Evolution of animal Piwi-interacting RNAs and prokaryotic CRISPRs

Piwi-interacting RNAs (piRNAs) and CRISPR RNAs (crRNAs) are two recently discovered classes of small noncoding RNA that are found in animals and prokaryotes, respectively. Both of these novel RNA species function as components of adaptive immune systems that protect their hosts from foreign nucleic acids-piRNAs repress transposable elements in animal germlines, whereas crRNAs protect their bacterial hosts from phage and plasmids. The piRNA and CRISPR systems are nonhomologous but rather have independently evolved into logically similar defense mechanisms based on the specificity of targeting via nucleic acid base complementarity. Here we review what is known about the piRNA and CRISPR systems with a focus on comparing their evolutionary properties. In particular, we highlight the importance of several factors on the pattern of piRNA and CRISPR evolution, including the population genetic environment, the role of alternate defense systems and the mechanisms of acquisition of new piRNAs and CRISPRs.

A review of metallothionein isoforms and their role in pathophysiology

The Metallothionein (MT) is a protein which has several interesting biological effects and has been demonstrated increase focus on the role of MT in various biological systems in the past three decades. The studies on the role of MT were limited with few areas like apoptosis and antioxidants in selected organs even fifty years after its discovery. Now acknowledge the exploration of various isoforms of MT such as MT-I, MT-II, MT-III and MT-IV and other isoforms in various biological systems.

Strong evidence exists that MT modulates complex diseases and the immune system in the body but the primary function of MT still remains unknown. This review's main objective is to explore the capability to specifically manipulate MT levels in cells and in animals to provide answers regarding how MT could impact those complex disease scenarios.

The experimental result mentioned in this review related among MT, zinc, cadmium, diabetic, heart disease, bone retardation, neuro toxicity, kidney dysfunction, cancer, and brain suggest novel method for exploration and contribute significantly to the growing scientist to research further in this field.

The polyphenol 3, 4, 5 - tri-hydroxy benzoic acid inhibits indian daboia russelli venom and its hemorrhagic complex induced local toxicity

Despite a long history on treatment and management of snakebite, as of now, no satisfactory cure exists to treat local toxicity, including anti-venom therapy. Several natural compounds from plants and their synthetic analogs have shown to be protective. In this study 3, 4, 5-tri-hydroxy benzoic acid, the gallic acid (GA) was tested against the local toxicity of Daboia russelli (DR) venom and its purified hemorrhagic complex (HC). GA inhibited in vitro proteolytic activity of both DR venom and HC but, it did not inhibit phospholipase activity of DR venom. GA inhibited hemorrhage, edema forming, dermo- and myonecrotic activities of both HC and DR venom in in vivo experiments. GA was particularly effective against hemorrhagic activity but, GA inhibition had a greater effect on HC when compared to DR venom. The inhibition was likely due to GA induced structural changes in HC as revealed by alterations in fluorescence emission and CD spectral properties. However, the inhibition was not due to chelating property of GA as suggested by UV-visible spectral studies. Inhibition of collagen type IV, laminin and fibronectin degradation essentially provided the biochemical basis for GA which inhibited local effects of HC as well as DR venom. Thus, the study appears highly promising to explore GA and its generics against ruthless local effects and perhaps systemic hemorrhage of DR and other snake bites as well. Further, these agents will possibly find an immense value in the regulation of matrix metalloproteases (MMPs) in processes such as wound healing, inflammation and in the treatment of cancer.

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

The metalloprotease, NN-PF3 from Naja naja venom inhibits platelet aggregation primarily by affecting α2β1 integrin

NN-PF3 is a non-toxic, anticoagulant, high-molecular-mass (67.81 kDa) metalloprotease from Indian cobra (Naja naja) venom. In the present study, NN-PF3 was investigated for the mechanism of inhibition of collagen-induced aggregation of human platelets. The complete inhibition of collagen-induced aggregation and partial inhibition of ADP- and epinephrine-induced aggregation has the respective IC(50) of 75 ± 5, 185 ± 10, and 232 ± 12 nM, whereas no inhibition of thrombin-, arachidonic acid-, and ristocetin-induced aggregation of platelets was observed in platelet-rich plasma. Further, native NN-PF3 and EDTA-inactivated NN-PF3 inhibited collagen-induced aggregation of washed platelets with respective IC(50) of 75 ± 4 and 180 ± 6 nM. The higher inhibitory effect of native NN-PF3 compared with EDTA-inactivated NN-PF3 suggests the enzymatic and non-enzymatic mechanism of inhibition. NN-PF3 pretreatment affected the collagen binding but not the fibrinogen, and fibronectin binding of washed platelets in adhesion assay suggested that the collagen receptors are affected. Western blot study using anti-integrin α2β1 mAb 6F1 suggested that NN-PF3 binds to integrin α2β1 in a primary structure-dependent manner only and is not cleaved. There was a drastic reduction in the intensity of several intracellular signaling phosphotyrosine protein bands when monoclonal anti-phosphotyrosine antibody was used, suggesting that the major activation pathway of platelets get affected, which occurs through glycoprotein VI. NN-PF3 did not bind to collagen as revealed by Western blot using anti-collagen mAb. Furthermore, neither the proteolytic cleavage of fibrinogen nor its degradation products by NN-PF3 contributed for the collagen-induced platelet aggregation inhibition.

Bio-conversion rate and optimum harvest intervals for Moina australiensis using digested piggery effluent and Chlorella vulgaris as a food source

The bio-conversion rate of Moina australiensis fed with Chlorella vulgaris grown on digested piggery effluent at three different feeding rates was determined and a 2, 3 and 4-day harvest interval strategy was investigated. This study indicates that C. vulgaris is a suitable food source for M. australiensis. A significant difference (P < or = 0.001) in the feeding rate against mean total populations was found among treatments. The increase in the amount of algae fed accelerated the production rate, and the population density peaked faster in the high C. vulgaris fed treatment. The BCR calculated from this experiment indicates that for every 1000 mg of C. vulgaris fed there was an increase of 437.9 mg of M. australiensis biomass produced. A significant difference (P < or = 0.001) in biomass production among the different harvest interval treatments was observed. The 2-day harvest interval treatment produced 7.78 g of M. australiensis followed by 6.89 g in the 3 day and 5.01 g in the 4-day harvest interval treatment. This study provides strong evidence that M. australiensis can utilise the bacterial blooms and bio-films associated with digested piggery effluent as a food source.

Inhibition of local effects of Indian Daboia/Vipera russelli venom by the methanolic extract of grape (Vitis vinifera L.) seeds

Although anti-venom therapy is available for the treatment of fatal bite by snakes, it offers less or no protection against the local effects such as dermo- and myonecrosis, edema, hemorrhage and inflammation at the bitten region. The viper species are known for their violent local effects and such effects have been commonly treated with plant extracts without any scientific validation in rural India. In this investigation, the methanolic extract of grapes (Vitis vinifera L.) seed was studied against the Indian Daboia/Vipera russelli venom-induced local effects. The extract abolished the proteolytic and hyaluronidase activities and also efficiently neutralized the hemorrhage, edema-inducing and myonecrotic properties of the venom. In addition, the extract also inhibited partially the pro-coagulant activity of the venom and abolished the degradation of Aalpha and Bbeta chains of human fibrinogen. Thus, the extract possesses potent anti-snake venom property, especially against the local effects of viper bites.

Magnetotransport and structural properties of nanocrystalline FeAgAl thin films

Structural and magnetotransport properties of metallic Fe(x)Ag(y)Al(z) nanogranular thin films were studied. These films with several compositions were prepared by dc magnetron sputtering. X-ray diffraction (XRD) measurements carried out on the samples show only Ag(111) peaks. The d-spacings determined from the Ag(111) peaks are smaller than the standard value for bulk Ag indicating a partial substitution of Fe and Al atoms in Ag matrix. Transmission electron diffraction (TEM) patterns show a number of Ag rings. Both XRD and TEM studies did not reveal any diffraction peaks due to Fe or Al. The average particle size determined from the TEM micrograph is 5.9 nm. This value is in good agreement with the grain size determined from the XRD patterns for the Al substituted samples. The MR was found to increase for smaller Al concentration and it decreases with further increase in Al content. In the samples investigated magnetoresistance ratio reaches a maximum value of about 4.5% for the Fe27Ag63Al10 film.

Structure, morphology and magnetization of Fe-Pd thin films

Several Fe(100-x)Pd(x0 thin films with x = 24-35 have been investigated to understand their structural, morphological and magnetic properties. The lattice spacing d111 obtained from the X-ray diffraction peaks shows a gradual increase with increasing x and this behaviour is attributed to the increasing substitution of Pd with larger atomic radius. While the atomic force microscopy images on selected samples showed surface roughness in the range 2-4 nm the scanning electron microscopy image of a Fe71Pd29 sample showed slightly dark and bright regions due to the large undulations of the surface of the films. We presume that these undulations are due to shape memory twin variants. In-plane magnetization measurements were carried out on selected films in applied magnetic fields up to 30 kOe. For three samples, the saturation magnetization is about 1300 emu/cc whereas for the Fe71Pd29 film it is about 950 emu/cc. The remanence ratio of the films is approximately in the range 50-70%. The behaviour of coercivity of our samples is believed to be due to grain size effect that generally plays a predominant role in thin films with nanometer size grains.

Nanogranular Fe-Cu-Ag thin films: structure, microstructure and giant magnetoresistance

Fe(x)Cu(y)Ag(z) granular thin films with several compositions were prepared by dc magnetron sputtering. These films consist of small Fe magnetic particles embedded in a nonmagnetic CuAg matrix. Structure, microstructure, morphology and magnetotransport properties were studied. The compositions of these samples were determined by energy-dispersive X-ray analysis. X-ray diffraction results showed strong Ag(111) peaks and broad Cu(111) peaks in all the samples. The variation of the (111) lattice spacings indicates a partial intermixing of Fe, Cu and Ag atoms. Microstructural studies using transmission electron microscopy (TEM) on a selected sample showed only Ag reflections and no reflection from Cu and Fe. Both XRD and TEM studies did not reveal any diffraction peak due to Fe and Cu for this sample. The fitting of the experimental grain size data obtained from TEM micrograph to the lognormal distribution function has allowed an estimation of the average grain diameter of 3.7 nm. The surface image of the Fe22Ag78 film observed using a scanning electron microscope showed the presence of droplet like Ag particles on the film surface. The Cu substitution results in smooth films without any Ag particles on the surface. Surface morphology by atomic force microscopy shows that the Fe39Cu13Ag48 film has a surface roughness of 0.75 nm. Finally, we have obtained a maximum giant magnetoresistance ratio of 3.2% in these films measured at 300 K for an in-plane magnetic field of 20 kOe.

Structure, microstructure, and giant magnetoresistance in nanogranular FeAgNi thin films

Structural, microstructural, and magnetoresistive properties of metallic Fe(x)Ag(y)Ni(z) granular thin films were studied. These films with several compositions were prepared by dc magnetron sputtering. X-ray diffraction (XRD) measurements carried out on the samples show only Ag(111) peaks. The d-spacings determined from the Ag(111) peaks are smaller than the standard value for bulk Ag indicating a partial intermixing of Fe and Ni atoms in Ag. The diffraction pattern obtained using Transmission electron microscope (TEM) shows a number of Ag rings. Both XRD and TEM studies did not reveal any diffraction peaks due to Fe or Ni. The average particle size determined from the TEM micrograph is 5.5 nm whereas that determined from the XRD patterns is always higher. The magnetoresistance ratio for all the samples lies in the range 3 to 4.3%, except for a sample.