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Background: Neuromyelitis optica is a relapsing–remitting disease characterized by a recurrent attack of optic neuritis and transverse myelitis; sometimes associated with acute brainstem syndrome. Systemic lupus erythematosus is an autoimmune multisystem disorder in which ocular involvement such as acute ischemic optic neuropathy is a rare manifestation. However, neuromyelitis optica can be associated with systemic lupus erythematosus. Case presentation: A 24-year-old Bangladeshi woman was admitted to the hospital with complaints of sudden, progressive, painless vision loss in both eyes, and progressive weakness in both lower limbs for 48 hours. She also gave a history of arthralgia, a photosensitive skin rash, intermittent fever, oral ulcerations, and alopecia for the last 2 months. On examination, the fundus was suggestive of bilateral acute ischemic neuropathy, and examinations of the lower limb revealed spastic paraparesis with sensory abnormality. Laboratory investigations revealed the presence of positive anti-aquaporin 4 antibody, strongly positive antinuclear antibody, and anti-ds DNA with the longitudinally extensive lesion on magnetic resonance imaging of the spinal cord. She was treated with methylprednisolone, hydroxychloroquine, and mycophenolate, and was discharged with improvement of her paraparesis. However, her vision did not improve substantially. Conclusion: The importance of this report is to shed some light on the occurrence of two devastating complications that is, bilateral acute ischemic optic neuropathy in systemic lupus erythematosus complicated by neuromyelitis optica, as well as evidence of rare presentations for systemic lupus erythematosus and treatment modalities of ischemic optic neuropathy with systemic lupus erythematosus. [ABSTRACT FROM AUTHOR]

Paediatric pneumonia is a respiratory infection that affects infants and young children under the age of 3. This disease is the leading cause of infant and child mortality in developing countries because of the weak immune system of young children. The difficulty and length of time required to identify the pathogen and causative agent are the main reasons for this high mortality rate. In addition, the identification of certain causative agents is particularly important for the treatment of paediatric pneumonia. In this study, we explored the possible mechanisms by which pathogenic Enterococcus faecalis induced pneumonia in vivo. The potential virulence factors of bacteria isolated from the intestines of paediatric pneumonia patients were determined. Taken together, the results suggested that lysophosphatidic acid (LTA) from pathogenic E. faecalis decreases the expression of platelet-activating factor receptor (PAFR), which in turn disrupts the function of intestinal tight junctions (Occ and Ccldn1), leading to the entry of LE-LTA into the bloodstream because of the disruption of the intestinal barrier. Although LTA can enter circulation, it cannot directly infiltrate the lungs, which indicates that lung inflammation in mice is not caused by the direct entry of LE-LTA into the lungs. We further found that LTA activates immune cells, such as CD8 + T cells and type 2 innate lymphocytes, in vivo. Interleukin-6 and interleukin-17 can produce large amounts of inflammatory factors and thus promote the development of pneumonia. In conclusion, our findings demonstrate that the LTA of pathogenic E. faecalis in the intestine is a virulence factor that can cause paediatric pneumonia. This study found that intestinal bacterial virulence factors can induce immune responses in the lungs and blood. These findings could provide further insight into the mechanism of infectious diseases in the lung that are caused by bacteria in the intestine. [ABSTRACT FROM AUTHOR]

Background: The sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome. Methods: All reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon's entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database. Results: A total of 2321 nonamers met the HCSS selection criteria of entropy < 0.25 and MI > 0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity. Conclusion: This work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens. [ABSTRACT FROM AUTHOR]

Background: Ebolavirus (EBOV) is responsible for one of the most fatal diseases encountered by mankind. Cellular T-cell responses have been implicated to be important in providing protection against the virus. Antigenic variation can result in viral escape from immune recognition. Mapping targets of immune responses among the sequence of viral proteins is, thus, an important first step towards understanding the immune responses to viral variants and can aid in the identification of vaccine targets. Herein, we performed a large-scale, proteome-wide mapping and diversity analyses of putative HLA supertype-restricted T-cell epitopes of Zaire ebolavirus (ZEBOV), the most pathogenic species among the EBOV family. Methods: All publicly available ZEBOV sequences (14,098) for each of the nine viral proteins were retrieved, removed of irrelevant and duplicate sequences, and aligned. The overall proteome diversity of the non-redundant sequences was studied by use of Shannon's entropy. The sequences were predicted, by use of the NetCTLpan server, for HLA-A2, -A3, and -B7 supertype-restricted epitopes, which are relevant to African and other ethnicities and provide for large (~86%) population coverage. The predicted epitopes were mapped to the alignment of each protein for analyses of antigenic sequence diversity and relevance to structure and function. The putative epitopes were validated by comparison with experimentally confirmed epitopes. Results & discussion: ZEBOV proteome was generally conserved, with an average entropy of 0.16. The 185 HLA supertype-restricted T-cell epitopes predicted (82 (A2), 37 (A3) and 66 (B7)) mapped to 125 alignment positions and covered ~24% of the proteome length. Many of the epitopes showed a propensity to co-localize at select positions of the alignment. Thirty (30) of the mapped positions were completely conserved and may be attractive for vaccine design. The remaining (95) positions had one or more epitopes, with or without non-epitope variants. A significant number (24) of the putative epitopes matched reported experimentally validated HLA ligands/T-cell epitopes of A2, A3 and/or B7 supertype representative allele restrictions. The epitopes generally corresponded to functional motifs/domains and there was no correlation to localization on the protein 3D structure. These data and the epitope map provide important insights into the interaction between EBOV and the host immune system. [ABSTRACT FROM AUTHOR]

Background: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. Results: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Ourmethodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis. Conclusion: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via the original article. [ABSTRACT FROM AUTHOR]

Background: Plasmodium vivax is one of the widespread human malarial parasites accounting for 75% of malaria epidemics. However, there is no baseline information about the status and nature of genetic variation of Plasmodium species circulating in various parts of Pakistan. The present study was aimed at observing the molecular epidemiology and genetic variation of Plasmodium vivax by analysing its merozoite surface protein-3α (msp-3α) and merozoite surface protein-3β (msp-3β) genes, by using suballele, species-specific, combined nested PCR/RFLP detection techniques. Methods: A total of 230 blood samples from suspected subjects tested slide positive for vivax malaria were collected from Punjab, Sindh, Khyber Pakhtunkhwa, and Balochistan during the period May 2012 to December 2013. Combined nested PCR/RFLP technique was conducted using Pvmsp-3α and Pvmsp-3β genetic markers to detect extent of genetic variation in clinical isolates of P. vivax in the studied areas of Pakistan. Results: By PCR, P. vivax, 202/230 (87.82%), was found to be widely distributed in the studied areas. PCR/RFLP analysis showed a high range of allelic variations for both msp-3α and msp-3β genetic markers of P. vivax, i.e., 21 alleles for msp-3α and 19 for msp-3β. Statistically a significant difference (p ≤ 0.05) was observed in the genetic diversity of the suballelic variants of msp-3α and msp-3β genes of P. vivax. Conclusion: It is concluded that P. vivax populations are highly polymorphic and diverse allelic variants of Pvmsp-3α and Pvmsp-3β are present in Pakistan. [ABSTRACT FROM AUTHOR]

Background: The rapid advancement of computer and information technology in recent years has resulted in the rise of e-learning technologies to enhance and complement traditional classroom teaching in many fields, including bioinformatics. This paper records the experience of implementing e-learning technology to support problem-based learning (PBL) in the teaching of two undergraduate bioinformatics classes in the National University of Singapore. Results: Survey results further established the efficiency and suitability of e-learning tools to supplement problem-based learning (PBL) in bioinformatics education. 63.16% of year three bioinformatics students showed a positive response regarding the usefulness of the Learning Activity Management System (LAMS) e-learning tool in guiding the learning and discussion process involved in problem-based learning and in enhancing the learning experience by breaking down PBL activities into a sequential workflow. On the other hand, 89.81% of year two bioinformatics students indicated that their revision process was positively impacted with the usage of LAMS for guiding the learning process, while 60.19% agreed that the breakdown of activities into a sequential step-by-step workflow by LAMS enhances the learning experience. Conclusion: We show that e-learning tools are useful for supplementing PBL in bioinformatics education. The results suggest that it is feasible to develop and adopt e-learning tools to supplement a variety of instructional strategies in the future. [ABSTRACT FROM AUTHOR]

