Metagenomic functional profiling: to sketch or not to sketch?

Motivation: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive.

Low Energy Intake Leads to Body Composition and Performance Decrements in a Highly-Trained, Female Athlete: The WANDER (Woman's Activity and Nutrition during an Extensive Hiking Route) Case Study.

Objective: This case study's purpose was to quantify energy intake vs energy expenditure during a thru-hiker's trek and assess its relationship to performance and health.

Methods: A highly trained, female thru-hiker (Age (yrs): 62, Ht (cm): 157, Wt (kg): 53.5, BMI (kg/m): 21.

Synthesizing the links between secure housing tenure and health for more equitable cities.

Millions of households in rich and poor countries alike are at risk of being unwilfully displaced from their homes or the land on which they live (i.e., lack secure tenure), and the urban poor are most vulnerable.

Application of a New Carbohydrate Food Quality Scoring System: An Expert Panel Report.

Carbohydrate foods (≥40% energy from carbohydrates) are the main source of energy in the US diet. In contrast to national-level dietary guidance, many regularly consumed carbohydrate foods are low in fiber and whole grains but high in added sugar, sodium, and/or saturated fat. Given the important contribution of higher-quality carbohydrate foods to affordable healthy diets, new metrics are needed to convey the concept of carbohydrate quality to policymakers, food industry stakeholders, health professionals, and consumers.

Neighborhood infrastructure-related risk factors and non-communicable diseases: a systematic meta-review.

Background: With rapid urbanization, the urban environment, especially the neighborhood environment, has received increasing global attention. However, a comprehensive overview of the association between neighborhood risk factors and human health remains unclear due to the large number of neighborhood risk factor-human health outcome pairs.

Method: On the basis of a whole year of panel discussions, we first obtained a list of 5 neighborhood domains, containing 33 uniformly defined neighborhood risk factors.

Development of a multidimensional housing and environmental quality index (HEQI): application to the American Housing Survey.

Background: Substandard housing conditions and hazardous indoor environmental exposures contribute to significant morbidity and mortality worldwide. Housing indices that capture the multiple dimensions of healthy housing are important for tracking conditions and identifying vulnerable households. However, most indices focus on physical deficiencies and repair costs and omit indoor environmental exposures, as few national data sources routinely collect this information.

Association of fruit and vegetable color with incident diabetes and cardiometabolic risk biomarkers in the United States Hispanic/Latino population.

Background: Color groups of fruits and vegetables (FV) are part of a healthy diet, but evidence for an association with cardiometabolic outcomes is inconsistent.

Objective: To examine the association between intake of FV of different colors with incident diabetes and cardiometabolic risk biomarkers among U.S.

A New Carbohydrate Food Quality Scoring System to Reflect Dietary Guidelines: An Expert Panel Report.

Existing metrics of carbohydrate food quality have been based, for the most part, on favorable fiber- and free sugar-to-carbohydrate ratios. In these metrics, higher nutritional quality carbohydrate foods are defined as those with >10% fiber and <10% free sugar per 100 g carbohydrate. Although fiber- and sugar-based metrics may help to differentiate the nutritional quality of various types of grain products, they may not aptly capture the nutritional quality of other healthy carbohydrate foods, including beans, legumes, vegetables, and fruits.

Assessment of elevated CO concentrations and heat stress episodes in soybean cultivars growing in heavy metal polluted soils: Crop nutritional quality and food safety.

The present study evaluated the interactive effects of global change and heavy metals on the growth and development of three soybean [Glycine max (L.) Merrill] cultivars and the consequences on yield and food safety. Soybean cultivars (Alim 3.

Neighbourhood, Built Environment and Children's Outdoor Play Spaces in Urban Ghana: Review of Policies and Challenges.

Although a great deal of research work has been done by social scientists on walkability and playability, the focus to a large extent has been on the global north. Research work on the urban built environment and children's play has not engaged Africa in general and Ghana in particular. More importantly, there is limited evidence of policies in terms of community-based practices and governmental policies and programmes for the promotion of play.

Metal solubility in the rhizosphere of a co-cropping system. The role of total carbon exudation, soluble proteins and plant interaction.

In the present study we assessed how modified rhizosphere pH and root exudation (total carbon (C) and soluble proteins released) affected lead (Pb) solubility as well as plant growth and Pb accumulation. A pot experiment with Pb polluted agricultural soils was performed, which involved growing two species, Capsicum annum (pepper) and Tagetes minuta, with the latter being a native herb indicated as potential phytoextractor of Pb, in monocrop and co-cropping conditions. Changes in plant growth, metal uptake as well as rhizosphere soil parameters (pH, EC) and total C and protein exudation were determined.

Effect of Pb-Polluted Soil on Soybean Growth and Associated Toxicological Risk.

Glycine max (L.) Merr. (soybean) has been mentioned as a potential accumulator of hazardous metals, such as Pb.

Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force.

The speed of protein synthesis can dramatically change when consecutively charged residues are incorporated into an elongating nascent protein by the ribosome. The molecular origins of this class of allosteric coupling remain unknown. We demonstrate, using multiscale simulations, that positively charged residues generate large forces that move the P-site amino acid away from the A-site amino acid.

Toward an Evidence-Based Definition and Classification of Carbohydrate Food Quality: An Expert Panel Report.

Carbohydrate-containing crops provide the bulk of dietary energy worldwide. In addition to their various carbohydrate forms (sugars, starches, fibers) and ratios, these foods may also contain varying amounts and combinations of proteins, fats, vitamins, minerals, phytochemicals, prebiotics, and anti-nutritional factors that may impact diet quality and health. Currently, there is no standardized or unified way to assess the quality of carbohydrate foods for the overall purpose of improving diet quality and health outcomes, creating an urgent need for the development of metrics and tools to better define and classify high-quality carbohydrate foods.

Assessment of lead tolerance on Glycine max (L.) Merr. at early growth stages.

Lead (Pb) contamination of agricultural soils, and subsequently of crops, has been widely reported. Soybean (Glycine max (L.) Merr.

Lead uptake and translocation pathways in soybean seedlings: the role of ion competition and transpiration rates.

Glycine max (L.) Merr. (soybean) crop plants have been found to have high lead (Pb) levels in aerial organs; however, knowledge about the processes involved in the incorporation, and subsequent translocation and accumulation of the metal in the plants is scarce.

Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation.

Regulation of gene expression starts from the transcription initiation. Regulated transcription initiation is critical for generating correct transcripts with proper abundance. The impact of epigenetic control, such as histone modifications and chromatin remodelling, on gene regulation has been extensively investigated, but their specific role in regulating transcription initiation is far from well understood.

Biosolid compost with wood shavings and yard trimmings alleviates stress and improves grain quality in soybean grown in lead polluted soils.

Heavy metals induce stress in plants, thereby affecting growth, crop quality, and food security. Most studies addressing the mitigation of these effects by soil amendment have focused on metals in soils and plant uptake, with there still being a great deal of uncertainty about how amendment application in polluted soils can modify plant stress response and, consequently, yield and food safety. Thus, the aim of this study was to evaluate the effect of biosolid compost amendment on stress response, growth, and lead accumulation in Glycine max, when applied to lead polluted agricultural soils.

Effects of co-cropping on soybean growth and stress response in lead-polluted soils.

Phytoremediation by co-cropping may be a promising approach to produce safe crops while remediating the soil. However, the effects of plant interaction, especially stress response, remain unclear. The aims of this study were to investigate the effect of co-cropping on plant growth, stress response and lead (Pb) uptake in soybean and Tagetes minuta, and to assess the feasibility of agricultural production in Pb-polluted soils.

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance.

Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families.

Availability of lead in agricultural soils amended with compost of biosolid with wood shavings and yard trimmings.

Lead-polluted agricultural soils are a serious problem for food safety, with organic amendment being a promising mitigation method from the environmental perspective. Therefore, the purpose of this study was to evaluate lead availability and the effectiveness of the application of compost of biosolid with wood shavings and yard trimmings in contaminated soils. The physicochemical (Pb distribution, organic matter, pH, electric conductivity, cation exchange capacity, nitrogen, phosphorus, carbon, carbonates, exchangeable cations, sodium) and biological parameters (the microbial activity obtained by fluorescein diacetate hydrolysis) in Pb-polluted and non-polluted agricultural soils were evaluated after the addition of biosolid with wood shavings and yard trimming compost.

YeasTSS: an integrative web database of yeast transcription start sites.

The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5' boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files.

Pb accumulation in spores of arbuscular mycorrhizal fungi.

Heavy metal (HM) pollution of soils is one of the most important and unsolved environmental problems affecting the world, with alternative solutions currently being investigated through different approaches. Arbuscular mycorrhizal fungi (AMF) are soil inhabitants that form symbiotic relationships with plants. This alleviates HM toxicity in the host plant, thereby enhancing tolerance.