We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and ...observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses.
The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages.
The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.
Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this ...premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of
Bos taurus
(cow) and
Bubalus bubalis
(buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90–96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera
Fibrobacter
,
Bacteroides
,
Clostridium
,
Prevotella
and
Ruminococcus
involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.
Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation ...sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.
The Philippines has an abundance of karst or forest over limestone landscapes, but only a small percentage of them have been studied and protected. Although the flora and fauna of karst forests are ...diverse and unique, little is known about the microflora that inhabits this ecosystem. The taxonomic and functional composition of bacteria and fungi in soil samples from three locations within three karst forest zones in Basey, Samar, Philippines were analyzed using Illumina shotgun metagenome sequencing. Proteobacteria and Actinobacteria bacterial sequences were most prevalent in the karst soil, followed by those of the Firmicutes, Acidobacteria, Chloroflexi, Planctomycetes, Cyanobacteria, Verrumicrobia, Bacteriodetes, and Deinococcus-Thermus. The most abundant fungal sequences belonged to Ascomycota, followed by Basidiomycota. An average of 33 million predicted protein features was detected across all sites. Enzyme pathways for nitrogen and sulfur metabolism, and several carbon fixation pathways, appeared nearly complete. To our knowledge, this is the first report to provide baseline information on the microbial community and their possible roles in karst forest ecosystem health in the Philippines, which may lead to identifying new microbes with specialized metabolism and promoting biodiversity conservation of karst forests in the Philippines. Furthermore, correlation analysis with plant diversity will reveal plant-microbe interaction leading to the understanding of the adaptation, abundance, survival, and diversity of microorganisms and plants.
Cilj rada bio je opisati potencijal rasta prasadi s osvrtom na hranidbene zahtjeve prasadi prije i nakon faze odbića. Rast prasadi je opisan sigmoidnom krivuljom koju karakterizira brzi porast ...tijekom prve faze te blagi pad u drugoj fazi proizvodnog ciklusa. Kako bi se smanjila depresija rasta tijekom prvih dana nakon odbića važno je osigurati razdoblje prilagodbe tijekom kojeg će prasad prijeći s hranidbe majčinim mlijekom na hranidbu krutom hranom. Iako prasad posjeduje veliki kapacitet za brzi porast nakon razdoblja odbića on može biti ograničen čimbenicima kao što su dob pri odbiću, hranidba, mikrobiološki ili fiziološki čimbenici. Suplemenati poput esencijalnih ulja, aminokiselina, selena ili kratkolančanih masnih kiselina u obrocima pozitivno utječu na zdravstveni status prasadi, ali i na njihov potencijal za rast tijekom kasnijih faza proizvodnog ciklusa. Izbalansiranom hranidbom u pogledaju energije i hranjivih tvari osiguravaju se optimalni uvjeti za postizanje zadovoljavajućih prirasta uz zadržavanje dobrog zdravstvenog statusa prasadi što čini preduvjet uspješne svinjogojske proizvodnje.
The aim of this study was to describe the growth potential of weaned piglets with reference to the nutritional requirements of piglets before
and after the weaning. Piglets growth is described by sigmoid curve that is characterized with a rapid increase during the first stages and a
slight decrease in the second stage of the production cycle. In order to reduce growth depression during the first days after the weaning, it is important to provide an adjustment period during which the piglets will switch from feeding with sow’s milk to solid feeding. Although piglets possess a large capacity for rapid growth after the weaning, it may be limited by factors such as age at the weaning, feeding, microbiological or physiological factors. The addition of supplements such as essential oils, amino acids, selenium or short-chain fatty acids
in meals have a positive effect on the health status of piglets, but also on their growth potential during the later stages of the production
cycle. A balanced diet in terms of energy and nutrients ensures optimal
conditions for achieving satisfactory growth and maintaining good health status of piglets, which is a prerequisite for successful pig production.
U ovom se članku promišlja o stvarnosti i pojmu milosrđa kako ga je iskusila i razumjela sveta Terezija Avilska. Ujedno se želi vidjeti koliko su njezina iskustva i promišljanja aktualna i izazovna ...za današnju teologiju. U prvome se dijelu pokušava pokazati aktualnost milosrđa kao teološke teme te u tom smislu i sustavno-teološki promišljati o milosrđu kod svete Terezije. Pokazat će se kako je milosrđe ne samo velika tema nego i polazište Terezijine teologije. U drugome se dijelu promišlja o odnosu milosrđa i spasenja. Iz toga se odnosa ponajbolje može shvatiti presudno značenje Božjega milosrđa za čovjeka. Tu će se tematizirati i tema mogućnosti vječne propasti te će se kroz predstavljanja nekih Terezijinih misli ponuditi poticaji za teologiju. U trećem dijelu pokazuje se kako je prema shvaćanju svete Terezije milosrđe konstanta duhovnoga života, stvarnost koja prati čitavi duhovni rast.
In questo articolo riflettiamo sulla realtà e sul concetto di misericordia come ne ha fatto esperienza e come viene inteso da santa Teresa d’Avila. Allo stesso tempo, desideriamo vedere quanto le sue esperienze e le sue riflessioni siano attuali e rappresentino una sfida per la teologia odierna. Nella prima parte cerchiamo di mostrare l’attualità della misericordia come concetto teologico e, in tal senso, riflettere pure in modo sistematico-teologico sulla misericordia in santa Teresa. Verrà dimostrato che la misericordia non è solo una tematica importante, ma anche il punto di partenza della teologia teresiana. Nella seconda parte svilupperemo l’importante tematica riguardante il rapporto fra misericordia e salvezza. Dall’osservazione di questo rapporto possiamo capire nel migliore dei modi il significato cruciale della misericordia divina per l’uomo. Qui verrà tematizzata anche la tematica della possibilità della dannazione eterna e verranno offerti, tramite la presentazione di alcune riflessioni teresiane, degli stimoli per la teologia. Nella terza parte viene mostrato come secondo santa Teresa la misericordia sia una costante della vita spirituale, una realtà che accompagna l’intera crescita spirituale.
RAST-F is a new full-core analysis code based on the two-step approach that couples a multi-group cross-section generation Monte-Carlo code MCS and a multi-group nodal diffusion solver. To ...demonstrate the feasibility of using MCS/RAST-F for fast reactor analysis, this paper presents the coupled nodal code verification results for the MET-1000 and CAR-3600 benchmark cores. Three different multi-group cross-section calculation schemes are employed to improve the agreement between the nodal and reference solutions. The reference solution is obtained by the MCS code using continuous-energy nuclear data. Additionally, the MCS/RAST-F nodal solution is verified with results based on cross-section generated by collision probability code TULIP. A good agreement between MCS/RAST-F and reference solution is observed with less than 120 pcm discrepancy in keff and less than 1.2% root-mean-square error in power distribution. This study confirms the two-step approach MCS/RAST-F as a reliable tool for the three-dimensional simulation of reactor cores with fast spectrum.
Decay heat (DH) is the heat produced through a radioactive decay of fission products during or after a reactor operation. It is known as the second largest source of power in the core after fission. ...Being such a strong contributor to reactor power, it should be accurately determined at any time of reactor operation. Currently, there are two main approaches for DH estimation used in reactor simulation codes. One approach is based on careful inventorying of all produced target nuclides and their individual contributions to total power. Alternatively, the other popular approach is based on collapsing all target fission products into a small number of groups similar to delayed neutron estimation techniques. However, the last (multigroup) method currently has limitations when used in some transient scenarios such as transients occurred in fresh fuel.
In this study, the multigroup method was further developed for reducing limitations while retaining the advantage in computation speed. Then, it was implemented into Reactor Analysis code for Steady state and Transient (RAST-K) and tested against other codes. As a result, the improved method was found capable of determining DH power at all tested stages of reactor operation under any tested operation scenario. In particular, the test simulations using the improved method showed better results in those scenarios that were under accuracy limitations of the original multigroup method. Overall, the quality of transient calculations in RAST-K was improved when using the newly implemented DH module.
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