Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Burkholderia sp. Strain USMB20, Isolated from Nodules of Mucuna bracteata.

Burkholderia sp. strain USMB20 is a plant growth-promoting rhizobacterium that was isolated from nodules of the leguminous cover crop Mucuna bracteata. The draft genome sequence of Burkholderia sp. strain USMB20 has an assembly size of 7.7 Mbp in 26 contigs with a GC content of 66.88%.

Draft Genome Sequence of Lactarius deliciosus Strain CBS 582.63 from the CBS-KNAW Culture Collection.

A type strain of Lactarius deliciosus was obtained from the CBS-KNAW culture collection. The mycelium was cultured using potato dextrose agar, and the extracted genomic DNA was subjected to PacBio genome sequencing. Upon assembly and annotation, the genome size was estimated to be 54 Mbp, with 12,753 genes.

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel.

The "ship" of the Arabian and North African deserts, the one-humped dromedary camel (Camelus dromedarius) has a remarkable capacity to survive in conditions of extreme heat without needing to drink water. One of the ways that this is achieved is through the actions of the antidiuretic hormone arginine vasopressin (AVP), which is made in a specialised part of the brain called the hypothalamo-neurohypophyseal system (HNS), but exerts its effects at the level of the kidney to provoke water conservation. Interestingly, our electron microscopy studies have shown that the ultrastructure of the dromedary HNS changes according to season, suggesting that in the arid conditions of summer the HNS is in an activated state, in preparation for the likely prospect of water deprivation. Based on our dromedary genome sequence, we have carried out an RNAseq analysis of the dromedary HNS in summer and winter. Amongst the 171 transcripts found to be significantly differentially regulated (>2 fold change, p value <0.05) there is a significant over-representation of neuropeptide encoding genes, including that encoding AVP, the expression of which appeared to increase in summer. Identification of neuropeptides in the HNS and analysis of neuropeptide profiles in extracts from individual camels using mass spectrometry indicates that overall AVP peptide levels decreased in the HNS during summer compared to winter, perhaps due to increased release during periods of dehydration in the dry season.

Development of electronic medical records for clinical and research purposes: the breast cancer module using an implementation framework in a middle income country- Malaysia.

BACKGROUND: Advances in medical domain has led to an increase of clinical data production which offers enhancement opportunities for clinical research sector. In this paper, we propose to expand the scope of Electronic Medical Records in the University Malaya Medical Center (UMMC) using different techniques in establishing interoperability functions between multiple clinical departments involving diagnosis, screening and treatment of breast cancer and building automatic systems for clinical audits as well as for potential data mining to enhance clinical breast cancer research in the future. RESULTS: Quality Implementation Framework (QIF) was adopted to develop the breast cancer module as part of the in-house EMR system used at UMMC, called i-Pesakit©. The completion of the i-Pesakit© Breast Cancer Module requires management of clinical data electronically, integration of clinical data from multiple internal clinical departments towards setting up of a research focused patient data governance model. The 14 QIF steps were performed in four main phases involved in this study which are (i) initial considerations regarding host setting, (ii) creating structure for implementation, (iii) ongoing structure once implementation begins, and (iv) improving future applications. The architectural framework of the module incorporates both clinical and research needs that comply to the Personal Data Protection Act. CONCLUSION: The completion of the UMMC i-Pesakit© Breast Cancer Module required populating EMR including management of clinical data access, establishing information technology and research focused governance model and integrating clinical data from multiple internal clinical departments. This multidisciplinary collaboration has enhanced the quality of data capture in clinical service, benefited hospital data monitoring, quality assurance, audit reporting and research data management, as well as a framework for implementing a responsive EMR for a clinical and research organization in a typical middle-income country setting. Future applications include establishing integration with external organization such as the National Registration Department for mortality data, reporting of institutional data for national cancer registry as well as data mining for clinical research. We believe that integration of multiple clinical visit data sources provides a more comprehensive, accurate and real-time update of clinical data to be used for epidemiological studies and audits.

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures.

Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.

Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681.

Here, we report the complete genome sequence of Paenibacillus durus type strain ATCC 35681, which can fix atmospheric nitrogen even in the presence of nitrate.

Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.

Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).

The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12.

Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different.

Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.

BACKGROUND: Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures. RESULTS: The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme. CONCLUSIONS: The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.

Xylanase Superproducer: Genome Sequence of a Compost-Loving Thermophilic Fungus, Thermomyces lanuginosus Strain SSBP.

We report here the draft genome sequence of Thermomyces lanuginosus strain SSBP, which was isolated from soil in South Africa. This fungus produces the largest amount of xylanase ever reported in the literature.

Draft genome sequence of the rubber tree Hevea brasiliensis.

BACKGROUND: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. RESULTS: Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. CONCLUSIONS: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.

Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12.

We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.

Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5.

Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring in Malaysia. Here, we report the complete genome of G. thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.

Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1.

Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.