Selective prediction of interaction sites in protein structures with THEMATICS

Background  

Methods are now available for the prediction of interaction sites in protein 3D structures. While many of these methods report high success rates for site prediction, often these predictions are not very selective and have low precision. Precision in site prediction is addressed using Theoretical Microscopic Titration Curves (THEMATICS), a simple computational method for the identification of active sites in enzymes. Recall and precision are measured and compared with other methods for the prediction of catalytic sites.     

The binding of anionic and nonionic surfactants to collagen through the hydrophobic effect

The adsorption of nonionic surfactants on hide powder previously treated with anionic surfactants has been studied. The adsorption of nonionic surfactants takes place through hydrophobic interactions. A mechanism has been proposed for this interaction, assuming that the nonionic surfactant has been fixed by means of secondary adsorption (hydrophobic interaction) after the primary adsorption of the anionic surfactant (ionic and hydrophobic interaction) which makes it possible.     

Genetic targeting of Card19 is linked to disrupted NINJ1 expression,impaired cell lysis,and increased susceptibility to Yersinia infection

Cell death plays a critical role in inflammatory responses. During pyroptosis, inflammatory caspases cleave Gasdermin D (GSDMD) to release an N-terminal fragment that generates plasma membrane pores that mediate cell lysis and IL-1 cytokine release. Terminal cell lysis and IL-1β release following caspase activation can be uncoupled in certain cell types or in response to particular stimuli, a state termed hyperactivation. However, the factors and mechanisms that regulate terminal cell lysis downstream of GSDMD cleavage remain poorly understood. In the course of studies to define regulation of pyroptosis during Yersinia infection, we identified a line of Card19-deficient mice (Card19^lxcn) whose macrophages were protected from cell lysis and showed reduced apoptosis and pyroptosis, yet had wild-type levels of caspase activation, IL-1 secretion, and GSDMD cleavage. Unexpectedly, CARD19, a mitochondrial CARD-containing protein, was not directly responsible for this, as an independently-generated CRISPR/Cas9 Card19 knockout mouse line (Card19^Null) showed no defect in macrophage cell lysis. Notably, Card19 is located on chromosome 13, immediately adjacent to Ninj1, which was recently found to regulate cell lysis downstream of GSDMD activation. RNA-seq and western blotting revealed that Card19^lxcn BMDMs have significantly reduced NINJ1 expression, and reconstitution of Ninj1 in Card19^lxcn immortalized BMDMs restored their ability to undergo cell lysis in response to caspase-dependent cell death stimuli. Card19^lxcn mice exhibited increased susceptibility to Yersinia infection, whereas independently-generated Card19^Null mice did not, demonstrating that cell lysis itself plays a key role in protection against bacterial infection, and that the increased infection susceptibility of Card19^lxcn mice is attributable to loss of NINJ1. Our findings identify genetic targeting of Card19 being responsible for off-target effects on the adjacent gene Ninj1, disrupting the ability of macrophages to undergo plasma membrane rupture downstream of gasdermin cleavage and impacting host survival and bacterial control during Yersinia infection.     

