Gene Variant of Barrier to Autointegration Factor 2 (Banf2w) Is Concordant with Female Determination in Cichlids

Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10⁻²⁶). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy–Weinberg equilibrium (p < 4.2 × 10⁻³), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD.     

Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks

Applications running on leadership platforms are more and more bottlenecked by storage input/output (I/O). In an effort to combat the increasing disparity between I/O throughput and compute capability, we created Adaptable IO System (ADIOS) in 2005. Focusing on putting users first with a service oriented architecture, we combined cutting edge research into new I/O techniques with a design effort to create near optimal I/O methods. As a result, ADIOS provides the highest level of synchronous I/O performance for a number of mission critical applications at various Department of Energy Leadership Computing Facilities. Meanwhile ADIOS is leading the push for next generation techniques including staging and data processing pipelines. In this paper, we describe the startling observations we have made in the last half decade of I/O research and development, and elaborate the lessons we have learned along this journey. We also detail some of the challenges that remain as we look toward the coming Exascale era. Copyright © 2013 John Wiley & Sons, Ltd.     

Kinetics of the chemical oxidation of polysulfide anions in aqueous solution

The kinetic properties of the chemical oxidation of aqueous polysulfide solutions have been studied in phosphate-buffered systems at pH 7-12, at temperatures between 20 and 40 degrees C, and ionic strength between 0.05 and 0.50 M. Polysulfide solutions were mixed with a buffer solution of known dissolved oxygen concentration, after which the decrease in the oxygen concentration of the solution was measured in time. The rate of oxygen consumption can be described by the empirical relation d[O2]/dt= -k[Sx(2-)][O2](0.59) . The reaction rate constant k is moderately dependent on pH and goes through a maximum at pH 10. The rate of oxygen consumption for polysulfide solutions is approximately four times higher than for sulfide solutions. At pH values below 9, reaction products were formed according to Sx(2-)+3/2O2-->S2O3(2-)+(x-2)S(0) . At pH values higher than 9, more thiosulfate and additional sulfide were formed, which is attributed to the low chemical stability of the sulfur of oxidation state zero, formed upon polysulfide oxidation. Our results strongly suggest that hydrolysis of this 'nascent' elemental sulfur to HS- and S2O3(2-) is faster than hydrolysis of crystalline inorganic sulfur or colloidal particles of biologically produced sulfur, and has a significant contribution already at 30 degrees C and pH 10.     

SP1 protein-based nanostructures and arrays

Controlled formation of complex nanostructures is one of the main goals of nanoscience and nanotechnology. Stable Protein 1 (SP1) is a boiling-stable ring protein complex, 11 nm in diameter, which self-assembles from 12 identical monomers. SP1 can be utilized to form large ordered arrays; it can be easily modified by genetic engineering to produce various mutants; it is also capable of binding gold nanoparticles (GNPs) and thus forming protein-GNP chains made of alternating SP1s and GNPs. We report the formation and the protocols leading to the formation of those nanostructures and their characterization by transmission electron microscopy, atomic force microscopy, and electrostatic force microscopy. Further control over the GNP interdistances within the protein-GNP chains may lead to the formation of nanowires and structures that may be useful for nanoelectronics.     

Biological black water treatment combined with membrane separation

Separate treatment of black (toilet) water offers the possibility to recover energy and nutrients. In this study three combinations of biological treatment and membrane filtration were compared for their biological and membrane performance and nutrient conservation: a UASB followed by effluent membrane filtration, an anaerobic MBR and an aerobic MBR. Methane production in the anaerobic systems was lower than expected. Sludge production was highest in the aerobic MBR, followed by the anaerobic MBR and the UASB-membrane system. The level of nutrient conservation in the effluent was high in all three treatment systems, which is beneficial for their recovery from the effluent. Membrane treatment guaranteed an effluent which is free of suspended and colloidal matter. However, the concentration of soluble COD in the effluent still was relatively high and this may seriously hamper subsequent nutrient recovery by physical-chemical processes. The membrane filtration behaviour of the three systems was very different, and seemed to be dominated by the concentration of colloidals in the membrane feed. In general, membrane fouling was the lowest in the aerobic MBR, followed by the membranes used for UASB effluent filtration and the anaerobic MBR.     

Structural features and properties of soluble products derived from Eucalyptus globulus hemicelluloses

Eucalyptus globulus wood samples were subjected to double hydrothermal processing to remove extractives in the first stage, and to cause the selective solubilisation of 4-O-methylglucuronoxylan in the second stage. The hemicellulose-derived products present in the liquors from the second hydrothermal stage (substituted xylooligosaccharides, denoted XOS) were refined by treatments with membranes and ion exchange. The purified XOS product was assayed for composition and characterised by HPLC-RI, HPAEC-PAD, HPSEC, MALDI-TOF-MS and NMR techniques. The results suggested the presence of neutral and acidic XOS with a degree of acetylation of about 0.6. The fermentability of the refined XOS product by faecal inocula was assessed by measuring both substrate consumption and formation of short-chain fatty acids.     

Management of Alluvial Aquifers in Two Southern African Ephemeral Rivers: Implications for IWRM

This paper summarises innovative research into the assessment of long-term groundwater recharge from flood events in dryland environments of the Kuiseb (Namibia) and the Buffels (South Africa) rivers. The integrated water resource management (IWRM) policies and institutions affecting the exploitation of groundwater resources in each of these developing countries are compared. The relatively large alluvial aquifer of the Kuiseb River (～240 Mm³) is recharged from irregular floods originating in the upper catchment. Reported abstraction of 4.6 Mm³ per year is primarily consumed in the town of Walvis Bay, although the groundwater decay (pumping and natural losses along the period 1983–2005) was estimated in 14.8 Mm³ per year. Recharge is variable, occurring in 11 out of 13 years in the middle Kuiseb River, but only in 11 out of 28 years in the middle-lower reaches. In contrast, the Buffels River has relatively minor alluvial aquifers (～11 Mm³) and recharge sources derive from both lateral subsurface flow and floodwater infiltration, the latter limited to a recharge maximum of 1.3 Mm³ during floods occurring once every four years. Current abstractions to supply the adjacent rural population and a few small-scale, irrigated commercial farms are 0.15 Mm³ yr^???1, well within the long-term sustainable yield estimated to be 0.7 Mm³ yr^???1. Since independence in 1990, Namibia’s water resource management approach has focussed on ephemeral river basin management of which the Kuiseb Basin Management Committee (KBMC) is a model. Here, some water points are managed independently by rural communities through committees while the national bulk water supplier provides for Walvis Bay Municipality from the lower aquifers. This provides a sense of local ownership through local participation between government, NGOs and CBOs (community-based organisations) in the planning and implementation of IWRM. Despite the potential for water resource development in the lower Buffels River, the scope for implementing IWRM is limited not only by the small aquifer size, but also because basin management in South Africa is considered only in the context of perennial rivers. Since 2001, water service delivery in the Buffels River catchment has become the responsibility of two newly created local municipalities. As municipal government gains experience, skills and capacity, its ability to respond to local needs related to water service delivery will be accomplished through local participation in the design and implementation of annual ‘integrated development plans’. These two case studies demonstrate that a variety of IWRM strategies in the drylands of developing countries are appropriate depending on scales of governance, evolving policy frameworks, scales of need and limitations inherent in the hydrological processes of groundwater resources.     

Pacemaker Activity of the Human Sinoatrial Node: An Update on the Effects of Mutations in HCN4 on the Hyperpolarization-Activated Current

Since 2003, several loss-of-function mutations in the HCN4 gene, which encodes the HCN4 protein, have been associated with sinus node dysfunction. In human sinoatrial node (SAN), HCN4 is the most abundant of the four isoforms of the HCN family. Tetramers of HCN subunits constitute the ion channels that conduct the hyperpolarization-activated “funny” current (I_f), which plays an important modulating role in SAN pacemaker activity. Voltage-clamp experiments on HCN4 channels expressed in COS-7, CHO and HEK-293 cells, as well as in Xenopus oocytes have revealed changes in the expression and kinetics of mutant channels, but the extent to which especially the kinetic changes would affect I_f flowing during a human SAN action potential often remains unresolved. In our contribution to the Topical Collection on Human Single Nucleotide Polymorphisms and Disease Diagnostics, we provide an updated review of the mutation-induced changes in the expression and kinetics of HCN4 channels and provide an overview of their effects on I_f during the time course of a human SAN action potential, as assessed in simulated action potential clamp experiments. Future research may solve apparent inconsistencies between data from clinical studies and data from in vitro and in silico experiments.