FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high-throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater –omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG-RAST repositories) covering all sequence-based -omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta-analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).     

Obesity--a risk factor for diabetic retinopathy in type 2 diabetes?

The aim of the study was to investigate whether obesity, independently or associated with other risk factors, increases the risk for the diabetic retinopathy in type 2 diabetic persons. Data of 156 diabetic persons that have consecutively attended the Outpatient Department in the Vuk Vrhovac Institute in Zagreb during two months period were studied. According to their body mass index (BMI) they were divided into three groups: group 1 (BMI < or = 25; n = 49), group 2 (BMI 26-29.9; n = 52) and group 3 (BMI > or = 30; n = 55). The three groups did not differ in age, duration of diabetes, treatment, cholesterol, HDL-cholesterol and triglycerides. With increase in BMI, we observed a significant deterioration of HbA1c and a significant increase in LDL-cholesterol, systolic and diastolic blood pressure. Statistical analyses shown that the prevalence of retinopathy increased significantly with higher body weight (gr. 1: 40.8%, gr. 2: 63.4%, gr. 3: 63.6%;p < 0.05), but also with correlation to quality of metabolic control (HbA1c) and systolic blood pressure. Therefore, obesity may be, because of its significant correlation to quality of metabolic control (HbA1c) and systolic blood pressure, considered as risk factor for diabetic retinopathy in type 2 diabetic persons.     

COPASAAR – A database for proteomic analysis of single amino acid repeats

Background  

Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat is responsible for causing the disease. The COPASAAR database is a new tool to facilitate the rapid analysis of single amino acid repeats at a proteome level. The database aims to simplify the comparison of repeat distributions between proteomes in order to provide a better understanding of their function and evolution.     

1H-NMR-based metabolomics for cancer targeting and metabolic engineering –A review

Nuclear magnetic resonance (NMR) spectroscopy acts as the best tool that can be used in tissue engineering scaffolds to investigate unknown metabolites. Moreover, metabolomics is a systems approach for examining in vivo and in vitro metabolic profiles, which promises to provide data on cancer metabolic alterations. However, metabolomic profiling allows for the activity of small molecules and metabolic alterations to be measured. Furthermore, metabolic profiling also provides high-spectral resolution, which can then be linked to potential metabolic relationships. An altered metabolism is a hallmark of cancer that can control many malignant properties to drive tumorigenesis. Metabolite targeting and metabolic engineering contribute to carcinogenesis by proliferation, and metabolic differentiation. The resulting the metabolic differences are examined with traditional chemometric methods such as principal component analysis (PCA), and partial least squares-discriminate analysis (PLS-DA). In this review, we examine NMR-based activity metabolomic platforms that can be used to analyze various fluxomics and for multivariant statistical analysis in cancer. We also aim to provide the reader with a basic understanding of NMR spectroscopy, cancer metabolomics, target profiling, chemometrics, and multifunctional tools for metabolomics discrimination, with a focus on metabolic phenotypic diversity for cancer therapeutics.     

A barcode of life database for the Cephalopoda? Considerations and concerns

The concept of a Barcode of Life Database (BoLD) for the Class Cephalopoda (Phylum Mollusca) was introduced at the Cephalopod International Advisory Council (CIAC) symposium in Hobart, Australia, February 2006. This suggestion was met with significant interest, concern and debate. This review attempts to describe the concept of the BoLD initiative and to outline considerations and concerns specific to a cephalopod BoLD. Jan M. Strugnell and Annie R. Lindgren contributed equally to this work.     

BIOPOP — A database of plant traits and internet application for nature conservation

In scientific literature there is a wealth of information about the ecological and life-history traits of plant species. This information would be very valuable for a functional analysis of the response of species and communities to environmental changes and subsequent vulnerability/viability analysis or predictive modelling. However, the information is scattered in a multiple of different sources. Researchers often are discouraged from searching all available information. We are compiling a database of plant traits of the flora of Germany. Our aim is to create a comprehensive, well documented database to be made freely accessible within FLORAWEB, an Internet portal of the German Federal Agency for Nature Conservation (BfN). An interactive user-interface will enable the data to be readily used for extracting biological risk factors and for decision-making in nature conservation.     

Extracellular Vesicles: A Prevalent Tool for Microbial Gene Delivery?

Genetic plasticity of prokaryotic microbial communities is largely dependent on the ongoing exchange of genetic determinants by Horizontal Gene Transfer (HGT). HGT events allow beneficial genetic transitions to occur throughout microbial life, thus promoting adaptation to changing environmental conditions. Here, the significance of secreted vesicles in mediating HGT between microorganisms is discussed, while focusing on the benefits gained by vesicle‐mediated gene delivery and its occurrence under different environmental cues. The potential use of secreted DNA‐harboring vesicles as a mechanism of currently unresolved HGT events in eukaryotic microbes is further discussed.     

Interleukin-1β and mitochondria damage, and the development of diabetic retinopathy

Mitochondrial dysfunction is considered to play an important role in the development of diabetic retinopathy. Recent evidence has also shown many similarities between diabetic retinopathy and a low grade chronic inflammatory disease. The aim of this study is to understand the interrelationship between proinflammtory mediator, IL-1β and mitochondrial dysfunction in the accelerated loss of capillary cells in the retina. Using IL-1β receptor gene knockout (IL-1R1^?/^?) diabetic mice, we have investigated the effect of regulation of IL-1β on mitochondrial dysfunction and mtDNA damage, and increased retinal capillary cell apoptosis and the development of retinopathy. Retinal mitochondrial dysfunction and mtDNA damage were significantly ameliorated in IL-1R1^?/^? mice, diabetic for ~10 months, compared to the wild-type diabetic mice. This was accompanied by protection of accelerated capillary cell apoptosis and the development of acellular capillaries, histopathology associated with diabetic retinopathy. Thus, mitochondrial damage could be one of the key events via which increased inflammation contributes to the activation of the apoptotic machinery resulting in the development of diabetic retinopathy, and the possible mechanism via which inflammation contributes to the development of diabetic retinopathy includes continuous fueling of the vicious cycle of mitochondrial damage, which could be disrupted by inhibitors of inflammatory mediators.     

Modulation of IL-1β and VEGF expression in rat diabetic retinopathy after PACAP administration

Diabetic retinopathy (DR) is a microvascular complication of diabetes. Hyperglycemic/hypoxic microenvironment concurs to aberrant angiogenesis characterizing the pathology and activates many downstream target genes including inflammatory cytokines and vasoactive peptides, such as interleukin-1β (IL-1β) and vascular endothelial growth factor (VEGF).It has been largely demonstrated that pituitary adenylate cyclase-activating peptide (PACAP) plays a protective effect in DR. In the present study, we investigated the role of PACAP to protect retinal tissue through IL-1β and VEGF expression. Diabetes was induced in rats by streptozotocin (STZ) injection, and one week later a single intravitreal injection of 100 μM PACAP was administrated. Analyses of IL-1β and VEGF levels were performed three weeks after diabetes induction.The results demonstrated that a single intraocular administration of PACAP significantly reduced the expression of IL-1β in diabetic animals. Moreover, it affects VEGF and its receptors (VEGFRs) levels and interferes with their retinal layers distribution as showed by confocal microscopy analysis. In particular, PACAP treatment downregulates VEGF and VEGFRs that are increasingly expressed in STZ-treated animals as compared to controls. These results indicate that PACAP plays an important role to attenuate the early phase of DR.     

CHLPEP—A database of chloroplast transit peptides

Transit peptides are N-terminal extensions that serve to route nuclearencoded proteins into chloroplasts. We have collected amino acid sequences for approximately 260 transit peptides, and have constructed a database that presently runs under FileMaker Plus on Macintosh personal computers. In addition, the collection is available as an ASCII-file, either in a tab-delimited format suitable for import into other database programs, or in a format with line-identifiers similar to the widely used Swiss Prot database. We hope that the plant molecular biology community will help us ensure that the collection is kept up to date by submitting new sequences directly to us.     

PRD: A protein�CRNA interaction database

Although protein–RNA interactions (PRIs) are involved in various important cellular processes, compiled data on PRIs are still limited. This contrasts with protein–protein interactions, which have been intensively recorded in public databases and subjected to network level analysis. Here, we introduce PRD, an online database of PRIs, dispersed across several sources, including scientific literature. Currently, over 10,000 interactions have been stored in PRD using PSI-MI 2.5, which is a standard model for describing detailed molecular interactions, with an emphasis on gene level data. Users can browse all recorded interactions and execute flexible keyword searches against the database via a web interface. Our database is not only a reference of PRIs, but will also be a valuable resource for studying characteristics of PRI networks.

Availability

PRD can be freely accessed at http://pri.hgc.jp/     

A Novel Role for Tm7sf2 Gene in Regulating TNFα Expression

We have explored the role of Tm7sf2 gene, which codifies for 3β-hydroxysterol Δ14-reductase, an endoplasmic reticulum resident protein, in the sensitivity to endoplasmic reticulum stress and in the resulting inflammatory response. We used mouse embryonic fibroblasts, derived from Tm7sf2^+/+ and Tm7sf2^−/− mice, to determine the in vitro effects of thapsigargin on NF-κB activation. Our results show that the Tm7sf2 gene controls the launch of the unfolded protein response and presides an anti-inflammatory loop thus its absence correlates with NF-κB activation and TNFα up-regulation. Our data also show that Tm7sf2 gene regulates liver X receptor activation and its absence inhibits LXR signalling. By expressing the hTm7sf2 gene in KO MEFs and observing a reduced NF-κB activation, we have confirmed that Tm7sf2 gene is linked to NF-κB activation. Finally we used genetically modified mice in an in vivo model of ER stress and of inflammation. Our results show a significant increase in renal TNFα expression after tunicamycin exposure and in the oedematogenic response in Tm7sf2^−/− mice. In conclusion, we have shown that the Tm7sf2 gene, to date involved only in cholesterol biosynthesis, also controls an anti-inflammatory loop thereby confirming the existence of cross talk between metabolic pathways and inflammatory response.     

EDAS—A database of alternatively spliced human genes

EDAS, an alternatively spliced human gene database, contains data on alignment of proteins, mRNAs, and ESTs. For 8324 human genes, the database contains information on all observed exons and introns and also elementary alternatives formed therefrom. The database allows one to filter the output data by varying the cutoff threshold according to the significance level. The database is available at http://www.genebee.msu.ru/edas/.