keyword
MENU ▼
Read by QxMD icon Read
search

genomic evolution

keyword
https://www.readbyqxmd.com/read/29156805/circulating-tumor-dna-shows-variable-clonal-response-of-breast-cancer-during-neoadjuvant-chemotherapy
#1
Ji-Yeon Kim, Donghyun Park, Dae-Soon Son, Seok Jin Nam, Seok Won Kim, Hae Hyun Jung, Yeon Jeong Kim, Gahee Park, Woong-Yang Park, Jeong Eon Lee, Yeon Hee Park
Circulating tumor DNA (ctDNA) correlates with tumor burden and provides early detection of treatment response and tumor genetic alterations in breast cancer (BC). In this study, we aimed to identify genetic alterations during the process of tumor clonal evolution and examine if ctDNA level well indicated clinical response to neoadjuvant chemotherapy (NAC) and BC recurrence. We performed targeted ultra-deep sequencing of plasma DNAs, matched germline DNAs and tumor DNAs from locally advanced BC patients. Serial plasma DNAs were collected at diagnosis, after the 1(st) cycle of NAC and after curative surgery...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156423/under-pressure-evolutionary-engineering-of-yeast-strains-for-improved-performance-in-fuels-and-chemicals-production
#2
REVIEW
Robert Mans, Jean-Marc G Daran, Jack T Pronk
Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci...
November 17, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29155284/the-dynamic-evolution-of-drosophila-innubila-nudivirus
#3
Tom Hill, Robert L Unckless
Viruses coevolve with their hosts to overcome host resistance and gain the upper hand in the evolutionary arms race. Drosophila innubila nudivirus (DiNV) is a double stranded DNA virus, closely related to Oryctes rhinoceros nudivirus (OrNV) and Kallithea virus. DiNV is the first DNA virus found to naturally infect Drosophila and therefore has the potential to be developed as a model for DNA virus immune defense and host/virus coevolution within its well-studied host system. Here we sequence and annotate the genome of DiNV and identify signatures of adaptation, revealing clues for genes involved in host-parasite coevolution...
November 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#4
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29154929/identification-of-genetic-variants-of-brucella-spp-through-genome-wide-association-studies
#5
Jagadesan Sankarasubramanian, Udayakumar S Vishnu, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp...
November 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29154857/astakines-in-arthropods-phylogeny-and-gene-structure
#6
Lena Ericsson, Irene Söderhäll
Astakine1 was isolated as a hematopoietic cytokine in the freshwater crayfish Pacifastacus leniusculus. In this study we detect and compare 79 sequences in GenBank, which we consider to be possible astakine orthologs, among which eleven are crustacean, sixteen are chelicerate and 52 are from insect species. Available arthropod genomes are searched for astakines, and in conclusion all astakine sequences in the current study have a similar exon containing CCXX(X), thus potentially indicating that they are homologous genes with the structure of this exon highly conserved...
November 14, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29154789/biosynthesis-of-microcystin-hepatotoxins-in-the-cyanobacterial-genus-fischerella
#7
Karina Heck, Danillo O Alvarenga, Tania K Shishido, Alessandro M Varani, Felipe A Dörr, Ernani Pinto, Leo Rouhiainen, Jouni Jokela, Kaarina Sivonen, Marli F Fiore
Microcystins (MCs) are serine/threonine phosphatase inhibitors synthesized by several members of the phylum Cyanobacteria. Mining the draft genome sequence of the nostocalean MC-producing Fischerella sp. strain CENA161 led to the identification of three contigs containing mcy genes. Subsequent PCR and Sanger sequencing allowed the assembling of its complete biosynthetic mcy gene cluster with 55,016 bases in length. The cluster encoding ten genes (mcyA-J) with a central bidirectional promoter was organized in a similar manner as found in other genera of nostocalean cyanobacteria...
November 14, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29153851/apobec-enzymes-as-targets-for-virus-and-cancer-therapy
#8
REVIEW
Margaret E Olson, Reuben S Harris, Daniel A Harki
Human DNA cytosine-to-uracil deaminases catalyze mutations in both pathogen and cellular genomes. APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H restrict human immunodeficiency virus 1 (HIV-1) infection in cells deficient in the viral infectivity factor (Vif), and have the potential to catalyze sublethal levels of mutation in viral genomes in Vif-proficient cells. At least two APOBEC3 enzymes, and in particular APOBEC3B, are sources of somatic mutagenesis in cancer cells that drive tumor evolution and may manifest clinically as recurrence, metastasis, and/or therapy resistance...
November 14, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/29153401/multiple-approaches-to-phylogenomic-reconstruction-of-the-fungal-kingdom
#9
Charley G P McCarthy, David A Fitzpatrick
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153400/deciphering-pathogenicity-of-fusarium-oxysporum-from-a-phylogenomics-perspective
#10
Yong Zhang, Li-Jun Ma
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153399/fungal-gene-cluster-diversity-and-evolution
#11
Jason C Slot
Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153166/a-100-year-review-practical-female-reproductive-management
#12
J S Stevenson, J H Britt
Basic knowledge of mechanisms controlling reproductive processes in mammals was limited in the early 20th century. Discoveries of physiologic processes and mechanisms made early in the last century laid the foundation to develop technologies and programs used today to manage and control reproduction in dairy cattle. Beyond advances made in understanding of gonadotropic support and control of ovarian and uterine functions in basic reproductive biology, advancements made in artificial insemination (AI) and genetics facilitated rapid genetic progress of economically important traits in dairy cattle...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29152135/evaluation-of-pre-analytical-conditions-and-comparison-of-the-performance-of-several-digital-pcr-assays-for-the-detection-of-major-egfr-mutations-in-circulating-dna-from-non-small-cell-lung-cancers-the-circan_0-study
#13
Jessica Garcia, Eric Dusserre, Valérie Cheynet, Pierre Paul Bringuier, Karen Brengle-Pesce, Anne-Sophie Wozny, Claire Rodriguez-Lafrasse, Gilles Freyer, Marie Brevet, Léa Payen, Sébastien Couraud
Non invasive somatic detection assays are suitable for repetitive tumor characterization or for detecting the appearance of somatic resistance during lung cancer. Molecular diagnosis based on circulating free DNA (cfDNA) offers the opportunity to track the genomic evolution of the tumor, and was chosen to assess the molecular profile of several EGFR alterations, including deletions in exon 19 (delEX19), the L858R substitution on exon 21 and the EGFR resistance mutation T790M on exon 20. Our study aimed at determining optimal pre-analytical conditions and EGFR mutation detection assays for analyzing cfDNA using the picoliter-droplet digital polymerase chain reaction (ddPCR) assay...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151869/when-evolution-is-the-solution-to-pollution-key-principles-and-lessons-from-rapid-repeated-adaptation-of-killifish-fundulus-heteroclitus-populations
#14
REVIEW
Andrew Whitehead, Bryan W Clark, Noah M Reid, Mark E Hahn, Diane Nacci
For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human-mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments...
September 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29151852/ancient-oncogenesis-infection-and-human-evolution
#15
REVIEW
Riaan F Rifkin, Marnie Potgieter, Jean-Baptiste Ramond, Don A Cowan
The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA...
December 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29151160/tolerance-improvement-of-corynebacterium-glutamicum-on-lignocellulose-derived-inhibitors-by-adaptive-evolution
#16
Xia Wang, Imrana Khushk, Yanqiu Xiao, Qiuqiang Gao, Jie Bao
Robustness of fermenting strains to lignocellulose derived inhibitors is critical for efficient biofuel and biochemical productions. In this study, the industrial fermenting strain Corynebacterium glutamicum S9114 was evolved for improved inhibitor tolerance using long-term adaptive evolution by continuously transferring into the inhibitors containing corn stover hydrolysate every 24 h, and finally a stably evolved C. glutamicum was obtained after 128 days of serial transfers. The evolved strain exhibited the highly increased conversion rate to the typical lignocellulose derived inhibitors including furfural, 5-hydroxymethylfurfural, vanillin, syringaldehyde, 4-hydroxybenzaldehyde, and acetic acid...
November 18, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29150926/viral-short-orfs-and-their-possible-functions
#17
REVIEW
Yaara Finkel, Noam Stern-Ginossar, Michal Schwartz
Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short Open Reading Frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and experimental limitations, however it has become clear over the past several years that translation of sORFs is pervasive and serves diverse functions. The development of ribosome profiling, allowing identification of translated sequences genome-wide, revealed wide-spread, previously unidentified translation events...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150903/phylogenetic-and-genetic-variation-analyses-of-porcine-circovirus-type-2-isolated-from-china
#18
S Yang, S Yin, Y Shang, B Liu, L Yuan, M U Zafar Khan, X Liu, J Cai
Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease, which is a growing problem in the swine industry worldwide. High nucleotide substitution occurs in the capsid (Cap) gene of PCV2, which allows the continuous evolution and the emergence of novel PCV2 strains. In this study, we sequenced 24 Chinese PCV2 strains collected from healthy and diseased pigs between 2013 and 2015. Analyses of the genome, Cap and phylogeny classified the 24 Chinese PCV2 strains as PCV-2a (four of 24), PCV-2b (five of 24) and PCV-2d (15 of 24)...
November 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29150608/rapid-neo-sex-chromosome-evolution-and-incipient-speciation-in-a-major-forest-pest
#19
Ryan R Bracewell, Barbara J Bentz, Brian T Sullivan, Jeffrey M Good
Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150513/high-prevalence-and-genetic-diversity-of-large-phicd211-phicdif1296t-like-prophages-in-clostridioides-difficile
#20
Julian R Garneau, Ognjen Sekulovic, Bruno Dupuy, Olga Soutourina, Marc Monot, Louis-Charles Fortier
Clostridioides difficile (formerly Clostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in C. difficile so far, with a genome of 131-kbp. It shares morphological and genomic similarity with other large siphophages like phage 949 infecting Lactococcus lactis and phage c-st infecting Clostridium botulinum...
November 17, 2017: Applied and Environmental Microbiology
keyword
keyword
53798
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"