Background: T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunological hotspots, has been observed in several antigens. These clusters may be exploited to facilitate the development of epitope-based vaccines by selecting a small number of hotspots that can elicit all of the required T-cell activation functions. Given the large size of pathogen proteomes, including of variant strains, computational tools are necessary for automated screening and selection of immunological hotspots. Results: Hotspot Hunter is a web-based computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes through analysis of antigenic diversity. It allows screening and selection of hotspots specific to four common HLA supertypes, namely HLA class I A2, A3, B7 and class II DR. The system uses Artificial Neural Network and Support Vector Machine methods as predictive engines. Soft computing principles were employed to integrate the prediction results produced by both methods for robust prediction performance. Experimental validation of the predictions showed that Hotspot Hunter can successfully identify majority of the real hotspots. Users can predict hotspots from a single protein sequence, or from a set of aligned protein sequences representing pathogen proteome. The latter feature provides a global view of the localizations of the hotspots in the proteome set, enabling analysis of antigenic diversity and shift of hotspots across protein variants. The system also allows the integration of prediction results of the four supertypes for identification of hotspots common across multiple supertypes. The target selection feature of the system shortlists candidate peptide hotspots for the formulation of an epitope-based vaccine that could be effective against multiple variants of the pathogen and applicable to a large proportion of the human population. Conclusion: Hotspot Hunter is publicly accessible at http://antigen.i2r.a-star.edu.sg/hh/. It is a new generation computational tool aiding in epitope-based vaccine design. [ABSTRACT FROM AUTHOR]

Background: Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines. Results: Our analysis showed that the number of unique protein sequences required to represent complete antigenic diversity of short peptides in dengue virus is significantly smaller than that required to represent complete protein sequence diversity. Short-peptide antigenic diversity shows an asymptotic relationship to the number of unique protein sequences, indicating that for large sequence sets (~200) the addition of new protein sequences has marginal effect to increasing antigenic diversity. A near-linear relationship was observed between the extent of antigenic diversity and the length of protein sequences, suggesting that, for the practical purpose of vaccine development, antigenic diversity of short peptides from dengue virus can be represented by short regions of sequences (~<100 aa) within viral antigens that are specific targets of immune responses (such as T-cell epitopes specific to particular human leukocyte antigen alleles). Conclusion: This study provides evidence that there are limited numbers of antigenic combinations in protein sequence variants of a viral species and that short regions of the viral protein are sufficient to capture antigenic diversity of T-cell epitopes. The approach described herein has direct application to the analysis of other viruses, in particular those that show high diversity and/or rapid evolution, such as influenza A virus and human immunodeficiency virus (HIV). [ABSTRACT FROM AUTHOR]

Background: Malaria is the leading cause of morbidity and mortality in Sudan. The entire population is at risk of contracting malaria to different levels. This study aimed to assess the effectiveness of communication for behavioural impact (COMBI) strategy in enhancing the utilization of long-lasting insecticidal nets (LLINs) among mothers of underfive children in rural areas. Methods: A randomized community trial was conducted in rural area of Kosti locality, White Nile State, Sudan, among mothers of under-five children, from January 2013 to February 2014. A total of 761 mothers from 12 villages were randomly selected, 412 mothers from intervention villages and 349 were from comparison villages. Results: The knowledge of mothers, in intervention villages, about malaria vector, personal protective measures (PPM) against malaria, and efficacy of LLINs was significantly increased from 86.9 to 97.3 %; 45.9 to 92 % and 77.7 to 96.1 % respectively. Knowledge about usefulness of PPM, types of mosquito nets and efficacy of LLINs was significantly higher in intervention villages compared to comparison villages (p < 0.05), (η2 = 0.64). Mothers in intervention villages increasingly perceived, post-intervention, that malaria was a serious disease (99.3 %), a preventable disease (98.8 %) and also LLINs as an effective intervention in malaria prevention (92.2 %). This resulted in an increase in the utilization rate of LLINs from 19.2 to 82.8 % in intervention villages compared to comparison villages (p < 0.05) [OR = 4.6, 95 %, CI = (3.72-5.72)], (η2 = 0.64). The average of mothers' knowledge about malaria was increased by 64 % (η2 = 0.64), the use of LLINs was increased by 79 % (η2 = 0.79) and a positive attitude towards malaria was 2.25 times higher in intervention villages than among mothers in the comparison villages. Conclusions: These results established the usefulness of COMBI strategy for increasing awareness about malaria, developing a positive perception towards malaria prevention and, increasing the utilization of LLINs. [ABSTRACT FROM AUTHOR]