Seasonal plant water uptake patterns in the saline southeast Everglades ecotone

The purpose of this study was to determine the seasonal water use patterns of dominant macrophytes coexisting in the coastal Everglades ecotone. We measured the stable isotope signatures in plant xylem water of Rhizophora mangle, Cladium jamaicense, and Sesuvium portulacastrum during the dry (DS) and wet (WS) seasons in the estuarine ecotone along Taylor River in Everglades National Park, FL, USA. Shallow soilwater and deeper groundwater salinity was also measured to extrapolate the salinity encountered by plants at their rooting zone. Average soil water oxygen isotope ratios (δ ¹⁸O) was enriched (4.8 ± 0.2‰) in the DS relative to the WS (0.0 ± 0.1‰), but groundwater δ ¹⁸O remained constant between seasons (DS: 2.2 ± 0.4‰; WS: 2.1 ± 0.1‰). There was an inversion in interstitial salinity patterns across the soil profile between seasons. In the DS, shallow water was euhaline [i.e., 43 practical salinity units (PSU)] while groundwater was less saline (18 PSU). In the WS, however, shallow water was fresh (i.e., 0 PSU) but groundwater remained brackish (14 PSU). All plants utilized 100% (shallow) freshwater during the WS, but in the DS R. mangle switched to a soil–groundwater mix (δ 55% groundwater) while C. jamaicense and S. portulacastrum continued to use euhaline shallow water. In the DS, based on δ ¹⁸O data, the roots of R. mangle roots were exposed to salinities of 25.4 ± 1.4 PSU, less saline than either C. jamaicense (39.1 ± 2.2 PSU) or S. portulacastrum (38.6 ± 2.5 PSU). Although the salinity tolerance of C. jamaicense is not known, it is unlikely that long-term exposure to high salinity is conducive to the persistence of this freshwater marsh sedge. This study increases our ecological understanding of how water uptake patterns of individual plants can contribute to ecosystem levels changes, not only in the southeast saline Everglades, but also in estuaries in general in response to global sea level rise and human-induced changes in freshwater flows.     

Competition between Hardwood Hammocks and Mangroves

A bstract The boundaries between mangroves and freshwater hammocks in coastal ecotones of South Florida are sharp. Further, previous studies indicate that there is a discontinuity in plant predawn water potentials, with woody plants either showing predawn water potentials reflecting exposure to saline water or exposure to freshwater. This abrupt concurrent change in community type and plant water status suggests that there might be feedback dynamics between vegetation and salinity. A model examining the salinity of the aerated zone of soil overlying a saline body of water, known as the vadose layer, as a function of precipitation, evaporation and plant water uptake is presented here. The model predicts that mixtures of saline and freshwater vegetative species represent unstable states. Depending on the initial vegetation composition, subsequent vegetative change will lead either to patches of mangrove coverage having a high salinity vadose zone or to freshwater hammock coverage having a low salinity vadose zone. Complete or nearly complete coverage by either freshwater or saltwater vegetation represents two stable steady-state points. This model can explain many of the previous observations of vegetation patterns in coastal South Florida as well as observations on the dynamics of vegetation shifts caused by sea level rise and climate change.     

Production of pectinases byAspergillus sp using differently pretreated lemon peel as the carbon source

Summary Aspergillus sp strains from decaying lemons were tested for extracellular pectinase production, testing differently pretreated lemon peel as the carbon source instead of pectin. It was found that the production of extracellular polygalacturonase was about the same and that of pectinesterase substantially higher when unwashed fresh lemon peel was used instead of pectin. The culture filtrate obtained showed a clarifying capacity similar to that of a commercial pectinase preparation, but the vitamin C of the juice was less affected by the treatment.     

Distinct functions of maternal and somatic Pat1 protein paralogs

We previously identified Xenopus Pat1a (P100) as a member of the maternal CPEB RNP complex, whose components resemble those of P-(rocessing) bodies, and which is implicated in translational control in Xenopus oocytes. Database searches have identified Pat1a proteins in other vertebrates, as well as paralogous Pat1b proteins. Here we characterize Pat1 proteins, which have no readily discernable sequence features, in Xenopus oocytes, eggs, and early embryos and in human tissue culture cells. xPat1a and 1b have essentially mutually exclusive expression patterns in oogenesis and embryogenesis. xPat1a is degraded during meiotic maturation, via PEST-like regions, while xPat1b mRNA is translationally activated at GVBD by cytoplasmic polyadenylation. Pat1 proteins bind RNA in vitro, via a central domain, with a preference for G-rich sequences, including the NRAS 5′ UTR G-quadruplex-forming sequence. When tethered to reporter mRNA, both Pat proteins repress translation in oocytes. Indeed, both epitope-tagged proteins interact with the same components of the CPEB RNP complex, including CPEB, Xp54, eIF4E1b, Rap55B, and ePAB. However, examining endogenous protein interactions, we find that in oocytes only xPat1a is a bona fide component of the CPEB RNP, and that xPat1b resides in a separate large complex. In tissue culture cells, hPat1b localizes to P-bodies, while mPat1a-GFP is either found weakly in P-bodies or disperses P-bodies in a dominant-negative fashion. Altogether we conclude that Pat1a and Pat1b proteins have distinct functions, mediated in separate complexes. Pat1a is a translational repressor in oocytes in a CPEB-containing complex, and Pat1b is a component of P-bodies in somatic cells.     

Bone quality and healing in a swine vascularized bone allotransplantation model using cyclosporine-based immunosuppression therapy

Although vascularized bone and joint allotransplantation is a promising new treatment option for reconstructing large bone defects, the need for immunosuppressive agents to prevent rejection in these procedures poses a major problem. This problem stems from the fact that several of these agents can cause harmful side effects, such as alterations in bone quality and healing. Therefore, the purpose of this study was to determine what effect the commonly used immunosuppressant regimen cyclosporine A-based combination therapy has on bone quality and healing. In 10 pigs, vascularized bone allografts with skin and muscle components (osteomyocutaneous free flaps) were transplanted from size-matched donor animals. Recipient animals received oral cyclosporine A/mycophenolate mofetil/prednisone therapy for 90 days. Bone quality was studied before and after transplantation by measuring the bone's acoustic velocity and density and calculating the bone's elastic coefficient. Bone healing was assessed using radiographic analysis. Four animals were lost as a result of graft rejection or immunosuppression-related complications before the 90-day endpoint of the study. Although bone specimens taken from the six animals that completed the 90-day protocol had histological signs of rejection, they all seemed to have normal bone healing. Posttransplant bone density values were significantly decreased (p < 0.05) (1544.7 +/- 47.5 kg/m3) as compared with pretransplant values (1722.7 +/- 44.1 kg/m3). Results of the acoustic velocity and elastic coefficients measurements showed a significant decrease (p < 0.05) in posttransplant values (from 3503.0 +/- 165.1 meters/sec to 2963.0 +/- 54.6 meters/sec and from 21.6 +/- 2.2 GPa to 13.6 +/- 0.5 GPa, respectively), indicating diminished bone quality. The findings indicate that cyclosporine A/mycophenolate mofetil/prednisone combination therapy is ineffective in preventing bone rejection, that it decreases bone quality, and that it is associated with systemic toxicity, suggesting that this immunosuppressive regimen at the doses used in this study is not ideal for vascularized bone allotransplantation procedures.     

Lethal and sublethal effects of selected insecticides and an insect growth regulator on the boll weevil (Coleoptera: Curculionidae) ectoparasitoid Catolaccus grandis (Hymenoptera: Pteromalidae)

A laboratory culture of Catolaccus grandis (Burks), an ectoparasitoid of the boll weevil, Anthonomus grandis grandis Boheman, was exposed to lethal and sublethal doses of insecticides and an insect growth regulator using a spray chamber bioassay. Materials tested were azinphos-methyl, endosulfan, fipronil, malathion, cyfluthrin, dimethoate, spinosad, methyl parathion, acephate, oxamyl, and tebufenozide. At full rates, spinosad was significantly less toxic to female C. grandis than other treatments except endosulfan. Fipronil and malathion were significantly more toxic to females than other treatments. Most of the chemicals tested were highly toxic to male C. grandis; spinosad was least toxic. At reduced rates, most of 4 selected chemicals tested were low in toxicity to C. grandis; however, a reduced rate of malathion was significantly more toxic to females than other treatments. No C. grandis pupae developed from parasitism during a 24-h treatment period with malathion or spinosad. The sex ratio of progeny from sprayed adults appeared to be unaffected by the treatments.