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gene evolution

Andrei Popescu, Andrei Haidar, Rodica Maricela Anghel
Recent years have brought major advances in the treatment of malignant melanoma. One such an advance is the treatment with BRAF tyrosine-kinase inhibitors in metastatic malignant melanomas that harbor mutations in the BRAF gene. The trials that have been performed in this setting have demonstrated superior response rates and increased overall survival, however they mostly included patients with melanomas carrying the more common V600E and V600K mutations, not being able to assess the benefit of these treatments in situations where more rare mutations of the BRAF gene are present...
November 27, 2017: Romanian Journal of Internal Medicine, Revue Roumaine de Médecine Interne
Lei Shan, Qi Wu, Le Wang, Lei Zhang, Fuwen Wei
Bitter taste receptor genes (TAS2Rs) mediate bitterness perception in mammals. It is believed that these genes evolved in response to species-specific diets. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens styani) in the order Carnivora are specialized herbivores with an almost exclusive bamboo diet (>90% bamboo). Because bamboo is full of bitter tasting compounds, we hypothesized that adaptive evolution have occurred at TAS2R genes in giant and red pandas throughout the course of their dietary shift...
November 23, 2017: Integrative Zoology
Zhongyi Zhu, Si Qiu, Kang Shao, Yong Hou
Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors...
November 22, 2017: Cell Biology and Toxicology
Alexis De Tiège, Yves Van de Peer, Johan Braeckman, Koen B Tanghe
Although classical evolutionary theory, i.e., population genetics and the Modern Synthesis, was already implicitly 'gene-centred', the organism was, in practice, still generally regarded as the individual unit of which a population is composed. The gene-centred approach to evolution only reached a logical conclusion with the advent of the gene-selectionist or gene's eye view in the 1960s and 1970s. Whereas classical evolutionary theory can only work with (genotypically represented) fitness differences between individual organisms, gene-selectionism is capable of working with fitness differences among genes within the same organism and genome...
November 22, 2017: History and Philosophy of the Life Sciences
Dariya K Sydykova, Benjamin R Jack, Stephanie J Spielman, Claus O Wilke
We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses...
2017: F1000Research
Leena Arora, Alka Narula
Advancements in Genome editing technologies have revolutionized the fields of functional genomics and crop improvement. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat)-Cas9 is a multipurpose technology for genetic engineering that relies on the complementarity of the guideRNA (gRNA) to a specific sequence and the Cas9 endonuclease activity. It has broadened the agricultural research area, bringing in new opportunities to develop novel plant varieties with deletion of detrimental traits or addition of significant characters...
2017: Frontiers in Plant Science
Giles E Hardingham, Priit Pruunsild, Michael E Greenberg, Hilmar Bading
Excitation-transcription coupling shapes network formation during brain development and controls neuronal survival, synaptic function and cognitive skills in the adult. New studies have uncovered differences in the transcriptional responses to synaptic activity between humans and mice. These differences are caused both by the emergence of lineage-specific activity-regulated genes and by the acquisition of signal-responsive DNA elements in gene regulatory regions that determine whether a gene can be transcriptionally induced by synaptic activity or alter the extent of its inducibility...
November 23, 2017: Nature Reviews. Neuroscience
Jinglei Wang, Yang Qiu, Xiaowu Wang, Zhen Yue, Xinhua Yang, Xiaohua Chen, Xiaohui Zhang, Di Shen, Haiping Wang, Jiangping Song, Hongju He, Xixiang Li
Glucosinolates (GSLs) and their hydrolysis products present in Brassicales play important roles in plants against herbivores and pathogens as well as in the protection of human health. To elucidate the molecular mechanisms underlying the formation of species-specific GSLs and their hydrolysed products in Raphanus sativus L., we performed a comparative genomics analysis between R. sativus and Arabidopsis thaliana. In total, 144 GSL metabolism genes were identified, and most of these GSL genes have expanded through whole-genome and tandem duplication in R...
November 22, 2017: Scientific Reports
Shubhra Agarwal, Prasith Baccam, Rakesh Aggarwal, Naga Suresh Veerapu
Many RNA viruses exist as an ensemble of genetically-diverse, replicating populations, known as mutant cloud. The genetic diversity (cloud size) and composition of this mutant cloud may influence several important phenotypic features of the virus, including its replication capacity. We applied a straightforward, bacterium-free approach using error-prone PCR coupled with reverse genetics to generate infectious mutant RNA clouds of varying genetic diversity from a genotype 1 strain of hepatitis E virus (HEV)...
November 22, 2017: Journal of Virology
Allan C Spradling
Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all Drosophila larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of Drosophila polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
N A Wyatt, J K Richards, R S Brueggeman, T L Friesen
Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, is a destructive pathogen in barley growing regions throughout the world. Typical yield losses due to NFNB range from 10-40%, however, complete loss has been observed on highly susceptible barley lines where environmental conditions favor the pathogen. Currently, genomic resources for this economically important pathogen are limited to a fragmented draft genome assembly and annotation with limited RNA support of the P. teres f...
November 22, 2017: G3: Genes—Genomes—Genetics
Hani Boshra, Wioleta M Zelek, Timothy R Hughes, Santiago Rodriguez de Cordoba, B Paul Morgan
CD59 is a membrane-bound regulatory protein that inhibits the assembly of the terminal membrane attack complex (C5b-9) of complement. From its original discovery in humans almost 30 years ago, CD59 has been characterized in a variety of species, from primates to early vertebrates, such as teleost fish. CD59 is ubiquitous in mammals; however, we have described circumstantial evidence suggesting that guinea pigs (Cavia porcellus) lack CD59, at least on erythrocytes. In this study, we have used a combination of phylogenetic analyses with syntenic alignment of mammalian CD59 genes to identify the only span of genomic DNA in C...
November 22, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
Peilin Liu, Lei Shi, Wei Zhang, Jianan He, Chunxiao Liu, Chunzhong Zhao, Siu Kai Kong, Jacky Fong Chuen Loo, Dayong Gu, Longfei Hu
BACKGROUND: More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted. METHODS: A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37...
November 22, 2017: Virology Journal
Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot, Nathalie Leblond-Bourget
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on "integrative and mobilizable elements" (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer...
November 22, 2017: Genes
Eyal Cohen, Zohar Zafrir, Tamir Tuller
The two major steps of gene expression are transcription and translation. While hundreds of studies regarding the effect of sequence features on the translation elongation process have been published, very few connect sequence features to the transcription elongation rate. We suggest, for the first time, that short transcript sub-sequences have a typical effect on RNA polymerase (RNAP) speed: we show that nucleotide 5-mers tend to have typical RNAP speed (or transcription rate), which is consistent along different parts of genes and among different groups of genes with high correlation...
November 22, 2017: RNA Biology
Alexandros G Brotis, Anastasia Tasiou, Theofanis Giannis, Athanasios Paschalis, Kostas N Fountas
BACKGROUND: The development, evolution and rupture of intracranial aneurysms is in part related to genetic factors. The role Collagen type I a2 genetic polymorphisms has not been clarified yet. MATERIAL AND METHODS: A meta-analysis was realized by means of a genotype model-fitting processes (allele contrast, recessive, dominant, additive, and co-dominant), and a model-free approach using the generalized odds ratio (ORG). The latter was assessed in association to the degree of dominance (h-index)...
November 22, 2017: International Journal of Neuroscience
Feng Liu, Zhe Jin, Yu Wang, Yuping Bi, James T Melton
Dictyotophycidae is a subclass of brown algae containing 395 species that are distributed worldwide. A complete plastid (chloroplast) genome (ptDNA or cpDNA) had not previously been sequenced from this group. In this study, the complete plastid genome of Dictyopteris divaricata (Okamura) Okamura (Dictyotales, Phaeophyceae) was characterized and compared to other brown algal ptDNAs. This plastid genome was 126,099 bp in size with two inverted repeats (IRs) of 6026 bp. The D. divaricata IRs contained rpl21, making its IRs larger than representatives from the orders Fucales and Laminariales, but was smaller than that from Ectocarpales...
November 21, 2017: Marine Biotechnology
Elizabeth Santin, Ricardo Mitsuo Hayashi, Jessica Caroline Wammes, Ricardo Gonzalez-Esquerra, Marcelo Falsarella Carazzolle, Caio César de Melo Freire, Paulo Sérgio Monzani, Anderson Ferreira da Cunha
Salmonella enterica serovar Heidelberg is a human pathogen also found in broilers. A strain (UFPR1) has been associated with field reports of resistance to short-chain organic acids (SCOA) in broilers in the South of Brazil, but was susceptible to a Bacillus subtilis-based probiotic added in feed in a related study. This work aimed to (i) report clinical symptoms caused by SH UFPR1 in broilers, (ii) study its susceptibility to some antibiotics in vitro, and (iii) SCOA in vivo; and (iv) relate these phenotypic observations with its genome characteristics...
2017: Frontiers in Veterinary Science
Andrey G Solovyev, Sergey Y Morozov
Fast accumulation of sequencing data on plant virus genomes and plant transcriptomes demands periodic re-evaluation of current views on the genome evolution of viruses. Here, we substantiate and further detail our previously mostly speculative model on the origin and evolution of triple gene block (TGB) encoding plant virus movement proteins TGB1, TGB2, and TGB3. Recent experimental data on functional competence of transport gene modules consisting of two proteins related to TGB1 and TGB2, as well as sequence analysis data on similarity of TGB2 and TGB3 encoded by a viral genome and virus-like RNAs identified in a plant transcriptomes, suggest that TGB evolution involved events of gene duplication and gene transfer between viruses...
2017: Frontiers in Plant Science
Nelson Garcia, Joachim Messing
The TEL2, TTI1, and TTI2 proteins are co-chaperones for heat shock protein 90 (HSP90) to regulate the protein folding and maturation of phosphatidylinositol 3-kinase-related kinases (PIKKs). Referred to as the TTT complex, the genes that encode them are highly conserved from man to maize. TTT complex and PIKK genes exist mostly as single copy genes in organisms where they have been characterized. Members of this interacting protein network in maize were identified and synteny analyses were performed to study their evolution...
2017: Frontiers in Plant Science
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