Draft genome sequence of Saccharopolyspora rectivirgula

We have sequenced the genome of Saccharopolyspora rectivirgula, the causative agent of farmer’s lung disease. The draft genome consists of 182 contigs totaling 3,977,051 bp, with a GC content of 68.9%

PENGEMBANGAN MODEL MANAJEMEN BERBASIS SEKOLAH YANG LEBIH MENGEDEPANKAN PELIBATAN PARTISIPASI MASYARAKAT UNTUK IMPLEMENTASI KURIKULUM 2013 DI BENGKULU

Penelitian ini bertujuan untuk mengembangkan model manajemen berbasis sekolah yang lebih mengedepankan pelibatan partisipasi masyarakat dalam rangka implementtasi kurikulum 2013 di Bengkulu. Penelitian tahun-1 ditujukan untuk mendeskripsikan faktor ekonomi, sosial, dan budaya masyarakat yang potensial berkontribusi terhadap pelaksanaan program sekolah. Berdasarkan data ekonomi, sosial, dan budaya tersebut maka pada tahun ke-2 peneliti akan memberikan penguatan pelibatan partisipasi masyarakat guna memberikan dukungan terhadap implementasi program sekolah, mengajak masyarakat untuk mengidentifikasi apa yang dapat mereka sumbangkan untuk kepentingan pendidikan di sekolah, dan sekolah menemukan cara yang tepat untuk meningkatkan partisipasi masyarakat. Pendekatan yang digunakan dalam mencapai tujuan tersebut antara lain dengan jalan: (1) menetapkan sekolah yang relevan dengan masalah dan bersedia menjadi subjek penelitian; (2) mengidentifikasi faktor ekonomi, sosial dan budaya masyarakat yang berpeluang memberikan kontribusi dalam pelaksanaan program sekolah; dan (3) memberikan penguatan terhadap komite sekolah agar dapat meningkatkan partisipasi masyarakat guna mendukung implementasi kurikulum 2013. Luaran penelitian tahun-1 antara lain berupa: (1) tersusun instrumen identifikasi potensi sekolah dan faktor ekonomi, sosial, dan budaya masyarakat yang potensial memberikan kontribusi pada pelaksanaan program sekolah; (2) deskripsi potensi sekolah yang dapat digunakan sebagai media pelibatan partisipasi masyarakat; (3) deskripsi faktor ekonomi, sosial, dan budaya masyarakat yang potensial memberikan kontribusi pada pelaksanaan program sekolah; dan (4) tersusun standar prosedur pelibatan partisipasi masyarakat dalam implementasi program sekolah. Semua hasil tesebut disajikan dalam (A) Laporan Penelitian; (B) Poster; (C) Makalah Seminar Internasional; (D) Proposal Penelitian Tahun-2

Run-Off Replication of Host-Adaptability Genes Is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii

The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes

Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS–associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (DABD-GLU = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response–related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS–associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10−4). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS–related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10−4); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10−4) and BMI–adjusted waist-to-hip ratio (P = 2.4×10−4). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

tRNA Gene Structures in Bacteria

In bacteria, tRNA molecules are produced as precursors with additional nucleotides both upstream and downstream of the tRNA coding sequence. To generate a mature tRNA, the endoribonuclease RNase P removes the upstream sequence, while a number of enzymes can remove the downstream sequence. In this thesis, the influence of such upstream and downstream sequences on the expression of mature functional tRNA was studied. It was found that in Escherichia coli, the presence of an upstream sequence positively influences tRNA expression. Furthermore, it was shown that the identity of the nucleotide immediatedly 5' of the canonical RNase P cleavage site in a tRNA precursor influenced RNase P cleavage site selection in vivo in E. coli, but not in Pseudomonas aeruginosa. Additionally, a stem-loop in the precursor just downstream of the tRNA increased this "miscleavage". This stem-loop resembled a rho-independent transcription terminator and overlapped the trpT gene in P. aeruginosa, but it only marginally influenced the expression of the downstream secE gene. The trpT and secE genes were found to be cotranscribed. The trpT-secE gene order was also conserved in the majority of bacteria investigated. The expression of tRNA genes during development in Streptomyces coelicolor was also studied. Here, the expression of most tRNA genes tested increased with time during development. Similarly, the expression of the RNase P RNA increased. The relative increase was quantified and correlated with different criteria related to gene structure and gene organisation, but no significant differences could be found. Moreover, a tRNALeuCAA UUA codon suppressor as well as the cognate bldA tRNA could restore differentiation to a developmentally blocked bldA deletion strain. For both tRNAs, the efficiency of restoration depended on the 5'- and 3'-flanks. In conclusion, both 5'- and 3'-flanking sequences influence tRNA expression, and bacteria respond differently to changes in their tRNA gene structures

Comparative genome analysis of Mycobacteria focusing on tRNA and non-coding RNA

Background: The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. Results: We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. Conclusions; Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria

Characterization of three Mycobacterium spp. with potential use in bioremediation by genome sequencing and comparative genomics

We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense and M. obuense are 6.93, 5.95 and 5.58 Mbps with GC-contents of 68.4, 69.2 and 67.9%, respectively. Comparative genomic analysis revealed that 3254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named M. ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds, and copper homeostasis. These are the first non-pathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus

The Mycobacterium phlei Genome : Expectations and Surprises

Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for the IV, phlei CCUG21000(T) type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is approximate to 0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phiei RIVM; 2) genes involved in polyamine metabolism and transport (potAD, potT) that are absent in other mycobacteria, and 3) strain specific variations in the number of sigma-factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155