Stable Isotopes Approach to Infer the Feeding Habit and Trophic Position of Freshwater Fishes in Tropical Lakes

A study was conducted on the stable isotope variation of muscle tissues from selected freshwater fish species from Temenggor Lake and Chenderoh Lake, Perak, Malaysia from December 2014 to March 2015. The objective is to assess the stable isotopes of δ13C to identify the carbon sources and δ15N of fish species from Temenggor and Chenderoh Lake, Perak, Malaysia to infer the trophic position of these fishes. Four types of fish species were analyzed by using stable isotope approach which were Hampala barb (Hampala macrolepidota), Oxygaster cyprinus (Oxygaster anomalura), Peacock Bass (Cichla ocellaris) and Nile Tilapia (Oreochromis niloticus). Stable isotopes of δ13C and δ15N were analysed using an elemental analyser Thermo Finnigan Flash EA 2000 connected to Finningan DELTA V AVANTAGE plus isotope ratio mass spectrometry by a ConFlo II interface. The δ13C values from both lakes implies a C3 phytoplankton as reported from the literature. Based on δ15N values of fish species, O. anomalura occupies the highest trophic level in Temenggor Lake, reflecting its carnivorous feeding habit despite its small size while C. ocellaris was the highest in Chenderoh Lake, implying its predatory behaviour. Further analysis should be carried out to incorporate primary producers and consumers to elucidate the food web in the tropical lake ecosystem. This study provides a reference record for conducting stable isotopes in the food web of tropical lake ecosystem for better management and deeper understanding of the ecosystem functioning

Determining how polymer-bubble interactions impact algal separation using the novel "Posi"-dissolved air flotation process

The novel dissolved air flotation (DAF) process that uses hydrophobically-modified polymers (HMPs) to generate positively charged bubbles (PosiDAF) has been shown to separate negatively charged algal cells without the need for coagulation-flocculation. Previous research has been limited to HMPs of poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) and, while they were effective at bench-scale, performance at pilot-scale was better using commercial poly(N,N-diallyl-N,N-dimethylammonium chloride) (PDADMAC). Hence, the aim of this research was to compare the effectiveness of PDADMAC modified with aliphatic and aromatic moieties in comparison to previously tested PDMAEMA HMPs in respect to algal cell separation and minimisation of effluent polymer concentration, as well as defining the underlying polymer-bubble interaction mechanisms. Polymer-bubble adhesion properties were measured using atomic force microscopy (AFM) while polymer concentration was monitored via zeta potential and, where possible, assays using fluorescence spectroscopy. Both PDADMAC functionalised with a fluorinated aromatic group (PDADMAC-BCF) and PDMAEMA modified with 1-bromodecane respectively, gave effective cell separation, while the treated effluent zeta potential values at maximum cell removal were lower than the other polymers trialled. The effluent polymer concentration when using PDADMAC-BCF was four times lower in comparison to another aromatically modified PDADMAC polymer. AFM studies indicated that, in contrast to the PDMAEMA-based polymers, the PDADMAC-based polymers did not adsorb closely to the bubble surface. The different polymer-bubble interactions indicate that separation mechanisms will also vary, potentially leading to differences in process effectiveness when explored at pilot scale

Gramene QTL database: development, content and applications

Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research

Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces

TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5αrh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5αrh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction. © 2011 Zhao et al

Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulanso

Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat) a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci) and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.Vicki Thomson, Ken P. Aplin, Alan Cooper, Susan Hisheh, Hitoshi Suzuki, Ibnu Maryanto, Grace Yap, Stephen C. Donnella

Gramene: a growing plant comparative genomics resource

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions

Advances in small lasers

M.T.H was supported by an Australian Research council Future Fellowship research grant for this work. M.C.G. is grateful to the Scottish Funding Council (via SUPA) for financial support.Small lasers have dimensions or modes sizes close to or smaller than the wavelength of emitted light. In recent years there has been significant progress towards reducing the size and improving the characteristics of these devices. This work has been led primarily by the innovative use of new materials and cavity designs. This Review summarizes some of the latest developments, particularly in metallic and plasmonic lasers, improvements in small dielectric lasers, and the emerging area of small bio-compatible or bio-derived lasers. We examine the different approaches employed to reduce size and how they result in significant differences in the final device, particularly between metal- and dielectric-cavity lasers. We also present potential applications for the various forms of small lasers, and indicate where further developments are required.PostprintPeer reviewe

Alpha-tocotrienol is the most abundant tocotrienol isomer circulated in plasma and lipoproteins after postprandial tocotrienol-rich vitamin E supplementation

<p>Abstract</p> <p>Background</p> <p>Tocotrienols (T3) and tocopherols (T), both members of the natural vitamin E family have unique biological functions in humans. T3 are detected in circulating human plasma and lipoproteins, although at concentrations significantly lower than α-tocopherol (α-T). T3, especially α-T3 is known to be neuropotective at nanomolar concentrations and this study evaluated the postprandial fate of T3 and α-T in plasma and lipoproteins.</p> <p>Methods</p> <p>Ten healthy volunteers (5 males and 5 females) were administered a single dose of vitamin E [526 mg palm tocotrienol-rich fraction (TRF) or 537 mg α-T] after 7-d pre-conditioning on a T3-free diet. Blood was sampled at baseline (fasted) and 2, 4, 5, 6, 8, and 24 h after supplementation. Concentrations of T and T3 isomers in plasma, triacylglycerol-rich particles (TRP), LDL, and HDL were measured at each postprandial interval.</p> <p>Results</p> <p>After TRF supplementation, plasma α-T3 and γ-T3 peaked at 5 h (α-T3: 4.74 ± 1.69 μM; γ-T3: 2.73 ± 1.27 μM). δ-T3 peaked earlier at 4 h (0.53 ± 0.25 μM). In contrast, α-T peaked at 6 h (30.13 ± 2.91 μM) and 8 h (37.80 ± 3.59 μM) following supplementation with TRF and α-T, respectively. α-T was the major vitamin E isomer detected in plasma, TRP, LDL, and HDL even after supplementation with TRF (composed of 70% T3). No T3 were detected during fasted states. T3 are detected postprandially only after TRF supplementation and concentrations were significantly lower than α-T.</p> <p>Conclusions</p> <p>Bio-discrimination between vitamin E isomers in humans reduces the rate of T3 absorption and affects their incorporation into lipoproteins. Although low absorption of T3 into circulation may impact some of their physiological functions in humans, T3 have biological functions well below concentration noted in this study.</p

A Cryogenic Silicon Interferometer for Gravitational-wave Detection

The detection of gravitational waves from compact binary mergers by LIGO has opened the era of gravitational wave astronomy, revealing a previously hidden side of the cosmos. To maximize the reach of the existing LIGO observatory facilities, we have designed a new instrument that will have 5 times the range of Advanced LIGO, or greater than 100 times the event rate. Observations with this new instrument will make possible dramatic steps toward understanding the physics of the nearby universe, as well as observing the universe out to cosmological distances by the detection of binary black hole coalescences. This article presents the instrument design and a quantitative analysis of the anticipated noise floor