CoaSim: A flexible environment for simulating genetic data under coalescent models

Background  

Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these.     

<Emphasis Type="Italic">Syzygium aromaticum</Emphasis> extract mediated,rapid and facile biogenic synthesis of shape-controlled (3D) silver nanocubes

The synthesis of metal nano materials with controllable geometry has received extensive attention of researchers from the past decade. In this study, we report an unexplored new route for rapid and facile biogenic synthesis of silver nanocubes (AgNCs) by systematic reduction of silver ions with crude clove (Syzygium aromaticum) extract at room temperature. The formation and plasmonic properties of AgNCs were observed and the UV–vis spectra show characteristic absorption peak of AgNCs with broaden region at 430 nm along with the intense (124), (686), (454) and (235) peak in X-ray diffraction pattern confirmed the formation and crystallinity of AgNCs. The average size of AgNC cubes were found to be in the range of ~80 to 150 nm and it was confirmed by particles size distribution, scanning and transmission electron microscopy with elemental detection by EDAX. Further FTIR spectra provide the various functional groups present in the S. aromaticum extract which are supposed to be responsible and participating in the reaction for the synthesis of AgNCs. The AgNCs casted over glass substrate show an electrical conductivity of ~0.55 × 10⁶ S/m demonstrating AgNCs to be a potential next generation conducting material due to its high conductivity. This work provides a novel and effective approach to control the shape of silver nanomaterial for impending applications. The current synthesis mode is eco-friendly, low cost and promises different potential applications such as biosensing, nanoelectronics, etc.     

The evolution of the long and short repetitive DNA sequences in sea urchins.

The rates of evolution of purified long and short repetitive DNA sequences were examined by hybridisation analysis between the DNAs from several species of sea urchins. We find that the rates of nucleotide substitution are very comparable within mutually retained sequences for the two classes of repetitive DNA. The loss of hybridisable sequences between species also occurs at similar rates among both the short and long repetitive DNA sequences. Between species that separated less than 50 million years ago, hybridisable short repetitive sequences are lost all through the spectrum of reiteration frequencies. The long repeats contain a few sequences which are highly conserved within all of the species examined, and which amount to approximately 1% of the total genome. The short repetitive class, on the other hand, does not seem to contain any such highly conserved elements. The long repetitive sequences internally appear to contain short 'units' of reiteration, which may comprise families within the long repetitive class. We find no evidence to indicate that the majority of long and short repetitive sequences evolve by different mechanisms or at different rates.     

Monoorganobismuth(III) dithiocarboxylates: Synthesis, structures and their utility as molecular precursors for the preparation of Bi2S3 films and nanocrystals

Synthesis of a series of monoorganobismuth dithiocarboxylate complexes, [RBi(S₂CAr)₂] (R = Me, Ph, tol; Ar = Ph, tol), has been reported. They have been characterized by elemental analyses and spectroscopic methods. Molecular structures of [RBi(S₂Ctol)₂] (R = Me or Ph) have been established by single crystal X-ray diffraction studies. The bismuth atom in these complexes adopts a square pyramidal configuration with the R group at the apical position. In the solid state, these complexes show supra-molecular association devoid of Bi?S secondary interactions. Thermolysis of [RBi(S₂Ctol)₂] (R = Me or Ph) in refluxing diphenylether yielded Bi₂S₃ nanocrystals which were characterized by XRD, EDAX and SEM. The complex [PhBi(S₂Ctol)₂] has been employed for deposition of thin films of Bi₂S₃ by AACVD.     

Faithful expression of GFP from the PLCbeta2 promoter in a functional class of taste receptor cells

Phospholipase C-type beta2 (PLCbeta2) is expressed in a subset of cells within mammalian taste buds. This enzyme is involved in the transduction of sweet, bitter, and umami stimuli and thus is believed to be a marker for gustatory sensory receptor cells. We have developed transgenic mice expressing green fluorescent protein (GFP) under the control of the PLCbeta2 promoter to enable one to identify these cells and record their physiological activity in living preparations. Expression of GFP (especially in lines with more than one copy integrated) is strong enough to be detected in intact tissue preparations using epifluorescence microscopy. By immunohistochemistry, we confirmed that the overwhelming majority of cells expressing GFP are those that endogenously express PLCbeta2. Expression of the GFP transgene in circumvallate papillae occurs at about the same time during development as endogenous PLCbeta2 expression. When loaded with a calcium-sensitive dye in situ, GFP-positive taste cells produce typical Ca2+ responses to a taste stimulus, the bitter compound cycloheximide. These PLCbeta2 promoter-GFP transgenic lines promise to be useful for studying taste transduction, sensory signal processing, and taste bud development.     

In vitro organogenesis and plant regeneration of Thymus serpyllum L.: an important aromatic medicinal plant

An efficient in vitro propagation system has been developed for the rapid micropropagation of Thymus serpyllum L. (Banajwain), an aromatic medicinal herb from nodal explant on MS medium. Phenolic leaching and high rate of contamination was the most significant problem in establishing in vitro culture of Thymus serpyllum which was overcome by preparing explants in an antioxidant ascorbic acid (1000 ppm) at 6°C for 45 min and addition of the same antioxidant (50 mgl⁻¹) to the MS medium. The frequency of shoot production was influenced by different cytokinins (Kn, BAP, and Kn + BAP) and 95.56% shoot induction was observed when MS medium was supplemented with 1.0 + 2.0 mgl⁻¹ (Kn + BAP). The maximum average number of shoots 16.93 ± 2.15 and average length (3.98 ± 0.55) was recorded when MS medium have 0.5 + 2.0 mgl⁻¹ (Kn + BAP). The in vitro regenerated microshoots were rooted on MS and half strength MS medium and there was significant difference in root induction on both media under the influence of auxins (IAA, IBA, and NAA). The maximum average number (11.67 ± 3.03) and average root length (3.88 ± 0.71) was reported in half MS medium having 1.0 mgl⁻¹ IBA. The complete regenerated plantlets were acclimatized under growth chamber before transferring to the earthen pots and showed 90% survival.

Graphical abstract

     

The effects of core muscle activation on dynamic trunk position and knee abduction moments: Implications for ACL injury

Anterior cruciate ligament (ACL) injury is one of the most common serious lower-extremity injuries experienced by athletes participating in field and court sports and often occurs during a sudden change in direction or pivot. Both lateral trunk positioning during cutting and peak external knee abduction moments have been associated with ACL injury risk, though it is not known how core muscle activation influences these variables. In this study, the association between core muscle pre-activation and trunk position as well as the association between core muscle pre-activation and peak knee abduction moment during an unanticipated run-to-cut maneuver were investigated in 46 uninjured individuals. Average co-contraction indices and percent differences between muscle pairs were calculated prior to initial contact for internal obliques, external obliques, and L5 extensors using surface electromyography. Outside tilt of the trunk was defined as positive when the trunk was angled away from the cutting direction. No significant associations were found between pre-activations of core muscles and outside tilt of the trunk. Greater average co-contraction index of the L5 extensors was associated with greater peak knee abduction moment (p=0.0107). Increased co-contraction of the L5 extensors before foot contact could influence peak knee abduction moment by stiffening the spine, limiting sagittal plane trunk flexion (a motion pattern previously linked to ACL injury risk) and upper body kinetic energy absorption by the core during weight acceptance.     

Biodegradation of feather keratin with a PEGylated protease of Chryseobacterium gleum

Present study deals with the covalent modification of keratinolytic protease of Chryseobacterium gleum with higher enzyme activity, improved stability, non-immunogenicity and reusability. Protease of C. gleum showing feather degradation ability was modified by covalent attachment to polyethylene glycol. This modification culminated the change in electrophoretic mobility of protease in acrylamide gel. The modified enzyme showed 1.4 times more catalytic activity with better stability than native in aqueous system containing whole feathers as keratin. It showed improved pH, thermal, storage and solvent stability with a broadened range of pH (7–9) and temperature (25–50 °C) than native. The differentiation between modified and native enzyme was authenticated through UV–vis spectroscopy, SEM, XRD, FTIR and DSC. This modification of protease proved to be non-immunogenic in rats. The enzyme extracted after first run could be used for several cycles which clearly demonstrated its reusability in catalytic bioprocess of keratin degradation.     

Receptor specific crosstalk and modulation of signaling upon heterodimerization between β1-adrenergic receptor and somatostatin receptor-5

In the present study we describe heterodimerization, trafficking, coupling to adenylyl cyclase and signaling in HEK-293 cells cotransfected with human-somatostatin receptor 5 (hSSTR5) and β₁-adrenergic receptor (β₁AR). hSSTR5/β₁AR exists as heterodimers in basal conditions which was further enhanced upon synergistic activation of both receptors. Activation of either β₁AR or hSSTR5 displayed dissociation of heterodimerization. In cotransfectants, β₁AR effect on cAMP was predominant; however, blocking β₁AR with antagonist resulted in 60% inhibition of forskolin-stimulated cAMP in the presence of hSSTR5 agonists. cAMP/PKA pathway in cotransfected cells was regulated in receptor-specific manner, in contrast, the status of pERK1/2 and pPI3K/AKT was predominantly regulated by hSSTR5. The expression levels of phosphorylated NFAT remained unchanged indicating blockade of calcineurin-mediated dephosphorylation and nuclear translocation of NFAT, the process predominantly regulated by pJNK in SSTR5 dependent manner. Taken together, the functional consequences of results described here might have relevance in the cardiovascular system where SSTR and AR subtypes play important roles.