Type-1 Diabetes Mellitus (T1DM) is regarded as a multifunctional, immune-related disease which causes massive destruction of islet β-cells in pancreas resulting in hyperglycemic, hypoinsulinemia and hyperlipidimic conditions. The aim of the present study, was to investigate the hypothesis that streptozotocin (STZ)-induced T1DM in Balb/c mice when treated with crude polysaccharide from seaweed, Dictyopteris divaricata (CDDP) depicts improvement in diabetes-related symptoms. Treatment with CDDP resulted in decreased body weight loss, improved food consumption and water intake disbalances. The CDDP effectively improved fasting blood glucose, oral glucose tolerance (OGTT), serum insulin, insulin secretion, rejuvenation of β-cells mass, serum lipid profile and pro-inflammatory cytokines levels. Additionally, treatment with CDDP increased the population of beneficial bacteria such as Firmicutes, Bacteroidetes and Lactobacillus at phylum, family and genus levels by 16S rRNA sequencing. Furthermore, immunohistological examination confirmed that CDDP reduces the inflammation and restored the structural morphology of colon and upraised the levels of insulin receptor substrate-1 (IRS-1), Mucin-2 (MUC-2) and tight-junction proteins (TJs) whereby maintaining the gut structures and barrier permeability. Thus, the above presented data, highlights the safe and therapeutic effects of crude polysaccharide (CDDP) from D. divaricata in the treatment and restoration of T1DM disorders and can be used as a food supplement alternative to diabetes medicine. [ABSTRACT FROM AUTHOR]

Background: Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments. Results: Herein, we present T3SEdb http://effectors.bic.nus.edu.sg/T3SEdb, a specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been defined for i) comprehensive annotation of experimental status of effectors, ii) submission and curation review of records by users of the database, and iii) the regular update of T3SEdb existing and new records. Keyword fielded and sequence searches (BLAST, regular expression) are supported for both experimentally verified and hypothetical T3SEs. More than 171 clusters of T3SEs were detected based on sequence identity comparisons (intra-cluster difference up to ∼60%). Owing to this high level of sequence diversity of T3SEs, the T3SEdb provides a large number of experimentally known effector sequences with wide species representation for creation of effector predictors. We created a reliable effector prediction tool, integrated into the database, to demonstrate the application of the database for such endeavours. Conclusions: T3SEdb is the first specialised database reported for T3SS effectors, enriched with manual annotations that facilitated systematic construction of a reliable prediction model for identification of novel effectors. The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments. [ABSTRACT FROM AUTHOR]

The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources. [ABSTRACT FROM AUTHOR]

Background: The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose considerable challenges in data processing and extraction of biological meaning. Moreover it has created an unmet need for the effective integration of these datasets to achieve insights into biological systems. While it has increased the demand for bioinformatics experts who can interface with biologists, it has also raised the requirement for biologists to possess a basic capability in bioinformatics and to communicate seamlessly with these experts. This may be achieved by embedding in their undergraduate and graduate life science education, basic training in bioinformatics geared towards acquiring a minimum skill set in computation and informatics. Results: Based on previous attempts to define curricula suitable for addressing the bioinformatics capability gap, an initiative was taken during the Workshops on Education in Bioinformatics and Computational Biology (WEBCB) in 2008 and 2009 to identify a minimum skill set for the training of future bioinformaticians and molecular biologists with informatics capabilities. The minimum skill set proposed is cross-disciplinary in nature, involving a combination of knowledge and proficiency from the fields of biology, computer science, mathematics and statistics, and can be tailored to the needs of the "-omics". Conclusion: The proposed bioinformatics minimum skill set serves as a guideline for biology curriculum design and development in universities at both the undergraduate and graduate levels. [ABSTRACT FROM AUTHOR]

Background: Biology has entered the era of big data with the advent of high-throughput omics technologies. Biological databases provide public access to petabytes of data and information facilitating knowledge discovery. Over the years, sequence data of pathogens has seen a large increase in the number of records, given the relatively small genome size and their important role as infectious and symbiotic agents. Humans are host to numerous pathogenic diseases, such as that by viruses, many of which are responsible for high mortality and morbidity. The interaction between pathogens and humans over the evolutionary history has resulted in sharing of sequences, with important biological and evolutionary implications. Results: This study describes a large-scale, systematic bioinformatics approach for identification and characterization of shared sequences between the host and pathogen. An application of the approach is demonstrated through identification and characterization of the Flaviviridae-human share-ome. A total of 2430 nonamers represented the Flaviviridae-human share-ome with 100% identity. Although the share-ome represented a small fraction of the repertoire of Flaviviridae (~ 0.12%) and human (~ 0.013%) non-redundant nonamers, the 2430 shared nonamers mapped to 16,946 Flaviviridae and 7506 human non-redundant protein sequences. The shared nonamer sequences mapped to 125 species of Flaviviridae, including several with unclassified genus. The majority (~ 68%) of the shared sequences mapped to Hepacivirus C species; West Nile, dengue and Zika viruses of the Flavivirus genus accounted for ~ 11%, ~ 7%, and ~ 3%, respectively, of the Flaviviridae protein sequences (16,946) mapped by the share-ome. Further characterization of the share-ome provided important structural-functional insights to Flaviviridae-human interactions. Conclusion: Mapping of the host-pathogen share-ome has important implications for the design of vaccines and drugs, diagnostics, disease surveillance and the discovery of unknown, potential host-pathogen interactions. The generic workflow presented herein is potentially applicable to a variety of pathogens, such as of viral, bacterial or parasitic origin. [ABSTRACT FROM AUTHOR]

Background: Organic mulches are widely used in crop production systems. Due to their benefits in improving soil fertility, retention of soil moisture and weed control. Field experiments were conducted during wheat growing seasons of 2018–2019 and 2019–2020 to evaluate the effects of Jatropha leaves mulch on the growth of wheat varieties 'Wadan-17' (rainfed) and 'Pirsabaq-2013' (irrigated) under well irrigated and water stress conditions (non-irrigated maintaining 40% soil field capacity). Jatropha mulch was applied to the soil surface at 0, 1, 3 and 5 Mg ha−1 before sowing grains in the field. Under conditions of water stress, Jatropha mulch significantly maintained the soil moisture content necessary for normal plant growth. Results: We noted a decrease in plant height, shoot and root fresh/dry weight, leaf area, leaf relative water content (LRWC), chlorophyll, and carotenoid content due to water stress. However, water stress caused an increase in leaf and root phenolics content, leaf soluble sugars and electrolytes leakage. We observed that Jatropha mulch maintained LRWC, plant height, shoot and root fresh/dry weight, leaf area and chlorophyll content under water stress. Moreover, water stress adverse effects on leaf soluble sugar content and electrolyte leakage were reversed to normal by Jatropha mulch. Conclusion: Therefore, it may be concluded that Jatropha leaves mulch will minimize water stress adverse effects on wheat by maintaining soil moisture and plant water status. [ABSTRACT FROM AUTHOR]

Mesenchymal stem cells hold the promise to treat not only several congenital and acquired bone degenerative diseases but also to repair and regenerate morbid bone tissues. Utilizing MSCs, several lines of evidences advocate promising clinical outcomes in skeletal diseases and skeletal tissue repair/regeneration. In this context, both, autologous and allogeneic cell transfer options have been utilized. Studies suggest that MSCs are transplanted either alone by mixing with autogenous plasma/serum or by loading onto repair/induction supportive resorb-able scaffolds. Thus, this review is aimed at highlighting a wide range of pertinent clinical therapeutic options of MSCs in the treatment of skeletal diseases and skeletal tissue regeneration. Additionally, in skeletal disease and regenerative sections, only the early and more recent preclinical evidences are discussed followed by all the pertinent clinical studies. Moreover, germane post transplant therapeutic mechanisms afforded by MSCs have also been conversed. Nonetheless, assertive use of MSCs in the clinic for skeletal disorders and repair is far from a mature therapeutic option, therefore, posed challenges and future directions are also discussed. Importantly, for uniformity at all instances, term MSCs is used throughout the review. [ABSTRACT FROM AUTHOR]

g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets. The comparative analyses between the co-aligned sequences of the two viral populations is based on a sliding window approach of size nine for statistical significance and data application to the major histocompatibility complex (MHC) and T-cell receptor (TCR) immune response mechanisms. The sequences at each of the aligned overlapping nonamer positions for the respective virus hosts are classified as four patterns of characteristic diversity motifs, as a basis for quantitative analyses: (i) "index", the most prevalent sequence; (ii) "major" variant, the second most common sequence and the single most prevalent variant of the index, with at least one amino acid mutation; (iii) "minor" variants, multiple different sequences, each with an incidence (percent occurrence) less than that of the major variant; and (iv) "unique" variants, each with only one occurrence in the alignment. The diversity motifs and their incidences at each of the nonamer positions allow evaluation of the mutation transmission dynamics and selectivity of the viral sequences in relation to the animal and the human hosts. g-FLUA2H is facilitated by a grid back-end for parallel processing of large sequence datasets. The web-application is publicly available at http://bioinfo.perdanauniversity.edu.my/g-FLUA2H. It can be used for a detailed characterization of the composition and incidence of mutations present in the proteomes of influenza viruses from animal and human host populations, for a better understanding of host tropism. [ABSTRACT FROM AUTHOR]

Background: Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results: We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an “.lzm” file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions: Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. [ABSTRACT FROM AUTHOR]

Objective: To determine the frequency and clinical features of bleeding disorders in the tribe as a result of consanguineous marriages. Design: Cross Sectional Study Introduction: Countries in which consanguinity is a normal practice, these rare autosomal recessive disorders run in close families and tribes. Here we describe a family, living in village Ali Murad Chandio, District Badin, labeled as haemophilia. Patients & Methods: Our team visited the village & developed the pedigree of the whole extended family, up to seven generations. Performa was filled by incorporating patients, family history of bleeding, signs & symptoms, and bleeding from any site. From them 144 individuals were screened with CBC, bleeding time, platelet aggregation studies & RiCoF. While for PT, APTT, VWF assay and Factor VIII assay, samples were kept frozen at -70 degrees C until tested. Results: The family tree of the seven generations comprises of 533 individuals, 63 subjects died over a period of 20 years and 470 were alive. Out of all those 144 subjects were selected on the basis of the bleeding history. Among them 98(68.1%) were diagnosed to have a bleeding disorder; 44.9% patients were male and 55.1% patients were female. Median age of all the patients was 20.81, range (4 months- 80 yrs). The results of bleeding have shown that majority had gum bleeding, epistaxis and menorrhagia. Most common bleeding disorder was Von Willebrand disease and Platelet functional disorders. Conclusion: Consanguineous marriages keep all the beneficial and adversely affecting recessive genes within the family; in homozygous states. These genes express themselves and result in life threatening diseases. Awareness, education & genetic counseling will be needed to prevent the spread of such common occurrence of these bleeding disorders in the community. [ABSTRACT FROM AUTHOR]

Background: Elevated intracranial pressure from cerebral edema is the major cause of early mortality in acute stroke. Current treatment strategies to limit cerebral edema are not particularly effective. Some novel anti-edema measures have shown promising early findings in experimental stroke models. Vasopressin antagonism in stroke is one such target which has shown some encouraging preliminary results. The aim of this report is to highlight the potential use of vasopressin antagonism to limit cerebral edema in patients after acute stroke.Case Presentation: A 57-year-old Caucasian man with new onset diplopia was diagnosed with vertebral artery aneurysm extending into the basilar circulation. He underwent successful elective vertebral artery angioplasty and coiling of the aneurysm. In the immediate post-operative period there was a decline in his neurological status and brain imaging revealed new midbrain and thalamic hemorrhage with surrounding significant brain edema. Treatment with conventional anti-edema therapy was initiated with no significant clinical response after which conivaptan; a mixed vasopressin antagonist was started. Clinical and radiological evaluation following drug administration showed rapid clinical improvement without identification of significant adverse effects.Conclusions: The authors have successfully demonstrated the safety and efficacy of using mixed vasopressin antagonist in treatment of stroke related brain edema, thereby showing its promise as an alternative anti-edema agent. Preliminary findings from this study suggest mixed vasopressin antagonism may have significant utility in the management of cerebral edema arising from cerebrovascular accident. Larger prospective studies are warranted to explore the role of conivaptan in the treatment of brain edema and neuroprotection. [ABSTRACT FROM AUTHOR]