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https://www.readbyqxmd.com/read/28228919/variation-in-morphometric-characters-in-four-sand-crab-albunea-symmysta-populations-collected-from-sumatra-and-java-island-indonesia
#1
Febi Ayu Pramithasari, Nurlisa Alias Butet, Yusli Wardiatno
Variation in morphometric characters in four sand crab (Albunea symmysta) populations from four intertidal areas in Sumatra (Aceh and Bengkulu) and Java (Cilacap and Yogyakarta) were studied. Crabs collected from the four sites were measured to obtain 10 morphometric characters, i.e., carapace length (CL), carapace width (CW), ocular peduncle length and width (LOP and WOP), telson length and width (LT and WT), merus length (ML), carpus length (CaL), propodus length (PL), and dactylus length (DL). Allometric relationships were established among three morphometric characters (CW, PL, and DL) for each site, in which CL was fixed on the abscissa as a reference variable...
January 2017: Tropical Life Sciences Research
https://www.readbyqxmd.com/read/28210467/diversity-and-distribution-of-culturable-lactic-acid-bacterial-species-in-indonesian-sayur-asin
#2
Wibowo Mangunwardoyo, Abinawanto, Andi Salamah, Endang Sukara, Sulistiani, Achmad Dinoto
BACKGROUND AND OBJECTIVES: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#3
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#4
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28187681/revision-and-cladistic-analysis-of-the-southeast-asian-leaf-dwelling-spider-genus-i-calapnita-i-simon-araneae-pholcidae
#5
Bernhard A Huber
The Southeast Asian pholcid genus Calapnita Simon, 1892 is revised, with descriptions of 17 new species, five of them in the phyllicola group (Borneo: C. lehi, C. kubah, C. bidayuh, C. bankirai; Malay Peninsula, Sumatra, Java: C. anai), 12 in the vermiformis group (Borneo: C. bario, C. bariengi, C. magaseng, C. dayak, C. lawangan, C. loksado; Sulawesi: C. bugis; Philippines: C. bohol, C. dinagat, C. mae, C. nunezae, C. maragusan). New records are listed for six of the eight previously described species. A morphological cladistic analysis supports the monophyly of Calapnita and of its two previously proposed species groups and presents several new phylogenetically informative characters...
January 13, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187630/sternaspidae-annelida-sedentaria-from-vietnam-with-description-of-three-new-species-and-clarification-of-some-morphological-features
#6
Anna E Zhadan, Alexander B Tzetlin, Sergio I Salazar-Vallejo
Five sternaspid species were found near Vietnam shores: Sternaspis britayevi sp. nov., S. costata von Marenzeller, 1879, S. nana sp. nov., S. papillosa sp. nov., and S. spinosa Sluiter 1882. Sternaspis britayevi is described from the shallow water in Vietnam inhabiting soft bottoms; it resembles S. spinosa described from Java and S. thorsoni Sendall & Salazar-Vallejo, 2013 described from the Persian Gulf, but differs in having a medially projected and markedly ribbed fan of the ventro-caudal shield and nearly parallel, distally widened and rounded branchial plates...
January 25, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187423/integrated-automatic-workflow-for-phylogenetic-tree-analysis-using-public-access-and-local-web-services
#7
Kasikrit Damkliang, Pichaya Tandayya, Unitsa Sangket, Ekawat Pasomsub
At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format...
November 28, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#8
Sophia Santos, Isabel Rocha
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments...
November 27, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187414/web-based-hybrid-dimensional-visualization-and-exploration-of-cytological-localization-scenarios
#9
Gökhan Kovanci, Mehmood Ghaffar, Björn Sommer
The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3...
December 21, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187410/jllumina-a-comprehensive-java-based-api-for-statistical-illumina-infinium-humanmethylation450-and-methylationepic-data-processing
#10
Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, Richard Röttger
Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187215/spatiotemporal-trends-in-the-southwest-monsoon-wind-driven-upwelling-in-the-southwestern-part-of-the-south-china-sea
#11
Poh Heng Kok, Mohd Fadzil Mohd Akhir, Fredolin Tangang, Mohd Lokman Husain
This study analyzes two wind-induced upwelling mechanisms, namely, Ekman transport and Ekman pumping that occur during the southwest monsoon. The results suggest that the coastline of the east coast of Peninsular Malaysia (ECPM) is affected by upwelling with spatiotemporal variations. Characterization of upwelling by using wind-induced upwelling indexes (UIW) indicate the existence of favorable upwelling conditions from May to September. Upwelling intensity increased in May and peaked in August before declining in September, decreasing intensity from the southern tip towards the northern tip along the coastline of the ECPM...
2017: PloS One
https://www.readbyqxmd.com/read/28186960/polyunphased-an-extension-to-polytomous-outcomes-of-the-unphased-package-for-family-based-genetic-association-analysis
#12
Alexandre Bureau, Jordie Croteau
Polytomous phenotypes arise when a disease has multiple subtypes or when two dichotomous phenotypes are analyzed simultaneously. Few software programs offer the option to analyze such phenotypes in family studies, and none implements conditional polytomous logistic regression for within-family analysis robust to population stratification. We introduce Polyunphased, an extension to polytomous phenotypes of the Unphased package, a flexible software tool for genetic association analysis in nuclear families. Like Unphased, Polyunphased is written in C++ and runs from the command line or from a Java graphical user interface...
February 10, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28185824/uncovering-the-mask-of-the-simulium-feuerborni-complex-diptera-simuliidae-description-of-a-new-pseudocryptic-species-simulium-pairoti-from-malaysia
#13
Zubaidah Ya'cob, Hiroyuki Takaoka, Van Lun Low, Mohd Sofian-Azirun
A black fly species of the Simulium feuerborni species-group of Simulium (Nevermannia) from Cameron Highland, Peninsular Malaysia, previously regarded as S. feuerborni Edwards, originally described from East Java, is described as Simulium pairoti sp. nov. based on complete life stages. High intraspecific variations in the arrangement of the six pupal gill filaments, length of the stalk of the ventral paired filaments, and length of the anterodorsal projection of the cocoon, are noted in this species. This new species is readily distinguished from its congeners by having the characters of male genitalia with simple lamellate ventral plate, short inwardly-twisted styles, several parameral hooks, and a simple narrow median sclerite...
February 7, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28181497/boninite-like-intraplate-magmas-from-manihiki-plateau-require-ultra-depleted-and-enriched-source-components
#14
Roman Golowin, Maxim Portnyagin, Kaj Hoernle, Folkmar Hauff, Andrey Gurenko, Dieter Garbe-Schönberg, Reinhard Werner, Simon Turner
The Ontong Java and Manihiki oceanic plateaus are believed to have formed through high-degree melting of a mantle plume head. Boninite-like, low-Ti basement rocks at Manihiki, however, imply a more complex magma genesis compared with Ontong Java basement lavas that can be generated by ∼30% melting of a primitive mantle source. Here we show that the trace element and isotope compositions of low-Ti Manihiki rocks can best be explained by re-melting of an ultra-depleted source (possibly a common mantle component in the Ontong Java and Manihiki plume sources) re-enriched by ≤1% of an ocean-island-basalt-like melt component...
February 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28158307/aspasia-a-toolkit-for-evaluating-the-effects-of-biological-interventions-on-sbml-model-behaviour
#15
Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C Coles, Marika C Kullberg, Jon Timmis
A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML)...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28155670/esap-plus-a-web-based-server-for-est-ssr-marker-development
#16
Piyarat Ponyared, Jiradej Ponsawat, Sissades Tongsima, Pusadee Seresangtakul, Chutipong Akkasaeng, Nathpapat Tantisuwichwong
BACKGROUND: Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#17
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin
BACKGROUND: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28151875/java-brucea-and-chinese-herbal-medicine-for-the-treatment-of-cholesterol-granuloma-in-the-suprasellar-and-sellar-regions-a-case-report-and-literature-review
#18
Zhe Sun, Yang Cao, Lin-Zhu Zhai
RATIONALE: A cholesterol granuloma (CG) is usually found in the middle ear, papilla, orbits, petrous apex, and choroid plexus, but is highly uncommon in the skull. In spite of benign clinicopathological lesions, bone erosion can be seen occasionally in the patient with CG. The optimal treatment strategy is radical surgery, but complete excision is usually impossible due to anatomical restrictions and a risk of injury to the key structures located nearby. Here, we report a patient with CGs in the suprasellar and sellar regions who was successfully treated with Java brucea and Chinese herbal medicine...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28138784/implementation-of-a-risk-orientated-hygiene-analysis-for-the-control-of-salmonella-java-in-the-broiler-production
#19
Franziska Kloska, Maximilian Casteel, Frederik Wilms-Schulze Kump, Günter Klein
This field study aimed to establish a risk-orientated hygiene analysis on two broiler farms in Northwestern Germany for the practical use in broiler housing to evaluate the success of disinfection procedures for eradicating S. Java. The risk-orientated hygiene analysis enables fast, reproducible and cost-effective testing of broiler farms and in turn helps minimize the public health risk ensuing from S. Java. Farms were tested before and after cleaning as well as after disinfection according to a risk-orientated hygiene analysis for the presence of Salmonella DNA with qPCR...
January 31, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28137712/sparse-network-modeling-and-metscape-based-visualization-methods-for-the-analysis-of-large-scale-metabolomics-data
#20
Sumanta Basu, William Duren, Charles R Evans, Charles F Burant, George Michailidis, Alla Karnovsky
MOTIVATION: Recent technological advances in mass spectrometry, development of richer mass spectral libraries and data processing tools have enabled large scale metabolic profiling. Biological interpretation of metabolomics studies heavily relies on knowledge-based tools that contain information about metabolic pathways. Incomplete coverage of different areas of metabolism and lack of information about non-canonical connections between metabolites limits the scope of applications of such tools...
January 30, 2017: Bioinformatics
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