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Annual Review of Genetics

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https://www.readbyqxmd.com/read/27893966/vaccination-via-chloroplast-genetics-affordable-protein-drugs-for-the-prevention-and-treatment-of-inherited-or-infectious-human-diseases
#1
Henry Daniell, Hui-Ting Chan, Elise K Pasoreck
Plastid-made biopharmaceuticals treat major metabolic or genetic disorders, including Alzheimer's, diabetes, hypertension, hemophilia, and retinopathy. Booster vaccines made in chloroplasts prevent global infectious diseases, such as tuberculosis, malaria, cholera, and polio, and biological threats, such as anthrax and plague. Recent advances in this field include commercial-scale production of human therapeutic proteins in FDA-approved cGMP facilities, development of tags to deliver protein drugs to targeted human cells or tissues, methods to deliver precise doses, and long-term stability of protein drugs at ambient temperature, maintaining their efficacy...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893965/single-cell-and-single-molecule-analysis-of-gene-expression-regulation
#2
Maria Vera, Jeetayu Biswas, Adrien Senecal, Robert H Singer, Hye Yoon Park
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893964/aneuploidy-in-cancer-and-aging
#3
Ryan M Naylor, Jan M van Deursen
Chromosomal instability (CIN), the persistent inability of a cell to faithfully segregate its genome, is a feature of many cancer cells. It stands to reason that CIN enables the acquisition of multiple cancer hallmarks; however, there is a growing body of evidence suggesting that CIN impairs cellular fitness and prevents neoplastic transformation. Here, we suggest a new perspective to reconcile this apparent paradox and share an unexpected link between aneuploidy and aging that was discovered through attempts to investigate the CIN-cancer relationship...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893963/regulated-proteolysis-in-bacteria-caulobacter
#4
Kamal Kishore Joshi, Peter Chien
Protein degradation is essential for all living things. Bacteria use energy-dependent proteases to control protein destruction in a highly specific manner. Recognition of substrates is determined by the inherent specificity of the proteases and through adaptor proteins that alter the spectrum of substrates. In the α-proteobacterium Caulobacter crescentus, regulated protein degradation is required for stress responses, developmental transitions, and cell cycle progression. In this review, we describe recent progress in our understanding of the regulated and stress-responsive protein degradation pathways in Caulobacter...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893962/proteopathic-strains-and-the-heterogeneity-of-neurodegenerative-diseases
#5
Lary C Walker
Most age-related neurodegenerative diseases are associated with the misfolding and aberrant accumulation of specific proteins in the nervous system. The proteins self-assemble and spread by a prion-like process of corruptive molecular templating, whereby abnormally folded proteins induce the misfolding and aggregation of like proteins into characteristic lesions. Despite the apparent simplicity of this process at the molecular level, diseases such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob, and others display remarkable phenotypic heterogeneity, both clinically and pathologically...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893961/the-genetics-of-enteropathogenic-escherichia-coli-virulence
#6
Jaclyn S Pearson, Cristina Giogha, Tania Wong Fok Lung, Elizabeth L Hartland
In many parts of the world, enteropathogenic Escherichia coli (EPEC) are a leading cause of death in children with diarrhea. Much of what we know about the pathogenesis of EPEC infections is based on the study of one or two prototypic strains that have provided deep insight into the precise mechanisms by which EPEC colonizes the intestine, evades host immunity, and spreads from person to person. In some cases, defining the biochemical activity of the host-interacting effector proteins from these prototypic strains has led to the discovery of novel post-translational protein modifications and new understandings of biology and host-pathogen interactions...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893960/eukaryotic-dna-polymerases-in-homologous-recombination
#7
Mitch McVey, Varandt Y Khodaverdian, Damon Meyer, Paula Gonçalves Cerqueira, Wolf-Dietrich Heyer
Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893959/monoallelic-gene-expression-in-mammals
#8
Andrew Chess
Monoallelic expression not due to cis-regulatory sequence polymorphism poses an intriguing problem in epigenetics because it requires the unequal treatment of two segments of DNA that are present in the same nucleus and that can indeed have absolutely identical sequences. Here, I focus on a few recent developments in the field of monoallelic expression that are of particular interest and raise interesting questions for future work. One development is regarding analyses of imprinted genes, in which recent work suggests the possibility that intriguing networks of imprinted genes exist and are important for genetic and physiological studies...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732796/mosquito-vectors-and-the-globalization-of-plasmodium-falciparum-malaria
#9
Alvaro Molina-Cruz, Martine M Zilversmit, Daniel E Neafsey, Daniel L Hartl, Carolina Barillas-Mury
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732795/a-life-investigating-pathways-that-repair-broken-chromosomes
#10
James E Haber
Double-strand breaks (DSBs) pose a severe challenge to genome integrity; consequently, cells have developed efficient mechanisms to repair DSBs through several pathways of homologous recombination and other nonhomologous end-joining processes. Much of our understanding of these pathways has come from the analysis of site-specific DSBs created by the HO endonuclease in the budding yeast Saccharomyces cerevisiae. I was fortunate to get in on the ground floor of analyzing the fate of synchronously induced DSBs through the study of what I coined "in vivo biochemistry...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732794/regulation-and-role-of-fungal-secondary-metabolites
#11
Juliane Macheleidt, Derek J Mattern, Juliane Fischer, Tina Netzker, Jakob Weber, Volker Schroeckh, Vito Valiante, Axel A Brakhage
