Relevant bibliographies by topics / Genetics and Genome Biology

Academic literature on the topic 'Genetics and Genome Biology'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Genetics and Genome Biology"

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Pennisi, E. "Genetics: From Genes to Genome Biology." Science 272, no. 5269 (June 21, 1996): 1736–38. http://dx.doi.org/10.1126/science.272.5269.1736.

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Pegoraro, Mirko, and Gareth D. Weedall. "Malaria in the ‘Omics Era’." Genes 12, no. 6 (May 30, 2021): 843. http://dx.doi.org/10.3390/genes12060843.

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Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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Smýkal, P. "Pea (Pisum sativum L.) in biology prior and after Mendel's discovery." Czech Journal of Genetics and Plant Breeding 50, No. 2 (June 12, 2014): 52–64. http://dx.doi.org/10.17221/2/2014-cjgpb.

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Pea (Pisum sativum L.) has been extensively used in early hybridization studies and it was the model organism of choice for Mendel’s discovery of the laws of inheritance, making pea part of the foundation of modern genetics. Pea has also been used as model for experimental morphology and physiology. However, subsequent progress in pea genomics has lagged behind many other plant species, largely as a consequence of its genome size and low economic significance. The availability of the genome sequences of five legume species (Medicago truncatula, Lotus japonicus, Glycine max, Cajanus cajan and Cicer aerietinum) offers opportunities for genome wide comparison. The combination of a candidate gene and synteny approach has allowed the identification of genes underlying agronomically important traits such as virus resistances and plant architecture. Useful genomic resources already exist and include several types of molecular marker sets as well as both transcriptome and proteome datasets. The advent of greater computational power and access to diverse germplasm collections enable the use of association mapping to identify genetic variation related to desirable agronomic traits. Current genomic knowledge and technologies can facilitate the allele mining for novel traits and their incorporation from wild Pisum sp. into elite domestic backgrounds. Fast neutron and targeting-induced local lesions in genomes (TILLING) pea mutant populations are available for reverse genetics approaches, BAC libraries for positional gene cloning as well as transgenic and in vitro regeneration for proof of function through gene silencing or over-expression. Finally, recently formed International Pea Genome Sequencing Consortium, holds promise to provide the pea genome sequence by 2015, a year of 150 anniversary of Mendel’s work.
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Teterina, Anastasia A., John H. Willis, and Patrick C. Phillips. "Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization." Genetics 214, no. 4 (February 28, 2020): 769–80. http://dx.doi.org/10.1534/genetics.119.303018.

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The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.
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Beacon, Tasnim H., James R. Davie, and Michael J. Hendzel. "Introduction: Genome Biology." Genome 64, no. 4 (April 2021): v—vii. http://dx.doi.org/10.1139/gen-2021-0003.

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Totikov, Azamat, Andrey Tomarovsky, Dmitry Prokopov, Aliya Yakupova, Tatiana Bulyonkova, Lorena Derezanin, Dmitry Rasskazov, et al. "Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology." Genes 12, no. 9 (August 28, 2021): 1336. http://dx.doi.org/10.3390/genes12091336.

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Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.
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Bult, C. J. "The Mouse Genome Database (MGD): integrating biology with the genome." Nucleic Acids Research 32, no. 90001 (January 1, 2004): 476D—481. http://dx.doi.org/10.1093/nar/gkh125.

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Shiloh, Y. "Cancer genetics: Tumor biology and genome technology converge." European Journal of Cancer 29 (January 1993): S9. http://dx.doi.org/10.1016/0959-8049(93)90650-5.

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Wixon, Jo. "Meeting Highlights: Genome Sequencing and Biology 2001." Comparative and Functional Genomics 2, no. 4 (2001): 243–51. http://dx.doi.org/10.1002/cfg.97.

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We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.
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Sung, Bong Hyun, Donghui Choe, Sun Chang Kim, and Byung-Kwan Cho. "Construction of a minimal genome as a chassis for synthetic biology." Essays in Biochemistry 60, no. 4 (November 30, 2016): 337–46. http://dx.doi.org/10.1042/ebc20160024.

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Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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Dissertations / Theses on the topic "Genetics and Genome Biology"

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Chew, Wei Leong. "Postnatal Genome Editing With CRISPR." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493352.

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Targeted genome editing holds tremendous promise for permanent correction of many genetic diseases. The recently developed CRISPR/Cas9 genome-editing tool exhibits facile programmability and robust gene-editing efficiency, and has been applied in cell cultures and animal tissues. However, multi-organ gene-editing in live mammals has not been examined or achieved. This study demonstrates genetic modification in multiple organs of postnatal mice by systemic delivery of CRISPR with adeno-associated viruses (AAVs). I resolved the AAV payload limitation by splitting Cas9 and reconstituting the native protein in vivo using scarless split-intein protein trans-splicing, which preserves full activity of Cas9. I determined that the delivery efficiency of AAV-CRISPR dictates gene-targeting rates in vivo, with the preferential gene-editing in liver and heart, and more modest editing efficiencies in skeletal muscle, brain and gonads, directly reflecting the infection profile of the virus serotype. To track CRISPR biodistribution, I established two reporter systems that apply in situ fluorescence activation to demarcate CRISPR-targeting events at single-cell resolution, identifying rare gene-edited cells that normally evade detection by sequencing. This exquisite detection sensitivity further allows evaluation of inter-generational transmission of gene-editing viruses. Finally, although Cas9 elicits host immune responses, these can be ameliorated by immunosuppression. I also identified a public Cas9-responsive T-cell clonotype and mapped the B-cell epitopes on Cas9 and AAV. Engineering tolerance to immunodominant epitopes may provide an avenue for avoiding immune rejection of AAV-CRISPR. The ability to create programmable genetic modifications in multiple organs of postnatal mammals provides a powerful tool for biological research, and foretells that the genomes of whole mammals may be rewritten at will.
Medical Sciences
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Omilian, Angela Ruggieri. "Features of Daphnia genome evolution." [Bloomington, Ind.] : Indiana University, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3243783.

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Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2006.
Title from PDF t.p. (viewed Nov. 18, 2008). Source: Dissertation Abstracts International, Volume: 67-12, Section: B, page: 6862. Adviser: Michael Lynch.
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Chung, Hattie. "Genome evolution in structured systems." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493565.

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The evolution of a genome is shaped by spatial interactions at multiple scales. At the angstrom level, structural constraints on both RNA molecules and proteins contribute to the evolution of a gene sequence. Such optimized genes are weaved together in a particular order, out of a near-infinite number of combinations, to result in a genome. The fate of a genome is intricately linked to the evolutionary fate of its host organism; in turn, the fate of an organism is governed by where it resides in space. In this dissertation, I investigate how structure shapes the evolution of a gene, genome content, and pathogen populations residing in a diseased human lung. Chapter 1 provides a brief historical overview of population genetics in structured environments. I motivate why it is important to determine the migration rate of new alleles. Chapter 2 investigates how pathogens evolve within the structure of the cystic fibrosis lung. I find that migration rate and mutation rate are on similar timescales. Selection, rather than spatial isolation, maintains diversity within a pathogen population. Chapter 3 presents a new method to probe how codon choice is optimized throughout a gene. I find that codon choice is dictated by preference for particular RNA secondary structures, rather than intrinsic properties of a codon. Chapter 4 describes an ongoing study of how rapidly P. aeruginosa populations evolve in short-term infections. Preliminary results show that gene duplication events can sweep through a population in just 11 days. Chapter 5 introduces ideas for future directions. I pose questions regarding how pathogens evolve molecular mimicry that can trigger autoimmune disease in the human host, and how cancer-inducing inflammation might be detected from mutational signatures in the microbiome.
Systems Biology
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Chen, Stacy Yen-chun. "Genome-wide analysis of yeast meiotic recombination landscape." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390037.

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Simonson, Matthew A. "Polygenic analysis of genome-wide SNP data." Thesis, University of Colorado at Boulder, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3562047.

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One of the central motivators behind genetic research is to understand how genetic variation relates to human health and disease. Recently, there has been a large-scale effort to find common genetic variants associated with many forms of disease and disorder using single nucleotide polymorphisms (SNPs). Several genome-wide association (GWAS) studies have successfully identified SNPs associated with phenotypes. However, the effect sizes attributed to individual variants is generally small, explaining only a very small amount of the genetic risk and heritability expected based on the estimates of family and twin studies. Several explanations exist for the inability of GWAS to find the "missing heritability."

The results of recent research appear to confirm the prediction made by population genetics theory that most complex phenotypes are highly polygenic, occasionally influenced by a few alleles of relatively large effect, and usually by several of small effect. Studies have also confirmed that common variants are only part of what contributes to the total genetic variance for most traits, indicating rare-variants may play a significant role.

This research addresses some of the most glaring weaknesses of the traditional GWAS approach through the application of methods of polygenic analysis. We apply several methods, including those that investigate the net effects of large sets of SNPs, more sophisticated approaches informed by biology rather than the purely statistical approach of GWAS, as well as methods that infer the effects of recessive rare variants.

Our results indicate that traditional GWAS is well complemented and improved upon by methods of polygenic analysis. We demonstrate that polygenic approaches can be used to significantly predict individual risk for disease, provide an unbiased estimate of a substantial proportion of the heritability for multiple phenotypes, identify sets of genes grouped into biological pathways that are enriched for associations, and finally, detect the significant influence of recessive rare variants.

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Wesolowska, Natalia. "Modification and nuclear organization of the Drosophila melanogaster genome." Thesis, The Johns Hopkins University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3575013.

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The success of Drosophila as a system for genetic analysis is closely linked to its amenability to genetic manipulation. Part 1 of the dissertation elucidates a novel scheme for long-range targeted manipulation of genes. We integrated an 80-kb genomic fragment at its endogenous locus, utilizing a targeted attP attachment site for the phiC31 integrase. We achieved single-copy reduction of the resulting region duplication by inducing recombinational DNA repair. We showed that this two-step scheme of integration and reduction is efficient and useful for delivering modifications. We established a vector configuration that facilitates the recovery of modifications. The integrating genomic fragment allowed for delivery of a new attachment site at 70 kb from the existing attP into a new locus, making it susceptible to targeted mutagenesis. We extrapolate that with this scheme, only 1 200 lines bearing att-sites throughout the genome would suffice to render all Drosophila genes amenable to targeted mutagenesis. Excitingly, this method should be readily applicable to other systems.

In Part 2 of the dissertation, I explored the question of telomere organization in Drosophila. Telomeres demarcate the ends of linear chromosomes to distinguish them from broken ends. In yeast, they cluster at the periphery of the nucleus establishing a compartment of silent chromatin. To bring insight into telomere organization in a higher organism, we followed EGFPlabeled Drosophila telomeric protein HOAP in vivo and found that the 16 telomeres cluster into 4-6 foci per nucleus in somatic tissues. Interestingly, HOAP signal intensity in the clusters doubles in interphase, potentially due to loading of HOAP to newly replicated telomeres. We tested several predictions about rules governing clustering. First, by inspecting mutant embryos that develop as haploids, we found that clustering is not mediated by associations between homologs. Second, by demonstrating clustering capability for a telomere of novel sequence, we eliminated DNA sequence homology and identity as important factors. Third, by marking both ends of a chromosome, we ruled out predominance of intra-chromosomal interactions. We propose that clustering is indiscriminate of sequence and is likely maintained by a yet undetermined factor.

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Badhwar, AmanPreet. "Identification and characterization of rearrangements in the vervet monkey genome." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=101702.

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Several mechanisms can lead to the reorganization of genomes during speciation, including centromere repositioning, new centromere emergence or other chromosomal rearrangements. Using a comparative karyotype approach, I determined that the vervet genome contains at least 12 evolutionary young centromere locations.
To study the evolutionary dynamics of centromere formation, I identified and validated the alpha-satellite repeat as a centromere-specific marker in the vervet using comparative genomics, sequence analysis and hybridization screening. I developed criteria to infer the position of vervet bacterial artificial chromosome (BAC) inserts based on alpha-satellite monomer content. In a complementary approach, I demarcated the pericentromeric boundaries in human and identified vervet BAC clones that mapped orthologously to these regions.
In addition to centromeric analyses, I developed methodologies to detect other genome rearrangements, in particular vervet deletion/human insertion and vervet translocation events. The tools and approaches developed in this thesis will prove useful in cataloguing additional vervet genome rearrangements.
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Young, Adrian. "The Evolutionary Feedback between Genetic Conflict and Genome Architecture." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11482.

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The advent of separate sexes set the stage for dramatic evolutionary innovation across a wide range of taxa. Much of this innovation is attributable to divergent evolutionary interests between now distinct sub-populations of males and females. Trade-offs inherent to these divergent life histories, coupled with a common genome, conspire to limit natural selection's ability to simultaneously maximize the fitness of both sexes. Such conflict between the sexes has therefore largely shaped the history of the genomes of sexual taxa. However, various aspects of the genomic environment—including genes' spatial distributions, abilities to regulate their expression, and rates of recombination—also feed back to influence future sex-specific evolutionary trajectories. Using various genomic resources and transcriptome sequences for the lab mouse, I test several theoretical predictions regarding this feedback between genetic conflict and features of genomic organization.
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Li, Hubo. "Genome-Wide RNAi Screens for Novel Regulators of Acute Myeloid Leukemia." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226105.

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Acute myeloid leukemia (AML) is a heterogeneous disease with complex molecular mechanisms. Recent advent of genomic technologies, such as copy number profiling, whole genome sequencing, and gene expression profiling has accumulated a plethora of large-scale data in AML cell lines and patient samples. However, the functional relevance of most genes identified by these methods has yet to be determined. To systematically characterize the genetic requirement in AML, we conducted genome-wide shRNA screens in 17 AML cell lines in parallel with 199 cell lines of other cancer types. We identified over 150 genes that were required for proliferation specifically by AML, but not other cancer cell lines. We further interrogated the requirements of primary screen hits in vivo with a secondary screen in a xenotransplantation model driven by the MLL-AF9 oncogenic fusion. Integrating both of the RNAi screens and additional gene expression data, we identified transcription factor ZEB2 as a top candidate for regulating AML proliferation. In human AML cells, ZEB2 inhibition impairs proliferation and promotes granulocytic differentiation. Mechanistically, we showed that ZEB2 interacts with the CtBP co-repressor complex, and transcriptionally represses genes involved in cell adhesion and migration. ZEB2’s relevance in AML is further demonstrated by its overexpression in MLL-rearranged AML, and by the epigenetic silencing of its negative regulators, miR-200 family microRNAs, in AML. Our results extend the role of ZEB2 beyond regulating epithelial-mesenchymal transition, and establish ZEB2 as a novel regulator of AML proliferation and differentiation. MicroRNA-like off-target effect is a major caveat of RNAi screens, which often leads to false positive discoveries. However, systematic analysis of off-target effects in large-scale RNAi screen data can also lead to the discovery of microRNAs with functional relevance. By analyzing the off-target effects in our AML screen, we identified several microRNAs as candidate suppressors for AML proliferation. We show that miR-105, miR-140, miR-501, and miR-532 are novel regulators of the myeloid oncogene MYB. In particular, miR-105 inhibits AML cell growth and miR-532 is associated with myeloid differentiation. The combination of the ZEB2 and microRNA work emphasizes the power of RNAi screens in the exploration of novel cancer regulators.
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Canver, Matthew. "Elucidation of Mechanisms of Fetal Hemoglobin Regulation by CRISPR/Cas9 Mediated Genome Editing." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493407.

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Despite nearly complete understanding of the genetics of the β-hemoglobinopathies for several decades, definitive treatment options have lagged behind. Fetal hemoglobin (HbF) reinduction represents a “silver bullet” for therapy of the β-globin disorders. Recent development of the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 nuclease system has allowed for facile manipulation of the genome for the study of genes and genetic elements. Here we developed CRISPR/Cas9-based methodology to reliably engender targeted genomic deletions ranging from 1.3 kilobases to over 1 megabase, which suggested an inverse relationship between deletion size and deletion frequency. Targeted deletion methods and Cas9-mediated in situ saturating mutagenesis were applied to the enhancer of the HbF repressor BCL11A, which revealed discrete vulnerabilities. This finding is consistent with emerging evidence in the field that large enhancers are comprised of constituent parts with some harboring the majority of the activity. The identified “Achilles heel” of the enhancer represents a promising therapeutic target. We further enhanced the resolution of the in situ saturating mutagenesis technique by using multiple Cas9 nucleases and variant-aware library design to identify functional sequences within the HBS1L-MYB intergenic region, a locus associated with elevated HbF levels. These data demonstrate the robustness of CRISPR/Cas9 mediated in situ saturating mutagenesis and targeted deletion to interrogate functional sequence within regulatory DNA. Harnessing the power of genome editing may usher in a second generation form of gene therapy for the β-globin disorders.
Medical Sciences
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Books on the topic "Genetics and Genome Biology"

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Post-genome biology of primates. Tokyo: Springer, 2012.

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Igor, Kovalchuk, and Kovalchuk Olga MD, eds. Transgenerational genome instability. Hauppauge, N.Y: Nova Science Publishers, 2009.

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Evolution, development, & the predictable genome. Greenwood Village, Colo: Roberts And Company Publishers, 2011.

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1944-, Adolph Kenneth W., ed. Human genome methods. Boca Raton: CRC Press, 1998.

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Genome instability and transgenerational effects. New York: Nova Science Publishers, 2010.

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1966-, Muse Spencer V., ed. A primer of genome science. 3rd ed. Sunderland, Mass: Sinauer Associates, 2009.

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Strachan, T. Human molecular genetics. 4th ed. New York: Garland Science, 2011.

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G, Zimm Georgianna, and Lindsley Dan L. 1925-, eds. The genome of Drosophila melanogaster. San Diego: Academic Press, 1992.

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Lewontin, Richard C. It ain't necessarily so: The dream of the human genome and other illusions. London: Granta, 2001.

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S, Rajadhyaksha Medha, ed. New biology and genetic diseases. New Delhi: Oxford University Press, 1999.

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Book chapters on the topic "Genetics and Genome Biology"

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Van Asselt, Austin J., and Erik A. Ehli. "Whole-Genome Genotyping Using DNA Microarrays for Population Genetics." In Methods in Molecular Biology, 269–87. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1920-9_16.

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Moore, Graham. "Exploiting Comparative Biology and Genomics to Understand a Trait in Wheat, Ph1." In Advances in Wheat Genetics: From Genome to Field, 137–46. Tokyo: Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55675-6_15.

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Dahiya, Rashmi, Taj Mohammad, and Md Imtaiyaz Hassan. "Role of Genome-Wide Association Studies in Host Genetics: Toward Understanding of Microbiome Association." In Metagenomic Systems Biology, 37–54. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-8562-3_2.

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Kobayashi, Ichizo. "Genetic Addiction: a Principle of Gene Symbiosis in a Genome." In Plasmid Biology, 105–44. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817732.ch6.

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Maliga, Pal, and Zora Svab. "Engineering the Plastid Genome of Nicotiana sylvestris, a Diploid Model Species for Plastid Genetics." In Methods in Molecular Biology, 37–50. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-61737-957-4_2.

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Obata, Masaomi, Mareki Ohtsuji, Yukiyasu Iida, Toshikazu Shirai, Sachiko Hirose, and Hioroyuki Nishimura. "Genome-Wide Genetic Study in Autoimmune Disease-Prone Mice." In Methods in Molecular Biology, 111–41. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0404-4_13.

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Johansson, Anna C. V., and Lars Feuk. "Characterizing and Interpreting Genetic Variation from Personal Genome Sequencing." In Methods in Molecular Biology, 343–67. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-507-7_17.

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Hill, Eric M., Cheng-Yi Chen, Florencia del Viso, Lacey R. Ellington, Shuonan He, Ahmet Karabulut, Ariel Paulson, and Matthew C. Gibson. "Manipulation of Gene Activity in the Regenerative Model Sea Anemone, Nematostella vectensis." In Methods in Molecular Biology, 437–65. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_23.

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AbstractWith a surprisingly complex genome and an ever-expanding genetic toolkit, the sea anemone Nematostella vectensis has become a powerful model system for the study of both development and whole-body regeneration. Here we provide the most current protocols for short-hairpin RNA (shRNA)-mediated gene knockdown and CRISPR/Cas9-targeted mutagenesis in this system. We further show that a simple Klenow reaction followed by in vitro transcription allows for the production of gene-specific shRNAs and single guide RNAs (sgRNAs) in a fast, affordable, and readily scalable manner. Together, shRNAknockdown and CRISPR/Cas9-targeted mutagenesis allow for rapid screens of gene function as well as the production of stable mutant lines that enable functional genetic analysis throughout the Nematostella life cycle.
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Deleye, Lieselot, Dieter De Coninck, Dieter Deforce, and Filip Van Nieuwerburgh. "Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis." In Methods in Molecular Biology, 27–42. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7514-3_3.

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Meyer-Ficca, Mirella L., and Ralph G. Meyer. "Genetic Approaches to Targeting Multiple PARP Genes in a Mammalian Genome." In Methods in Molecular Biology, 349–76. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-270-0_21.

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Conference papers on the topic "Genetics and Genome Biology"

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"NGRI1, PIP4K2A, and HTR2K contain possible genetics." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-408.

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"Mitochondrial genetics of amphipods: revealing mechanisms of diversity." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-153.

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"Understanding the role of genetics in comorbidity." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-220.

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"Fundamental and applied aspects of microbiome genetics." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-277.

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"Seeking an optimal approach to variant calling in medical genetics." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-215.

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"766 BGRS/SB-2022 Medical genetics and cancer studies based on next-gen sequencing presented at the bioinformatics conferences and young scientists schools." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-442.

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"Genetic regulation of wheat inflorescence development." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-191.

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Kim, Moon K., Byeongsoo Lim, and Wing Kam Liu. "Multiscale Elastic Network Model for Macromolecular Machines." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13090.

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In the early year of this century the human genome sequencing project was successfully completed so that we can understand all the human genes and their corresponding protein sequences. Now our interests have naturally moved from genetics to proteomics in which we challenge to elucidate the relationship between functions and structures of proteins. In particular, understanding large conformational changes occurring at molecular machinery systems or protein assemblies have received great attentions. However, it has been rarely studied both experimentally and theoretically because of limitation of experimental setup for capturing real time protein dynamics and computing power, respectively.
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"Genetic aspects of internet-dependence in teenagers." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-160.

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"Inter- vs. intraspecific genetic variability of morphologically similar Ligophorus species." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-166.

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Reports on the topic "Genetics and Genome Biology"

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Dawson, William O., Moshe Bar-Joseph, Charles L. Niblett, Ron Gafny, Richard F. Lee, and Munir Mawassi. Citrus Tristeza Virus: Molecular Approaches to Cross Protection. United States Department of Agriculture, January 1994. http://dx.doi.org/10.32747/1994.7570551.bard.

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Citrus tristeza virus (CTV) has the largest genomes among RNA viruses of plants. The 19,296-nt CTV genome codes for eleven open reading frames (ORFs) and can produce at least 19 protein products ranging in size from 6 to 401 kDa. The complex biology of CTV results in an unusual composition of CTV-specific RNAs in infected plants which includes multiple defective RNAs and mixed infections. The complex structure of CTV populations poses special problems for diagnosis, strain differentiation, and studies of pathogenesis. A manipulatable genetic system with the full-length cDNA copy of the CTV genome has been created which allows direct studies of various aspects of the CTV biology and pathology. This genetic system is being used to identify determinants of the decline and stem-pitting disease syndromes, as well as determinants responsible for aphid transmission.
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Konisky, J. Genetics and molecular biology of methanogen genes. Final report. Office of Scientific and Technical Information (OSTI), October 1997. http://dx.doi.org/10.2172/555346.

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Palsson, Bernhard O., Ali Ebrahim, and Steve Federowicz. The OME Framework for genome-scale systems biology. Office of Scientific and Technical Information (OSTI), December 2014. http://dx.doi.org/10.2172/1169326.

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Gunsalus, R. P. Molecular biology and genetics of the acetate-utilizing methanogenic bacteria. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/6967641.

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Robert P. Gunsalus. Molecular Biology and Genetics of the Acetate-Utilizing Methanogenic Bacteria. Office of Scientific and Technical Information (OSTI), July 2003. http://dx.doi.org/10.2172/859404.

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Boore, Jeffrey. Why Evolutionary Biology and Genome Sciences Need Each Other. Office of Scientific and Technical Information (OSTI), May 2005. http://dx.doi.org/10.2172/840341.

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Moore, Gloria A., Gozal Ben-Hayyim, Charles L. Guy, and Doron Holland. Mapping Quantitative Trait Loci in the Woody Perennial Plant Genus Citrus. United States Department of Agriculture, May 1995. http://dx.doi.org/10.32747/1995.7570565.bard.

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As is true for all crops, production of Citrus fruit is limited by traits whose characteristics are the products of many genes (i.e. cold hardiness). In order to modify these traits by marker aided selection or molecular genetic techniques, it is first necessary to map the relevant genes. Mapping of quantitative trait loci (QTLs) in perennial plants has been extremely difficult, requiring large numbers of mature plants. Production of suitable mapping populations has been inhibited by aspects of reproductive biology (e.g. incompatibility, apomixis) and delayed by juvenility. New approaches promise to overcome some of these obstacles. The overall objective of this project was to determine whether QTLs for environmental stress tolerance could be effectively mapped in the perennial crop Citrus, using an extensive linkage map consisting of various types of molecular markers. Specific objectives were to: 1) Produce a highly saturated genetic linkage map of Citrus by continuing to place molecular markers of several types on the map. 2) Exploiting recently developed technology and already characterized parental types, determine whether QTLs governing cold acclimation can be mapped using very young seedling populations. 3) Determine whether the same strategy can be transferred to a different situation by mapping QTLs influencing Na+ and C1- exclusion (likely components of salinity tolerance) in the already characterized cross and in new alternative crosses. 4) Construct a YAC library of the citrus genome for future mapping and cloning.
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Wall, Judy D. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria. Office of Scientific and Technical Information (OSTI), December 2014. http://dx.doi.org/10.2172/1166017.

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Wall, J. Genetics and molecular biology of hydrogen metabolism in sulfate reducing bacteria. Office of Scientific and Technical Information (OSTI), January 1990. http://dx.doi.org/10.2172/6892389.

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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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