IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.

BACKGROUND: The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map dynamic changes in polyclonal responses precise framework and complementarity determining region annotation of rearranging genes is pivotal. Most sequence annotation tools are designed primarily for use with human and mouse antibody sequences which use databases with fixed species lists, applying very specific assumptions which select against unique structural characteristics. For this reason, data agnostic tools able to learn from presented data can be very useful with new species or with novel datasets. RESULTS: We have developed IgMAT, which utilises a reduced amino acid alphabet, that incorporates multiple HMM alignments into a single consensus to automatically annotate immunoglobulin sequences from most organisms. Additionally, the software allows the incorporation of user defined databases to better represent the species and/or antibody class of interest. To demonstrate the accuracy and utility of IgMAT, we present analysis of sequences extracted from structural data and immunoglobulin sequence datasets from several different species. CONCLUSIONS: IgMAT is fully open-sourced and freely available on GitHub ( https://github.com/TPI-Immunogenetics/igmat ) for download under GPLv3 license. It can be used as a CLI application or as a python module to be integrated in custom scripts.

The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation.

Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.

The Current State of Pediatric Emergency Medicine Training in Emergency Medicine Residencies.

BACKGROUND: Several studies show that emergency medicine (EM) physicians are less comfortable caring for pediatric patients than adults. The state of pediatric training has not been comprehensively evaluated since 2000. OBJECTIVES: We sought to describe current pediatric education in EM residencies and to evaluate EM Program Director (PD) confidence in graduating trainees' abilities to care for pediatric patients. METHODS: We conducted an anonymous, cross-sectional survey study of EM PDs in August 2020. We collected program demographics, clinical rotations, and didactic methods. We used Likert scales to measure PD confidence in graduating residents' competence to care for pediatric and adult patients. RESULTS: We found e-mail addresses for 249 (93%) of 268 EM programs. One hundred nineteen (48%) PDs completed the survey. We include denominators to account for unanswered questions. Sixty-eight (59%) of 116 programs spend 10% to 20% of clinical time seeing pediatric patients. One hundred ten (91%) of 119 require a pediatric emergency medicine (PEM) rotation, 88/119 (83%) require pediatric intensive care, and 34/119 (29%) require neonatal intensive care. Seventy (62%) of 113 have curricula designed by PEM-trained faculty, 96/113 (85%) have PEM attendings teach lectures, and 77/113 (68%) spend 10% to 20% of didactic time on pediatric topics. Twenty-three (23%) of 106 PDs stated not all residents graduate with competence in pediatric resuscitation compared with 2/106 (2%) for adult resuscitation ( P < 0.05). CONCLUSIONS: Program directors report less confidence in graduating residents' competence in caring for pediatric patients compared with adult patients. We propose ideas to strengthen the quality of pediatric education in EM residencies.

Causes of deaths in neonates and children aged 1-59 months in Nigeria: verbal autopsy findings of 2019 Verbal and Social Autopsy study.

BACKGROUND: Nigeria has one of the highest under-five mortality rates in the world. Identifying the causes of these deaths is crucial to inform changes in policy documents, design and implementation of appropriate interventions to reduce these deaths. This study aimed to provide national and zonal-level estimates of the causes of under-five death in Nigeria in the 2013-2018 periods. METHODS: We conducted retrospective inquiries into the cause of deaths of 948 neonates and 2,127 children aged 1-59 months as identified in the 2018 Nigeria Demographic and Health Survey (NDHS). The verbal autopsy asked about signs and symptoms during the final illness. The Physician Coded Verbal Autopsy (PCVA) and Expert Algorithm Verbal Autopsy (EAVA) methods were employed to assign the immediate and underlying cause of deaths to all cases. RESULT: For the analysis, sampling weights were applied to accommodate non-proportional allocation. Boys accounted for 56 percent of neonatal deaths and 51.5 percent of the 1-59-months old deaths. About one-quarter of under-5 mortality was attributed to neonatal deaths, and 50 percent of these neonatal deaths were recorded within 48 h of delivery. Overall, 84 percent of the under-5 deaths were in the northern geopolitical zones. Based on the two methods for case analysis, neonatal infections (sepsis, pneumonia, and meningitis) were responsible for 44 percent of the neonatal deaths, followed by intrapartum injury (PCVA: 21 percent vs. EAVA: 29 percent). The three main causes of death in children aged 1-59 months were malaria (PCVA: 23 percent vs. EAVA: 35 percent), diarrhoea (PCVA: 17 percent vs. EAVA: 23 percent), and pneumonia (PCVA: 10 percent vs. EAVA: 12 percent). In the North West, where the majority of under-5 (1-59 months) deaths were recorded, diarrhoea was the main cause of death (PCVA: 24.3 percent vs. EAVA: 30 percent). CONCLUSION: The causes of neonatal and children aged 1-59 months deaths vary across the northern and southern regions. By homing on the specific causes of mortality by region, the study provides crucial information that may be useful in planning appropriately tailored interventions to significantly reduce under-five deaths in Nigeria.

Health beliefs and (timely) use of facility-based care for under-five children: lessons from the qualitative component of Nigeria's 2019 VASA.

BACKGROUND: Nigeria's under-five health outcomes have improved over the years, but the mortality rates remain unacceptably high. The qualitative component of Nigeria's 2019 verbal and social autopsy (VASA) showed that caregivers' health beliefs about causes of illnesses and efficacious treatment options contribute to non-use/delay in use of facility-based healthcare for under-five children. This study explored how these health beliefs vary across zones and how they shape how caregivers seek healthcare for their under-five children. METHODS: Data for this study come from the qualitative component of the 2019 Nigeria VASA, comprising 69 interviews with caregivers of under-five children who died in the five-year period preceding the 2018 Nigeria Demographic and Health Survey (NDHS); and 24 key informants and 48 focus group discussions (FGDs) in 12 states, two from each of the six geo-political zones. The transcripts were coded using predetermined themes on health beliefs from the 2019 VASA (qualitative component) using NVivo. RESULTS: The study documented zonal variation in belief in traditional medicine, biomedicine, spiritual causation of illnesses, syncretism, and fatalism, with greater prevalence of beliefs discouraging use of facility-based healthcare in the southern zones. Driven by these beliefs and factors such as availability, affordability, and access to and perceived quality of care in health facilities, caregivers often choose one or a combination of traditional medicines, care from medicine vendors, and faith healing. Most use facility-based care as the last option when other methods fail. CONCLUSION: Caregivers' health beliefs vary by zones, and these beliefs influence when and whether they will use facility-based healthcare services for their under-five children. In Nigeria's northern zones, health beliefs are less likely to deter caregivers from using facility-based healthcare services, but they face other barriers to accessing facility-based care. Interventions seeking to reduce under-five deaths in Nigeria need to consider subnational differences in caregivers' health beliefs and the healthcare options they choose based on those beliefs.

Early Growth and Cognitive Development in Children Born Preterm: Relevance of Maternal Body Mass Index.

OBJECTIVE: Maternal prepregnancy body mass index (BMI) represents a surrogate marker of fetal exposures to the maternal metabolism during pregnancy. Yet, it remains poorly understood whether this marker indicates risk of altered trajectories in postnatal growth and development in children born preterm. This study aimed to determine whether maternal prepregnancy BMI is associated with altered growth and development in children born preterm. STUDY DESIGN: A retrospective cohort study evaluated prepregnancy BMI as the exposure for childhood outcomes using linear regression and mixed effects models. The 38 children included in this follow-up evaluation originally participated in a prospective, observational cohort study to determine longitudinal levels of lipid species in preterm human milk expressed by women who delivered prior to 32 weeks. Childhood outcomes in this study were anthropometric measures during hospitalization (n = 38), after discharge through 36 months (n = 34) and Bayley-III developmental scores through 18 months corrected age (n = 26). RESULTS: In 38 children born prior to 32 weeks, higher maternal prepregnancy BMI was independently associated with higher preterm infant growth velocity during hospitalization, but not associated with in-hospital change in length or head circumference and/or postdischarge growth. In univariate linear regression models, higher maternal BMI was associated with lower cognitive scores at 18 months corrected age. This significant association remained in an adjusted model accounting for relevant influences on early childhood development. CONCLUSION: Increasing maternal prepregnancy BMI may reflect risk of altered growth and cognitive development in children born preterm. KEY POINTS: · Maternal BMI was associated with early preterm infant weight gain.. · Maternal BMI was not associated with postdischarge growth.. · Increased maternal BMI may be associated with lower cognitive function scores in offspring..

Neurodiversity in medical education: How can we improve postgraduate learning for neurodiverse doctors?

Recently, there has been an important drive to increase diversity in medical education, which could potentially translate to improved outcomes for patients. Despite this, evidence on how to support neurodiverse doctors is limited. In this article the author reflects on their experience of postgraduate medical education as a doctor with Attention Deficit Hyperactivity Disorder (ADHD) and considers how the learning environment can be improved to help neurodiverse doctors reach their potential. This includes increasing the diversity of senior role models, using a cognitive apprenticeship model, employing teaching strategies which allow learners to elaborate their individual thought processes, and providing appropriate timely feedback.

Randomized Controlled Trial of Early Docosahexaenoic Acid and Arachidonic Acid Enteral Supplementation in Very Low Birth Weight Infants.

OBJECTIVE: To determine feasibility of providing a concentrated emulsified long-chain polyunsaturated fatty acids (LCPUFA) supplement to very low birth weight infants, and to evaluate blood LCPUFA concentrations at 2 and 8 weeks of study supplementation. STUDY DESIGN: This prospective, randomized, double-blind, placebo-controlled trial randomized infants to receive (1) LCPUFA-120 (a supplement of 40 mg/kg/day docosahexaenoic acid [DHA] and 80 mg/kg/day arachidonic acid [ARA]; DHA:ARA at 1:2 ratio), (2) LCPUFA-360 (a supplement of 120 mg/kg/day DHA and 240 mg/kg/day ARA), or (3) sunflower oil (placebo control). Infants received supplement daily for 8 weeks or until discharge, whichever came first. Whole blood LCPUFA levels (wt%; g/100 g) were measured at baseline, 2 weeks, and 8 weeks. RESULTS: Infants were 28 weeks of gestation (IQR, 27-30 weeks of gestation) and weighed 1040 g (IQR, 910-1245 g). At 2 weeks, the change in blood DHA (wt%) from baseline differed significantly among groups (sunflower oil, n = 6; -0.63 [IQR, -0.96 to -0.55]; LCPUFA-120: n = 12; -0.14 [IQR, -0.72 to -0.26]; LCPUFA-360, n = 12; 0.46 [IQR, 0.17-0.81]; P = .002 across groups). Change in blood ARA (wt%) also differed by group (sunflower oil: -2.2 [IQR, -3.9 to -1.7]; LCPUFA-120: 0.1 [IQR, -2.1 to 1.1] vs LCPUFA-360: 2.9 IQR, 1.5 to 4.5]; P = .0002). Change from baseline to 8 weeks significantly differed between groups for DHA (P = .02) and ARA (P = .003). CONCLUSIONS: Enteral LCPUFA supplementation supported higher blood DHA by 2 weeks. LCPUFA supplementation at 360 mg of combined DHA and ARA is likely necessary to reduce declines as well as allow increases in whole blood concentrations in the first 8 weeks of life. TRIAL REGISTRATION: Clinicaltrials.gov: NCT03192839.

High Prevalence of Burnout Among US Emergency Medicine Residents: Results From the 2017 National Emergency Medicine Wellness Survey.

STUDY OBJECTIVE: Previous work shows that emergency medicine attending physicians have higher-than-average rates of burnout. Preliminary data suggest that emergency medicine residents are also at risk for burnout. The objective of this study was to conduct the first national survey assessment of US emergency medicine residents to determine the prevalence of burnout. METHODS: This prospective 2017 National Emergency Medicine Resident Wellness Survey study was conducted through the Wellness Think Tank, whereby emergency medicine residents from 247 residencies across the United States were invited to participate in a national survey. The primary measure of burnout was the Maslach Burnout Inventory-Human Services Survey. In accordance with others' work, "burnout" was defined as a dichotomous variable represented by high levels of emotional exhaustion or depersonalization. Because of interpretative variability with the survey tool, we also calculated burnout rates by using a more restrictive definition and a more inclusive definition that have been reported in the literature. RESULTS: Surveys were completed by 1,522 residents (21.1% of all US emergency medicine residents), representing 193 of 247 US emergency medicine residency programs (78.1%). Within this sample, the prevalence of burnout was 76.1% (95% confidence interval 74.0% to 78.3%). With alternative definitions applied, burnout prevalence rates for this same sample were 18.2% (95% confidence interval 16.3% to 20.1%) with the more restrictive definition and 80.9% (95% confidence interval 78.9% to 82.9%) with the more inclusive definition. CONCLUSION: The majority of US emergency medicine residents responding to this survey reported symptoms consistent with burnout, highlighting that physician burnout in the emergency medicine profession seems to begin as early as residency training. These findings may provide a baseline against which future work can be compared.

Associations between evaporative cooling and dust-mite allergens, endotoxins, and ß-(1 → 3)-d-glucans in house dust: A study of low-income homes.

Recent work suggests that evaporative coolers increase the level and diversity of bioaerosols, but this association remains understudied in low-income homes. We conducted a cross-sectional study of metropolitan, low-income homes in Utah with evaporative coolers (n = 20) and central air conditioners (n = 28). Dust samples (N = 147) were collected from four locations in each home and analyzed for dust-mite allergens Der p1 and Der f1, endotoxins, and ß-(1 â†’ 3)-d-glucans. In all sample locations combined, Der p1 or Der f1 was significantly higher in evaporative cooler versus central air conditioning homes (OR = 2.29, 95% CI = 1.05-4.98). Endotoxin concentration was significantly higher in evaporative cooler versus central air conditioning homes in furniture (geometric mean (GM) = 8.05 vs 2.85 EU/mg, P < .01) and all samples combined (GM = 3.60 vs 1.29 EU/mg, P = .03). ß-(1 â†’ 3)-d-glucan concentration and surface loads were significantly higher in evaporative cooler versus central air conditioning homes in all four sample locations and all samples combined (P < .01). Our study suggests that low-income, evaporative cooled homes have higher levels of immunologically important bioaerosols than central air-conditioned homes in dry climates, warranting studies on health implications and other exposed populations.

Considerations for Preterm Human Milk Feedings When Caring for Mothers Who Are Overweight or Obese.

BACKGROUND: Mother's milk is the recommended source of nutrition for all newborns. Preterm infants may be further compromised by maternal factors that impede successful lactation and alter milk composition. PURPOSE: To review and summarize the state of the science regarding implications of maternal overweight and obesity on successful lactation and associated alterations in preterm mother's milk composition. METHODS/SEARCH STRATEGY: PubMed, EMBASE, and Web of Science searches were performed using relevant key words to identify references addressing maternal overweight or obesity, prematurity, human milk, and lactation. FINDINGS/RESULTS: In the United States, more than half of women enter pregnancy with an overweight or obese body mass index. These women have increased risk of adverse pregnancy outcomes and obstetric complications that can undermine successful initiation and continuation of lactation, including preterm birth. Maternal overweight and obesity are also associated with alterations in mother's milk composition. IMPLICATIONS FOR PRACTICE: Mother-preterm infant dyads affected by maternal overweight and obesity are at risk for barriers to initiation and continuation of lactation. Support for early initiation of milk expression is needed. Continued support, especially during the first weeks of lactation, can facilitate sustained milk production. IMPLICATIONS FOR RESEARCH: Considerable knowledge gaps remain in this area of human milk science. Future research is needed to facilitate more comprehensive understanding of differences in milk composition associated with maternal overweight and obesity and their impact on clinical outcomes in the preterm infant.

Energy and Protein Intake During the Transition from Parenteral to Enteral Nutrition in Infants of Very Low Birth Weight.

OBJECTIVE: To evaluate the association between nutrition delivery practices and energy and protein intake during the transition from parenteral to enteral nutrition in infants of very low birth weight (VLBW). STUDY DESIGN: This was a retrospective analysis of 115 infants who were VLBW from a regional neonatal intensive care unit. Changes in energy and protein intake were estimated during transition phase 1 (0% enteral); phase 2 (>0, ≤33.3% enteral); phase 3 (>33.3, ≤66.7% enteral); phase 4 (>66.7, <100% enteral); and phase 5 (100% enteral). Associations between energy and protein intake were determined for each phase for parenteral nutrition, intravenous lipids, central line, feeding fortification, fluid restriction, and excess non-nutritive fluid intake. RESULTS: In phases 2 and 3, infants receiving feeding fortification received less protein than infants who were unfortified (-1.1 and -0.3 g/kg/d, respectively; P < .001). However, this negative association was not observed after adjusting for relevant nutrition delivery practices. Despite greater enteral protein intake during phases 2 and 3 (0.3 and 0.8 g/kg/d, respectively; P < .001), infants with early fortification received less parenteral protein than infants who were unfortified (-1.4 and -1.1 g/kg/d, respectively; P < .001). Similar patterns were observed for energy intake. Protein intake declined during phases 3 and 4. CONCLUSIONS: Infants paradoxically received less protein and energy on days with early fortification, suggesting that clinicians may lack easily accessible data to detect the association between nutrition delivery practices and overall nutrition in infants who are VLBW.

Quasispecies evolution of the prototypical genotype 1 porcine reproductive and respiratory syndrome virus early during in vivo infection is rapid and tissue specific.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious threat to the pig industry worldwide. Increasing evidence suggests that microevolution within a quasispecies population can give rise to high sequence heterogeneity in PRRSV; potentially impacting the pathogenicity of the virus. Here, we report on micro-evolutionary events taking place within the viral quasispecies population in lung and lymph node 3 days post infection (dpi) following experimental in vivo infection with the prototypical Lelystad PRRSV (LV). Sequence analysis revealed 16 high frequency single nucleotide variants (SNV) or differences from the reference LV genome which are assumed to be representative of the consensus inoculum genome. Additionally, 49 other low frequency SNVs were also found in the inoculum population. At 3 dpi, a total of 9 and 10 SNVs of varying frequencies could already be detected in the LV population infecting the lung and lymph nodes, respectively. Interestingly, of these, three and four novel SNVs emerged independently in the two respective tissues when compared to the inoculum. The remaining variants, though already present at lower frequencies in the inoculum, were positively selected and their frequency increased within the quasispecies population. Hence, we were able to determine directly from tissues infected with PRRSV the repertoire of genetic variants within the viral quasispecies population. Our data also suggest that microevolution of these variants is rapid and some may be tissue-specific.

Nutritional Practices and Growth in Premature Infants After Surgical Necrotizing Enterocolitis.

OBJECTIVE: The aim of the study was to describe the nutritional provisions received by infants with surgical necrotizing enterocolitis (NEC) and the associated effects on short-term growth. METHODS: Through the Children's Hospitals Neonatal Database, we identified infants born ≤32 weeks' gestation with surgical NEC from 5 regional neonatal intensive care units for 4 years. Excluded infants had isolated intestinal perforation and died <14 days postoperatively. Infants were stratified by their median parenteral protein dose (low [LP] or high [HP] protein) for the first postoperative week. The primary outcome was postoperative weight growth velocity. Growth (weight, length, and head circumference [HC]) was measured and the effects related to protein dose were estimated using multivariable analyses. RESULTS: There were 103 infants included; the median parenteral protein dose received was 3.27 g ·â€Škg ·â€Šday (LP: 2.80 g ·â€Škg ·â€Šday; HP: 3.87 g ·â€Škg ·â€Šday). Postoperative weight (11.5 ±â€Š6.5 g ·â€Škg ·â€Šday) and linear growth (0.9 ±â€Š0.2 cm/wk) were similar regardless of dose (P > 0.3 between groups for weight and length). Unadjusted and independent associations were identified with HC changes and HP dose (ß = 0.1 cm/wk, P = 0.03) after adjusting for gestational age, the presence of severe bronchopulmonary dysplasia, short bowel syndrome, blood stream infection, severe intraventricular hemorrhage, small for gestational age, and calorie intake. Eventual nonsurvivors received 18% less protein and 14% fewer calories over the first postoperative month. CONCLUSIONS: Postoperative protein doses in infants with surgical NEC appear related to increases in HC. The influence of postoperative nutritional support on risk of adverse outcomes deserves further attention.

Growth and Development in Extremely Low Birth Weight Infants After the Introduction of Exclusive Human Milk Feedings.

Objective To estimate associations of exclusive human milk (EHM) feedings with growth and neurodevelopment through 18 months corrected age (CA) in extremely low birth weight (ELBW) infants. Study Design ELBW infants admitted from July 2011 to June 2013 who survived were reviewed. Infants managed from July 2011 to June 2012 were fed with bovine milk-based fortifiers and formula (BOV). Beginning in July 2012, initial feedings used a human milk-based fortifier to provide EHM feedings. Infants were grouped on the basis of feeding regimen. Primary outcomes were the Bayley-III cognitive scores at 6, 12, and 18 months and growth. Results Infants (n = 85; 46% received EHM) were born at 26 ± 1.9 weeks (p = 0.92 between groups) weighing 776 ± 139 g (p = 0.67 between groups). Cognitive domain scores were similar at 6 months (BOV: 96 ± 7; EHM: 95 ± 14; p = 0.70), 12 months (BOV: 97 ± 10; EHM: 98 ± 9; p = 0.86), and 18 months (BOV: 97 ± 16; EHM: 98 ± 14; p = 0.71) CA. Growth velocity prior to discharge (BOV: 12.1 ± 5.2 g/kg/day; EHM: 13.1 ± 4.0 g/kg/day; p = 0.33) and subsequent growth was similar between groups. Conclusion EHM feedings appear to support similar growth and neurodevelopment in ELBW infants as compared with feedings containing primarily bovine milk-based products.

Early docosahexaenoic and arachidonic acid supplementation in extremely-low-birth-weight infants.

BACKGROUND: Extremely-low-birth-weight (ELBW) infants accrue large deficits in docosahexaenoic acid (DHA) and arachidonic acid (ARA) and require improved supplementation strategies. We hypothesized that once daily DHA+ARA drops applied to buccal mucosa will increase blood levels. METHODS: Thirty ELBW infants were randomized to receive DHA 20 mg/kg/d + ARA 40 or 60 mg/kg/d + ARA 120 mg/kg/d or placebo within 72 h of age for 8 wk duration. Red blood cell phospholipid levels of DHA (primary) and ARA (secondary) were measured at 2 and 8 wk of age. RESULTS: Twenty-eight survivors with a median birth weight of 806 g completed dosing and sampling. Red blood cell levels were similar between the three groups at 2 wk (DHA: 4.62 wt% (interquartile range (IQR) 4.1-5.5) for all, P = 0.29 between groups; ARA: 21.1 wt% (IQR 18.78-22.6) for all, P = 0.41 between groups) and 8 wk (DHA: 6.0 wt% (IQR 5.1-7.1) for all, P = 0.57 between groups; ARA: 20.1 wt% (IQR 18.3-23.1) for all, P = 0.63 between groups). DHA in all infants showed a median increase of 31% from 2 to 8 wk (P < 0.04). ARA levels did not significantly change over time (P > 0.6). CONCLUSION: Daily buccal DHA and ARA supplements did not affect fatty acid levels in ELBW infants.

Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications.

Phosphoinositide 3-kinases (PI3Ks) are involved in important cellular functions and represent desirable targets for drug discovery efforts, especially related to oncology; however, the four PI3K subtypes (α, ß, γ, and δ) have highly similar binding sites, making the design of selective inhibitors challenging. A series of inhibitors with selectivity toward the ß subtype over δ resulted in compound 3(S), which has entered a phase I/Ib clinical trial for patients with advanced PTEN-deficient cancer. Interestingly, X-ray crystallography revealed that the modifications making inhibitor 3(S) and related compounds selective toward the ß-isoform do not interact directly with either PI3Kß or PI3Kδ, thereby confounding rationalization of the SAR. Here, we apply explicit solvent molecular dynamics and solvent thermodynamic analysis using WaterMap in an effort to understand the unusual affinity and selectivity trends. We find that differences in solvent energetics and water networks, which are modulated upon binding of different ligands, explain the experimental affinity and selectivity trends. This study highlights the critical role of water molecules in molecular recognition and the importance of considering water networks in drug discovery efforts to rationalize and improve selectivity.

Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is the most common form of leukemia in adults in the Western hemisphere. Tumor-specific chromosomal translocations, characteristic findings in several human malignancies that directly lead to malignant transformation, have not been identified in CLL. Using paired-end transcriptome sequencing, we identified recurrent and reciprocal RNA chimeras involving yippee like 5 (YPEL5) and serine/threonine-protein phosphatase PP1-beta-catalytic subunit (PPP1CB) in CLL. Two of seven index cases (28%) harbored the reciprocal RNA chimeras in our initial screening. Using quantitative real-time PCR (q real-time PCR), YPEL5/PPP1CB and PPP1CB/YPEL5 fusion transcripts were detected in 97 of 103 CLL samples (95%) but not in paired normal samples, benign lymphocytes, or various unrelated cancers. Whole-genome sequencing and Southern blotting demonstrated no evidence for a genomic fusion between YPEL5 and PPP1CB. YPEL5/PPP1CB chimera, when introduced into mammalian cells, expressed a truncated PPP1CB protein that demonstrated diminished phosphatase activity. PPP1CB silencing resulted in enhanced proliferation and colony formation of MEC1 and JVM3 cells, implying a role in the pathogenesis of mature B-cell leukemia. These studies uncover a potential role for recurrent RNA chimeras involving phosphatases in the pathogenesis of a common form of leukemia.

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response.

Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory tumor necrosis factor (TNF). The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steady-state total RNA and should be useful in many biological settings.

Linking fat intake, the intestinal microbiome, and necrotizing enterocolitis in premature infants.

Components of diet, including the total amounts and specific types of fat, affect the composition of the intestinal microbiome in both animal models and cohort studies of humans. Amounts of total fat and specific fatty acids (FA) are some of the most variable nutritional components of breast milk. Evaluations of the microbiome in premature infants have shown decreased diversity of species and increased proportions of potentially pathogenic bacteria. Microbial patterns in premature infants may be affected by nutritional fat intake, altering risk of diseases such as necrotizing enterocolitis. Dietary FA may also impact disease susceptibility through molecular mechanisms. Specifically, intestinal Toll-like receptor 4 expression is altered by manipulation of FA in murine models. Abnormal increased expression of Toll-like receptor 4, the receptor for lipopolysaccharide, has been implicated in necrotizing enterocolitis. This report will review the role of dietary fat in the composition of the intestinal microbiome, the extreme variability of FA intake in premature infants, and associations of both dysbiosis and FA intake with the development of necrotizing enterocolitis.