Using the theoretical domains framework to determine the barriers and facilitators to medication adherence in Parkinson's disease.

Background: Patient medication adherence in Parkinson's Disease (PD) is often suboptimal. This may lead to poor symptom management, greater disease burden, decreased quality of life and increased healthcare costs. Use of psychological theory such as the Theoretical Domains Framework (TDF) has effectively captured barriers and facilitators to medication adherence in other long-term conditions. Applying this framework to medication adherence in PD could provide a better understanding of the challenges to inform the development of effective interventions. Objectives: The aim of the study was to apply the TDF to determine the barriers and facilitators to medication adherence in people with PD. Methodology: This qualitative study employed online interviews to explore medication adherence in a small group of people with PD recruited via Parkinson's UK and social media. A semi-structured interview schedule was designed informed by the 14 TDF domains. All interviews were audio-recorded, transcribed verbatim and mapped to the TDF using Framework Analysis. Results: Twelve participants diagnosed with PD were interviewed, 11 of whom were currently taking prescribed medication plus another self-medicating with Vitamin B1. All TDF domains were evident in the data. Predominant facilitators were Domains 1 - Knowledge, 6 - Social Influence, and 12 - Beliefs about Consequences and barriers were 7 - Reinforcement, 10 - Memory, Attention and Decision Processes, and 11 - Environmental Context and Resources. Other themes were not related to medication adherence. Conclusion: In this small group, all data relating to the barriers and facilitators for medication adherence in PD were successfully mapped onto the TDF. This indicates the utility of the framework for determining and structuring the factors to consider when providing medication support for this patient population in an accessible and coherent way. Further quantitative studies are needed to determine the extent to which these factors can be generalised to other PD patients.

Bone and soft tissue tumors: clinicoradiologic-pathologic molecular-genetic correlation of novel fusion spindled, targetable-ovoid, giant-cell-rich, and round cell sarcomas.

BACKGROUND: New entities in the classification of bone and soft tissue tumors have been identified by use of advanced molecular-genetic techniques, including next-generation sequencing. Clinicoradiologic and pathologic correlation supports diagnostic classification. METHODS: Tumors from four morphologically grouped areas are selected to enhance diagnosis and awareness among the multidisciplinary team. These include select round cell tumors, spindle cell tumors, targetable tyrosine kinase/RAS::MAPK pathway-ovoid (epithelioid to spindled) tumors, and giant-cell-rich tumors of bone and soft tissue. RESULTS: Round cell tumors of bone and soft tissue include prototypical Ewing sarcoma, newer sarcomas with BCOR genetic alteration and CIC-rearranged, as well as updates on FUS/EWSR1::NFATc2, an EWSR1 non-ETS tumor that is solid with additional amplified hybridization signal pattern of EWSR1. This FUS/EWSR1::NFATc2 fusion has now been observed in seemingly benign to low-grade intraosseous vascular-rich and simple (unicameral) bone cyst tumors. Select spindle cell tumors of bone and soft tissue include rhabdomyosarcoma with FUS/EWSR1::TFCP2, an intraosseous high-grade spindle cell tumor without matrix. Targetable tyrosine-kinase or RAS::MAPK pathway-tumors of bone and soft tissue include NTRK, ALK, BRAF, RAF1, RET, FGFR1, ABL1, EGFR, PDGFB, and MET with variable ovoid myopericytic to spindled pleomorphic features and reproducible clinicopathologic and radiologic clues to their diagnosis. Giant-cell-rich tumors of bone, joint, and soft tissue are now respectively characterized by H3F3A mutation, CSF1 rearrangement (targetable), and HMGA2::NCOR2 fusion. CONCLUSION: This article is an update for radiologists, oncologists, surgeons, and pathologists to recognize these novel ovoid, spindled, giant-cell-rich, and round cell tumors, for optimal diagnostic classification and multidisciplinary team patient care.

Personal observations on COVID-19 and the conduct and application of biomedical science.

We begin by describing our observations of the ways in which the conduct of research has changed during the COVID-19 pandemic and go on to comment on the quality of the scientific advice that is provided to UK citizens, and especially to schools. Researchers, like many, have suffered from the effects of the pandemic. Those hardships notwithstanding, we suggest that research into COVID-19 has benefitted from a 'seed corn' of discovery science that has provided the basis for routine diagnostic PCR and antibody tests; for structural analyses of the way in which the SARS-CoV-2 virus interacts with cells; for the development of new treatments (and the debunking of ineffective ones); for studies of the genetics of susceptibility to SARS-CoV-2; and for the development of vaccines. The speed of dissemination of research has benefitted from the widespread use of pre-prints, and researchers and funders have become more nimble in their approaches to research and more willing to change their priorities in the face of the pandemic. In our experience, the advice provided to schools on the basis of this research was, however, often published at the last minute and was frequently flawed or inconsistent. This has led to a widening of the attainment gap between children from disadvantaged backgrounds and their peers and it has exacerbated the digital divide and holiday hunger. The consequences will be felt for many years to come and will jeopardize diversity in research and other careers.

Accumulation of Insensitive Munition Compounds in the Earthworm Eisenia andrei from Amended Soil: Methodological Considerations for Determination of Bioaccumulation Factors.

The present study investigates the bioaccumulation of the insensitive munition compounds 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO), developed for future weapons systems to replace current munitions containing sensitive explosives. The earthworm Eisenia andrei was exposed to sublethal concentrations of DNAN or NTO amended in Sassafras sandy loam. Chemical analysis indicated that 2- and 4-amino-nitroanisole (2-ANAN and 4-ANAN, respectively) were formed in DNAN-amended soils. The SumDNAN (sum of DNAN, 2-ANAN, and 4-ANAN concentrations) in soil decreased by 40% during the 14-d exposure period. The SumDNAN in the earthworm body residue increased until day 3 and decreased thereafter. Between days 3 and 14, there was a 73% decrease in tissue uptake that was greater than the 23% decrease in the soil concentration, suggesting that the bioavailable fraction may have decreased over time. By day 14, the DNAN concentration accounted for only 45% of the SumDNAN soil concentration, indicating substantial DNAN transformation in the presence of earthworms. The highest bioaccumulation factor (BAF; the tissue-to-soil concentration ratio) was 6.2 ± 1.0 kg/kg (dry wt) on day 3 and decreased to 3.8 ± 0.8 kg/kg by day 14. Kinetic studies indicated a BAF of 2.3 kg/kg, based on the earthworm DNAN uptake rate of 2.0 ± 0.24 kg/kg/d, compared with the SumDNAN elimination rate of 0.87 d-1 (half-life = 0.79 d). The compound DNAN has a similar potential to bioaccumulate from soil compared with trinitrotoluene. The NTO concentration in amended soil decreased by 57% from the initial concentration (837 mg NTO/kg dry soil) during 14 d, likely due to the formation of unknown transformation products. The bioaccumulation of NTO was negligible (BAF ≤ 0.018 kg/kg dry wt). Environ Toxicol Chem 2021;40:1713-1725. © 2021 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo.

BACKGROUND: Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions. RESULTS: We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature. Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition. CONCLUSIONS: In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.

Distribution of Lactococcus spp. in New York State dairy farms and the association of somatic cell count resolution and bacteriological cure in clinical mastitis samples.

We investigated the distribution of pathogenic non-agalactiae gram-positive, catalase-negative cocci (GPCN) in a convenience sample of New York State dairy farms. Our primary objective with the clinical mastitis (CM) GPCN samples was to evaluate somatic cell count (SCC) resolution and bacteriological cure of Streptococcus dysgalactiae or Streptococcus uberis versus Lactococcus lactis or Lactococcus garvieae in cows that received an approved intramammary treatment. In phase I, we assessed the distribution of the GPCN and SCC resolution. In phase II, we evaluated the SCC resolution and bacteriological cure in CM samples from the 4 farms with the highest prevalence of L. lactis or L. garvieae in phase I. In phase I, 8,868 CM and subclinical mastitis (SCM) milk samples were received from 143 farms. The GPCN samples identified by culture were confirmed with MALDI-TOF. From the 473 MALDI-TOF-confirmed GPCN samples, 155 were S. dysgalactiae (33%); 150, S. uberis (32%); 112, L. lactis (24%); 16, L. garvieae (3%); and 40, other GPCN (8%). From these, 277 were CM samples and 127 were eligible for the evaluation of SCC resolution, which was defined as SCC ≤200,000 cells/mL in a composite sample 15 to 60 d post-diagnosis. The odds of SCC resolution in CM samples was evaluated with multivariable logistic regression, and the odds were 6.1 [95% confidence interval (CI):2.7-13.9] times higher for S. dysgalactiae or S. uberis compared with L. lactis or L. garvieae. In phase II, a total of 1,662 CM and SCM samples were evaluated with microbiological methods as in phase I, of which 211 samples were confirmed by MALDI-TOF: 39% were S. dysgalactiae (n = 61) and S. uberis (n = 21); 55%, L. lactis (n = 114) and L. garvieae (n = 2); and 6%, other GPCN (n = 13). In total, 168 CM samples were eligible for analysis and 118 were included in the final SCC resolution model. Similar statistical methods as in phase I were performed, and the odds of SCC resolution were 2.4 (95% CI: 1.1-5.5) times higher for S. dysgalactiae or S. uberis compared with L. lactis or L. garvieae. Bacteriological cure was defined as having a different or negative culture on a quarter sample taken 14 to 28 d after initial diagnosis. The odds of bacteriological cure (n = 121) were 8.0 (95% CI: 2.5-25.6) times higher for S. dysgalactiae or S. uberis compared with L. lactis or L. garvieae. Differences in SCC resolution and bacteriological cure between these groups may dictate a different management approach.

Evaluation of powdered 0.5% chlorhexidine acetate-based postmilking teat dip compared with a foamed 1% iodine-based postmilking teat dip under cold weather conditions in northern New York.

The objective of this trial was to compare a powdered 0.5% chlorhexidine acetate-based postmilking teat dip with a foamed 1% iodine-based postmilk teat dip during winter on clinical mastitis, subclinical mastitis (somatic cell count ≥200,000 cells/mL), linear score, teat skin condition, teat end score for hyperkeratosis, and risk of developing a new intramammary infection (IMI). Holstein cows (n = 331) housed in freestall and tiestall barns on one farm were blocked by pen, parity, lactation stage, and lactation performance. They were assigned randomly to a powdered chlorhexidine postmilking teat dip (PD; Derma Soft n' Dry, IBA Inc., Millbury, MA) or a foamed iodine-based postmilking teat dip (ID; FS-103, IBA Inc.). Treatments were applied for 6 wk starting January 4, 2016, for 3 milkings per day. Milk samples were collected from each quarter at the beginning and end of the trial and analyzed for aerobic culture and somatic cell count. Cows that had a clinical mastitis event during the trial were quarter sampled for aerobic culture at the time of clinical event. Teat skin condition and teat end score for hyperkeratosis were evaluated at the beginning, middle, and end of the trial based on a 3- and 5-point scale, respectively. No treatment difference was observed for linear score or teat skin condition. Teat end score was greater for ID cows compared with PD cows (2.72 vs. 2.77) at the conclusion of the trial. At the beginning of trial 102 PD quarters and 129 ID quarters had an IMI identified on aerobic culture, 402 PD and 457 ID quarters cultured negative, and 109 PD and 125 ID samples were classified as "no significant growth." At the conclusion of the trial, 129 PD and 101 ID quarters had an IMI. Use of PD resulted in a greater risk for developing a new IMI, based on bacteriological culture, at the conclusion of the trial as compared with ID (relative risk = 1.51; confidence interval: 1.10-2.07). Additionally, use of PD resulted in a greater risk as compared with ID of coagulase-negative staphylococci (relative risk = 1.5; confidence interval: 1.10-2.25) and Staphylococccus aureus (relative risk = 2.30; confidence interval: 1.04-5.07) to be present at the conclusion of the trial. In conclusion, use of PD led to a lower teat end score, an increase in new IMI, and an increased risk of coagulase-negative staphylococci and Staph. aureus compared with ID after 6 wk of product use.

Facts and challenges in respiratory neurobiology.

Respiratory neurobiology has been a lead discipline in the field of neuroscience for almost a century. Despite this, research studies on the fundamental synaptic and cellular processes underlying the generation and modulation of breathing movements suffered a significant decline during the last decade. We still believe that respiratory neurobiology is one of the most exciting and imperative fields of neuroscience. With the first white paper concerned with the central control of breathing, we want to celebrate the global importance of breathing research.

Cooperation Between T-Box Factors Regulates the Continuous Segregation of Germ Layers During Vertebrate Embryogenesis.

A wild-type vertebrate embryo first generates its head and then extends its main body axis by successively appending trunk and tail. This rostro-caudal (head-to-tail) development is initiated by a set of morphogenetic movements known as gastrulation that recruits multipotent cells into one of the three morphologically distinct germ layers: ectoderm, endoderm, and mesoderm. These primordial tissues go on to form complementary sets of connective tissues and organs to build the head and at least some of the trunk. In contrast, the tail appears to be formed without clear germ layer segregation from a terminally located growth zone (the tailbud). Recent research shows that the tailbud retains some pregastrulation multipotency to generate derivatives of different germ layers such as spinal cord (ectoderm) and skeletal muscle (mesoderm). This review discusses the emerging role of T-box transcription factors in this process and their intricate relationship with other genetic components to regulate multipotency and germ layer segregation during axial elongation-from gastrulation to the termination of tail growth.

Modeling Mercury in Proteins.

Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively nontoxic, other forms such as Hg(2+) and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg(2+) can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg(2+) to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed molecular picture and circumvent issues associated with toxicity. Here, we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intraprotein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand-binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confer mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multiscale model of environmental mercury cycling.

The unconscious, myth, and the rule of law: Reflections on the persistence of gender inequality.

Social order, to remain stable, needs the voluntary compliance of the majority of the population. Such consent requires normative justification. The rational foundation of the rule of law and the democratic state rests on the presumption of the equality of every citizen. Male domination of females nevertheless remains universal even in the most advanced democratic nation states because it is legitimized by the shared assumption that patriarchy reflects the will of God or is dictated by nature. Freud's diagnosis of patriarchy as a collective neurosis of the group mind negates every possible normative justification that can be made for gender hierarchy. Freud made extensive references to myth in developing his analysis of the neurotic foundations of social order. An analysis of the structure of myth suggests that ideological seduction rather than God, nature or biology determines male dominance.

The Hubbard dimer: a density functional case study of a many-body problem.

This review explains the relationship between density functional theory and strongly correlated models using the simplest possible example, the two-site Hubbard model. The relationship to traditional quantum chemistry is included. Even in this elementary example, where the exact ground-state energy and site occupations can be found analytically, there is much to be explained in terms of the underlying logic and aims of density functional theory. Although the usual solution is analytic, the density functional is given only implicitly. We overcome this difficulty using the Levy-Lieb construction to create a parametrization of the exact function with negligible errors. The symmetric case is most commonly studied, but we find a rich variation in behavior by including asymmetry, as strong correlation physics vies with charge-transfer effects. We explore the behavior of the gap and the many-body Green's function, demonstrating the 'failure' of the Kohn-Sham (KS) method to reproduce the fundamental gap. We perform benchmark calculations of the occupation and components of the KS potentials, the correlation kinetic energies, and the adiabatic connection. We test several approximate functionals (restricted and unrestricted Hartree-Fock and Bethe ansatz local density approximation) to show their successes and limitations. We also discuss and illustrate the concept of the derivative discontinuity. Useful appendices include analytic expressions for density functional energy components, several limits of the exact functional (weak- and strong-coupling, symmetric and asymmetric), various adiabatic connection results, proofs of exact conditions for this model, and the origin of the Hubbard model from a minimal basis model for stretched H2.

Examination of the perception of sweet- and bitter-like taste qualities in sucralose preferring and avoiding rats.

Sucralose avoiding rats detect a bitter-like taste quality in concentrations of sucralose that are strongly preferred over water by sucralose preferring rats. Here, we investigated whether sucralose preferrers (SP) also detect a bitter-like quality in sucralose that may be masked by an increased perception of sucralose's sweet-like quality. A microstructural analysis of sucralose intake revealed that, at concentrations they avoided in preference tests, sucralose avoiders (SA) consumed smaller and fewer bouts of sucralose than SP. Interestingly, the concentration-dependent increase in sucralose preference in SP was not associated with larger bouts or increased lick rate, two measures that are expected to increase with increasing perceived sweetness. This suggests that SP can detect an aversive quality in sucralose, but this perception of a presumably bitter-like quality may be masked by increased salience of a sweet-like quality that sustains high levels of intake in SP. Further evidence for increased sweet-taste perception in SP, relative to SA, was obtained in a second study in which SP consumed more of a palatable sweet-milk diet than SA. These are the first data to suggest that SP are not blind to the bitter-like quality in sucralose, and that there may be differences in sweet-taste perception between SP and SA.

Early life growth trajectories and future risk for overweight.

OBJECTIVE: Standard approaches have found that rapid growth during the first 2 years of life is a risk factor for overweight in later childhood. Our objective was to test whether growth velocity, independent of concurrent size, was associated with overweight using a nonlinear random-effects model that allows for enhanced specifications and estimations. METHODS: Longitudinal data from a birth cohort in Mexico (n=586) were used to estimate growth trajectories over 0-24 months for body mass index (BMI), length and weight using the SuperImposition by Translation and Rotation (SITAR) models. The SITAR models use a nonlinear random-effects model to estimate an average growth curve for BMI, length and weight and each participant's deviation from this curve on three dimensions-size, velocity and timing of peak velocity. We used logistic regression to estimate the association between overweight status at 7-9 years and size, velocity and timing of BMI, length and weight trajectories during 0-24 months. We tested whether any association between velocity and overweight varied by relative size during 0-24 months or birth weight. RESULTS: SITAR models explained the majority of the variance in BMI (73%), height (86%) and weight (85%) between 0-24 months. When analyzed individually, relative BMI/length/weight (size) and BMI/length/weight velocity during 0-24 months were each associated with increased odds of overweight in late childhood. Associations for timing of peak velocity varied by anthropometric measure. However, in the mutually adjusted models, only relative BMI/length/weight (size) remained statistically significant. We found no evidence that any association between velocity and overweight varied by size during 0-24 months or birth weight. CONCLUSIONS: After mutual adjustment, size during 0-24 months of life (as opposed to birth size), but not velocity or timing of peak velocity, was most consistently associated with overweight in later childhood.

Lessons learned from developing a drug evidence base to support pharmacovigilance.

OBJECTIVE: This work identified challenges associated with extraction and representation of medication-related information from publicly available electronic sources. METHODS: We gained direct observational experience through creating and evaluating the Drug Evidence Base (DEB), a repository of drug indications and adverse effects (ADEs), and supplemented this through literature review. We extracted DEB content from the National Drug File Reference Terminology, from aggregated MEDLINE co-occurrence data, and from the National Library of Medicine's DailyMed. To understand better the similarities, differences and problems with the content of DEB and the SIDER Side Effect Resource, and Vanderbilt's MEDI Indication Resource, we carried out statistical evaluations and human expert reviews. RESULTS: While DEB, SIDER, and MEDI often agreed on medication indications and side effects, cross-system shortcomings limit their current utility. The drug information resources we evaluated frequently employed multiple, disparate vaguely related UMLS concepts to represent a single specific clinical drug indication or adverse effect. Thus, evaluations comparing drug-indication and drug-ADE coverage for such resources will encounter substantial numbers of false negative and false positive matches. Furthermore, our review found that many indication and ADE relationships are too complex - logically and temporally - to represent within existing systems. CONCLUSION: To enhance applicability and utility, future drug information systems deriving indications and ADEs from public resources must represent clinical concepts uniformly and as precisely as possible. Future systems must also better represent the inherent complexity of indications and ADEs.

Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development.

In this paper, we use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium, two cell types that are closely associated during development. High-throughput sequencing identified 754 genes whose transcripts are enriched threefold or more in blood and/or vascular endothelial cells compared with the rest of the embryo at 26-28 h post fertilisation. Of these genes, 388 were classified as novel to these cell types after cross-reference with PubMed and the zebrafish information network (ZFIN). Analysis by quantitative PCR and in situ hybridisation showed that 83% (n=41) of these novel genes are expressed in blood or vascular endothelium. Of 10 novel genes selected for knockdown by antisense morpholino oligonucleotides, we confirmed that two, tmem88a and trim2a, are required for primitive erythropoiesis and myelopoiesis. Our results provide a catalogue of genes whose expression is enriched in the developing blood and endothelium in zebrafish, many of which will be required for the development of those cell types, both in fish and in mammals.

Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation.

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.

Is the burden of overweight shifting to the poor across the globe? Time trends among women in 39 low- and middle-income countries (1991-2008).

BACKGROUND: Overweight prevalence has increased globally; however, current time trends of overweight prevalence by social class in lower income countries have not been fully explored. METHODS: We used repeated cross-sectional, nationally representative data from the Demographic and Health Surveys on women aged 18-49 years with young children (n=421,689) in 39 lower-income countries. We present overweight (body mass index ≥ 25 kg m⁻²) prevalence at each survey wave, prevalence difference and prevalence growth rate for each country over time, separately by wealth quintile and educational attainment. We present the correlation between nation wealth and differential overweight prevalence growth by wealth and education. RESULTS: In the majority of countries, the highest wealth and education groups still have the highest prevalence of overweight and obesity. However, in a substantial number of countries (14% when wealth is used as the indicator of socioeconomic status and 28% for education) the estimated increases in overweight prevalence over time have been greater in the lowest- compared with the highest-wealth and -education groups. Gross domestic product per capita was associated with a higher overweight prevalence growth rate for the lowest-wealth group compared with the highest (Pearson's correlation coefficient: 0.45). CONCLUSIONS: Higher (vs lower) wealth and education groups had higher overweight prevalence across most developing countries. However, some countries show a faster growth rate in overweight in the lowest- (vs highest-) wealth and -education groups, which is indicative of an increasing burden of overweight among lower wealth and education groups in the lower-income countries.