A newly identified population of Gambusia affinis (Baird and Girard, 1853), a non-native invasive species, in Lake Kenyir, Malaysia: Implications for management

Gambusia affinis (Baird and Girard, 1853), a notorious non-native invasive fish species, has negatively impacted aquatic ecosystems around the world. This species was recently identified in Lake Kenyir, one of the largest impoundments in SouTheast Asia, using DNA barcoding. The coxI sequence of Gambusia caught in Lake Kenyir was compared with the sequences of topotypic voucher specimens of G. affinis and two other candidate Poeciliidae. The species was found to cluster with G. affinis but not with monophyletic clades of either G. holbrooki or P. reticulata thus confirming species identity. The fish is yet to be widely established in the lake with the current distribution limited to areas of anthropogenic disturbance

Gene family encoding the major toxins of lethal \u3ci\u3eAmanita\u3c/i\u3e mushrooms

Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode α-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. α-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable ‘‘toxin’’ region capable of encoding a wide variety of peptides of 7–10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes

Rapid optimization of enzyme mixtures for deconstruction of diverse pretreatment/biomass feedstock combinations

<p>Abstract</p> <p>Background</p> <p>Enzymes for plant cell wall deconstruction are a major cost in the production of ethanol from lignocellulosic biomass. The goal of this research was to develop optimized synthetic mixtures of enzymes for multiple pretreatment/substrate combinations using our high-throughput biomass digestion platform, GENPLAT, which combines robotic liquid handling, statistical experimental design and automated Glc and Xyl assays. Proportions of six core fungal enzymes (CBH1, CBH2, EG1, β-glucosidase, a GH10 endo-β1,4-xylanase, and β-xylosidase) were optimized at a fixed enzyme loading of 15 mg/g glucan for release of Glc and Xyl from all combinations of five biomass feedstocks (corn stover, switchgrass, <it>Miscanthus</it>, dried distillers' grains plus solubles [DDGS] and poplar) subjected to three alkaline pretreatments (AFEX, dilute base [0.25% NaOH] and alkaline peroxide [AP]). A 16-component mixture comprising the core set plus 10 accessory enzymes was optimized for three pretreatment/substrate combinations. Results were compared to the performance of two commercial enzymes (Accellerase 1000 and Spezyme CP) at the same protein loadings.</p> <p>Results</p> <p>When analyzed with GENPLAT, corn stover gave the highest yields of Glc with commercial enzymes and with the core set with all pretreatments, whereas corn stover, switchgrass and <it>Miscanthus </it>gave comparable Xyl yields. With commercial enzymes and with the core set, yields of Glc and Xyl were highest for grass stovers pretreated by AP compared to AFEX or dilute base. Corn stover, switchgrass and DDGS pretreated with AFEX and digested with the core set required a higher proportion of endo-β1,4-xylanase (EX3) and a lower proportion of endo-β1,4-glucanase (EG1) compared to the same materials pretreated with dilute base or AP. An optimized enzyme mixture containing 16 components (by addition of α-glucuronidase, a GH11 endoxylanase [EX2], Cel5A, Cel61A, Cip1, Cip2, β-mannanase, amyloglucosidase, α-arabinosidase, and Cel12A to the core set) was determined for AFEX-pretreated corn stover, DDGS, and AP-pretreated corn stover. The optimized mixture for AP-corn stover contained more exo-β1,4-glucanase (i.e., the sum of CBH1 + CBH2) and less endo-β1,4-glucanase (EG1 + Cel5A) than the optimal mixture for AFEX-corn stover. Amyloglucosidase and β-mannanase were the two most important enzymes for release of Glc from DDGS but were not required (i.e., 0% optimum) for corn stover subjected to AP or AFEX. As a function of enzyme loading over the range 0 to 30 mg/g glucan, Glc release from AP-corn stover reached a plateau of 60-70% Glc yield at a lower enzyme loading (5-10 mg/g glucan) than AFEX-corn stover. Accellerase 1000 was superior to Spezyme CP, the core set or the 16-component mixture for Glc yield at 12 h, but the 16-component set was as effective as the commercial enzyme mixtures at 48 h.</p> <p>Conclusion</p> <p>The results in this paper demonstrate that GENPLAT can be used to rapidly produce enzyme cocktails for specific pretreatment/biomass combinations. Pretreatment conditions and feedstock source both influence the Glc and Xyl yields as well as optimal enzyme proportions. It is predicted that it will be possible to improve synthetic enzyme mixtures further by the addition of additional accessory enzymes.</p

Alkaline peroxide pretreatment of corn stover: effects of biomass, peroxide, and enzyme loading and composition on yields of glucose and xylose

<p>Abstract</p> <p>Background</p> <p>Pretreatment is a critical step in the conversion of lignocellulose to fermentable sugars. Although many pretreatment processes are currently under investigation, none of them are entirely satisfactory in regard to effectiveness, cost, or environmental impact. The use of hydrogen peroxide at pH 11.5 (alkaline hydrogen peroxide (AHP)) was shown by Gould and coworkers to be an effective pretreatment of grass stovers and other plant materials in the context of animal nutrition and ethanol production. Our earlier experiments indicated that AHP performed well when compared against two other alkaline pretreatments. Here, we explored several key parameters to test the potential of AHP for further improvement relevant to lignocellulosic ethanol production.</p> <p>Results</p> <p>The effects of biomass loading, hydrogen peroxide loading, residence time, and pH control were tested in combination with subsequent digestion with a commercial enzyme preparation, optimized mixtures of four commercial enzymes, or optimized synthetic mixtures of pure enzymes. AHP pretreatment was performed at room temperature (23°C) and atmospheric pressure, and after AHP pretreatment the biomass was neutralized with HCl but not washed before enzyme digestion. Standard enzyme digestion conditions were 0.2% glucan loading, 15 mg protein/g glucan, and 48 h digestion at 50°C. Higher pretreatment biomass loadings (10% to 20%) gave higher monomeric glucose (Glc) and xylose (Xyl) yields than the 2% loading used in earlier studies. An H₂O₂loading of 0.25 g/g biomass was almost as effective as 0.5 g/g, but 0.125 g/g was significantly less effective. Optimized mixtures of four commercial enzymes substantially increased post-AHP-pretreatment enzymatic hydrolysis yields at all H₂O₂concentrations compared to any single commercial enzyme. At a pretreatment biomass loading of 10% and an H₂O₂loading of 0.5 g/g biomass, an optimized commercial mixture at total protein loadings of 8 or 15 mg/g glucan gave monomeric Glc yields of 83% or 95%, respectively. Yields of Glc and Xyl after pretreatment at a low hydrogen peroxide loading (0.125 g H₂O₂/g biomass) could be improved by extending the pretreatment residence time to 48 h and readjusting the pH to 11.5 every 6 h during the pretreatment. A Glc yield of 77% was obtained using a pretreatment of 15% biomass loading, 0.125 g H₂O₂/g biomass, and 48 h with pH adjustment, followed by digestion with an optimized commercial enzyme mixture at an enzyme loading of 15 mg protein/g glucan.</p> <p>Conclusions</p> <p>Alkaline peroxide is an effective pretreatment for corn stover. Particular advantages are the use of reagents with low environmental impact and avoidance of special reaction chambers. Reasonable yields of monomeric Glc can be obtained at an H₂O₂concentration one-quarter of that used in previous AHP research. Additional improvements in the AHP process, such as peroxide stabilization, peroxide recycling, and improved pH control, could lead to further improvements in AHP pretreatment.</p

Conditional deletion of the bcl-x gene from mouse mammary epithelium results in accelerated apoptosis during involution but does not compromise cell function during lactation

In the mammary gland Bcl-x is the most abundant cell survival factor from the Bcl-2 family. Since Bcl-x null mice die around day 12 of embryogenesis, the relevance of this protein in organ development and function is poorly understood. In erythroid cells bcl-x gene expression is controlled by cytokines and the transcription factor Stat5 (signal transducer and activator of transcription). However, we identified that bcl-x RNA levels in mammary tissue from prolactin receptor- and Stat5-null mice were indistinguishable from wild type mice. We have proposed that Bcl-x might control the survival of mammary epithelial cells throughout pregnancy, lactation, and the early stages of involution, and we have now tested this hypothesis through the conditional deletion of the bcl-x gene from mouse mammary epithelium. Conditional (floxed) bcl-x alleles were excised from alveolar cells during pregnancy using a Cre transgene under the control of the whey acidic protein gene promoter. Deletion of the bcl-x gene from the entire epithelial compartment (ducts and alveoli) was achieved by expressing Cre-recombinase under control of the mouse mammary tumor virus long terminal repeat. The absence of Bcl-x did not compromise proliferation and differentiation of mammary ductal and alveolar epithelial cells in virgin mice and during pregnancy and lactation. However, epithelial cell death and tissue remodeling were accelerated in the bcl-x conditional knockout mice during the first stage of involution. Concomitant deletion of the bax gene did not significantly modify the Bcl-x phenotype. Our results suggest that Bcl-x is not essential during mammopoiesis, but is critical for controlled apoptosis during the first phase of involution. Published by Elsevier Science Ireland Ltd

In situ XAFS of acid-resilient iridate pyrochlore oxygen evolution electrocatalysts under operating conditions

Pyrochlore iridates (Na,Ca)2-xIr2O6?H2O are acid-stable electrocatalysts that are candidates for use in electrolysers and fuel cells. Ir LIII-edge X-ray absorption fine structure spectroscopy in 1 M H2SO4 at oxygen evolution conditions suggests the involvement of the electrons from the conduction band of the metallic particles, rather than just surface iridium reacting

Influence of carbon source on the expression of Cochliobolus carbonum xylan-degrading enzyme genes

The expression of four Cochliobolus carbonum endo-1,4-b-xylanase genes (XYL1, XYL2, XYL3, XYL4), and an exo-1,4-b-xylosidase gene (XYP1) was studied following the growth of the fungus in minimal medium containing glucose, sucrose, xylose, xylan, pectin, or cellulose. The XYL1 and XYL2 genes were expressed only when the culture medium contained xylan or cellulose. Both XYL3 and XYL4 are induced by xylose and xylan, and XYP1 expression is induced by xylose, xylan, pectin and cellulose. None of these genes is expressed in glucose or sucrose media. The differential expression of these enzymes may provide means for the fungus to adapt to different conditions

Gene Transfer of Engineered Calmodulin Alleviates Ventricular Arrhythmias in a Calsequestrin-Associated Mouse Model of Catecholaminergic Polymorphic Ventricular Tachycardia

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a familial arrhythmogenic syndrome characterized by sudden death. There are several genetic forms of CPVT associated with mutations in genes encoding the cardiac ryanodine receptor (RyR2) and its auxiliary proteins including calsequestrin (CASQ2) and calmodulin (CaM). It has been suggested that impairment of the ability of RyR2 to stay closed (ie, refractory) during diastole may be a common mechanism for these diseases. Here, we explore the possibility of engineering CaM variants that normalize abbreviated RyR2 refractoriness for subsequent viral-mediated delivery to alleviate arrhythmias in non-CaM-related CPVT

Structures of mixed manganese ruthenium oxides (Mn1−xRux)O2(Mn_{1−x}Ru_x)O_2 crystallised under acidic hydrothermal conditions

A synthesis method for the preparation of mixed manganese–ruthenium oxides is presented along with a detailed characterisation of the solids produced. The use of 1 M aqueous sulfuric acid mediates the redox reaction between KRuO$_4$, KMnO$_4$ and Mn$^{2+}$ to form ternary oxides. At reaction temperature of 100°C the products are mixtures of α-MnO$_2$ (hollandite-type) and β-MnO$_2$ (rutile-type), with some evidence of Ru incorporation in each from their expanded unit cell volumes. At reaction temperature of 200°C solid-solutions β-Mn$_{1−x}$Ru$_x$O$_2$ are formed and materials with x ≤ 0.6 have been studied. The amount of Ru included in the oxide is greater than expected from the ratio of metals used in the synthesis, as determined by elemental analysis, implying that some Mn remains unreacted in solution. Powder X-ray diffraction (XRD) shows that while the unit cell volume expands in a linear manner, following Vegard's law, the tetragonal lattice parameters, and the a/c ratio, do not follow the extrapolated trends: this anisotropic behaviour is consistent with the different local coordination of the metals in the end members. Powder XRD patterns show increased peak broadening with increasing ruthenium content, which is corroborated by electron microscopy that shows nanocrystalline material. X-ray absorption near-edge spectra show that the average oxidation state of Mn in the solid solutions is reduced below +4 while that of Ru is increased above +4, suggesting some redistribution of charge. Analysis of the extended X-ray absorption fine structure provides complementary local structural information, confirming the formation of a solid solution, while X-ray photoelectron spectroscopy shows that the surface oxidation states of both Ru and Mn are on average lower than +4, suggesting a disordered surface layer may be present in the materials

ARSENIC REMOVAL IN WATER TREATMENT FACILITIES: SURVEY OF GEOCHEMICAL FACTORS AND PILOT PLANT EXPERIMENTS

Midwest Technology Assistance Center for Small Community Water Supplies (MTAC)Ope