Structural insights of Mycobacterium GTPase‐Obg and anti‐sigma‐F factor Usfx interaction

An essential protein for bacterial growth, GTPase‐Obg (Obg), is known to play an unknown but crucial role in stress response as its expression increases in Mycobacterium under stress conditions. It is well reported that Obg interacts with anti‐sigma‐F factor Usfx; however, a detailed analysis and structural characterization of their physical interaction remain undone. In view of above‐mentioned points, this study was conceptualized for performing binding analysis and structural characterization of Obg‐Usfx interaction. The binding studies were performed by surface plasmon resonance, while in silico docking analysis was done to identify crucial residues responsible for Obg‐Usfx interaction. Surface plasmon resonance results clearly suggest that N‐terminal and G domains of Obg mainly contribute to Usfx binding. Also, binding constants display strong affinity that was further evident by intermolecular hydrogen bonds and hydrophobic interactions in the predicted complex. Strong interaction between Obg and Usfx supports the view that Obg plays an important role in stress response, essentially required for Mycobacterium survival. As concluded by various studies that Obg is crucial for Mycobacterium survival under stress, this structural information may help us in designing novel and potential inhibitors against resistant Mycobacterium strains.     

Partitioning of MLX-Family Transcription Factors to Lipid Droplets Regulates Metabolic Gene Expression

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Leaching requirement conceptual models for reactive salt

Accurate prediction of the leaching requirements (Lr) of crops and striving to attain them is essential for efficient irrigation water use. Solute modeling was extended to develop four Lr conceptual models that do not neglect solute reactions in the root-zone, surface evaporation, and the influence of immobile wetted pore space. The models were based on: (i) the water movement equation which included an exponential water-uptake function (-e) or the 40-30-20-10 water-uptake function (-4); (ii) the solute movement equation for a reactive salt of a linear reaction term (the Lrchem-e and Lrchem-4 models); or the employment of output (salinity of soil solution, EC vs concentration factor, CF) of the SAO comprehensive chemical model (the LrSAO-e and LrSAO-4 models); and (iii) the inclusion of an effective soil solution volume in the transport equations. The root-zone average relative effective soil solution volume νeff (L | L50, p) was of sigmoidal response to leaching fraction (L) with two adjustable parameters L50 and p; the root-zone average reduced retention coefficient decreased linearly with L; and salt concentration at soil surface was related to salt concentration of irrigation water (ECi) by the fraction of irrigation water that evaporated (∈). The resulted concentration profiles indicated the salt behaved as a conservative one down to a threshold depth (xs) below of which salt was retained and precipitated. The depth of the conservative-salt front, xs increased with L and the 40-30-20-10 water-uptake pattern overestimated the xs depth relative to the exponential pattern. Concentration profiles were integrated to compute the root-zone average salinity, which was converted to crop salt-tolerance threshold (AE). The four conceptual models were successfully calibrated using experimental AE/ECi vs. Lr data with the input parameter values: ς = 0.27, p = 1.44, L50 = 0.16, ω = 2, and ∈ = 0 or 0.1 for the exponential or the 40-30-20-10 pattern, respectively; where ς is relative root length parameter and ω is a weighing parameter. No significant difference existed between the four model correlations at the 0.05 level. The four models require ECi and AE of the crop as input for Lr prediction. Sensitivity analysis revealed predicted Lr was sensitive the least to error in ∈. For tolerant and moderately tolerant crops Lr was sensitive the most to ς, and for sensitive crops to L50 and p. Model verification and validation were discussed. In deriving the present Lr models, no osmotic adjustment was required and both the exponential and the 40-30-20-10 water uptake patterns were, equivalently, applicable. This revised version was published online in July 2006 with corrections to the Cover Date.     

Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system

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Activation of the PDGF β Receptor by a Persistent Artificial Signal Peptide

Most eukaryotic transmembrane and secreted proteins contain N-terminal signal peptides that mediate insertion of the nascent translation products into the membrane of the endoplasmic reticulum. After membrane insertion, signal peptides typically are cleaved from the mature protein and degraded. Here, we tested whether a small hydrophobic protein selected for growth promoting activity in mammalian cells retained transforming activity while also acting as a signal peptide. We replaced the signal peptide of the PDGF β receptor (PDGFβR) with a previously described 29-residue artificial transmembrane protein named 9C3 that can activate the PDGFβR in trans. We showed that a modified version of 9C3 at the N-terminus of the PDGFβR can function as a signal peptide, as assessed by its ability to support high level expression, glycosylation, and cell surface localization of the PDGFβR. The 9C3 signal peptide retains its ability to interact with the transmembrane domain of the PDGFβR and cause receptor activation and cell proliferation. Cleavage of the 9C3 signal peptide from the mature receptor is not required for these activities. However, signal peptide cleavage does occur in some molecules, and the cleaved signal peptide can persist in cells and activate a co-expressed PDGFβR in trans. Our finding that a hydrophobic sequence can display signal peptide and transforming activity suggest that some naturally occurring signal peptides may also display additional biological activities by interacting with the transmembrane domains of target proteins.     

Potential stocks of reef fish-based ecosystem services in the Kuroshio Current region: Their relationship with latitude and biodiversity

The latitudinal decline of species richness is a general spatial pattern of biodiversity, and it applies to marine species as well. Based on a latitudinal gradient of marine species richness, potential stocks of marine ecosystem services are expected to be higher in lower latitudes through increment in biodiversity. However, little is known about the relationships of the marine ecosystem services with latitude and biodiversity. We estimated the latitudinal patterns and relationships with the biodiversity of potential stocks of three major reef fish-based ecosystem services (fisheries production, aquarium fish production, and recreational diving) at ten coral habitats from tropical to temperate zones in the Kuroshio Current region (8°37′N–33°24′N) using field survey data and information from relevant websites and administrative statistics. We found a latitudinal declin from south to north in potential stocks of aquarium fish production and diving in this region, whereas the peaks of fisheries production were found around both tropical and sub-tropical zones. Our results also showed strong positive effects of biodiversity on potential stocks of the three ecosystem services, highlighting the importance of conserving diverse fish species to sustain multiple services at high levels. Broad spatial patterns of the reef fish-based ecosystem services are useful as baselines for future evaluation of their changes. As the effects of climate change on reef fishes are predicted to vary among different latitude zones, our estimates of the ecosystem services infer specific management and economic actions for the respective zones against climate change.     

An Extreme Value Analysis of Pollutant Concentrations in Surface Soils Due to Atmospheric Deposition

Risk assessments often rely on deterministic models using long-term averages or “steady-state” values of input variables. Such models do not provide the information needed to estimate acute exposures. This study uses extreme value theory to examine the frequency and magnitude of daily pollutant concentrations in surface soils predicted at six U.S. locations. Concentrations are predicted using a deposition-leaching model and 50 years of historical precipitation data. A stochastic model also is used to generate 1000 years of precipitation data as modeling inputs for each location. The annual maximum concentrations at each site are fitted to a Gumbel type I distribution to estimate occurrence probability. For soluble pollutants, the predicted concentration varied substantially with precipitation, and the maximum daily concentrations exceeded annual averages by 4 to 8 times. Observed and synthetic precipitation data produced similar results at most study locations, though the synthetic data provided a slightly better fit to the Gumbel type I distribution. The precipitation model allows the generation of representative precipitation data that extend limited historical records. The extreme value analysis facilitates the evaluation of maximum pollutant concentrations, return periods, and other statistics that are important in evaluating acute exposures.     

Protein expression by Streptococcus uberis in co-culture with bovine mammary epithelial cells

Three strains of Streptococcus uberis isolated from dairy cows with mastitis were co-cultured with a bovine mammary epithelial cell line (MAC-T) in Dulbecco's modified Eagle's medium without fetal bovine serum. Protein profiles from culture supernatants and bacterial pellets among different treatments were compared by electrophoresis. There were proteins induced or having increased expression in both supernatant and surface-associated samples from S. uberis co-cultured with MAC-T cells. Some of these proteins were recognized by antibodies in serum obtained from a cow infected by S. uberis . In supernatant samples, there were two distinct protein bands at 35 and 36.8 kDa for all three strains of S. uberis co-cultured with MAC-T cells. These two bands were absent when bacterial protein synthesis was inhibited by chloramphenicol. This study clearly indicates that bacterial protein expression was regulated in response to co-culture with mammary epithelial cells.