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Songhe Zhang, Si Pang, Peifang Wang, Chao Wang, Chuan Guo, Felix Gyawu Addo, Yi Li
Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations...
October 26, 2016: Scientific Reports
Changlin Liu, Fazhen Zhao, Jingping Yan, Chunsheng Liu, Siwei Liu, Siqing Chen
Golden cuttlefish Sepia esculenta Hoyle is an economically important cephalopod species. However, artificial hatching is currently challenged by low survival rate of larvae due to abnormal embryonic development. Dissecting the genetic foundation and regulatory mechanisms in embryonic development requires genomic background knowledge. Therefore, we carried out a transcriptome sequencing on Sepia embryos and larvae via mRNA-Seq. 32,597,241 raw reads were filtered and assembled into 98,615 unigenes (N50 length at 911 bp) which were annotated in NR database, GO and KEGG databases respectively...
October 22, 2016: International Journal of Molecular Sciences
David A Balota, Andrew J Aschenbrenner, Melvin J Yap
There has been growing interest in dynamic changes in the lexical processing system across trials, which have typically been assessed via linear mixed effect modelling. In the current study, we explore the influence of previous trial lexicality and previous trial perceptual degradation on the effect of lexicality and degradation on the current trial. The results of analyses of three datasets (two previously published studies and a new study) provide evidence for a robust four-way interaction among previous trial lexicality and degradation and current trial lexicality and degradation effects...
October 26, 2016: Quarterly Journal of Experimental Psychology: QJEP
Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé
BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH...
2016: PeerJ
Sandeep J Joseph, Ben Li, Robert A Petit Iii, Zhaohui S Qin, Lyndsey Darrow, Timothy D Read
In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S...
2016: PeerJ
Miguel Jesus Nunes Ramos, João Lucas Coito, Joana Fino, Jorge Cunha, Helena Silva, Patrícia Gomes de Almeida, Maria Manuela Ribeiro Costa, Sara Amâncio, Octávio S Paulo, Margarida Rocheta
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp...
October 24, 2016: Plant Molecular Biology
Hao Ma, Gregory M Weber, Hairong Wei, Jianbo Yao
Many factors have been reported to affect rainbow trout egg quality, among which, postovulatory aging is one of the most significant causes as reared rainbow trout do not usually volitionally oviposit the ovulated eggs. In order to uncover the genetic regulation underling egg deterioration caused by postovulatory aging in rainbow trout, mitochondrial genome-encoded small RNA (mitosRNAs) were analyzed from unfertilized eggs on Days 1, 7, and 14 postovulation with fertilization rates of 91.8, 73.4, and less than 50 %, respectively...
October 24, 2016: Marine Biotechnology
Suzanne Adlof, Gwen Frishkoff, Jennifer Dandy, Charles Perfetti
Word learning can build the high-quality word representations that support skilled reading and language comprehension. According to the partial knowledge hypothesis, words that are partially known, also known as "frontier words" (Durso & Shore, 1991), may be good targets for instruction precisely because they are already familiar. However, studies investigating this question have produced mixed findings, and individual differences in baseline knowledge have complicated results both within and across studies...
March 2016: Reading and Writing
Sameera Khan, Reza Hamedy, Yuejuan Lei, Rikke S Ogawa, Shane N White
INTRODUCTION: Anxiety is an emotion characterized by feelings of tension, worried thoughts, and physical changes. Dental anxiety has been associated with pain, fear, care avoidance, and more invasive treatments including nonsurgical root canal treatment (NSRCT). The very words root canal are deeply embedded in societal consciousness. Better understanding of dental anxiety may prevent treatment avoidance. The purpose of this study was to conduct a systematic review of NSRCT-associated anxiety...
October 21, 2016: Journal of Endodontics
Carsten P Bramlage, Mina Nasiri-Sarvi, Joan Minguet, Peter Bramlage, Gerhard Anton Müller
BACKGROUND AND AIMS: Arterial hypertension is a major cause of death worldwide. For the most part, treatment for hypertension can be performed on an outpatient basis. However, some patients also require inpatient treatment, and the contributing factors for this remain unknown. Therefore, the primary objective of the present study was to determine which patient characteristics are associated with inpatient treatment for arterial hypertension. METHODS: Here, we conducted a mono-centric study of 103 hypertensive subjects, who were treated as inpatients in the Department of Nephrology and rheumatology of the university medical faculty of Göttingen...
October 24, 2016: BMC Research Notes
P O'Mahoney, M Khazova, M Higlett, T Lister, S Ibbotson, E Eadie
BACKGROUND: Daylight PDT (dPDT) is an effective and nearly painless treatment for field-change actinic keratosis. Measuring the protoprophyrin-IX (PpIX)-weighted exposure dose can give an indication of when conditions are most viable for effective dPDT. It would be advantageous for practitioners if more detailed information of exposure dose and appropriate treatment conditions were available. Where sophisticated measurement equipment is unavailable, simpler and more cost-effective methods of dose measurement are desirable...
October 24, 2016: British Journal of Dermatology
B N Keel, J W Keele, W M Snelling
Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences...
October 24, 2016: Animal Genetics
Bor L Tang
Hexanucleotide repeat expansion in an intron of Chromosome 9 open reading frame 72 (C9orf72) is the most common genetic cause of Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). While functional haploinsufficiency of C9orf72 resulting from the mutation may play a role in ALS/FTD, the actual cellular role of the protein has been unclear. Recent findings have now shown that C9orf72 physically and functionally interacts with multiple members of the Rab small GTPases family, consequently exerting important influences on cellular membrane traffic and the process of autophagy...
2016: Frontiers in Cellular Neuroscience
Huma Siddiqui, Tsute Chen, Ardita Aliko, Piotr M Mydel, Roland Jonsson, Ingar Olsen
BACKGROUND: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present. OBJECTIVE: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation...
2016: Journal of Oral Microbiology
Ryo Nakao, Keita Matsuno, Yongjin Qiu, Junki Maruyama, Nao Eguchi, Naganori Nao, Masahiro Kajihara, Kentaro Yoshii, Hirofumi Sawa, Ayato Takada, Chihiro Sugimoto
Ticks harbour various microorganisms, some of which act as pathogens of humans and animals. The recent advancement of genome sequencing technologies revealed that a wide range of previously unrecognised microorganisms exist in ticks. Continuous cell lines established from ticks could play a key role in the isolation of such microorganisms; however, tick cells themselves have been known to harbour symbiotic microorganisms. The present study aimed to characterise putative RNA viral sequences detected in the culture supernatant of one of the most frequently used tick cell lines, ISE6, which was derived from embryos of the blacklegged tick Ixodes scapularis...
October 15, 2016: Ticks and Tick-borne Diseases
Mahnaz Ashoorkhani, Ali Bozorgi, Reza Majdzadeh, Hamed Hosseini, Ali Yoonessi, Ali Ramezankhani, Hassan Eftekhar
BACKGROUND: Hypertension is one of the most important and well-known risk factors for cardiovascular diseases. Unfortunately, in spite of effective treatments, adherence to the regular use of drugs and other nondrug treatments, such as lifestyle improvement, is often poor. This study evaluates the effectiveness of an educational, supportive intervention - in the form of a Blood Pressure Management Application (BPMAP) - on self-management in patients with primary hypertension on controlling the determinant factors of hypertension, and on adherence to treatment...
October 21, 2016: Trials
Alemayehu Desalegn, Asamer Tsegaw, Destaye Shiferaw, Haile Woretaw
BACKGROUND: Refractive error is the main cause of visual impairment in the world. Spectacles are the most frequently used options for correcting refractive errors. In addition, they can be used for protection and fashion. It is the simplest, cheapest and only method used in developing countries like Ethiopia. This study aims to explore the knowledge, attitude, practice and associated factors towards spectacles use among adult population of Gondar town, northwest Ethiopia. METHODS: Community based cross sectional study was conducted on 780 participants using a pre-tested structured questionnaire in Gondar...
October 21, 2016: BMC Ophthalmology
Arvind Y M Sundaram, Timothy Hughes, Shea Biondi, Nathalie Bolduc, Sarah K Bowman, Andrew Camilli, Yap C Chew, Catherine Couture, Andrew Farmer, John P Jerome, David W Lazinski, Andrew McUsic, Xu Peng, Kamran Shazand, Feng Xu, Robert Lyle, Gregor D Gilfillan
BACKGROUND: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures...
October 21, 2016: BMC Genomics
Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian, Henry Horng-Shing Lu
BACKGROUND: It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length)...
October 6, 2016: BMC Bioinformatics
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