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https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#1
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#2
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773976/facing-the-challenges-of-neuropeptide-gene-knockouts-why-do-they-not-inhibit-reproduction-in-adult-teleost-fish
#3
REVIEW
Vance L Trudeau
Genetic manipulation of teleost endocrine systems started with transgenic overexpression of pituitary growth hormone. Such strategies enhance growth and reduce fertility, but the fish still breed. Genome editing using transcription activator-like effector nuclease in zebrafish and medaka has established the role of follicle stimulating hormone for gonadal development and luteinizing hormone for ovulation. Attempts to genetically manipulate the hypophysiotropic neuropeptidergic systems have been less successful...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29773831/dnajc17-is-localized-in-nuclear-speckles-and-interacts-with-splicing-machinery-components
#4
A Pascarella, G Ferrandino, S C Credendino, C Moccia, F D'Angelo, B Miranda, C D'Ambrosio, P Bielli, O Spadaro, M Ceccarelli, A Scaloni, C Sette, M De Felice, G De Vita, E Amendola
DNAJC17 is a heat shock protein (HSP40) family member, identified in mouse as susceptibility gene for congenital hypothyroidism. DNAJC17 knockout mouse embryos die prior to implantation. In humans, germline homozygous mutations in DNAJC17 have been found in syndromic retinal dystrophy patients, while heterozygous mutations represent candidate pathogenic events for myeloproliferative disorders. Despite widespread expression and involvement in human diseases, DNAJC17 function is still poorly understood. Herein, we have investigated its function through high-throughput transcriptomic and proteomic approaches...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773647/altered-sterol-metabolism-in-budding-yeast-affects-mitochondrial-iron-sulfur-fe-s-cluster-synthesis
#5
Diane M Ward, Opal S Chen, Liangtao Li, Jerry Kaplan, Shah Alam Bhuiyan, Selvamuthu K Natarajan, Martin Bard, James E Cox
Ergosterol synthesis is essential for cellular growth and viability of the budding yeast Saccharomyces cerevisiae, and intracellular sterol distribution and homeostasis are therefore highly regulated in this species. Erg25 is an iron-containing C4-methyl sterol oxidase that contributes to the conversion of 4,4-dimethylzymosterol to zymosterol, a precursor of ergosterol. The ERG29 gene encodes an endoplasmic reticulum (ER)-associated protein, and here we identified a role for Erg29 in the methyl sterol oxidase step of ergosterol synthesis...
May 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29773624/complete-genome-sequence-of-mycobacterium-marinum-atcc-927-t-obtained-using-nanopore-and-illumina-sequencing-technologies
#6
Mitsunori Yoshida, Hanako Fukano, Yuji Miyamoto, Keigo Shibayama, Masato Suzuki, Yoshihiko Hoshino
Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29773570/hdna2-nuclease-helicase-promotes-centromeric-dna-replication-and-genome-stability
#7
Zhengke Li, Bochao Liu, Weiwei Jin, Xiwei Wu, Mian Zhou, Vincent Wenzhe Liu, Ajay Goel, Zhiyuan Shen, Li Zheng, Binghui Shen
DNA2 is a nuclease/helicase that is involved in Okazaki fragment maturation, replication fork processing, and end resection of DNA double-strand breaks. Similar such helicase activity for resolving secondary structures and structure-specific nuclease activity are needed during DNA replication to process the chromosome-specific higher order repeat units present in the centromeres of human chromosomes. Here, we show that DNA2 binds preferentially to centromeric DNA The nuclease and helicase activities of DNA2 are both essential for resolution of DNA structural obstacles to facilitate DNA replication fork movement...
May 17, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29770973/genome-wide-based-model-predicting-recovery-from-portosystemic-shunting-after-liver-shunt-attenuation-in-dogs
#8
Lindsay Van den Bossche, Frank G van Steenbeek, Maarten F Weber, Bart Spee, Louis C Penning, Freek J van Sluijs, Flin Zomerdijk, Marian J A Groot Koerkamp, Jan Rothuizen, Iwan A Burgener, Anne Kummeling
BACKGROUND: In dogs with congenital portosystemic shunt (CPSS), recovery after surgical CPSS attenuation is difficult to predict. OBJECTIVES: Our aim was to build a model with plasma albumin concentration and mRNA expression levels of hepatic gene products as predictors of recovery from portosystemic shunting after surgery. ANIMALS: Seventy-three client-owned dogs referred for surgical attenuation of CPSS. METHODS: A prediction model was constructed using 2 case-control studies of recovered and nonrecovered dogs after surgical CPSS attenuation...
