MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses

Linking similar proteins structurally is a challenging task that may help in finding the novel members of a protein family. In this respect, identification of conserved sequence can facilitate understanding and classifying the exact role of proteins. However, the exact role of these conserved elements cannot be elucidated without structural and physiochemical information. In this work, we present a novel desktop application MotViz designed for searching and analyzing the conserved sequence segments within protein structure. With MotViz, the user can extract a complete list of sequence motifs from loaded 3D structures, annotate the motifs structurally and analyze their physiochemical properties. The conservation value calculated for an individual motif can be visualized graphically. To check the efficiency, predicted motifs from the data sets of 9 protein families were analyzed and MotViz algorithm was more efficient in comparison to other online motif prediction tools. Furthermore, a database was also integrated for storing, retrieving and performing the detailed functional annotation studies. In summary, MotViz effectively predicts motifs with high sensitivity and simultaneously visualizes them into 3D strucures. Moreover, MotViz is user-friendly with optimized graphical parameters and better processing speed due to the inclusion of a database at the back end. MotViz is available at http://www.fi-pk.com/motviz.html.     

Effect of obesity on high-density lipoprotein metabolism

Reduced levels of high-density lipoproteins (HDL) in non-obese and obese states are associated with increased risk for the development of coronary artery disease. Therefore, it is imperative to determine the mechanisms responsible for reduced HDL in obese states and, conversely, to examine therapies aimed at increasing HDL levels in these individuals. This paper examines the multiple causes for reduced HDL in obese states and the effect of exercise and diet--two non-pharmacologic therapies--on HDL metabolism in humans. In general, the concentration of HDL-cholesterol is adversely altered in obesity, with HDL-cholesterol levels associated with both the degree and distribution of obesity. More specifically, intra-abdominal visceral fat deposition is an important negative correlate of HDL-cholesterol. The specific subfractions of HDL that are altered in obese states include the HDL2, apolipoprotein A-I, and pre-beta1 subfractions. Decreased HDL levels in obesity have been attributed to both an enhancement in the uptake of HDL2 by adipocytes and an increase in the catabolism of apolipoprotein A-I on HDL particles. In addition, there is a decrease in the conversion of the pre-beta1 subfraction, the initial acceptor of cholesterol from peripheral cells, to pre-beta2 particles. Conversely, as a means of reversing the decrease in HDL levels in obesity, sustained weight loss is an effective method. More specifically, weight loss achieved through exercise is more effective at raising HDL levels than dieting. Exercise mediates positive effects on HDL levels at least partly through changes in enzymes of HDL metabolism. Increased lipid transfer to HDL by lipoprotein lipase and reduced HDL clearance by hepatic triglyceride lipase as a result of endurance training are two important mechanisms for increases in HDL observed from exercise.     

Microresonator mass sensors for detection of Bacillus anthracis Sterne spores in air and water

Towards the goal of developing a real-time monitoring device for microorganisms, we demonstrate the use of microcantilevers as resonant mass sensors for detection of Bacillus anthracis Sterne spores in air and liquid. The detection scheme was based on measuring resonant frequency decrease driven by thermally induced oscillations, as a result of the added mass of the spores with the use of a laser Doppler vibrometer (LDV). Viscous effects were investigated by comparing measurements in air and deionized (DI) water along with theoretical values. Moreover, biological experiments were performed which involved suspending spores onto the cantilevers and performing mass detection in air and water. For detection of spores in water, the cantilevers were functionalized with antibodies in order to fix the spores onto the surface. We demonstrate that as few as 50 spores on the cantilever can be detected in water using the thermal noise as excitation source. Measurement sensitivity of 9.23 Hz/fg for air and 0.1 Hz/fg for water were obtained. These measurements were compared with theoretical values and sources of improvement in cantilever sensitivity in a viscous medium were also discussed. It is expected that by driving the cantilevers and using higher order modes, detection of a single spore in liquids should be achievable.     

Female transfer between one-male groups of proboscis monkey (<Emphasis Type="Italic">Nasalis larvatus</Emphasis>)

Successful or unsuccessful female transfers were observed seven times during a 32-month field study of proboscis monkeys (Nasalis larvatus) inhabiting a riverine forest along a tributary of the Kinabatangan River, Sabah, Malaysia. In all cases, the females voluntarily left their own groups and immediately joined with another one. When adult females tried to shift to other groups, adult males called them back to their own groups, but appeared to be indifferent to subadult females. When the adult females returned, the males never attacked the females physically, but instead often emitted herding sounds to them. One subadult female was repelled by a resident adult female. When one adult female transferred into a new one-male group, she left her behind son in an all-male group. The number of females often fluctuated in most study groups, with this fluctuation being more prominent among subadult females than adult females. It is likely that female transfer in proboscis monkeys is not a rare occurrence and that it is especially common among sub-adult females.     

Direct differentiation of somatic embryos on different regions of intact seedlings of Azadirachta in response to thidiazuron

Direct differentiation of somatic embryos occurs in high-frequency and at high density in response to 1.0 microM TDZ, on different regions-hypocotyl, epicotyl, cotyledonary-node, cotyledons and leaves-of intact seedlings of Azadirachta. One-week-old seedlings on this medium exhibited stress symptoms as visible by the loss of root formation and reduction in the elongation of hypocotyl and epicotyl. Globular somatic embryos were more abundant on hypocotyl, epicotyl, stem tip and leaves. The arrest of embryos at this stage was possibly due to their presence in high density. Well-developed somatic embryos were present on the cotyledons and the cotyledonary-node. These embryos on isolation and transfer to hormone-free medium regenerated readily to form plantlets. The possible role of stress in thidiazuron-induced somatic embryo formation is discussed.     

Oscillatory burst discharge generated through conditional backpropagation of dendritic spikes.

Gamma frequencies of burst discharge (>40 Hz) have become recognized in select cortical and non-cortical regions as being important in feature extraction, neural synchrony and oscillatory discharge. Pyramidal cells of the electrosensory lateral line lobe (ELL) of Apteronotus leptorhynchus generate burst discharge in relation to specific features of sensory input in vivo that resemble those recognized as gamma frequency discharge when examined in vitro. We have shown that these bursts are generated by an entirely novel mechanism termed conditional backpropagation that involves an intermittent failure of dendritic Na+ spike conduction. Conditional backpropagation arises from a frequency-dependent broadening of dendritic spikes during repetitive discharge, and a mismatch between the refractory periods of somatic and dendritic spikes. A high threshold class of K+ channel, AptKv3.3, is expressed at high levels and distributed over the entire soma-dendritic axis of pyramidal cells. AptKv3.3 channels are shown to contribute to the repolarization of both somatic and dendritic spikes, with pharmacological blockade of dendritic Kv3 channels revealing an important role in controlling the threshold for burst discharge. The entire process of conditional back-propagation and burst output is successfully simulated using a new compartmental model of pyramidal cells that incorporates a cumulative inactivation of dendritic K+ channels during repetitive discharge. This work is important in demonstrating how the success of spike backpropagation can control the output of a principle sensory neuron, and how this process is regulated by the distribution and properties of voltage-dependent K+ channels.     

Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae.

We have reported the isolation of linking clones of HindIII and EcoRI fragments, altogether spanning a 230-kb continuous stretch of chromosome VI. The presence or absence of autonomously replicating sequence (ARS) activities in all of these fragments has been determined by using ARS searching vectors containing CEN4. Nine ARS fragments were identified, and their positions were mapped on the chromosome. Structures essential for and/or stimulative to ARS activity were determined for the ARS fragments by deletions and mutations. The organization of functional elements composed of core and stimulative sequences was found to be variable. Single core sequences were identified in eight of nine ARSs. The remaining ARS (ARS603) essential element is composed of two core-like sequences. The lengths of 3'- and 5'-flanking stimulative sequences required for the full activity of ARSs varied from ARS to ARS. Five ARSs required more than 100 bp of the 3'-flanking sequence as stimulative sequences, while not more than 79 bp of the 3' sequence was required by the other three ARSs. In addition, five ARSs had stimulative sequences varying from 127 to 312 bp in the 5'-flanking region of the core sequence. In general, these stimulative activities were correlated with low local delta Gs of unwinding, suggesting that the low local delta G of an ARS is an important element for determining the efficiency of initiation of replication of ARS plasmids.     

Microevolutionary patterns in the common caiman predict macroevolutionary trends across extant crocodilians

Both extinct and extant crocodilians have repeatedly diversified in skull shape along a continuum, from narrow‐snouted to broad‐snouted phenotypes. These patterns occur with striking regularity, although it is currently unknown whether these trends also apply to microevolutionary divergence during population differentiation or the early stages of speciation. Assessing patterns of intraspecific variation within a single taxon can potentially provide insight into the processes of macroevolutionary differentiation. For example, high levels of intraspecific variation along a narrow‐broad axis would be consistent with the view that cranial shapes can show predictable patterns of differentiation on relatively short timescales, and potentially scale up to explain broader macroevolutionary patterns. In the present study, we use geometric morphometric methods to characterize intraspecific cranial shape variation among groups within a single, widely distributed clade, Caiman crocodilus. We show that C. crocodilus skulls vary along a narrow/broad‐snouted continuum, with different subspecies strongly clustered at distinct ends of the continuum. We quantitatively compare these microevolutionary trends with patterns of diversity at macroevolutionary scales (among all extant crocodilians). We find that morphological differences among the subspecies of C. crocodilus parallel the patterns of morphological differentiation across extant crocodilians, with the primary axes of morphological diversity being highly correlated across the two scales. We find intraspecific cranial shape variation within C. crocodilus to span variation characterized by more than half of living species. We show the main axis of intraspecific phenotypic variation to align with the principal direction of macroevolutionary diversification in crocodilian cranial shape, suggesting that mechanisms of microevolutionary divergence within species may also explain broader patterns of diversification at higher taxonomic levels.     

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.     

Unfolding during urea denaturation of a low molecular weight phytocystatin (thiol protease inhibitor) purified from Phaseolus mungo (Urd)

In the present study, two phytocystatins were purified to homogeneity as peaks I and II with molecular weights of 19 kDa and 17 kDa, respectively, as determined by SDS-PAGE and mass spectrometry. Both PMCs I and II were purified with a greater than 1000-fold purification and overall yield of about 16-18%. The effect of urea on PMC I and II was analysed by fluorescence and Circular Dichroism (CD) spectroscopy. Fluorescence studies suggest a red shift of the maximum emission at higher urea concentrations. PMC I and II are extremely stable protein inhibitors with regards to temperature and pH stability. FTIR studies show predominant alpha-helical structure in both the cystatins. CD analysis results show change in urea concentration-dependent loss in ellipticity, as well as in the shape of the CD spectrum compared to the intact phytocystatin.