Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations

The Protein Journal - Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory...     

Elasmobranchs of the Persian (Arabian) Gulf: ecology, human aspects and research priorities for their improved management

Given widespread concern about the status of elasmobranch fishes globally, information on this group in the Persian (Arabian) Gulf is reviewed comprehensively for the first time. The Arabian region may be of overlooked significance to elasmobranch biogeography, and the environmentally unique Gulf has some highly distinctive elements of biodiversity: an endemic and critically endangered rajid skate, a rarely recorded carcharhinid shark, and preliminary molecular studies which indicate intriguing levels of distinctness from conspecifics elsewhere in the Indo-Pacific. Elasmobranchs also have a long history of association with, and exploitation by, humans around the Gulf. Despite this, Gulf elasmobranchs have been poorly researched, probably due to their low esteem as food. Information is scattered through a variety of literature, and only a handful of published works have been primarily concerned with aspects relevant to management. Key areas of concern include large reported landings by Iran; the export of fins to east Asian markets (particularly through the United Arab Emirates); potentially increasing demand for elasmobranchs for pharmaceutical products and human consumption; a reported change in elasmobranch community structure along the Iranian coast; and major degradation of the Gulf’s shallow, semi-enclosed environment. Priorities for research in the near future should include: resolution of taxonomic issues; species-level monitoring and reporting of fisheries landings by all Gulf states (including the species, pathways and fisheries involved in the fin trade locally); establishing the degree of connectivity of Gulf populations to those in adjacent waterbodies; and identification of key spatio-temporal sensitivities.     

The membrane-proximal region of the thrombopoietin receptor confers its high surface expression by JAK2-dependent and -independent mechanisms

Janus tyrosine kinase 2 (JAK2) is essential for signaling by the thrombopoietin (TpoR) and erythropoietin (EpoR) receptors. In the absence of JAK2 most EpoR molecules are retained in the endoplasmic reticulum in an Endo H-sensitive form. In contrast, we show that in the absence of JAK2 a large fraction of the TpoR is processed to the mature Endo H-resistant form and reaches the cell surface. By studying chimeras of the TpoR and EpoR we show that high surface expression of the TpoR is entirely conferred by the membrane-proximal region of the intracellular domain that includes the juxtamembrane, Box 1, and Box 2 regions. The TpoR intracellular domain shows similar effects on receptor endocytosis rate as that of the EpoR, but does stabilize the mature receptor isoform from degradation. Co-expression of JAK2 further stabilizes mature TpoR and thus further increases its surface expression. This JAK2 effect depends on the Box 1 region, the only JAK2 interacting site in the TpoR. By contrast, EpoR requires Box 1 as well as the flanking 20 residues on the C-terminal side for JAK2 interaction and JAK2-dependent surface expression. Our study suggests that whereas cell surface expression of type I cytokine receptors requires their cognate JAKs, the mechanisms governing receptor-JAK interactions differ among receptors interacting with the same JAK protein.     

Characterization of R-ras3/m-ras null mice reveals a potential role in trophic factor signaling

R-Ras3/M-Ras is a member of the RAS superfamily of small-molecular-weight GTP-binding proteins. Previous studies have demonstrated high levels of expression in several regions of the central nervous system, and a constitutively active form of M-Ras promotes cytoskeletal reorganization, cellular transformation, survival, and differentiation. However, the physiological functions of M-Ras during embryogenesis and postnatal development have not been elucidated. By using a specific M-Ras antibody, we demonstrated a high level of M-Ras expression in astrocytes, in addition to neurons. Endogenous M-Ras was activated by several trophic factors in astrocytes, including epidermal growth factor (EGF), basic fibroblast growth factor, and hepatocyte growth factor. Interestingly, M-Ras activation by EGF was more sustained compared to prototypic Ras. A mouse strain deficient in M-Ras was generated to investigate its role in development. M-Ras null mice appeared phenotypically normal, and there was a lack of detectable morphological and neurological defects. In addition, primary astrocytes derived from Mras(-/-) mice did not appear to display substantial alterations in the activation of both the mitogen-activated protein kinase and phosphatidylinositol 3-kinase pathways in response to trophic factors.     

The methamphetamine-sensitive circadian oscillator (MASCO) in mice

The suprachiasmatic nucleus (SCN) orchestrates synchrony among many peripheral oscillators and is required for circadian rhythms of locomotor activity and many physiological processes. However, the unique effects of methamphetamine (MAP) on circadian behavior suggest the presence of an SCN-independent, methamphetamine-sensitive circadian oscillator (MASCO). Substantial data collected using rat models show that chronic methamphetamine dramatically lengthens circadian period of locomotor activity rhythms and induces rhythms in animals lacking an SCN. However, the anatomical substrate and the molecular components of the MASCO are unknown. The response to MAP is less well studied in mice, a model that would provide the genetic tools to probe the molecular components of this extra-SCN oscillator. The authors tested the effects of chronic MAP on 2 strains of intact and SCN-lesioned mice in constant dark and constant light. Furthermore, they applied various MAP availability schedules to SCN-lesioned mice to confirm the circadian nature of the underlying oscillator. The results indicate that this oscillator has circadian properties. In intact mice, the MASCO interacts with the SCN in a manner that is strain, sex, and dose dependent. In SCN-lesioned mice, it induces robust free-running locomotor rhythmicity, which persists for up to 14 cycles after methamphetamine is withdrawn. In the future, localization of the MASCO and characterization of its underlying molecular mechanism, as well as its interactions with other oscillators in the body, will be essential to a complete understanding of the organization of the mammalian circadian system.     

West Nile Virus Capsid Degradation of Claudin Proteins Disrupts Epithelial Barrier Function

During acute infection, West Nile virus (WNV) has been reported to infect a variety of cell types in various tissues of both experimentally and naturally infected hosts. Virus infects epithelial cells in the skin, kidney, intestine, and testes, although the importance of these findings is unclear. In the current study, we have observed that WNV infection of kidney tubules in mice coincides with the loss of expression of several members of the claudin family. Proteins of this family are often involved in epithelial barrier formation and function. WNV infection of epithelial cells in culture resulted in a decrease in the transepithelial electrical resistance, an increase in the efflux of mannitol across the monolayer, and a loss of intracellular levels of claudin-1 to -4. WNV capsid alone was sufficient for the degradation event, which was mediated through lysosomal proteases. Since epithelial cells are frequent sites of WNV infection, these observations imply a potential mechanism for virus dissemination and extraneural pathogenesis.West Nile Virus (WNV) is a mosquito-borne flavivirus that first appeared in the United States in 1999. Since that time, the virus has spread across the continental United States, causing significant morbidity and mortality. Roughly 20% of WNV infections are symptomatic, and approximately 1 out of every 150 infections progresses to encephalitis and/or meningitis (39, 42). Following the bite of a carrier mosquito, WNV infection of the host is thought to initiate in the Langerhans cells of the skin (13). Viral replication continues in the regional tissue and lymph nodes, which results in the dissemination of the virus into the bloodstream. Replication then proceeds at several sites throughout the host, including the kidneys, heart, connective tissue, smooth muscle, spleen, and ultimately the brain (46). Infection of the nervous system is characteristic of the most severe cases of WNV disease, often resulting in death or long-term neurologic sequelae (26). Pathologies associated with extraneural sites of infection have also been reported, including acute renal failure (11, 24).Epithelial cells are major targets of WNV infection in vivo in both humans and experimentally infected rodents. In a hamster model of WNV infection, virus can be detected in the epithelial cells of the kidney up to 60 days postinfection, suggesting that this tissue may be a site of viral persistence (53). Infection of kidney epithelium has also been found in WNV-infected mice (20) and dogs (12). In WNV-infected humans, epithelial cell infection has also been demonstrated in several organs, including the kidney, lung, pancreas, thyroid, intestine, and testes (4). These studies suggest that the epithelial cells may play an important role in WNV pathogenesis. However, the growth characteristics of WNV in epithelial cells and the effect of WNV on the polarity and permeability functions of polarized epithelial cells have not been investigated. One important feature of epithelial cells is the presence of tight junctions (TJ). TJ are intercellular contacts between endothelial or epithelial cells which allow the formation of polarized cells with discrete apical and basolateral plasma membrane domains and separate physiologically distinct apical and basolateral fluid compartments (22). Macromolecules larger than 30 Å in diameter are generally excluded from the TJ, but permeability to small ions varies depending on tissue-specific requirements and local physiological stimuli (2, 23). TJ are thus not static seals but dynamic structures subject to transient changes in permeability (30). The TJ is composed of the transmembrane proteins occludin, claudin (a family of more than 20 members), and junctional adhesion molecule (a family of four known members). These proteins mediate cell-cell interactions and regulate junctional permeability. The transmembrane proteins interact on their cytoplasmic side with several other components of the TJ. These include zonula occludens 1, 2, and 3 (ZO-1 to -3, which belong to a family of membrane-associated guanylate kinase homologues). ZO-1 is thought to nucleate the initial formation of the TJ and to provide a scaffold for TJ assembly. This process is thought to require the interaction of ZO-1 with the adherens junction (1, 7).In this study, we show that WNV infection of epithelial cells in vivo and in vitro results in a loss of claudin protein expression. The loss of claudin expression coincides with perturbation of the permeability functions of cultured epithelial cells as measured by a reduction in transepithelial electrical resistance (TER) and an increase in the efflux of [¹⁴C]mannitol across the cell monolayer. Expression of WNV capsid alone was sufficient to mediate these events. Epithelial cells are likely to be targets for WNV infection from the earliest times of exposure (e.g., the keratinocytes at the site of the mosquito bite) and also may be sites of long-term persistence. Therefore, the effect of the virus on the TJ, a crucial component of epithelial function, suggests a possible mechanism of virus spread, as well as potentially contributing to pathogenesis.     

Discovery of N-{N-[(3-cyanobenzene) sulfonyl]-4(R)-(3,3-difluoropiperidin-1-yl)-(l)-prolyl}-4-[(3′,5′-dichloro-isonicotinoyl) amino]-(l)-phenylalanine (MK-0617), a highly potent and orally active VLA-4 antagonist

A series of prolyl-N-isonicotinoyl-(L)-4-aminophenylalanine derivatives substituted at the proline 4-position with cyclic amines was evaluated as VLA-4 antagonists. The ring size and presence or absence of fluorine affected potency and receptor occupancy. The analog with 3,3-difluoropiperidine at the proline 4-position (13) was the most potent compound and had very good duration of receptor occupancy in vitro. The ethyl ester prodrug of 13 demonstrated excellent receptor occupancy after oral dosing in rats.     

Evaluation of the Australian weed risk assessment system for the prediction of plant invasiveness in Canada

The Australian Weed Risk Assessment system has been tested in a number of countries and geographical areas since its introduction in 1997, and is widely considered to be an accurate method of predicting the risk of invasiveness of new plant introductions. We evaluated the system against 152 plant species with at least a 50-year introduction history in Canada, including major and minor weeds and species which have not naturalized. Four questions that referred explicitly to Australian conditions were replaced with appropriate equivalent questions for Canada. The weediness of each species was independently rated by a panel of Canadian agricultural, botanical, and conservation experts. Using the standard cut-off scores, the system correctly rejected all major and 86% of minor weeds. However, it also incorrectly rejected 44% of non-weedy species. The diagnostic power of the system, as measured by the receiver operating characteristic curve, was similar to but somewhat lower than that found in other regions where the system has been evaluated. Answers to 23 of the 49 questions were not significantly associated with experts’ weediness ratings, indicating that a simplified system could give equally reliable results for Canada. Experts’ ratings were strongly related to cold-hardiness, suggesting that the system could be improved by making better use of data on climatic tolerances. We suggest that performance would also be improved by combining likelihood- and consequence-related scores in a multiplicative rather than additive way.     

Integrating genetic and network analysis to characterize genes related to mouse weight

Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker data from an F2 mouse intercross to examine the large-scale organization of the gene co-expression network in liver, and annotate several gene modules in terms of 22 physiological traits. We identify chromosomal loci (referred to as module quantitative trait loci, mQTL) that perturb the modules and describe a novel approach that integrates network properties with genetic marker information to model gene/trait relationships. Specifically, using the mQTL and the intramodular connectivity of a body weight–related module, we describe which factors determine the relationship between gene expression profiles and weight. Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest.