Archeota, Spring 2018

https://scholarworks.sjsu.edu/saasc_archeota/1007/thumbnail.jp

A Small Family of Elements with Long Inverted Repeats is Located Near Sites of Developmentally Regulated DNA Rearrangement in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions

Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family

BACKGROUND: The bacterial cell wall is the target of many antibiotics and cell envelope constituents are critical to host-pathogen interactions. To combat resistance development and virulence, a detailed knowledge of the individual factors involved is essential. Members of the LytR-CpsA-Psr family of cell envelope-associated attenuators are relevant for beta-lactam resistance, biofilm formation, and stress tolerance, and they are suggested to play a role in cell wall maintenance. However, their precise function is still unknown. This study addresses the occurrence as well as sequence-based characteristics of the LytR-CpsA-Psr proteins. RESULTS: A comprehensive list of LytR-CpsA-Psr proteins was established, and their phylogenetic distribution and clustering into subgroups was determined. LytR-CpsA-Psr proteins were present in all Gram-positive organisms, except for the cell wall-deficient Mollicutes and one strain of the Clostridiales. In contrast, the majority of Gram-negatives did not contain LytR-CpsA-Psr family members. Despite high sequence divergence, the LytR-CpsA-Psr domains of different subclusters shared a highly similar, predicted mixed alpha/beta-structure, and conserved charged residues. PhoA fusion experiments, using MsrR of Staphylococcus aureus, confirmed membrane topology predictions and extracellular location of its LytR-CpsA-Psr domain. CONCLUSIONS: The LytR-CpsA-Psr domain is unique to bacteria. The presence of diverse subgroups within the LytR-CpsA-Psr family might indicate functional differences, and could explain variations in phenotypes of respective mutants reported. The identified conserved structural elements and amino acids are likely to be important for the function of the domain and will help to guide future studies of the LytR-CpsA-Psr proteins

The development and analysis of future agricultural landscapes

Alternative futures studies provide a way for policy-makers and stakeholders to investigate the future impacts of different management strategies by providing representations of possible outcomes. An alternative futures study was undertaken by the Pacific Northwest-Ecosystem Research Consortium for the Willamette River Basin, Oregon, USA, to determine how this regional system would respond to various drivers of change. To support this effort required the development of a simulation model that generates future agricultural landscapes in response to these drivers of change and the evaluation of the resulting landscapes to derive information useful for policy analysis and community discussions. These goals were achieved by creating a characterization of the initial agricultural system, developing an agricultural land-cover change model, and finally, integrating this model with scenario elements to produce the final agricultural landscape evolution model. An important part of the initial landscape characterization was determining the crop suitability class of the basin's agricultural soils for 14 commonly grown crops. Suitability rankings were generated by using rough-set rule induction to create predictive if-then rules that related a soil's biophysical characteristics to crop production and then applying these rules to all the agricultural soils in the basin. After characterizing the agricultural system, a spatially explicit, multi-attribute decision model was developed to simulate a grower's crop-selection decision. This model used attributes describing a field's biophysical conditions and each crop's agronomic, economic, and management characteristics to select a field's preferred crop from a list of crop alternatives. Next, rules and constraints were formulated for each of the three policy scenarios: a continuation of current trends, an increased reliance on market forces to determine land use, and an increased emphasis on environmental restoration programs. The initial agricultural landscape depiction, crop selection model, and scenario rules were used to generate three future landscapes, each depicting an alternative state of the agricultural system in the year 2050. Then, landscape metrics and screening models were used to assess the agronomic and environmental condition of each agricultural landscape. Finally, this information was placed into the context of the Willamette River Basin, with suggestions for policy development and analysis

Induction kinetics of the Staphylococcus aureus cell wall stress stimulon in response to different cell wall active antibiotics

BACKGROUND: Staphylococcus aureus activates a protective cell wall stress stimulon (CWSS) in response to the inhibition of cell wall synthesis or cell envelope damage caused by several structurally and functionally different antibiotics. CWSS induction is coordinated by the VraSR two-component system, which senses an unknown signal triggered by diverse cell wall active agents. RESULTS: We have constructed a highly sensitive luciferase reporter gene system, using the promoter of sas016 (S. aureus N315), which detects very subtle differences in expression as well as measuring > 4 log-fold changes in CWSS activity, to compare the concentration dependence of CWSS induction kinetics of antibiotics with different cell envelope targets. We compared the effects of subinhibitory up to suprainhibitory concentrations of fosfomycin, D-cycloserine, tunicamycin, bacitracin, flavomycin, vancomycin, teicoplanin, oxacillin, lysostaphin and daptomycin. Induction kinetics were both strongly antibiotic- and concentration-dependent. Most antibiotics triggered an immediate response with induction beginning within 10 min, except for tunicamycin, D-cycloserine and fosfomycin which showed lags of up to one generation before induction commenced. Induction characteristics, such as the rate of CWSS induction once initiated and maximal induction reached, were strongly antibiotic dependent. We observed a clear correlation between the inhibitory effects of specific antibiotic concentrations on growth and corresponding increases in CWSS induction kinetics. Inactivation of VraR increased susceptibility to the antibiotics tested from 2- to 16-fold, with the exceptions of oxacillin and D-cycloserine, where no differences were detected in the methicillin susceptible S. aureus strain background analysed. There was no apparent correlation between the induction capacity of the various antibiotics and the relative importance of the CWSS for the corresponding resistance phenotypes. CONCLUSION: CWSS induction profiles were unique for each antibiotic. Differences observed in optimal induction conditions for specific antibiotics should be determined and taken into account when designing and interpreting CWSS induction studies

Values of sleep/wake, activity/rest, circadian rhythms, and fatigue prior to adjuvant breast cancer chemotherapy.

Fatigue is the most prevalent and distressing symptom experienced by patients receiving adjuvant chemotherapy for early stage breast cancer. Higher fatigue levels have been related to sleep maintenance problems and low daytime activity in patients who have received chemotherapy, but knowledge describing these relationships prior to chemotherapy is sparse. The Piper Integrated Fatigue Model guided this study, which describes sleep/wake, activity/rest, circadian rhythms, and fatigue and how they interrelate in women with Stage I, II, or IIIA breast cancer during the 48 hours prior to the first adjuvant chemotherapy treatment. The present report describes these variables in 130 females, mean age=51.4 years; the majority were married and employed. Subjective sleep was measured by the Pittsburgh Sleep Quality Index and fatigue was measured by the Piper Fatigue Scale. Wrist actigraphy was used to objectively measure sleep/wake, activity/rest, and circadian rhythms. Mean Pittsburgh Sleep Quality Index score was 6.73+/-3.4, indicating poor sleep. Objective sleep/wake results were within normal limits established for healthy individuals, except for the number and length of night awakenings. Objective activity/rest results were within normal limits except for low mean daytime activity. Circadian rhythm mesor was 132.3 (24.6) and amplitude was 97.2 (22.8). Mean Piper Fatigue Scale score was 2.56+/-2, with 72% reporting mild fatigue. There were significant relationships between subjective and objective sleep, but no consistent patterns. Higher total and subscale fatigue scores were correlated with most components of poorer subjective sleep quality (r=0.25-0.42, P\u3c or =0.005)

Update on Transanal NOTES for Rectal Cancer: Transitioning to Human Trials

The feasibility of natural orifice translumenal endoscopic surgery (NOTES) resection for rectal cancer has been demonstrated in both survival swine and fresh human cadaveric models. In preparation for transitioning to human application, our group has performed transanal NOTES rectal resection in a large series of human cadavers. This experience both solidified the feasibility of resection and allowed optimization of technique prior to clinical application. Improvement in specimen length and operative time was demonstrated with increased experience and newer platforms. This extensive laboratory experience has paved the way for successful clinical translation resulting in an ongoing clinical trial. To date, based on published reports, 4 human subjects have undergone successful hybrid transanal NOTES resection of rectal cancer. While promising, instrument limitations continue to hinder a pure transanal approach. Careful patient selection and continued development of new endoscopic and flexible-tip instruments are imperative prior to pure NOTES clinical application

Conducting Research with Tribal Communities: Sovereignty, Ethics, and Data-Sharing Issues

When conducting research with American Indian tribes, informed consent beyond conventional Institutional Review Board (IRB) review is needed because there may be potential for adverse consequences at a community or governmental level that are unrecognized by academic researchers. This paper reviews sovereignty, research ethics, and data-sharing considerations when doing community-based participatory health-related or natural resource-related research with American Indian nations and presents a model material and data-sharing agreement that meets tribal and university requirements. Only tribal nations themselves can identify potential adverse outcomes, and they can do this only if they understand the assumptions and methods of the proposed research. Tribes much be truly equal partners in study design, data collection, interpretation, and publication. Advances in protection of intellectual property rights are also applicable to IRB reviews, as are principles of sovereignty and indigenous rights, all of which affect data ownership and control. Academic researchers engaged in tribal projects should become familiar with all three areas: sovereignty, ethics and informed consent, and intellectual property rights (IPR). We recommend developing an agreement with tribal partners that reflects both health-related IRB and natural resource-related IPR considerations