Analysis of Taca Overexpression on Phenotypic Characteristics of Sinorhizobium meliloti

Sinorhizobium meliloti is a nitrogen-fixing bacterium that forms a symbiosis with legumes. These bacteria colonize plant roots within nodules and undergo a novel cell cycle as a symbiont. Free-living in soil, it undergoes asymmetrical cell division with one round of DNA replication per cell cycle. We are interested in identifying cell cycle regulators and understanding their function during free-living growth and symbiosis. We hypothesize that TacA is a cell cycle regulator since deletion of the TacA ortholog in Caulobacter crescentus shows morphology, motility, and cell membrane defects. To test this, we examined IPTG-induced overexpression of tacA for exopolysaccharide, membrane, and motility defects. Our results show low IPTG levels decrease motility of wild type and ?cbrA strains. Surprisingly, higher amounts of IPTG restore motility to each strain’s original level. Additionally, tacA overexpression causes a membrane defect in WT that is similar to ?cbrA, while tacA does not appear to regulate exopolysaccharide production. In conclusion, tacA overexpression has several cell cycle phenotypes, which makes it a good candidate for further investigation. S. meliloti is an important model organism, not only for its potential to replace synthetic nitrogen fertilizers, but also because it is related to bacteria that cause brucellosis and plant tumors

PAID TO PUMP: How a tax credit could discourage conservation of the High Plains Aquifer

In 1965’s United States v. Shurbet case, an irrigator from Texas asserted his claim for a depletion tax deduction for groundwater pumped from the High Plains Aquifer. He argued that the unique conditions of the southern High Plains region - a plateau where the shallow aquifer is recharged only through precipitation at a slow rate - meant the groundwater resource would be depleted in time. The state argued that groundwater was not fundamentally an exhaustible natural deposit, but the Supreme Court concluded the tax deduction was appropriate given the “peculiar” conditions in the area. It was stated the decision was not meant to establish a precedent regarding cost depletion of groundwater. The findings of the Shurbet case were intended to be limited to the southern High Plains region. However, in a 1980 lawsuit against the IRS, the Gigot brothers of Kansas sought to expand the deduction to allow depletion of the aquifer beneath their 30,000 acre farm in Kansas. The case was settled in the district court with a ruling allowing the brothers’ deductions to continue, thereby extending the Shurbet decision to include all landowners extracting from the approximately 174,000 square miles of land overlying the High Plains Aquifer. Currently, the estimated value of the credit is highest in parts of northern Texas, eastern Colorado, western Kansas, and south central Nebraska

Assessing explanatory factors for variation in on-farm irrigation in US maize-soybean systems

Irrigation exhibits large variation across producer fields, even within same region and year. A knowledge gap exists relative to factors that explain this variation, in part due to lack of availability of high-quality irrigation data from multiple field-years. This study assessed sources of variation in irrigation using a large database collected during 9 years (2005–2013) from ca. 1400 maize and soybean producer fields in Nebraska, central USA (total of 12,750 field-year observations). The study area is representative of ca. 4.5 million ha of irrigated land sown with maize and soybean. Influence of biophysical (weather, soil, and crop type) and behavioral (producer skills, risk aversion) factors on irrigation was investigated. Field irrigation distributions showed a substantial number of fields received irrigation amounts that were well above average irrigation for same region-year. Variation in irrigation across fields, within the same region, was as large as year-to-year variation. Seasonal water deficit (defined as total reference evapotranspiration minus precipitation), soil available water holding capacity, and crop type explained about half of observed variation in field irrigation, indicating that producers adjusted irrigation depending upon siteyear variation in these parameters. However, half of the variation in irrigation remained unexplained, indicating that producer behavior and skills play also an important role. There was evidence of a “neighbor” effect as fields that received large irrigation were surrounded by other fields with similarly large irrigation. Likewise, fields with above- or below-average irrigation in one year remained consistently above and below regional average irrigation, respectively, in other years despite similarity in weather and soil among fields. These findings indicate that irrigation decisions are influenced by both biophysical and behavioral factors, making predictions of field and regional irrigation extremely difficult. This study highlights the value of collecting on-farm irrigation data to understand producer decision-making and find opportunities to improve current water management in irrigated crop systems

Observational Study Design in Veterinary Pathology, Part 1: Study Design

Observational studies are the basis for much of our knowledge of veterinary pathology and are highly relevant to the daily practice of pathology. However, recommendations for conducting pathology-based observational studies are not readily available. In part 1 of this series, we offer advice on planning and conducting an observational study with examples from the veterinary pathology literature. Investigators should recognize the importance of creativity, insight, and innovation in devising studies that solve problems and fill important gaps in knowledge. Studies should focus on specific and testable hypotheses, questions, or objectives. The methodology is developed to support these goals. We consider the merits and limitations of different types of analytic and descriptive studies, as well as of prospective vs retrospective enrollment. Investigators should define clear inclusion and exclusion criteria and select adequate numbers of study subjects, including careful selection of the most appropriate controls. Studies of causality must consider the temporal relationships between variables and the advantages of measuring incident cases rather than prevalent cases. Investigators must consider unique aspects of studies based on archived laboratory case material and take particular care to consider and mitigate the potential for selection bias and information bias. We close by discussing approaches to adding value and impact to observational studies. Part 2 of the series focuses on methodology and validation of methods

Urinary Epidermal Growth Factor as a Marker of Disease Progression in Children With Nephrotic Syndrome.

