Bioinformatics and Genetics Quiz
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Which of the following tools are used in bioinformatics for analyzing biological data?

  • Statistical analysis tools
  • Visualization software
  • Algorithms for data comparison
  • All of the above (correct)

    • What type of biological variations are analyzed in genome-wide association studies (GWAS)?

    Single Nucleotide Polymorphisms (SNP)

    In bioinformatics, _________ refers to the study of proteins and their structures.

    proteomics

    Match the following concepts with their descriptions:

    <p>cDNAs = Complementary DNAs synthesized from mRNA SNP = Genetic variation at a single nucleotide Microarray = A tool to analyze gene expression Proteomics = The large-scale study of proteins</p> Signup and view all the answers

    What is the primary function of the Eyeless/PAX6 gene in Drosophila?

    <p>Controlling eye development</p> Signup and view all the answers

    PAX6 mutations in humans can lead to the complete absence of eyes.

    <p>False</p> Signup and view all the answers

    What structural domain is unique to the PAX6 protein and is responsible for binding DNA?

    <p>paired box domain</p> Signup and view all the answers

    PAX6 is known to regulate approximately _____ genes involved in eye development.

    <p>300</p> Signup and view all the answers

    Match the following PAX6-related terms with their descriptions:

    <p>Aniridia = Phenotype associated with PAX6 mutations leading to no iris CRISPR = Technology used for precise DNA editing Eyeless Protein = Controls eye development in <em>Drosophila</em> Imaginal disks = Cells that will give rise to adult structures in insects</p> Signup and view all the answers

    Which statement accurately describes the role of CRISPR in genetic engineering?

    <p>It uses gRNA to cleave DNA at specific locations.</p> Signup and view all the answers

    What is a common phenotype resulting from mutations in PAX6 in humans?

    <p>Aniridia</p> Signup and view all the answers

    Mouse PAX6 can function normally in flies.

    <p>True</p> Signup and view all the answers

    When CRISPR is used, the _______ protein is responsible for cleaving DNA.

    <p>Cas9</p> Signup and view all the answers

    Which of the following statements is true regarding PAX6?

    <p>PAX6's amino acid sequence is conserved among species.</p> Signup and view all the answers

    What primary risk does 23andMe FDA-approved genetic testing assess?

    <p>Genetic risk information based on SNPs</p> Signup and view all the answers

    23andMe's Genetic Health Risk tests can be used to diagnose medical conditions.

    <p>False</p> Signup and view all the answers

    What is the main purpose of 23andMe's data sharing from customers?

    <p>To develop a high-value database for research organizations.</p> Signup and view all the answers

    PAX6 is a transcription factor that is conserved across a wide range of ________.

    <p>species</p> Signup and view all the answers

    Match the following terms with their definitions:

    <p>SNP = A variation at a single nucleotide position in a DNA sequence. Transcription Factor = A protein that influences the transcription of a gene. Cis-regulatory sequence = A DNA sequence that regulates the transcription of nearby genes. Homolog = A gene related by descent from a common ancestor.</p> Signup and view all the answers

    What percentage of 23andMe customers agrees to share their data for research purposes?

    <p>80%</p> Signup and view all the answers

    The TATA box is a DNA recognition sequence for the transcription factor RNA polymerase.

    <p>False</p> Signup and view all the answers

    Name one of the principal investors in 23andMe.

    <p>Google</p> Signup and view all the answers

    The transcription factor PAX6 is essential for ________ development.

    <p>eye</p> Signup and view all the answers

    Alberto Gutierrez represents which agency?

    <p>Food and Drug Administration</p> Signup and view all the answers

    Match the following genes to their respective organisms:

    <p>ey = Drosophila Sey = Mouse PAX6 = Human</p> Signup and view all the answers

    What aspect of human health are 23andMe tests primarily focused on?

    <p>Genetic Health Risks</p> Signup and view all the answers

    Direct to Consumer (DCT) testing allows consumers to access their genetic information without a healthcare provider.

    <p>True</p> Signup and view all the answers

    What are the two binding domains known for PAX6?

    <p>Homeobox and PAX domain</p> Signup and view all the answers

    Which statement correctly defines the difference between a risk factor and a genetic determinant?

    <p>A risk factor makes disease more likely, while a genetic determinant results in the disease.</p> Signup and view all the answers

    Sporadic mutations can be both inherited and somatic in nature.

    <p>True</p> Signup and view all the answers

    What does the acronym NGS stand for?

    <p>Next Generation Sequencing</p> Signup and view all the answers

    In cancer research, mutations that occur in the germline can be described as __________ mutations.

    <p>heritable</p> Signup and view all the answers

    Match the following terms to their correct descriptions:

    <p>SNP = Single nucleotide change Monogenic = Risk from a single gene Polygenic = Interaction of many genes Somatic = Mutations not in germline</p> Signup and view all the answers

    Which of the following is a disadvantage of estimating Genetic Health Risk using SNPs?

    <p>They can be inaccurate due to the complexity of polygenic traits.</p> Signup and view all the answers

    Next Generation Sequencing is currently not utilized by the NHS.

    <p>False</p> Signup and view all the answers

    What are the two main categories of mutations discussed in the content?

    <p>Sporadic and inherited mutations</p> Signup and view all the answers

    A __________ is an allele that results in the disease, such as mutations in APP, PS1, PS2.

    <p>genetic determinant</p> Signup and view all the answers

    Which of these is NOT a characteristic of functional genomics?

    <p>Involves only single gene modeling.</p> Signup and view all the answers

    Polygenic risk can only be quantified through rare genetic markers.

    <p>False</p> Signup and view all the answers

    What is the term for mutations that are acquired in the body cells and are not inheritable?

    <p>Somatic mutations</p> Signup and view all the answers

    Next Generation Screening (NGS) in the NHS can lead to faster diagnoses for patients, limiting the _________ of uncertainty.

    <p>diagnostic odyssey</p> Signup and view all the answers

    Match the following cancer risk factors with their characteristics:

    <p>Diet = Modifiable risk factor Family history = Non-modifiable risk factor Smoking = Modifiable risk factor Age = Non-modifiable risk factor</p> Signup and view all the answers

    What can consumers do with their DNA data as provided by 23andMe?

    <p>Download raw DNA data</p> Signup and view all the answers

    23andMe shares consumer identifying information with third parties without consent.

    <p>False</p> Signup and view all the answers

    What is one common reason consumers profile their DNA?

    <p>Risk prediction for diseases</p> Signup and view all the answers

    23andMe's method of analyzing DNA involves a device known as an ________.

    <p>Illumina Microchip</p> Signup and view all the answers

    Match the following reports offered by 23andMe with their main purpose:

    <p>Health dispositions = Determines genetic risk for diseases Traits = Fun facts about genetic traits Carrier status = Identifies problematic alleles for children Genetic ancestry = Explores heritage and lineage</p> Signup and view all the answers

    Which of the following is an ethical concern regarding genetic testing?

    <p>Impersonal results about high cancer risk</p> Signup and view all the answers

    The oligonucleotide used in SNP detection can detect SNPs at any location in the genome.

    <p>False</p> Signup and view all the answers

    What is a limitation of SNP detection using microarrays?

    <p>Can only detect SNPs at known loci</p> Signup and view all the answers

    FDA required 23andMe to demonstrate that their process of measuring SNPs is _______.

    <p>analytically valid</p> Signup and view all the answers

    Match the following types of DNA reports with their features:

    <p>Health dispositions = Complicated disease risk statistics Traits = Fun insights about physical attributes Carrier status = Potential issues for offspring Risk information = Information about probabilities of diseases</p> Signup and view all the answers

    What genetic risk factor is specifically discussed in relation to late-onset Alzheimer’s disease?

    <p>APOE 4/4 alleles</p> Signup and view all the answers

    Consumers can instantly access all the information from their DNA tests as soon as their samples are processed.

    <p>False</p> Signup and view all the answers

    What is one factor leading to the high medical literacy among the population?

