SMS: A Novel Approach for Bacterial Strain Genome Reconstruction in Multiple Samples

BackgroundThe analysis of the bacterial strains is important for the understanding of drug resistance. Despite the existence of dozens of computational tools for bacterial strain studies, most of them are developed for the limited number of known bacterial strains. Almost all remaining tools are designed to analyze individual samples or local regions instead of the entire bacterial genomes. With multiple shotgun metagenomic samples routinely generated in a project, it is necessary to create methods to reconstruct novel bacterial strain genomes in multiple samples.ResultsWe developed a novel computational approach called SMS to de novo reconstruct bacterial Strain genomes from Multiple shotgun sequencing Samples. Tested on 702 simulated and 195 experimental datasets, SMS reliably identified the strain number, strain abundance, and strain polymorphisms. Compared with two existing approaches, SMS showed superior performance in terms of more accurate estimation of the strain number, abundance and variations.ConclusionsSMS is a useful tool for novel bacterial strain reconstruction in multiple shotgun metagenomic samples.

Cage aggression in group-housed laboratory male mice: an international data crowdsourcing project

Aggression in group-housed laboratory mice is a serious animal welfare concern. Further understanding of the causes of mouse aggression could have a significant impact on a large number of laboratory animals. The NC3Rs led a crowdsourcing project to collect data on the prevalence and potential triggers of aggression in laboratory mice. The crowdsourcing approach collected data from multiple institutions and is the first time such an approach has been applied to a laboratory animal welfare problem. Technicians observed group-housed, male mice during daily routine cage checks and recorded all incidents of aggression-related injuries. In total, 44 facilities participated in the study and data was collected by 143 animal technicians. A total of 788 incidents of aggression-related injuries were reported across a sample population of 137,580 mice. The mean facility-level prevalence of aggression-related incidents reported across facilities was equivalent to 15 in 1,000 mice. Key factors influencing the prevalence of aggression included strain; number of mice per cage; how mice were selected into a cage; cage cleaning protocols; and transfer of nesting material. Practical recommendations have been provided to minimise aggressive behaviour in group-housed, male mice based upon the results of the study and taking into consideration the current published literature.

EFFECT OF TEMPERATURE AND SODIUM CHLORIDE CONCENTRATION ON GROWTH OF Staphylococcus aureus MUTANTS

The study included the identification of Staphylococcus aureus (wild type and mutant) isolates. All these isolates were identified as coagulase and catalase positive and able to ferment mannitol. Strain number 24 was chosen & undergone mutation with NTG to isolate temperature sensitive osmotically fragile (TOF) mutants. TOF mutants were successfully isolated by exposing the cell suspension to 200 Mg/ml of NTG for 75 minutes. The results of characterization of TOF mutants, showed that these mutants were identical to their mother strain morphologically and biochemically. The result of this mutation is to make the lysozyme able to lyse the cell wall of the TOF mutants in pattern similar to lysostaphin . Antibiotic sensitivity pattern was demonstrated for all the isolates and multiple resistance of some isolates were detected. The obtained results showed that the two mutant isolates were resistant to Methicillin, Benzathin, Penicillin, Cloxacillin Sodium and Lincomycin, wherease these isolates were sensitive to Amoxicillin, Cefotaxine Sodium, Cephalexin Sodium and Tetracyclin but intermediate in resistance to Clindamycin. The effect of different temperature showed that the growth of the mother strain (strain No.24) increased with the increase of temperature.The mutant strains (3M,10M) are not stable in the different temperature and their growth is very low at 40C. The effect of different NaCl concentration showed that the growth of the mother strain (strain No.24) and the 2 mutant strain (3M,10M) would increase with the increase of the NaCl concentration but decrease at NaCl concentration = 1.5 M .

Productivity of Krivovir Strain and its Importance on Sheep Farming in Republic of Serbia

The area of central Serbia is very suitable for sheep production, because of it’s hilly and mountainous configuration. Such area is rich in pastures for ruminants. In the territory of central Serbia, representative of autochthonous (indigenous) sheep breeds is pramenka (zackel) with its differentiated strains: Sjenica strain, Svrljig strain, Krivovir strain, Karakachan strain, Pirot strain, Lipa strain and Bardoka (White Metohian strain). Aim of this study was to investigate Krivovir strain: number of controlled heads and their part in total sheep population, their productivity parameters and milk parameters. In this study, total of 789 adult animals were observed. Average observed body weight (BW) of lambs were: BW on birth 3.22 kg, BW after 30 days 10.55 kg and BW on weaning 24.99 kg, while BW of adult sheep was 50.52 kg. Fertility index was 1.17 and average wool production was 2.88 kg. Average lactation after weaning lasted for 100 days, with milk production 65.16 kg, 3.91% protein and 6.72% milk fat. Krivovir strain is participating with 0.4% of total number of controlled sheep in central Serbia. Although in small number, this strain is irreplaceable in sustainable systems because they are evolutionary adapted to the conditions in which they are reared and because of their contribution to gene pool and agro-biodiversity.

Detection of Bacterial Leaf Blight Resistance Genes in Indigenous Glutinous Rice Landraces

Bacterial leaf blight disease (BLB) caused by Xanthomonas oryzae pv is one of the most widespread devastating diseases of rice worldwide. In this study, a total of 86 indigenous glutinous rice landraces were examined for BLB resistant genes included Xa4, xa5, and Xa7 by using molecular markers. The results indicated that 37 samples carrying resistant genes, in which Xa4 was found in 11 samples, xa5 determined in 6 samples, Xa7 was in 19 samples, respectively. However, both of Xa7 and Xa4 were observed in only one sample. The resistant level against 10 bacterial strains carrying the resistant genes was also evaluated. We found that the number 6, 9, and 8 out of the 10 bacterial strains were resistant to the landraces which carried the Xa4, xa5, and Xa7. The bacterial strain number 5 was revealed highly toxic, causing infection of all samples. The agronomical traits, yield and yield components of 37 rice landraces included the resistant genes (Xa4, xa5 and Xa7) were evaluated. Our findings may provide useful genetic sources in indigenous glutinous rice landraces to further develop BLB resistant rice lines via molecular breeding program.

Performance Of Mentik Wangi Rice Generation M1 From The Results Of Gamma Ray Irradiation

<p>Mentik wangi is one of the local rice varieties in Indonesia less attractive to farmers. That is because the rice Mentik wangi has some weakness, namely a long harvest time, easy to collapse, and the results less than the maximum productivity. To increase the interest of farmers in rice cultivation Mentik wangi, then an attempt is made to improve the quality of rice Mentik wangi properties with plant breeding techniques one of which is a genetic mutation using gamma radiation. This study was conducted to determine the performance (performance) of rice Mentik wangi (M1) results of gamma-ray radiation that is expected to have a positive properties of new or better than its origin. This research was conducted in paddy fields in the village of Nangsri Lor, District Kebakkramat, Karanganyar and implemented in September 2015 to January 2016. Data were analyzed by descriptive with sorting and comparing each individual plant at each radiation dose to the average control accurately and objective. The results showed that gained some plants that could potentially be a mutant plant that has better properties (positive) that appears at the variable plants from each individual plant, ie the number of lines T16 with a radiation dose of 300 gray tall plants are very short 86 cm, strain number T204 with a radiation dose of 200 gray pick the highest panicle length of 33.5 cm, strain number T133 with a radiation dose of 100 gray has a total number of tillers and productive tiller high of 17 rods (total) and 11 rods (productive), strain number T133 with radiation dose of 200 gray had the highest number of filled grain and 624 grain strain T70 numbers with a radiation dose of 100 gray had the highest percentage of filled grain at 96%, and the number of lines T (1-7) with a radiation dose of 100 gray and strain number T ( 1-9) with a radiation dose of 200 gray had a shorter harvesting time is 110 days.<strong></strong></p>

Identification and characterization of Pseudomonas fluorescensstrains effective against Xanthomonasoryzaepv. oryzae causing bacterial blight of rice in Punjab, India

For the control of bacterial blight of rice caused by Xanthomonasoryzaepv. oryzae, sixty four Pseudomonas fluorescens strains were recovered from rice and wheat rhizosphere. These strains were identified on the basis of internal transcribed spacer (ITS) region. It was observed that the strains showing fluorescence in the selective media showed the amplification of the targeted P. fluorescens specific ITS region. The strains were also characterized for the production of the antibiotic 2, 4-diacetylphloroglucinol (DAPG) using phlDlocus. The characteristic 750bp region was amplified in all the DAPG producing strains. These strains were evaluated against X. oryzae in vitro by dual culture method. The P. fluorescens strains found effective in vitro were further tested in field for their antagonistic potentiality and disease suppression ability. P. fluorescens strain number Pf-4-R showed maximum inhibition i.e. of 5.5 mm against the test pathogen X. oryzaepv. oryzae. Talc based powder formulation of the effective strain Pf-4-R used for field evaluation, showed that pre-inoculation foliar sprays were effective in controlling bacterial blight of rice with disease suppression efficiency ranging from 29.6 to 65.6 percent in different treatments.

USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.

USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.