Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins

Phosphorylation is a major post‐translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase‐substrate pairs identified by the Kinase‐Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.     

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

Diatoms are one of the most successful groups of unicellular eukaryotic algae. Successive endosymbiotic events contributed to their flexible metabolism, making them competitive in variable aquatic habitats. Although the recently sequenced genomes of the model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana have provided the first insights into their metabolic organization, the current knowledge on diatom biochemistry remains fragmentary. By means of a genome‐wide approach, we developed DiatomCyc, a detailed pathway/genome database of P. tricornutum. DiatomCyc contains 286 pathways with 1719 metabolic reactions and 1613 assigned enzymes, spanning both the central and parts of the secondary metabolism of P. tricornutum. Central metabolic pathways, such as those of carbohydrates, amino acids and fatty acids, were covered. Furthermore, our understanding of the carbohydrate model in P. tricornutum was extended. In particular we highlight the discovery of a functional Entner–Doudoroff pathway, an ancient alternative for the glycolytic Embden–Meyerhof–Parnas pathway, and a putative phosphoketolase pathway, both uncommon in eukaryotes. DiatomCyc is accessible online ( http://www.diatomcyc.org ), and offers a range of software tools for the visualization and analysis of metabolic networks and ‘omics’ data. We anticipate that DiatomCyc will be key to gaining further understanding of diatom metabolism and, ultimately, will feed metabolic engineering strategies for the industrial valorization of diatoms.     

Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya,North East India reveals novel genes

Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.     

Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large‐scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.     

The power of data synthesis to shape the future of the restoration community and capacity

Restoration efforts will be taking place over the next decade(s) in the largest scope and capacity ever seen. Immense commitments, goals, and budgets are set, with impactful wide‐reaching potential benefits for people and the environment. These are ambitious aims for a relatively new branch of science and practice. It is time for restoration action to scale up, the legacy of which could impact over 350 million hectares targeted for the U.N. Decade on Ecosystem Restoration. However, restoration still proceeds on a case‐by‐case, trial by error basis and restoration outcomes can be variable even under similar conditions. The ability to put each case into context—what about it worked, what did not, and why—is something that the synthesis of data across studies can facilitate. The link between data synthesis and predictive capacity is strong. There are examples of extremely ambitious and successful efforts to compile data in structured, standardized databases which have led to valuable insights across regional and global scales in other branches of science. There is opportunity and challenge in compiling, standardizing, and synthesizing restoration monitoring data to inform the future of restoration practice and science. Through global collation of restoration data, knowledge gaps can be addressed and data synthesized to advance toward a more predictive science to inform more consistent success. The interdisciplinary potential of restoration ecology sits just over the horizon of this decade. Through truly collaborative synthesis across foci within the restoration community, we have the opportunity to rapidly reach that potential and achieve extraordinary outcomes together.     

Environmental Profile of Brazilian Green Coffee (6 pp)

Goal, Scope and Background

Brazil is the world's biggest producer of coffee beans with approx. a 30% market share. Depending on climate conditions, approx. 30 million bags of coffee beans are exported annually from Brazil, while domestic consumption is around 10 million bags, which makes Brazil the world's third largest coffee-consuming country. Therefore, the goal of this paper is to present the LCA of green coffee produced in Brazil for the reference crops 2001/02 and 2002/03 in order to generate detailed production inventory data as well as to identify the potential environmental impacts of its tillage in order to realize how to reduce those impacts and increase the environmental sustainability of this product. Only the inputs and outputs relative to the coffee tillage were considered. The production of fertilizers, correctives and pesticides were not included in the boundary, but only their amounts. The functional unit selected for this study was 1,000 kg of green coffee destined for exportation.

Methods

The LCI was performed according to the ISO 14040 standard series. All information considered in this study (use of water, fossil based energy, fertilizers and chemicals) were taken up in in-depth data collection and evaluation by questionnaires applied on a farm level and/or received by mail. Four Brazilian coffee producer regions were evaluated: Cerrado Mineiro, South of Minas Gerais State, the Marília and Alta Mogiana regions in São Paulo State. These regions have the following geographic coordinates: 44 to 50° W longitude and 18 to 24° S latitude. The data refer to a production of 420,000 coffee bean bags and a productive area of approx. 14,300 ha. The varieties of coffee beans considered in this study were Mundo Novo, Catuaí (yellow and red), Icatu (yellow and red), Catucaí (yellow and red) and Obatã. Farm specific data along with agricultural production data have been combined to elaborate a coffee cultivation inventory, which will be applied in an emissions estimation.

Results and Conclusion

The production of 1,000 kg of green coffee in Brazil requires approx. 11,400 kg of water, 94 kg of diesel, 270 kg of fertilizers as NPK, 900 kg of total fertilizers, 620 kg of correctives, 10 kg of pesticides and 0.05 hectare of annual land use. Outputs related to these functional units are approx. 3,000 kg of waste water from coffee washing, 8,500 kg of waste water from the wet method and 750 kg of organic residue that is reincorporated to the tillage as fertilizer. The publication of an LCI of agricultural products is a fundamental step for understanding the potential environmental impacts of each tillage and then establishes the basis for product sustainability. In this way, this work is the first Brazilian initiative for applying LCA to coffee cultivation.

Recommendation and Perspective

Different agricultural practices demonstrate different environmental profiles. The amount of agricultural pesticide is directly related to agricultural practices as tillage rotation, density of plants, etc. This study supplied important results for a better correlation of the agricultural practices and potential environmental impacts of coffee. Future updates of this study will show the evolution of the natural resource management such as land use, new agricultural practices, lower fertilizers and chemicals use.     

贵州省安顺市土地资源信息空间数据库的建立与应用

1　引　　言要制订不会危及环境的土地资源开发和保护计划 ,必须首先掌握可靠的、较新的有关土地资源的时空信息[3 ] .近年来 ,以ＧＩＳ和遥感技术为主的现代信息科学技术在土地覆盖/利用调查与填图[2 ,6] 、土地资源动态变化监测[13 ] 、土地质量退化与土壤侵蚀监测[5,8] 、土地资源评价[12 ] 与管理[10 ] 中得到了广泛应用 .这些技术可以较好地解决以往传统方法在获取、分析和处理大量、复杂土地信息中的众多限制 ,使我们得以动态地、综合地分析土地资源环境信息[4,7] .贵州省安顺市地处我国西南岩溶山区 ,生态环境脆弱 ,土地资源相对不足…     

Incidence and mortality of pancreatic cancer on a rapid rise in Taiwan, 1999–2012

BackgroundAccumulating data has revealed a rapidly rising incidence of pancreatic cancer in Western countries, but convincing evidence from the East remains sparse. We aimed to quantify how the incidence and mortality rates of pancreatic malignancy changed over time in Taiwan, and to develop future projection for the next decade.MethodsThis nationwide population-based study analyzed the Taiwan National Cancer Registry and the National Cause of Death Registry to calculate the annual incidence and mortality rates of pancreatic malignancy from 1999 to 2012 in this country. The secular trend of the incidence was also examined by data from the National Health Insurance Research Database.ResultsA total of 21,986 incident cases of pancreatic cancer and 20,720 related deaths occurred during the study period. The age-standardized incidence rate increased from 3.7 per 100,000 in 1999 to 5.0 per 100,000 in 2012, with a significant rising trend (P < 0.01). The increase was nationwide, consistently across subgroups stratified by age, gender, geographic region, and urbanization. Data from the National Health Insurance Research Database corroborated the rise of incident pancreatic cancer. Mortality also increased with time, with the age-standardized rate rising from 3.5 per 100,000 in 1999 to 4.1 per 100,000 in 2012 (P < 0.01). In accordance with the incidence, the mortality trend was consistent in all subgroups. Both the incidence and mortality were projected to further increase by approximately 20% from 2012 to 2027.ConclusionThe incidence and mortality of pancreatic cancer have been rapidly rising and presumably will continue to rise in Taiwan.     

细菌sRNA数据库

细菌sRNA是一类长度在50～500 nt的调控小RNA（small regulatory RNA）,主要通过与靶标mRNA或靶标蛋白质结合发挥多种生物学功能。目前,随着生物信息学与高通量测序的应用,发现了越来越多的细菌sRNA,开发了多个相关数据库。为了sRNA工作者系统了解与应用这些数据,本文拟对包含细菌sRNA的综合数据库和细菌sRNA专业数据库作一概述,并对sRNA数据库的未来发展进行展望。