Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Rationale, design, and methodology for the healthy mothers-healthy children study: A randomized controlled trial

Background: Hispanic women and children who become overweight or obese are at risk for developing prediabetes, type 2 diabetes, and cardiovascular disease later in life. Interdisciplinary interventions which target Hispanic women and their 3-5-year old children to improve nutrition and physical activity behaviors, manage adiposity and weight in mothers, and prevent excessive adiposity and weight gain trajectory in their children offer promise to break the intergenerational cycle. Methods: Using a randomized two-group, repeated measures experimental design, the goal of the proposed study is to investigate the efficacy of a 12-week nutrition and physical activity program including education, coping skills training, and home-based intervention in Hispanic women and their 3-5-year old children. The program includes 6 months of continued monthly contact to help overweight and obese Hispanic mothers and their children improve adiposity, weight (trajectory for children), health behaviors (nutrition and physical activity), and self-efficacy We will partner with two federally qualified health departments in Durham and Chatham counties, North Carolina to enroll participants. We will partner with community centers to deliver the intervention. A total of 294 Hispanic women with a BMI ≥ 25 kg/m2 and 294 Hispanic 3-5-year old children with a ≥ 25th BMI percentile will be enrolled over 4 years and randomized to the experimental or equal attention control group. Data will be collected at Time 1 (0 months [baseline]) to Time 2 (9 months [completion of the intervention]) and Time 1 to Time 3 (15 months [after 6 months with no contact from the study staff]). Data collected will include adiposity and weight in mothers and children (primary outcomes). Secondary outcomes will include health behaviors and self-efficacy in the mothers and in the children. We will also evaluate the cost of delivering the program for public health departments. We will use general linear mixed models to test the hypotheses. Discussion: Decreasing overweight and obesity in Hispanic women and slowing adiposity and weight gain trajectory in young Hispanic children is urgently needed to decrease morbidity, mortality, and future health care costs. Trial registration: NCT03866902. (March 7, 2019)

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

Triticum aestivum cDNAs homologous to nuclear-encoded mitochondrion-localized small heat shock proteins.

Two cDNAs, TaHSP23.5 and TaHSP23.6, encoding proteins with homology to mitochondrion-localized (MT) small heat shock proteins (sHSPs) were isolated from a heat shock cDNA library from Triticum aestivum (wheat). TaHSP23.5 specified a 214 amino acid protein and TaHSP23.6 specified a 216 amino acid protein. Amino acid sequence identity was only 45.7% between the two proteins. However, both proteins showed greater identity to MT sHSPs of other plant species than to any other sHSPs from wheat. Amino acid sequence alignments with other MT sHSPs identified the putative amino terminus of the mature proteins and consensus regions specific to this class of sHSPs. Transcripts of both genes were absent from control tissues, but strongly induced by heat stress. Phylogenetic analysis indicates that these two wheat genes arose by duplication after the divergence of monocots and dicots

Prescribed fire increases plant–pollinator network robustness to losses of rare native forbs

Restoration efforts often focus on changing the composition and structure of invaded plant communities, with two implicit assumptions: (1) functional interactions with species of other trophic levels, such as pollinators, will reassemble automatically when native plant diversity is restored and (2) restored communities will be more resilient to future stressors. However, the impact of restoration activities on pollinator richness, plant–pollinator interaction network structure, and network robustness is incompletely understood. Leveraging a restoration chronosequence in Pacific Northwest prairies, we examined the effects of restoration-focused prescribed fire and native forb replanting on floral resources, pollinator visitation, and plant–pollinator network structure. We then simulated the effects of plant species loss/removal scenarios on secondary extinction cascades in the networks. Specifically, we explored three management-relevant plant loss scenarios (removal of an abundant exotic forb, removal of an abundant forb designated a noxious weed, and loss of the rarest native forb) and compared them to control scenarios. Pyrodiversity and proportion of area recently burned increased the abundance and diversity of floral resources, with concomitant increases in pollinator visitation and diversity. Pyrodiversity also decreased network connectance and nestedness, increased modularity, and buffered networks against secondary extinction cascades. Rare forbs contributed disproportionately to network robustness in less restored prairies, while removal of typical “problem” plants like exotic and noxious species had relatively small impacts on network robustness, particularly in prairies with a long history of restoration activities. Restoration actions aimed mainly at improving the diversity and abundance of pollinator-provisioning plants may also produce plant–pollinator networks with increased resilience to plant species losses. © 2023 The Authors. Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Parental knowledge, beliefs and behaviours for oral health of toddlers residing in rural Victoria

Background: Little is known about the oral health of children under the age of four years. The determinants of early childhood caries (ECC) in this young age group are also not well understood despite a growing recognition that early interventions may deliver the greatest benefits. The aim of this study was to examine the oral health‐related knowledge, attitudes and reported behaviours of parents of children aged 12–24 months living in rural areas of Victoria, Australia. Methods: A robust theoretical model was utilized to identify oral health‐related behaviours and their antecedent and reinforcing conditions within the context of this specific population group. Two hundred and ninety‐four parent/child dyads were recruited through their maternal and child health nurses as part of a larger intervention trial. Parents completed a self‐report questionnaire. Results: Knowledge regarding risk and protective factors amongst parents was variable and sometimes at odds with contemporary evidence. Knowledge of the role of early infection with S. mutans was very low, with high levels of behaviours that may promote early transmission reported. Tooth cleaning was reported by most parents at least sometimes, however a large proportion lacked confidence and this was significantly related to the frequency of the cleaning. Parents were confused about the fluoride status of their water supplies. Most parents believed fluoride toothpaste reduced the risk of ECC but did not know whether it should be used with toddlers. Conclusions: The results of this study have implications for efforts to prevent dental decay in this very young age group. Health care professionals other than dentists need support to provide information and promote confidence with regard to optimal fluoride exposure. Attention should also be given to the contribution of early contact with particular bacteria in oral health education and promotion programmes

The Impact of Age on Mortality, Impairment, and Disability among Adults with Acute Traumatic Spinal Cord Injury

Given the potential effects of age on mortality, impairment, and disability among individuals with traumatic spinal cord injury [(SCI), we examined these issues using a large, prospectively accrued clinical database. This study includes all patients who were enrolled in the Third National Spinal Cord Injury Study (NASCIS 3). Motor, sensory, and pain outcomes were assessed using NASCIS scores. Functional outcome was evaluated using the Functional Independence Measure (FIM). Data analyses included regression models adjusted for major potential confounders (i.e., sex, ethnicity, Glasgow Coma Scale [GCS] score, blood alcohol concentration on admission, drug protocol, cause, and level and severity of SCI). Mortality rates among older people (≥65 years) were significantly greater than those of younger individuals at 6 weeks, at 6 months, and at 1 year following SCI (38.6% versus 3.1%; p < 0.0001). Among survivors, age was not significantly correlated with motor recovery or change in pain scores in the acute and chronic stages after SCI based on regression analyses adjusted for major confounders. However, older individuals experienced greater functional deficit (based on FIM scores) than younger individuals, despite experiencing similar rates of sensorimotor recovery (based on NASCIS scores). Our results suggest that older individuals have a substantially increased mortality rate during the first year following traumatic SCI in comparison with younger patients. Among survivors, the potential of older patients with SCI to neurologically improve within the first year post-injury does not appear to translate into similar functional recovery compared to that seen in younger individuals. Given this fact, rehabilitation protocols that are more focused on functional recovery may reduce disability among older people with acute traumatic SCI

Serum organochlorine levels and breast cancer: a nested case-control study of Norwegian women

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