Introduction: Childhood-onset nephrotic syndrome has a variable clinical course. Improved predictive markers of long-term outcomes in children with nephrotic syndrome are needed. This study tests the association between baseline urinary epidermal growth factor (uEGF) excretion and longitudinal kidney function in children with nephrotic syndrome. Methods: The study evaluated 191 participants younger than 18 years enrolled in the Nephrotic Syndrome Study Network, including 118 with their first clinically indicated kidney biopsy (68 minimal change disease; 50 focal segmental glomerulosclerosis) and 73 with incident nephrotic syndrome without a biopsy. uEGF was measured at baseline for all participants and normalized by the urine creatinine (Cr) concentration. Renal epidermal growth factor (EGF) mRNA was measured in the tubular compartment microdissected from kidney biopsy cores from a subset of patients. Linear mixed models were used to test if baseline uEGF/Cr and EGF mRNA expression were associated with change in estimated glomerular filtration rate (eGFR) over time. Results: Higher uEGF/Cr at baseline was associated with slower eGFR decline during follow-up (median follow-up = 30 months). Halving of uEGF/Cr was associated with a decrease in eGFR slope of 2.0 ml/min per 1.73 m Conclusion: uEGF/Cr may be a useful noninvasive biomarker that can assist in predicting the long-term course of kidney function in children with incident nephrotic syndrome

Effect of obesity on constant workrate exercise in hyperinflated men with COPD

<p>Abstract</p> <p>Background</p> <p>Chronic obstructive pulmonary disease (COPD) and a high body mass index (BMI) can both affect pulmonary volumes as well as exercise tolerance, but their combined effect on these outcomes is not well known. The aim of this study was to investigate the effects of increased BMI during constant workrate cycle ergometry in patients with COPD.</p> <p>Methods</p> <p>Men with COPD and hyperinflation were divided according to World Health Organization BMI classification: 84 normal BMI (NBMI), 130 overweight (OW) and 64 obese (OB). Patients underwent spirometric and lung volumes assessment and an incremental cycling exercise test. This was followed by a constant workrate exercise test (CET) at 75% of peak capacity. Inspiratory capacity and Borg dyspnea scores were measured at baseline, during and at the end of CET.</p> <p>Results and discussion</p> <p>FEV₁% predicted was not different across BMI classes. Total lung capacity and functional residual capacity were significantly lower in OB and OW compared to NBMI patients. Peak VO₂in L·min^-1was significantly higher in OB and OW patients than in NBMI patients. CET time was not different across BMI classes (p = 0.11). Changes in lung volumes and dyspnea during CET were not different between BMI categories.</p> <p>Conclusions</p> <p>OB and OW patients with COPD had a higher peak VO₂than their lean counterparts. Endurance time, dyspnea and changes in lung volumes during CET were similar between BMI categories.</p

Increasing vegetable intakes: rationale and systematic review of published interventions

Purpose While the health benefits of a high fruit and vegetable consumption are well known and considerable work has attempted to improve intakes, increasing evidence also recognises a distinction between fruit and vegetables, both in their impacts on health and in consumption patterns. Increasing work suggests health benefits from a high consumption specifically of vegetables, yet intakes remain low, and barriers to increasing intakes are prevalent making intervention difficult. A systematic review was undertaken to identify from the published literature all studies reporting an intervention to increase intakes of vegetables as a distinct food group. Methods Databases—PubMed, PsychInfo and Medline—were searched over all years of records until April 2015 using pre-specified terms. Results Our searches identified 77 studies, detailing 140 interventions, of which 133 (81 %) interventions were conducted in children. Interventions aimed to use or change hedonic factors, such as taste, liking and familiarity (n = 72), use or change environmental factors (n = 39), use or change cognitive factors (n = 19), or a combination of strategies (n = 10). Increased vegetable acceptance, selection and/or consumption were reported to some degree in 116 (83 %) interventions, but the majority of effects seem small and inconsistent. Conclusions Greater percent success is currently found from environmental, educational and multi-component interventions, but publication bias is likely, and long-term effects and cost-effectiveness are rarely considered. A focus on long-term benefits and sustained behaviour change is required. Certain population groups are also noticeably absent from the current list of tried interventions

Patient-directed self-management of pain (PaDSMaP) compared to treatment as usual following total knee replacement; a randomised controlled trial

Background Self-administration of medicines by patients whilst in hospital is being increasingly promoted despite little evidence to show the risks and benefits. Pain control after total knee replacement (TKR) is known to be poor. The aim of the study was to determine if patients operated on with a TKR who self-medicate their oral analgesics in the immediate post-operative period have better pain control than those who receive their pain control by nurse-led drug rounds (Treatment as Usual (TAU)). Methods A prospective, parallel design, open-label, randomised controlled trial comparing pain control in patient-directed self-management of pain (PaDSMaP) with nurse control of oral analgesia (TAU) after a TKR. Between July 2011 and March 2013, 144 self-medicating adults were recruited at a secondary care teaching hospital in the UK. TAU patients (n = 71) were given medications by a nurse after their TKR. PaDSMaP patients (n = 73) took oral medications for analgesia and co-morbidities after two 20 min training sessions reinforced with four booklets. Primary outcome was pain (100 mm visual analogue scale (VAS)) at 3 days following TKR surgery or at discharge (whichever came soonest). Seven patients did not undergo surgery for reasons unrelated to the study and were excluded from the intention-to-treat (ITT) analysis. Results ITT analysis did not detect any significant differences between the two groups’ pain scores. A per protocol (but underpowered) analysis of the 60% of patients able to self-medicate found reduced pain compared to the TAU group at day 3/discharge, (VAS -9.9 mm, 95% CI -18.7, − 1.1). One patient in the self-medicating group over-medicated but suffered no harm. Conclusion Self-medicating patients did not have better (lower) pain scores compared to the nurse-managed patients following TKR. This cohort of patients were elderly with multiple co-morbidities and may not be the ideal target group for self-medication

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe