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Hege Smith Tunsjø, Sumana Kalyanasundaram, Colin Charnock, Truls Michael Leegaard, Aina E F Moen
Current clinical diagnostic procedures have shortcomings in the differentiation of Staphylococcus argenteus from Staphylococcus aureus. This article presents three cases of Staphylococcus argenteus obtained from clinical samples. The initial results from biochemical and molecular methods led to an incorrect identification of the isolates as methicillin-resistant Staphylococcus aureus. Whole genome sequencing and real-time PCR targeting the nonribosomal peptide synthetase gene led to their correct identification as methicillin-resistant Staphylococcus argenteus...
June 2018: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
David Cheishvili, Surabhi Parashar, Niaz Mahmood, Ani Arakelian, Richard Kremer, David Goltzman, Moshe Szyf, Shafaat A Rabbani
Osteoporosis is one of the most common age-related progressive bone diseases in elderly people. Approximately one in three women and one in five men are predisposed to developing OP. In postmenopausal women a reduction in bone mineral density (BMD) leads to an increased risk of fractures. In the current study we delineated the DNA methylation signatures in whole blood samples of postmenopausal osteoporotic women. We obtained whole blood DNA from 22 normal women and 22 postmenopausal osteoporotic women (51-89 years) from the Canadian Multicenter Osteoporosis Study (CaMos) cohort...
June 20, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Fang Yu, Ai-Ping Liang
The complete mitochondrial genome (mitogenome) of Ugyops sp. (Hemiptera: Delphacidae) was sequenced, making it the first determined mitogenome from the subfamily Asiracinae, the basal clade of the family Delphacidae. The mitogenome was 15,259 bp in length with A + T content of 77.65% and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The gene order was identical with that of the ancestral insect. The nucleotide composition analysis indicated that the whole mitogenome was strongly A-skewed (0...
May 1, 2018: Journal of Insect Science
Daniel J Leite, Luís Baudouin-Gonzalez, Sawa Iwasaki-Yokozawa, Jesus Lozano-Fernandez, Natascha Turetzek, Yasuko Akiyama-Oda, Nikola-Michael Prpic, Davide Pisani, Hiroki Oda, Prashant P Sharma, Alistair P McGregor
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterised and compared the homeobox repertoires in a range of arachnids...
June 19, 2018: Molecular Biology and Evolution
Henrik Christensen, Magne Bisgaard
The aim of the investigation was to investigate the phylogeny of the 49 type strains of species of Pasteurellaceae and three genomospecies, which are available with whole genomic sequences. The genomes were downloaded from National Center for Biotechnological Information and for three species of Avibacterium sequenced in the present investigation. From the predicted protein sequences of proteins, which were conserved in all genomes, 31 proteins were randomly selected for the study. The protein sequences were concatenated for each taxon, and a multiple alignment reconstructed for the 52 taxa...
June 20, 2018: International Journal of Systematic and Evolutionary Microbiology
Eva Bártová, Soňa Legartová, Jana Krejčí, Petra Řezníčková, Alena Svobodová Kovaříková, Jana Suchánková, Radek Fedr, Evgeny Smirnov, Matúš Hornáček, Ivan Raška
We studied how deficiency in lamins A/C and lamina-associated polypeptide 2α (Lap2α) affects DNA repair after irradiation. A-type lamins and Lap2α were not recruited to local DNA lesions and did not accumulate to γ-irradiation-induced foci (IRIF), as it is generally observed for well-known marker of DNA lesions, 53BP1 protein. At micro-irradiated chromatin of lmna double knockout (dn) and Lap2α dn cells, 53BP1 protein levels were reduced, compared to locally irradiated wild-type counterpart. Decreased levels of 53BP1 we also observed in whole populations of lmna dn and Lap2α dn cells, irradiated by UV light...
June 19, 2018: Journal of Cellular Biochemistry
Saad M Al Shareef, Sulman Basit, Sha Li, Corinne Pfister, Sylvain Pradervand, Michel Lecendreux, Geert Mayer, Yves Dauvilliers, Vincenzo Salpietro, Henry Houlden, Ahmed S BaHammam, Mehdi Tafti
Kleine-Levin syndrome (KLS) is a rare periodic hypersomnia with associated behavioural abnormalities but with often favourable prognosis. There is excess risk of KLS in first-degree relatives, suggesting a strong genetic contribution. So far, no mutation is identified in KLS and comprehensive genetic analysis of affected individuals is lacking. Here we performed whole genome single-nucleotide polymorphism (SNP) genotyping and exome sequencing in a large family with seven affected members. The identified gene with a mutation was resequenced in 38 sporadic KLS patients and the expression of the gene product was mapped in the mouse brain...
June 19, 2018: Journal of Sleep Research
Asima Rani, Syed Kashif Nawaz, Muhammad Arshad, Shazia Irfan
Background: Toll-like receptors (TLRs) of the human immune mechanism play important role in the detection of invading pathogens. TLRs specifically recognize the pathogen-associated molecular patterns (PAMPs) from pathogens and start the effective response. Single nucleotide polymorphisms (SNPs) in the TLRs can mediate their functions. Present study evaluated the importance of rs4986790 polymorphism of TLR4 gene in susceptibility towards malaria, clinical outcomes of the disease and responsible species of malaria...
May 2018: Iranian Journal of Public Health
Ignacio Ferrés, Gregorio Iraola
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes...
2018: PeerJ
Wei Liu, Zhidan Xiao, Chao Fan, Nonghui Jiang, Xiangchun Meng, Xu Xiang
Litchi ( Litchi chinensis ) is an important subtropical fruit tree with high commercial value. However, the short and centralized fruit maturation period of litchi cultivars represents a bottleneck for litchi production. Therefore, the development of novel cultivars with extremely early fruit maturation period is critical. Previously, we showed that the genotypes of extremely early-maturing (EEM), early-maturing (EM), and middle-to-late-maturing (MLM) cultivars at a specific locus SNP51 (substitution type C/T) were consistent with their respective genetic background at the whole-genome level; a homozygous C/C genotype at SNP51 systematically differentiated EEM cultivars from others...
2018: Frontiers in Plant Science
Zetao Cheng, Yuqian Yan, Shuping Jing, Wen-Gang Li, Wei-Wei Chen, Jing Zhang, Min Li, Shan Zhao, Na Cao, Junxian Ou, Suhui Zhao, Xianbo Wu, Bin Cao, Qiwei Zhang
Human adenovirus type 55 (HAdV-B55) is a recently identified acute respiratory disease (ARD) pathogen in HAdV species B with a recombinant genome between renal HAdV-B11 and respiratory HAdV-B14. Since HAdV-B55 first appeared in China school in 2006, no more ARD cases associated with it had been reported until 2011, when there was an outbreak of adult severe community-acquired pneumonia (CAP) in Beijing, China. Reported here is the bioinformatics analysis of the re-emergent HAdV-B55 responsible for this outbreak...
2018: Frontiers in Microbiology
Tomoo Osumi, Shin-Ichi Tsujimoto, Moe Tamura, Meri Uchiyama, Kazuhiko Nakabayashi, Kohji Okamura, Masanori Yoshida, Daisuke Tomizawa, Akihiro Watanabe, Hiroyuki Takahashi, Tsukasa Hori, Shohei Yamamoto, Kazuko Hamamoto, Masahiro Migita, Hiroko Ogata-Kawata, Toru Uchiyama, Hiroe Kizawa, Hitomi Ueno-Yokohata, Ryota Shirai, Masafumi Seki, Kentaro Ohki, Junko Takita, Takeshi Inukai, Seishi Ogawa, Toshio Kitamura, Kimikazu Matsumoto, Kenichiro Hata, Nobutaka KIyokawa, Susumu Goyama, Motohiro Kato
Translocations of retinoic acid receptor-α (RARA), typically PML-RARA, are a genetic hallmark of acute promyelocytic leukemia (APL). However, because a small fraction of APL lack translocations of RARA, we focused here on APL cases without RARA translocation to elucidate the molecular etiology of RARA-negative APL. We performed whole-genome sequencing, PCR, and FISH for five APL cases without RARA translocations. Four of five RARA-negative APL cases had translocations involving retinoic acid receptor-β (RARB) translocations, and TBL1XR1-RARB was identified as an in-frame fusion in three cases; one case had an RARB rearrangement detected by FISH, although the partner gene could not be identified...
June 19, 2018: Cancer Research
Adam G Sowalsky, Huihui Ye, Manoj Bhasin, Eliezer M Van Allen, Massimo Loda, Rosina T Lis, Laleh Montaser-Kouhsari, Carla Calagua, Fen Ma, Joshua W Russo, Rachel J Schaefer, Olga S Voznesensky, Zhenwei Zhang, Glenn J Bubley, Bruce Montgomery, Elahe A Mostaghel, Peter S Nelson, Mary-Ellen Taplin, Steven P Balk
Primary prostate cancer (PCa) can have extensive microheterogeneity, but its contribution to the later emergence of metastatic castration-resistant PCa (mCRPC) remains unclear. In this study, we microdissected residual PCa foci in radical prostatectomies from 18 men treated with neoadjuvant intensive androgen deprivation therapy (leuprolide, abiraterone acetate, and prednisone) and analyzed them for resistance mechanisms. Transcriptome profiling showed reduced but persistent androgen receptor (AR) activity in residual tumors with no increase in neuroendocrine differentiation...
June 19, 2018: Cancer Research
Miguel J Xavier, Lisa A Mitchell, Kristen E McEwan, Rodney Scott, Robert John Aitken
The Big Blue® λSelect-cII selection system has been employed along with whole-exome sequencing, to examine the susceptibility of the male germ line to mutation in two challenging situations: (i) exposure to a chemotherapeutic regime including bleomycin, etoposide and cis-platinum (BEP) and (ii) the ageing process. A 3-week exposure to BEP induced complete azoospermia associated with a loss of developing germ cells and extensive vacuolization of Sertoli cell cytoplasm. Following cessation of treatment, spermatozoa first appeared in the caput epididymis after 6 weeks and by 12 weeks motile spermatozoa could be recovered from the cauda, although the count (P < 0...
June 19, 2018: Reproduction: the Official Journal of the Society for the Study of Fertility
Vicente M Cabrera, Patricia Marrero, Khaled K Abu-Amero, Jose M Larruga
BACKGROUND: The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya...
June 19, 2018: BMC Evolutionary Biology
Zahid Rasul Niazi, Naqab Khan, Samiullah Khan, Mehboob Alam, Mohammad A Kamal
BACKGROUND: Neurodegenerative disorder are persistently increasing and relentlessly affecting the individuals, families and society as whole. Regrettably these disorders are resistant to the available drugs, the outcomes are only palliative while the side effects of the therapy harm the patient compliance as well as treatment. Drugs from venomous source have been considered as an effective alternative for such types of disorders, particularly neurodegenerative diseases. Due to emerging advancement in the field of proteomics, genomics and molecular biology, characterization and screening of these novel compounds become more assessable...
June 14, 2018: Protein and Peptide Letters
Eyal Privman, Pnina Cohen, Amir B Cohanim, Oksana Riba-Grognuz, DeWayne Shoemaker, Laurent Keller
The fire ant Solenopsis invicta and its close relatives are highly invasive. Enhanced social cooperation may facilitate invasiveness in these and other invasive ant species. We investigated whether invasiveness in Solenopsis fire ants was accompanied by positive selection on sociobiological traits by applying a phylogenomics approach to infer ancient selection, and a population genomics approach to infer recent and ongoing selection in both native and introduced S. invicta populations. A combination of whole-genome sequencing of 40 haploid males and reduced-representation genomic sequencing of 112 diploid workers identified 1,758,116 and 169,682 polymorphic markers, respectively...
June 19, 2018: Molecular Ecology
Venugopal S Vineeth, Usha R Dutta, Karthik Tallapakka, Aneek Das Bhowmik, Ashwin Dalal
Rett syndrome is a neurodevelopmental disorder affecting the nervous, musculoskeletal and gastroenteric systems. Affected individuals show normal neonatal development for 6-18 months followed by sudden growth arrest, psychomotor retardation and a broad spectrum of clinical features. Sequence variants in MECP2 gene have been identified as the major genetic etiology accounting for 90-95% of patients. Apart from MECP2, pathogenic sequence variants and copy number variants of FOXG1 gene lead to congenital type of Rett syndrome which is a more severe form and characterised by absence of early normal development as seen in classical Rett syndrome...
June 16, 2018: Gene
Johan Gimonet, Anne-Catherine Portmann, Coralie Fournier, Leen Baert
This work shows that an incubation time reduced to 4-5 h to prepare a culture for DNA extraction followed by an automated DNA extraction can shorten the hands-on time, the turnaround time by 30% and increase the throughput while maintaining the WGS quality assessed by high quality Single Nucleotide Polymorphism analysis.
June 16, 2018: Journal of Microbiological Methods
Charlotte J Houldcroft, Sunando Roy, Sofia Morfopoulou, Ben K Margetts, Daniel P Depledge, Juliana Cudini, Divya Shah, Julianne R Brown, Erika Yara Romero, Rachel Williams, Elaine Cloutman-Green, Kanchan Rao, Joseph F Standing, John Hartley, Judith Breuer
Background: Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission among patients in a paediatric tertiary hospital. Methods: We developed a target-enriched adenovirus WGS technique for clinical samples and retrospectively sequenced 107 adenovirus-positive residual diagnostic samples, including viraemias (>5x104 copies/ml), from 37 patients collected January 2011 - March 2016...
June 4, 2018: Journal of Infectious Diseases
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