Reaction time: Does it relate to weight status in children?

It has been recently reported that reaction time (RT) is related to weight status [measured by body mass index (BMI)] in young, adult and older people. However, there is little evidence for children, and the similar studies included small sample of participants. The aim of this study was to evaluate the relationship between a new RT test and weight status among a sample of 7–11 year old schoolboys. Therefore, 533 apparently healthy schoolboys underwent clinical reaction time (RT_clin) measurements and standard anthropometry. Participants according to different obesity indices [waist circumference (WC), waist to height ratio (WHtR), BMI and fat%] were assigned to different weight status categories. Results indicated that time of RT_clin decreased as age of the boys increased (F = 63; P < 0.01). No significant difference was observed for RT_clin among the BMI, WC, WHtR and fat% categories after controlling for age (P > 0.05). In conclusion, it seems that there is no relationship between simple RT (measured by RT_clin) and weight status in the boys. Additional studies for finding relationship between RT and weight status are needed by including larger samples of participants, various age groups and various RT tests.     

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. Two main factors affect the utility of potential prediction tools: their accuracy must enable extraction of reliable structural information on the proteins of interest, and their runtime must be low to keep pace with sequencing data being generated at a constantly increasing speed. Here, we present NetSurfP-2.0, a novel tool that can predict the most important local structural features with unprecedented accuracy and runtime. NetSurfP-2.0 is sequence-based and uses an architecture composed of convolutional and long short-term memory neural networks trained on solved protein structures. Using a single integrated model, NetSurfP-2.0 predicts solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of the input sequences. We assessed the accuracy of NetSurfP-2.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features. We observe a correlation of 80% between predictions and experimental data for solvent accessibility, and a precision of 85% on secondary structure 3-class predictions. In addition to improved accuracy, the processing time has been optimized to allow predicting more than 1000 proteins in less than 2 hours, and complete proteomes in less than 1 day.     

Cryoenzymology: How to practice kinetic and structural studies

For a full understanding of an enzyme reaction pathway, one must identify the reaction intermediates and obtain their structures and rates of interconversion. It is impossible to obtain all this information under normal conditions. An approach is to work suboptimally, in particular at subzero temperatures. This is cryoenzymology, an approach that implies both kinetic and structural measurements on enzyme systems below 0°C. To work below 0°C one must add an antifreeze so cryoenzymology means perturbation by two agents: temperature and antifreeze, usually an organic solvent. Certain precautions are needed with these agents, which we will discuss here. In particular, we discuss the importance of choosing the right solvent: this requires extensive exploratory studies but it is the key for the successful practice of cryoenzymology. Each system has its particularities and its own ‘good’ solvent. Cryoenzymology is not only a way of reducing reaction rates, it is also a way of perturbing one's system. Thus, it is a method that allows for the accumulation of intermediates that cannot be observed under normal conditions by slowing down their kinetics of formation, by changes in rate limiting steps or by shifts in equilibria. We illustrate the usefulness of cryoenzymology by myosin and actomyosin ATPases and by creatine, arginine and 3-phosphoglycerate kinases. We also discuss recent results obtained by X-ray crystallography.     

PROTEUS: a suite of programs for prediction of structural features of proteins using an Apple lie

We have implemented several algorithms, developed by variousauthors for predicting structural features of proteins fromtheir primary structure, on an Apple lle and collected themin a suite, named PROTEUS. This suite incorporates: (i) methodsfor predicting secondary structure; (ii) the algorithm for computingthe hydropathy profile using one out of five available setsof parameters; (ii) the algorithms for calculating the hydrophobicmoment plot; and (iv) for performing the amphipathic analysisusing one out of four available sets of parameters. The suitehas a utility program for storing on a disk the sequence tobe analysed. As an example, we applied some of the methods includedin PROTEUS to predict the structure of a mitochondnal leaderpeptide. The results suggest the occurrence of structural featurespossibly related to the import of proteins into mitochondria. Received on April 30, 1987; accepted on July 21, 1987     

The current status of ethnobiological research in Latin America: gaps and perspectives

Background

Recent reviews have demonstrated an increase in the number of papers on ethnobiology in Latin America. Among factors that have influenced this increase are the biological and cultural diversity of these countries and the general scientific situation in some countries. This study aims to assess the panorama of ethnobiological research in Latin America by analyzing its evolution, trends, and future prospects.

Methods

To conduct this study, we searched for papers in the Scopus (http://www.scopus.com) and Web of Science (http://www.isiknowledge.com) databases. The search was performed using combinations of keywords and the name of each Latin American country. The following countries were included in this study: Argentina, Bolivia, Brazil, Chile, Colombia, Costa Rica, Cuba, Ecuador, Guatemala, Haiti, Honduras, Mexico, Panama, Paraguay, Peru, Venezuela, and Uruguay.

Results and conclusions

According to our inclusion criteria, 679 ethnobiological studies conducted in Latin America were found for the period between 1963 and 2012. Of these studies, 289 (41%) were conducted in Brazil, 153 in Mexico (22%), 61 in Peru (9%), 58 in Argentina (8%), 45 in Bolivia (6%), and 97 (14%) in other Latin American countries. The increased number of publications related to this area of knowledge in recent years demonstrates the remarkable growth of ethnobiology as a science. Ethnobiological research may be stimulated by an increase in the number of scientific events and journals for study dissemination and by the creation of undergraduate courses and graduate programs to train ethnoscientists who will produce high-quality studies, especially in certain countries.

     

How do subordinate and dominant species in semi-natural mountain grasslands relate to productivity and land-use change?

Changes in agricultural practices of semi-natural mountain grasslands are expected to modify plant community structure and shift dominance patterns. Using vegetation surveys of 11 sites in semi-natural grasslands of the Swiss Jura and Swiss and French Alps, we determined the relative contribution of dominant, subordinate and transient plant species in grazed and abandoned communities and observed their changes along a gradient of productivity and in response to abandonment of pasturing.The results confirm the humpbacked diversity–productivity relationship in semi-natural grassland, which is due to the increase of subordinate species number at intermediate productivity levels. Grazed communities, at the lower or higher end of the species diversity gradient, suffered higher species loss after grazing abandonment. Species loss after abandonment of pasturing was mainly due to a higher reduction in the number of subordinate species, as a consequence of the increasing proportion of dominant species.When plant biodiversity maintenance is the aim, our results have direct implications for the way grasslands should be managed. Indeed, while intensification and abandonment have been accelerated since few decades, our findings in this multi-site analysis confirm the importance of maintaining intermediate levels of pasturing to preserve biodiversity.     

The effect of race on the incidence of low birth weight: persistence of effect after controlling for socioeconomic, educational, marital, and risk status

The purpose of this study was to determine whether the elevated risk for low birth weight (LBW) infants among black mothers would persist when biologic, behavioral, and socioeconomic factors (as measured by socioeconomic status, level of education, and marital status) were controlled. It was found that the odds ratios for the risk of LBW for blacks/whites persisted above 1.5, regardless of what subgroups were used and what factors were controlled. The black/white odds ratios were, however, less than 2.0 when cigarette smoking was not a risk factor and higher than 2.0 when it was. In fact, the highest odds ratios, up to 2.65, occurred among the smoking group. These data suggest that smoking may have a more strongly negative effect among black than white pregnant mothers. In general, the effect of race on the LBW risk was much less strong than that of risk factors that can be influenced, such as adverse maternal practices.     

The interplay of pineal hormones and socioeconomic status leading to colorectal cancer disparity

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. Despite increased screening options and state-of-art treatments offered in clinics, racial differences remain in CRC. African Americans (AAs) are disproportionately affected by the disease; the incidence and mortality are higher in AAs than Caucasian Americans (CAs). At the time of diagnosis, AAs more often present with advanced stages and aggressive CRCs, primarily accounting for the racial differences in therapeutic outcomes and mortality. The early incidence of CRC in AAs could be attributed to race-specific gene polymorphisms and lifestyle choices associated with socioeconomic status (SES). Altered melatonin-serotonin signaling, besides the established CRC risk factors (age, diet, obesity, alcoholism, and tobacco use), steered by SES, glucocorticoid, and Vitamin D status in AAs could also account for the early incidence in this racial group. This review focuses on how the lifestyle factors, diet, allelic variants, and altered expression of specific genes could lead to atypical serotonin and melatonin signaling by modulating the synthesis, secretion, and signaling of these pineal hormones in AAs and predisposing them to develop more aggressive CRC earlier than CAs. Crosstalk between gut microbiota and pineal hormones and its impact on CRC pathobiology is addressed from a race-specific perspective. Lastly, the status of melatonin-focused CRC treatments, the need to better understand the perturbed melatonin signaling, and the potential of pineal hormone-directed therapeutic interventions to reduce CRC-associated disparity are discussed.     

The binding of calcium to fibrinogen: some structural features.

Experiments are described which suggest that structural features are related to the existence of three high affinity calcium-binding sites in the fibrinogen molecule. The circular dichroism spectra analysis shows that the binding of calcium to this protein does not entail an overall conformational change. However several calcium-induced protective effects may be observed: 1. At pH 5.0 calcium-free fibrinogen is slightly acid-denatured. This denaturation is counteracted by the presence of calcium, whereas magnesium ions have no effect. 2. A temperature transition shift of 3 degrees C is measured in the presence of bound calcium during thermal denaturation, whereas magnesium ions have no effect. 3. Resistance to proteolysis by plasmin is observed when calcium is bound to fibrinogen. The velocity of the splitting of the earliest plasmin-succeptible bonds is reduced in the presence of calcium, whereas magnesium ions have no effect. It can be concluded from these results that the calcium binding centers are located in a more or less flexible zone of the molecule probably involving the C-terminal part of the Aalpha chain. And that the calcium divalent cation stabilizes a more compact structure of the fibrinogen molecule.     

The need for broader ecological and socioeconomic tools to evaluate the effectiveness of coral restoration programs

Coral reef restoration initiatives are burgeoning in response to the need for novel management strategies to address dramatic global declines in coral cover. However, coral restoration programs typically lack rigor and critical evaluation of their effectiveness. A review of 83 peer‐reviewed papers that used coral transplantation for reef restoration reveals that growth and survival of coral fragments were the most widely used indicators of restoration success, with 88% of studies using these two indicators either solely (55%) or in combination with a limited number of other ecological factors (33%). In 53% of studies, reef condition was monitored for 1 year or less, while only 5% of reefs were monitored for more than 5 years post‐transplantation. These results highlight that coral reef restoration science has focused primarily on short‐term experiments to evaluate the feasibility of techniques for ecological restoration and the initial establishment phase post‐transplantation, rather than on longer‐term outcomes for coral reef communities. Here, we outline 10 socioecological indicators that comprehensively evaluate the effectiveness of coral reef restoration across the four pillars of sustainability (i.e. environmental, sociocultural, governance, and economic contributions to sustainable communities). We recommend that evaluations of the effectiveness of coral restoration programs integrate ecological indicators with sociocultural, economic, and governance considerations. Assessing the efficacy of coral restoration as a tool to support reef resilience will help to guide future efforts and ensure the sustainable maintenance of reef ecosystem goods and services.     

The association between socioeconomic status and exposure to mobile telecommunication networks in children and adolescents

A potential association between socioeconomic status (SES) and self‐reported use of mobile phones has been investigated in a few studies. If measured exposure to mobile phone networks differs by SES in children, it has not yet been studied. Interview data of 1,481 children and 1,505 adolescents on participants' mobile phone use, socio‐demographic characteristics and potential confounders were taken from the German MobilEe‐study. Sociodemographic data was used to stratify participants into three “status groups” (low, middle, high). Using a personal dosimeter, we obtained an exposure profile over 24 h for each of the participants. Exposure levels during waking hours were expressed as mean percentage of the reference level. Children with a low SES were more likely to own a mobile phone (OR 2.1; 95% CI: 1.1–3.9) and also reported to use their mobile phone longer per day (OR 2.4; 95% CI: 1.1–5.4) than children with a high SES. For adolescents, self‐reported duration of mobile phone use per day was also higher with a low SES (OR: 3.4; 95% CI: 1.4–8.4) compared with a high SES. No association between SES and measured exposure to mobile telecommunication networks was seen for children or adolescents. Mobile phone use may differ between status groups with higher use among disadvantaged groups. However, this does not result in higher overall exposure to mobile telecommunication networks. Whether short duration of own mobile phone use or the small numbers of participants with a low SES are causal, have to be investigated in further studies. Bioelectromagnetics 31:20–27, 2010. © 2009 Wiley‐Liss, Inc.     

Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: How to relate microarray expression data with genomic sequences

The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in Escherichia coli. Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10 nt for relaxation-induced genes and to 11 nt for relaxation-repressed genes. The helical periodicities in the subsets of promoters recognized by RNA polymerase with different sigma factors were also studied. A special procedure was developed for the study of correlations between the intensities of periodicities in promoter sequences and the expression levels of corresponding genes. Significant correlations of expression with the AT content and with AT periodicities about 10, 11, and 50 nt indicate their role in regulation of supercoiling-sensitive genes.     

Cumulative incidence of self-reported diabetes in Croatian adult population in relation to socioeconomic status and lifestyle habits

The aim of this study was to determine the 5-year cumulative incidence of self-reported diabetes mellitus in relation to various socioeconomic and lifestyle factors in Croatian adult population. The analysis included 2909 participants of the Croatian Health Cohort Study (CroHort) aged 20-79 years (median 55, interquartile range 43-67; 69% women) with no history of diabetes. There were 163 new cases of diabetes (5-year cumulative incidence 5.6%), without significant differences according to sex. Significant predictors of diabetes were age, body mass index, waist and hip circumference in bivariate logistic regression, and being married or living in partnership (OR = 1.57, 95% CI 1.08-2.28; p = 0.018), body mass index (OR =1.11, 95% CI 1.07-1.14; p < 0.001) and age (OR = 1.02, 95% CI 1.01-1.03; p = 0.004) in multivariate model. Our results indicate that approximately 1% of the Croatian adult population develops diabetes each year. Association of living in partnership with higher diabetes incidence requires further investigation.     

Growth and nutritional status of Khasi boys in Northeast India relating to exogamous marriages and socioeconomic classes

The Khasis are one of the matrilineal tribes of Meghalaya in Northeast India. They belong to the Indo-Mongoloid racial stock, and speak the Monkhmer language of the Austro-Asiatic group. They have their own traditional religion (Niam Khasi), but about 65% of them have converted to Christianity. A few Khasi members have also embraced Islam through matrimonial relationship with immigrant Muslim males. The present study was based on a cross-sectional sample of 1,351 urban Khasi boys aged 3-18 years belonging to these three religious groups, with a view to understanding the effects of socioeconomic factors on growth and nutritional status, using anthropometric variables such as weight and height. The findings showed that about 60%, 29%, and 6% of these boys were below -2 Z-scores of the US National Center for Health Statistics (NCHS) references in respect of weight for age, height for age, and body mass index for age, respectively. The logistic regression coefficient (beta +/- standard error) indicated that the prevalence of low weight for age (below -2 Z-scores of the NCHS references) was positively associated with age (0.088 +/- 0.014, P<0.0001), while it was inversely associated with household income (-1.216 +/- 0.030, P<0.0001). Likewise, low height for age Z-score was negatively associated with household income (-1.056 +/- 0.130, P<0.0001), although such a relationship was not significant in the case of low body mass index for age (-0.169 +/- 0.229, P>0.05). There were also significant differences between religious groups in respect of anthropometric variables. Allowing for household income, the ANCOVA test indicated that Muslim Khasi boys, who were the offspring of intermarriages between Khasi females and immigrant Muslim males, were significantly heavier and taller than Christian and Niam Khasi boys almost across ages. From about 3-10 years of age, Muslim Khasi boys were, on average, comparable to the 5th and 25th percentiles of the NCHS references of height and weight, respectively. Although it looks as though genetic mechanisms like heterosis and/or gene flow might also be associated with the larger body size in Muslim boys, such a conjecture could only be substantiated or refuted by further studies concerning genetic and more socioeconomic data on both immigrant and nonimmigrant populations.     

Applying the polio model to New Zealand: The contingent role of socioeconomic status in infectious disease mortality

Objectives

The traditional polio model depicts a positive relationship between the disease and socioeconomic status (SES), with higher SES associated with exposure to the poliovirus beyond infancy/early childhood and a higher mortality rate. This study uses occupation data from non-Māori New Zealand death registrations and the Census to assess evidence for differential mortality by SES during the polio epidemics of 1916, 1924–25, and 1936–37.

Materials and Methods

Polio deaths were classified by father's occupation using the Caversham Project scheme, which includes nine collapsible urban occupational strata and codes rural occupations separately. Evidence for differential mortality and differences in age at death between rural and urban areas and among urban occupational strata was assessed using nonparametric Mann–Whitney U, Kruskal–Wallis, Jonckheere-Terpstra, and chi-square tests.

Results

There was limited evidence of either differential mortality or differences in age at death among collapsed urban strata, mainly in 1924/25, only partially meeting the expectations of the traditional polio model. For 1916 only, the rural group had a higher proportion of deaths (χ² (1, n = 95) = 8.341, p = 0.0039, φ = 0.30)) and higher age at death (U = 828.00, p = 0.026, r = −0.23).

Discussion

These results suggest that rural New Zealand was more isolated from poliovirus infection prior to 1916, but thereafter rural and urban groups faced more similar exposure patterns and mortality—at least among non-Māori. The degree to which occupational categories reflect conditions of exposure requires further research.

     

How to build a pathogen detector: structural basis of NB-LRR function

Many plant disease resistance (R) proteins belong to the family of nucleotide-binding-leucine rich repeat (NB-LRR) proteins. NB-LRRs mediate recognition of pathogen-derived effector molecules and subsequently activate host defence. Their multi-domain structure allows these pathogen detectors to simultaneously act as sensor, switch and response factor. Structure-function analyses and the recent elucidation of the 3D structures of subdomains have provided new insight in how these different functions are combined and what the contribution is of the individual subdomains. Besides interdomain contacts, interactions with chaperones, the proteasome and effector baits are required to keep NB-LRRs in a signalling-competent, yet auto-inhibited state. In this review we explore operational models of NB-LRR functioning based on recent advances in understanding their structure.     

How to untwist an alpha-helix: structural principles of an alpha-helical barrel

Recent crystallographic studies have revealed that 12 alpha-helices can pack in an anti-parallel fashion to form a hollow cylinder of nearly uniform radius. In this architecture, which we refer to as an alpha-barrel, the helices are inclined with respect to the cylindrical axis, and thus they curve and twist. As with conventional coiled-coils, the helices of the barrel associate via "knobs-into-holes" interactions; however, their packing is distinct in several important ways. First, the alpha-barrel helices untwist in comparison with the helices found in two-stranded coiled-coils and, as a consequence of this distortion, their knobs approach closely one end of the complementary holes. This effect defines a requirement for particular size and shape of the protruding residues, and it is associated with a relative axial translation of the paired helices. Second, as each helix packs laterally with two neighbours, the helices have two sequence patterns that are phased to match the two interfaces. The two types of interface are not equivalent and, as one travels around the circumference of the cylinder's interior, they alternate between one type where the knobs approach the holes straight-on, and a second type in which they are inclined. The choice of amino acid depends on the interface type, with small hydrophobic side-chains preferred for the direct contacts and larger aliphatic side-chains for the inclined contacts. Third, small residues are found preferentially on the inside of the tube, in order to make the "wedge" angle between helices compatible with a 12-member tube. Finally, hydrogen-bonding interactions of side-chains within and between helices support the assembly. Using these salient structural features, we present a sequence template that is compatible with some underlying rules for the packing of helices in the barrel, and which may have application to the design of higher-order assemblies from peptides, such as nano-tubes. We discuss the general implications of relative axial translation in coiled-coils and, in particular, the potential role that this movement could play in allosteric mechanisms.     

Monitoring population size of mammals using a spotlight-count-based abundance index: How to relate the number of counts to the precision?

Abundance indices are widely used to study changes in population size in wildlife management. However, a truly appropriate measure of precision is often lacking in such studies. Statistically, the two crucial issues regarding the use of an abundance index are sampling and observability, which lead one to consider two kinds of errors, namely sampling and observation errors. The purpose of this methodological paper is to relate the number of counts to the precision of an abundance index by introducing the Hansen–Hurwitz–Bershad model which takes into account both sampling and observation errors. We illustrate this statistical approach in the case of a European rabbit (Oryctolagus cuniculus) abundance index based on spotlight counts, for two fixed spatial sampling units located in different ecological contexts. We show (i) that the usual sampling variance estimator is a downward-biased estimator of the total variance of the abundance index, (ii) that the bias of the usual variance estimator does not decrease when increasing the sampling size, (iii) that correlated observation errors may have a dramatic impact on the total variance, especially when the sampling size increases. The acknowledgement that the (pure) sampling variance underestimates the total variance because of observation errors is a statistical result that is neither widely known nor appreciated by most wildlife ecologists. The magnitude of this underestimation may be important and, therefore, observation errors cannot be always considered as a priori negligible in assessing the precision of a count-based abundance index.