Figure 18.1 Stages of Childbirth. The stages of childbirth include Stage 1, early cervical dilation; Stage 2, full dilation and expulsion of the newborn; and Stage 3, delivery of the placenta and associated fetal membranes. (The position of the newborn’s shoulder is described relative to the mother). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 16.2. Structure of Sperm. Sperm cells are divided into a head, containing DNA; a mid-piece, containing mitochondria; and a tail, providing motility. The acrosome is oval and somewhat flattened. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.1 Kidneys. The kidneys are slightly protected by the ribs and are surrounded by fat for protection (not shown). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.2 Left Kidney. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.3 Blood Flow in the Kidney. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.4. Blood Flow in the Nephron. The two capillary beds are clearly shown in this figure. The efferent arteriole is the connecting vessel between the glomerulus and the peritubular capillaries and vasa recta. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.5 Bladder. (a) Anterior cross section of the bladder. (b) The detrusor muscle of the bladder (source: monkey tissue) LM × 448. (Micrograph provided by the Regents of the University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.6. Female and Male Urethras. The urethra transports urine from the bladder to the outside of the body. This image shows (a) a female urethra and (b) a male urethra. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.7 Net Filtration Pressure. The NFP is the sum of osmotic and hydrostatic pressures. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.8 Urine Color. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 15.9 Nitrogen Wastes. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.2 Endocrine System. Endocrine glands and cells are located throughout the body and play an important role in maintaining equilibrium (homeostasis). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.3 Negative Feedback Loop. The release of adrenal glucocorticoids is stimulated by the release of hormones from the hypothalamus and pituitary gland. This signaling is inhibited when glucocorticoid levels become elevated by causing negative signals to the pituitary gland and hypothalamus. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.4 Anterior Pituitary. The anterior pituitary manufactures seven hormones. The hypothalamus produces separate hormones that stimulate or inhibit hormone production in the anterior pituitary. Hormones from the hypothalamus reach the anterior pituitary via the hypophyseal portal system. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.5 Hormonal Regulation of Growth. Growth hormone (GH) directly accelerates the rate of protein synthesis in skeletal muscle and bones. Insulin-like growth factor 1 (IGF-1) is activated by growth hormone and indirectly supports the formation of new proteins in muscle cells and bone. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.6 Posterior Pituitary. Neurosecretory cells in the hypothalamus release oxytocin (OT) or ADH into the posterior lobe of the pituitary gland. These hormones are stored or released into the blood via the capillary plexus. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.8 Adrenal Glands. Both adrenal glands sit atop the kidneys and are composed of an outer cortex and an inner medulla, all surrounded by a connective tissue capsule. The cortex can be subdivided into additional zones, all of which produce different types of hormones. LM × 204. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 14.9 Pancreas. The pancreatic exocrine function involves the acinar cells secreting digestive enzymes that are transported into the small intestine by the pancreatic duct. Its endocrine function involves the secretion of insulin (produced by beta cells) and glucagon (produced by alpha cells) within the pancreatic islets. These two hormones regulate the rate of glucose metabolism in the body. The micrograph reveals pancreatic islets. LM × 760. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.1 Components of the Digestive System. All digestive organs play integral roles in the life-sustaining process of digestion. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.2 Mouth. The mouth includes the lips, tongue, palate, gums, and teeth. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.3 Tongue. This superior view of the tongue shows the locations and types of lingual papillae. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.4 Esophagus. The upper esophageal sphincter controls the movement of food from the pharynx to the esophagus. The lower esophageal sphincter controls the movement of food from the esophagus to the stomach. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.5 Stomach. The stomach has four major regions: the cardia, fundus, body, and pylorus. The addition of an inner oblique smooth muscle layer gives the muscularis the ability to vigorously churn and mix food. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.6 Small Intestine. The three regions of the small intestine are the duodenum, jejunum, and ileum. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.7 Large Intestine. The large intestine includes the cecum, colon, and rectum. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.8 Accessory Organs. The liver, pancreas, and gallbladder are considered accessory digestive organs, but their roles in the digestive system are vital. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.9 Exocrine and Endocrine Pancreas. The pancreas has a head, a body, and a tail. It delivers pancreatic juice to the duodenum through the pancreatic duct. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.10 Gallbladder. The gallbladder stores and concentrates bile, and releases it into the two-way cystic duct when it is needed by the small intestine. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.11. Peristalsis. Peristalsis moves food through the digestive tract with alternating waves of muscle contraction and relaxation. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 13.12. Digestive Processes. The digestive processes are ingestion, propulsion, mechanical digestion, chemical digestion, absorption, and defecation. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.2 Upper Airway. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.3 Pseudostratified Ciliated Columnar Epithelium. Respiratory epithelium is pseudostratified ciliated columnar epithelium. Seromucous glands provide lubricating mucus. LM × 680. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.4 Divisions of the Pharynx. The pharynx is divided into three regions: the nasopharynx, the oropharynx, and the laryngopharynx. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.7 Trachea. (a) The tracheal tube is formed by stacked, C-shaped pieces of hyaline cartilage. (b) The layer visible in this cross-section of tracheal wall tissue between the hyaline cartilage and the lumen of the trachea is the mucosa, which is composed of pseudostratified ciliated columnar epithelium that contains goblet cells. LM × 1220. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.8 Respiratory Zone. Bronchioles lead to alveolar sacs in the respiratory zone, where gas exchange occurs. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.9 Structures of the Respiratory Zone. (a) The alveolus is responsible for gas exchange. (b) A micrograph shows the alveolar structures within lung tissue. LM × 178. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.10 Gross Anatomy of the Lungs. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 12.12 Inspiration and Expiration. Inspiration and expiration occur due to the expansion and contraction of the thoracic cavity, respectively. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.1 Anatomy of the Lymphatic System. Lymphatic vessels in the arms and legs convey lymph to the larger lymphatic vessels in the torso. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.2 Lymphatic Capillaries. Lymphatic capillaries are interlaced with the arterioles and venules of the cardiovascular system. Collagen fibers anchor a lymphatic capillary in the tissue (inset). Interstitial fluid slips through spaces between the overlapping endothelial cells that compose the lymphatic capillary.From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.3 Major Trunks and Ducts of the Lymphatic System. The thoracic duct drains a much larger portion of the body than does the right lymphatic duct. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.5 Clonal Selection and Expansion of T Lymphocytes. Stem cells differentiate into T cells with specific receptors, called clones. The clones with receptors specific for antigens on the pathogen are selected for and expanded. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.6 Structure and Histology of a Lymph Node. Lymph nodes are masses of lymphatic tissue located along the larger lymph vessels. The micrograph of the lymph nodes shows a germinal center, which consists of rapidly dividing B cells surrounded by a layer of T cells and other accessory cells. LM × 128. (Micrograph provided by the Regents of the University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.8. Locations and Histology of the Tonsils. (a) The pharyngeal tonsil is located on the roof of the posterior superior wall of the nasopharynx. The palatine tonsils lay on each side of the pharynx. (b) A micrograph shows the palatine tonsil tissue. LM × 40. (Micrograph provided by the Regents of the University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.9 Mucosa-associated Lymphoid Tissue (MALT) Nodule. LM × 40. (Micrograph provided by the Regents of the University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.10 Cooperation between Innate and Adaptive Immune Responses. The innate immune system enhances adaptive immune responses so they can be more effective. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.14 Kaposi’s Sarcoma Lesions. (credit: National Cancer Institute). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 11.15 Autoimmune Disorders: Rheumatoid Arthritis and Lupus. (a) Extensive damage to the right hand of a rheumatoid arthritis sufferer is shown in the x-ray. (b) The diagram shows a variety of possible symptoms of systemic lupus erythematosus. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 10.3 Systemic Arteries. The major systemic arteries shown here deliver oxygenated blood throughout the body. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 10.11 Emigration. Leukocytes exit the blood vessel and then move through the connective tissue of the dermis toward the site of a wound. Some leukocytes, such as the eosinophil and neutrophil, are characterized as granular leukocytes. They release chemicals from their granules that destroy pathogens; they are also capable of phagocytosis. The monocyte differentiates into a [pb_glossary id="411"]macrophage[/pb_glossary] that then [pb_glossary id="413"]phagocytizes[/pb_glossary] the pathogens. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 10.16 Atherosclerosis. (a) Atherosclerosis can result from plaques formed by the buildup of fatty, calcified deposits in an artery. (b) Plaques can also take other forms, as shown in this micrograph of a coronary artery that has a buildup of connective tissue within the artery wall. LM × 40. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 10.17 Varicose Veins. Varicose veins are commonly found in the lower limbs. (credit: Thomas Kriese). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 9.1. Position of the Heart in the Thorax. The heart is located within the thoracic cavity, medially between the lungs in the mediastinum. It is about the size of a fist, is broad at the top, and tapers toward the base. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 9.7. ECG Tracing Correlated to the Cardiac Cycle. This diagram correlates an ECG tracing with the electrical and mechanical events of a heart contraction. Each segment of an ECG tracing corresponds to one event in the cardiac cycle. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 9.8. Arteries of the Thoracic and Abdominal Regions The thoracic aorta gives rise to the arteries of the visceral and parietal branches. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.2 Gray Matter and White Matter. A brain removed during an autopsy, with a partial section removed, shows white matter surrounded by gray matter. Gray matter makes up the outer cortex of the brain. (credit: modification of work by “Suseno”/Wikimedia Commons). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.3 The Cerebrum. The cerebrum is a large component of the CNS in humans, and the most obvious aspect of it is the folded surface called the cerebral cortex. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.4 Lobes of the Cerebral Cortex. The cerebral cortex is divided into four lobes. Extensive folding increases the surface area available for cerebral functions. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.6 The Brain Stem. The brain stem comprises three regions: the midbrain, the pons, and the medulla. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.7 The Cerebellum. The cerebellum is situated on the posterior surface of the brain stem. Descending input from the cerebellum enters through the large white matter structure of the pons. Ascending input from the periphery and spinal cord enters through the fibers of the inferior olive. Output goes to the midbrain, which sends a descending signal to the spinal cord. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.8 Parts of a Neuron. The major parts of the neuron are labeled on a multipolar neuron from the CNS. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.9 Neuron Classification by Shape. Unipolar cells have one process that includes both the axon and dendrite. Bipolar cells have two processes, the axon, and a dendrite. Multipolar cells have more than two processes, the axon, and two or more dendrites. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.10 Other Neuron Classifications. Three examples of neurons that are classified on the basis of other criteria. (a) The pyramidal cell is a multipolar cell with a cell body that is shaped something like a pyramid. (b) The Purkinje cell in the cerebellum was named after the scientist who originally described it. (c) Olfactory neurons are named for the functional group to which they belong. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.11 Glial Cells of the CNS. The CNS has astrocytes, oligodendrocytes, microglia, and ependymal cells that support the neurons of the CNS in several ways. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.12 Glial Cells of the PNS. The PNS has satellite cells and Schwann cells. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.13 Somatic, Autonomic, and Enteric Structures of the Nervous System. Somatic structures include the spinal nerves, both motor and sensory fibers, as well as the sensory ganglia (posterior root ganglia and cranial nerve ganglia). Autonomic structures are found in the nerves also but include the sympathetic and parasympathetic ganglia. The enteric nervous system includes the nervous tissue within the organs of the digestive tract. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.14 Broca’s and Wernicke’s Areas. Two important integration areas of the cerebral cortex associated with language function are Broca’s and Wernicke’s areas. The two areas are connected through the deep white matter running from the posterior temporal lobe to the frontal lobe. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 8.15 Hemorrhagic Stroke. (a) A hemorrhage into the tissue of the cerebrum results in a large accumulation of blood with additional edema in the adjacent tissue. The hemorrhagic area causes the entire brain to be disfigured as suggested here by the lateral ventricles being squeezed into the opposite hemisphere. (b) A CT scan shows an intraparenchymal hemorrhage within the parietal lobe. (credit b: James Heilman). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 7.1 The Three Types of Muscle Tissue. The body contains three types of muscle tissue: (a) skeletal muscle, (b) smooth muscle, and (c) cardiac muscle. (Micrographs provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.1 Axial and Appendicular Skeleton. The axial skeleton supports the head, neck, back, and chest and thus forms the vertical axis of the body. It consists of the skull, vertebral column (including the sacrum and coccyx), and the thoracic cage, formed by the ribs and sternum. The appendicular skeleton is made up of all bones of the upper and lower limbs. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.2 Vertebral Column. The adult vertebral column consists of 24 vertebrae, plus the sacrum and coccyx. The vertebrae are divided into three regions: cervical C1–C7 vertebrae, thoracic T1–T12 vertebrae, and lumbar L1–L5 vertebrae. The vertebral column is curved, with two primary curvatures (thoracic and sacrococcygeal curves) and two secondary curvatures (cervical and lumbar curves). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.3 Thoracic Cage. The thoracic cage is formed by the (a) sternum and (b) 12 pairs of ribs with their costal cartilages. The ribs are anchored posteriorly to the 12 thoracic vertebrae. The sternum consists of the manubrium, body, and xiphoid process. The ribs are classified as true ribs (1–7) and false ribs (8–12). The last two pairs of false ribs are also known as floating ribs (11–12). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.5 Bones of the Hands. The eight carpal bones form the base of the hand. These are arranged into proximal and distal rows of four bones each. The metacarpal bones form the palm. The thumb and fingers consist of the phalanx bones. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.8 Movements of the Body, Part 1. Synovial joints give the body many ways in which to move. (a) and (b) Flexion and extension motions are in the sagittal (anterior and posterior) plane of motion. These movements take place at the shoulder, hip, elbow, knee, wrist, metacarpophalangeal, metatarsophalangeal, and interphalangeal joints. (c) and (d) Anterior bending of the head or vertebral column is flexion, while any posterior-going movement is extension. (e) Abduction and adduction are motions of the limbs, hand, fingers, or toes in the coronal (medial and lateral) plane of movement. Moving the limb or hand laterally away from the body, or spreading the fingers or toes, is abduction. Adduction brings the limb or hand toward or across the midline of the body or brings the fingers or toes together. Circumduction is the movement of the limb, hand, or fingers in a circular pattern, using the sequential combination of flexion, adduction, extension, and abduction motions. Adduction/abduction and circumduction take place at the shoulder, hip, wrist, metacarpophalangeal, and metatarsophalangeal joints. (f) Turning of the head side to side or twisting of the body is rotation. Medial and lateral rotation of the upper limb at the shoulder or lower limb at the hip involves turning the anterior surface of the limb toward the midline of the body (medial or internal rotation) or away from the midline (lateral or external rotation). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.9 Movements of the Body, Part 2. (g) Supination of the forearm turns the hand to the palm forward position in which the radius and ulna are parallel, while forearm pronation turns the hand to the palm backward position in which the radius crosses over the ulna to form an “X.” (h) Dorsiflexion of the foot at the ankle joint moves the top of the foot toward the leg, while plantar flexion lifts the heel and points the toes. (i) Eversion of the foot moves the bottom (sole) of the foot away from the midline of the body, while foot inversion faces the sole toward the midline. (j) Protraction of the mandible pushes the chin forward, and retraction pulls the chin back. (k) Depression of the mandible opens the mouth, while elevation closes it. (l) Opposition of the thumb brings the tip of the thumb into contact with the tip of the fingers of the same hand and reposition brings the thumb back next to the index finger. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.10 Abnormal Curvatures of the Vertebral Column. (a) Scoliosis is an abnormal lateral bending of the vertebral column. (b) An excessive curvature of the upper thoracic vertebral column is called kyphosis. (c) Lordosis is an excessive curvature in the lumbar region of the vertebral column. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 6.12. Types of Fractures. Compare healthy bone with different types of fractures: (a) closed fracture, (b) open fracture, (c) transverse fracture, (d) spiral fracture, (e) comminuted fracture, (f) impacted fracture, (g) greenstick fracture, and (h) oblique fracture. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.3 Epidermis. The epidermis is epithelium composed of multiple layers of cells. The basal layer consists of cuboidal cells, whereas the outer layers are squamous, keratinized cells, so the whole epithelium is often described as being keratinized stratified squamous epithelium. LM × 40. (Micrograph provided by the Regents of University of Michigan Medical School © 2012). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.4 Layers of the Dermis. This stained slide shows the two components of the dermis—the papillary layer and the reticular layer. Both are made of connective tissue with fibers of collagen extending from one to the other, making the border between the two somewhat indistinct. The dermal papillae extending into the epidermis belong to the papillary layer, whereas the dense collagen fiber bundles below belong to the reticular layer. LM × 10. (credit: modification of work by “kilbad”/Wikimedia Commons). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.6 Hair. Hair follicles originate in the epidermis and have many different parts. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.7 Nails. The nail is an accessory structure of the integumentary system. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.8 Eccrine Gland. Eccrine glands are coiled glands in the dermis that release sweat that is mostly water. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.9 Aging. Generally, skin, especially on the face and hands, starts to display the first noticeable signs of aging, as it loses its elasticity over time. (credit: Janet Ramsden). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.10 Moles. Moles range from benign accumulations of melanocytes to melanomas. These structures populate the landscape of our skin. (credit: the National Cancer Institute). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.11 Basal Cell Carcinoma. Basal cell carcinoma can take several different forms. Similar to other forms of skin cancer, it is readily cured if caught early and treated. (credit: John Hendrix, MD). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.12 Squamous Cell Carcinoma Squamous cell carcinoma presents here as a lesion on a nose. (credit: the National Cancer Institute). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.13 Melanoma. Melanomas typically present as large brown or black patches with uneven borders and a raised surface. (credit: the National Cancer Institute). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.14 Vitiligo. Individuals with vitiligo experience depigmentation that results in lighter colored patches of skin. The condition is especially noticeable on darker skin. (credit: Klaus D. Peter). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.15 Eczema. Eczema is a common skin disorder that presents as a red, flaky rash. (credit: “Jambula”/Wikimedia Commons). From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.16. Acne. Acne is a result of over-productive sebaceous glands, which leads to the formation of blackheads and inflammation of the skin. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 5.17 Calculating the Size of a Burn. The size of a burn will guide decisions made about the need for specialized treatment. Specific parts of the body are associated with a percentage of body area. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 4.1 Structures of the Ear. The external ear contains the auricle, ear canal, and tympanic membrane. The middle ear contains the ossicles and is connected to the pharynx by the Eustachian tube. The inner ear contains the cochlea and vestibule, which are responsible for audition and equilibrium, respectively. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 4.2 Cross Section of the Cochlea. The three major spaces within the cochlea are highlighted. The scala tympani and scala vestibuli lie on either side of the cochlear duct. The organ of Corti, containing the mechanoreceptor hair cells, is adjacent to the scala tympani, where it sits atop the basilar membrane. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 4.4 The Eye in the Orbit. The eye is located within the orbit and surrounded by soft tissues that protect and support its function. The orbit is surrounded by cranial bones of the skull. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 4.5. Structure of the Eye. The sphere of the eye can be divided into anterior and posterior chambers. The wall of the eye is composed of three layers: the fibrous tunic, vascular tunic, and neural tunic. Within the neural tunic is the retina, with three layers of cells and two synaptic layers in between. The center of the retina has a small indentation known as the fovea. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 4.6 Comparison of Color Sensitivity of Photopigments. Comparing the peak sensitivity and absorbance spectra of the four photopigments suggests that they are most sensitive to particular wavelengths. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 3.1 Levels of Structural Organization of the Human Body. The organization of the body often is discussed in terms of six distinct levels of increasing complexity, from the smallest chemical building blocks to a unique human organism. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 3.2. Organ Systems of the Human Body. Organs that work together are grouped into organ systems. From Betts et al., 2013. Licensed under CC BY 4.0 [Image description.]


Figure 3.4. Regions of the Human Body. The human body is shown in anatomical position in an (a) anterior view and a (b) posterior view. The regions of the body are labeled in boldface. From Betts et al., 2013. Licensed under CC BY 4.0 [Image description.]


Figure 3.5. Directional Terms Applied to the Human Body. Paired directional terms are shown as applied to the human body. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 3.6. Dorsal and Ventral Body Cavities. The ventral cavity includes the thoracic and abdominopelvic cavities and their subdivisions. The dorsal cavity includes the cranial and spinal cavities. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 3.7. Tissue Membranes. The two broad categories of tissue membranes in the body are (1) connective tissue membranes, which include synovial membranes, and (2) epithelial membranes, which include mucous membranes, serous membranes, and the cutaneous membrane, in other words, the skin. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Figure 3.8. Serous Membrane. Serous membrane lines the pericardial cavity and reflects back to cover the heart—much the same way that an underinflated balloon would form two layers surrounding a fist. From Betts et al., 2013. Licensed under CC BY 4.0. [Image description.]


Exit gunshot wound, gross


Entrance-exit wound, close proximity from low angle of bullet entrance, gross


Intermediate range gunshot wound, gross


Gunshot entrance wound with GSR,
microsopic


Blood spatter on hand, gross


Contact range gunshot wound, gross


Sooting of hand, gross


Hip prosthesis, radiograph.


Femoral neck fracture, radiographs.


Femur with osteoporosis, radiograph.


Vertebral bone with osteoporosis, low power microscopic.


Vertebral bone with osteoporosis and compressed fracture, gross.


Vertebral bone with osteoporosis, gross.


Normal vertebral bone, polarized, medium power microscopic.


Normal vertebral bone and marrow, low power microscopic.


Normal vertebral bone, gross.


A QTL for  osteoporosis  on the human chromosome 20


Example of a genome-wide scan for QTL of  osteoporosis


Bacteria are classified by their shape.


Taq polymerase which is used in Polymerase Chain Reaction(PCR)


BMC, Part of Springer Nature


The homepage of the journal website


Example cover page of the journal


Two-colored rose chimera


Chimeric trait distribution by generation


African violets exhibiting chimerism


The green cells in the centres of the leaves of this  Pelargonium  plant have formed from the epithelium cell layer, which has normal chlorophyll. That cell layer does not extend all the way to the edges of the leaves, which therefore show the chlorophyll-deficient cells of other developmental layers. This is a periclinal chimera.


Taxus  mosaic


Boiling Springs Lake, California, is where the first natural chimeric virus was found in 2012. [ 47 ]


A chimeric mouse with her  offspring , which carry the  agouti coat color gene ; note her pink eye


Cherry tree, consolidated "V" graft


Tape has been used to bind the rootstock and scion at the graft, and tar to protect the scion from desiccation.


A grafted tree showing two differently coloured blossoms


Graft particular to plum cherry. The scion is the largest in the plant, due to the imperfect union of the two. It can be seen on the enlarged trunk: this accumulation of starch is an indication of imperfection.


An example of approach grafting by  Axel Erlandson .


Depiction of general-purpose grafting knives


Grafting process (Uzbekistan)


T budding


Successful cleft graft after 2 years' growth


Same graft after 4 years' growth


Graft needing attention the following season


Successful whip graft


Successful stub graft, healed


A " husband and wife tree "  blackthorn , ( Prunus spinosa ), the result of natural grafting


Possible deliberate grafts on a  sessile oak  in  Ayrshire , Scotland


A domestic half-sider budgerigar


During pregnancy, a two-way traffic of immune cells may occur through the  placenta . Exchanged cells can multiply and establish long-lasting cell lines that are immunologically active even decades after giving birth.


Grafted tomato plants


Cryptocarya williwilliana  showing leaf venation and variegated leaves.


Variegation of fruits and wood in  Ficus carica  'Panascè', a bicolor (yellow-green) common fig cultivar. This Italian cultivar is a  chimera .


Leaves of  red clover  ( Trifolium pratense ) have a typical v-shaped variegation.


Variegated foliage used in an English garden. Plants shown include  Aralia elata  'Aureovariegata' and  Carex ornithopoda  'Variegata'


Gregor Mendel


The chemical structure of a four base pair fragment of a  DNA   double helix . The  sugar - phosphate  backbone chains run in opposite directions with the  bases  pointing inward,  base-pairing   A  to  T  and  C  to  G  with  hydrogen bonds .


Micrographic   karyogram  of human male, showing 23 pairs of chromosomes. The largest  chromosomes  are around 10 times the size of the smallest. [ 53 ]


Schematic  karyogram  of a human, with annotated  bands and sub-bands . It shows dark and white regions on  G banding . It shows 22  homologous chromosomes , both the male (XY) and female (XX) versions of the  sex chromosome  (bottom right), as well as the  mitochondrial genome  (at bottom left).  Further information:  Karyotype


Schematic of a single-stranded RNA molecule illustrating a series of three-base  codons . Each three- nucleotide  codon corresponds to an  amino acid  when translated to protein.


Protein coding genes are transcribed to an  mRNA  intermediate, then translated to a functional  protein . RNA-coding genes are transcribed to a functional  non-coding RNA  ( PDB :  3BSE ,  1OBB ,  3TRA ).


Inheritance of a gene that has two different  alleles  (blue and white). The gene is located on an  autosomal chromosome . The white allele is  recessive  to the blue allele. The probability of each outcome in the children's generation is one quarter, or 25 percent.


Depiction of numbers of genes for representative  plants  (green),  vertebrates  (blue),  invertebrates  (orange),  fungi  (yellow),  bacteria  (purple), and  viruses  (grey). An inset on the right shows the smaller genomes expanded 100-fold area-wise. [ 87 ] [ 88 ] [ 89 ] [ 90 ] [ 91 ] [ 92 ] [ 93 ] [ 94 ]


Gene functions in the minimal  genome  of the  synthetic organism ,  Syn 3 [ 105 ]


Comparison of conventional plant breeding with transgenic and cisgenic genetic modification


This stylistic diagram shows a gene in relation to the  double helix  structure of  DNA  and to a  chromosome  (right). The chromosome is X-shaped because it is dividing.  Introns  are regions often found in  eukaryote  genes that are removed in the  splicing  process (after the DNA is transcribed into RNA): Only the  exons  encode the  protein . The diagram labels a region of only 55 or so bases as a gene. In reality, most genes are hundreds of times larger.


pre-mRNA splice patterns showing constitutive exons and introns and the inserted fragment. Orange lines show alternative splicing outcomes as dictated by the exonic sequences and intronic sequences (yellow and green bands) that influence splicing. These sequences may be splicing enhancers or silencers, polypyrimidine tract binding protein sites or other elements.


A typical cycle for constructing a minigene.


The domains found in anillin across species


Figure 1: Splice variants of  Bok  mRNA and the resulting proteins .  Bok  mRNA comprises five exons and two alternative start codons for translation (AUG). Exons are visualized as arrows and boxes in different colors; ovals indicate sequences that code for Bcl-2 homology domains (BH1, BH2, BH3, BH4) or the transmembrane domain (TM). In the Bok-S variant, the BH3 domain is truncated and fused to the shortened BH1 domain. Another known variant, Bok-P, lacks the BH4 domain and contains a truncated BH3 domain.


BPIFA1 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFA2 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFA3 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFB1 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFB2 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFB3 is a member of the BPI-fold gene family and the BPI/LBP/PLUN protein superfamily


BPIFB4 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


BPIFB6 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily


The general location where the gene C2orf27A is on chromosome 2. Reference:  http://ghr.nlm.nih.gov/chromosome=2   Archived  2016-03-09 at the  Wayback Machine


Given that NBEA is present in mainly mammals, gene duplication is believed to originate from chromosome 13 to chromosome 2. The duplication event involves the exons 2, 9, and 10 of chromosome 13 onto chromosome 2, becoming exons 1, 2, and 3 of C2orf27A.


Chromosome 2


See the red band: 2q37.1.


Top Ten Predicted Biological Processes (GO) as of July 16, 2022, via Archs4. https://maayanlab.cloud/archs4/gene/C2ORF72


In this figure, in this case, I listed three possible phosphorylation sites: Serine-294, Threonine-286, and Serine-277.


AlphaFold C2Orf72 protein structure prediction, as of July 16, 2022. https://alphafold.ebi.ac.uk/entry/A6NCS6


I-TASSER for Protein Structure Prediction (Performed Calculation Approximately in July 2021 for C2Orf72's Predicted Amino Acid Sequence, Raw Form). [ 22 ]


c9orf135 location on chromosome 9 and the neighboring genes.


Splice Variants of c9orf135 based on NCBI AceView


Cytogenetic band: 12q23.2 [ 6 ]


Tertiary structure  for C12orf42 protein. [ 7 ]


This protein cartoon illustrates the location of, the domain DUF4607 and two nuclear localization sequences.


Illustrates the translocation that occurred that led to a deletion in chromosome 12. Where chromosome 12q23 cross-fused with TRDREC and TRAJ61 segment. This interfered with C12orf42 gene. [ 19 ]


Location of C15orf39 on chromosome 15. [ 3 ]


Expression of C15orf39 in human tissues. [ 6 ]


In-situ hybridization of C15orf39 in fetal and adult reticulocytes. [ 7 ]


Domains of C15orf39. P = Phosphorylation, A = Acetylation, SUMO = Sumoylation, O = O-glycosylation.


Conceptual translation of C15orf39 C-terminal showing predicted PTM and secondary structure.


Predicted tertiary structure for C-terminal end of C15orf39. [ 17 ]


Phylogenetic tree for select C15orf39 orthologs. [ 26 ]


Rate of sequence divergence for C15orf39, Fibrinogen, and Cytochrome C in orthologs. [ 27 ]


Location of C20orf96 as well as neighboring genes, as given by NCBI Gene


The location of  CCDC180  on human chromosome 9 within locus 9q22.33 is marked with a line.


Here are shown the major domains present within the protein CCDC180: Domains of Unknown Function 4455 and 4456, two coiled-coil domains, and a glutamic acid rich domain.


A model of CCDC180 secondary and tertiary structure predicted by the University of Michigan I-TASSER server [ 6 ]


Translation of the mRNA and protein sequence for the human protein CCDC180, including domains, secondary structure, exon splice sites, and post-translation modification sites


GEO Profile for the expression of the human protein CCDC180 in normal tissues [ 13 ]


The amino acid changes per 100 (m) in a selection of orthologs of CCDC180 versus time of divergence of the species from human in millions of years. This is compared to Cytochrom C and Fibrinogen to indicate the relatively high speed of evolution of the CCDC180 protein.


The image shows the exact location of CXorf49 on the minus strand of the X chromosome.


Image of the protein with the domain of unknown function.


This phylogenetic tree made with CRUSTALW on SDSC Biology Workbench [ 6 ]   shows how CXorf49 in Human (Hsa), Chimpanzee(Ptro), Malayan flying lemur(Gava), Sheep (Ovari), Pacific walrus(Ord), Aardvark(Oafaf), Chinese tree shrew (Tuchi) and House mouse(Mmus) has diverged over time.


Novel genes can emerge from ancestrally non-genic regions through poorly understood mechanisms.  (A)  A non-genic region first gains transcription and an  open reading frame  (ORF), in either order, facilitating the birth of a  de novo  gene. The ORF is for illustrative purposes only, as de novo genes may also , or lack an ORF, as with  RNA genes .  (B)  Overprinting. A novel ORF is created that overlaps with an existing ORF, but in a different frame.  (C)  Exonization. A formerly  intronic  region becomes alternatively spliced as an exon, such as when repetitive sequences are acquired through  retroposition  and new splice sites are created through  mutational  processes. Overprinting and exonization may be considered as special cases of de novo gene birth.


Novel genes can be formed from ancestral genes through a variety of mechanisms. [ 1 ]   (A)  Duplication and divergence. Following duplication, one copy experiences relaxed selection and gradually acquires novel function(s).  (B)  Gene fusion. A hybrid gene formed from some or all of two previously separate genes. Gene fusions can occur by different mechanisms; shown here is an interstitial deletion.  (C)  Gene fission. A single gene separates to form two distinct genes, such as by duplication and differential degeneration of the two copies. [ 2 ]   (D)   Horizontal gene transfer . Genes acquired from other species by horizontal transfer undergo divergence and neofunctionalization.  (E)  Retroposition. Transcripts may be reverse transcribed and integrated as an intronless gene elsewhere in the genome. This new gene may then undergo divergence.


Annotated features of TMEM261 protein including topology and important sites for phosphorylation and Myristoylation as well DUF4536 and transmembrane helical domains.


Some proteins found to interact with TMEM261


Tissue expression of TMEM261 showing tissue enriched gene (TEG) expression  [ 27 ]


D4Z4 array with three D4Z4 repeats and the 4qA allele      CEN   centromeric  end   TEL   telomeric  end      NDE box   non-deleted element   PAS   polyadenylation  site      triangle   D4Z4 repeat   trapezoid   partial D4Z4 repeat      white box   pLAM   gray boxes   DUX4 exons 1, 2, 3      arrows       corner   promoters   straight   RNA transcripts       black   sense   red   antisense       blue   DBE-T   dashes   dicing sites


Structure of FAM63B protein showing the domain of unknown function, bipartite tryptophan binding motif, hydrophobic stretchm, and KDEL signal.


Predicted protein structure of FAM63B as determined by iTASSER.


The phylogenetic tree from TimeTree shows a time calibration for the evolution of FAM63B among humans (Has), prairie voles (Moc), polar bears (Uma), Western clawed frogs (Xtr), and Western Indian Ocean coelacanth (Latimeria chalumnae, Lch). The fish is the most diverged, followed by the amphibian, and the mammals, especially humans, are the least diverged. This is as expected in accordance with the evolutionary history of organisms on Earth, and FAM63B shows no great exception to the rule.


Genomic region of 3' UTR of gene FAM151A


FAM151A Expression in HPA RNA-seq normal tissues [ 9 ]


Antibody staining of FAM151A in human kidney tissue


FAM151A tertiary structure as predicted by AlphaFold2


Shannon information content  of amino acid residues for 20 aligned FAM151A sequences.


Figure 1.  FAM180b is located on Chromosome 11p11.2


Figure 2.  Secondary Structure of FAM180b


Figure 3.  Tertiary Structure of FAM180b


Figure 4.  RPKM tissue expression


Figure 5.  Gene expression in fetal human tissues


A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with a homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.


Types of Gene Conversion.


Micrographic  karyogram  of a human male. Shows 2 sets of the 22 autosomal chromosomes and the 23rd chromosome set with one X and one Y.


Schematic  karyogram  of a human, showing an overview of the  human genome , with 22  homologous chromosomes , both the female (XX) and male (XY) versions of the  sex chromosome  (bottom right), as well as the  mitochondrial genome  (to scale at bottom left). Further information:  Karyotype


Genes which control hair colour are polymorphic.


Figure 1. Common mechanisms of gene duplication.


A diagram showing the three possible isoforms for the c1orf173 protein.


A diagram showing the two DUF domains and phosphorylation sites (in red) on the domains. Phosphorylated O-Glcnac sites also appear in grey.


Drosophila  with the  antennapedia  mutant phenotype exhibit homeotic transformation of the antennae into leg-like structures on the head.


The vnd/NK-2 homeodomain-DNA complex. Helix 3 of the homeodomain binds in the major groove of the DNA and the N-terminal arm binds in the minor groove, in analogy with other homeodomain-DNA complexes.


Hox gene expression in  Drosophila melanogaster .


Homeotic selector gene complexes in the fruit fly  Drosophila melanogaster


Drosophila melanogaster


Sterol Regulatory Element Binding Protein


Small nuclear ribonucleoprotein-associated proteins B and B'


Human chromosome 14 - 550 bphs


Simplified diagram of Imd signalling as found in the  fruit fly .


Fruit flies  infected by GFP-producing bacteria. Red-eyed flies lacking antimicrobial peptide genes are susceptible to infection, while white-eyed flies have a wild-type immune response.


Pea aphids have lost Imd signalling


Expression of IEG  c-Fos  in neurons responding to stimulation with potassium treatment


Diagram of human chromosome 17 with KIAA0753 location indicated


Phylogenetic tree displaying the relationship between KIAA0753 in humans and its orthologs


Shows the four variants of human KIAA0753 and their exon locations


Microarray profile showing ubiquitous expression of KIAA0753 in humans


KNOP1 expression in Human tissues [ 5 ]


Domains of KNOP1:The green box is domain DUF5595:The blue box is domain SMAP:The green line is region of interaction for ZNF106 [ 19 ]


KNOP1 Conceptual Translation


Schematic illustration made using DOG software showing the domain of unknown function (DUF4641) as well as the location of secondary structures such as alpha helices, and post-translation modifications such as SUMO sites.


Displays the modeled secondary structures of LOC101059915 with the red indicating alpha helices, and the yellow indicating possible beta sheets.


Shows the unrooted branching of select orthologs for LOC10105519.


Conceptual translation of LSMEM1 for humans


Phylogenetic tree for select orthologs of LSMEM1


Human LSMEM1 evolutionary rate in comparison to a fast-evolving and a slow-evolving protein.


E. coli , the bacterium in which MCR-1 was first identified.


Simplified diagram of cytoplasmic protein degradation by the proteasome, transport into endoplasmic reticulum by TAP complex, loading on MHC class I, and transport to the surface for presentation


Pathway showing how MHC-II distribution is controlled within Immature Dendritic Cells.


This ideogram, using a red oval, depicts the location of NBEAL1 on human chromosome 2.


I-TASSER predicted this 3D structure for amino acids 1-1500 of NBEAL1.


Predicted structure via I-TASSER of NBEAL1, amino acids 1501-2694.


The different post-translational modifications are illustrated in this conceptually annotated transcript.


This unrooted phylogenetic tree, produced by Biology Workbench, [ 18 ]  illustrates the evolution of NBEAL1.


Using Biology Workbench, a Multiple Sequence Alignment was done to illustrate the highly conserved aspects of NBEAL1 in close orthologs to the  homo sapiens  gene.


Location of NBPF1 in relation to other genes on chromosome 1


Amino acid sequence of NBPF1 that shows the locations DUF1220 domains(blue) and coiled coil domains(yellow).


This is the predicted nuclear localization signal of NBPF1 using the program PSORT II.


Predicted Structure of Stat-1 and Stat3b-like DNA binding domains in NBPF1 using Phyre2


Expression for NBPF1 based on NCBI GEO Profiles, whole tissue expression profile


This shows the predicted relationship between NBPF1 similarity based on a multiple sequence alignment.


Rooted phylogenetic tree of NBPF1 paralogs based on multiple sequence alignment.


NEDD9 structure


NEDD9 mediated signaling


Structure of NR4A1 protein.


Nuclear gene location


OCC-1 Phylogenetic Tree


MSA for the Occludin/ELL Domain in OCEL1 and its five human paralogs. The beginnings and ends of each paralog were trimmed.


Tertiary structure of the human OCEL1 protein as predicted by iTASSER. [ 14 ] [ 15 ]


RNA folding of the 3’ UTR in OCEL1 generated with RNAfold Web Server. [ 27 ]


Tandem out-of-phase overlap of the human mitochondrial genes ATP8 (+1 frame, in red) and ATP6 (+3 frame, in blue) [ 10 ]


A  cladogram  indicating the likely evolutionary trajectory of the gene-dense pX region in  human T-lymphotropic virus 1  (HTLV1), a  deltaretrovirus  associated with blood cancers. This region contains numerous overlapping genes, several of which likely originated  de novo  through overprinting. [ 9 ]


Overlapping genes in the bacteriophage ΦX174 genome. There are 11 genes in this genome (A, A*, B-H, J, K). Genes B, K, E overlap with genes A, C, D. [ 29 ]


The  RNA silencing suppressor p19  from  tomato bushy stunt virus , a protein encoded by an overprinted gene. The protein specifically binds  siRNAs  produced as part of the plant's  RNA silencing  defense against viruses. [ 30 ]


The image shows a polycystic kidney disease, caused by mutation in the  GANAB  gene.


Predicted 3D structure of RESF1


This  phylogenetic tree  shows inferred evolutionary relationships of the human RESF1 gene and 20 of its  orthologs .


This graph shows the molecular evolution of the RESF1 gene in comparison to the evolution of cytochrome C and fibrinogen alpha.


Diagram of the SKIDA1 protein.


A predicted 3D structure of SKIDA1. The Ski/Sno/Dac domain, DUF4584, and C-Terminal region (amino acids 844-908) are annotated.


SKIDA1 is highly expressed in  Purkinje cells  in the cerebellum.


Expression of SKIDA1 in the house mouse fetal heart increases, then decreases with age.


Schematic of Human SMIM15 Domains


Figure 1. Conceptual Translation for the Human SMIM15


A table with accession number,  chromosome  location, strand location, size, and known aliases.


