An investigation into reduced milk production following dietary alteration on an Irish dairy farm

A nutritional evaluation of an Irish dairy herd indicated gross overfeeding of late lactation cows, over-conditioning of cows at parturition and a high rate of body condition loss in early lactation. Metabolisable-energy based nutritional modelling software was used to guide recommended dietary changes to prevent excessive condition gain in late lactation. Immediately following the implementation of the changes there was an unexpected reduction in performance affecting both milk yield and protein concentration. An investigation into the poor performance revealed underestimation of peak milk yield; over-estimation of maize silage quality; a large difference in the concentrate being fed compared to the concentrate recommended, and failure of the blend of concentrate ingredients to maintain the intended proportions in the in-parlour feeding system. The estimated maximum cumulative effect of these errors was to cause undersupply of energy and protein in the recommended diet of 16% and 3% respectively to cows in early lactation. Use of a net-energy nutritional model would have indicated a requirement for a higher energy supply in this case. This report highlights the challenges in obtaining accurate on-farm data for use in dairy cow nutritional models

Summer-Season Populations of Epibenthic Marine Fishes in the Indian River Lagoon System, Florida

Epibenthic marine fish populations were sampled in order to establish quantitative base-line data for use in long term monitoring of the northern Indian River lagoon system, Florida. Fish samples were taken by trawling monthly at 8 fixed stations from June through September, 1979 and 1980. Fifty-seven fish species representing 29 families were collected. The fish community was numerically dominated by a very few species. Anchoa mitchilli alone accounted for 87% of the 105,853 individuals collected. Abundance, domin ance, and species diversity were compared among the three lagoon subdivisions, Mosquito Lagoon, Indian River, and Banana River. Greater numbers of fishes were collected in the Indian River, while the highest diversity levels were in the Banana River. Although most species were collected in all three subareas, gross inequities occurred in the numbers of individuals taken. For example, Mosquito Lagoon produced significantly more Micropogonias undulatus and Leiostomus xanthurus than either the Indian or Banana rivers. Significantly more Syngnathus scovelli and Anchoa mitchilli were collected in the Indian River than in the Banana River, and the Banana River produced significantly more Lagodon rhomboides than the Indian River. The only measured environmental parameters that appeared to play significant roles in determining fish populations were vegetative cover and salinity. An importance value (IV) index, combining relative abundance, relative frequency of capture, and relative size (biomass) per individual, was calculated for each species in the community. Dominance ranking by IV has advantages over dominance ranking by relative abundance alone and is calculable for making comparisons in a long-term monitoring study

Description of the updated nutrition calculation of the Oxford WebQ questionnaire and comparison with the previous version among 207,144 participants in UK Biobank.

PURPOSE: The Oxford WebQ is a web-based 24-h dietary assessment method which has been used in UK Biobank and other large prospective studies. The food composition table used to calculate nutrient intakes has recently been replaced with the UK Nutrient Databank, which has food composition data closer in time to when participants completed the questionnaire, and new dietary variables were incorporated. Here we describe the updated version of the Oxford WebQ questionnaire nutrient calculation, and compare nutrient intakes with the previous version used. METHODS: 207,144 UK Biobank participants completed ≥ 1 Oxford WebQs, and means and standard deviations of nutrient intakes were averaged for all completed 24-h dietary assessments. Spearman correlations and weighted kappa statistics were used to compare the re-classification and agreement of nutrient intakes between the two versions. RESULTS: 35 new nutrients were incorporated in the updated version. Compared to the previous version, most nutrients were very similar in the updated version except for a few nutrients which showed a difference of > 10%: lower with the new version for trans-fat (- 20%), and vitamin C (- 15%), but higher for retinol (+ 42%), vitamin D (+ 26%) and vitamin E (+ 20%). Most participants were in the same (> 60%) or adjacent (> 90%) quintile of intake for the two versions. Except for trans-fat (r = 0.58, κ = 0.42), very high correlations were found between the nutrients calculated using the two versions (r > 0.79 and κ > 0.60). CONCLUSION: Small absolute differences in nutrient intakes were observed between the two versions, and the ranking of individuals was minimally affected, except for trans-fat

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay.

As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation

Loss of Tumor Suppressor TMEM127 Drives Ret-Mediated Transformation Through Disrupted Membrane Dynamics

Internalization from the cell membrane and endosomal trafficking of receptor tyrosine kinases (RTKs) are important regulators of signaling in normal cells that can frequently be disrupted in cancer. The adrenal tumor pheochromocytoma (PCC) can be caused by activating mutations of the rearranged during transfection (RET) receptor tyrosine kinase, or inactivation of TMEM127, a transmembrane tumor suppressor implicated in trafficking of endosomal cargos. However, the role of aberrant receptor trafficking in PCC is not well understood. Here, we show that loss of TMEM127 causes wildtype RET protein accumulation on the cell surface, where increased receptor density facilitates constitutive ligand-independent activity and downstream signaling, driving cell proliferation. Loss of TMEM127 altered normal cell membrane organization and recruitment and stabilization of membrane protein complexes, impaired assembly, and maturation of clathrin-coated pits, and reduced internalization and degradation of cell surface RET. In addition to RTKs, TMEM127 depletion also promoted surface accumulation of several other transmembrane proteins, suggesting it may cause global defects in surface protein activity and function. Together, our data identify TMEM127 as an important determinant of membrane organization including membrane protein diffusability and protein complex assembly and provide a novel paradigm for oncogenesis in PCC where altered membrane dynamics promotes cell surface accumulation and constitutive activity of growth factor receptors to drive aberrant signaling and promote transformation

Tropical montane cloud forest: Environmental drivers of vegetation structure and ecosystem function

Abstract:Tropical montane cloud forests (TMCF) are characterized by short trees, often twisted with multiple stems, with many stems per ground area, a large stem diameter to height ratio, and small, often thick leaves. These forests exhibit high root to shoot ratio, with a moderate leaf area index, low above-ground production, low leaf nutrient concentrations and often with luxuriant epiphytic growth. These traits of TMCF are caused by climatic conditions not geological substrate, and are particularly associated with frequent or persistent fog and low cloud. There are several reasons why fog might result in these features. Firstly, the fog and clouds reduce the amount of light received per unit area of ground and as closed-canopy forests absorb most of the light that reaches them the reduction in the total amount of light reduces growth. Secondly, the rate of photosynthesis per leaf area declines in comparison with that in the lowlands, which leads to less carbon fixation. Nitrogen supply limits growth in several of the few TMCFs where it has been investigated experimentally. High root : shoot biomass and production ratios are common in TMCF, and soils are often wet which may contribute to N limitation. Further study is needed to clarify the causes of several key features of TMCF ecosystems including high tree diameter : height ratio.This is the author accepted manuscript. The final version is available from Cambridge University Press via http://dx.doi.org/10.1017/S026646741500017

Collaborative fisheries research reveals reserve size and age determine efficacy across a network of marine protected areas

A variety of criteria may influence the efficacy of networks of marine protected areas (MPA) designed to enhance biodiversity conservation and provide fisheries benefits. Meta-analyses have evaluated the influence of MPA attributes on abundance, biomass, and size structure of harvested species, reporting that MPA size, age, depth, and connectivity influence the strength of MPA responses. However, few empirical MPA evaluation studies have used consistent sampling methodology across multiple MPAs and years. Our collaborative fisheries research program systematically sampled 12 no-take or highly protective limited-take MPAs and paired fished reference areas across a network spanning 1100 km of coastline to evaluate the factors driving MPA efficacy across a large geographic region. We found that increased size and age consistently contributed to increased fish catch, biomass, and positive species responses inside MPAs, while accounting for factors such as latitude, primary productivity, and distance to the nearest MPA. Our study provides a model framework to collaboratively engage diverse stakeholders in fisheries research and provide high-quality data to assess the success of conservation strategies

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

Peer reviewedPublisher PD

Participation in collaborative fisheries research improves the perceptions of recreational anglers towards marine protected areas

Collaborative fisheries research programs engage stakeholders in data collection efforts, often with the benefit of increasing transparency about the status and management of natural resources. These programs are particularly important in marine systems, where management of recreational and commercial fisheries have historically been contentious. One such program is the California Collaborative Fisheries Research Program (CCFRP), which was designed in 2006 to engage recreational anglers in the scientific process and evaluate the efficacy of California’s network of marine protected areas. CCFRP began on the Central Coast of California and expanded statewide in 2017 to include six partner institutions in three regions: Northern, Central, and Southern California. To date, over 2,000 volunteer anglers have participated in the program, with many anglers volunteering for multiple years. However, the impacts of outreach, education, and collaborative research on those anglers at the statewide scale are currently unknown. Thus, the objective of the current study was to survey the statewide pool of volunteer anglers to assess the degree to which participation in CCFRP has influenced angler perceptions of MPAs, fisheries management, and conservation. We received 259 completed surveys out of a pool of 1,386 active anglers, equating to an 18.7% response rate. Participation in CCFRP resulted in a significant, positive impact on anglers’ attitudes towards MPAs in California across all regions. Anglers who participated in six or more CCFRP fishing trips had a more positive perception of MPAs than those who participated in fewer trips. Volunteer anglers across all regions perceived that they caught larger fishes, a higher abundance of fishes, and a greater diversity of species inside MPAs, consistent with the ecological findings of the program. These results highlight the benefits of involving community members in collaborative scientific research. Collaboration between researchers and the broader community increases transparency and trust between stakeholders, and results in greater understanding of natural resource dynamics, ultimately producing better management outcomes

Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance)

PURPOSE: Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581. PATIENTS AND METHODS: C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables. RESULTS: Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P < .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk. CONCLUSION: ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis