testset.csv

user_input,reference_contexts,reference,persona_name,query_style,query_length,synthesizer_name
What recognition did the Institute of Primate Research receive from the African Network of Drugs and Diagnostics Innovation?,"['JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND \nTECHNOLOGY- KAREN CAMPUS\nREPORT ON THE INTERNSHIP AT THE INSTITUTE OF \nPRIMATE RESEARCH SUBMITTED TO DEPARTMENT OF \nREPRODUCTIVE HEALTH AND BIOLOGY.\nDURATION   5TH May to 11th August 2014\nWRITTEN BY: BENSON NYABUTI MAINYE2SIGNATORY PAGE\n \nNAME: MAINYE BENSON NYABUTI\nREG NUMBER: JKC-B06-0042/2011\nSIGNATURE ...............................................\nDATE: ..........................................................\n \n \n \nSUPERVISOR\nI hereby confirm and that the above named student was attached to  the \ndepartment of Reproductive health and biology at the Institute of  Primate \nResearch under my supervision.\n \nNAME: ………………………………………………..\n \nSIGNATURE:…………………………………………\n \nDATE:………………………………………………….\n \n 3 ACKNOWLEDGEMENTS\nFirstly, I would like to take this opportunity to thank the management and \nhuman resource of the Institute of primate research (IPR) for giving me an \nopportunity to carry out an internship at IPR. It was an honor and privilege to be \npart of the team at the short time I’ve been here.\nI have learned a lot during my stay at the institute, I have gotten vast practical \nknowledge relating to microbiology, medical techniques among others that I will \napply in during course and research.\nIn addition, special thanks everyone in the reproductive health and biology, \nthose in the animal science department staff who took their time to explain \nvarious practical aspects and willing ness to assist.\nI am also grateful for the guidance provided by my supervisor Dr. Atunga \nNyachieo for his support and assessment during internship period.\nLastly, I would like to thank the institute of primate research fraternity for \nallowing a smooth running of activities facilitating an easy time during my \ninternship period. Last but not least I would like to thank my parents for their \nencouragement and moral support as well as financial support.4 INTRODUCTION\nThe Institute of research is connected to the family of the late Louis Seymour \nBazett Leakey. Ever since it was established it has grown with help of support \nfrom   Kenya Government, World Health Organization’s Special Programmes in \nHuman Reproduction and Tropical Diseases, and the European Community.  \nIn 2011, it was recognized by the African Network of Drugs and Diagnostics \nInnovation (ANDI) as a Centre of Excellence in Preclinical Research and for its \nwork in health innovation. This new status was conferred to IPR by the ANDI \nStakeholders and Donors Conference held in Addis Ababa Ethiopia on October \n24-27th 2011. The criterion for its recognition was based on its achievements in \npreclinical research and development of new candidate drugs, vaccines and \ndiagnostics for infectious and non-infectious diseases. In addition, it is a World \nHealth Organization collaborating center in human reproduction to add icing to \nthe IPR cake.\nIPR is under ISO 9001:2008 certification which sets out requirements for a \nquality management system. This allows activities to be conducted to give \nimproved performance in the organization.5Table Of Contents\nSIGNATORY PAGE 2\nACKNOWLEDGEMENTS 3\nINTRODUCTION 4\n']","In 2011, the Institute of Primate Research was recognized by the African Network of Drugs and Diagnostics Innovation (ANDI) as a Centre of Excellence in Preclinical Research for its work in health innovation.",Research Biologist,POOR_GRAMMAR,MEDIUM,single_hop_specific_query_synthesizer
What are the key features of a molecular biology laboratory?,['1.0 Good Laboratory Practice and Procedures 6\n1.5 Quality control 6\n 2.0 Department of Reproductive health and biology 7\n2.0.1 Reproductive diseases laboratory LAB A 8\n2.0.2 FACS ROOM 9\n2.0.3 Molecular biology laboratory 10\n3.0 Department of pathology and diagnostics 23\n3.0.1 Diagnostics 23\n3.0.2 HISTOPATHOLOGY LABORATORY 30\n3.0.3 Rodents’ facility 40\n4.0 Department of tropical and infectious disease 46\n4.0.1 Schistosomiasis laboratory 46\n4.0.2 Malaria laboratory 51\n4.0.3 Virology lab 54\n'],"The molecular biology laboratory is part of the Department of Reproductive Health and Biology, which focuses on various aspects of reproductive diseases.",Research Biologist,WEB_SEARCH_LIKE,MEDIUM,single_hop_specific_query_synthesizer
What is the role of the copper intrauterine device in reproductive health research?,"['CONCLUSION 55\nREFERENCES 5661.0 Good Laboratory Practice and Procedures\nBefore I go into the particulars of the laboratories; it is important to mention \na number of principles of good laboratory practice. They include:\n1.Strict adherence to the standard practice and procedures.\n2.Using Personal protective clothing which forms a barrier between \npersonnel and the infectious materials (gloves, laboratory coat and \ngoogles).\n3.All equipment and working surfaces should properly cleaned and \ndisinfected after contact with blood or other potentially infectious \nmaterials.\n4.When working with infectious agents, chemical, biological, hazardous, \nradioactive being aware of potential hazards, and being conversant \nwith practices and procedures required for safe handling of these \nmaterials.\n1.5 Quality control\n1.According to ISO 9001:2008 requirements; there is an aspect on \nmanagement. For example, an aspect in management like Document \ncontrol adequate filling has been done regarding animal test results and \naspect of management and organizational requirements.72.0 Department of Reproductive health and biology \nThis department is concerned with basic and applied research on the aspects of reproductive \nhealth, reproductive biology, physiology and immunology that is important in the understanding \nof both human and non-human primate’s reproduction and fertility/infertility.\nDuring research they developed an ideal research model that is, the baboon Papio anubis to \nstudy various issues related to reproductive biology.\nThe reasons include: \n\uf0b7It is not an endangered species; there numbers are not declining to an extent they are \ngetting extinct.\n\uf0b7It is most abundant in Kenya\n\uf0b7Closeness in terms of:- \nPhylogeny-compared to human beings, the baboon possesses 42 chromosomes whereas the \nhuman being possesses 46 chromosomes.\nAnatomy-if you look at the anatomy of the female reproductive tract of a baboon it is quite \nsimilar to that of female human being, however, the size differs.\nImmunology \nReprophysiology refers to the study of maternal female hormone system which includes \nactivities of various endocrine organs from puberty till menopause.\nThey also have a big body size enabling complicated surgery and repeated blood sampling.\nFemale reproductive biology lab/reproductive diseases laboratory \nFemale baboon\nReproductive cycle\nGestation about 6months/170 days\nWeaning 6 months\nLitter size average 1 \nAnimals under observation are assigned numbers. That is, the female baboon for instance. \nThe numbers 1-8 are given which corresponds with a particular phase of the female \nreproductive cycle.\nFor example8Menstruation phase is assigned the number 7\nLuteal phase 0&6\nOvulation phase 1-5\nGestation 8\nIn addition, perineal inflation and deflation (sex skin) - makes it easier for the cycle to be \ndetermined .\n2.0.1 Reproductive diseases laboratory LAB A\nThey are several projects going on in the reproductive diseases laboratory ;\nEndometriosis is a condition in which cells that are normally found inside the uterus \n(endometrial cells) are found growing outside of the uterus. That is, the lining of the inside of \nthe uterus is found outside of it. Endometrial cells are the cells that shed every month during \nmenstruation, and so endometriosis is most likely to affect women during their childbearing \nyears. \nThe baboon Papio anubis  is being as model to study this disease.\nCopper intrauterine device (I.U.D) project \n5 Baboons are under study. Some of the aims of the study were to investigate the implication \nof the device with Chlamydia, to observe if there were changes in the microbiota.\nHow it works\nThe intra uterine device is one of the ways of preventing pregnancy via preventing fertilization of the \negg by damaging or killing the sperm. It also affects the uterine lining. \nThe copper I.U.D is toxic to the sperm. It makes the uterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\nKhat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\nStudent project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus']","The copper intrauterine device (I.U.D) project involves studying its implications with Chlamydia and observing changes in the microbiota. The I.U.D works by preventing pregnancy through damaging or killing sperm and affecting the uterine lining, as it is toxic to sperm and causes the uterus and fallopian tubes to produce fluid that kills sperm.",Research Biologist,MISSPELLED,SHORT,single_hop_specific_query_synthesizer
How Neopterin is measured in the lab?,"['Laboratories in the department 2.0.2 Facs room Equipment FACS CALIBUR Use: Allows user to perform both cell analysis and cell sorting in a single bench top system. It allows enumeration of lymphocyte subsets, stem cells, residual white blood cells and reticulocytes. ELISA reader Use: Measures and quantitates the color differences in the 96 wells of the plate. How it works It uses spectrophotometry; they emit light at one wave length, and measure the amount of light absorbed and reflected by an object such as Neopterin. When it is exposed to a wavelength it will emit a certain wavelength of light when exposed light of 450nm. The amount of absorption will be measured thus quantifying the amount of substance. Fridges Used: Used to store reagents and samples.102.0.3 Molecular biology laboratory This laboratory is involved in the study of biology at a molecular level using specialized equipment such as thermo cycler, real time polymerase chain reaction and Loop mediated isothermal amplification. The first molecular technique that was demonstrated was the polymerase chain reaction. The polymerase chain reaction is used to amplify small pieces of Deoxyribonucleic acid (D.N.A) to make millions copies of the product. They are several variations of this technique; it has been manipulated to be used for diagnostic purposes. LAMP (loop mediated isothermal amplification) Use: Amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. Principle This method employs DNA polymerase and four specifically designed primers that recognize a total of six regions of the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. This serves as a template for DNA synthesis primed by an outer primer releases a single stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem–loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem–loop DNA and a new stem–loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 109 copies of target in less than an hour. The final products are stem–loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity ( Keiko Watanabe et al., 2000) 11Projects Objective : Isolation of DNA to detect Trypanosoma brucei brucei DNA in different samples obtained from vervet monkeys ( Chlorocebus pygerythus ) Materials and apparatus \uf0b7Whole blood, Serum, Cerebrospinal fluid, Urine and saliva \uf0b7Vortex \uf0b7Microcentrifuge \uf0b7Reaction tubes \uf0b7Zymo research kit \uf0b7Micropipette Procedure 1.Added 400µl of genomic lysis buffer (breaks down cells and mimics the internal conditions of the cell to preserve the lysate) to 100µl of blood, serum, urine, cerebrospinal fluid (c.s.f) and saliva in a ratio of 4:1 ratio. 2.Mixed completely by vortexing 4-6 seconds, and then let it stand for 5minutes at room temperature. 3.Transferred the mixture to a Zymo –SpinTM column in a collection tube. 4.Centrifuged art 1000xg for one minute. Discard the collection tube with flow through. 5.Transferred the zymo-spinTM column to a new collection tube. 6.Added 200µl of DNA prewash buffer to the spin column. 7.Centrifuged at 10,000xg for 1minute. 8.Added 500µl of g-DNA wash buffer to the spin column. 9.Centrifuged at 10,000xg for 1 minute. 10.Transferred the spin column to a clean microcentrifuge tube. Added ≥50ml DNA elution buffer or water to the spin column. 11.Incubated 2-5minutes at room temperature and then centrifuge at top speed for 30 seconds to elute the DNA. 12.The eluted DNA can be used immediately for molecular based applications or stored ≤ -20oC for']","Neopterin is measured using an ELISA reader, which quantifies color differences in the 96 wells of the plate. It works through spectrophotometry, emitting light at one wavelength and measuring the amount of light absorbed and reflected by Neopterin when exposed to light of 450nm.",Benson Nyabuti Mainye,POOR_GRAMMAR,MEDIUM,single_hop_specific_query_synthesizer
How does the fluid produced by the uterus and fallopian tubes affect sperm in relation to cell analysis techniques used in the laboratory?,"['<1-hop>\n\nLaboratories in the department 2.0.2 Facs room Equipment FACS CALIBUR Use: Allows user to perform both cell analysis and cell sorting in a single bench top system. It allows enumeration of lymphocyte subsets, stem cells, residual white blood cells and reticulocytes. ELISA reader Use: Measures and quantitates the color differences in the 96 wells of the plate. How it works It uses spectrophotometry; they emit light at one wave length, and measure the amount of light absorbed and reflected by an object such as Neopterin. When it is exposed to a wavelength it will emit a certain wavelength of light when exposed light of 450nm. The amount of absorption will be measured thus quantifying the amount of substance. Fridges Used: Used to store reagents and samples.102.0.3 Molecular biology laboratory This laboratory is involved in the study of biology at a molecular level using specialized equipment such as thermo cycler, real time polymerase chain reaction and Loop mediated isothermal amplification. The first molecular technique that was demonstrated was the polymerase chain reaction. The polymerase chain reaction is used to amplify small pieces of Deoxyribonucleic acid (D.N.A) to make millions copies of the product. They are several variations of this technique; it has been manipulated to be used for diagnostic purposes. LAMP (loop mediated isothermal amplification) Use: Amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. Principle This method employs DNA polymerase and four specifically designed primers that recognize a total of six regions of the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. This serves as a template for DNA synthesis primed by an outer primer releases a single stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem–loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem–loop DNA and a new stem–loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 109 copies of target in less than an hour. The final products are stem–loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity ( Keiko Watanabe et al., 2000) 11Projects Objective : Isolation of DNA to detect Trypanosoma brucei brucei DNA in different samples obtained from vervet monkeys ( Chlorocebus pygerythus ) Materials and apparatus \uf0b7Whole blood, Serum, Cerebrospinal fluid, Urine and saliva \uf0b7Vortex \uf0b7Microcentrifuge \uf0b7Reaction tubes \uf0b7Zymo research kit \uf0b7Micropipette Procedure 1.Added 400µl of genomic lysis buffer (breaks down cells and mimics the internal conditions of the cell to preserve the lysate) to 100µl of blood, serum, urine, cerebrospinal fluid (c.s.f) and saliva in a ratio of 4:1 ratio. 2.Mixed completely by vortexing 4-6 seconds, and then let it stand for 5minutes at room temperature. 3.Transferred the mixture to a Zymo –SpinTM column in a collection tube. 4.Centrifuged art 1000xg for one minute. Discard the collection tube with flow through. 5.Transferred the zymo-spinTM column to a new collection tube. 6.Added 200µl of DNA prewash buffer to the spin column. 7.Centrifuged at 10,000xg for 1minute. 8.Added 500µl of g-DNA wash buffer to the spin column. 9.Centrifuged at 10,000xg for 1 minute. 10.Transferred the spin column to a clean microcentrifuge tube. Added ≥50ml DNA elution buffer or water to the spin column. 11.Incubated 2-5minutes at room temperature and then centrifuge at top speed for 30 seconds to elute the DNA. 12.The eluted DNA can be used immediately for molecular based applications or stored ≤ -20oC for', '<2-hop>\n\nuterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\n Khat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\n Student project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus papio) affects baboons is similar to Herpes Simplex \nVirus-1, thus, she is using it as a model to study Herpes simplex virus -1)\nOther projects:9OVART Ovary transplantation\nIt could have been done in the following ways:\nThe ovary to be transplanted is thawed. The procedure is done in open surgery and involves \nreconnecting tiny blood vessels to the ovary. This enables steady blood flow to the ovary which is \nvital to its function. After a few months the ovary may be fully functional.\nAlternatively, ovary tissue can be transplanted to defective ovary instead of the whole ovary tissue.\nAlso, in the past characterization of the rotavirus strains was carried out in the past.\n future use.1213.Prepared the LAMP reaction tubes of Dhat( Trypanosoma brucei detection reagent) no. of samples+ 2 tubes for controls) 14.Sealed the aluminum bag immediately. 15.Pipetted 25µl of the sample solution and close the lid of the lamp reaction tube. 16.Pipetted 25 µl of the negative control HAT (NC HAT) into a lamp reaction tube. 17.Pipetted 25 µl of the positive control HAT (PC HAT) into a lamp reaction tube. 18.Turned the reaction tubes upside-down to collect the solution in the cap (reconstitute the LAMP reagents for 2 minutes with a timer). 19.Inverted the LAMP reaction tube 5 times (Move the solution from the cap to the bottom or bottom to cap) N.B Avoid any bubbles. 20.Started the LAMP reaction for 40 minute at 65oC. Results Negative sample: No fluorescent light is emitted. Graphs according to the LAMP program Y-axis optical density X-axis time Positive control has a steep rise then levels out Negative control is on the negative axes Interpretation The drug administered to the animals was effective since no T.brucei brucei DNA was found in the samples. Moreover, the reaction tube can be set into the Visual Check unit, illuminated and the results checked. For a valid run the follow results must be obtained \uf0b7Positive control: Green fluorescent light is emitted. \uf0b7Negative control: No fluorescent light is emitted. 13']","The fluid produced by the uterus and fallopian tubes contains white blood cells, copper ions, enzymes, and prostaglandins, which can kill sperm. In the laboratory, cell analysis techniques such as those performed using the FACS Calibur allow for the enumeration of lymphocyte subsets and other cell types, which could be relevant in studying the effects of this fluid on sperm viability and function.",,,,multi_hop_abstract_query_synthesizer
"How does DNA purification contribute to diagnostics in pathology laboratories, particularly in the context of Toxoplasma gondii detection?","['<1-hop>\n\ne of DNA since it has intercalated with DNA.  The DNA band \ncan also be cut out and can be dissolved to retrieve the purified DNA. Sybr green can be used instead of \nethidium bromide.21 Purification of DNA \nThermo scientific GeneJET PCR Purification Kit\nPrinciple\nA reaction mixture containing the DNA is combined with the binding buffer and added to a purification \ncolumn. A chaotrophic agent in the binding buffer denatures protein and promotes DNA binding in a \nsilica membrane in the column. As an added advantage the binding buffer contains a color indicator that \nallows easy monitoring of the solution pH for optimal DNA binding. Impurities are removed in a single \nwash step. Purified DNA is eluted from the column using an elution buffer. The recovered DNA is ready \nfor use in downstream applications. As an example this method was used to purify DNA isolated by Mr. \nShadrack Lekerepes who was the principal investigator of this research project.\n Toxoplasma project\nA few individuals have been involved in this project. They all had different objectives regarding these \nprotozoa. Some of them include:\nTo make a standard kit to diagnose Toxoplasma gondii  that can be used in LAMP thermocycler \n(objective)\n Procedure\nIn order to make the kit isolated DNA template of the parasite had to be obtained.\nIt involved making a standard master mix \nAfter adding the template DNA and the primers in a reaction tube \nIt was then placed in the Thermocycler \nAfter a period of time, amplification proceeded but the positive and negative control did not get amplified \nas required in some instances. Thus, the contents of the master mix were reviewed.22Real time polymerase chain reaction\nUse \nqTOWER 2.0/2.2 is a thermal cycler for amplifying DNA by way of the polymerase chain\nReaction (PCR) licensed for real-time PCR experiments. The license is limited to applications outside of \nvitro diagnostics (research use only).\nThe integrated detector enables the measurement of the sample fluorescence in up to six spectral channels \nduring the PCR, with the filters used in the color or FRET modules being exactly matched to the \nproperties of the most frequently used fluorescence dyes, thereby, permitting a sensitive and selective \ndetection of fluorescent PCR products.\nAnalytik Jena offers a number of color or FRET modules of which up to six can be installed \nsimultaneously in the device. Replacement and retrofit of color or FRET modules can be easily \naccomplished.\nqTOWER 2.0/2.2 is an open platform for real-time PCR and supports intercalating dyes as well as \nindividual samples and kits of various manufacturers. qTOWER 2.0/2.2 can be used in different \napplications, such as expression analyses, genotyping and the detection of pathogens.233.0 ', '<2-hop>\n\nDiagnostics & Pathology laboratories. This inevitably encompasses the health care, provision of veterinary and related technical services during the carrying out of scientific procedures and investigations utilizing laboratory animals for instance, non-human primates. 3.0.1 Diagnostics Diagnosis is the identification of the cause of a disorder such as a disease. It is involved hematology, bacteriology, parasitology and mycology; however, this was not done during my rotation. Parasitology The first technique that was demonstrated formalin ether technique. It is used to concentrate a wide variety of fecal specimens from fresh or preserved specimen. The stool is emulsified in formol water/ 10 % formalin the suspension is strained to remove fecal particles, diethyl ether is added and the mixed suspension is centrifuged. Cysts, oocysts, eggs and larvae are fixed and sedimented and the fecal debris is separated in a layer between ether and the formol water. Diagram for formol ether sedimentation technique Purpose : To determine eggs and larvae of parasitic worms and cysts of protozoa in fecal specimens of infested animals.24Materials \uf0b7Fresh or formalin fixed stool \uf0b710% formol saline \uf0b7Diethyl-Ether or ethyl acetate \uf0b715ml conical tubes \uf0b7Wash bottles \uf0b7Microscope slides \uf0b7Cover slips \uf0b7Bulb pipettes Procedure 1.Pour about 4ml of formol saline solution into screw cap container. 2.Add about 2g of feces. Using a glass rod or an applicator stick to emulsify the fecal samples. 3.Pass the emulsified stool via 4 layer gauze into a clean labelled 15ml centrifuge tube and make up the volume to 7ml. 4.Add 3ml of diethyl ether or ethylene acetate; replace the ca p and shake vigorously for 1 minute. 5.Loosen the cap to release trapped gas, balance with another tube of the same volume and centrifuge at 500xg for ten minutes. 6.Dislodge the interphase between ether and formol saline then discard the supernatant by turning the tube upside down. 7.Remove the fats from the sides of the tube using a cotton swab and add a little 10% formol saline to resuspend the pellet. 8.Take a small volume of the well-mixed deposit and put it on a clean microscope slide, add a drop of lugol’s iodine and carefully place a cover slip on top. 9.Mount the slide onto the microscope stage and examine using 10x then 40x objective lens 10.To scan for ova and cysts such as Entamoeba spp (4-8 nuclei), Iodomoeba species (bulls eye appearance take up iodine), Blastocytis hominis cyst (nucleus surrounded by 25granules), Balantidium coli (has two nuclei- a macro and micronuclei, Trichuria trichuris egg (has typical polar caps suggesting a lemon shape), Strongyles spp and Strongloides spp eggs. Hematology Observation of different white blood cells I observed previously stained blood smears; The blood smears were stained using the giemsa stain. It is used to differentiate nuclear and or cytoplasmic morphology of platelets, red blood cells, white blood cells and parasites. Cytoplasm color Nucleus and lobulation Neutrophil Pink Purple 2-5 lobes Eosinophil(dark outline on cell membrane)Orange-red Purple 1-3 Basophil Purple granules obscure the nucleusPurple, figure 8 nucleus Monocytes Pale cytoplasm Purple nucleus. Can also possess vacuoles Lymphocyte blue purple Differential Leukocyte count Before reporting, an individual should choose what method to count the leukocytes it could be battlement or horizontal. In a differential leukocyte count-the status of the different blood cells is reported such as; 1.Lobulation of polymorphonuclear neutrophils can be looked at <2 lobes -shift to left26 >3 lobes –shift to right Inclusion bodies 2.Red cells Can be report as macro, micro and normal Size of the cell-sickle, ovalocytes, sphreocytes Shape leptocyte or hematocytes Staining Inclusion bodies like parasites of malaria273.Platelets Distribution 8-25 per field Size Bacteriology Gram stain procedure Vaginal swabs smears were made in the past from female baboons Papio anubis']","DNA purification is crucial for diagnostics in pathology laboratories as it allows for the isolation of DNA templates necessary for accurate detection of pathogens like Toxoplasma gondii. The purification process involves using a binding buffer and a purification column, which ensures that impurities are removed and the DNA is ready for downstream applications. In the context of Toxoplasma detection, a standard kit was developed that required the isolation of the parasite's DNA template, which was then amplified using techniques such as real-time polymerase chain reaction (PCR). This method enhances the reliability of diagnostics by providing a clear and purified DNA sample for analysis.",,,,multi_hop_abstract_query_synthesizer
"How does the process of cell analysis in the laboratory relate to the study of the uterus and fallopian tubes, particularly in terms of the fluid they produce that affects sperm?","['<1-hop>\n\nLaboratories in the department 2.0.2 Facs room Equipment FACS CALIBUR Use: Allows user to perform both cell analysis and cell sorting in a single bench top system. It allows enumeration of lymphocyte subsets, stem cells, residual white blood cells and reticulocytes. ELISA reader Use: Measures and quantitates the color differences in the 96 wells of the plate. How it works It uses spectrophotometry; they emit light at one wave length, and measure the amount of light absorbed and reflected by an object such as Neopterin. When it is exposed to a wavelength it will emit a certain wavelength of light when exposed light of 450nm. The amount of absorption will be measured thus quantifying the amount of substance. Fridges Used: Used to store reagents and samples.102.0.3 Molecular biology laboratory This laboratory is involved in the study of biology at a molecular level using specialized equipment such as thermo cycler, real time polymerase chain reaction and Loop mediated isothermal amplification. The first molecular technique that was demonstrated was the polymerase chain reaction. The polymerase chain reaction is used to amplify small pieces of Deoxyribonucleic acid (D.N.A) to make millions copies of the product. They are several variations of this technique; it has been manipulated to be used for diagnostic purposes. LAMP (loop mediated isothermal amplification) Use: Amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. Principle This method employs DNA polymerase and four specifically designed primers that recognize a total of six regions of the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. This serves as a template for DNA synthesis primed by an outer primer releases a single stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem–loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem–loop DNA and a new stem–loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 109 copies of target in less than an hour. The final products are stem–loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity ( Keiko Watanabe et al., 2000) 11Projects Objective : Isolation of DNA to detect Trypanosoma brucei brucei DNA in different samples obtained from vervet monkeys ( Chlorocebus pygerythus ) Materials and apparatus \uf0b7Whole blood, Serum, Cerebrospinal fluid, Urine and saliva \uf0b7Vortex \uf0b7Microcentrifuge \uf0b7Reaction tubes \uf0b7Zymo research kit \uf0b7Micropipette Procedure 1.Added 400µl of genomic lysis buffer (breaks down cells and mimics the internal conditions of the cell to preserve the lysate) to 100µl of blood, serum, urine, cerebrospinal fluid (c.s.f) and saliva in a ratio of 4:1 ratio. 2.Mixed completely by vortexing 4-6 seconds, and then let it stand for 5minutes at room temperature. 3.Transferred the mixture to a Zymo –SpinTM column in a collection tube. 4.Centrifuged art 1000xg for one minute. Discard the collection tube with flow through. 5.Transferred the zymo-spinTM column to a new collection tube. 6.Added 200µl of DNA prewash buffer to the spin column. 7.Centrifuged at 10,000xg for 1minute. 8.Added 500µl of g-DNA wash buffer to the spin column. 9.Centrifuged at 10,000xg for 1 minute. 10.Transferred the spin column to a clean microcentrifuge tube. Added ≥50ml DNA elution buffer or water to the spin column. 11.Incubated 2-5minutes at room temperature and then centrifuge at top speed for 30 seconds to elute the DNA. 12.The eluted DNA can be used immediately for molecular based applications or stored ≤ -20oC for', '<2-hop>\n\nuterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\n Khat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\n Student project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus papio) affects baboons is similar to Herpes Simplex \nVirus-1, thus, she is using it as a model to study Herpes simplex virus -1)\nOther projects:9OVART Ovary transplantation\nIt could have been done in the following ways:\nThe ovary to be transplanted is thawed. The procedure is done in open surgery and involves \nreconnecting tiny blood vessels to the ovary. This enables steady blood flow to the ovary which is \nvital to its function. After a few months the ovary may be fully functional.\nAlternatively, ovary tissue can be transplanted to defective ovary instead of the whole ovary tissue.\nAlso, in the past characterization of the rotavirus strains was carried out in the past.\n future use.1213.Prepared the LAMP reaction tubes of Dhat( Trypanosoma brucei detection reagent) no. of samples+ 2 tubes for controls) 14.Sealed the aluminum bag immediately. 15.Pipetted 25µl of the sample solution and close the lid of the lamp reaction tube. 16.Pipetted 25 µl of the negative control HAT (NC HAT) into a lamp reaction tube. 17.Pipetted 25 µl of the positive control HAT (PC HAT) into a lamp reaction tube. 18.Turned the reaction tubes upside-down to collect the solution in the cap (reconstitute the LAMP reagents for 2 minutes with a timer). 19.Inverted the LAMP reaction tube 5 times (Move the solution from the cap to the bottom or bottom to cap) N.B Avoid any bubbles. 20.Started the LAMP reaction for 40 minute at 65oC. Results Negative sample: No fluorescent light is emitted. Graphs according to the LAMP program Y-axis optical density X-axis time Positive control has a steep rise then levels out Negative control is on the negative axes Interpretation The drug administered to the animals was effective since no T.brucei brucei DNA was found in the samples. Moreover, the reaction tube can be set into the Visual Check unit, illuminated and the results checked. For a valid run the follow results must be obtained \uf0b7Positive control: Green fluorescent light is emitted. \uf0b7Negative control: No fluorescent light is emitted. 13']","In the laboratory, cell analysis is performed using equipment such as the FACS Calibur, which allows for the enumeration of various cell types, including lymphocytes and stem cells. This technique is crucial for understanding cellular interactions and responses. In the context of the uterus and fallopian tubes, it has been observed that these structures produce a fluid containing white blood cells, copper ions, enzymes, and prostaglandins, which plays a significant role in the reproductive process by affecting sperm viability. The analysis of these cells and fluids can provide insights into reproductive health and the mechanisms by which the uterine environment influences sperm function.",,,,multi_hop_abstract_query_synthesizer
"What role do the uterus and fallopian tubes play in reproductive health, particularly in relation to cell analysis techniques used in molecular biology?","['<1-hop>\n\nLaboratories in the department 2.0.2 Facs room Equipment FACS CALIBUR Use: Allows user to perform both cell analysis and cell sorting in a single bench top system. It allows enumeration of lymphocyte subsets, stem cells, residual white blood cells and reticulocytes. ELISA reader Use: Measures and quantitates the color differences in the 96 wells of the plate. How it works It uses spectrophotometry; they emit light at one wave length, and measure the amount of light absorbed and reflected by an object such as Neopterin. When it is exposed to a wavelength it will emit a certain wavelength of light when exposed light of 450nm. The amount of absorption will be measured thus quantifying the amount of substance. Fridges Used: Used to store reagents and samples.102.0.3 Molecular biology laboratory This laboratory is involved in the study of biology at a molecular level using specialized equipment such as thermo cycler, real time polymerase chain reaction and Loop mediated isothermal amplification. The first molecular technique that was demonstrated was the polymerase chain reaction. The polymerase chain reaction is used to amplify small pieces of Deoxyribonucleic acid (D.N.A) to make millions copies of the product. They are several variations of this technique; it has been manipulated to be used for diagnostic purposes. LAMP (loop mediated isothermal amplification) Use: Amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. Principle This method employs DNA polymerase and four specifically designed primers that recognize a total of six regions of the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. This serves as a template for DNA synthesis primed by an outer primer releases a single stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem–loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem–loop DNA and a new stem–loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 109 copies of target in less than an hour. The final products are stem–loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity ( Keiko Watanabe et al., 2000) 11Projects Objective : Isolation of DNA to detect Trypanosoma brucei brucei DNA in different samples obtained from vervet monkeys ( Chlorocebus pygerythus ) Materials and apparatus \uf0b7Whole blood, Serum, Cerebrospinal fluid, Urine and saliva \uf0b7Vortex \uf0b7Microcentrifuge \uf0b7Reaction tubes \uf0b7Zymo research kit \uf0b7Micropipette Procedure 1.Added 400µl of genomic lysis buffer (breaks down cells and mimics the internal conditions of the cell to preserve the lysate) to 100µl of blood, serum, urine, cerebrospinal fluid (c.s.f) and saliva in a ratio of 4:1 ratio. 2.Mixed completely by vortexing 4-6 seconds, and then let it stand for 5minutes at room temperature. 3.Transferred the mixture to a Zymo –SpinTM column in a collection tube. 4.Centrifuged art 1000xg for one minute. Discard the collection tube with flow through. 5.Transferred the zymo-spinTM column to a new collection tube. 6.Added 200µl of DNA prewash buffer to the spin column. 7.Centrifuged at 10,000xg for 1minute. 8.Added 500µl of g-DNA wash buffer to the spin column. 9.Centrifuged at 10,000xg for 1 minute. 10.Transferred the spin column to a clean microcentrifuge tube. Added ≥50ml DNA elution buffer or water to the spin column. 11.Incubated 2-5minutes at room temperature and then centrifuge at top speed for 30 seconds to elute the DNA. 12.The eluted DNA can be used immediately for molecular based applications or stored ≤ -20oC for', '<2-hop>\n\nuterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\n Khat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\n Student project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus papio) affects baboons is similar to Herpes Simplex \nVirus-1, thus, she is using it as a model to study Herpes simplex virus -1)\nOther projects:9OVART Ovary transplantation\nIt could have been done in the following ways:\nThe ovary to be transplanted is thawed. The procedure is done in open surgery and involves \nreconnecting tiny blood vessels to the ovary. This enables steady blood flow to the ovary which is \nvital to its function. After a few months the ovary may be fully functional.\nAlternatively, ovary tissue can be transplanted to defective ovary instead of the whole ovary tissue.\nAlso, in the past characterization of the rotavirus strains was carried out in the past.\n future use.1213.Prepared the LAMP reaction tubes of Dhat( Trypanosoma brucei detection reagent) no. of samples+ 2 tubes for controls) 14.Sealed the aluminum bag immediately. 15.Pipetted 25µl of the sample solution and close the lid of the lamp reaction tube. 16.Pipetted 25 µl of the negative control HAT (NC HAT) into a lamp reaction tube. 17.Pipetted 25 µl of the positive control HAT (PC HAT) into a lamp reaction tube. 18.Turned the reaction tubes upside-down to collect the solution in the cap (reconstitute the LAMP reagents for 2 minutes with a timer). 19.Inverted the LAMP reaction tube 5 times (Move the solution from the cap to the bottom or bottom to cap) N.B Avoid any bubbles. 20.Started the LAMP reaction for 40 minute at 65oC. Results Negative sample: No fluorescent light is emitted. Graphs according to the LAMP program Y-axis optical density X-axis time Positive control has a steep rise then levels out Negative control is on the negative axes Interpretation The drug administered to the animals was effective since no T.brucei brucei DNA was found in the samples. Moreover, the reaction tube can be set into the Visual Check unit, illuminated and the results checked. For a valid run the follow results must be obtained \uf0b7Positive control: Green fluorescent light is emitted. \uf0b7Negative control: No fluorescent light is emitted. 13']","The uterus and fallopian tubes produce fluid that kills sperm, containing white blood cells, copper ions, enzymes, and prostaglandins. In the context of reproductive health, cell analysis techniques such as those performed in molecular biology laboratories can be utilized to study the effects of these fluids on sperm viability and overall reproductive health. Techniques like polymerase chain reaction (PCR) and LAMP (loop-mediated isothermal amplification) can amplify DNA from samples taken from the reproductive system, allowing for detailed analysis of cellular responses and interactions.",,,,multi_hop_abstract_query_synthesizer
"What are the key requirements for conducting PCR, and how does it relate to the study of the β-lactoglobulin gene in East African goats?","['<1-hop>\n\nPCR Requirements \nPCR buffer for stabilization of pH for optimum functioning of enzyme for example\nMagnesium Chloride MgCl 2 increase Taq polymerase activity \ndNTps deoxynucleotide triphosphate building blocks for new DNA strands\nDouble distilled water dilutes other reagents to correct concentrations \nTaq polymerase synthesis new strands complimentary to the target sequence \nPrimers (Forward& Reverse primers) - sites for polymerase to begins synthesizing DNA\nTemplate DNA17 Diagram of PCR summary  (Occurs in the thermocycler) \nThe cycles are variable depending on how many DNA strands are required. The times can also vary to \nspecifics of the investigator.18', ""<2-hop>\n\nn concentrations has been associated with increased production of reactive oxygen species. \nIt also allows estimation of the extent of oxidative stress elicited by the immune system.\nNeopterin can also correlate with the extent and activity of a disease and is useful in monitor during the \ntherapy in patients suffering from Borrelia .\n Principle\nThe Neopterin ELISA employs an enzyme immunoassay technique to quantitate neopterin in a serum \nsample.\nEnzyme immunoassays depend on the ability of a specific antibody to bind to its corresponding antigen. \nTo quantitate the antigen, the enzyme-conjugate (labeled) and native (unlabeled) of the antigen compete \nfor a limited number of binding sites on its specific antibody. As more unlabeled antigen is added to the \nreaction, it takes up more antibody binding sites allowing less enzyme-labeled antigen to be bound. This \nproceeds until equilibrium between the free and the antibody –bound antigen occurs. \nIn the neopterin ELISA, the sample and the enzyme conjugate are added to an antibody-coated assay well \nand incubated at room temperature for two hours. Following a wash step to remove all unbound labelled \nand unlabeled neopterin, substrate (TMB) is added and color development is allowed to proceed for 30 \nminutes. The enzyme reaction is rapidly terminated by the addition of a stopping solution (dilute sulfuric \nacid) and the absorbance is read at 450nm. The resulting absorbance is inversely proportional to the \namount of neopterin in the standard and the sample. \nSummary\n1.Incubation (Sample and enzyme conjugate)\n2.Wash (removes unlabeled  or unlabeled neopterin)\n3.Add substrate (3,31,5,51Tetramethylbenzidine)144.Add stopping solution H 2SO 4\nEnzyme conjugate concentrate Neopterin-horseradish concentrate\n Results \nPositive and negative wells that possess or do not possess the neopterin in the ELISA plate as shown from \nELISA reader printout.\nThis is followed by Calculations.\nAverage the absorbance of all duplicates. Subtract the averaged non-specific binding (NSB) absorbance \nfrom the average obtained above.\nThis yields a net absorbance. Divide the net absorbance by the net zero standard absorbance (B 0) to obtain \nthe % bound (% B/B 0)\n%B/B0 =  X 100\nAbs= average absorbance of the duplicate wells \nNSB= non-specific binding (also the blank)\nSample= particular serum or standard being calculated \nZero standard= 0 ng/ml standard or 100% binding wells\nConstruct graph\n%bound (Y-axis) versus the concentration \nX-axis the concentration of Neopterin standards\nHelps in the determination of the concentration of neopterin in each sample of the vervet monkeys.15Restriction Fragment Length Polymorphism\nAim: To study polymorphism in β-lactoglobulin gene in a small East African goat breed using PCR \nRestriction Fragment Length Polymorphism and Sequencing\nβ-lactoglobulin protein is a protein found in goat milk and it affects the quality. \nβ-lactoglobulin gene codes protein β-lactoglobulin in milk \nCharacteristics of the gene ( β-lactoglobulin gene)\nIt has 7 exons and 6 introns \nThe β-lactoglobulin area has 426 base pairs \nProcedure \nTo get the area of interest DNA must be extracted from the blood sample using a DNA extraction kit\nThis is followed by Digestion was done aided by Sac II restriction enzyme in order to isolate the region of \ninterest will recognize the 5’......... CCGC^GG……..3’ and 3'.......G G^C G C C.......5'\nThis is followed by the polymerase chain reaction to amplify the DNA fragments containing the β-\nlactoglobulin gene.\nThen sequencing is done 10µl DNA+ Taq polymerase takes 3-9 hours to prepare.\nElectrophoresis was done as a confirmatory to test if amplification has occurred appropriately\nOn the next day, a kit was used to purify the DNA for sequencing to be transported to Europe for \nsequencing.16""]","The key requirements for conducting PCR include a PCR buffer to stabilize pH, Magnesium Chloride (MgCl2) to increase Taq polymerase activity, deoxynucleotide triphosphates (dNTPs) as building blocks for new DNA strands, double distilled water to dilute other reagents, Taq polymerase for synthesizing new strands complementary to the target sequence, and primers for initiating the synthesis of DNA. In the study of the β-lactoglobulin gene in a small East African goat breed, DNA is extracted from blood samples, and PCR is used to amplify the DNA fragments containing the β-lactoglobulin gene, which is crucial for understanding the genetic factors affecting milk quality in goats.",,,,multi_hop_specific_query_synthesizer
"What is the significance of HVP-2 in the study of Herpes Simplex Virus-1, and how does the baboon model contribute to this research?","['<1-hop>\n\nuterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\n Khat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\n Student project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus papio) affects baboons is similar to Herpes Simplex \nVirus-1, thus, she is using it as a model to study Herpes simplex virus -1)\nOther projects:9OVART Ovary transplantation\nIt could have been done in the following ways:\nThe ovary to be transplanted is thawed. The procedure is done in open surgery and involves \nreconnecting tiny blood vessels to the ovary. This enables steady blood flow to the ovary which is \nvital to its function. After a few months the ovary may be fully functional.\nAlternatively, ovary tissue can be transplanted to defective ovary instead of the whole ovary tissue.\nAlso, in the past characterization of the rotavirus strains was carried out in the past.\n future use.1213.Prepared the LAMP reaction tubes of Dhat( Trypanosoma brucei detection reagent) no. of samples+ 2 tubes for controls) 14.Sealed the aluminum bag immediately. 15.Pipetted 25µl of the sample solution and close the lid of the lamp reaction tube. 16.Pipetted 25 µl of the negative control HAT (NC HAT) into a lamp reaction tube. 17.Pipetted 25 µl of the positive control HAT (PC HAT) into a lamp reaction tube. 18.Turned the reaction tubes upside-down to collect the solution in the cap (reconstitute the LAMP reagents for 2 minutes with a timer). 19.Inverted the LAMP reaction tube 5 times (Move the solution from the cap to the bottom or bottom to cap) N.B Avoid any bubbles. 20.Started the LAMP reaction for 40 minute at 65oC. Results Negative sample: No fluorescent light is emitted. Graphs according to the LAMP program Y-axis optical density X-axis time Positive control has a steep rise then levels out Negative control is on the negative axes Interpretation The drug administered to the animals was effective since no T.brucei brucei DNA was found in the samples. Moreover, the reaction tube can be set into the Visual Check unit, illuminated and the results checked. For a valid run the follow results must be obtained \uf0b7Positive control: Green fluorescent light is emitted. \uf0b7Negative control: No fluorescent light is emitted. 13', '<2-hop>\n\nCONCLUSION 55\nREFERENCES 5661.0 Good Laboratory Practice and Procedures\nBefore I go into the particulars of the laboratories; it is important to mention \na number of principles of good laboratory practice. They include:\n1.Strict adherence to the standard practice and procedures.\n2.Using Personal protective clothing which forms a barrier between \npersonnel and the infectious materials (gloves, laboratory coat and \ngoogles).\n3.All equipment and working surfaces should properly cleaned and \ndisinfected after contact with blood or other potentially infectious \nmaterials.\n4.When working with infectious agents, chemical, biological, hazardous, \nradioactive being aware of potential hazards, and being conversant \nwith practices and procedures required for safe handling of these \nmaterials.\n1.5 Quality control\n1.According to ISO 9001:2008 requirements; there is an aspect on \nmanagement. For example, an aspect in management like Document \ncontrol adequate filling has been done regarding animal test results and \naspect of management and organizational requirements.72.0 Department of Reproductive health and biology \nThis department is concerned with basic and applied research on the aspects of reproductive \nhealth, reproductive biology, physiology and immunology that is important in the understanding \nof both human and non-human primate’s reproduction and fertility/infertility.\nDuring research they developed an ideal research model that is, the baboon Papio anubis to \nstudy various issues related to reproductive biology.\nThe reasons include: \n\uf0b7It is not an endangered species; there numbers are not declining to an extent they are \ngetting extinct.\n\uf0b7It is most abundant in Kenya\n\uf0b7Closeness in terms of:- \nPhylogeny-compared to human beings, the baboon possesses 42 chromosomes whereas the \nhuman being possesses 46 chromosomes.\nAnatomy-if you look at the anatomy of the female reproductive tract of a baboon it is quite \nsimilar to that of female human being, however, the size differs.\nImmunology \nReprophysiology refers to the study of maternal female hormone system which includes \nactivities of various endocrine organs from puberty till menopause.\nThey also have a big body size enabling complicated surgery and repeated blood sampling.\nFemale reproductive biology lab/reproductive diseases laboratory \nFemale baboon\nReproductive cycle\nGestation about 6months/170 days\nWeaning 6 months\nLitter size average 1 \nAnimals under observation are assigned numbers. That is, the female baboon for instance. \nThe numbers 1-8 are given which corresponds with a particular phase of the female \nreproductive cycle.\nFor example8Menstruation phase is assigned the number 7\nLuteal phase 0&6\nOvulation phase 1-5\nGestation 8\nIn addition, perineal inflation and deflation (sex skin) - makes it easier for the cycle to be \ndetermined .\n2.0.1 Reproductive diseases laboratory LAB A\nThey are several projects going on in the reproductive diseases laboratory ;\nEndometriosis is a condition in which cells that are normally found inside the uterus \n(endometrial cells) are found growing outside of the uterus. That is, the lining of the inside of \nthe uterus is found outside of it. Endometrial cells are the cells that shed every month during \nmenstruation, and so endometriosis is most likely to affect women during their childbearing \nyears. \nThe baboon Papio anubis  is being as model to study this disease.\nCopper intrauterine device (I.U.D) project \n5 Baboons are under study. Some of the aims of the study were to investigate the implication \nof the device with Chlamydia, to observe if there were changes in the microbiota.\nHow it works\nThe intra uterine device is one of the ways of preventing pregnancy via preventing fertilization of the \negg by damaging or killing the sperm. It also affects the uterine lining. \nThe copper I.U.D is toxic to the sperm. It makes the uterus and the fallopian tubes produce fluid that \nkills the sperm. This fluid contains white blood cells, copper ions, enzymes and prostaglandins.\nKhat project\nAim: To study effects of khat on expectant baboons.\nThe weight of the female baboon and the infant were weighed, temperature recorded and blood drawn \nin the surgery room.  I haven’t caught wind of any developments of this project.\nStudent project concerning Herpes virus Miss Sharon Chepkwony\nIt has been found out that HVP-2(herpes virus']","HVP-2, or herpes virus papio, is significant in the study of Herpes Simplex Virus-1 as it has been found to affect baboons in a manner similar to the human herpes simplex virus. This similarity allows researchers, like Miss Sharon Chepkwony, to use HVP-2 as a model to study the characteristics and behaviors of Herpes Simplex Virus-1. The baboon model is particularly valuable due to the anatomical and physiological similarities between baboons and humans, which enhances the understanding of the virus's impact and potential treatments.",,,,multi_hop_specific_query_synthesizer
What are the key components required for PCR and how does the purification process of DNA facilitate downstream applications?,"['<1-hop>\n\nPCR Requirements \nPCR buffer for stabilization of pH for optimum functioning of enzyme for example\nMagnesium Chloride MgCl 2 increase Taq polymerase activity \ndNTps deoxynucleotide triphosphate building blocks for new DNA strands\nDouble distilled water dilutes other reagents to correct concentrations \nTaq polymerase synthesis new strands complimentary to the target sequence \nPrimers (Forward& Reverse primers) - sites for polymerase to begins synthesizing DNA\nTemplate DNA17 Diagram of PCR summary  (Occurs in the thermocycler) \nThe cycles are variable depending on how many DNA strands are required. The times can also vary to \nspecifics of the investigator.18', '<2-hop>\n\ne of DNA since it has intercalated with DNA.  The DNA band \ncan also be cut out and can be dissolved to retrieve the purified DNA. Sybr green can be used instead of \nethidium bromide.21 Purification of DNA \nThermo scientific GeneJET PCR Purification Kit\nPrinciple\nA reaction mixture containing the DNA is combined with the binding buffer and added to a purification \ncolumn. A chaotrophic agent in the binding buffer denatures protein and promotes DNA binding in a \nsilica membrane in the column. As an added advantage the binding buffer contains a color indicator that \nallows easy monitoring of the solution pH for optimal DNA binding. Impurities are removed in a single \nwash step. Purified DNA is eluted from the column using an elution buffer. The recovered DNA is ready \nfor use in downstream applications. As an example this method was used to purify DNA isolated by Mr. \nShadrack Lekerepes who was the principal investigator of this research project.\n Toxoplasma project\nA few individuals have been involved in this project. They all had different objectives regarding these \nprotozoa. Some of them include:\nTo make a standard kit to diagnose Toxoplasma gondii  that can be used in LAMP thermocycler \n(objective)\n Procedure\nIn order to make the kit isolated DNA template of the parasite had to be obtained.\nIt involved making a standard master mix \nAfter adding the template DNA and the primers in a reaction tube \nIt was then placed in the Thermocycler \nAfter a period of time, amplification proceeded but the positive and negative control did not get amplified \nas required in some instances. Thus, the contents of the master mix were reviewed.22Real time polymerase chain reaction\nUse \nqTOWER 2.0/2.2 is a thermal cycler for amplifying DNA by way of the polymerase chain\nReaction (PCR) licensed for real-time PCR experiments. The license is limited to applications outside of \nvitro diagnostics (research use only).\nThe integrated detector enables the measurement of the sample fluorescence in up to six spectral channels \nduring the PCR, with the filters used in the color or FRET modules being exactly matched to the \nproperties of the most frequently used fluorescence dyes, thereby, permitting a sensitive and selective \ndetection of fluorescent PCR products.\nAnalytik Jena offers a number of color or FRET modules of which up to six can be installed \nsimultaneously in the device. Replacement and retrofit of color or FRET modules can be easily \naccomplished.\nqTOWER 2.0/2.2 is an open platform for real-time PCR and supports intercalating dyes as well as \nindividual samples and kits of various manufacturers. qTOWER 2.0/2.2 can be used in different \napplications, such as expression analyses, genotyping and the detection of pathogens.233.0 ']","The key components required for PCR include PCR buffer for stabilizing pH, Magnesium Chloride (MgCl2) to increase Taq polymerase activity, deoxynucleotide triphosphates (dNTPs) as building blocks for new DNA strands, double distilled water to dilute reagents, Taq polymerase for synthesizing new strands complementary to the target sequence, and primers for polymerase to begin synthesizing DNA. The purification process of DNA involves combining a reaction mixture with a binding buffer and adding it to a purification column, where a chaotropic agent denatures proteins and promotes DNA binding. This process removes impurities in a single wash step, allowing the purified DNA to be eluted and ready for use in downstream applications.",,,,multi_hop_specific_query_synthesizer
What role does alcohol play in the staining process described in the context?,"['<1-hop>\n\nStaining \nRemove the slides from a drying oven and allow them to come at room temperature. Paraffin \nwax tissue processing method allows use of different stains. The type of stain to be used depends \non what the requestor is interested in demonstrating. Since H&E allow general view of various \nstructures of the processed tissue, all stains are first stained with this stain along other stains. \nHistopathological procedures \nHaematoxylin and Eosin staining technique\nPurpose\nThis method is used to demonstrate the general structures and layers of the tissue.\nMaterials\nXylene \nVarying concentrations of alcohol (80, 95 and 100%)\nHarris Haematoxylin stain\nAmmonia water or 0.3% Lithium carbonate\n5% Acid alcohol\nStaining racks\nTissue sections\nA timer\nProcedure\nThe following table shows the step-by-step procedure that has been adopted \nTable 4: Staining schedule \nReagent                                                                                             Time\nXylene                                                                                             5minutes\n100% ethanol                                                                                  5minutes\n95% ethanol                                                                                    5minutes3780% ethanol                                                                                    3minutes\nWater washes                                                                                  1minute\nHarris haematoxylin                                                                       10-15minutes\nWater wash                                                                                     1minute\n5% acid alcohol                                                                               2dips\nWater wash                                                                                      1minute\nAmmonia water                                                                               45seconds\nWater wash                                                                                       1minute\nEosin                                                                                                 1minute\n95% Ethanol                                                                                       14dips\n95% Ethanol                                                                                       14dips\n100% Ethanol                                                                                     14dips\nXylene                                                                                               5minutes\nXylene                                                                                               5minutes\nThe slides remain in xylene overnight as they await mounting.\nMounting of slides\nUsing a clean Pasteur pipette, place a mountant DPX onto a clean dust free cover slip such it \nmakes a thin horizontal or vertical line. Using a clean pair of forceps gradually lower the cover \nslip onto the stained section on the slide and firmly tilt it into position for them to dry.\nAlternatively, you can put some mountant onto a cover slip then pick it carefully touching it with \nthe stained slide is then inverted, the cover slip tilted carefully into position of the stained section \nand slide is allowed to dry. (This method was employed) \nFunctions of reagents\nXylene  used in different stages of H&E staining.\na)Deparaffinization- removal of paraffin38b)Clearing- displacement of alcohol from tissue sections with clearant to assure \nmiscibility when coverslipping with xylene-toluene or other petroleum –based \nmounting media.\nAlcohols- acid alcohol and ethanol \nAlso used in different stages was used to achieve\na)Hydration-the introduction of water into the tissue section. This was done by passing the \nslides slowly via a series of de']","Alcohol is used in different stages of the H&E staining process for hydration, which involves the introduction of water into the tissue section. Specifically, varying concentrations of alcohol (80%, 95%, and 100%) are utilized to displace the xylene and ensure proper miscibility when coverslipping with mounting media.",,,,multi_hop_specific_query_synthesizer