Temporal dynamics and relationship between climate,limnological variables and zooplankton composition in climate-sensitive Lake Bosumtwi,Ghana

The community composition and the factors affecting seasonal and interannual dynamics of zooplankton in Lake Bosumtwi were studied biweekly at a central index station during 2005 and 2006. The lake zooplankton community was species poor. Mesocyclops bosumtwii was numerically superior seasonally and interannually and was endemic to the lake. Minor constituents included Moina micrura, six rotifer species (except for Hexarthra intermedia) and Chaoborus ceratopogones larvae. Low variance of cyanobacteria-dominated phytoplankton biomass underlined stable zooplankton community structure. Emergence of rare species of rotifers occurred seasonally. The climatic signature on the lake’s stratification and mixing regime was strongly influenced by atmospheric temperature, but weakly by wind strength, because of sheltering of the lake by high crater walls. Increasing mixing depth entrained high TP concentrations from below the thermocline seasonally, but reflected poorly in the phytoplankton biomass behaviour. Total zooplankton abundance did not differ seasonally, but varied markedly from year to year in its timing and magnitude. Herbivores were squeezed between food limitation and high predation pressure from Chaoborus all year round. The low fish planktivory (high fishing pressure) on Chaoborus may create a trophic bottleneck restricting energy transfer efficiency from zooplankton to fish.     

Bringing microbial diversity into focus: high‐resolution analysis of iron mats from the Lō‘ihi Seamount

Thirty kilometers south of the island of Hawai‘i lies the Lō‘ihi Seamount, an active submarine volcano that hosts a network of low‐temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers – the metabolic byproduct of iron‐oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō‘ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō‘ihi and has broad implications for our understanding of these globally distributed communities.     

A Proposed Set of Ethical Practice Guidelines in the Assessment and Treatment of Pelvic Floor Disorders

The treatment of pelvic floor disorders using biofeedback, behavioral therapies, and other applied psychophysiological treatments has been well documented as effective. Practitioners must take due care to ensure that they practice within the boundaries of what is common practice for their discipline and within the scope of practice allowed by their professional license as outlined by the appropriate state licensing law(s), the ethical principles and practice guidelines and standards for their discipline, and those of the Association of Applied Psychophysiology and Biofeedback if using a biofeedback assessment or treatment. Being competent to provide a particular treatment does not necessarily make it legal and/or ethical. This paper provides a set of recommended practice guidelines for use in the assessment and treatment of pelvic floor disorders. Please note that they have not at this time been endorsed as an official position of the Association of Applied Psychophysiology and Biofeedback or any other professional organization.     

The FEATURE framework for protein function annotation: modeling new functions,improving performance,and extending to novel applications

Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient to annotate the molecular functions of these structures. Techniques that combine structural and functional modeling can be valuable for functional annotation. FEATURE is a flexible framework for modeling and recognition of functional sites in macromolecular structures. Here, we present an overview of the main components of the FEATURE framework, and describe the recent developments in its use. These include automating training sets selection to increase functional coverage, coupling FEATURE to structural diversity generating methods such as molecular dynamics simulations and loop modeling methods to improve performance, and using FEATURE in large-scale modeling and structure determination efforts.     

High capacity substrates as a platform for a DNA probe array genotyping assay

Colloidal silica particles were deposited on a glass substrate to produce high-capacity porous supports for high-density DNA probe arrays. Porous surfaces were used to increase the addressable surface area and number of probes available for hybridization. Surfaces derived from 70-100 nm size particles deposited in films from 0.15 to 2 microns thick exhibited excellent performance in light-directed oligonucleotide synthesis. Evaluation of these substrates in a genotyping assay is reported.     

Factors affecting the virulence of entomopathogenic nematodes to engorged female Boophilus annulatus ticks

The laboratory trials rank the virulence of entomopathogenic nematode strains (3 heterorhabditids and 6 steinernematids) to engorged female Boophilus annulatus ticks according to 3 parameters of the infection process: the effect of exposure time on tick mortality, the quantity of nematodes that penetrate ticks, and the rate of tick mortality after the injection of 1, 2, or 3 nematodes. Exposure of the ticks to heterorhabditid strains for 6 hr resulted in >80% mortality, but only 20 or 65% mortality after exposure to most steinernematids. The quantity of nematodes recovered per tick exposed to nematodes for 6 days averaged from 16 to 141. For steinernematids, a negative correlation was obtained between tick mortality and the average quantity of nematodes recovered. Injecting 1 infective juvenile from 1 of 2 heterorhabditid strains into each tick resulted in close to 100% mortality. Increasing the quantity of nematodes injected into each tick had little or no additive effect on tick mortality.     

Molecular-genetic analysis of dual-stranded DNA break repair in saccharomyces yeasts

DNA double-strand breaks (DSB) are the most dangerous damage to genetic material caused by ionizing radiation and some chemical agents. Nonrestored DSB lead to chromosomal rearrangements, genetic instability, and cell death. On the other hand, DSB normally occur in cells in the course of normal gene functioning. DSB repair not only protects cells from adverse consequences and maintains stability of genetic material but is directly involved in the most important processes of cell life, such as meiosis and humoral immunity in vertebrates. The diverse mechanisms of homologous and nonhomologous recombination underlie DSB repair. In this respect, yeast are the best-studied object. In this review, genetic control and molecular models of the recombination DNA DSB repair in Saccharomyces cerevisiae are considered. Evidence has accumulated that indicates the higher eukaryotes retained the basic set of the repair pathways characteristic of bacteria and lower eukaryotes. However, different repair mechanisms predominate in yeast as compared to higher eukaryotes. Therefore, the results obtained in yeast experiments may be applicable to higher eukaryotes.     

Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway

The ability to stimulate recombination in a site-specific manner in mammalian cells may provide a useful tool for gene knockout and a valuable strategy for gene therapy. We previously demonstrated that psoralen adducts targeted by triple-helix-forming oligonucleotides (TFOs) could induce recombination between tandem repeats of a supF reporter gene in a simian virus 40 vector in monkey COS cells. Based on work showing that triple helices, even in the absence of associated psoralen adducts, are able to provoke DNA repair and cause mutations, we asked whether intermolecular triplexes could stimulate recombination. Here, we report that triple-helix formation itself is capable of promoting recombination and that this effect is dependent on a functional nucleotide excision repair (NER) pathway. Transfection of COS cells carrying the dual supF vector with a purine-rich TFO, AG30, designed to bind as a third strand to a region between the two mutant supF genes yielded recombinants at a frequency of 0.37%, fivefold above background, whereas a scrambled sequence control oligomer was ineffective. In human cells deficient in the NER factor XPA, the ability of AG30 to induce recombination was eliminated, but it was restored in a corrected subline expressing the XPA cDNA. In comparison, the ability of triplex-directed psoralen cross-links to induce recombination was only partially reduced in XPA-deficient cells, suggesting that NER is not the only pathway that can metabolize targeted psoralen photoadducts into recombinagenic intermediates. Interestingly, the triplex-induced recombination was unaffected in cells deficient in DNA mismatch repair, challenging our previous model of a heteroduplex intermediate and supporting a model based on end joining. This work demonstrates that oligonucleotide-mediated triplex formation can be recombinagenic, providing the basis for a potential strategy to direct genome modification by using high-affinity DNA binding ligands.     

Environmental factors affecting sexual differentiation in the entomopathogenic nematode Heterorhabditis bacteriophora

The present study was aimed at determining the influence of various environmental factors on sex differentiation (SD) in the entomopathogenic nematode Heterorhabditis bacteriophora HP88 strain, under in vivo and in vitro culture conditions. Injection of individual nematodes into last instars of Galleria mellonella resulted in development of a similar number of females and hermaphrodites (35-40%) and 20-25% males. Increasing the number of nematodes injected into the insect did not change these proportions. In smaller insects (0.7-1.5 cm long), an increase in the proportion of hermaphrodites was recorded as compared with larger size cadavers (2.4-2.7 cm long). When individual hermaphrodites were placed on NGM, the proportion of hermaphrodites, females and male progeny was 63%, 31%, and 6%, respectively. Rearing on richer medium ("Dog-food" agar) resulted in reduction in the proportion of hermaphrodites. Nematodes introduced to the symbiotic bacterium obtained from other nematode strains (IS-5 and IS-33) developed similarly to the culture reared on the HP88 bacteria. Rearing the nematodes at a temperature range between 21 degrees C to 30 degrees C also did not have a significant effect on the sexual differentiation among nematodes cultured on NGM. The proportion of hermaphrodites increased as the starvation period of hatching nematode juveniles lengthened (>6 hr). The data obtained in the present study strongly suggest that the main factor affecting sex differentiation in H. bacteriophora is the nutrition source. The practical and biological implications of the results are discussed.