Recombination networks as genetic markers in a human variation study of the Old World

We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.     

Bioremediation of chromium contaminated environments

Bioremediation is the most promising and cost effective technology widely used nowadays to clean up both soils and wastewaters containing organic or inorganic contaminants. Discharge of chromium containing wastes has led to destruction of many agricultural lands and water bodies. Utilisation of chromium(Cr) reducing microbes and their products has enhanced the efficiency of the process of detoxification of Cr(VI) to Cr(III). This review focuses mainly on the current technologies prevalent for remediation like natural attenuation, anaerobic packed bed bioreactors (using live cells, Cr(VI) reductases or their byproducts) and use of engineered microorganisms. Treatment of wastewaters by biosorption or using biofilms and immobilized microbial cells are also discussed.     

Mitochondrial Dysfunction in Rabies Virus-Infected Human and Canine Brains

Neurochemical Research - Rabies is a fatal encephalitis caused by the Rabies lyssavirus (RABV). The presence of minimal neuropathological changes observed in rabies indicates that neuronal...     

SlHyPRP1 and DEA1, the multiple stress responsive eight-cysteine motif family genes of tomato (Solanum lycopersicum L.) are expressed tissue specifically,localize and interact at cytoplasm and plasma membrane in vivo

Owing to rapid global climate change, the occurrence of multiple abiotic stresses is known to influence the outburst of biotic stress factors which affects crop productivity. Therefore, it is essential to understand the molecular and cell biology of key genes associated with multiple stress responses in crop plants. SlHyPRP1 and DEA1, the members of eight-cysteine motif (8CM) family genes have been recently identified as putative regulators of multiple stress responses in tomato (Solanum lycopersicum L.). In order to gain deeper insight into cell and molecular biology of SlHyPRP1 and DEA1, we performed their expression analysis in three tomato cultivars and in vivo cell biological analysis. The semi-quantitative PCR and qRT-PCR results showed the higher expression of SlHyPRP1 and DEA1 in leaf, stem, flower and root tissues as compared to fruit and seed tissues in all three cultivars. The expression levels of SlHyPRP1 and DEA1 were found to be relatively higher in a wilt susceptible tomato cultivar (Arka Vikas) than a multiple disease resistant cultivar (Arka Abhed). In vivo cell biological analysis through Gateway cloning and Bi-FC assay revealed the predominant sub-cellular localization and strong protein–protein interaction of SlHyPRP1 and DEA1 at the cytoplasm and plasma membrane. Moreover, SlHyPRP1 showed in vivo interaction with stress responsive proteins WRKY3 and MST1. Our findings suggest that SlHyPRP1 with DEA1 are co-expressed with tissue specificity and might function together by association with WRKY3 and MST1 in plasma membrane for regulating multiple stress responses in the tomato plant.Electronic supplementary materialThe online version of this article (10.1007/s12298-020-00913-z) contains supplementary material, which is available to authorized users.Keyword: Eight-cysteine motif, Hybrid proline rich proteins, Multiple stresses, Tissue specific expression, Plasma membrane, Protein-protein interaction     

A limited-trust capacity model for mitigating threats of internal malicious services in cloud computing

Hidden persistent malware in guest virtual machine instances are among the most common internal threats in cloud computing, affecting the security of both cloud customers and providers. With the growing sophistication of modern malware, traditional methods are becoming increasingly ineffective for tackling cloud security problems. Moreover, given the pay-per-use model of clouds, consumption of resources by these malwares and malicious services can cause huge losses to both the cloud provider and customer. Thus, it is important to develop mechanisms that can limit the scale of malicious attacks in order to minimize their resources consumption. Trust management is a fundamental technique for assessing and increasing the reliability and security of cloud services. Unfortunately, majority of existing mechanisms for trust management in clouds have limitations that prevent them from being fully effective. In this paper, we propose a novel limited-trust capacity model to mitigate the threats of internal malicious software and services in cloud computing using concepts from flow networks to reduce the scale of malicious software or services. Our limited-trust capacity model can be utilized in the following two ways: (1) to manage the trust relationship among the guest services and to evaluate the threats of unknown malicious services, and (2) to minimize risk associated with renting cloud services and limiting the resource drain caused by malicious guest services. Finally, experimental results show that our limited-trust capacity model can effectively restrict the scale of malicious services and significantly mitigate the threats of internal attacks.     

Biological and molecular correlates between induced dedifferentiation and spore germination in Dictyostelium.

When developing cultures of Dictyostelium discoideum are disaggregated at any time prior to cell wall formation and challenged to reinitiate development, amoebae will progress through the original sequence of morphogenetic stages, but the second time through they will do so in roughly one-tenth the original time, a process known as 'rapid recapitulation'. However, if disaggregated cells are suspended in nutrient medium, they enter a program of dedifferentiation during which they lose the capacity to rapidly recapitulate after an 80 minute lag period in a process known as 'erasure'. Here we show that cells that have completed the morphogenetic program and emerge from spore coats in the process of germination have also erased. In addition, the germination-specific 270 gene family is expressed during induced dedifferentiation in a unique fashion, and a germination-defective mutant exhibits a dramatic delay in erasure without concomitant defects in the program of gene regulation accompanying induced dedifferentiation. These results suggest for the first time that induced dedifferentiation and spore germination share some common processes in converting cells from a developmental to vegetative state.     

Differential regulation of metalloprotease steady-state mRNA levels by IL-1 and FGF in rabbit articular chondrocytes.

The expression of collagenase and stromelysin is believed to be coordinately regulated. In this report however, we provide evidence that suggests subtle differences may exist in the early events of the induction of these enzymes. Rabbit articular chondrocytes treated with interleukin-1, either alone or in combination with fibroblast growth factor, accumulated steady-state mRNA levels for both the enzymes, with the latter treatment more effective in inducing greater levels and within a shorter time. Further, the induction of the enzymes by either protocol was blocked by cycloheximide co-treatment. Cycloheximide added 1 h post-stimulation with interleukin-1 + fibroblast growth factor failed to block stromelysin mRNA expression, but was able to block collagenase steady-state mRNA levels. Transforming growth factor-beta, another inhibitor of metallprotease induction, showed no such differential activity. The results suggest that collagenase and stromelysin may have subtle variations in their induction pathways. Our studies further show that the enzyme induction by interleukin-1 alone or in combination with fibroblast growth factor occurs through different, but related mechanisms.     

Heat shock proteins: Molecules with assorted functions

Heat shock proteins (Hsps) or molecular chaperones, are highly conserved protein families present in all studied organisms. Following cellular stress, the intracellular concentration of Hsps generally increases several folds. Hsps undergo ATP-driven conformational changes to stabilize unfolded proteins or unfold them for translocation across membranes or mark them for degradation. They are broadly classified in several families according to their molecular weights and functional properties. Extensive studies during the past few decades suggest that Hsps play a vital role in both normal cellular homeostasis and stress response. Hsps have been reported to interact with numerous substrates and are involved in many biological functions such as cellular communication, immune response, protein transport, apoptosis, cell cycle regulation, gametogenesis and aging. The present review attempts to provide a brief overview of various Hsps and summarizes their involvement in diverse biological activities.     

Parathyroid hormone (1-34) regulates integrin expression in vivo in rat osteoblasts.

Intermittent administration of parathyroid hormone (PTH) activates new sites of bone formation by stimulating osteoblast differentiation and function resulting in an increase in bone mass. Because integrins have been shown to play a crucial role in osteoblast differentiation and bone formation, in the present study, we evaluated whether human PTH (1-34) upon administration to rats, influenced integrin expression in osteoblastic cells isolated from the metaphysis and the diaphysis of rat long bones. Initial immunohistochemical evaluation of bone sections demonstrated that the osteoblasts expressed at least alphav, alpha2, alpha3, and alpha5beta1 integrins. Immunocolocalization studies for integrins and vinculin established that alphav, alpha2, and alpha5beta1, but not alpha3 integrins were present in the focal adhesion sites of osteoblasts attached to FN coated surfaces. Osteoprogenitor cells isolated from metaphyseal (but not diaphyseal) marrow of rats injected with intermittent PTH (1-34) exhibited greater alphav and reduced alpha2 levels, with no apparent changes in alpha3, and alpha5beta1 integrin levels, as assessed by immunohistochemistry, Northern, and Western blot analyses. However, these changes were not observed on the same cells treated with PTH in vitro. These observations suggest that integrin modulation by PTH is likely to be indirect and that selective phenotypic expression of integrin subtypes is part of the cascade of events that lead to PTH (1-34) mediated osteoblast differentiation.