    <p>Increased access to universities</p> Signup and view all the answers

    The genetic analysis results are delivered through a _______ portal.

    <p>personalized</p> Signup and view all the answers

    Why might individuals choose not to learn about genetic risks?

    <p>Desire to avoid anxiety over potential illnesses</p> Signup and view all the answers

    What is the primary purpose of aligning small fragments of sequence data to a Ref Seq?

    <p>To spot small variations like SNPs</p> Signup and view all the answers

    Aligning to a Ref Seq is equally useful for identifying large genomic changes as it is for SNPs.

    <p>False</p> Signup and view all the answers

    What does SNP stand for?

    <p>Single Nucleotide Polymorphism</p> Signup and view all the answers

    SNPs are useful in associating _________ with genes.

    <p>diseases</p> Signup and view all the answers

    Match the types of genomic changes with their descriptions:

    <p>SNPs = Single nucleotide variations Deletions = Loss of a segment of DNA Mutations = Changes in DNA sequence that occur less frequently Copy number variation = Variations in the amount of DNA present</p> Signup and view all the answers

    Which type of sequencing is typically better for identifying large genomic changes?

    <p>Long read sequencing</p> Signup and view all the answers

    Most SNPs identified in the Human Genome Project are located in coding regions.

    <p>False</p> Signup and view all the answers

    What is the relevance of SNPs in the context of personalized medicine?

    <p>They help identify the right drug at the right dosage for individuals.</p> Signup and view all the answers

    A genomic clone requires special vectors such as _________ or BACs.

    <p>YACs</p> Signup and view all the answers

    What does the term 'contig' refer to in genomic sequencing?

    <p>A continuous stretch of DNA sequences</p> Signup and view all the answers

    According to the content, gaps in sequence alignment are generally unhelpful.

    <p>False</p> Signup and view all the answers

    Name one significant transcription factor mentioned in the content.

    <p>PAX6</p> Signup and view all the answers

    To express a gene in a transgenic animal, one needs a large amount of ________ DNA for the right enhancers.

    <p>upstream and downstream</p> Signup and view all the answers

    Match the alignment strategies with their purposes:

    <p>Local alignment = Identifying similar regions Global alignment = Matching entire sequences Gap allowance = Facilitating domain detection Scoring alignments = Determining optimal matches</p> Signup and view all the answers

    What is the primary purpose of using homologous recombination in gene editing?

    <p>To introduce an altered version of a gene</p> Signup and view all the answers

    Nonhomologous end joining does not introduce any errors when repairing double-strand breaks in DNA.

    <p>False</p> Signup and view all the answers

    What is the role of the 5’ cap in mRNA?

    <p>It promotes translation and provides stability to the mRNA molecule.</p> Signup and view all the answers

    The process of converting primary RNA into mRNA includes splicing, capping, and __________.

    <p>polyadenylation</p> Signup and view all the answers

    Which of the following statements about polyadenylation is correct?

    <p>The poly A tail is crucial for mRNA export and stability.</p> Signup and view all the answers

    CDNA is directly comparable to RNA sequences in databases.

    <p>False</p> Signup and view all the answers

    What is the function of the 3’ untranslated region (UTR) in mRNA?

    <p>It regulates the stability of the mRNA and can affect polyadenylation.</p> Signup and view all the answers

    The reference sequence (Ref Seq) is curated by the __________ to represent the best data for genes.

    <p>NCBI</p> Signup and view all the answers

    Why may a reference sequence not be the most common variant?

    <p>It represents an accurate depiction of the transcript.</p> Signup and view all the answers

    The 5’ UTR is critical for the initiation of translation.

    <p>True</p> Signup and view all the answers

    Why is mRNA considered unstable during certain conditions like an infection?

    <p>To ensure that cytokines are only produced when needed and not maintained long-term.</p> Signup and view all the answers

    Mature proteins are secreted via __________ insertion, where they are fed into the ER as they are synthesized.

    <p>cotranslational</p> Signup and view all the answers

    What is the primary purpose of the BLAST tool?

    <p>To identify local regions of alignment between sequences</p> Signup and view all the answers

    The BLOSUM 62 matrix is used for scoring nucleotide alignments.

    <p>False</p> Signup and view all the answers

    What are exons?

    <p>Regions shared between genomic DNA and mRNA.</p> Signup and view all the answers

    BLAST can map ________ and ________ structure in genomic DNA.

    <p>exon, intron</p> Signup and view all the answers

    Which of the following is a characteristic of protein sequence alignments?

    <p>They use a scoring matrix based on amino acid frequency</p> Signup and view all the answers

    DNA sequence alignments only accept gaps that improve the score.

    <p>True</p> Signup and view all the answers

    What does a low E-value indicate in a BLAST result?

    <p>A highly reliable alignment.</p> Signup and view all the answers

    A ________ blot is used to visualize sequence identity.

    <p>dot</p> Signup and view all the answers

    Match the following components of nucleic acid alignments with their roles:

    <p>Identity = Represented as a positive alignment Mismatch = Indicates a difference in nucleotides Gap = Represents an insertion or deletion Score = Overall assessment of alignment quality</p> Signup and view all the answers

    What do conserved amino acids in protein alignment scoring reflect?

    <p>The importance and rarity of certain amino acids</p> Signup and view all the answers

    The primary size of the word used in BLAST for DNA sequences is typically 5 nucleotides.

    <p>False</p> Signup and view all the answers

    What might a high score in a BLAST alignment indicate?

    <p>High homology or similarity between sequences.</p> Signup and view all the answers

    BLAST performs comparisons on a ________ basis.

    <p>pairwise</p> Signup and view all the answers

    Which of the following reasons makes protein sequence alignments more sensitive than DNA alignments?

    <p>Proteins consist of 20 different amino acids</p> Signup and view all the answers

    What is a significant advantage of Next Generation Sequencing (NGS) compared to traditional Sanger sequencing?

    <p>Massively parallel processing</p> Signup and view all the answers

    Sanger sequencing incorporates labeled nucleotides that terminate the DNA strand elongation.

    <p>False</p> Signup and view all the answers

    What are the typical read lengths for NGS?

    <p>250-500 bp</p> Signup and view all the answers

    Sanger sequencing requires a __________ to initiate the DNA synthesis.

    <p>primer</p> Signup and view all the answers

    Match the following sequencing technologies with their primary characteristics:

    <p>Sanger Sequencing = Uses ddNTPs and generates longer reads NGS (Illumina) = Massively parallel, produces short reads PacBio = Single molecule, long read sequencing Nanopore Sequencing = Real-time sequencing with long reads</p> Signup and view all the answers

    What is the role of bioinformatics in NGS?

    <p>To analyze and assemble short sequence reads</p> Signup and view all the answers

    Adult stem cells are primarily responsible for the creation of embryos.

    <p>False</p> Signup and view all the answers

    What sequencing method is currently dominant for short reads?

    <p>Illumina</p> Signup and view all the answers

    The process of detecting DNA clusters in NGS allows researchers to __________ quickly.

    <p>sequence</p> Signup and view all the answers

    Match the type of error in NGS assembly with its example:

    <p>Likely sequence error = C instead of G in a DNA sequence Poor coverage = Few reads mapping to a region Real variant = Consistent appearance of a different nucleotide</p> Signup and view all the answers

    What is one disadvantage of NGS?

    <p>Struggles with copy number variations</p> Signup and view all the answers

    The cost of sequencing a genome has significantly decreased since the Human Genome Project.

    <p>False</p> Signup and view all the answers

    What is the purpose of adding adaptors in NGS?

    <p>To attach fragments to the flow cell</p> Signup and view all the answers

    In NGS, __________ can be created during PCR amplification.

    <p>errors</p> Signup and view all the answers

    What is the primary role of quiescence in stem cells?

    <p>To temporarily withdraw from the cell cycle</p> Signup and view all the answers

    Asymmetric division results in both daughter cells remaining as stem cells.

    <p>False</p> Signup and view all the answers

    Where do neurons migrate from in adult mice?

    <p>Subventricular zone</p> Signup and view all the answers

    The _______ are known to project into cerebrospinal fluid and coordinate neurogenesis during development.

    <p>neural stem cells</p> Signup and view all the answers

    Match the following cell types with their descriptions:

    <p>Neural stem cells = Pluripotent cells found in the brain Transient amplifying cells = Cells that rapidly divide before differentiating Neuroblasts = Immature nerve cells that develop into neurons Astrocytes = Supportive cells in the nervous system</p> Signup and view all the answers

    What determines the fate of daughter cells during cell division in certain environments?

    <p>The orientation of the mitotic spindle</p> Signup and view all the answers

    Stochastic outcomes in cell division are completely random and cannot be modeled.

    <p>False</p> Signup and view all the answers

    What is the primary characteristic of embryonic stem cells?

    <p>They are pluripotent.</p> Signup and view all the answers

    Asymmetric division results in one daughter cell maintaining ____ cell characteristics.

    <p>stem</p> Signup and view all the answers

    What is the role of ependymal cells in the subventricular zone?

    <p>To line the ventricles and project into CSF</p> Signup and view all the answers

    What is one primary function of stem cells in the gut?

    <p>Replace apoptotic cells</p> Signup and view all the answers

    Stem cells can undergo unlimited self-renewal indefinitely.

    <p>False</p> Signup and view all the answers

    What term is used for daughter cells that can no longer self-renew indefinitely?

    <p>Progenitor cells</p> Signup and view all the answers

    Stem cells differentiate into __________ cells that perform specialized functions.

    <p>differentiated</p> Signup and view all the answers

    Match the type of stem cell with its description:

    <p>Unipotent = Can differentiate into one cell type Multipotent = Can differentiate into several cell types Pluripotent = Can differentiate into almost all cell types Totipotent = Can differentiate into any cell type, including the placenta</p> Signup and view all the answers

    What characterizes dividing stem cells?

    <p>One stays a stem cell and the other differentiates</p> Signup and view all the answers

    GFP can be used to trace daughter cells from stem cells.

    <p>True</p> Signup and view all the answers

    What environmental factor may cause damage to gut epithelial cells?

    <p>Food or microbiome</p> Signup and view all the answers

    Aspirin is known to promote __________, helping to maintain gut health.

    <p>apoptosis</p> Signup and view all the answers

    Match the following tools or substances to their functions:

    <p>Tamoxifen = Activates Cre-recombinase Cre-recombinase = Cuts DNA sequences GFP = Tracks cell lineages LoxP sites = Recognized by Cre-recombinase</p> Signup and view all the answers

    What happens to daughter cells as they push out from the gut stem cells?

    <p>They undergo differentiation and further division.</p> Signup and view all the answers

    Hematopoietic stem cells (HSC) can regenerate the entire bone marrow.

    <p>True</p> Signup and view all the answers

    What is the main reason for stem cells to produce progenitor cells?

    <p>To reduce the burden of replication</p> Signup and view all the answers

    Stem cells are known to reside at the bottom of __________.

    <p>crypts</p> Signup and view all the answers

    Select the INCORRECT statement about organoids.

    <p>Organoids often contain a vasculature and patrolling immune cells.</p> Signup and view all the answers

    Organoids are useful in drug discovery for the following reasons EXCEPT:

    <p>Organoids are easier to grow in culture than established cell lines.</p> Signup and view all the answers

    Organoids can aid in understanding disease mechanisms.

    <p>True</p> Signup and view all the answers

    What is a limitation of current organoid technology?

    <p>Lack of vasculature and limited control over heterogeneity.</p> Signup and view all the answers

    To be useful, organoids need to be fully ________.

    <p>characterized</p> Signup and view all the answers

    Match the following characteristics of organoids with their descriptions:

    <p>Organoid resemblance = Resembles various tissues Stem cell origin = Derived from adult or IPSC stem cells Drug discovery = Assists in testing drug efficacy Limitations = Lacks complete vasculature and immune cells</p> Signup and view all the answers

    Organoids can perform all functions of natural tissues.

    <p>False</p> Signup and view all the answers

    What do researchers hope to achieve by fine-tuning organoid production?

    <p>To get the right kinds of connections among cells.</p> Signup and view all the answers

    What method is used to determine the amount of mRNA present in a sample?

    <p>Quantitative PCR (qPCR)</p> Signup and view all the answers

    Organoids are used to study gene expression in just one type of cell.

    <p>False</p> Signup and view all the answers

    What is the primary functional test for organoids derived from islets?

    <p>Their ability to secrete insulin in response to glucose.</p> Signup and view all the answers

    The process of _________ involves converting mRNA into cDNA to analyze gene expression.

    <p>reverse transcription</p> Signup and view all the answers

    Match the following staining techniques with their purposes:

    <p>H&amp;E staining = General tissue structure visualization Immunostaining = Detect specific proteins in cells DAPI staining = Nuclear visualization cDNA synthesis = Convert mRNA to cDNA</p> Signup and view all the answers

    What do organoids derived from liver tumors help researchers understand?

    <p>Growth differences between various tumors</p> Signup and view all the answers

    Single cell sequencing allows the examination of mRNA from multiple cells simultaneously.

    <p>False</p> Signup and view all the answers

    Why are housekeeping genes important in quantitative PCR?

    <p>They serve as control genes to compare the expression levels of target genes.</p> Signup and view all the answers

    The organoid should ideally resemble the original _______ from which it was derived.

    <p>tissue</p> Signup and view all the answers

    Match the following markers to what they indicate in liver cancer organoids:

    <p>AFP = Hepatocellular carcinoma marker EpCAM = Colorectal carcinoma marker DAPI = Nuclear stain H&amp;E = General tissue staining</p> Signup and view all the answers

    What size are organoids typically in diameter?

    <p>1-2 mm</p> Signup and view all the answers

    Organoids can be generated only from induced pluripotent stem cells (iPSCs).

    <p>False</p> Signup and view all the answers

    What is one application of organoids in personalized medicine?

    <p>Testing drug sensitivity or developing specific treatments for individuals.</p> Signup and view all the answers

    Organoids are considered an improvement over traditional cell lines because they maintain the __________ of the tissue.

    <p>complexity</p> Signup and view all the answers

    Match the types of stem cells with their corresponding uses:

    <p>Adult Stem Cells (ASC) = Used for gut organoids Induced Pluripotent Stem Cells (iPSC) = Used for brain organoids Cancer Stem Cells = Derived from biopsies for cancer research Embryoid bodies = Initial structure formed from iPSCs</p> Signup and view all the answers

    What key challenge do organoids face regarding their structure?

    <p>Absence of stromal components and vasculature</p> Signup and view all the answers

    Organoids can be grown in environments that mimic the host tissue.

    <p>True</p> Signup and view all the answers

    What is the significance of using organoids derived from healthy and diseased tissue?

    <p>They allow comparison to study disease mechanisms and treatment effects.</p> Signup and view all the answers

    Validation of organoids typically involves using __________ and immunostaining.

    <p>microscopy</p> Signup and view all the answers

    Match the following organoid applications with their descriptions:

    <p>Disease Modelling = Studying the mechanisms of diseases using organoids Drug Discovery = Testing drug efficacy on patient-derived organoids Diagnostics = Using organoids to identify disease states Regeneration = Examining repair mechanisms in tissue-specific organoids</p> Signup and view all the answers

    Which of the following is a reason for using organoids in drug discovery?

    <p>They provide a more accurate model than traditional cell lines</p> Signup and view all the answers

    Organoids are typically less accessible for experimental procedures than animal models.

    <p>False</p> Signup and view all the answers

    List one method used to pattern stem cells during organoid development.

    <p>Using commercial morphogens to block differentiation.</p> Signup and view all the answers

    The goal of organoid development is to recapitulate the __________ and behavior of host tissue.

    <p>architecture</p> Signup and view all the answers

    What is the primary purpose of using homologous recombination in genetic engineering?

