Identification of Novel Candidate Risk Genes for Myelomeningocele Within the Glucose Homeostasis/Oxidative Stress and Folate/One-Carbon Metabolism Networks

BACKGROUND: Neural tube defects (NTDs) are the second most common complex birth defect, yet, our understanding of the genetic contribution to their development remains incomplete. Two environmental factors associated with NTDs are Folate and One Carbon Metabolism (FOCM) and Glucose Homeostasis and Oxidative Stress (GHOS). Utilizing next-generation sequencing of a large patient cohort, we identify novel candidate genes in these two networks to provide insights into NTD mechanisms. METHODS: Exome sequencing (ES) was performed in 511 patients, born with myelomeningocele, divided between European American and Mexican American ethnicities. Healthy control data from the Genome Aggregation database were ethnically matched and used as controls. Rare, high fidelity, nonsynonymous predicted damaging missense, nonsense, or canonical splice site variants in independently generated candidate gene lists for FOCM and GHOS were identified. We used a gene-based collapsing approach to quantify mutational burden in case and controls, with the control cohort estimated using cumulative allele frequencies assuming Hardy-Weinberg equilibrium. RESULTS: We identified 45 of 837 genes in the FOCM network and 22 of 568 genes in the GHOS network as possible NTD risk genes with p \u3c 0.05. No nominally significant risk genes were shared between ethnicities. Using a novel approach to mutational burden we identify 55 novel NTD risk associations. CONCLUSIONS: We provide a means of utilizing large publicly available sequencing datasets as controls for sequencing projects examining rare disease. This approach confirmed existing risk genes for myelomeningocele and identified possible novel risk genes. Lastly, it suggests possible distinct genetic etiologies for this malformation between different ethnicities

Integrating ecology into macroevolutionary research

On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, ‘Integrating Ecology into Macroevolutionary Research’. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns

Appetite, appetite hormone and energy intake responses to two consecutive days of aerobic exercise in healthy young men

Single bouts of exercise do not cause compensatory changes in appetite, food intake or appetite regulatory hormones on the day that exercise is performed. It remains possible that such changes occur over an extended period or in response to a higher level of energy expenditure. This study sought to test this possibility by examining appetite, food intake and appetite regulatory hormones (acylated ghrelin, total peptide-YY, leptin and insulin) over two days, with acute bouts of exercise performed on each morning. Within a controlled laboratory setting, 15 healthy males completed two, 2-day long (09:00–16:00) experimental trials (exercise and control) in a randomised order. On the exercise trial participants performed 60 min of continuous moderate-high intensity treadmill running (day one: 70.1 ± 2.5% VO2peak, day two: 70.0 ± 3.2% VO2max (mean ± SD)) at the beginning of days one and two. Across each day appetite perceptions were assessed using visual analogue scales and appetite regulatory hormones were measured from venous blood samples. Ad libitum energy and macronutrient intakes were determined from meals provided two and six hours into each day and from a snack bag provided in-between trial days. Exercise elicited a high level of energy expenditure (total = 7566 ± 635 kJ across the two days) but did not produce compensatory changes in appetite or energy intake over two days (control: 29,217 ± 4006 kJ; exercise: 28,532 ± 3899 kJ, P > 0.050). Two-way repeated measures ANOVA did not reveal any main effects for acylated ghrelin or leptin (all P > 0.050). However a significant main effect of trial (P = 0.029) for PYY indicated higher concentrations on the exercise vs. control trial. These findings suggest that across a two day period, high volume exercise does not stimulate compensatory appetite regulatory changes

Role of vitamin D supplementation in modifying outcomes after surgery:a systematic review of randomised controlled trials