May 17, 2018: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29770864/agrobacterium-mediated-transformation-of-yeast-and-fungi
#9
Paul J J Hooykaas, G Paul H van Heusden, Xiaolei Niu, M Reza Roushan, Jalal Soltani, Xiaorong Zhang, Bert J van der Zaal
Two decades ago, it was discovered that the well-known plant vector Agrobacterium tumefaciens can also transform yeasts and fungi when these microorganisms are co-cultivated on a solid substrate in the presence of a phenolic inducer such as acetosyringone. It is important that the medium has a low pH (5-6) and that the temperature is kept at room temperature (20-25 °C) during co-cultivation. Nowadays, Agrobacterium-mediated transformation (AMT) is the method of choice for the transformation of many fungal species; as the method is simple, the transformation efficiencies are much higher than with other methods, and AMT leads to single-copy integration much more frequently than do other methods...
May 17, 2018: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/29770504/black-pepper-piper-nigrum-essential-oil-demonstrates-tissue-remodeling-and-metabolism-modulating-potential-in-human-cells
#10
Xuesheng Han, Cody Beaumont, Damian Rodriguez, Tyler Bahr
Very few studies have investigated the biological activities of black pepper essential oil (BPEO) in human cells. Therefore, in the current study, we examined the biological activities of BPEO in cytokine-stimulated human dermal fibroblasts by analyzing the levels of 17 important protein biomarkers pertinent to inflammation and tissue remodeling. BPEO exhibited significant antiproliferative activity in these skin cells and significantly inhibited the production of Collagen I, Collagen III, and plasminogen activator inhibitor 1...
May 17, 2018: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/29770349/single-step-precision-genome-editing-in-yeast-using-crispr-cas9
#11
Azat Akhmetov, Jon M Laurent, Jimmy Gollihar, Elizabeth C Gardner, Riddhiman K Garge, Andrew D Ellington, Aashiq H Kachroo, Edward M Marcotte
Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended modification. Here, we describe a CRISPR-Cas9 mediated genome editing protocol for modifying any yeast gene of interest (either essential or nonessential) in a single-step transformation without any selectable marker...
March 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29770142/subcellular-localization-screening-of-colletotrichum-higginsianum-effector-candidates-identifies-fungal-proteins-targeted-to-plant-peroxisomes-golgi-bodies-and-microtubules
#12
Guillaume P Robin, Jochen Kleemann, Ulla Neumann, Lisa Cabre, Jean-Félix Dallery, Nicolas Lapalu, Richard J O'Connell
The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum , encodes a large inventory of putative secreted effector proteins that are sequentially expressed at different stages of plant infection, namely appressorium-mediated penetration, biotrophy and necrotrophy. However, the destinations to which these proteins are addressed inside plant cells are unknown. In the present study, we selected 61 putative effector genes that are highly induced in appressoria and/or biotrophic hyphae. We then used Agrobacterium -mediated transformation to transiently express them as N -terminal fusions with fluorescent proteins in cells of Nicotiana benthamiana for imaging by confocal microscopy...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29769357/evolution-of-genomic-variation-in-the-burrowing-owl-in-response-to-recent-colonization-of-urban-areas
#13
Jakob C Mueller, Heiner Kuhl, Stefan Boerno, Jose L Tella, Martina Carrete, Bart Kempenaers
When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl ( Athene cunicularia ), a species that colonized South American cities just a few decades ago...
May 16, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29769342/cotesia-congregata-bracovirus-circles-encoding-ptp-and-ankyrin-genes-integrate-into-the-dna-of-parasitized-manduca-sexta-hemocytes
#14
Germain Chevignon, Georges Periquet, Gabor Gyapay, Nathalie Vega-Czarny, Karine Musset, Jean-Michel Drezen, Elisabeth Huguet
Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as template for the production of double stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production hence impeding viral replication in caterpillar hosts during parasitism. Here we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta , by the wasp Cotesia congregata Sequences sharing similarities with Host integration Motifs (HIM) involved in integration into DNA of Microplitis demolitor bracovirus (MdBV) circles, could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769334/reovirus-nonstructural-protein-%C3%AF-ns-acts-as-an-rna-stability-factor-promoting-viral-genome-replication
#15
Paula F Zamora, Liya Hu, Jonathan J Knowlton, Roni M Lahr, Rodolfo A Moreno, Andrea J Berman, B V Venkataram Prasad, Terence S Dermody
Viral nonstructural proteins, which are not packaged into virions, are essential for replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. Reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, activities of σNS during individual steps of the reovirus replication cycle are poorly understood...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769309/etoposide-induced-protein-2-4-functions-as-a-regulator-of-the-calcium-atpase-and-protects-pancreatic-%C3%AE-cell-survival
#16
Lin Yuan, Huiyu Wang, Qi Liu, Zhe Wang, Mingshu Zhang, Yan Zhao, Kuo Liang, Liangyi Chen, Tao Xu, Pingyong Xu
Calcium homeostasis is essential for maintaining the viability and function of pancreatic β cells and plays a key role in preventing the development of diabetes. Decreased levels of ATPase sarco-plasmic/endoplasmic reticulum Ca2+ -transporting 2 (ATP2a2), the main calcium pump in β cells, are often found in individuals with diabetes and in diabetic animal models. However, the regulators of ATP2a2 and the molecular mechanisms responsible for controlling ATP2a2 activity remain unclear. Etoposide-induced protein 2...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29769291/key-transport-and-ammonia-recycling-genes-involved-in-aphid-symbiosis-respond-to-host-plant-specialization
#17
Dohyup Kim, Bushra F Minhas, Hongmei Li-Byarlay, Allison K Hansen
Microbes are known to influence insect-plant interactions; however, it is unclear if host-plant diet influences the regulation of nutritional insect symbioses. The pea aphid, Acyrthosiphon pisum , requires its nutritional endosymbiont, Buchnera , for the production of essential amino acids. We hypothesize that key aphid genes that regulate the nutritional symbioses respond to host-plant diet when aphids feed on a specialized (alfalfa) compared to a universal host-plant diet (fava), which vary in amino acid profiles...
May 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29769087/replacement-of-feline-foamy-virus-bet-by-feline-immunodeficiency-virus-vif-yields-replicative-virus-with-novel-vaccine-candidate-potential
#18
Carmen Ledesma-Feliciano, Sarah Hagen, Ryan Troyer, Xin Zheng, Esther Musselman, Dragana Slavkovic Lukic, Ann-Mareen Franke, Daniel Maeda, Jörg Zielonka, Carsten Münk, Guochao Wei, Sue VandeWoude, Martin Löchelt
BACKGROUND: Hosts are able to restrict viral replication to contain virus spread before adaptive immunity is fully initiated. Many viruses have acquired genes directly counteracting intrinsic restriction mechanisms. This phenomenon has led to a co-evolutionary signature for both the virus and host which often provides a barrier against interspecies transmission events. Through different mechanisms of action, but with similar consequences, spumaviral feline foamy virus (FFV) Bet and lentiviral feline immunodeficiency virus (FIV) Vif counteract feline APOBEC3 (feA3) restriction factors that lead to hypermutation and degradation of retroviral DNA genomes...
May 16, 2018: Retrovirology
https://www.readbyqxmd.com/read/29769016/whole-genome-sequencing-data-of-1110-mycobacterium-tuberculosis-isolates-identifies-insertions-and-deletions-associated-with-drug-resistance
#19
Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam, Stephen Kwok-Wing Tsui
BACKGROUND: Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. RESULTS: Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance...
May 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29768419/a-secreted-heat-shock-protein-90-of-trichomonas-vaginalis
#20
Meetali Singh, Divya Beri, Rishi Kumar Nageshan, Leena Chavaan, Darshak Gadara, Mukta Poojary, Suraj Subramaniam, Utpal Tatu
Trichomonas vaginalis is a causative agent of Trichomoniasis, a leading non-viral sexually transmitted disease worldwide. In the current study, we show Heat shock protein 90 is essential for its growth. Upon genomics analysis of the parasite, it was found to possess seven ORFs which could potentially encode Hsp90 isoforms. We identified a cytosolic Hsp90 homolog, four homologs which can align to truncated cytosolic Hsp90 gene products along with two Grp94 homologs (ER isoform of Hsp90). However, both Grp94 orthologs lacked an ER retention motif...
May 16, 2018: PLoS Neglected Tropical Diseases
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