    <p>To knock out or delete genes</p> Signup and view all the answers

    Induced pluripotent stem cells (iPSC) must originate from human embryonic stem cells.

    <p>False</p> Signup and view all the answers

    What type of stem cells are derived from a blastocyst and can form chimeras?

    <p>Embryonic stem cells (ES cells)</p> Signup and view all the answers

    Fibroblasts can be reprogrammed to generate __________ stem cells.

    <p>induced pluripotent</p> Signup and view all the answers

    Match the following processes with their descriptions.

    <p>G418 selection = Used to select reprogrammed cells Homologous recombination = Introduces precise modifications near a cut site iPSC reprogramming = Converts somatic cells back to pluripotent state CRISPR-Cas9 = Uses guide RNA to make double-strand breaks</p> Signup and view all the answers

    Which of the following is NOT a reason for preferring iPSC over human embryonic stem cells?

    <p>Embryonic stem cells are pluripotent</p> Signup and view all the answers

    Using CRISPR-Cas9, the cleavage site must be located within the region to be altered.

    <p>False</p> Signup and view all the answers

    What do embryoid bodies differentiate into when treated with specific factors?

    <p>Neurons and glial cells</p> Signup and view all the answers

    The process of __________ allows scientists to introduce specific mutations into IPSC.

    <p>gene editing</p> Signup and view all the answers

    Match the following stem cell applications with their uses.

    <p>Cell Replacement Therapy = Transplants from bone marrow Immunomodulation = Use of mesenchymal stem cells Regeneration = Potential applications in heart and pancreas</p> Signup and view all the answers

    Which of the following describes a chimera in mouse genetics?

    <p>A mouse made up of both host and new cells</p> Signup and view all the answers

    The G418 resistance gene is an effective system for selecting all reprogrammed cells.

    <p>False</p> Signup and view all the answers

    Name a common type of cell from which iPSCs can be generated.

    <p>Fibroblasts or epithelial cells</p> Signup and view all the answers

    CRISPR-Cas9 uses __________ RNA to guide the editing process.

    <p>guide</p> Signup and view all the answers

    Match the following types of stem cells with their characteristics.

    <p>Embryonic Stem Cells = Pluripotent, can make any cell type Induced Pluripotent Stem Cells = Reprogrammed somatic cells Hemopoietic Stem Cells = Found in bone marrow</p> Signup and view all the answers

    Study Notes

    Stem Cell Biology Study Notes

    • Stem cells are undifferentiated cells capable of self-renewal and producing differentiated progeny.
    • Adult stem cells are crucial for tissue renewal and repair.
    • Stem cells can be difficult to identify in adult tissues due to their low numbers, frequent turnover, and differentiation.
    • Stem cell divisions result in one daughter cell remaining a stem cell, and one differentiating.
    • Stem cells often generate progenitor cells to expand the pool of differentiated cells.
    • Progenitor cells divide, generating differentiated cells, but they cannot do so indefinitely.
    • Stem cells in the gut reside in crypts, continuously dividing to replace lost epithelial cells.
    • Cell lineage tracing experiments, often using transgenic mice, genetically label stem cells, allowing their progeny to be observed.
    • Stem cells are categorized by potency: unipotent, multipotent, pluripotent, and totipotent.
    • Hematopoietic stem cells (HSCs) are a type of multipotent hematopoietic stem cells, demonstrating their capacity in transplant experiments by regenerating the entire bone marrow.
    • A stem cell niche is a specialized microenvironment consisting of cells and secreted molecules supporting stem cell survival and quiescence.
    • Asymmetric divisions in stem cells maintain the stem cell pool, while symmetric division increases the number of stem cells.
    • Neural stem cells reside in the subventricular zone of the brain and can generate neurons.
    • Embryonic stem cells (ESCs) are pluripotent, allowing generation of transgenic mice.
    • Induced pluripotent stem cells (iPSCs) are created from somatic cells, offering an alternative to using embryonic cells.
    • IPSCs can be differentiated into various cell types, and their use in cancer modeling.
    • Clinical use of patient-derived organoids involves randomization between current treatments and new treatments.
    • Organoids are useful in modeling human tissues and disease processes in a simplified, often 3D, environment.
    • Organoids are generated from stem cells by manipulating factors to guide the self-assembly of a tissue-like structure.
    • Characterisation of organoids involves validating presence of cellular components and functionalities, such as protein expression and functional assay (e.g. drug sensitivity/response).
    • Standardisation in organoid production improves reproducibility and consistency of experiments.

    Organoid Study Notes

    • Organoids are self-organizing 3D cell cultures that mimic the architecture and behaviour of tissues. They can arise from various sources, including stem cells, cancer cells, or biopsies.
    • Organoids are generated for various tissues, including the gut, pancreas, and brain.
    • Organoids offer advantages over cell lines and animal models due to their human cells, accessibility, lack of immortal cell lines, and more complex tissue properties.
    • Limitations of organoids include potential need for vascularization, immune system components, stromal cells, and heterogeneity.
    • Organoids are used for studying development, regeneration, diagnostics, disease modelling, drug discovery, and personalized medicine.

    Bioinformatics Study Notes

    • Bioinformatics provides tools for managing and analyzing biological data.
    • Sequence analysis and protein structure analysis knowledge are critical for bioscience researchers.
    • Various biological datasets are now widely accessible, including cDNA, whole genomes, copy number variations, microarray results, single-cell RNA-Seq, GWAS, SNPs, chromatin modifications, amino acid sequences, protein structures, proteomics data, and protein-interaction maps.
    • GenBank, DBBJ, and ENA are extensive, publicly accessible databases for sequence data.
    • Whole genome sequencing data is increasing exponentially due to next-generation sequencing (NGS).
    • Bioinformatics plays a huge role in genomic medicine.
    • Local, regional, and national workflows are being implemented for genomic medicine.
    • Understanding sporadic vs. inherited diseases, risk factors, genetic determinants, monogenic vs. polygenic risks, and causative vs. linked SNPs are critical components of bioinformatics for genetic health risk prediction.
    • Direct-to-consumer (DCT) genetic testing, like 23andMe, allows individuals to access their genetic information, analyze health dispositions, traits, and carrier status.
    • DCT genetic testing uses Illumina microarrays for SNP detection, offering a lower cost entry point (with some FDA regulatory hurdles).
    • Sequence alignments are critical in bioinformatics, often facilitated by tools like BLASTN and BLASTP, enabling identification of similar genes/regions across sequences.
    • NGS (Next-Generation Sequencing), a massively parallel sequencing technology, has revolutionized bioinformatics analysis, producing short reads from millions of DNA segments in parallel. It is capable of sequencing entire genomes.
    • Sanger sequencing is still relevant, while NGS has become cheaper and faster, though long-read sequencing methods may be necessary for certain analyses of genomic variation, such as copy number variations and chromosomal rearrangements.
    • Bioinformatics is integral for NGS assembly to analyze short reads and determine variations like SNPs.
    • Bioinformatic methods, such as BLAST, enable alignment of DNA sequences, like mRNA to genomic sequences, allowing the location of exons, introns, and potentially mutations.
    • Database tools like RefSeq (reference sequence for transcripts and corresponding genomic sequences) are often utilised for this kind of analysis.
    • Identification of conserved genes/domains across sequences aids understanding evolutionary relationships and functional similarities.
    • Various matrices like BLOSUM 62 can be used for quantitative scoring of protein sequence alignments.

    MCQ Answer Key

    • (These answers are based on the provided text and may not be exhaustive.)*

    • Select the correct statement: 2. Somatic mutations refer to mutations in cells outside of the germline so are not inheritable.

    • Select the correct statement: 2. Functional genomics explains how genomic data explains the phenotype.

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    Description

    Test your knowledge on bioinformatics tools, genetic studies, and the PAX6 gene. This quiz covers various aspects of biological data analysis, genome-wide association studies, protein structures, and genetic engineering. Evaluate your understanding of crucial genetic concepts and their implications in both model organisms and humans.

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