Fungi have the capability to produce a tremendous number of so-called secondary metabolites, which possess a multitude of functions, e.g., communication signals during coexistence with other microorganisms, virulence factors during pathogenic interactions with plants and animals, and in medical applications. Therefore, research on this topic has intensified significantly during the past 10 years and thus knowledge of regulatory mechanisms and the understanding of the role of secondary metabolites have drastically increased...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732793/deciphering-combinatorial-genetics
#12
Alan S L Wong, Gigi C G Choi, Timothy K Lu
High-order interactions among components of interconnected genetic networks regulate complex functions in biological systems, but deciphering these interactions is challenging. New strategies are emerging to decode these combinatorial genetic interactions across a wide range of organisms. Here, we review advances in multiplexed and combinatorial genetic perturbation technologies and high-throughput profiling platforms that are enabling the systematic dissection of complex genetic networks. These rapidly evolving technologies are being harnessed to probe combinatorial gene functions in functional genomics studies and have the potential to advance our understanding of how genetic networks regulate sophisticated biological phenotypes, to generate novel therapeutic strategies, and to enable the engineering of complex artificial gene networks...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732792/cell-specific-targeting-of-genetically-encoded-tools-for-neuroscience
#13
Lucas Sjulson, Daniela Cassataro, Shamik DasGupta, Gero Miesenböck
Genetically encoded tools for visualizing and manipulating neurons in vivo have led to significant advances in neuroscience, in large part because of the ability to target expression to specific cell populations of interest. Current methods enable targeting based on marker gene expression, development, anatomical projection pattern, synaptic connectivity, and recent activity as well as combinations of these factors. Here, we review these methods, focusing on issues of practical implementation as well as areas for future improvement...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732791/plant-transgenerational-epigenetics
#14
Leandro Quadrana, Vincent Colot
Transgenerational epigenetics is defined in opposition to developmental epigenetics and implies an absence of resetting of epigenetic states between generations. Unlike mammals, plants appear to be particularly prone to this type of inheritance. In this review, we summarize our knowledge about transgenerational epigenetics in plants, which entails heritable changes in DNA methylation. We emphasize the role of transposable elements and other repeat sequences in the creation of epimutable alleles. We also argue that because reprogramming of DNA methylation across generations seems limited in plants, the inheritance of DNA methylation defects results from the failure to reinforce rather than reset this modification during sexual reproduction...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27732790/interorgan-communication-pathways-in-physiology-focus-on-drosophila
#15
Ilia A Droujinine, Norbert Perrimon
Studies in mammals and Drosophila have demonstrated the existence and significance of secreted factors involved in communication between distal organs. In this review, primarily focusing on Drosophila, we examine the known interorgan communication factors and their functions, physiological inducers, and integration in regulating physiology. Moreover, we describe how organ-sensing screens in Drosophila can systematically identify novel conserved interorgan communication factors. Finally, we discuss how interorgan communication enabled and evolved as a result of specialization of organs...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27686281/the-ecology-and-evolution-of-cancer-the-ultra-microevolutionary-process
#16
Chung-I Wu, Hurng-Yi Wang, Shaoping Ling, Xuemei Lu
Although tumorigenesis has been accepted as an evolutionary process ( 20 , 102 ), many forces may operate differently in cancers than in organisms, as they evolve at vastly different time scales. Among such forces, natural selection, here defined as differential cellular proliferation among distinct somatic cell genotypes, is particularly interesting because its action might be thwarted in multicellular organisms ( 20 , 29 ). In this review, selection is analyzed in two stages of cancer evolution: Stage I is the evolution between tumors and normal tissues, and Stage II is the evolution within tumors...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27686280/conservation-and-variability-of-meiosis-across-the-eukaryotes
#17
Josef Loidl
Comparisons among a variety of eukaryotes have revealed considerable variability in the structures and processes involved in their meiosis. Nevertheless, conventional forms of meiosis occur in all major groups of eukaryotes, including early-branching protists. This finding confirms that meiosis originated in the common ancestor of all eukaryotes and suggests that primordial meiosis may have had many characteristics in common with conventional extant meiosis. However, it is possible that the synaptonemal complex and the delicate crossover control related to its presence were later acquisitions...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27648643/the-plant-microbiota-systems-level-insights-and-perspectives
#18
Daniel B Müller, Christine Vogel, Yang Bai, Julia A Vorholt
Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that the plant microbiota plays a role in plant growth and can provide protection from invading pathogens. Apart from intense research on crop plants, Arabidopsis is emerging as a valuable model system to investigate the drivers shaping stable bacterial communities on leaves and roots and as a tool to decipher the intricate relationship among the host and its colonizing microorganisms...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27648642/genome-wide-analysis-of-rna-secondary-structure
#19
Philip C Bevilacqua, Laura E Ritchey, Zhao Su, Sarah M Assmann
Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27648641/control-of-meiotic-crossovers-from-double-strand-break-formation-to-designation
#20
Stephen Gray, Paula E Cohen
Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis is the process of homologous recombination, whereby DNA double-strand breaks are introduced into the genome and are subsequently repaired to generate either noncrossovers or crossovers. Although homologous recombination is essential for chromosome pairing during prophase I, the resulting crossovers are critical for maintaining homolog interactions and enabling accurate segregation at the first meiotic division...
November 23, 2016: Annual Review of Genetics
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