Effect of a trematode infection on growth,reproduction, and mortality of shorthead sculpin

Environmental Biology of Fishes - Shorthead sculpin (Cottus confusus Bailey and Bond, 1963) in Birch Creek, Idaho, were infected with the trematode Euryhelmis cotti (Simon, 1972). Our objective was...     

Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU

Emerging data show a rise in colorectal cancer (CRC) incidence in young men and women that is often chemoresistant. One potential risk factor is an alteration in the microbiome. Here, we investigated the role of TGF-β signaling on the intestinal microbiome and the efficacy of chemotherapy for CRC induced by azoxymethane and dextran sodium sulfate in mice. We used two genotypes of TGF-β-signaling-deficient mice (Smad4^+/? and Smad4^+/?Sptbn1^+/?), which developed CRC with similar phenotypes and had similar alterations in the intestinal microbiome. Using these mice, we evaluated the intestinal microbiome and determined the effect of dysfunctional TGF-β signaling on the response to the chemotherapeutic agent 5-Fluoro-uracil (5FU) after induction of CRC. Using shotgun metagenomic sequencing, we determined gut microbiota composition in mice with CRC and found reduced amounts of beneficial species of Bacteroides and Parabacteroides in the mutants compared to the wild-type (WT) mice. Furthermore, the mutant mice with CRC were resistant to 5FU. Whereas the abundances of E. boltae, B.dorei, Lachnoclostridium sp., and Mordavella sp. were significantly reduced in mice with CRC, these species only recovered to basal amounts after 5FU treatment in WT mice, suggesting that the alterations in the intestinal microbiome resulting from compromised TGF-β signaling impaired the response to 5FU. These findings could have implications for inhibiting the TGF-β pathway in the treatment of CRC or other cancers.     

Iris: Interactive all‐in‐one graphical validation of 3D protein model iterations

Iris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.     

A comprehensive biochemical characterization of settlement stage leptocephalus larvae of bonefish (Albula vulpes)

Little is known about early development of the near-threatened bonefish (Albula vulpes), a member of superorder Elopomorpha. Members of Elopomorpha are partially defined by their synapomorphic leptocephalus larval stage, for which the nutritional requirements are not well understood. Characterizing the nutritional profile, including major nutrients (such as lipids) used for energetic processes, can help to gain a better understanding of the nutritional requirements for leptocephalus larvae. A total of 24 settlement stage A. vulpes leptocephalus larvae were collected at Long Caye Island, Belize. Samples were used to determine various biochemical characteristics including lipid class, fatty acid and glycosaminoglycan compositions. Each of these biochemical components plays a role in early developmental processes such as cellular membrane formation and is crucial for healthy development. Biochemical characteristics of settlement stage A. vulpes leptocephalus are presented in this study for the first time. The dominant lipid classes and fatty acids detected in these samples were consistent with prior studies using closely related species like the Japanese eel, indicating possible similarities in diets at this stage. In the future, similar analyses can be applied to other species that share the leptocephalus life stage to determine if nutritional requirements at this stage of development are unique to this species. The findings in this study will also help to facilitate the establishment of adequate aquaculture systems for captive bonefish, ultimately leading to improved management strategies for wild bonefish habitats.     

Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns

There is an emerging consensus that achieving global tuberculosis control targets will require more proactive case finding approaches than are currently used in high-incidence settings. Household contact tracing (HHCT), for which households of newly diagnosed cases are actively screened for additional infected individuals is a potentially efficient approach to finding new cases of tuberculosis, however randomized trials assessing the population-level effects of such interventions in settings with sustained community transmission have shown mixed results. One potential explanation for this is that household transmission is responsible for a variable proportion of population-level tuberculosis burden between settings. For example, transmission is more likely to occur in households in settings with a lower tuberculosis burden and where individuals mix preferentially in local areas, compared with settings with higher disease burden and more dispersed mixing. To better understand the relationship between endemic incidence levels, social mixing, and the impact of HHCT, we developed a spatially explicit model of coupled household and community transmission. We found that the impact of HHCT was robust across settings of varied incidence and community contact patterns. In contrast, we found that the effects of community contact tracing interventions were sensitive to community contact patterns. Our results suggest that the protective benefits of HHCT are robust and the benefits of this intervention are likely to be maintained across epidemiological settings.     

The Enrichment of Plasmid Dnas,in Bacterial Cell Lysates,Using an Alkaline-pH Procedure that Does Not Permanently Denature Them.

Abstract

The method described permits the enrichment of large (greater than or eoual to 54 kb), small (less than or equal to 2.1 kb), or intermediate sizes of plasmid DNAs. It is a modification of the plasmid enrichment method described by Currier and Nester (Anal. Biochem., 76, 431-441, 1976) in that it defers the alkali denaturation step until the pH and temperature can be controlled. This prevents permanent alkali denaturation of some plasmids. In general, total cellular nucleic acids are precipitated with either ethanol or isopropanol after lysates, in 3% w/v NaCl, are extracted with a phenol-chloroform mixture. The nucleic acids are then treated at an alkaline-pH (12.3-12.4), in a buffer, at 0°C, for a minimum time of 15 min. Denatured DNA, in 3% w/v NaCl, is removed with phenol. The RNA- containing, plasmid enriched fraction, is once again precipitated with either ethanol or isopropanol, dried in a vacuum, and redissolved. Samples are then digested with various restriction enzymes and/or examined directly on agarose gels after treatment with RNAase A.