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https://www.readbyqxmd.com/read/28822948/bacterial-and-archaeal-community-distribution-and-stabilization-of-anaerobic-sludge-in-a-strengthen-circulation-anaerobic-sca-reactor-for-municipal-wastewater-treatment
#1
Bo Yang, Hui Xu, Junfeng Wang, Xinshan Song, Yuhui Wang, Fang Li, Qing Tian, Chunyan Ma, Daoyuan Wang, Junhong Bai, Wolfgang Sand
In this study, a SCA reactor was employed for municipal wastewater treatment at a mesophilic temperature (30°C) under different hydraulic retention times (HRT) and upflow velocities (Vup) to investigate granule sludge stability and spatial microbial distribution. The stable COD removal efficiency readied at HRT of 15, 12, 9 and 6h, and Vup ranging from 0.6 to 5.9mh(-1). EPS fraction analysis of granule sludge shows that municipal wastewater was mainly attributed to the enrichment influence of polysaccharide and tightly bound-EPS...
August 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28822795/strategies-for-analyzing-bisulfite-sequencing-data
#2
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28822354/3d-brain-organoids-derived-from-pluripotent-stem-cells-promising-experimental-models-for-brain-development-and-neurodegenerative-disorders
#3
REVIEW
Chun-Ting Lee, Raphael M Bendriem, Wells W Wu, Rong-Fong Shen
Three-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), appear to recapitulate the brain's 3D cytoarchitectural arrangement and provide new opportunities to explore disease pathogenesis in the human brain. Human iPSC (hiPSC) reprogramming methods, combined with 3D brain organoid tools, may allow patient-derived organoids to serve as a preclinical platform to bridge the translational gap between animal models and human clinical trials...
August 20, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28821885/the-expression-profiles-of-mirna-mrna-of-early-response-in-genetically-improved-farmed-tilapia-oreochromis-niloticus-liver-by-acute-heat-stress
#4
Jun Qiang, Wen J Bao, Fan Y Tao, Jie He, Xia H Li, Pao Xu, Lan Y Sun
Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are commercially important fish that are cultured in China. GIFT are highly susceptible to diseases when exposed to high temperatures in summer. Better understanding the GIFT regulatory response to heat stress will not only help in determining the relationship between heat stress signalling pathways and adaption mechanisms, but will also contribute to breeding new high-temperature tolerant strains of GIFT. In this study, we built control (28 °C) and heat-treated (37...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821582/identification-of-%C3%AE-enolase-as-a-prognostic-and-diagnostic-precancer-biomarker-in-oral-submucous-fibrosis
#5
Swarnendu Bag, Debabrata Dutta, Amrita Chaudhary, Bidhan Chandra Sing, Mousumi Pal, Ajoy Kumar Ray, Rita Banerjee, Ranjan Rashmi Paul, Amit Basak, Amit Kumar Das, Jyotirmoy Chatterjee
AIMS: Diagnostic ambiguities regarding the malignant potentiality of oral submucous fibrosis (OSF), an oral precancerous condition having dysplastic and non-dysplastic isoforms are the major failure for early intervention of oral squamous cell carcinoma (OSCC) patients. Our goal is to identify proteomic signatures from biopsies that can be used as precancer diagnostic marker for patient suffering from OSF. METHODS: The high throughput techniques adopting de novo peptide sequencing (1D SDS-PAGE coupled nanoLC MALDI tandem mass spectrometry (MS/MS)-based peptide mass fingerprint), immunohistochemistry (IHC), Western blot (WB) and real-time PCR (RT-PCR) analysis are considered for such biomarker identification and multilevel validations...
August 18, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28821295/coexistence-of-congenital-left-ventricular-aneurysm-and-prominent-left-ventricular-trabeculation-in-a-patient-with-ldb3-mutation-a-case-report
#6
Shengshuai Shan, Xiaoxiao He, Lin He, Min Wang, Chengyun Liu
BACKGROUND: The coexistence of congenital left ventricular aneurysm and abnormal cardiac trabeculation with gene mutation has not been reported previously. Here, we report a case of coexisting congenital left ventricular aneurysm and prominent left ventricular trabeculation in a patient with LIM domain binding 3 gene mutation. CASE PRESENTATION: A 30-year-old Asian man showed paroxysmal sinus tachycardia and Q waves in an electrocardiogram health check. There were no specific findings in physical examinations and serological tests...
August 19, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28820478/detection-of-interactions-between-proteins-by-using-legendre-moments-descriptor-to-extract-discriminatory-information-embedded-in-pssm
#7
Yan-Bin Wang, Zhu-Hong You, Li-Ping Li, Yu-An Huang, Hai-Cheng Yi
Protein-protein interactions (PPIs) play a very large part in most cellular processes. Although a great deal of research has been devoted to detecting PPIs through high-throughput technologies, these methods are clearly expensive and cumbersome. Compared with the traditional experimental methods, computational methods have attracted much attention because of their good performance in detecting PPIs. In our work, a novel computational method named as PCVM-LM is proposed which combines the probabilistic classification vector machine (PCVM) model and Legendre moments (LMs) to predict PPIs from amino acid sequences...
August 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28820204/droplet-microfluidics-for-synthetic-biology
#8
REVIEW
Philip C Gach, Kosuke Iwai, Peter W Kim, Nathan J Hillson, Anup K Singh
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28819774/whole-exome-sequencing-of-wild-derived-inbred-strains-of-mice-improves-power-to-link-phenotype-and-genotype
#9
Peter L Chang, Emily Kopania, Sara Keeble, Brice A J Sarver, Erica Larson, Annie Orth, Khalid Belkhir, Pierre Boursot, François Bonhomme, Jeffrey M Good, Matthew D Dean
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation...
August 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819199/transcriptome-analysis-of-the-effects-of-shell-removal-and-exogenous-gibberellin-on-germination-of-zanthoxylum-seeds
#10
Jikang Sun, Ping Wang, Tao Zhou, Jian Rong, Hao Jia, Zhiming Liu
The zanthoxylum seeds are oil-rich and have a very thick, dense and oily shell. In the natural conditions the seeds have a very low germination rate. Prior to treatment with GAs to promote germination, the seeds were usually soaked in sulfuric acid to remove shells easily. A high-throughput sequencing of mRNAs was performed to investigate the effects of the above treatments on the germination of zanthoxylum seeds. Seven libraries were assembled into 100,982 unigenes and 59,509 unigenes were annotated. We focused on the expression profiles of the key genes related to the oil metabolisms and hormone regulations during seed germination...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819187/administration-of-mesenchymal-stromal-cells-before-renal-ischemia-reperfusion-attenuates-kidney-injury-and-may-modulate-renal-lipid-metabolism-in-rats
#11
Pauline Erpicum, Pascal Rowart, Laurence Poma, Jean-Marie Krzesinski, Olivier Detry, François Jouret
Mesenchymal stromal cells (MSC) have been demonstrated to attenuate renal ischemia/reperfusion (I/R) damage in rodent models. The mechanisms of such nephro-protection remain largely unknown. Furthermore, the optimal timing of MSC administration has been poorly investigated. Here, we compare the impact of MSC injection 7 days before (MSCD - 7) versus 1 day after (MSCD + 1) renal I/R in rats. Control groups received equivalent volumes of saline at similar time-points (SD - 7 and SD + 1). Right nephrectomy was performed, and left renal ischemia lasted 45 min...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819150/the-g%C3%AE-i-giv-binding-interface-is-a-druggable-protein-protein-interaction
#12
Vincent DiGiacomo, Alain Ibáñez de Opakua, Maria P Papakonstantinou, Lien T Nguyen, Nekane Merino, Juan B Blanco-Canosa, Francisco J Blanco, Mikel Garcia-Marcos
Heterotrimeric G proteins are usually activated by the guanine-nucleotide exchange factor (GEF) activity of GPCRs. However, some non-receptor proteins are also GEFs. GIV (a.k.a Girdin) was the first non-receptor protein for which the GEF activity was ascribed to a well-defined protein sequence that directly binds Gαi. GIV expression promotes metastasis and disruption of its binding to Gαi blunts the pro-metastatic behavior of cancer cells. Although this suggests that inhibition of the Gαi-GIV interaction is a promising therapeutic strategy, protein-protein interactions (PPIs) are considered poorly "druggable" targets requiring case-by-case validation...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818911/complete-genome-sequence-of-a-naturally-occurring-simian-foamy-virus-isolate-from-rhesus-macaque-sfvmmu_k3t
#13
Subhiksha Nandakumar, Eunhae H Bae, Arifa S Khan
The full-length genome sequence of a simian foamy virus (SFVmmu_K3T), isolated from a rhesus macaque (Macaca mulatta), was obtained using high-throughput sequencing. SFVmmu_K3T consisted of 12,983 bp and had a genomic organization similar to that of other SFVs, with long terminal repeats (LTRs) and open reading frames for Gag, Pol, Env, Tas, and Bet.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818813/nitrogen-loss-from-anaerobic-ammonium-oxidation-coupled-to-iron-iii-reduction-in-a-riparian-zone
#14
Bangjing Ding, Zhengkui Li, Yunbin Qin
Anaerobic ammonium oxidation coupled to iron(III) reduction (termed Feammox) is a recently discovered pathway of nitrogen cycling. However, little is known about the pathways of N transformation via Feammox process in riparian zones. In this study, evidence for Feammox in riparian zones with or without vegetation cover was demonstrated using isotope tracing technique and high-throughput sequencing technology. The results showed that Feammox could occur in riparian zones, and demonstrated that N2 directly from Feammox was dominant Feammox pathway...
August 14, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28818754/daily-thanatomicrobiome-changes-in-soil-as-an-approach-of-postmortem-interval-estimation-an-ecological-perspective
#15
Joe Adserias-Garriga, Marta Hernández, Narciso M Quijada, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization...
August 7, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28818587/phenanthrene-responsive-micrornas-and-their-targets-in-wheat-roots
#16
Jinfeng Li, Le Yue, Yu Shen, Yu Sheng, Xinhua Zhan, Guohua Xu, Baoshan Xing
MicroRNAs (miRNAs) play key roles in plant growth, development and responses to abiotic stress. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants. However, it is yet unknown how miRNAs work during PAH uptake by plant roots. Thus, in this study we ascertain phenanthrene (a model PAH)-responsive miRNAs using small RNA high-throughput deep sequencing and their target genes in wheat roots. We identified 108 conserved and non-conserved miRNA members belonging to 82 miRNA families and found 11 differentially expressed miRNAs, among which four miRNAs (miR156, miR164, miR171a and miR9678-3p) were up-regulated and the other seven miRNAs (miR398, miR531, miR1121, miR5048-5p, miR9653b, miR9773 and miR9778) were down-regulated...
August 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28818036/ecccl-parallelized-gpu-implementation-of-ensemble-classifier-chains
#17
Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider
BACKGROUND: Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this context, the concept of Classifier Chains has been shown to improve prediction accuracy, especially when applied as Ensemble Classifier Chains. However, these techniques lack computational efficiency when applied on large amounts of data, e.g., derived from next-generation sequencing experiments...
August 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28817650/snorna-and-pirna-expression-levels-modified-by-tobacco-use-in-women-with-lung-adenocarcinoma
#18
Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton de Sa Carvalho, Fabio Passetti
Lung cancer is one of the most frequent types of cancer worldwide. Most patients are diagnosed at advanced stage and thus have poor prognosis. Smoking is a risk factor for lung cancer, however most smokers do not develop lung cancer while 20% of women with lung adenocarcinoma are non-smokers. Therefore, it is possible that these two groups present differences besides the smoking status, including differences in their gene expression signature. The altered expression patterns of non-coding RNAs in complex diseases make them potential biomarkers for diagnosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28817636/uncovering-robust-patterns-of-microrna-co-expression-across-cancers-using-bayesian-relevance-networks
#19
Parameswaran Ramachandran, Daniel Sánchez-Taltavull, Theodore J Perkins
Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths...
2017: PloS One
https://www.readbyqxmd.com/read/28817224/a-novel-post-hoc-method-for-detecting-index-switching-finds-no-evidence-for-increased-switching-on-the-illumina-hiseq-x
#20
Gregory L Owens, Marco Todesco, Emily B M Drummond, Sam Yeaman, Loren H Rieseberg
High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that 'index switching', where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may...
August 17, 2017: Molecular Ecology Resources
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