Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data‐model integration

In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data‐model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model‐data benchmarking; and data assimilation and ecological forecasting. This community‐driven approach is a key to meeting the pressing needs of science and society in the 21st century.     

Epidemio-Clinico-Microbiological Study of Mycotic Keratitis in North-West Region of Rajasthan

Aim and Objectives

Mycotic keratitis, with its diverse clinical presentation and difficulties in treatment, makes it a challenging task for clinicians and an important object of study. The aim of present study was to determine the frequency of occurrence and epidemiological association with identification of fungal isolates from mycotic keratitis cases.

Materials and Methods

This was a prospective and observational study conducted in Mycology Laboratory, Department of Microbiology, S.P. Medical College, Bikaner, on corneal scrapings and swabs of a total of 480 patients attending the Ophthalmology OPD, P.B.M. Hospital, Bikaner, during July 2005 to June 2012.

Results

Out of 480 suspected cases, 180 were found to be positive for fungus by smear/culture examination. Increased incidence was seen in the months of May to September with Aspergillus fumigatus being the most common isolate.

Conclusion

Mycotic keratitis, though an age-old disease, still presented with challenging aspects of diagnosis and treatment. The study showed fungal keratitis is prevalent in rural parts of north-west Rajasthan, mainly found in males (age group 21–40 years) with low socio-economic status (farm or factory workers). The most common cause of fungal keratitis was found to be species of Aspergillus.

     

Common Variants in CLDN2 and MORC4 Genes Confer Disease Susceptibility in Patients with Chronic Pancreatitis

A recent genome-wide association study (GWAS) identified association with variants in X-linked CLDN2 and MORC4, and PRSS1-PRSS2 loci with chronic pancreatitis (CP) in North American patients of European ancestry. We selected 9 variants from the reported GWAS and replicated the association with CP in Indian patients by genotyping 1807 unrelated Indians of Indo-European ethnicity, including 519 patients with CP and 1288 controls. The etiology of CP was idiopathic in 83.62% and alcoholic in 16.38% of 519 patients. Our study confirmed a significant association of 2 variants in CLDN2 gene (rs4409525—OR 1.71, P = 1.38 x 10^-09; rs12008279—OR 1.56, P = 1.53 x 10^-04) and 2 variants in MORC4 gene (rs12688220—OR 1.72, P = 9.20 x 10^-09; rs6622126—OR 1.75, P = 4.04x10^-05) in Indian patients with CP. We also found significant association at PRSS1-PRSS2 locus (OR 0.60; P = 9.92 x 10^-06) and SAMD12-TNFRSF11B (OR 0.49, 95% CI [0.31–0.78], P = 0.0027). A variant in the gene MORC4 (rs12688220) showed significant interaction with alcohol (OR for homozygous and heterozygous risk allele -14.62 and 1.51 respectively, P = 0.0068) suggesting gene-environment interaction. A combined analysis of the genes CLDN2 and MORC4 based on an effective risk allele score revealed a higher percentage of individuals homozygous for the risk allele in CP cases with 5.09 fold enhanced risk in individuals with 7 or more effective risk alleles compared with individuals with 3 or less risk alleles (P = 1.88 x 10^-14). Genetic variants in CLDN2 and MORC4 genes were associated with CP in Indian patients.     

Thermal microdevices for biological and biomedical applications

Temperature strongly influences the form and function of biologically important macromolecules and cells. Advances in microfabrication technology have enabled highly localized and accurate temperature control and manipulation, allowing the investigation of thermal effects on biological microsystems. This paper reviews progress in this field, with emphasis on techniques and microdevices with biomedical applications. Recent advances in the study of thermal effects on cellular behavior, enabled by MEMS-based structures are reported. These studies focus on investigating thermal interactions between the cell and its microenvironment. Thermal-based tools for concentration and purification of biologically important macromolecules like DNA and proteins are summarized. These tools address common issues in protein/DNA research, like concentration, separation and purification of samples. With the increasing research focus on the integration of biomedicine with engineering technologies and the several incentives of miniaturization, MEMS-based devices are likely to become increasingly prevalent in biology and medicine. Thermal engineering is expected to continue to play an important role in the improvement of current microdevices and the development of new ones.     

A LCMT1-PME-1 methylation equilibrium controls mitotic spindle size

Leucine carboxyl methyltransferase-1 (LCMT1) and protein phosphatase methylesterase-1 (PME-1) are essential enzymes that regulate the methylation of the protein phosphatase 2A catalytic subunit (PP2AC). LCMT1 and PME-1 have been linked to the regulation of cell growth and proliferation, but the underlying mechanisms have remained elusive. We show here an important role for an LCMT1-PME-1 methylation equilibrium in controlling mitotic spindle size. Depletion of LCMT1 or overexpression of PME-1 led to long spindles. In contrast, depletion of PME-1, pharmacological inhibition of PME-1 or overexpression of LCMT1 led to short spindles. Furthermore, perturbation of the LCMT1-PME-1 methylation equilibrium led to mitotic arrest, spindle assembly checkpoint activation, defective cell divisions, induction of apoptosis and reduced cell viability. Thus, we propose that the LCMT1-PME-1 methylation equilibrium is critical for regulating mitotic spindle size and thereby proper cell division.     

Formulating gels for decreased mucociliary transport using rheologic properties: Polyacrylic acids

The purpose of these studies was to identify the rheologic properties of polyacrylic acid gels necessary for optimal reductions in mucociliary clearance. The mucociliary transport of 2 bioadhesive polyacrylic acid polymers, polycarbophil and carbopol, was assessed in vitro by measuring their clerance rates across explants of ciliated bovine tracheal tissue. The viscoelastic properties of polymer gels were measured in the presence of mucus using controlled stress rheometry. Combinations of apparent viscosity (η) and complex modulus (G^*) were found to be the most useful parameters in the identification of polyacrylic acid formulations capable of decreasing mucociliary transport rate (MTR). A narrow range of η and G^* values suitable for reducing mucociliary clearance, while remaining sufficiently fluid for intranasal administration, were identified. The correlations between the rheologic parameters of the polycarbophil gels and their mucociliary transport rates were used to identify other polyacrylic acid gels that also had suitable mucociliary clearance properties, demonstrating that these parameters can be used to direct the optimization of formulations using simple in vitro rheologic testing. Published: April 20, 2007     

Genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859

We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen.