Biomechanical profiling of Caenorhabditis elegans motility

Caenorhabditis elegans locomotion is a stereotyped behavior that is ideal for genetic analysis. We integrated video microscopy, image analysis algorithms, and fluid mechanics principles to describe the C. elegans swim gait. Quantification of body shapes and external hydrodynamics and model-based estimates of biomechanics reveal that mutants affecting similar biological processes exhibit related patterns of biomechanical differences. Therefore, biomechanical profiling could be useful for predicting the function of previously unstudied motility genes.     

Peptide Scaffolds: Flexible Molecular Structures With Diverse Therapeutic Potentials

Peptide scaffolds are diverse chemical structures providing a major base for drug development. Nature modifies a premature peptide with respect to a basic scaffold structure to create a mature and active peptide. Mimicking the natural scaffolds with desirable modifications i.e., scaffold-hopping will decrease the enormous efforts of chemical syntheses and testing for drug development. We have surveyed the scaffold-based compounds being used for anticancer, antiinfective, antiinflammatory and antidiabetic activities. Synthetic peptidomimetics like aptamers, dendrimers, arylamide foldamers, β peptides, d peptides etc. provide an anticipative picture for the therapeutic use of scaffold structures. Free energy based conformational analysis of peptidomimetics provides details of their structure–activity relationships. Diverse forms of such peptidomimetics with respect to their structure and applications are discussed alongwith the mimetics which reached clinical trials. The review gives an insight into the future panoramas of drug development and identifies few peptide scaffolds having diverse potential with chemical modifications.     

More than multiple introductions: Multiple taxa contribute to the genesis of the invasive California’s wild artichoke thistle

The history of some invasive species is so complex that their origins can be difficult to determine. One example of such invasive species is the California invasive known as “wild artichoke thistle” (Cynara cardunculus var. sylvestris), found in natural and disturbed ecosystems. Wild artichoke thistle is a Mediterranean native and the progenitor of two domesticated horticultural taxa, artichoke and cardoon. Different hypotheses regarding the origins of California plants have included introductions by 19th century Italian immigrants and the de-domestication (evolutionary reversion to wild-type morphology) of feral (escaped, free-living) cultivars. Using microsatellite markers, we compared the genetic constitutions of 12 artichoke thistle populations in California with possible progenitor populations: 17 Spanish and Italian wild populations and eight different artichoke and cardoon cultivars. Each California population was compared with its putative progenitors using STRUCTURE analysis. Our results suggest that California's artichoke thistle populations are polyphyletic. Surprisingly, two-thirds of California's populations closely matched populations from the Iberian Peninsula. Three populations matched domesticated artichoke. One population appears to have wild and cultivar hybrid ancestry. Alleles specific to Italian populations were found at low frequencies in some California plants, suggesting that Italian wild plants may have been in California, but have left a trivial genetic legacy. Given that the de-domesticated plants in this study appear to be as invasive as the wild taxon, we conclude with a discussion of the role that ferality and de-domestication may have in plant invasions.     

Computational and Structural Investigation of Deleterious Functional SNPs in Breast Cancer BRCA2 Gene

In this work, we have analyzed the genetic variation that can alter the expression and the function in BRCA2 gene using computational methods. Out of the total 534 SNPs, 101 were found to be non synonymous (nsSNPs). Among the 7 SNPs in the untranslated region, 3 SNPs were found in 5′ and 4 SNPs were found in 3′ un-translated regions (UTR). Of the nsSNPs 20.7% were found to be damaging by both SIFT and PolyPhen server among the 101 nsSNPs investigated. UTR resource tool suggested that 2 SNPs in the 5′ UTR region and 4 SNPs in the 3′ UTR regions might change the protein expression levels. The mutation from asparagine to isoleucine at the position 3124 of the native protein of BRCA2 gene was most deleterious by both SIFT and PolyPhen servers. A structural analysis of this mutated protein and the native protein was made which had an RMSD value of 0.301 nm. Based on this work, we proposed that this most deleterious nsSNP with an SNPid rs28897759 is an important candidate for the cause of breast cancer by BRCA2 gene.     

Role of TNF-alpha in prenatal alterations in dams of mice under thermal stress

The possible involvement of cytokines such as tumour necrosis factor-alpha (TNF-alpha), interleukin-1 beta (IL-1 beta) and interferon-gamma (IFN-gamma) that are suspected of causing pregnancy loss and miscarriage has been investigated in dams of mice subjected to hyperthermia. Thermal stress was induced by exposing mice dams at 40+/-2 degrees C for 4 h every day during the different phases of the gestation period whereas the normothermic animals were housed at 22+/-2 degrees C. The effect of maternal thermal stress was measured in pregnant mice at different phases of the gestation period namely, blastogenesis-implantation phase (days 0-5 postconceptionem [p.c.]), organogenesis or embryogenesis phase (days 6-15 p.c.) and fetogenesis phase (days 16-20 p.c.). Uterine examination of dams subjected to hyperthermia on days 6-15 p.c. showed maximum reduction in live fetus number, gestational index and maximum pre and postimplantation loss in comparison with dams housed in normothermic environment and dams exposed to thermal stress between days 0-5 and 16-20 p.c. Maximum resorption rate and number of non-viable fetuses were observed in dams exposed to hyperthermia during days 6-15 p.c. Elevated levels of TNF-alpha and IL-1 beta were observed in the amniotic fluid of dams subjected to hyperthermia during days 6-15 p.c. but IFN-gamma levels remained unaltered. Single intraperitoneal (i.p.) administration of recombinant mouse TNF-alpha at a dose of 1 and 0.5 ng/mice in dams on day 6 in normothermic condition resulted in a reduced number of live fetuses. Administration of anti-TNF-alpha antibody i.p. at a dose of 10 microg/dam on day 6 p.c. and subjected to thermal stress between days 6-15 p.c. increased marginally the number of fetuses but failed to attain statistical significance in comparison with days 6-15 p.c. thermally stressed dams without antibody treatment. It is concluded that the induction of TNF-alpha, in the amniotic fluid is associated with thermal stress during pregnancy and may be linked to the reproductive performances of dams. This study will help in understanding the mechanism of thermal injury in pregnant subjects.     

Assessment of microbial diversity in effluent treatment plants by culture dependent and culture independent approaches

Microbial community structure of two distinct effluent treatment plants (ETPs) of pesticide and pharmaceutical industries was assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16S rRNA gene sequencing, (ii) diversity index analysis - operational taxonomic units (OTUs). A total of 38 and 44 bacterial OTUs having 85-99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. Fifty percent of the OTUs were related to uncultured bacteria. These OTUs had a Shannon diversity index value of 2.09-2.33 for culturables and in the range of 3.25-3.38 for unculturables. The high species evenness values of 0.86 and 0.95 indicated the vastness of microbial diversity retrieved by these approaches. The dominant cultured bacteria indicative of microbial diversity in functional ETPs were Alcaligenes, Bacillus and Pseudomonas. Brevundimonas, Citrobacter, Pandoraea and Stenotrophomonas were specific to pesticide ETP and Agrobacterium, Brevibacterium, Micrococcus, Microbacterium, Paracoccus and Rhodococcus were specific to pharmaceutical ETP. These microbes can thus be maintained and exploited for efficient functioning and maintenance of ETPs.     

TRAINING, VALIDATION AND MAINTENANCE OF A PANEL TO EVALUATE THE TEXTURE OF DRY BEANS (PHASEOLUS VULGARIS L.)

The inclusion of dry beans in diets has clear health benefits. However, consumers in developed countries mainly choose beans for their sensory qualities, especially for their texture. This article describes the constitution, training and validation of a panel of judges to evaluate the texture of dry beans. The judges were trained in the perception of different textures, analyzed a wide range of beans and selected seed-coat roughness, seed-coat perceptibility and creaminess/mealiness of the cotyledon as the main attributes to be scored. After training, the panel was capable of discriminating between different varieties of beans and even between beans of the same variety grown at different locations. The analysis of the behavior of the panel in a standard tasting session 2 years after its formation showed that periodic inclusion of samples from the extremes of the scales for the attributes during tasting sessions was sufficient to keep the panel trained.

PRACTICAL APPLICATIONS

This article could serve as a guide for the training of sensory panels to evaluate the texture of dry beans. It describes the selection of the attributes on which the analysis is based, references for the extreme values of the attributes and how to train the panel. It also provides a practical example of the analysis of the behavior of the panel some time after training.     

Gating at the mouth of the acetylcholine receptor channel: energetic consequences of mutations in the alphaM2-cap

Gating of nicotinic acetylcholine receptors from a C(losed) to an O(pen) conformation is the initial event in the postsynaptic signaling cascade at the vertebrate nerve-muscle junction. Studies of receptor structure and function show that many residues in this large, five-subunit membrane protein contribute to the energy difference between C and O. Of special interest are amino acids located at the two transmitter binding sites and in the narrow region of the channel, where C<-->O gating motions generate a low<-->high change in the affinity for agonists and in the ionic conductance, respectively. We have measured the energy changes and relative timing of gating movements for residues that lie between these two locations, in the C-terminus of the pore-lining M2 helix of the alpha subunit ('alphaM2-cap'). This region contains a binding site for non-competitive inhibitors and a charged ring that influences the conductance of the open pore. alphaM2-cap mutations have large effects on gating but much smaller effects on agonist binding, channel conductance, channel block and desensitization. Three alphaM2-cap residues (alphaI260, alphaP265 and alphaS268) appear to move at the outset of channel-opening, about at the same time as those at the transmitter binding site. The results suggest that the alphaM2-cap changes its secondary structure to link gating motions in the extracellular domain with those in the channel that regulate ionic conductance.