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Christian Schori, Christian Trachsel, Jonas Grossmann, Ioanna Zygoula, Daniel Barthelmes, Christian Grimm
Purpose: In contrast to neovascular AMD (nAMD), no treatment option exists for dry AMD. Hence, the identification of specific biomarkers is required to facilitate diagnosis and therapy of dry AMD. Methods: The proteome of 34 vitreous humor samples (dry AMD: n = 6; nAMD: n = 10; proliferative diabetic retinopathy [PDR]: n = 9; epiretinal membrane [ERM]: n = 9) was analyzed by liquid chromatography coupled mass spectrometry. Then, label-free relative quantification of dry AMD, nAMD, and PDR relative to ERM, which was defined as the reference group, was performed...
March 20, 2018: Investigative Ophthalmology & Visual Science
Carl-Erik Tornqvist, Megan Taylor, Yiwei Jiang, Joseph Evans, C Robin Buell, Shawn M Kaeppler, Michael D Casler
Flowering is an important developmental event in switchgrass (), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN...
July 2018: Plant Genome
Stella Salvo, Jason Cook, Alvar R Carlson, Candice N Hirsch, Shawn M Kaeppler, Heidi F Kaeppler
Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications. Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response. The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( L.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems...
July 2018: Plant Genome
Rujirat Hatrongjit, Anusak Kerdsin, Yukihiro Akeda, Shigeyuki Hamada
A multiplex PCR was described to simultaneously detect mcr-1 and frequently occurring carbapenem-resistant genes including bla KPC , bla NDM , bla IMP , and bla OXA-48-like in a single reaction. The PCR product sizes of these 4 carbapenem-resistant genes were 232 bp, 438 bp, 621 bp, and 798 bp for bla IMP , bla OXA-48-like , bla NDM , and bla KPC , respectively, whereas mcr-1 revealed 1126 bp of PCR product. This protocol accurately detected those resistant genes in agreement with the reference strains, 127 local carbapenem-resistant Enterobacteriaceae, 8 mcr-1 carrying Enterobacteriaceae, and 62 carbapenem-susceptible Enterobacteriaceae...
2018: MethodsX
Michael D Roberts, Cody T Haun, Christopher B Mobley, Petey W Mumford, Matthew A Romero, Paul A Roberson, Christopher G Vann, John J McCarthy
Numerous reports suggest there are low and high skeletal muscle hypertrophic responders following weeks to months of structured resistance exercise training (referred to as low and high responders herein). Specifically, divergent alterations in muscle fiber cross sectional area (fCSA), vastus lateralis thickness, and whole body lean tissue mass have been shown to occur in high versus low responders. Differential responses in ribosome biogenesis and subsequent protein synthetic rates during training seemingly explain some of this individual variation in humans, and mechanistic in vitro and rodent studies provide further evidence that ribosome biogenesis is critical for muscle hypertrophy...
2018: Frontiers in Physiology
Karel Kopejtka, Jürgen Tomasch, Boyke Bunk, Cathrin Spröer, Irene Wagner-Döbler, Michal Koblížek
Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales...
July 18, 2018: Extremophiles: Life Under Extreme Conditions
Zhi-Yu Duan, Guang-Yan Cai, Ji-Jun Li, Ru Bu, NanNan Wang, Pei Yin, Xiang-Mei Chen
Recent studies have indicated that urinary sediment miRNAs not only are able to serve as non-invasive diagnostic biomarkers for IgA nephropathy (IgAN) but may also be closely related to several clinical and pathological indicators. However, the lack of a suitable internal reference miRNA has hampered research into urinary sediment miRNAs. To date, U6 has been used as a reference gene in urinary sediment miRNA studies mostly based on the results from studies using tissue samples and cell lines. In a total of 330 IgAN patients, 164 disease control patients and 130 normal control patients, there was no significant difference in U6 levels...
July 18, 2018: Scientific Reports
Lindsay A Holden, Meharji Arumilli, Marjo K Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H Brown, Hannes Lohi
Dogs are excellent animal models for human disease. They have extensive veterinary histories, pedigrees, and a unique genetic system due to breeding practices. Despite these advantages, one factor limiting their usefulness is the canine genome reference (CGR) which was assembled using a single purebred Boxer. Although a common practice, this results in many high-quality reads remaining unmapped. To address this whole-genome sequence data from three breeds, Border Collie (n = 26), Bearded Collie (n = 7), and Entlebucher Sennenhund (n = 8), were analyzed to identify novel, non-CGR genomic contigs using the previously validated pseudo-de novo assembly pipeline...
July 18, 2018: Scientific Reports
Luyao Zhang, Hongyao Yu, Otto Hemminki, Asta Försti, Kristina Sundquist, Kari Hemminki
Familial risks for testicular cancer (TC) are among the highest of all cancers. However, data are limited for histological types of TC and for possible familial associations of TC with other cancers. We used the nationwide Swedish Family-Cancer Database for years 1958 to 2015 to analyse familial relative risks (RR) for 11,138 TC patients when first-degree relatives were diagnosed with TC or other cancer in reference to those without a family history. A total of 191 familial TCs were found, which accounted for 2...
July 18, 2018: Scientific Reports
Jeremy R B Newman, Patrick Concannon, Manuel Tardaguila, Ana Conesa, Lauren M McIntyre
Alternative splicing leverages genomic content by allowing the synthesis of multiple transcripts and, by implication, protein isoforms, from a single gene. However, estimating the abundance of transcripts produced in a given tissue from short sequencing reads is difficult and can result in both the construction of transcripts that do not exist, and the failure to identify true transcripts. An alternative approach is to catalog the events that make up isoforms (splice junctions and exons). We present here the Event Analysis (EA) approach, where we project transcripts onto the genome and identify overlapping/unique regions and junctions...
July 18, 2018: G3: Genes—Genomes—Genetics
Hua Wei Zhang, Xing Yu Meng, An Feng Li, Yu Ying Yang, Hua Ji Qiu
Long non-coding RNAs (lncRNAs) are designated as the transcripts longer than 200 nucleotides without protein-coding capacity. As a category of important gene regulatory factors, lncRNAs regulate the expression of target genes at epigenetic, transcription and post-transcriptional levels by various mechanisms, such as chromatin remodeling, DNA modification, transcription inhibition and RNA-RNA interactions, etc. In recent years, studies have shown that many lncRNAs can be induced by viruses or interferon (IFN) and to regulate the expression of related antiviral genes in IFN-mediated antiviral innate immune responses...
July 20, 2018: Yi Chuan, Hereditas
Imane Cherkaoui Jaouad, Abdelali Zrhidri, Wafaa Jdioui, Jaber Lyahyai, Laure Raymond, Grégory Egéa, Mohamed Taoudi, Said El Mouatassim, Abdelaziz Sefiani
BACKGROUND: Autosomal recessive primary microcephaly (MCPH) is a rare genetically heterogeneous disorder of neurogenic brain development characterized by a reduced head circumference at birth with no remarkable anomalies of brain architecture and variable degrees of intellectual impairment. Clinical and genetic heterogeneity in genetic disorders represent a major diagnostic challenge. CASE PRESENTATION: Two patients, 11 and 9 years old, born from consanguineous parents, were referred to the department of medical genetics at the National Institute of Health in Rabat...
July 18, 2018: BMC Medical Genetics
Odile Lalainasoa Rivoarilala, Benoît Garin, Felamboahangy Andriamahery, Jean Marc Collard
BACKGROUND: The prevalence of bacteria producing CTX-M Extended-Spectrum β-lactamases (ESBLs) has increased around the world and some of them became a major cause of infections such as bloodstream or urinary tract infections (UTI). We developed a loop-mediated isothermal amplification (LAMP) assay for a simple, rapid and sensitive detection of the four most common CTX-M groups, namely CTX-M groups 1, 2, 8 and 9. METHODS: LAMP primers targeting the four ESBLs CTX-M groups were designed using the Primer Explorer V4 software...
2018: PloS One
Sasha-Kay V Clarke, Sherline E Brown
Diaphorina citri Kuwayama (Hemiptera: Psyllidae), also known as the Asian citrus psyllid, is a vector of the citrus huanglongbing (HLB) disease. D. citri transmits all three known strains of the HLB pathogen: Candidatus Liberibacter africanus, Candidatus Liberibacter americanus, and Candidatus Liberibacter asiaticus. The study involved 92 psyllids representing the Caribbean Basin and reference samples representing countries within Asia, North America, and South America. This study was aimed at characterizing D...
July 17, 2018: Journal of Economic Entomology
Jean-Michel Claverie, Thi Ngan Ta
Motivation: More than 20 years ago, our laboratory published an original statistical test (referred to as the Audic-Claverie (AC) test in the literature) to identify differentially expressed genes from the pairwise comparison of counts of "expressed sequence tags" determined in different conditions. Despite its antiquity and the publications of more sophisticated packages, this original publication continued to gather more than 200 citations per year, indicating the persistent usefulness of the simple AC test for the community...
July 18, 2018: Bioinformatics
Arif O Khan
PURPOSE: Early-onset retinal dystrophy is usually isolated but can also be the presenting manifestation of an undiagnosed systemic disease. The purpose of this report is to highlight the initial presentation of a girl with early-onset retinal dystrophy and chronic dermatitis who was found to have an undiagnosed congenital disorder of glycosylation (SRD5A3-CDG). METHODS: Retrospective case report. RESULTS: A 13-year-old Baluchi girl was referred for evaluation of low vision since soon after birth...
July 18, 2018: Ophthalmic Genetics
Sobia Aleem
BACKGROUND: Diabetes Mellitus (DM) is an advanced and chronic endocrine disorder characterized by an insufficiency of insulin secretion from pancreatic β-cells and liver, adipose tissues, and skeletal muscles. OBJECTIVE: The main objective of this study is to understand the mechanism and genes which are responsible for the prevalence of diabetes. The study also covers various types of diabetic complications with special reference to insulin role and defects. METHODS: The scientific literature and patents were reviewed and analyzed based on their suitability and relevance to the theme of the study...
July 17, 2018: Recent Patents on Inflammation & Allergy Drug Discovery
Robert Lücking, David L Hawksworth
There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi , given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science...
June 2018: IMA Fungus
Hanna Marti, Nicole Borel, Deborah Dean, Cory A Leonard
Pigs are the natural hosts of Chlamydia suis , the only Chlamydia species known to spontaneously acquire homotypic resistance conferred by a class C tetracycline resistance gene. Various susceptibility assays have existed for several years, but there is no widely accepted, standardized assay to determine chlamydial antibiotic susceptibility. In this study, we developed new approaches to determine the in vitro susceptibility of Chlamydia to different antibiotics in view of existing protocols. Specifically, the minimal inhibitory concentration (MIC) is based on a consensus of both inclusion number reduction and alteration of inclusion size and morphology upon antibiotic exposure...
2018: Frontiers in Microbiology
Roma Sinha, Mathu Malar C, Raghwan, Subhadeep Das, Sonali Das, Mohammad Shadab, Rukhsana Chowdhury, Sucheta Tripathy, Nahid Ali
Leishmania donovani possesses a complex heteroxenic life cycle where infective metacyclic promastigotes are pre-adapted to infect their host and cope up with intracellular stress. Exploiting the similarities between cultured and sandfly derived promastigotes, we used early and late passage cultured promastigotes to show specific changes at genome level which compromise pathogen fitness reflected in gene expression and infection studies. The pathogen loses virulence mostly via transcriptional and translational regulations and long-time cultivation makes them struggle to convert to virulent metacyclics...
2018: Frontiers in Microbiology
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