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https://www.readbyqxmd.com/read/29150926/viral-short-orfs-and-their-possible-functions
#1
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/29149615/rethinking-unconventional-translation-in-neurodegeneration
#2
REVIEW
Fen-Biao Gao, Joel D Richter, Don W Cleveland
Eukaryotic translation is tightly regulated to ensure that protein production occurs at the right time and place. Recent studies on abnormal repeat proteins, especially in age-dependent neurodegenerative diseases caused by nucleotide repeat expansion, have highlighted or identified two forms of unconventional translation initiation: usage of AUG-like sites (near cognates) or repeat-associated non-AUG (RAN) translation. We discuss how repeat proteins may differ due to not just unconventional initiation, but also ribosomal frameshifting and/or imperfect repeat DNA replication, expansion, and repair, and we highlight how research on translation of repeats may uncover insights into the biology of translation and its contribution to disease...
November 16, 2017: Cell
https://www.readbyqxmd.com/read/29149047/new-insights-into-phasmatodea-chromosomes
#3
Thomas Liehr, Olesya Buleu, Tatyana Karamysheva, Alexander Bugrov, Nikolai Rubtsov
Currently, approximately 3000 species of stick insects are known; however, chromosome numbers, which range between 21 and 88, are known for only a few of these insects. Also, centromere banding staining (C-banding) patterns were described for fewer than 10 species, and fluorescence in situ hybridization (FISH) was applied exclusively in two Leptynia species. Interestingly, 10-25% of stick insects (Phasmatodea) are obligatory or facultative parthenogenetic. As clonal and/or bisexual reproduction can affect chromosomal evolution, stick insect karyotypes need to be studied more intensely...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29146883/a-landscape-of-germline-mutations-in-a-cohort-of-inherited-bone-marrow-failure-patients
#4
Olivier Bluteau, Marie Sebert, Thierry Leblanc, Régis Peffault de Latour, Samuel Quentin, Elodie Lainey, Lucie Hernandez, Jean-Hugues Dalle, Flore Sicre de Fontbrune, Etienne Lengline, Raphael Itzykson, Emmanuelle Clappier, Nicolas Boissel, Naddia Vasquez, Mélanie Da Costa, Julien Masliah-Planchon, Wendy Cuccuini, Anna Raimbault, Louis De Jaegere, Lionel Adès, Pierre Fenaux, Sébastien Maury, Claudine Schmitt, Marc Muller, Carine Domenech, Nicolas Blin, Bénédicte Bruno, Isabelle Pellier, Mathilde Hunault, Stéphane Blanche, Arnaud Petit, Guy Leverger, Gérard Michel, Yves Bertrand, André Baruchel, Gérard Socié, Jean Soulier
Bone marrow failure (BMF) in children and young adults is often suspected to be inherited, but in many cases diagnosis remains uncertain. We studied a cohort of 179 patients (from 173 families) with BMF of suspected inherited origin but unresolved diagnosis after medical evaluation and Fanconi anemia exclusion. All patients had cytopenias, and 12.0% presented ≥5% bone marrow blast cells. Median age at genetic evaluation was 11 years; 20.7% of patients were aged ≤2 years and 36.9% were ≥18 years. We analyzed genomic DNA from skin fibroblasts using whole-exome sequencing, and were able to assign a causal or likely causal germline mutation in 86 patients (48...
November 16, 2017: Blood
https://www.readbyqxmd.com/read/29143653/phylogenetic-study-of-the-endemic-species-oxytropis-almaatensis-fabaceae-based-on-nuclear-ribosomal-dna-its-sequences
#5
Shyryn Almerekova, Nashtay Mukhitdinov, Saule Abugalieva
BACKGROUND: Oxytropis almaatensis Bajt. is a rare, narrow endemic species of the Trans-Ili Alatau mountains in Kazakhstan. Up to now, no studies regarding the taxonomy and variation of key morphological traits of O. almaatensis were undertaken. The purpose of this analysis was to evaluate phenotypic variation of O. almaatensis and assess the position of the species within the genus based on nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacer (ITS) region. RESULTS: Two populations of O...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143601/morphological-description-and-dna-barcoding-study-of-sand-rice-agriophyllum-squarrosum-chenopodiaceae-collected-in-kazakhstan
#6
Yuliya Genievskaya, Saule Abugalieva, Aibatsha Zhubanysheva, Yerlan Turuspekov
BACKGROUND: Sand rice (Agriophyllum squarrosum (L.) Moq.) is an annual shrub-like plant adapted to the mobile sand dunes in desert and semi-desert regions of Asia. It has a balanced nutrient composition with relatively high concentration of lipids and proteins, which results in its nutrition being similar to legumes. Sand rice's proteins contain the full range of essential amino acids. However, calories content is more similar to wheat. These features together with desert stress resistance make sand rice a potential food crop resilient to ongoing climate change...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143375/an-immunoinformatics-approach-to-define-t-cell-epitopes-from-polyketide-and-non-ribosomal-peptide-synthesis-proteins-of-mycobacterium-tuberculosis-as-potential-vaccine-candidates
#7
S Dhivya, V Baskar, S R Kumar, R Sathishkumar
The role of polyketide and non-ribosomal proteins from the class of small molecule metabolism of Mycobacterium tuberculosis is well documented in envelope organization, virulence, and pathogenesis. Consequently, the identification of T cell epitopes from these proteins could serve to define potential antigens for the development of vaccines. Fourty-one proteins from polyketide and non-ribosomal peptide synthesis of small molecule metabolism proteins of M tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nanomeric peptides...
November 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29142804/analytical-study-of-effective-biodegradation-of-p-cresol-using-serratia-marcescens-abhi001-application-in-bioremediation
#8
Tripti Singh, Neha Srivastava, A K Bhatiya, P K Mishra
This study evaluated the capability of Serratia marcescens ABHI001 to effectively degrade p-cresol through different techniques. The molecular identity of the laboratory isolate S. marcescens ABHI001 was confirmed through the 16S ribosomal DNA gene pattern, and its morphological features were investigated through field-emission scanning electron microscopy. In addition, the degradation behavior of the isolate for cresol was verified using several techniques, including UV-visible spectroscopy, followed by high-performance liquid chromatography (HPLC), gas chromatography, and Fourier transform infrared spectroscopy...
December 2017: 3 Biotech
https://www.readbyqxmd.com/read/29139335/shprh-as-a-new-player-in-ribosomal-rna-transcription-and-its-potential-role-in-homeostasis-of-ribosomal-dna-repeats
#9
Deokjae Lee, Jun Hong Park, Shinseog Kim, Seon-Gyeong Lee, Kyungjae Myung
There are hundreds of copies of rDNA repeats in mammalian chromosomes and the ratio of active, poised, or inactive rDNA is regulated in epigenetic manners. Recent studies demonstrated that a post-DNA replication repair enzyme, SHPRH affects rRNA transcription by recognizing epigenetic markers on rDNA promoters and unveiled potential links between DNA repair and ribosome biogenesis (1) . This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity...
November 15, 2017: Transcription
https://www.readbyqxmd.com/read/29134144/composition-diversity-and-function-of-intestinal-microbiota-in-pacific-white-shrimp-litopenaeus-vannamei-at-different-culture-stages
#10
Shenzheng Zeng, Zhijian Huang, Dongwei Hou, Jian Liu, Shaoping Weng, Jianguo He
Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt...
2017: PeerJ
https://www.readbyqxmd.com/read/29133437/abnormal-microglia-and-enhanced-inflammation-related-gene-transcription-in-mice-with-conditional-deletion-of-ctcf-in-camk2a-cre-expressing-neurons
#11
Bryan E McGill, Ruteja A Barve, Susan E Maloney, Amy Strickland, Nicholas Rensing, Peter Wang, Michael Wong, Richard Head, David F Wozniak, Jeffrey Milbrandt
CCCTC-binding factor (CTCF) is an 11 zinc finger DNA-binding domain protein that regulates gene expression by modifying three dimensional chromatin structure. Human mutations in CTCF cause intellectual disability and autistic features. Knocking out Ctcf in mouse embryonic neurons is lethal by neonatal age, but the effects of CTCF deficiency in postnatal neurons are less well studied. We knocked out Ctcf postnatally in glutamatergic forebrain neurons under the control of Camk2a-CreCtcf(loxP/loxP) ;Camk2a-Cre+ (Ctcf CKO) mice of both sexes were viable and exhibited profound deficits in spatial learning/memory, impaired motor co-ordination, and decreased sociability by 4 months of age...
November 13, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29127501/characterization-of-a-novel-yeast-species-metschnikowia-persimmonesis-kctc-12991bp-kiom-g15050-type-strain-isolated-from-a-medicinal-plant-korean-persimmon-calyx-diospyros-kaki-thumb
#12
Young Min Kang, Ji Eun Choi, Richard Komakech, Jeong Hwan Park, Dae Wook Kim, Kye Man Cho, Seung Mi Kang, Sang Haeng Choi, Kun Chul Song, Chung Min Ryu, Keun Chul Lee, Jung-Sook Lee
The yeast strain Metschnikowia persimmonesis Kang and Choi et al., sp. nov. [type strain KIOM_G15050 = Korean Collection for Type Cultures (KCTC) 12991BP] was isolated from the stalk of native persimmon cultivars (Diospyros kaki Thumb) obtained from different regions of South Korea and was characterized phenotypically, genetically, and physiologically. The isolate grew between 4 and 40 °C (optimum temperature: 24-28 °C), pH 3-8 (pH optimum = 6.0), and in 0-4% NaCl solution (with optimal growth in absence of NaCl)...
November 10, 2017: AMB Express
https://www.readbyqxmd.com/read/29127415/sequencing-and-characterization-of-the-complete-mitochondrial-genome-of-japanese-swellshark-cephalloscyllium-umbratile
#13
Ke-Cheng Zhu, Yin-Yin Liang, Na Wu, Hua-Yang Guo, Nan Zhang, Shi-Gui Jiang, Dian-Chang Zhang
To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29125596/contrasting-the-relative-importance-of-species-sorting-and-dispersal-limitation-in-shaping-marine-bacterial-versus-protist-communities
#14
Wenxue Wu, Hsiao-Pei Lu, Akash Sastri, Yi-Chun Yeh, Gwo-Ching Gong, Wen-Chen Chou, Chih-Hao Hsieh
A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29121118/diversity-and-characterization-of-bacteria-associated-with-the-deep-sea-hydrothermal-vent-crab-austinograea-sp-comparing-with-those-of-two-shallow-water-crabs-by-16s-ribosomal-dna-analysis
#15
Na Zhang, Chengwen Song, Minxiao Wang, Yuan Liu, Min Hui, Zhaoxia Cui
For deep-sea hydrothermal vent crabs, recent investigations have revealed some epibiotic bacteria, but no study has described the bacterial community associated with the gill and intestine. In this study, the microbiota attached to the gill and intestine of the hydrothermal vent crab Austinograea sp. and two shallow-water crab species (Eriocheir sinensis and Portunus trituberculatus) were compared by high-throughput sequencing of 16S rDNA genes. The highest and lowest diversity in bacterial communities were observed in the gill and intestine of Austinograea sp...
2017: PloS One
https://www.readbyqxmd.com/read/29119858/eimeria-taggarti-n-sp-a-novel-coccidian-apicomplexa-eimeriorina-in-the-prostate-of-an-antechinus-flavipes
#16
Jemima Amery-Gale, Joanne Maree Devlin, Liliana Tatarczuch, David Augustine Taggart, David J Schultz, Jenny A Charles, Ian Beveridge
A novel coccidian species was discovered in the prostate of an Antechinus flavipes (yellow-footed antechinus) in South Australia, during the period of post-mating male antechinus immunosuppression and mortality. This novel coccidian is unusual because it develops extra-intestinally and sporulates endogenously within the prostate gland of its mammalian host. Histological examination of prostatic tissue revealed dense aggregations of spherical and thin-walled tetrasporocystic, dizoic sporulated coccidian oocysts within tubular lumina, with unsporulated oocysts and gamogonic stages within the cytoplasm of glandular epithelial cells...
November 10, 2017: Journal of Parasitology
https://www.readbyqxmd.com/read/29116037/patient-age-as-a-factor-of-antibiotic-resistance-in-methicillin-resistant-staphylococcus-aureus
#17
Alexander Garcia, Thierry Delorme, Payman Nasr
PURPOSE: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of nosocomial infections. A thorough understanding of the epidemiology and distribution of MRSA allows the development of better preventive measures and helps to control or reduce the rate of infection among the general population. METHODOLOGY: A retrospective survey was performed on 511 cases of MRSA infections from inpatient, outpatient and nursing home populations over a 12-month period...
November 8, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29114487/prevalence-of-trypanosome-infection-in-tsetse-flies-from-oji-river-and-emene-axis-of-enugu-state-nigeria-a-preliminary-report
#18
Kenechukwu Chibuike Onyekwelu, Fidelis Ebele Ejezie, Anthonius Anayochukwu Eze, Joy Ebele Ikekpeazu, Richard Chukwunonye Ezeh, Godknows Chizurumoke Edeh
Introduction: Trypanosomes are protozoan parasites of vertebrates transmitted by blood-sucking tsetse fly. Trypanosomes remain a constant threat to the lives of humans and animals throughout large regions of Africa. Aims and Objectives: This study investigated the presence, prevalence, and species of trypanosome parasite in tsetse flies caught in two areas of no previous documented history of trypanosome infection. Materials and Methods: For this purpose, 63 and 77 nonterenal tsetse flies were collected from Oji River and Emene areas of Enugu State Nigeria, respectively...
July 2017: Tropical Parasitology
https://www.readbyqxmd.com/read/29114356/comparative-analysis-of-chromosomal-localization-of-ribosomal-and-telomeric-dna-markers-in-three-species-of-pyrgomorphidae-grasshoppers
#19
REVIEW
Olesya G Buleu, Ilyas Y Jetybayev, Alexander G Bugrov
The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815), Pyrgomorpha guentheri (Burr, 1899) and Atractomorpha lata (Mochulsky, 1866). Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20) and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29114353/a-chromosomal-analysis-of-nepa-cinerea-linnaeus-1758-and-ranatra-linearis-linnaeus-1758-heteroptera-nepidae
#20
Robert B Angus, Constance Jeangirard, Desislava Stoianova, Snejana Grozeva, Valentina G Kuznetsova
An account is given of the karyotypes and male meiosis of the Water Scorpion Nepa cinerea Linnaeus, 1758 and the Water Stick Insect Ranatra linearis (Linnaeus, 1758) (Heteroptera, Nepomorpha, Nepidae). A number of different approaches and techniques were tried: the employment of both male and female gonads and mid-guts as the sources of chromosomes, squash and air-drying methods for chromosome preparations, C-banding and fluorescence in situ hybridization (FISH) for chromosome study. We found that N. cinerea had a karyotype comprising 14 pairs of autosomes and a multiple sex chromosome system, which is X1X2X3X4Y (♂) / X1X1X2X2X3X3X4X4 (♀), whereas R...
2017: Comparative Cytogenetics
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