Conceptual Translation of SMIM23. Labeled are the start and stop codon, exon splice sites,  polyadenylation signal  as well as singly conserved based highlighted in yellow, alpha helices with arrows, transmembrane domain in purple, domains of unknown function in blue, and a repeat domain is underlined.


Schematic of protein. Marking locations of notable features that were confirmed with some level of confidence. Here red stands for phosphorylation site and grey stands for C-terminal GPI-modification site. The transmembrane domain in relation to the rest of the protein is shown.


Predicted structure of SMIM23 by I-Tasser program.


A phylogenetic tree of the SMIM23 gene in various animals as seen in the table included. Abbreviations refer to the different common names i.e. Hu SMIM23 refers to the human gene.


Ideogram of the SPMIP10 Gene Location on Chromosome 5. The gene location is indicated by the red line.


SPMIP10 predicted tertiary structure. Generated using AlphaFold.


SPMIP10 predicted tertiary structure. Generated using iTasser.


SPMIP10 Microarray Expression Schematic in the Human Brain. Yellow boxes indicate areas of dense expression in the posterior lobe. Data obtained from the Allen Brain Atlas website.


SPMIP10 Transcription Regulation Diagram. Two predicated enhancers (E2405703 and E2405704) and an initiation region (Tex43_1) are labeled.


Annotated Conserved Post-translational Modifications for SPMIP10 Diagram. Longer ticks indicate higher confidence scores.


Graph 1: Corrected sequence divergence vs estimated date of divergence for SPMIP10, Cytochrome C and Fibrinogen Alpha.


Products that contain retinoic acid should be avoided during pregnancy.


Indirect gene therapy


Direct gene therapy


Bystander effect


Pin  (A) and  thrum  (B) flowers of  Primula vulgaris  are controlled by a supergene.


Location of TMEM33 on human chromosome 4 [ 2 ]


Transcription factors with the highest matrix binding affinity to GXP_4428588 [ 6 ]


All eleven human transcripts of TMEM33 aligned. The transcripts a, b, c, d, and e encode viable TMEM33 isoforms and the other six do not. [ 7 ]


SUSIO prediction of TMEM33 amino acid arrangement in human cellular membrane [ 9 ]


Orthologs of TMEM33 and their divergence from human TMEM33 as obtained from NCBI


Conceptual Translation of TMEM61


MyHits Motif Scan with evalues


Ali2D configured Helix Beta distribution


IBS configuration of TMEM61 with post-translation modification


Glycosylation of TMEM61


I-TASSER Predicted 3D model of TMEM61


TMEM61 transcription factors


Immunochemistry of TMEM61 and expression in the Human body


Protein evolution


Orthologs of TMEM61


This image depicts the various transcript variants of TMEM156. It can be observed here that there are two variants that have protein coding function and two that are just processed transcripts.


This image depicts the interaction of the protein with the membrane of the  endoplasmic reticulum . It can be seen here that the protein crosses the membrane three times. [ 11 ]


Phyre software was used to create a predicted 3-D structure of TMEM156. It can be seen that this protein is composed vastly of alpha helices. The N terminus is on the top of the image and the C terminus is located on the bottom.


I-TASSER software was used to predict the tertiary structure of TMEM156. It is evident that the protein is composed primarily of alpha helices as seen by the magenta coils.


Location of TVP23A on Chromosome 16 (red line)


Protein structure of TVP23A as predicted by iTASSER


A VUS is a common result in genetic testing


Since the  Human Genome Project  first sequenced the  human genome  in 2001 at a cost of US$100 million, costs have fallen precipitously, outpacing even  Moore's law , and were ≈US$1,000 in 2015. More widely available genome sequencing has led to more available data on variants of uncertain significance.


A patient displaying dystopia canthorum as well as the hypoplastic blue irises, which are both physical features associated with type 1 Waardenburg syndrome.


Crystal structure of Wnt8 (rainbow coloring) bound to the cysteine rich domain of Frizzled8 (green).


Figure 2. Wnt binds to (activates) the receptor. Axin is removed from the "destruction complex." β-Cat moves into the nucleus, binds to a transcription factor on DNA, and activates transcription of a protein. "P" represents  phosphate .


Figure 1. Wnt does not bind to the receptor. Axin, GSK and APC form a "destruction complex," and β-Cat is destroyed.


Canonical Wnt pathway


Noncanonical PCP pathway


Noncanonical Wnt/calcium pathway


Diagram illustrating the interaction between the Wnt and insulin signaling pathways


The schematic diagram of ZFNs


A pair of ZFNs, each with three zinc fingers binding to target DNA, are shown introducing a double-strand break, at the FokI domain, depicted in yellow. Subsequently, the double strand break is shown as being repaired through either  homology-directed repair  or  non-homologous end joining . [ 3 ]


A 23andMe 2021 genome testing kit


A 23andMe 2013 genome testing kit


BioModels Database Pipeline


Figure 1. The CCDS data set screenshot showing the report for Itm2a protein (CCDS 30349).


a) Various sources submit data, and each variation is assigned a unique submitted SNP number ID (ss#). b) dbSNP compiles identical ss# records into one reference SNP cluster (rs#) containing data from each ss#. c) Users can retrieve data for specific rs# records and analyze these variations. d) Data from dbSNP aids clinical and applied research. The ss# and rs# IDs in this figure are examples only. NCBI, National Center for Biotechnology Information; OMIM, Online Mendelian Inheritance in Man; GWAS, genome wide association study.


A segment of the human reference genome, viewed using  Ensembl  with the DECIPHER track enabled. Red bars represent individual mutations for anonymous patients with deletions across this region, while green bars represent patients with duplications across this region. The region shown encompasses the segment of chromosome missing in patients with  17q21.3 recurrent microdeletion syndrome .


A schematic representation of a chromosome deletion. DECIPHER maps small deletions detected in patients to the reference genome produced by the  Human Genome Project .


Karyotype visualisation in Ensembl Genomes


Visualisation of a custom track labelled "Reads" in Ensembl Genomes


BioMart view in Ensembl Plants.


Variant Effect Predictor Output file


Nucleotide sequence data in book form.


The EBI at the  Wellcome Trust Genome Campus  in  Hinxton ,  UK  which hosts the European Nucleotide Archive.


The EMBL Nucleotide Sequence Database (EMBL-Bank) has increased in size from around 600 entries in 1982 to over 2.5×10 8  by December 2012. [ 16 ]


The SRA has grown rapidly since 2008. [ 21 ]  As of 2011, most SRA sequence data was produced by  Illumina 's Genome Analyzer. [ 22 ]


Screenshot of the ENA browser  web interface , showing an HTML record.


Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.


CD-ROM of Genbank v100


Growth in GenBank base pairs, 1982 to 2018, on a  semi-log scale


Timeline of the GENCODE project


GENCODE pipeline diagram. The schema shows the flow of data between manual annotation and automated annotation through specialized prediction pipelines to provide hints to first-pass annotation and quality control (QC). Annotated gene models are subject to experimental validation, and the AnnoTrack tracking system contains data from all these sources and is used to highlight differences, coordinate QC, and track outcomes. Manual and automated annotation processes produce the GENCODE data set and also used to QC the completed annotation.


GTF file example where it is shown TAB-separated standard GTF columns (1-9)


Gene prioritization workflow of human diseases : Typical lists come from linkage regions, chromosomal aberrations, association study loci, deferentially expressed gene lists or genes identified by sequencing variants. Alternatively, the complete genome can be prioritized, but substantially more false positives would then be expected.


The process of database compilation and curation  The curated data may comprise a process from practical experience and literature review to web publication of the database [ 14 ]


Pathway Hogeneity vs Associated Genes  Showing the concept that diseases have large association with a variety of genes, a mean pathway homogeneity values of single diseases and random controls are plotted for four networks binned by the number of associated gene products per disease.  This graph shows how difficult is to correlate a bigger number of diseases vs concordance in 4 different databases, hence Gene Disease Databases test these relationships


DisGeNET gene-disease association ontology   The description of each association type in this ontology is: #Therapeutic Association: The gene/protein has a therapeutic role in the amelioration of the disease. #Biomarker Association: The gene/protein either plays a role in the etiology of the disease (e.g. participates in the molecular mechanism that leads to disease) or is a biomarker for a disease. #Genetic Variation Association: Used when a sequence variation (a mutation, a SNP) is associated to the disease phenotype, but there is still no evidence to say that the variation causes the disease. In some cases the presence of the variants increase the susceptibility to the disease. In general, the NCBI SNP identifiers are provided. #Altered Expression Association: Alterations in the function of the protein by means of altered expression of the gene are associated with the disease phenotype. #Post-translational Modification Association: Alterations in the function of the protein by means of post-translational modifications (methylation or phosphorylation of the protein) are associated with the disease phenotype.  [ 1 ]


Relationships in Gene Diseases


The logo of IMGT


OneZoom


Fig. 1. Dynamic Tumor Frequency Grid.


Fig. 2. Advanced Search example.


Fig. 3. PDX Like Me search example.


An overview of data provided by PomBase and ways to access it.


A theoretical ncRNA alignment from 6 species. Secondary structure base pairs are coloured in blocks and identified in the secondary structure consensus sequence (bottom line) by the < and > symbols.


The SRA has grown rapidly since 2008. [ 4 ]  As of 2011, most SRA sequence data was produced by  Illumina 's Genome Analyzer. [ 5 ]


Logo of the Y Chromosome Haplotype Reference Database (YHRD) version 4.0


Many organisms, including  aspen trees , reproduce by cloning, often creating large groups of organisms with the same  DNA . One example depicted here is  quaking aspen .


Cloning cell-line colonies using cloning rings


Propagating plants from  cuttings , such as grape vines, is an ancient form of cloning.


The  taxidermied  body of Dolly the sheep


Dolly clone


Sontarans  in  Doctor Who  are a cloned warrior race.


Diagram of the ways to reprogram cells along with the development of humans


Diagram of SCNT process


Overview of iPS cells


Stem cell treatments


Human therapeutic cloning laws by country     Legal      Legal within the limits of  Islam      Illegal      No data, not specified or depends on  state  legislation


Human therapeutic cloning laws by  U.S. state      Legal      Illegal      No data, not specified or unclear


Relationship between fully differentiated "old" cells, pluripotent stem cells produced through classical cloning, and "young" cells produced by partial cloning.


A.  Morula  and B. cross section of a blastula displaying the  blastocoel  and  blastoderm  of early animal  embryonic development


Clonal expansion  and monoclonal versus polyclonal proliferation


Schematic representation of the  pBR322  plasmid, one of the first plasmids widely used as a cloning vector.


The pUC plasmid has a high copy number, contains a multiple cloning site (polylinker), a gene for ampicillin antibiotic selection, and can be used for blue-white screen.


An LB agar plate showing the result of a blue white screen.   White colonies may contain an insert in the plasmid it carries, while the blue ones are unsuccessful clones.


A  magnolia  stem cutting has been coaxed to form new roots, and is now a complete plant.


Cutting from  Coleus scutellarioides  – after 14 days the roots are 6 cm long.


Softwood cuttings of elm ( Ulmus ) are kept under a water mist to prevent them from drying out while they form roots.


Cuttings from a variety of plants.


Ficus cuttings rooting in water


Scheme of appropriate type of stem cuttings according to season. [ 26 ]  Key: eq.: equinox , sol.:  solstice , HW: hardwood, SR: semi-ripe, SW: softwood.


A plastic cold frame with semi-white plastic, used to keep the cuttings humid and semi-shaded


Propagated by cuttings,  Inch Plants  can be moved easily as its  stolons  cling lightly to the ground.


Pelargonium x hortorum  ( garden geraniums ) are propagated by seeds and cuttings.


Nerium  can readily root after being placed in water or in compost.


Snake plants  are propagated by leaf cuttings or by dividing the  rhizome  (variegated plants will keep their yellow edges only by division).


The  common grapevine  is propagated from a  shoot  taken from a mother vine.


The  Pyrenean ibex , also known as the bouquetin (French) and bucardo (Spanish), is the only animal to have survived de-extinction past birth through cloning.


Pictured above is the process used to clone the  Pyrenean ibex . The tissue culture was taken from the last living, female Pyrenean ibex named Celia. The egg was taken from a  goat  ( Capra hircus ) and the nucleus removed to ensure the offspring was purely Pyrenean ibex. The egg was implanted into a surrogate goat mother for development.


The woolly mammoth is a current prime candidate for de-extinction through cloning or genome editing.


Taxidermised specimen of Celia, the  endling  of her subspecies


A bull from the Taurus Project, a project aiming to de-extinct the aurochs through back breeding modern domesticated cattle.


Living quagga, 1870


The last known thylacine, allegedly named "Benjamin", died from neglect in the Hobart Zoo in 1936.


Martha , the last known passenger pigeon


Skeleton of the bush moa


Maclear's rat, naturalist's painting


Model based on modern research at  Oxford University Museum of Natural History


Model of Steller's sea cow


Sudan , the final male northern white rhinoceros was euthanised due to age-related illnesses on the Ol Pejeta Conservancy in 2018


Stuffed male (bottom right) and female (upper left) specimens at the  Natural History Musuem, London


Ornithologist, professor  Alfred Otto Gross  holding Booming Ben, the last known heath hen


One of the final two remaining wild turtles at Dong Mo Lake in  Son Tay , Vietnam


The Carolina parakeet is a prime candidate for de-extinction due to the genome already being sequenced


The Heck horse was the result of the first attempts at back breeding domesticated horses to recreate the Tarpan, an extinct subspecies of wild horses


The woolly rhinoceros is a prime, but polemic candidate for de-extinction due to the critically endangered status of its closest living relative


Museum specimens of the  Xerces blue , an extinct butterfly


Glyphs  of  Paschalococos , an extinct genus of palm trees native to Easter Island


Methuselah, the first resurrected Judean date palm through germination of 2000 year old seeds found in the  Masada  excavations in the 1960s


Gaya, a female member of the rastreador Brasileiro breed that was revived through  preservation breeding


The balm of Gilead, a historical herbal perfume that the recently discovered/de-extinct Commiphora is believed to be an ingredient of in  The Old City of Jerusalem , Israel


Drawing of the Montreal melon, a de-extinct cultiver of melon


The  cloning  process that produced Dolly


Human egg cell


Diagram of a human egg cell


Ovum and sperm fusing together


The process of fertilizing an ovum (top to bottom).


Gene expression pattern determined by histochemical GUS assays in  Physcomitrella patens . The Polycomb gene FIE is expressed (blue) in unfertilized egg cells of the moss  Physcomitrella patens  (right) and expression ceases after fertilization in the developing diploid sporophyte (left). In situ GUS staining of two female sex organs ( archegonia ) of a transgenic plant expressing a translational fusion of FIE-uidA under control of the native FIE promoter


The San Diego Zoo established the first "frozen zoo" program in 1972.


A  Przewalski's horse


Diagram of trans-species cloning of the Pyrenean ibex


Electric Green GloFish Tetra


An ordinary Zebra Danio


A "Galactic Purple" GloFish shark


The  Zangersheide  stud farm (shown here with their  branding ) has been a driving force behind the development of horse cloning.


Genopole  d'Évry supported the creation of Cryozootech, France's first commercial horse cloning company.


Allegory of the triumph of  capitalism  over communism at  Texas A&M University , the first research institution on the American continent to successfully clone a horse.


One of the fears introduced by cloning is that it will jeopardize traditional horse breeding and reproduction techniques.


Dolly (taxidermy)


A  sticky end  ligation


Mycocepurus smithii  plate


Close up of a head of a  Mycocepurus smithii


BTX ECM 2001 Electrofusion generator used for nuclear transfer applications


Neural progenitors (green) in  olfactory bulb  with astrocytes (blue).


Example of the pattern of division of a progenitor cell (PC) which results in the production of an intermediate progenitor cell (IPC). Both cells later produce one or two neural cells (N).


Model of a  woolly mammoth  at the  Royal BC Museum


Model depicting the calf "Dima", Stuttgart


Modern elephants are highly  gregarious , as shown by these  Sri Lankan elephants


Dolly the sheep  on display at the  National Museum of Scotland


Schematic model of somatic cell nuclear transfer. This technique has been used to create clones of an organism or in therapeutic medicine.


Schematic of CRISPR based gene editing technique


Somatic cell nuclear transfer can create clones for both reproductive and therapeutic purposes.


BTX ECM 2001 electrofusion generator used for SCNT and Cloning applications


Human  blastocyst , showing the  inner cell mass  (top, right)


Pluripotent, embryonic stem cells originate as inner cell mass (ICM) cells within a blastocyst. These stem cells can become any tissue in the body, excluding a placenta. Only cells from an earlier stage of the embryo, known as the  morula , are totipotent, able to become all tissues in the body and the extraembryonic placenta.


Human  embryonic  stem cells   A: Stem cell colonies that are not yet differentiated.   B:  Nerve  cells, an example of a  cell type  after differentiation.


Human mesenchymal stem cells


Stem cell division and differentiation A: stem cell; B: progenitor cell; C: differentiated cell; 1: symmetric stem cell division; 2: asymmetric stem cell division; 3: progenitor division; 4: terminal differentiation


Diseases and conditions where stem cell treatment is being investigated


This image diagrams the procedure of subcloning as outlined to the left.


Diagram of TA Cloning.


Tong Dizhou (1955)


Cross-sectional  micrograph  of the human umbilical cord.  H&E stain . Labelled   allantoic duct  is also known as the  urachus .


Vaginal ultrasonography  of an embryo of a  gestational age  of eight weeks and three days. The embryo is surrounded by the thin membranes of the  amniotic sac , the umbilical cord is seen in the center, attaching the embryo to the  placenta .


A  knotted cord  on a newborn baby


The umbilical cord is about to be cut with scissors via caesarean section


Umbilical cord clamp


A day-old baby with the cord stump still attached.


A 7 cm (2.75 in) long detached umbilical cord.


Production of new individuals along a leaf margin of the air plant,  Kalanchoe pinnata . The small plant in front is about 1 cm tall. The concept of "individual" is stretched by this process.


Kalanchoe daigremontiana  produces plantlets along the margins of its leaves. When they are mature enough, they drop off and root in any suitable soil beneath.


Vegetative reproduction from a stem cutting less than a week old. Some species are more conducive to this means of propagation than others.


A bulb of  Muscari  has reproduced vegetatively underground to make two bulbs, each of which produces a flower stem.


'Lipstick' hybrid strawberry  ( Comarum palustre  ×  Fragaria × ananassa ) using  stolons  to grow new plants


Watsonia meriana , near the end of flowering, has  cormlets  that eventually drop and root.


Red  mangrove  seeds germinate while still on the parent tree.


A graphical representation of the typical human  karyotype


The human mitochondrial DNA


DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/T polymorphism).


Map of the migration of modern humans out of Africa, based on  mitochondrial DNA . Colored rings indicate thousand years before present.


Genetic distance map by Magalhães et al. (2012)


Genetic variation


Genetic variation of Eurasian populations showing different frequency of West- and East-Eurasian components. [ 56 ]


Human genetic variation calculated from genetic data representing 346  microsatellite  loci taken from 1484 individuals in 78 human populations. The upper graph illustrates that as populations are further from East Africa, they have declining genetic diversity as measured in average number of microsatellite repeats at each of the loci. The bottom chart illustrates  isolation by distance . Populations with a greater distance between them are more dissimilar (as measured by the Fst statistic) than those which are geographically close to one another. The horizontal axis of both charts is geographic distance as measured along likely routes of human migration. (Chart from Kanitz et al. 2018)


Chart showing human genetic clustering [ 83 ]


Individuals mostly have genetic variants which are found in multiple regions of the world. Based on data from "A unified genealogy of modern and ancient genomes". [ 84 ]


Ternary plot  showing average admixture of five North American ethnic groups. Individuals that self-identify with each group can be found at many locations on the map, but on average groups tend to cluster differently.


HIV attachment


The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism)


Types of single-nucleotide polymorphism (SNPs)


Associations between SNPs, methylation patterns and gene expression of biological traits


Changes in the number and order of genes (A-D) create genetic diversity within and between populations.


Locations of population samples of 1000 Genomes Project. [ 18 ]  Each circle represents the number of sequences in the final release.


An illustration of a Manhattan plot depicting several strongly associated risk loci


A horse showing the characteristic tiger eye.


This  palomino  is homozygous for Tiger-eye 2, and has blue eyes. [ 2 ]


Three major single-chromosome mutations:  deletion  (1),  duplication  (2) and  inversion  (3).


A red  tulip  exhibiting a partially yellow petal due to a  somatic mutation  in a cell that formed that petal


Prodryas persephone , a Late  Eocene  butterfly


A  covalent   adduct  between the  metabolite  of  benzo[ a ]pyrene , the major  mutagen  in  tobacco smoke , and DNA [ 41 ]


Five types of chromosomal mutations


Types of small-scale mutations


The structure of a  eukaryotic  protein-coding gene. A mutation in the  protein coding region  (red) can result in a change in the amino acid sequence. Mutations in other areas of the gene can have diverse effects. Changes within  regulatory sequences  (yellow and blue) can effect  transcriptional  and  translational  regulation of  gene expression .


Point mutations classified by impact on protein


Selection of disease-causing mutations, in a standard table of the  genetic code  of  amino acids [ 50 ]


The distribution of fitness effects (DFE) of mutations in  vesicular stomatitis virus . In this experiment, random mutations were introduced into the virus by site-directed mutagenesis, and the  fitness  of each mutant was compared with the ancestral type. A fitness of zero, less than one, one, more than one, respectively, indicates that mutations are lethal, deleterious, neutral, and advantageous. [ 69 ]


This figure shows a simplified version of loss-of-function, switch-of-function, gain-of-function, and conservation-of-function mutations.


A mutation has caused this  moss rose  plant to produce flowers of different colours. This is a  somatic  mutation that may also be passed on in the  germline .


Tevenphage


BRCA  mutations are inherited in a  genetically dominant  fashion, from either parent.


The BRCA genes are tumour suppressor genes pictured here on their respective chromosomes. BRCA 1 has the cytogenetic location 17q21 or the q arm of Chromosome 17 at position 21. BRCA 2 has the cytogenetic location 13q12.3 or the q arm of Chromosome 13 at position 12.3. Both genes produce proteins that help repair damaged DNA, keeping the genetic material of the cell stable. A damaged BRCA gene in either location can lead to increased risk of cancer, particularly breast or ovarian in women.


Calico Sheep


A tabby mother and her kittens, showing different colorations


Two amber tabby  Norwegian Forest cats , showing the colour difference with age. On the left a female kitten, on the right a male adult.


A mackerel tabby with the classic "M" on forehead


Agouti hair showing alternating bands along the shaft


Rosette  pattern in a  Bengal .


Female black tortoiseshell and white cat


Blue tortoiseshell and white (diluted calico)  British Shorthair


Agouti hair of a brown tabby with phaeomelanin (red pigment) and eumelanin (black or brown pigment).


Black and white bicolor kitten with fever coat expression over the black fur


Down, awn and guard hairs of a domestic tabby cat


Wavy fur of a Devon Rex cat


Hairless cats are often born even without  whiskers


Figure comparing the effects of exposure to genotoxic agents (aneugens and clastogens) on DNA. Aneugens induce mis-segregation of chromosomes into daughter cells while clastogens break the DNA and chromosome.


Summary of theories of the mechanisms of chromosomal aberrations: A, ‘classic’ breaks theory; B, ‘mis-repair of breaks’ theory; C, ‘repair-created breaks’ theory. Adapted from Bignold. [ 4 ]


Deletion on a chromosome


Three chromosomal abnormalities with ISCN nomenclature, with increasing complexity:  (A)  A tumour karyotype in a male with loss of the Y chromosome,  (B)  Prader–Willi Syndrome i.e. deletion in the 15q11-q12 region and  (C)  an arbitrary karyotype that involves a variety of autosomal and allosomal abnormalities. [ 6 ]


Human  karyotype  with annotated bands and sub-bands as used for the nomenclature of chromosome abnormalities. It shows dark and white regions as seen on  G banding . Each row is vertically aligned at  centromere  level. It shows 22  homologous   autosomal  chromosome pairs, both the female (XX) and male (XY) versions of the two  sex chromosomes , as well as the  mitochondrial genome  (at bottom left).  Further information:  Karyotype


Figure. 1. Chemical structure of apurinic site present in a fragment of single-stranded DNA.


Chromosomes on the left show possible disease gene locations (as identified by any of the below methods) for affected individuals. Red area in the 'composite chromosome' on the right signifies the overlap of these regions, and thus the most probable location of the disease gene


DNA damage in non-replicating cells, if not repaired and accumulated can lead to aging. DNA damage in replicating cells, if not repaired can lead to either apoptosis or to cancer.


Initiation of  DNA demethylation  at a  CpG site . In adult somatic cells DNA methylation typically occurs in the context of CpG dinucleotides ( CpG sites ), forming  5-methylcytosine -pG, or 5mCpG. Reactive oxygen species (ROS) may attack guanine at the dinucleotide site, forming  8-hydroxy-2'-deoxyguanosine  (8-OHdG), and resulting in a 5mCp-8-OHdG dinucleotide site.  The  base excision repair  enzyme  OGG1  targets 8-OHdG and binds to the lesion without immediate excision. OGG1, present at a 5mCp-8-OHdG site recruits  TET1  and TET1 oxidizes the 5mC adjacent to the 8-OHdG.  This initiates demethylation of 5mC. [ 83 ]


Diagram of DNA mismatch repair pathways. The first column depicts mismatch repair in eukaryotes, while the second depicts repair in most bacteria. The third column shows mismatch repair, to be specific in  E. coli .


Micrograph  showing loss of staining for  MLH1  in  colorectal adenocarcinoma  in keeping with DNA mismatch repair (left of image) and benign colorectal mucosa (right of image).


DNA damage resulting in multiple broken chromosomes


Structure of the base-excision repair enzyme  uracil-DNA glycosylase  excising a hydrolytically-produced uracil residue from DNA. The uracil residue is shown in yellow.


The main double-strand break repair pathways


DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide  ester  bond between the phosphate backbone and the deoxyribose nucleotides.


DNA repair rate is an important determinant of cell pathology.


Most life span influencing genes affect the rate of DNA damage.


A chart of common DNA damaging agents, examples of lesions they cause in DNA, and pathways used to repair these lesions. Also shown are many of the genes in these pathways, an indication of which genes are epigenetically regulated to have reduced (or increased) expression in various cancers. It also shows genes in the error-prone microhomology-mediated end joining pathway with increased expression in various cancers.


Initiation of  DNA demethylation  at a  CpG site . In adult somatic cells DNA methylation typically occurs in the context of CpG dinucleotides ( CpG sites ), forming  5-methylcytosine -pG, or 5mCpG. Reactive oxygen species (ROS) may attack guanine at the dinucleotide site, forming  8-hydroxy-2'-deoxyguanosine  (8-OHdG), and resulting in a 5mCp-8-OHdG dinucleotide site. The  base excision repair  enzyme  OGG1  targets 8-OHdG and binds to the lesion without immediate excision. OGG1, present at a 5mCp-8-OHdG site recruits  TET1  and TET1 oxidizes the 5mC adjacent to the 8-OHdG. This initiates demethylation of 5mC. [ 132 ]


Founder effect: The original population (left) could give rise to different founder populations (right).


The small founding population experiences a loss of heterozygosity after multiple generations. ("Genetic Drift" by Boundless, 2015. [ 15 ] )


Different types of indel mutation. Panel C is simply a deletion and not a frameshift mutation.


The  central dogma  model


The  translation  process


The three letter code, the  codon


Example of different types of point mutations


A deletion mutation alters every codon following it, and can make protein synthesis stop prematurely by forming a  stop codon .


Frequency of mutations on BRCA1 gene on chromosome 17


Frequency of mutations on BRCA2 gene on chromosome 13


A schematic showing the ways a fusion gene can occur at a chromosomal level


Schematic of a region of a chromosome before and after a duplication event


Evolutionary fate of duplicate genes


Human  karyotype  with annotated bands and sub-bands as used for the nomenclature of chromosome abnormalities. It shows dark and white regions as seen on  G banding . Each row is vertically aligned at  centromere  level. It shows 22  homologous   autosomal  chromosome pairs, both the female (XX) and male (XY) versions of the two  sex chromosomes , as well as the  mitochondrial genome  (at bottom left).  Further information:  Karyotype


Definition of  transitions  and  transversions . They are a common mutation caused by genotoxic compounds.


Ames test procedure to test for gene mutations present in the various bacterial strains


Overview of the use of the SOS response for genotoxicity testing


Transmittance of a  de novo  mutation in germ cells to offspring.


The CRISPR editing system is able to target specific DNA sequences and, using a donor DNA template, can repair mutations within this gene.


Location of the Glycerol Kinase gene on the X chromosome


The  metabolic pathway  of  glycolysis  releases energy by converting  glucose  to  pyruvate  by via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.


Diagram of an example of a hemoglobin mutation


A mutated hemoglobin protein


Johns Hopkins Hospital in Baltimore, Maryland


There is a wide variety of mitochondrial DNA genotypes in the maternal pool, which is represented by the bottle. The two genotypes in this maternal pool are represented by blue and yellow. When generated, each oocyte receives a small subsampling of mitochondrial DNA molecules in differing proportions. This is represented by the conveyor belt with oocytes, each one unique, as they are produced. [ 9 ]


Sequence illustrating heteroplasmy genotype of 16169 C/T in  Nicholas II of Russia . [ 17 ]


Antennapedia mutation


An illustration of an insertion at chromosome level


Orpington  hen exhibiting typical self-blue  plumage  due to lavender ( lav ) gene on black background.


Pekin Bantam  hen exhibiting the effect of lavender on a red  plumage  background


Figure 1. Incomplete lineage sorting. The gene G has two versions (alleles), G0 and G1. The ancestor of A, B and C originally had only one version of gene G, G0. At some point, a mutation occurred and the ancestral population became polymorphic, with some individuals having G0 and others G1. When species A split off, it retained only G1, while the ancestor of B and C remained polymorphic. When B and C diverged, B retained only G1 and C only G0; neither were now polymorphic in G. The tree for gene G shows A and B as sisters, whereas the species tree shows B and C as sisters.


A cat with the  Japanese Bobtail  mutation


A  Manx cat


Munchkin cat  with thick, short legs


A female polydactl cat with opposable thumbs.


American curl  cat with curled ears.


Scottish Fold  cat with folded ears.


Hairless  Sphynx cat .


An example of loss of heterozygosity over time, in  bottlenecking population . Different  alleles  painted in different colors. A  diploid  population of 10 individuals, that bottlenecked down to three individuals repeatedly, resulted in all individuals homozygous.


Copy-neutral LOH/uniparental disomy


SNP array Virtual karyotype of a colorectal carcinoma (whole genome view) demonstrating deletions, gains, amplifications, and acquired UPD (copy-neutral LOH).


Micronuclei ( B, C ) and nuclear abnormalities ( A, D ) in peripheral blood erythrocytes of penguins  Pygoscelis papua.


Micrograph  showing  tumor-infiltrating lymphocytes  in a case of  colorectal cancer  with evidence of MSI-H on  immunostaining .  H&E stain .


Example of Microsatellite Instability in a DNA Electropherogram Trace


Detection of microsatellite instability by real-time PCR


This image shows an example of missense mutation. One of the nucleotides (adenine) is replaced by another nucleotide (cytosine) in the DNA sequence. This results in an incorrect amino acid (proline) being incorporated into the protein sequence.


Wild type (left) and mutated (right) form of lamin A (pdb id: 1IFR). Normally, Arginine 527 (blue) forms  salt bridge  with glutamate 537 (magenta), but R527L substitution results in breaking this interaction (leucine has a nonpolar tail and therefore cannot form a static salt bridge).


Micrograph  showing loss of staining for  MLH1  in  colorectal adenocarcinoma  in keeping with DNA mismatch repair (left of image) and benign colorectal mucosa (right of image).


A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.


The  international   pictogram  for chemicals that are sensitising, mutagenic,  carcinogenic  or  toxic to reproduction


A  DNA adduct  (at center) of the mutagenic  metabolite  of  benzo[ a ]pyrene  from  tobacco smoke


Fruits and vegetables are rich in antioxidants.


The  blue lobster , an example of a mutant


Wild-type  Physcomitrella  and  knockout mosses : Deviating phenotypes induced in gene-disruption library transformants.  Physcomitrella  wild-type and transformed plants were grown on minimal Knop medium to induce differentiation and development of  gametophores . For each  plant , an overview (upper row, scale bar corresponds to 1 mm) and a close-up (bottom row, scale bar equals 0.5 mm) is shown. A,  Haploid  wild-type moss plant completely covered with leafy gametophores and close-up of wild-type leaf. B–E, Different mutants. [ 1 ]


The accumulation of replication-driven mutations with sex and age


Recently reported estimates of the human genome-wide mutation rate. The human  germline  mutation rate is approximately 0.5×10 −9  per  basepair  per year. [ 1 ]


Generation time  affects mutation rates: The long-lived woody bamboos (tribes  Arundinarieae  and  Bambuseae ) have lower mutation rates (short branches in the  phylogenetic tree ) than the fast-evolving herbaceous bamboos ( Olyreae ).


Transitions  (Alpha) and  transversions  (Beta).


Painting of  Hugo de Vries , making a painting of an  evening primrose , the plant which had apparently produced new forms by large mutations in his experiments, by  Thérèse Schwartze , 1918


Étienne Geoffroy Saint-Hilaire  believed that "monstrosities" could immediately found new species in a single large jump or  saltation .


Rudolph Albert von Kölliker revived Geoffroy's saltationist ideas, calling his theory  heterogenesis . It depended on a nonmaterial directive force ( orthogenesis ).


Drawing of  William Bateson , 1909, by the biologist  Dennis G. Lillie


Wilhelm Johannsen 's "pure line" experiments seemed to show that evolution could not work on continuous variation.


Papilio polytes  has 3 forms with differing wing patterns, here the "Romulus" morph.  Reginald Punnett  argued that this  polymorphism  demonstrated discontinuous evolution. However,  Ronald Fisher  showed that this could have arisen by small changes in additional modifier genes.


Thomas Hunt Morgan 's work on  Drosophila melanogaster  found many small Mendelian factors for natural selection to work on.


John Christopher Willis 's  The Course of Evolution by Differentiation Or Divergent Mutation Rather Than by Selection , 1940


Masatoshi Nei  argues that evolution is often mutation-limited. [ 52 ]


Charles Darwin in 1868


Pictured on the left is a diagram of normal translation occurring without mutation. Blue circles are the peptides already translated while the grey circles are peptides going to be translated next. In the center is a diagram a nonsense mutation where the UUG codon is translated to the stop codon UAG. The stop codon recruits a release factor, terminating translation. On the right is a diagram of the tRNA suppression mechanism where the codon and the tRNA are both mutated, resulting in tRNA suppression. The mutated Tyr tRNA has the anticodon AUC which recognizes the UAG stop codon, continuing protein translation. [ 9 ]


Selection of notable mutations, ordered in a standard table of the  genetic code  of  amino acids . [ 11 ]  nonsense mutations are marked by red arrows.


An example of point mutations at an amino acid site coding for  lysine . The  missense mutations  may be classed as point accepted mutations if the mutated protein is not rejected by natural selection.


PAM250 matrix with both halves filled in.


Point mutations of a codon, classified by their impact on protein sequence


Schematic of a single-stranded RNA molecule illustrating a series of three-base  codons . Each three- nucleotide  codon corresponds to an  amino acid  when translated to protein. When one of these codons is changed by a point mutation, the corresponding amino acid of the protein is changed.


A to G point mutation detected with Sanger sequencing


Transitions  (Alpha) and transversions (Beta).


Depurination mutation results in one normal strand and one shortened strand after replication.


Mosaicism arises after the zygote has formed and a mutation occurs during development. The mutated cell line can be passed down to offspring if the germ cells are affected.


Formation of thymine dimer lesion in DNA. The  photon  causes two consecutive bases on one strand to bind together, destroying the normal base-pairing double-strand structure in that area.


Cyclobutane dimer (CPD) (left), 6,4-dimer (6-4PP) (right)


Melanoma , a type of skin cancer


Resistance to a drug


"Gallus ex Persia", illustration from the  Ornithologiae Tomus Alter  of  Ulisse Aldrovandi , 1600


Illustration from the  Geflügel-Album  of  Jean Bungartz , 1885


This is a diagram of a hard selective sweep. It shows the different steps (a beneficial mutation occurs, increases in frequency and fixes in a population) and the effect on nearby genetic variation.


This is a diagram of a soft selective sweep from standing genetic variation. It shows the different steps (a neutral mutation becomes beneficial, increases in frequency and fixes in a population) and the effect on nearby genetic variation.


This is a diagram of a multiple origin  soft selective sweep  from recurrent mutation. It shows the different steps (a beneficial mutation occurs and increases in frequency, but before it fixes the same mutation occur again on a second genomic background, together, the mutations fix in the population) and the effect on nearby genetic variation.


Seneca white deer inside the depot


Spikelets of  Einkorn wheat ,  Triticum monococcum


Shattering in many crops involves  dehiscence  of the mature fruit, for example, in  Brassica napus .


Point substitution mutations of a codon, classified by their impact on protein sequence


Hydra oligactis  with two buds. Reproduction by  budding  is an exception to the rule that somatic mutations can not be inherited.


UV light  can damage DNA by causing  pyrimidine dimers . Adjacent bases bond with each other, instead of across the “ladder”. The distorted DNA molecule does not function properly. Mutation can result if mistakes occur in  DNA repair  or replication.


A visual representation of a splice site mutation instance [ 3 ]


Foliage of a dwarf Alberta spruce ( Picea glauca  var.  albertiana  'Conica'), with a branch showing reversion [ 1 ]  to the normal Alberta white spruce growth habit of larger leaves and longer internodes.


Diagram of the surveyor nuclease assay workflow


Illustration of a transition: each of the 4 nucleotide changes between purines or between pyrimidines (in blue). The 8 other changes are  transversions  (in red).


Illustration of a transversion: each of the 8 nucleotide changes between a purine and a pyrimidine (in red). The 4 other changes are  transitions  (in blue).


Mutations (red marks) in segments of the genome are reflected in proteins produced from them through transcription and translation. Some proteins are fragmented into peptides that can then be presented as antigens on the surface of cell membranes by major histocompatibility complexes (MHCs). If presented antigens accumulate enough mutations, they can bind and activate T-cells which can then initiate immune mediated cell death.


TMB Variation within and between Different Cancer Types found in TCGA (a colorblind palette was used to make this figure and the TCGA mutation file, mc3.v0.2.8.PUBLIC.maf.gz, was obtained in July 2020 from:  https://gdc.cancer.gov/about-data/publications/mc3-2017 )


Factors such as tumor cell content, tissue preprocessing, choice of sequencing technology, downstream bioinformatic pipelines, and TMB cutoffs can influence TMB calculations.


Gerty Cori  and  Carl Cori  jointly won the  Nobel Prize  in 1947 for their discovery of the  Cori cycle  at RPMI.


DNA structure ( 1D65 ) [ 24 ]


The main elements that compose the human body shown from most abundant (by mass) to least abundant


Structures of some common lipids. At the top are  cholesterol  and  oleic acid . [ 40 ]  The middle structure is a  triglyceride  composed of  oleoyl ,  stearoyl , and  palmitoyl  chains attached to a  glycerol  backbone. At the bottom is the common  phospholipid ,  phosphatidylcholine . [ 41 ]


The general structure of an α-amino acid, with the  amino  group on the left and the  carboxyl  group on the right


Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined as a dipeptide


A schematic of  hemoglobin . The red and blue ribbons represent the protein  globin ; the green structures are the  heme  groups.


Examples of protein structures from the  Protein Data Bank


Members of a protein family, as represented by the structures of the  isomerase   domains


The structure of  deoxyribonucleic acid  (DNA); the picture shows the monomers being put together.


Structural elements of common nucleic acid constituents. Because they contain at least one phosphate group, the compounds marked  nucleoside monophosphate ,  nucleoside diphosphate  and  nucleoside triphosphate  are all nucleotides (not phosphate-lacking  nucleosides ).


Schematic relationship between biochemistry,  genetics , and  molecular biology