Background: There is increasing evidence to suggest vitamin D plays a role in immune and vascular function; hence, it may be of biological and clinical relevance for patients undergoing major surgery. With a greater number of randomised studies being conducted evaluating the impact of vitamin D supplementation on surgical patients, it is an opportune time to conduct further analysis of the impact of vitamin D on surgical outcomes. Methods: MEDLINE, EMBASE and the Cochrane Trials Register were interrogated up to December 2023 to identify randomised controlled trials of vitamin D supplementation in surgery. The risk of bias in the included studies was assessed using the Cochrane Risk of Bias tool. A narrative synthesis was conducted for all studies. The primary outcome assessed was overall postoperative survival. Results: We screened 4883 unique studies, assessed 236 full-text articles and included 14 articles in the qualitative synthesis, comprising 1982 patients. The included studies were highly heterogeneous with respect to patient conditions, ranging from open heart surgery to cancer operations to orthopaedic conditions, and also with respect to the timing and equivalent daily dose of vitamin D supplementation (range: 0.5–7500 mcg; 20–300 000 IU). No studies reported significant differences in overall survival or postoperative mortality with vitamin D supplementation. There was also no clear evidence of benefit with respect to overall or intensive care unit length of stay. Discussion: Numerous studies have reported the benefits of vitamin D supplementation in different surgical settings without any consistency. However, this systematic review found no clear evidence of benefit, which warrants the supposition that a single biological effect of vitamin D supplementation does not exist. The observed improvement in outcomes in low vitamin D groups has not been convincingly proven beyond chance findings. Trial registration number: CRD42021232067

Modeling NH4NO3 over the San Joaquin Valley During the 2013 DISCOVER-AQ Campaign

The San Joaquin Valley (SJV) of California experiences high concentrations of PM2.5 (particulate matter with aerodynamic diameter 2.5 m) during episodes of meteorological stagnation in winter. Modeling PM2.5 NH4NO3 during these episodes is challenging because it involves simulating meteorology in complex terrain under low wind speed and vertically stratified conditions, representing complex pollutant emissions distributions, and simulating daytime and nighttime chemistry that can be influenced by the mixing of urban and rural air masses. A rich dataset of observations related to NH4NO3 formation was acquired during multiple periods of elevated NH4NO3 during the DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) field campaign in SJV in January and February 2013. Here, NH4NO3 is simulated during the SJV DISCOVER-AQ study period with the Community Multiscale Air Quality (CMAQ) model version 5.1, predictions are evaluated with the DISCOVER-AQ dataset, and process analysis modeling is used to quantify HNO3 production rates. Simulated NO3- generally agrees well with routine monitoring of 24-h average NO3-, but comparisons with hourly average NO3- measurements in Fresno revealed differences at higher time resolution. Predictions of gas-particle partitioning of total nitrate (HNO3 + NO3-) and NHx (NH3 + NH4+) generally agreed well with measurements in Fresno, although partitioning of total nitrate to HNO3 was sometimes overestimated at low relative humidity in afternoon. Gas-particle partitioning results indicate that NH4NO3 formation is limited by HNO3 availability in both the model and ambient. NH3 mixing ratios are underestimated, particularly in areas with large agricultural activity, and the spatial allocation of NH3 emissions could benefit from additional work, especially near Hanford. HNO3 production via daytime and nighttime pathways is reasonably consistent with the conceptual model of NH4NO3 formation in SJV, and production peaked aloft between about 160 and 240 m in the model. During a period of elevated NH4NO3, the model predicted that the OH + NO2 pathway contributed 46% to total HNO3 production in SJV and the N2O5 heterogeneous hydrolysis pathway contributed 54%. The relative importance of the OH + NO2 pathway for HNO3 production is predicted to increase as NOx emissions decrease

Multi-Messenger Gravitational Wave Searches with Pulsar Timing Arrays: Application to 3C66B Using the NANOGrav 11-year Data Set

When galaxies merge, the supermassive black holes in their centers may form binaries and, during the process of merger, emit low-frequency gravitational radiation in the process. In this paper we consider the galaxy 3C66B, which was used as the target of the first multi-messenger search for gravitational waves. Due to the observed periodicities present in the photometric and astrometric data of the source of the source, it has been theorized to contain a supermassive black hole binary. Its apparent 1.05-year orbital period would place the gravitational wave emission directly in the pulsar timing band. Since the first pulsar timing array study of 3C66B, revised models of the source have been published, and timing array sensitivities and techniques have improved dramatically. With these advances, we further constrain the chirp mass of the potential supermassive black hole binary in 3C66B to less than $(1.65\pm0.02) \times 10^9~{M_\odot}$ using data from the NANOGrav 11-year data set. This upper limit provides a factor of 1.6 improvement over previous limits, and a factor of 4.3 over the first search done. Nevertheless, the most recent orbital model for the source is still consistent with our limit from pulsar timing array data. In addition, we are able to quantify the improvement made by the inclusion of source properties gleaned from electromagnetic data to `blind' pulsar timing array searches. With these methods, it is apparent that it is not necessary to obtain exact a priori knowledge of the period of a binary to gain meaningful astrophysical inferences.Comment: 14 pages, 6 figures. Accepted by Ap

A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis and crossover resolution in the barley desynaptic mutant des10

Although meiosis is evolutionarily conserved, many of the underlying mechanisms show species-specific differences. These are poorly understood in large genome plant species such as barley (Hordeum vulgare) where meiotic recombination is very heavily skewed to the ends of chromosomes. The characterization of mutant lines can help elucidate how recombination is controlled. We used a combination of genetic segregation analysis, cytogenetics, immunocytology and 3D imaging to genetically map and characterize the barley meiotic mutant DESYNAPTIC 10 (des10). We identified a spontaneous exonic deletion in the orthologue of MutL-Homolog 3 (HvMlh3) as the causal lesion. Compared with wild-type, des10 mutants exhibit reduced recombination and fewer chiasmata, resulting in the loss of obligate crossovers and leading to chromosome mis-segregation. Using 3D structured illumination microscopy (3D-SIM), we observed that normal synapsis progression was also disrupted in des10, a phenotype that was not evident with standard confocal microscopy and that has not been reported with Mlh3 knockout mutants in Arabidopsis. Our data provide new insights on the interplay between synapsis and recombination in barley and highlight the need for detailed studies of meiosis in nonmodel species. This study also confirms the importance of early stages of prophase I for the control of recombination in large genome cereals.Isabelle Colas, Malcolm Macaulay, James D. Higgins, Dylan Phillips, Abdellah Barakate ... Robbie Waugh ... et al

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Validation of elemental and isotopic abundances in late-M spectral types with the benchmark HIP 55507 AB system

M dwarfs are common host stars to exoplanets but often lack atmospheric abundance measurements. Late-M dwarfs are also good analogs to the youngest substellar companions, which share similar $T_{\rm eff}\sim2300-2800~K$. We present atmospheric analyses for the M7.5 companion HIP 55507 B and its K6V primary star with Keck/KPIC high-resolution ($R\sim35,000$) $K$ band spectroscopy. First, by including KPIC relative radial velocities between the primary and secondary in the orbit fit, we improve the dynamical mass precision by 60% and find $M_B=88.0_{-3.2}^{+3.4}$ $M_{\rm Jup}$, putting HIP 55507 B above the stellar-substellar boundary. We also find that HIP 55507 B orbits its K6V primary star with $a=38^{+4}_{-3}$ AU and $e=0.40\pm0.04$. From atmospheric retrievals of HIP 55507 B, we measure $\rm [C/H]=0.24\pm0.13$, $\rm [O/H]=0.15\pm0.13$, and $\rm C/O=0.67\pm0.04$. Moreover, we strongly detect $\rm ^{13}CO$ ($7.8\sigma$ significance) and tentatively detect $\rm H_2^{18}O$ ($3.7\sigma$ significance) in companion's atmosphere, and measure $\rm ^{12}CO/^{13}CO=98_{-22}^{+28}$ and $\rm H_2^{16}O/H_2^{18}O=240_{-80}^{+145}$ after accounting for systematic errors. From a simplified retrieval analysis of HIP 55507 A, we measure $\rm ^{12}CO/^{13}CO=79_{-16}^{+21}$ and $\rm C^{16}O/C^{18}O=288_{-70}^{+125}$ for the primary star. These results demonstrate that HIP 55507 A and B have consistent $\rm ^{12} C/^{13}C$ and $\rm ^{16}O/^{18}O$ to the $<1\sigma$ level, as expected for a chemically homogeneous binary system. Given the similar flux ratios and separations between HIP 55507 AB and systems with young, substellar companions, our results open the door to systematically measuring $\rm ^{13}CO$ and $\rm H_2^{18}O$ abundances in the atmospheres of substellar or even planetary-mass companions with similar spectral types.Comment: Accepted to ApJ, 28 pages, 14 figure