meta-PPISP: a meta web server for protein-protein interaction site prediction

A number of complementary methods have been developed for predicting protein-protein interaction sites. We sought to increase prediction robustness and accuracy by combining results from different predictors, and report here a meta web server, meta-PPISP, that is built on three individual web servers: cons-PPISP (http://pipe.scs.fsu.edu/ppisp.html), Promate (http://bioportal.weizmann.ac.il/promate), and PINUP (http://sparks.informatics.iupui.edu/PINUP/). A linear regression method, using the raw scores of the three servers as input, was trained on a set of 35 nonhomologous proteins. Cross validation showed that meta-PPISP outperforms all the three individual servers. At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets. AVAILABILITY: meta-PPISP can be accessed at http://pipe.scs.fsu.edu/meta-ppisp.html     

Determination of natural moisturizing factors in the skin: Raman microspectroscopy versus HPLC

Background: Natural moisturizing factor (NMF) is used as genotypic and phenotypic biomarker in diagnostics. This study is a side-to-side comparison of two different methods to determine NMF in atopic dermatitis patients: Raman microspectroscopy and stratum corneum tape stripping followed by HPLC.

Results: Measured NMF values were significantly correlated (R²?=?.61; p?<?.0001), both methods demonstrated a concentration-depth dependence of NMF and reduced NMF levels in the carriers of filaggrin null mutations. Good agreement between measurements of left and right arms indicated robustness and good reproducibility of both methods.

Conclusions: Both methods showed comparable performance, choice of method will rather be influenced by practical consideration.     

Ecology of Microbial Saprophytes and Pathogens in Tissue Culture and Field-Grown Plants: Reasons for Contamination Problems In Vitro

This review compares published surveys of microbial populations in plant tissue and cell cultures with the microbial saprophytes and pathogens found on field grown plants and microbial populations in the laboratory environment. From this comparison and the measured reduction in contamination after improvements in working practices in the laboratory, conclusions can be drawn about the importance of the explant and the laboratory as sources of contamination.

Mechanisms of pathogenicity in vitro are described to explain why bacteria, fungi, and yeasts that are not pathogenic to plants in the field become pathogens in plant tissue cultures. Conversely, plant metabolism and its effect on the tissue culture environment are described to explain why prokaryotes, viruses, and viroids that cause disease in the field can stay latent in vitro.

Detection methods for latent contaminants in plant tissue cultures are summarized, and the strategies and methods for prevention or treatment of contamination are discussed.     

Epidermal growth factor,growth differentiation factor-15, and survivin as novel biocompatibility markers in children on chronic dialysis

Context: Chronic dialysis results in aggravation of apoptosis and cell damage, triggered by bioincompatibility of dialysis membranes and peritoneal fluids.

Objective: The aim of study was to assess the usefulness of epidermal growth factor (EGF), growth differentiation factor (GDF)-15, and survivin as novel markers of biocompatibility in dialyzed children.

Materials and methods: Parameters were assessed by ELISA in 19 patients on hemodialysis and 22 children on peritoneal dialysis.

Results: Serum concentrations of analyzed parameters in children on chronic dialysis differed significantly from controls and depended strongly on the dialysis technique.

Conclusions: EGF, GDF-15, and survivin may serve as new biocompatibility markers in children on chronic dialysis.     

Global profiling of protein complexes: current approaches and their perspective in biomedical research

Introduction: Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes – an important aspect of their function – has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research.

Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated.

Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.     

Assessing prey provisioned to Common Buzzard Buteo buteo chicks: a comparison of methods

Capsule: Methods of assessing raptor diet carry significant inherent biases which can vary over time.

Aims: To compare methods of assessing Common Buzzard Buteo buteo diet composition and assess how any differences vary between years.

Methods: Diet was assessed at 32 Common Buzzard nests on an area of upland heather moorland in Britain, managed for Red Grouse Lagopus lagopus scotica, over three years. Data obtained from nest cameras were compared with data from prey remains and regurgitated pellets.

Results: Diet composition differed between methods in all years. Methodological differences varied between years in relation to an almost twelve-fold change in Field Vole abundance, a key prey of Common Buzzards, while abundances of alternative prey changed little. Small mammals were underestimated by prey remains in all three years, while herpetofauna were underestimated by prey remains and pellets in two years. Large birds were overestimated by prey remains, significantly so in one year. Pellets overestimated invertebrates in all years. By combining prey remains and pellets, significant yearly variations in biases were eliminated, although the combined measure overestimated large birds and invertebrates.

Conclusion: Our results suggest that future studies should consider not only how chosen methods may affect results, but also how effects can differ between years.     

Circulating microparticles in cardiovascular disease: going on stage!

Context: Cardiovascular diseases (CVDs) are the leading cause of death worldwide. In spite of the fact that treatments are based on risk calculators which in turn are based on population characteristics, it is well known that these methods have definite levels of uncertainty. Recently, more precise diagnostic or predictive methods have been developed based on indicators of vascular and/or cardiac damage in order to supplement this risk evaluation.

Objective: In this review, we describe the main discoveries leading to the idea of using circulating microparticles as a promising and complementary tool in the evaluation of cardiovascular risk.

Methods: A Medline search for the terms cardiovascular diseases, microparticles, miRNAs, diagnosis, prognosis, biomarkers and microvesicles was performed.

Results: We found (i) nine articles, which were relevant to forming the idea of using microparticles as biomarkers in CVDs, and (ii) 15 and 12 experimental clinical studies which describe their potential in primary and secondary CVD prevention, respectively.

Conclusions: The levels of circulating microparticles have been associated with cardiovascular damage in asymptomatic patients as well as in patients who suffered a cardiovascular event, becoming promising diagnostics or prediction biomarkers in recent years.     

Mineral and Carbohydrate Nutrition of Plant Cell and Tissue Cultures

Recent advances in our understanding of the mineral (and carbohydrate) nutrition of cultured plant cells and tissues are reviewed. The methods used for empirical selection of nutrient composition of culture media for different plant genera/species and types of culture are critically evaluated.

The acquisition of nutrients is discussed in terms of their physical availability in the culture medium and uptake from the medium. The effect on uptake of factors such as pH and water potential and the relationship with growth rates and medium depletion are examined in detail.

Finally, some effects of nutrients on morphogenesis of plants are reviewed.     

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota

Introduction: Describing the human hut gut microbiota is one the most exciting challenges of the 21^st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions.

Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species.

Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.     

Fungal silver nanoparticles: synthesis,application and challenges

Purpose: This paper aims to summarize recent developments regarding the synthesis, application and challenges of fungal AgNPs. Possible methods to overcome the challenge of synthesis and reduce the toxicity of AgNPs have been discussed.

Materials and methods: This review consults and summary a large number of papers.

Results: Silver nanoparticles (AgNPs) have great potential in many areas, as they possess multiple novel characteristics. Conventional methods for AgNPs biosynthesis involve chemical agents, causing environmental toxicity and high energy consumption. Fungal bioconversion is a simple, low-cost and energy-efficient biological method, which could successfully be used for AgNPs synthesis. Fungi can produce enzymes that act as both reducing and capping agents, to form stable and shape-controlled AgNPs.

Conclusions: AgNPs have great potential in the medical and food industries, due to their antimicrobial, anticancer, anti-HIV, and catalytic activities. However, the observed in vitro and in vivo toxicity poses considerable challenges in the synthesis and application of AgNPs.     

Nestin is highly expressed in foetal spinal cord isolated from placenta previa patients and promotes inflammation by enhancing NF-κB activity

Purpose: Nestin is expressed in various tissues of the embryo in patients with placenta previa, while the regulatory mechanism still unknown.

Materials and methods: All participants terminated pregnancy. Among them, 75 patients with placenta previa were assigned to the case group and 80 healthy pregnant women with normal placenta were assigned to the control group. Expression of nestin and CDK5 in foetal spinal cord tissues was detected by Western blot and quantitative real-time RT-PCR methods. The enzyme-linked immunosorbent assay (ELISA) was used to determine the serum expression of some pro-inflammatory cytokines in placenta previa patients. The interaction between nestin and CDK5 was evaluated by immunoprecipitation and siRNA inhibition of nestin was performed to estimate its effect on NF-κB activity in foetal spinal cord tissues.

Results: Along with increased expression of nestin and CDK5 in foetal spinal cord tissues in the case group, IL-1β, IL-6, TNF-α and IFN-γ were increased in the serum of placenta previa patients. siRNA inhibition analysis indicated that nestin interacted with CDK5 and regulated NF-κB activity in foetal spinal cord tissues.

Conclusions: Nestin is highly expressed and the interaction between nestin and CDK5 might lead to the progress of placenta previa through its regulation on NF-κB.     

The status of the Ring Ouzel Turdus torquatus in the UK in 2012

Capsule: There were up to 6348 Ring Ouzel territories in the UK in 2012.

Aims: To produce estimates of the size of the Ring Ouzel breeding population in the UK and its constituent countries.

Methods: A stratified random selection of tetrads was surveyed within the known breeding range, except for the remaining breeding areas on Dartmoor and historical sites elsewhere, which were surveyed in their entirety. The methods followed those devised for the first UK-wide survey in 1999, using playback of song at specific points along tetrad transect lines.

Results: The UK population estimate in 2012 was 5332 (95% confidence limits (CL), 4096–6875) territories, a non-significant decline of 29% since 1999. There were no significant differences in the population changes in England, Scotland and Wales between the two surveys. An estimation of survey efficiency found that 84% of territories were located by the national survey methods, suggesting that the UK population in 2012 could have been as many as 6348 (95% CL, 4825–8198) territories.

Conclusion: The results suggest that the UK Ring Ouzel population has continued to decline since 1999. Ongoing and future research should determine where the main threats to the population are: on the breeding or wintering grounds, or during migration.     

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis

Introduction: The study of microbial communities based on the combined analysis of genomic and proteomic data – called metaproteogenomics – has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment.

Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications.

Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.     

Mass spectrometric analysis of glycosylated viral proteins

Introduction: Viral diseases contribute much to human and animal suffering and enormous efforts are directed at developing appropriate vaccines for protection. Glycoproteins constitute much of the viral surfaces and are obvious targets for such vaccine development. This review describes mass spectrometric methods used for the structural determination of these compounds.

Areas covered: The review describes the structures of the N- and O-linked glycans found on glycoproteins and mass spectrometric methods for their ionization and fragmentation. The steps, such as determination of glycan attachment sites and the structures of the attached glycans following their release from the glycoproteins are described and examples are given of the uses of the various analytical methods using mainly influenza, Ebola and HIV as representative examples. Also included are tables listing work on many other viruses.

Expert commentary: Recent technological advances, such as the introduction of ion mobility techniques, have greatly improved analyses in this area and have enabled larger amounts of information to be gathered in shorter time periods on ever smaller amounts of material. Such techniques should greatly accelerate the discovery of vaccine targets and lead to the production of vaccines for diseases not currently available.     

Proteogenomics in the context of the Human Proteome Project (HPP)

Introduction: The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue.

Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference.

Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.     

Sex hormone-binding globulin and thrombin generation in women using hormonal contraception

Objectives: We investigated the impact of serum sex hormone-binding globulin (SHBG) on thrombin generation (TG) in women according to hormonal contraception.

Patients and methods: A cross-sectional study of SHBG and TG measured via calibrated automated thrombography was conducted in 150 healthy women, including 75 users of combined oral contraceptives (COC), 22 users of progestin-only contraceptives (POC) and 53 nonusers.

Results: COC but not POC-users had significantly higher SHBG levels compared with nonusers. In hormonal contraceptive users, SHBG was positively associated with both activated protein C (APC) resistance and baseline TG, and protein S and prothrombin were important mediators.

Conclusion: These data provide further evidence that SHBG may be used as a biomarker in assessing prothrombotic profile of hormonal contraception.     

Clinical translation of MS-based,quantitative plasma proteomics: status,challenges, requirements,and potential

Introduction: Aided by the advent of advanced mass spectrometry (MS)-based technologies and methodologies, quantitative proteomics has emerged as a viable technique to capture meaningful data for candidate biomarker evaluation. To aid clinical translation, these methods generally utilize a bottom-up strategy with isotopically labeled standards and a targeted form of MS measurement.

Areas covered: This article reviews the status, challenges, requirements, and potential of translating current, MS-based methods to the clinical laboratory. The described methods are discussed and contrasted within a fit-for-purpose approach, while different resources for quality control, quantitative analysis, and data interpretation are additionally provided.

Expert commentary: Although great strides have been made over the past five years in developing reliable quantitative assays for plasma protein biomarkers, it is crucial for investigators to have an understanding of the clinical validation process, a major roadblock in translational research. Continued progress in method design and validation of protein assays is necessary to ultimately achieve widespread adoption and regulatory approval.     

Mutation in the beta3 subunit of Guanine nucleotide-binding protein (GNB3) gene is not associated with Type II diabetes mellitus risk: a case–control study of a North Indian population

Context: Genetics play a major role in development and pathophysiology of Type 2 diabetes mellitus (T2DM).

Objective: To asses the association of Guanine nucleotide-binding protein (GNB3) (C825T) gene's polymorphism with T2DM.

Materials and methods: A case–control study including 400 North Indians was performed using Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR-RFLP) approach to analyze genetic polymorphism.

Results: No significant difference was observed in genotype and allele frequencies of GNB3 gene on comparing cases with controls.

Discussion: Our study is in agreement with studies on Polish, Japanese, Hispanic-American and Danish populations who observed no significant association between GNB3 (C825T) polymorphism and T2DM.

Conclusion: GNB3 (C825T) polymorphism is not associated with T2DM.     

Post-mortem interval estimative through determination of catalase and Δ-aminolevulinate dehydratase activities in hepatic,renal, skeletal muscle and cerebral tissues of Swiss mice

Purpose: Determining the post-mortem interval (PMI) is one of the challenging tasks in forensic science due to the lack of quick and inexpensive methods. Our objective is to develop innovative and alternative means for PMI evaluation.

Methods: The relationship between PMI and enzymatic modifications in mice tissues was described. After being sacrificed, Swiss mice were randomly divided into groups according to the time elapsed since death. The activities of catalase (CAT) and δ-aminolevulinate dehydratase (δ-ALA-D) were determined in hepatic, renal, skeletal muscle and cerebral tissues.

Results: CAT activity increased in kidney and brain 6?h after death and this increase remained for up to 24?h in the brain and 48?h in the kidney. δ-ALA-D had its activity decreased in the liver and kidneys in 6?h. In the skeletal muscle, δ-ALA-D activity was reduced only 48?h after death. Conversely, an increase on δ-ALA-D activity was observed in the brain at 6?h, followed by its decrease at 24 and 48?h.

Conclusion: With the association of this set of results, it is possible to provide an estimate of PMI. Additionally, these results can be used as an auxiliary parameter associated with other methods to estimate PMI.