Structure and reorientational dynamics of angiotensin I and II: a microscopic physical insight

We present a study of structural analysis and reorientational dynamics of Angiotensin I (AngI) and Angiotensin II (AngII) in aqueous solution. AngI is a decapeptide that acts as a precursor to the octapeptide AngII in the Renin-Angiotensin-Aldosterone system for blood pressure regulation. Experimental structural characterization of these peptides, carried out with circular dichroism and infrared spectroscopy, showed that the angiotensins are mostly disordered but exhibit a measurable population of ordered structures at room temperature. Interestingly, these change from the unordered polyproline-like conformation for AngI to a more compact and ordered conformation for AngII as the length of the peptide is decreased. Anisotropy decay measurements with picosecond time resolution indicate slower overall tumbling and a greater amplitude of internal motion in AngI compared to AngII, consistent with more compact and less flexible structure of the active form of the peptide. To model the microscopic behavior of the peptides, 2-μs molecular dynamics simulation trajectories were generated for AngI and AngII, at 300?K using the OPLS-AA potential and SPC water. The structures sampled in the simulations mostly agree with the experimental results, showing the prevalence of disordered structures, turns, and polyproline helices. Additionally, the computational results predict fewer sampled conformations, tighter side-chain packing and marked increase of Phe8 solvent accessibility upon AngI truncation to AngII. Our combined approach of experiment and extensive computer simulation thus yields new information on the conformational dynamics of the angiotensins, helping provide insight into the structural basis for the potency of AngI relative to AngII.     

Strain improvement of <Emphasis Type="Italic">Sporosarcina pasteurii</Emphasis> for enhanced urease and calcite production

Phenotypic mutants of Sporosarcina pasteurii (previously known as Bacillus pasteurii) (MTCC 1761) were developed by UV irradiation to test their ability to enhance urease activity and calcite production. Among the mutants, Bp M-3 was found to be more efficient compared to other mutants and wild-type strain. It produced the highest urease activity and calcite production compared to other isolates. The production of extracellular polymeric substances and biofilm was also higher in this mutant than other isolates. Microbial sand plugging results showed the highest calcite precipitation by Bp M-3 mutant. Scanning electron micrography, energy-dispersive X-ray and X-ray diffraction analyses evidenced the direct involvement of bacteria in CaCO₃ precipitation. This study suggests that calcite production by the mutant through biomineralization processes is highly effective and may provide a useful strategy as a sealing agent for filling the gaps or cracks and fissures in any construction structures.     

Paradigm for disease deconvolution in rare neurodegenerative disorders in Indian population: insights from studies in cerebellar ataxias

Cerebellar ataxias are a group of rare progressive neurodegenerative disorders with an average prevalence ranges from 4.8 to 13.8 in 100,000 individuals. The inherited disorders affect multiple members of the families, or a community that is endogamous or consanguineous. Presence of more than 3000 mutations in different genes with overlapping clinical symptoms, genetic anticipation and pleiotropy, as well as incomplete penetrance and variable expressivity due to modifiers pose challenges in genotype–phenotype correlation. Development of a diagnostic algorithm could reduce the time as well as cost in clinicogenetic diagnostics and also help in reducing the economic and social burden of the disease. In a unique research collaboration spanning over 20 years, we have been able to develop a paradigm for studying cerebellar ataxias in the Indian population which would also be relevant in other rare diseases. This has involved clinical and genetic analysis of thousands of families from diverse Indian populations. The extensive resource on ataxia has led to the development of a clinicogenetic algorithm for cost-effective screening of ataxia and a unique ataxia clinic in the tertiary referral centre in All India Institute of Medical Sciences. Utilizing a population polymorphism scanning approach, we have been able to dissect the mechanisms of repeat instability and expansion in many ataxias, and also identify founders, and trace the mutational histories in the Indian population. This provides information for genetic testing of at—risk as well as protected individuals and populations. To dissect uncharacterized cases which comprises more than 50% of the cases, we have explored the potential of next-generation sequencing technologies coupled with the extensive resource of baseline data generated in-house and other public domains. We have also developed a repository of patient-derived peripheral blood mononuclear cells, lymphoblastoid cell lines and neuronal lineages (derived from iPSCs) for ascribing functionality to novel genes/mutations. Through integrating these technologies, novel genes have been identified that has broadened the diagnostic panel, increased the diagnostic yield to over 75%, helped in ascribing pathogenicity to novel mutations and enabled understanding of disease mechanisms. It has also provided a platform for testing novel molecules for amelioration of pathophysiological phenotypes. This review through a perspective on CAs suggests a generic paradigm from diagnostics to therapeutic interventions for rare disorders in the context of heterogeneous Indian populations.     

Effect of calcifying bacteria on permeation properties of concrete structures

Microbially enhanced calcite precipitation on concrete or mortar has become an important area of research regarding construction materials. This study examined the effect of calcite precipitation induced by Sporosarcina pasteurii (Bp M-3) on parameters affecting the durability of concrete or mortar. An inexpensive industrial waste, corn steep liquor (CSL), from starch industry was used as nutrient source for the growth of bacteria and calcite production, and the results obtained with CSL were compared with those of the standard commercial medium. Bacterial deposition of a layer of calcite on the surface of the specimens resulted in substantial decrease of water uptake, permeability, and chloride penetration compared with control specimens without bacteria. The results obtained with CSL medium were comparable to those obtained with standard medium, indicating the economization of the biocalcification process. The results suggest that calcifying bacteria play an important role in enhancing the durability of concrete structures.     

Characterization of Urease and Carbonic Anhydrase Producing Bacteria and Their Role in Calcite Precipitation

Urease and carbonic anhydrase (CA) are key enzymes in the chemical reaction of living organisms and have been found to be associated with calcification in a number of microorganisms and invertebrates. Three bacterial strains designated as AP4, AP6, and AP9 were isolated from highly alkaline soil samples using the enrichment culture technique. On the basis of various physiological tests and 16S rRNA sequence analysis, these three bacteria were identified as Bacillus sp., B. megaterium, and B. simplex. Further, these Bacillus species have been characterized for the production of urease and CA in the process of biocalcification. One of the isolates, AP6 produced 553 U/ml of urease and 5.61 EU/ml CA. All the strains were able to produce significant amount of exopolymeric substances and biofilm. Further, efficacy of these strains was tested for calcite production ability and results were correlated with urease and CA. Isolate AP6 precipitated 2.26 mg calcite/cell dry mass (mg). Our observations strongly suggest that it is not only urease but CA also plays an important role in microbially induced calcium carbonate precipitation process. The current work demonstrates that urease and CA producing microbes can be utilized in biocalcification as a sealing agent for filling the gaps or cracks and fissures in constructed facilities and natural formations alike.     

Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction

TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1′s binding epitope on TL1A. HDX coupled with electron-transfer dissociation MS provided residue-level epitope information. The HDX dataset, in combination with solvent accessible surface area (SASA) analysis and computational modeling, revealed a discontinuous epitope within the predicted interaction interface of TL1A and DR3. The epitope regions span a distance within the approximate size of the variable domains of mAb1′s heavy and light chains, indicating it uses a unique mechanism of action to block the TL1A/DR3 interaction.     

Sustainable bio-bricks prepared with synthetic urine enabled by biomineralization reactions

In this study, mineralization during brick preparation was performed with ureolytic bacterium, Lysinibacillus fusiformis that use urine as a substrate, omitting the heat that is normally required. Artificial urine for reasons of standardization was used to grow the bacterium for bio-bricks made of clay and cement, but their mineralization was enabled by biological activity instead of by heat. Scanning electron microscopy and energy dispersion X-ray spectroscopy were conducted to analyse the microstructures formed by L. fusiformis that precipitated various minerals in synthetic urine. The brick specimens were tested for compressive strength that was 59% more than control ones, whereas porosity of bio-bricks was 13% compared to 22% of control specimens. The minerals formed in the bio-bricks confirmed as struvite, apatite and calcite by Fourier-transform infrared spectroscopy and X-ray diffraction spectra, were responsible for improved strength and reduced porosity. The research provided evidence in utilizing ureolytic bacteria as a mode to mineralize clay in brick production with the use of (artificial) urine as a substrate.     

Genetic diversity and population structure of sickleweed (Falcaria vulgaris; Apiaceae) in the upper Midwest USA

Sickleweed (Falcaria vulgaris), an introduced species native to Europe and Asia, grows as an aggressive weed in some areas of the upper Midwest in the United States. We are reporting genetic diversity and population structure of sickleweed populations using microsatellite markers and nuclear and chloroplast DNA sequences. Populations showed high genetic differentiation but did not show significant geographic structure, suggesting random establishment of different genotypes at different sites was likely due to human mediated multiple introductions. Three genetic clusters revealed by microsatellite data and presence of six chlorotypes supported our hypothesis of multiple introductions. Chloroplast DNA sequence data revealed six chlorotypes nested into two main lineages suggesting at least two introductions of sickleweed in the upper Midwest. Some individuals exhibited more than two alleles at several microsatellite loci suggesting occurrence of polyploidy, which could be a post-introduction development to mitigate the inbreeding effects. High genetic variation in the introduced range attributable to multiple introductions and polyploidy may be inducing the evolution of invasiveness in sickleweed. Results of this study provide valuable insights into the evolution of sickleweed and baseline data for designing proper management practices for controlling sickleweed in the United States.