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Please answer the letter of option truthfully
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A
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| Q:In one taxonomic classification, Archaea, Eukarya, and Bacteria represent the three major domains of life. Eukarya utilize the general transcription factors TBP (TATA-binding protein) and TFIIB in transcription, whereas Bacteria do not. At least one member of Archaea has a protein similar to TBP and a protein similar... |
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Single-stranded binding proteins are proteins that play a critical role in DNA replication. During replication, the double-stranded DNA molecule must be separated into two single strands in order to serve as a template for the synthesis of new DNA strands.... | What is the role of single-stranded binding proteins in DNA replication, and how do they prevent the reannealing of DNA strands? |
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Silencers are specific DNA sequences that serve as binding sites for negative regulators, or repressors, that can inhibit or suppress gene expression. When a repressor protein binds to a silencer site, it can prevent the transcription machinery from access... | What are silencers in DNA regulation, and how do they function to control gene expression? |
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LOD scores are a statistical measure that is used to calculate the probability that two loci in the genome are linked, or in a state of linkage disequilibrium. This information can be used to study the inheritance patterns of different genetic traits, and ... | What is the significance of LOD scores in genetic research, and how are they used to study the relationship between different loci in the genome? |
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CRISPR/Cas9 is a genome editing tool that is derived from a bacterial defense system against viruses. It is used to make precise changes to DNA sequences in cells and organisms. The CRISPR/Cas9 system works by using a guide RNA molecule to target a specifi... | What is CRISPR/Cas9 and how is it used as a genome editing tool? |
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When using CRISPR/Cas9 to knock-in DNA, a repair template must be added to guide insertion of a construct.
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| What must be added when using CRISPR/Cas9 to knock-in DNA in order to guide insertion of a construct? |
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When using CRISPR/Cas9 that introduce a double strand break to knock-out target DNA, nonhomologous end joining enzymes repair the gap introduced by this Cas9 variant.
### Response:
| What repairs the gap introduced by CRISPR/Cas9 that introduces a double strand break to knock-out target DNA? |
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The BLM helicase is a protein that plays a role in regulating Homologous Recombination, a process involved in DNA repair. When the BLM gene is mutated, it can cause Bloom syndrome, a rare genetic disorder characterized by increased risk of cancer and other... | What is the BLM helicase and what role does it play in regulating Homologous Recombination? What happens when it is mutated? |
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The shine-dalgarno sequence plays a crucial role in bacterial translation initiation by serving as a recognition site for the 16s rRNA of the 30s ribosomal subunit. This sequence is located upstream of the start codon in the mRNA molecule and base-pairs wi... | What is the role of the shine-dalgarno sequence in bacterial translation initiation? |
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The Kozak sequence is a consensus sequence in eukaryotes that surrounds the start codon of a messenger RNA (mRNA) molecule. It aids in translation initiation by providing a recognition site for the ribosome, which is the molecular machine responsible for t... | What is the Kozak sequence, and how does it aid in translation initiation in eukaryotes? |
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One co-transcriptional modification involves the addition of a 7-methylguanosine cap at the 5' end.
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| What is one co-transcriptional modification that involves the addition of a 7-methylguanosine cap at the 5' end? |
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Linkage disequilibrium is a measure of the non-random association between alleles at different loci, and it is typically measured in a population, not in a family. Linkage disequilibrium can be influenced by a variety of factors, such as genetic drift, sel... | In what context is linkage disequilibrium measured, and is it measured in a family or a population? |
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No, homologous recombination is not considered to be error-prone. Homologous recombination is a DNA repair mechanism that is used by cells to repair double-stranded breaks in DNA. It involves the exchange of genetic material between two similar or identica... | Is homologous recombination considered to be error-prone? |
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In Homologous Recombination, dsDNA breaks are recognized by the ATM protein and the FA Core Complex, which activate BRCA1/2 to recruit enzymes to repair the break.
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| What are the proteins involved in recognizing and repairing double-stranded DNA (dsDNA) breaks in Homologous Recombination? |
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If two linked genes have a recombination frequency of 15%, they are approximately 15 centiMorgans (cM) apart. The recombination frequency is a measure of the likelihood that two genes on the same chromosome will be separated during meiosis. The higher the ... | How can you estimate the distance between two linked genes if their recombination frequency is 15%? |
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Homologous Recombination occurs after the S phase of the cell cycle. During Homologous Recombination, a sister chromatid is used as a template for repair of damaged DNA. This process involves the exchange of genetic information between two DNA molecules wi... | When and what is used as a template for Homologous Recombination during the cell cycle? |
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DNA methylation at CpG islands represses transcription. CpG islands are regions of DNA that contain a high frequency of CpG dinucleotides. Methylation of CpG islands can prevent the binding of transcription factors and other proteins that are required for ... | What is the role of DNA methylation at CpG islands in transcription? |
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At its core, the CRISPR/Cas9 system utilizes an endonuclease called Cas9 and a guide RNA that binds to a complementary target DNA sequence. The guide RNA directs Cas9 to the target DNA, where it cleaves the DNA, allowing for precise editing of the genome.
... | What are the two main components of the CRISPR/Cas9 system and how do they function? |
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A Southwestern blot is a laboratory technique used to identify DNA-binding proteins. It involves transferring proteins from a gel onto a membrane, and then using labeled oligonucleotide probes to detect specific DNA-binding proteins. The probes are designe... | What is a Southwestern blot and what is its purpose? |
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A missense mutation is a type of mutation that occurs when a nucleotide substitution codes for a different amino acid. This can result in a change in the protein's primary structure, which can affect its function. Depending on the location of the missense ... | What is a missense mutation, and how can it affect the function of a protein? |
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A knock-in transgenic mouse is a genetically modified mouse that has had a specific gene inserted into its genome through targeted gene editing techniques. This is in contrast to a knock-out mouse, which has had a specific gene removed. Knock-in mice are o... | What is a knock-in transgenic mouse? |
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A frameshift mutation is a type of genetic mutation that occurs when there is a deletion or insertion of a number of nucleotides that is not divisible by 3. This results in a shift in the reading frame of the gene, and all subsequent nucleotides are read i... | What is a frameshift mutation and how does it differ from other types of genetic mutations? |
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"The genome of... the Denisovans that once interbred with us has been sequenced... About 100,000 recent changes in our genome have occurred after the split from the Denisovans.... DNA from fossils unearthed in Denisova Cave in southern Siberia in 2008 reve... | What is the DNA of a human being? |
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Some prokaryotes express proton pumps called bacteriorhodopsins, archaerhodopsins, proteorhodopsins, and xanthorhodopsins to carry out phototrophy. Like animal visual pigments, these contain a retinal chromophore (although it is an all- trans, rather than... | Can you provide an explanation for Rhodopsin and Microbial Rhodopsins? |
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Preliminary DNA sequencing from a 38,000-year-old bone fragment of a femur found at Vindija Cave, Croatia, in 1980 showed Neanderthals and modern humans share about 99.5% of their DNA.
"DNA from the left shinbone of a skeleton, known as K14, which was exca... | What is the importance of DNA in humans? |
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Please answer with one of the option in the bracket
### Response:
C: Alternative pre-mRNA splicing
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| Q:A group of investigators is studying the effects of aberrant protein isoforms on the pathogenesis of lung cancer. They observe that three protein isoforms are transcribed from the same 30,160 base-pair-long DNA segment on chromosome 13q. The canonical protein has a primary peptide sequence of 1186 amino acids. The se... |
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Please answer with one of the option in the bracket
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A: Binding of met-tRNA to 60S complex
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| Q:An investigator is studying the genotypes of wingless fruit flies using full exome sequencing. Compared to wild-type winged fruit flies, the wingless fruit flies are found to have a point mutation in the gene encoding wing bud formation during embryogenesis. The point mutation in the gene causes the mRNA transcript t... |
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Question: is this a 2) strong advice, 1) weak advice 0) no advice?
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This is no advice
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| To further characterize the molecular events leading to chromatin condensation, we performed ChIP experiments using anti-HDAC1, HDAC2, HDAC3, MeCP2, MBD3, Kaiso, and NCoR antibodies, demonstrating HDAC1, HDAC2, and MeCP2, but not HDAC3, MBD3, Kaiso, and NCoR, to be involved in BIM silencing (Figure 5, D and E). |
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Question: is this a 2) strong advice, 1) weak advice 0) no advice?
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This is no advice
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| Using ChIP experiments, we demonstrated the involvement of histone H3 tail deacetylation, a well-known marker of chromatin condensation [50], in BIM silencing (Figure 4, A and B). |
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Question: is this a 2) strong advice, 1) weak advice 0) no advice?
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This is a weak advice
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| Taken together, evidence has shown that the interaction between DICER1 and CRC demonstrates the importance of miRNA-related SNPs (miR-SNPs), which alter miRNA levels and thereby influence mRNA transcription, in DICER. |
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This is no advice
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| Genome-wide association study (GWAS)-identified single-nucleotide polymorphisms (SNPs) are tag SNPs located in both transcribed and non-coding regulatory DNA regions, rather than representing causal or functional variants for disease. |
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Question: is this a 2) strong advice, 1) weak advice 0) no advice?
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This is no advice
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| To identify functional variants or genes for melanoma susceptibility, we used functional mapping and annotation (FUMA) to perform functional annotation of the summary statistics of 2541 significant melanoma risk SNPs (P < 5 √ó 10-8) identified by GWAS. |
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Please summerize the given abstract to a title
### Response:
The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes
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| Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain whi... |
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Characterization of Hspb8 in Zebrafish
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| Hspb8 is a member of the small heat shock protein (sHSP) family. Its expression is known to be upregulated under heat shock. This protein interacts with different partners and can, therefore, be involved in various processes relevant to tissue integrity and functioning. In humans, mutations in the gene encoding Hspb8 c... |
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An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
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| The number of samples in biological experiments are continuously increasing, but complex protocols and human experimentation in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machin... |
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### Response:
Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions
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| The widespread and versatile prokaryotic CRISPR–Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR–Cas system was added to the Cas e... |
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Cell Atlases as Roadmaps in Health and Disease.
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| The recent advent of methods for high-throughput single-cell and spatial profiling have opened the way to complete the 150-year-old endeavor of identifying all cell types in the human body, by their distinctive molecular profiles, and to relate this information to other cellular descriptions, physiological phenotypes, ... |
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Strategies for mitochondrial gene editing
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| Mitochondria, as the energy factory of cells, participate in metabolism processes and play a critical role in the maintenance of human life activities. Mitochondria belong to semi-automatic organelles, which have their own genome different from nuclear genome. Mitochondrial DNA (mtDNA) mutations can cause a series of d... |
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A high-throughput approach to profile RNA structure
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| Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as S... |
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Characterization of a Programmable Argonaute Nuclease from the Mesophilic Bacterium Rummeliibacillus suwonensis
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| Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from Kurthia massiliensis can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos,... |
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Rapid Degradation of Host mRNAs by Stimulation of RNase E Activity by Srd of Bacteriophage T4.
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| Escherichia coli messenger RNAs (mRNAs) are rapidly degraded immediately after bacteriophage T4 infection, and the host RNase E contributes to this process. Here, we found that a previously uncharacterized factor of T4 phage, Srd ( S: imilarity with R: po D: ), was involved in T4-induced host mRNA degradation. The rapi... |
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Efficient Conversion of Glycerol to Ethanol by an Engineered Saccharomyces cerevisiae Strain.
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| Glycerol is an eco-friendly solvent that enhances plant biomass decomposition via glycerolysis in many pretreatment methods. Nonetheless, inefficient conversion of glycerol to ethanol by natural Saccharomyces cerevisiae limits its use in these processes. Here, we have developed an efficient glycerol-converting yeast st... |
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ModFOLD8: accurate global and local quality estimates for 3D protein models
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| Methods for estimating the quality of 3D models of proteins are vital tools for driving the acceptance and utility of predicted tertiary structures by the wider bioscience community. Here we describe the significant major updates to ModFOLD, which has maintained its position as a leading server for the prediction of gl... |
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### Response:
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA.
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| Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic react... |
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PISCES: A pipeline for the Systematic, Protein Activity-based Analysis of Single Cell RNA Sequencing Data
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| While single-cell RNA sequencing provides a new window on physiologic and pathologic tissue biology and heterogeneity, it suffers from low signal-to-noise ratio and a high dropout rate at the individual gene level, thus challenging quantitative analyses. To address this problem, we introduce PISCES (Protein-activity In... |
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Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals
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| BACKGROUND: Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated... |
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Leveraging sequences missing from the human genome to diagnose cancer
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| Cancer diagnosis using cell-free DNA (cfDNA) can significantly improve treatment and survival but has several technical limitations. Here, we show that tumor-associated mutations create neomers, DNA sequences 11-18bp in length that are absent in the human genome, that can accurately detect cancer subtypes and features.... |
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### Response:
Synthetic mRNAs; Their Analogue Caps and Contribution to Disease
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| The structure of synthetic mRNAs as used in vaccination against cancer and infectious diseases contain specifically designed caps followed by sequences of the 5′ untranslated repeats of β-globin gene. The strategy for successful design of synthetic mRNAs by chemically modifying their caps aims to increase resistance to... |
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Low-cost, chromatic confocal endomicroscope for cellular imaging in vivo.
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| We have developed a low-cost, chromatic confocal endomicroscope (CCE) that can image a cross-section of the tissue at cellular resolution. In CCE, a custom miniature objective lens was used to focus different wavelengths into different tissue depths. Therefore, each tissue depth was encoded with the wavelength. A custo... |
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### Response:
These Are the Genes You're Looking For: Finding Host Resistance Genes
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| Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial inf... |
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### Response:
Systematic analysis of alternative splicing in time course data using Spycone
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| During disease progression or organism development, alternative splicing (AS) may lead to isoform switches (IS) that demonstrate similar temporal patterns and reflect the AS co-regulation of such genes. Tools for dynamic process analysis usually neglect AS. Here we propose Spycone (https://github.com/yollct/spycone), a... |
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Human mitochondrial RNA polymerase: evaluation of the single-nucleotide-addition cycle on synthetic RNA/DNA scaffolds.
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| The human mitochondrial RNA polymerase (h-mtRNAP) serves as both the transcriptase for expression and the primase for replication of mitochondrial DNA. As such, the enzyme is of fundamental importance to cellular energy metabolism, and defects in its function may be related to human disease states. Here we describe in ... |
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### Response:
A High-Throughput Yeast Two-Hybrid Protocol to Determine Virus-Host Protein Interactions
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| The yeast two-hybrid (Y2H) system is a powerful method to identify and analyze binary protein interactions. In the field of virology, the Y2H system has significantly increased our knowledge of structure and function of viral proteins by systematically assessing intraviral protein interactions. Several comprehensive ap... |
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Phylogenetic nomenclature and evolution of mannose-binding lectin (MBL2) haplotypes
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| BACKGROUND: Polymorphisms of the mannose-binding lectin gene (MBL2) affect the concentration and functional efficiency of the protein. We recently used haplotype-specific sequencing to identify 23 MBL2 haplotypes, associated with enhanced susceptibility to several diseases. RESULTS: In this work, we applied the same me... |
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Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques
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| In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to expl... |
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### Response:
Research Advances in Gametogenesis and Embryogenesis Using Pluripotent Stem Cells
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| The previous studies of human gametogenesis and embryogenesis have left many unanswered questions, which hinders the understanding of the physiology of these two vital processes and the development of diagnosis and treatment strategies for related diseases. Although many results have been obtained from animal studies, ... |
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### Response:
Origin and Isoform Specific Functions of Exchange Proteins Directly Activated by cAMP: A Phylogenetic Analysis
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| Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates... |
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Myosin-X is dispensable for spindle morphogenesis and positioning in the mouse oocyte.
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| Off-center spindle positioning in mammalian oocytes enables asymmetric divisions in size, important for subsequent embryogenesis. The migration of the meiosis I spindle from the oocyte center to its cortex is mediated by F-actin. Specifically, an F-actin-cage surrounds the microtubule spindle and applies forces to it. ... |
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### Response:
AbGradCon 2021: Lessons in Digital Meetings, International Collaboration, and Interdisciplinarity in Astrobiology
### Response:
| The Astrobiology Graduate Conference (AbGradCon) is an annual conference both organized for and by early career researchers, postdoctoral fellows, and students as a way to train the next generation of astrobiologists and develop a robust network of cohorts moving forward. AbGradCon 2021 was held virtually on September ... |
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### Response:
The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii
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| [Figure: see text] |
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### Response:
Molecular basis for substrate recognition and catalysis by a marine bacterial laminarinase.
### Response:
| Laminarin is an abundant algal polysaccharide that serves as carbon storage and fuel to meet the nutrition demands of heterotrophic microbes. Laminarin depolymerization catalyzed by microbial extracellular enzymes initiates remineralization, a key process in ocean biogeochemical cycles. Here, we described a glycoside h... |
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### Response:
A cotton NAC transcription factor GhirNAC2 plays positive roles in drought tolerance via regulating ABA biosynthesis.
### Response:
| NAC protein is a large plant specific transcription factor family, which plays important roles in the response to abiotic stresses. However, the regulation mechanism of most NAC proteins in drought stress remains to be further uncovered. In this study, we elucidated the molecular functions of a NAC protein, GhirNAC2, i... |
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### Response:
Utilizing Plant Synthetic Biology to Improve Human Health and Wellness
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| Plants offer a vast source of bioactive chemicals with the potential to improve human health through the prevention and treatment of disease. However, many potential therapeutics are produced in small amounts or in species that are difficult to cultivate. The rapidly evolving field of plant synthetic biology provides t... |
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### Response:
Pichia pastoris: A highly successful expression system for optimal synthesis of heterologous proteins
### Response:
| One of the most important branches of genetic engineering is the expression of recombinant proteins using biological expression systems. Nowadays, different expression systems are used for the production of recombinant proteins including bacteria, yeasts, molds, mammals, plants, and insects. Yeast expression systems su... |
### Instruction:
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### Response:
Super Resolution Microscopy Reveals that Caveolin-1 Is Required for Spatial Organization of CRFB1 and Subsequent Antiviral Signaling in Zebrafish
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| Understanding spatial distribution and dynamics of receptors within unperturbed membranes is essential for elucidating their role in antiviral signaling, but conventional studies of detergent-resistant membrane fractions cannot provide this information. Caveolae are integral to numerous signaling pathways and these mem... |
### Instruction:
Please summerize the given abstract to a title
### Response:
Wide Horizons of CRISPR-Cas-Derived Technologies for Basic Biology, Agriculture, and Medicine
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| The discovery and subsequent repurposing of the CRISPR (clustered regularly interspaced short palin-dromic repeats) and Cas proteins (CRISPR-associated proteins) has revolutionized our ability to manipulate DNA and RNA sequences in vitro, ex vivo, and in vivo In this introductory chapter, we present a brief overview of... |
### Instruction:
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### Response:
Genome sequencing and comparative genome analysis of 6 hypervirulent Klebsiella pneumoniae strains isolated in China
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| Hypervirulent Klebsiella pneumoniae (hvKP) has been increasingly reported over the past three decades and causes severe infections. To increase our understanding of hvKP at the genome level, genome sequencing and comparative genome analysis were performed on 6 hvKPs. The whole genome DNA from 6 hvKPs with different cap... |
### Instruction:
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### Response:
A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome
### Response:
| Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is comple... |
### Instruction:
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### Response:
iDRP-PseAAC: Identification of DNA Replication Proteins Using General PseAAC and Position Dependent Features
### Response:
| DNA replication is one of the specific processes to be considered in all the living organisms, specifically eukaryotes. The prevalence of DNA replication is significant for an evolutionary transition at the beginning of life. DNA replication proteins are those proteins which support the process of replication and are a... |
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### Response:
VIRUSBreakend: Viral Integration Recognition Using Single Breakends
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| MOTIVATION: Integration of viruses into infected host cell DNA can cause DNA damage and disrupt genes. Recent cost reductions and growth of whole genome sequencing has produced a wealth of data in which viral presence and integration detection is possible. While key research and clinically relevant insights can be unco... |
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### Response:
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models
### Response:
| We present a new technique for the rapid modeling and construction of scientifically accurate mesoscale biological models. The resulting 3D models are based on a few 2D microscopy scans and the latest knowledge available about the biological entity, represented as a set of geometric relationships. Our new visual-progra... |
### Instruction:
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### Response:
Pre-meiotic, 24-nt reproductive phasiRNAs are abundant in anthers of wheat and barley but not rice and maize
### Response:
| Two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs and their patterns of accumulation have been described in maize and rice anthers. Their precise function remains unclear, but some studies have shown that they support male fertility. The important role of phasiRNAs in anthers underpins our current study ... |
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### Response:
Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture.
### Response:
| This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed ... |
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### Response:
Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas
### Response:
| Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of... |
### Instruction:
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### Response:
The path of messenger RNA through the ribosome.
### Response:
| Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back ... |
### Instruction:
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### Response:
A new method to analyze protein sequence similarity using Dynamic Time Warping
### Response:
| Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol se... |
### Instruction:
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### Response:
AgNAC1, a celery transcription factor, related to regulation on lignin biosynthesis and salt tolerance
### Response:
| The NAC transcription factor participates in various biotic and abiotic stress responses and plays a critical role in plant development. Lignin is a water-insoluble dietary fiber, but it is second only to cellulose in abundance. Celery is the main source of dietary fiber, but its quality and production are limited by v... |
### Instruction:
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### Response:
LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2
### Response:
| The constant emergence of COVID-19 variants reduces the effectiveness of existing vaccines and test kits. Therefore, it is critical to identify conserved structures in SARS-CoV-2 genomes as potential targets for variant-proof diagnostics and therapeutics. However, the algorithms to predict these conserved structures, w... |
### Instruction:
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### Response:
Tackling malaria transmission at a single cell level in an endemic setting in sub-Saharan Africa
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| Studying malaria transmission biology using scRNA-sequencing provides information on within-host strain diversity and transcriptional states. Here, we comment on our collaborative efforts at establishing single-cell capacities in sub-Saharan Africa and the challenges encountered in Mali’s endemic setting. |
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Please summerize the given abstract to a title
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Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli
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| Vitamin B12 (or cobalamin) is an enzymatic cofactor essential both for mammals and bacteria. However, cobalamin can be synthesized only by few microorganisms so most bacteria need to take it up from the environment through the TonB-dependent transport system. The first stage of cobalamin import to E. coli cells occurs ... |
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Targeted intracellular delivery of Cas13 and Cas9 nucleases using bacterial toxin-based platforms
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| Targeted delivery of therapeutic proteins toward specific cells and across cell membranes remains major challenges. Here, we develop protein-based delivery systems utilizing detoxified single-chain bacterial toxins such as diphtheria toxin (DT) and botulinum neurotoxin (BoNT)-like toxin, BoNT/X, as carriers. The system... |
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Adaptive laboratory evolution for growth coupled microbial production
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| Adaptive laboratory evolution (ALE) is a powerful tool to select for strains with growth-coupled phenotypes. When coupled with next-generation sequencing and omic technologies, genotype-to-phenotype relationships and the molecular mechanisms underlying desired complex phenotypes can now be uncovered using ALE. However,... |
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Please summerize the given abstract to a title
### Response:
Agrobacterium fabrumatu0526-Encoding Protein Is the Only Chemoreceptor That Regulates Chemoattraction toward the Broad Antibacterial Agent Formic Acid
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| Soil-born plant pathogens, especially Agrobacterium, generally navigate their way to hosts through recognition of the root exudates by chemoreceptors. However, there is still a lack of appropriate identification of chemoreceptors and their ligands in Agrobacterium. Here, Atu0526, a sCache-type chemoreceptor from Agroba... |
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Please summerize the given abstract to a title
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Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour
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| BACKGROUND: Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good syst... |
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Please summerize the given abstract to a title
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Genome sequences published outside of Standards in Genomic Sciences, July - October 2012
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| The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in... |
### Instruction:
Please summerize the given abstract to a title
### Response:
Single-Cell Studies of Phage λ: Hidden Treasures Under Occam's Rug.
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| Studies over more than half a century have resulted in what some consider a complete narrative for the life cycle of bacteriophage λ. However, this narrative is only complete within the limited resolution offered by the traditional genetic and biochemical approaches that were used to create it. A recent series of studi... |
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Please summerize the given abstract to a title
### Response:
Human Codon Usage: The Genetic Basis of Pathogen Latency
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| Infectious diseases pose two main compelling issues. First, the identification of the molecular factors that allow chronic infections, that is, the often completely asymptomatic coexistence of infectious agents with the human host. Second, the definition of the mechanisms that allow the switch from pathogen dormancy to... |
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Please summerize the given abstract to a title
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bletl ‐ A Python package for integrating BioLector microcultivation devices in the Design‐Build‐Test‐Learn cycle
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| Microbioreactor (MBR) devices have emerged as powerful cultivation tools for tasks of microbial phenotyping and bioprocess characterization and provide a wealth of online process data in a highly parallelized manner. Such datasets are difficult to interpret in short time by manual workflows. In this study, we present t... |
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LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
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| Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read p... |
### Instruction:
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### Response:
Defeated by the nines: nine extracellular strategies to avoid microbe-associated molecular patterns recognition in plants
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| Recognition of microbe-associated molecular patterns (MAMPs) by cell-surface receptors is pivotal in host-microbe interactions. Both pathogens and symbionts establish plant-microbe interactions using fascinating intricate extracellular strategies to avoid recognition. Here we distinguish nine different extracellular st... |
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Please summerize the given abstract to a title
### Response:
Fast, Flexible, and Exact Minimum Flow Decompositions via ILP
### Response:
| Minimum flow decomposition (MFD) (the problem of finding a minimum set of paths that perfectly decomposes a flow) is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics (e.g. RNA assembly). However, because this problem and its variants are NP-hard... |
### Instruction:
Please summerize the given abstract to a title
### Response:
Coiled coil protein origami: from modular design principles towards biotechnological applications.
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| The design of new protein folds represents a grand challenge for synthetic, chemical and structural biology. Due to the good understanding of the principles governing its pairing specificity, coiled coil (CC) peptide secondary structure elements can be exploited for the construction of modular protein assemblies acting... |
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Please summerize the given abstract to a title
### Response:
Comparative phylogenomics of pathogenic bacteria by microarray analysis
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| DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate betwe... |
### Instruction:
Please summerize the given abstract to a title
### Response:
Bacteriophage T4 Escapes CRISPR Attack by Minihomology Recombination and Repair
### Response:
| Bacteria and bacteriophages (phages) have evolved potent defense and counterdefense mechanisms that allowed their survival and greatest abundance on Earth. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is a bacterial defense system that inactivates the invading phage genome b... |
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Please summerize the given abstract to a title
### Response:
High-level ribosomal frameshifting directs the synthesis of IS150 gene products.
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| IS150 contains two tandem, out-of-phase, overlapping genes, ins150A and ins150B, which are controlled by the same promoter. These genes encode proteins of 19 and 31 kD, respectively. A third protein of 49 kD is a transframe gene product consisting of domains encoded by both genes. Specific -1 ribosomal frameshifting is... |
### Instruction:
Please summerize the given abstract to a title
### Response:
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level
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| BACKGROUND: Cellular communication is an essential feature of multicellular organisms. Binding of ligands to their homologous receptors, which activate specific cell signaling pathways, is a basic type of cellular communication and intimately linked to many degeneration processes leading to diseases. MAIN BODY: This st... |
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### Response:
DeepTracer: Fast Cryo-EM Protein Structure Modeling and Special Studies on CoV-related Complexes
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| Information about macromolecular structure of protein complexes such as SARS-CoV-2, and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for fast de novo... |
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### Response:
The carbon footprint of bioinformatics
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| Bioinformatic research relies on large-scale computational infrastructures which have a non-zero carbon footprint. So far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this study, we estimate the bioinformatic carbon footprint (in kilograms of CO2 equivalent units... |
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### Response:
Triggered Assembly of a DNA-Based Membrane Channel
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| [Image: see text] Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics’ value for science and technology yet is difficult to achieve with poorly controlled building materials. Here, we use defined DNA blocks to rationally... |
### Instruction:
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### Response:
Toward a translationally independent RNA-based synthetic oscillator using deactivated CRISPR-Cas
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| In synthetic circuits, CRISPR-Cas systems have been used effectively for endpoint changes from an initial state to a final state, such as in logic gates. Here, we use deactivated Cas9 (dCas9) and deactivated Cas12a (dCas12a) to construct dynamic RNA ring oscillators that cycle continuously between states over time in b... |
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