Termites in the woodwork

Termites eat and digest wood, but how do they do it? Combining advanced genomics and proteomics techniques, researchers have now shown that microbes found in the termites' hindguts possess just the right tools. Most animals, from insects to mammals, carry complex communities of microbes in their digestive tracts. In the case of wood-eating termites, these gut microbes are particularly important: they are thought to provide most of the capabilities needed for efficient digestion of wood, which is otherwise a largely inaccessible food source. They also help to compensate for the paucity of some nutrients in wood, for example by fixing atmospheric nitrogen, and they synthesize essential amino acids and other compounds for their hosts [1, 2]. Despite their importance, relatively little is known about gut microbes in termites. This is partly because gut microbes are often difficult to grow in pure culture (as is the case for most microbes sampled from natural environments). Furthermore, a single termite can harbor a very complex assemblage of hundreds of different microbial lineages, whose members may vary widely in terms of abundance and growth rates. Without access to cultivated strains, researchers have to rely on so-called 'cultivation-independent' molecular techniques to analyze such communities. A clever combination of these techniques has now been applied to a section of the termite hindgut, aiming to identify molecular tools used by the microbes in this compartment to degrade wood [3]. Here, we review the procedures and results of this study, and discuss insights into the biological system as well as implications for the generation of biofuels

STRING and STITCH: known and predicted interactions between proteins and chemicals

Information on protein-protein and protein-chemical interactions is essential for understanding cellular functions. The STRING and STITCH web resources integrate interaction evidence derived from pathways, automatic literature mining, primary experimental data, and genomic context. The resulting interaction networks cover 1.5 million proteins from 373 organisms and 68,000 chemicals

STRING 8—a global view on proteins and their functional interactions in 630 organisms

Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures. Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.or

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWA DI DALAM LEMBAGA PEMASYARAKATAN

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWADI LEMBAGA PEMASYARAKATAN Agusriadi Dahlan Ali Suhaimi ABSTRAKLembaga Pemasyarakatan sebelumnya disebut Penjara adalah tempat orang-orang yang melakukan kriminalitas dan pelanggaran hukum lainnya agar mereka dapat menyadari kesalahannya dan mempertanggungjawabkan apa yang telah mereka perbuat. Hukuman yang mereka terima sebagai balasan yang setimpal terhadap perbuatan mereka, meskipun nilai-nilai kemanusiaan beserta hak asasinya kurang diperhatikan. Lembaga Pemasyarakatan merupakan tempat yang stressfull atau menekan yang dapat berpengaruh terhadap fisik dan kejiwaan (psikologi) seseorang ditambah kecemasan yang berlebihan sehingga muncul depresi yang mengakibatkan seseorang melakukan bunuh diri. Akibat stress melahirkan depresi dan depresi biasanya akan terjadi kegoncangan kejiwaan yang luar biasa yang dapat mengakibatkan seseorang menjadi tidak waras (gila). Undang-Undang No.12/1995 tentang Lembaga Pemasyarakatan maupun Peraturan Pemerintah No. 99 Tahun 2012 tentang Perubahan Kedua Atas Peraturan Pemerintah Nomor 32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan tidak menjelaskan ketentuan terhadap narapidana yang gila di dalam lapas sebagaimana yang pernah terjadi di Lapas Kelas II-A Lambaro, Aceh Besar dan Rutan Klas I Tanjung Gusta, Medan. Selanjutnya yang bersangkutan dikirim ke Lapas Kelas Klass II-B Meulaboh tanggal 27 Januari 2014. Selama tujuh hari di Lapas Klass II-B Meulaboh Zabir bin Ilyas kemudian di titipkan di Rumah Sakit Jiwa Banda Aceh karena penyakitnya sudah mencapai stadium empat untuk mendapatkan perawatan dan penyembuhan kejiwaannya. Bagaimanakah pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan. Kemudian bagaimanakah kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan, dan bagaimana status hukum bagi narapidana yang sembuh dari gangguan kejiwaan. Penelitian dan pengkajian ini bertujuan untuk mengetahui pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lapas dan mengidentifikasi kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan serta mengetahui status hukum bagi narapidana yang sembuh dari gangguan kejiwaan.Metode yang digunakan adalah metode penelitian yuridis-normatif dengan menggunakan jenis penelitian deskriptis analisis dalam rangka untuk menemukan aturan hukum, prinsip-prinsip hukum, norma maupun doktrin-doktrin hukum dengan pendekatan undang-undang, kasus. Sumber data adalah data sekunder berupa bahan hukum primer, bahan hukum sekunder, dan bahan hukum tersier.Hasil penelitian menunjukkan bahwa Pengaturan tentang perawatan narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan di Indonesia belum diatur, baik dalam Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan maupun PP No. 99 Tahun 2012 tentang PP No. 99 Tahun 2012 tentang Perubahan Kedua Atas PP No.32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan. Namun bila narapidana sakit atau gangguan kesehatan lainnya yang tidak termasuk gangguan kejiwaan ada aturan tentang perawatan medis. Adapun mengenai narapidana yang mengalami gangguan kejiwaan di Lembaga Pemasyarakatan di Indonesia hingga kini belum ada kepastian hukum karena kasus seperti ini sangat langka terjadi di Indonesia. Pihak otoritas hanya menggunakan hak diskresi yang dimilikinya untuk menyelesaikan kasus tersebut sebagaimana terjadi di Lapas Porong Surabaya. Tetapi di Aceh kasus ini baru pertama kali terjadi yang dialami Zabir bin Ilyas pada tahun 2014. Pimpinan Lapas memutuskan memasukkan Zabir bin Ilyas ke Rumah Sakit Jiwa Banda Aceh. Terkait status hukum narapidana yang sembuh dari gangguan kejiwaan masih tetap sebagai tersangka (ditahan). Tidak ada keringanan hukuman apalagi sampai dibebaskan sebelum masa hukuman habis dijalankan. Hingga kini tidak ada satupun aturan yang mengatur baik secara implisit maupun ekplisit yang mengatur tentang narapidana yang sembuh dari penyakit kejiwaan (gila).Disarankan kepada Pemerintah agar merevisi Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan dan memasukkan salah satu pasal yang mengatur mengenai narapidana yang mengalami gangguan kejiwaan di dalam Lembaga Pemasyarakatan. Agar terwujudnya kepastian hukum di Indonesia mengenai narapidana yang mengalami gangguan kejiwaan dalam lebaga pemasyarakatan untuk membuat regulasi legal baik berupa undang-undang khusus atau melalui Peraturan Pemerintah. Kemudian disarankan agar narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan dapat dibebaskan dan dikembalikan ke keluarganya atau dimasukkan ke rumah sakit jiwa hingga sembuh.Kata Kunci : Pembinaan, Narapidana, Gangguan Jiwa, Lembaga Pemasyarakatan.Banda Ace

Termites in the woodwork

Metagenomic analysis of termite gut flora reveals a diversity of wood-degrading enzymes

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available

Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments

Microbial Co-occurrence Relationships in the Human Microbiome

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.National Institutes of Health (U.S.) (grant CA139193)Fonds Wetenschappelijk Onderzoek – VlaanderenJuvenile Diabetes Research Foundation InternationalNational Institutes of Health (U.S.) (grant NIH U54HG004969)Crohn's and Colitis Foundation of AmericaNational Science Foundation (U.S.) (NSF DBI-1053486)United States. Army Research Office (ARO W911NF-11-1-0473)National Institutes of Health (U.S.) (grant NIH 1R01HG005969

STRING 8--a global view on proteins and their functional interactions in 630 organisms

International audienceno abstrac

Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

海洋ウイルスの種組成と炭素の鉛直輸送の相関を確認 --ウイルスによる地球環境の制御を示唆. 京都大学プレスリリース. 2021-01-15.The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics