Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.

The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures.

Although visceral adipocytes located within the body's central core are maintained at approximately 37°C, adipocytes within bone marrow, subcutaneous, and dermal depots are found primarily within the peripheral shell and generally exist at cooler temperatures. Responses of brown and beige/brite adipocytes to cold stress are well studied; however, comparatively little is known about mechanisms by which white adipocytes adapt to temperatures below 37°C. Here, we report that adaptation of cultured adipocytes to 31°C, the temperature at which distal marrow adipose tissues and subcutaneous adipose tissues often reside, increases anabolic and catabolic lipid metabolism, and elevates oxygen consumption. Cool adipocytes rely less on glucose and more on pyruvate, glutamine, and, especially, fatty acids as energy sources. Exposure of cultured adipocytes and gluteal white adipose tissue (WAT) to cool temperatures activates a shared program of gene expression. Cool temperatures induce stearoyl-CoA desaturase-1 (SCD1) expression and monounsaturated lipid levels in cultured adipocytes and distal bone marrow adipose tissues (BMATs), and SCD1 activity is required for acquisition of maximal oxygen consumption at 31°C.

Effect of feeding Bengal gram residual forage-based pelleted total mixed ration on growth performance, nutrient availability, carcass traits and composition in finisher Barbari kids.

The study aimed to assess the impact of feeding Bengal gram residual forage-based pelleted Total Mixed Ration (TMR) with varying concentrate (C) to roughage (R) ratios on feed intake, nutrient utilization, growth, and carcass characteristics in Barbari kids. Sixteen weaned male Barbari kids (av. age, 233 ± 11 days; weight, 13.86 ± 0.76 kg) were divided into two groups (T1 and T2), each receiving different pelleted diets (TMR) with distinct concentrate to roughage ratios (T1 with 60:40; T2 with 40:60). The kids were fed for 133 days, and a digestion trial was conducted at the end of the study. After completion, all kids were slaughtered. Although, kids under T1 consumed higher (P < 0.001) amount of dry matter, and crude protein compared to T2, which was due to a higher concentrate to roughage ratio in T1. But, the average daily body weight gain (ADG) of finisher kids was 88.53, and 79.83 g/d/kid in T1 and T2, respectively; however, the difference was non-significant. Digestibility of organic matter, crude protein, and total carbohydrate was also greater in T1 compared to T2. Total digestible nutrients intake was higher (P < 0.001) in T1; similarly intake of digestible energy, and metabolizable energy were significantly increased (P < 0.01) in T1 compared to T2. Concentrations of volatile fatty acids and NH3-nitrogen were also enhanced (P < 0.05) in T1 compared to T2. We observed similar carcass weight, and dressing percentage in both groups, and carcass composition remained unaffected. The pelleted diet containing greater ratio of concentrate: roughage (60:40) had no additional benefits in terms of ADG, and carcass traits in finisher kids. Therefore, it may be concluded that the Bengal gram residual forage-based pelleted TMR diet containing C40: R60 (TDN 57.13%, DCP 7.64%, ME 9.11MJ/kg feed) is suitable for optimizing growth performance with desirable carcass traits, and meat composition in finisher Barbari kids reared under the intensive system.

Molecular and immune signatures, and pathological trajectories of fatal COVID-19 lungs defined by in situ spatial single-cell transcriptome analysis.

Despite intensive studies during the last 3 years, the pathology and underlying molecular mechanism of coronavirus disease 2019 (COVID-19) remain poorly defined. In this study, we investigated the spatial single-cell molecular and cellular features of postmortem COVID-19 lung tissues using in situ sequencing (ISS). We detected 10 414 863 transcripts of 221 genes in whole-slide tissues and segmented them into 1 719 459 cells that were mapped to 18 major parenchymal and immune cell types, all of which were infected by SARS-CoV-2. Compared with the non-COVID-19 control, COVID-19 lungs exhibited reduced alveolar cells (ACs) and increased innate and adaptive immune cells. We also identified 19 differentially expressed genes in both infected and uninfected cells across the tissues, which reflected the altered cellular compositions. Spatial analysis of local infection rates revealed regions with high infection rates that were correlated with high cell densities (HIHD). The HIHD regions expressed high levels of SARS-CoV-2 entry-related factors including ACE2, FURIN, TMPRSS2 and NRP1, and co-localized with organizing pneumonia (OP) and lymphocytic and immune infiltration, which exhibited increased ACs and fibroblasts but decreased vascular endothelial cells and epithelial cells, mirroring the tissue damage and wound healing processes. Sparse nonnegative matrix factorization (SNMF) analysis of niche features identified seven signatures that captured structure and immune niches in COVID-19 tissues. Trajectory inference based on immune niche signatures defined two pathological routes. Trajectory A primarily progressed with increased NK cells and granulocytes, likely reflecting the complication of microbial infections. Trajectory B was marked by increased HIHD and OP, possibly accounting for the increased immune infiltration. The OP regions were marked by high numbers of fibroblasts expressing extremely high levels of COL1A1 and COL1A2. Examination of single-cell RNA-seq data (scRNA-seq) from COVID-19 lung tissues and idiopathic pulmonary fibrosis (IPF) identified similar cell populations consisting mainly of myofibroblasts. Immunofluorescence staining revealed the activation of IL6-STAT3 and TGF-ß-SMAD2/3 pathways in these cells, likely mediating the upregulation of COL1A1 and COL1A2 and excessive fibrosis in the lung tissues. Together, this study provides a spatial single-cell atlas of cellular and molecular signatures of fatal COVID-19 lungs, which reveals the complex spatial cellular heterogeneity, organization, and interactions that characterized the COVID-19 lung pathology.

Can Hierarchical Transformers Learn Facial Geometry?

Human faces are a core part of our identity and expression, and thus, understanding facial geometry is key to capturing this information. Automated systems that seek to make use of this information must have a way of modeling facial features in a way that makes them accessible. Hierarchical, multi-level architectures have the capability of capturing the different resolutions of representation involved. In this work, we propose using a hierarchical transformer architecture as a means of capturing a robust representation of facial geometry. We further demonstrate the versatility of our approach by using this transformer as a backbone to support three facial representation problems: face anti-spoofing, facial expression representation, and deepfake detection. The combination of effective fine-grained details alongside global attention representations makes this architecture an excellent candidate for these facial representation problems. We conduct numerous experiments first showcasing the ability of our approach to address common issues in facial modeling (pose, occlusions, and background variation) and capture facial symmetry, then demonstrating its effectiveness on three supplemental tasks.

Sketching and sampling approaches for fast and accurate long read classification.

BACKGROUND: In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read. RESULTS: Existing tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a "screen") of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read's similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy. CONCLUSIONS: The sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching .

Sapling: accelerating suffix array queries with learned data models.

MOTIVATION: As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The suffix array is a widely used data structure to accelerate alignment, but the binary search algorithm used to query, it requires widespread memory accesses, causing a large number of cache misses on large datasets. RESULTS: Here, we present Sapling, an algorithm for sequence alignment, which uses a learned data model to augment the suffix array and enable faster queries. We investigate different types of data models, providing an analysis of different neural network models as well as providing an open-source aligner with a compact, practical piecewise linear model. We show that Sapling outperforms both an optimized binary search approach and multiple widely used read aligners on a diverse collection of genomes, including human, bacteria and plants, speeding up the algorithm by more than a factor of two while adding <1% to the suffix array's memory footprint. AVAILABILITY AND IMPLEMENTATION: The source code and tutorial are available open-source at https://github.com/mkirsche/sapling. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Photocatalytic performance and interaction mechanism of reverse micelle synthesized Cu-TiO2 nanomaterials towards levofloxacin under visible LED light.

The degradation performance of Cu-TiO2 nanomaterials towards levofloxacin (LFX) antibiotic was investigated under an environmentally benign visible LED light source. Cu-TiO2 nanomaterials were prepared using the reverse micelle sol-gel method with different copper content ranging from 0.25 to 1.0 wt% concerning titania. Characterization of Cu-TiO2 samples was performed by XRD, TEM, UV-Vis, BET, ICP-MS, FTIR and XPS techniques. 0.5 wt% Cu-TiO2 showed crystallite size below 6 nm, surface area (69.85 m2/g) and significant visible light absorption capacity. Both Cu1+ and Cu2+ are formed in lower Cu-doped TiO2 samples, whereas only Cu2+ is present in higher Cu-doped TiO2 samples as evident in XPS analysis. 0.5 wt% Cu-TiO2 has shown the optimum photocatalytic degradation of 75.5% under 6 h. of a visible light source. FTIR analysis of LFX adsorbed Cu-TiO2 materials indicated the pollutant-catalyst interaction, where the declining trend was observed in photocatalytic degradation efficiency for higher Cu-doped TiO2 samples due to copper-LFX complex formation. Copper-LFX complexes are formed due to the presence of Cu2+ in higher Cu-doped TiO2 nanomaterials, which might have hindered the photocatalytic activity under visible light. Effects of initial pollutant concentration, catalyst loading and visible light intensity on the degradation of LFX are studied. Photocatalytic degradation pathways of LFX using best performing Cu-TiO2 material were also proposed based on the LC-MS analysis.

Effect of supplementation of phytogenic feed additives on intake, in vitro fermentation, growth performance and carcass traits in weaned Barbari kids reared under intensive feeding.

Twenty-four weaned male Barbari kids (age 144.67 days; weight 11.99 ± 0.49 kg) were divided equally into three groups (T1, T2, and T3) in order to investigate the effect of supplementation of phytogenic feed additives (herbal mixture) in the complete pelleted feed on growth performance, in vitro rumen fermentation and carcass quality in kids reared under stall-fed condition. Treatment groups were as follows: T1, concentrate mixture (40%) plus arhar (Cajanus cajan) straw (60%) in total mixed ration (TMR) form fed ad libitum; T2, T1 diet in complete feed pellets form fed ad libitum; and T3, T1 diet in complete feed pellets form supplemented with herbal mixture (Tulsi/Haldi/Amla/Arni; ratio 1:1:1:1 on DM basis) at 0.5% in complete feed fed ad libitum. The experimental kids in each group were allowed for feeding for 8 months by following the respective feeding schedule. Rumen fermentation pattern under in vitro system was also studied using the same three diets as substrates. After 240 days of feeding, all goats were slaughtered following standard protocol. Total body weight gain (kg) and average daily gain (ADG, g/day/kid) were 18.57, 22.26, and 23.06 kg, and 79.91, 101.49, and 100.18 g in T1, T2, and T3 treatments, respectively. Pelleting of TMR (T2) and supplementation of herbal mixture in pelleted feed (T3) increased (P < 0.001) average daily weight gain in Barbari kids compared to T1 (TMR). Average dry matter intake (DMI, g/day/kid) during growth trial was greater (P < 0.05) in T3 (1079.17) than T1 (849.76) and T2 (968.76). Feed conversion efficiency was 8.92, 9.48, and 8.68% in T1, T2, and T3, respectively. The difference was statistically non-significant among the treatments. Supplementation of herbal mixture in the complete pelleted substrate had adjunct effect on improvement of TCA-precipitable-N and total VFAs in the incubation medium under in vitro system. Carcass weight (kg) tended to increase in finisher kids under T2 (16.58) and T3 (16.70) than T1 (14.61), but the variation was non-significant. The dressing percentage was similar among three treatments. Similarly, the muscle protein, fat, and cholesterol contents remained unaffected by different dietary treatments. Therefore, it may be concluded that densification of feeds in the form of complete pelleted feed and further supplementation with potential phytogenic feed additives increased total DMI and ADG and tended to enhance meat production potential in finisher Barbari kids without changing the meat chemical composition.

Companion Animals Emerged as an Important Reservoir of Carbapenem-Resistant Enterobacteriaceae: A Report from India.

The emergence and spread of carbapenem-resistant Enterobacteriaceae (CRE) are perceived as a serious public-health threat world-wide. Despite sporadic reports, no systemic study has been carried out on CRE in companion animals in Indian subcontinent. In total, 237 canine specimens collected from five veterinary polyclinics in and around Kolkata were analyzed for isolation, antimicrobial resistance profiling and molecular characterization of carbapenem-resistant (CR) E. coli. Of the 29 CR isolates, 19 were identified as metallo-ß-lactamase producers (MP-CRE) and 10 as metallo-ß-lactamase non-producers (MNP-CRE). Eleven of them were extended spectrum ß-lactamase and/or AmpC type ß-lactamase producers and harboured fluoroquinolone-, tetracycline-, sulfonamide- and aminoglycoside-resistant genes. Beside uropathogenic virulence determinants, they carried the adhesion factors mediating biofilm production which was remarkably higher in 6 MP-CRE and one MNP-CRE isolates. Although the CRE were of diverse origin including the healthy and the diseased dogs, these were more frequently isolated from canine pyometra. The MP-CRE harboured plasmids of IncF and IncA/C types. Phylo-type B1 was observed in 38% of the CR isolates, followed by A0 in 31% and rest were attributed to A1 and D1. The Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) revealed that these isolates were genetically diverse and constituted of a heterogenous population. Detection of CRE in pet dogs despite the fact that carbapenems are not used in animals in India emphasizes the need for active surveillance to identify the transmission and dynamics of such pathogens in companion animals.

Application of Pomegranate by-Products in Muscle Foods: Oxidative Indices, Colour Stability, Shelf Life and Health Benefits.

In recent years, considerable importance is given to the use of agrifood wastes as they contain several groups of substances that are useful for development of functional foods. As muscle foods are prone to lipid and protein oxidation and perishable in nature, the industry is in constant search of synthetic free additives that help in retarding the oxidation process, leading to the development of healthier and shelf stable products. The by-products or residues of pomegranate fruit (seeds, pomace, and peel) are reported to contain bioactive compounds, including phenolic and polyphenolic compounds, dietary fibre, complex polysaccharides, minerals, vitamins, etc. Such compounds extracted from the by-products of pomegranate can be used as functional ingredients or food additives to harness the antioxidant, antimicrobial potential, or as substitutes for fat, and protein in various muscle food products. Besides, these natural additives are reported to improve the quality, safety, and extend the shelf life of different types of food products, including meat and fish. Although studies on application of pomegranate by-products on various foods are available, their effect on the physicochemical, oxidative changes, microbial, colour stabilizing, sensory acceptability, and shelf life of muscle foods are not comprehensively discussed previously. In this review, we vividly discuss these issues, and highlight the benefits of pomegranate by-products and their phenolic composition on human health.

Edible Mushrooms as Functional Ingredients for Development of Healthier and More Sustainable Muscle Foods: A Flexitarian Approach.

Consumers are increasingly interested in nutritious, safe and healthy muscle food products with reduced salt and fat that benefit their well-being. Hence, food processors are constantly in search of natural bioactive ingredients that offer health benefits beyond their nutritive values without affecting the quality of the products. Mushrooms are considered as next-generation healthy food components. Owing to their low content of fat, high-quality proteins, dietary fibre and the presence of nutraceuticals, they are ideally preferred in formulation of low-caloric functional foods. There is a growing trend to fortify muscle food with edible mushrooms to harness their goodness in terms of nutritive, bioactive and therapeutic values. The incorporation of mushrooms in muscle foods assumes significance, as it is favourably accepted by consumers because of its fibrous structure that mimics the texture with meat analogues offering unique taste and umami flavour. This review outlines the current knowledge in the literature about the nutritional richness, functional bioactive compounds and medicinal values of mushrooms offering various health benefits. Furthermore, the effects of functional ingredients of mushrooms in improving the quality and sensory attributes of nutritionally superior and next-generation healthier muscle food products are also highlighted in this paper.

KinVis: a visualization tool to detect cryptic relatedness in genetic datasets.

MOTIVATION: It is important to characterize individual relatedness in terms of familial relationships and underlying population structure in genome-wide association studies for correct downstream analysis. The characterization of individual relatedness becomes vital if the cohort is to be used as reference panel in other studies for association tests and for identifying ethnic diversities. In this paper, we propose a kinship visualization tool to detect cryptic relatedness between subjects. We utilize multi-dimensional scaling, bar charts, heat maps and node-link visualizations to enable analysis of relatedness information. AVAILABILITY AND IMPLEMENTATION: Available online as well as can be downloaded at http://shiny-vis.qcri.org/public/kinvis/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Application of nanoemulsion-based approaches for improving the quality and safety of muscle foods: A comprehensive review.

Recently, there has been growing interest in implementing innovative nanoscience-based technologies to improve the health, safety, and quality of food products. A major thrust in this area has been to use nanoemulsions because they can easily be formulated with existing food ingredients and technologies. In particular, oil-in-water nanoemulsions, which consist of small oil droplets (<200 nm) dispersed in water, are being utilized as delivery systems for various hydrophobic substances in foods, including nutrients, nutraceuticals, antioxidants, antimicrobials, colors, and flavors. In this article, we focus on the application of nanoemulsion-based delivery systems for improving the quality, safety, nutritional profile, and sensory attributes of muscle foods, such as meat and fish. The article also critically reviews the formulation and fabrication of food-grade nanoemulsions, their potential benefits and limitations in muscle food systems.

Impact of maternal overweight and obesity on milk composition and infant growth.

Overweight and obesity (OW/OB) impact half of the pregnancies in the United States and can have negative consequences for offspring health. Studies are limited on human milk alterations in the context of maternal obesity. Alterations in milk are hypothesized to impact offspring development during the critical period of lactation. We aimed to evaluate the relationships between mothers with OW/OB (body mass index [BMI] ≥25 kg/m2 ), infant growth, and selected milk nutrients. We recruited mother-infant dyads with pre-pregnancy OW/OB and normal weight status. The primary study included 52 dyads with infant growth measures through 6 months. Thirty-two dyads provided milk at 2 weeks, which was analysed for macronutrients, long-chain fatty acids, and insulin. We used multivariable linear regression to examine the association of maternal weight status with infant growth, maternal weight status with milk components, and milk components with infant growth. Mothers with OW/OB had infants with higher weight-for-length (WFL) and BMI Z-scores at birth. Mothers with OW/OB had higher milk insulin and dihomo-gamma-linolenic, adrenic, and palmitic acids and reduced conjugated linoleic and oleic acids. N6 long-chain polyunsaturated fatty acid (LC-PUFA)-driven factor 1 was associated with higher WFL, lower length-for-age (LFA), and lower head circumference-for-age Z-scores change from 2 weeks to 2 months in human milk-fed infants, whereas N6 LC-PUFA-driven factor 5 was associated with lower LFA Z-score change. Human milk composition is associated with maternal pre-pregnancy weight status and composition may be a contributing factor to early infant growth trajectory.

Dragon fruit (Hylocereus undatus) peel as antioxidant dietary fibre on quality and lipid oxidation of chicken nuggets.

In this study, the efficacy of dragon fruit peel (DFP) powder as antioxidant dietary fibre (ADF), at two different concentrations (T1-1.5% and T2-3.0%), on quality improvement and susceptibility to lipid oxidation of chicken nuggets during 20 days of refrigerated storage was assessed. DFP, rich in dietary fibre (56.91%) with higher insoluble dietary fibre, phenolics (36-39 mgGAE/100 g) content and possessing good radical scavenging activity as well as reducing power, contained 10.36% protein, 4.48% fat and 2.34% ash. HPLC analysis revealed presence of high concentrations of gallic and ferulic acid, among the phenolics. Incorporation of DFP in nuggets although decreased the pH but improved emulsion stability as well as cooking yield and had higher protein, ash and lower fat content. Further, the treated nuggets had significantly (p < 0.05) higher dietary fibre and total phenolics content than control. Incorporation of DFP decreased the hardness, gumminess and chewiness and improved (p < 0.05) the products' redness values. Sensory evaluation of the products revealed significant improvement in the appearance score and non-significant (p > 0.05) increase in the scores of other attributes compared to control samples. DFP significantly decreased lipid peroxidation, odour scores and microbial load in chicken nuggets during 20 days of storage period. From the study, it could be deduced that DFP rich in bioactive components had positive influence on the nutritional quality of chicken nuggets and could also be used as ADF in muscle food without affecting the quality and acceptability of products.

ZnO/Curcumin Nanocomposites for Enhanced Inhibition of Pseudomonas aeruginosa Virulence via LasR-RhlR Quorum Sensing Systems.

The indiscriminate and excessive use of antibiotics has ultimately led to the emergence of bacterial resistant mutants or superbugs. These superbugs are difficult to control with conventional antibiotics. Disabling quorum sensing (QS), a population-density-dependent cell-to-cell communication process used by bacteria to coordinate the expression of virulence genes and biofilm formation, with dietary phytochemicals is emerging as a non-antibiotic strategy to inhibit bacterial pathogenicity. Although curcumin is an anti-QS agent and its delivery to cells has been a challenge due to poor bioavailability, ZnO/curcumin nanocomposites (ZnC-NCs) were fabricated with enhanced delivery of curcumin inside the bacterial superbug Pseudomonas aeruginosa PAO1 for effective inhibition of its QS and biofilm formation. Sustained release of curcumin from ZnC-NCs was observed where 51% curcumin at pH 7.2 and 83% curcumin at pH 5.5 were released within 48 h. ZnC-NCs also decreased the production of virulence factors and biofilm formation without affecting planktonic cell growth. Both LasR and RhlR QS systems were inhibited by ZnC-NCs. ZnC-NCs were also capable of protecting both mice as well as lung epithelial cells from killing by PAO1. The superoxide anions (O2·-) were also found as key players in suppressing PAO1 QS systems by ZnC-NCs. Overall, ZnC-NCs enhanced curcumin bioavailability for effective inhibition of QS signaling in P. aeruginosa via LasR-RhlR suppression and O2·- generation.

Serum Polyunsaturated Fatty Acids in Middle Childhood and Body Mass Index Change Through Adolescence.

BACKGROUND: Polyunsaturated fatty acids (PUFA) status in childhood may be associated with adiposity development. OBJECTIVE: To assess associations of serum PUFA biomarkers in childhood with change in body mass index (BMI)-for-age Z scores (BMIZ) through adolescence. METHODS: We quantified serum PUFA at ages 5 and 10 years among 418 children from Santiago, Chile. BMI was measured at 5, 10, and 16 years. We compared BMIZ change through age 16 years between quartiles of PUFA at 5 and 10 years and PUFA change 5-10 years by fitting growth curves from mixed effects models. RESULTS: At age 5 years, serum docosahexaenoic acid was inversely associated with BMIZ change from ages 5 to 16 years. At age 10 years, arachidonic acid (AA) was nonlinearly positively related to BMIZ change from ages 10 to 16 years. Change in AA and the Δ5-desaturase (D5D) activity index between 5 and 10 years were each positively associated with BMIZ change from ages 10 to 16 years. Change in eicosapentaenoic acid was inversely associated with change in BMIZ. CONCLUSIONS: Serum long-chain n-3 PUFA in middle childhood were associated with less BMI gain through adolescence, whereas AA and D5D activity was related to greater BMI gain.

Inhibition of lipid and protein oxidation in raw ground pork by Terminalia arjuna fruit extract during refrigerated storage.

OBJECTIVE: Terminalia arjuna plant, specially its leaves, bark, and roots, are widely used in traditional herbal medicine due to presence of bioactive components and being a rich source of natural antioxidants. But its fruit has not been used for any such purposes despite its potential to retard oxidation. Hence, the antioxidant potential of Arjuna fruit extract (AFE) in retarding lipid and protein oxidation of raw ground pork was evaluated during refrigerated storage for 9 days. METHODS: The AFEs were prepared using different solvents viz. ethanol (EH), water, ethanol: water (60:40) and methanol:hot water (60:40). The AFEs were analysed for total phenolic content (TPC), 2, 2-diphenyl-1-picrylhydrazyl radical scavenging activity and reducing power. Water extract (WE) and ethanol-water extract (EH-WE) were selected and incorporated at 1.0% into freshly minced pork meat and compared with a synthetic antioxidant, in retarding lipid and protein oxidation during storage. RESULTS: The TPC in AFEs using different solvents ranged from 11.04 to 16.53 mg gallic acid equivalents/g and extracts exhibited appreciable scavenging activity ranging from 50.02% to 58.62%. Arjuna extracts significantly (p<0.05) improved the colour score of meat samples by reducing the formation of metmyoglobin during storage. Both the AFEs (WE and EH-WE) significantly (p<0.05) lowered the thiobarbituric acid reactive substances value, peroxide formation and formation of protein carbonyls in raw pork than control sample during storage. Upon sensory evaluation of all samples, it was found that AFE treatment could prolong the storage period of meat samples, without influencing the colour and odour score, up to 6 days. CONCLUSION: AFEs used at 1% improved the oxidative stability, colour and odour score and prolonged the refrigerated shelf life of ground pork up 6 days. Therefore, AFE could be explored as an alternative natural antioxidant in retarding lipid and protein oxidation in meat products.

Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota.

Background: trans-10,cis-12 Conjugated linoleic acid (t10,c12-CLA) is a dietary supplement that promotes weight loss by increasing fat oxidation and energy expenditure. We previously reported that in the absence of t10,c12-CLA, mice forced to lose equivalent body weight by food restriction (FR) do not exhibit increases in fat oxidation or energy expenditure but have improved glucose metabolism, consistent with FR as a metabolically healthy weight-loss method. Objective: Because diet is a primary determinant of gut bacterial populations, we hypothesized that the disparate metabolic effects accompanying weight loss from t10,c12-CLA or FR could be related to altered intestinal microbiota. Methods: Ten-week-old male LDL receptor-deficient (Ldlr-/-) mice were fed a high-fat, high-sucrose diet (HFHS; 36% lard fat, 36.2% sucrose + 0.15% cholesterol) for 12 wk (baseline), then switched to the HFHS diet alone (obese control), HFHS + 1% c9,t11-CLA (obese fatty acid control), HFHS + 1% t10,c12-CLA (weight-loss-inducing fatty acid), or HFHS + FR (weight-loss control group with 75-85% ad libitum HFHS food intake) for a further 8 wk. Fecal microbial content, short-chain fatty acids (butyrate, acetate), tissue CLA concentrations, and intestinal nutrient transporter expression were quantified. Results: Mice fed t10,c12-CLA or assigned to FR lost 14.5% of baseline body weight. t10,c12-CLA-fed mice had elevated concentrations of fecal butyrate (2-fold) and plasma acetate (1.5-fold) compared with HFHS-fed controls. Fecal α diversity decreased by 7.6-14% in all groups. Butyrivibrio and Roseburia, butyrate-producing microbes, were enriched over time by t10,c12-CLA. By comparing with each control group, we also identified bacterial genera significantly enriched in the t10,c12-CLA recipients, including Lactobacillus, Actinobacteria, and the newly identified Ileibacterium valens of the Allobaculum genus, whereas other taxa were enriched by FR, including Clostridiales and Bacteroides. Conclusion: Modalities resulting in equivalent weight loss but with divergent metabolic effects are associated with compositional differences in the mouse intestinal microbiota.