Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare

Predicting Insulin Resistance in a Pediatric Population With Obesity

OBJECTIVES

Insulin resistance (IR) affects children and adolescents with obesity and early diagnosis is crucial to prevent long-term consequences. Our aim was to identify predictors of IR and develop a multivariate model to accurately predict IR.

METHODS

We conducted a cross-sectional analysis of demographical, clinical, and biochemical data from a cohort of patients attending a specialized Paediatric Nutrition Unit in Portugal over a 20-year period. We developed multivariate regression models to predict IR. The participants were randomly divided into 2 groups: a model group for developing the predictive models and a validation group for cross-validation of the study.

RESULTS

Our study included 1423 participants, aged 3-17 years old, randomly divided in the model (n = 879) and validation groups (n = 544). The predictive models, including uniquely demographic and clinical variables, demonstrated good discriminative ability [area under the curve (AUC): 0.834-0.868; sensitivity: 77.0%-83.7%; specificity: 77.0%-78.7%] and high negative predictive values (88.9%-91.6%). While the diagnostic ability of adding fasting glucose or triglycerides/high density lipoprotein cholesterol index to the models based on clinical parameters did not show significant improvement, fasting insulin appeared to enhance the discriminative power of the model (AUC: 0.996). During the validation, the model considering demographic and clinical variables along with insulin showed excellent IR discrimination (AUC: 0.978) and maintained high negative predictive values (90%-96.3%) for all models.

CONCLUSION

Models based on demographic and clinical variables can be advantageously used to identify children and adolescents at moderate/high risk of IR, who would benefit from fasting insulin evaluation.

Pasture-finishing of bison improves animal metabolic health and potential health-promoting compounds in meat

BACKGROUND

With rising concerns regarding the effects of red meat on human and environmental health, a growing number of livestock producers are exploring ways to improve production systems. A promising avenue includes agro-ecological practices such as rotational grazing of locally adapted ruminants. Additionally, growing consumer interest in pasture-finished meat (i.e., grass-fed) has raised questions about its nutritional composition. Thus, the goal of this study was to determine the impact of two common finishing systems in North American bison-pasture-finished or pen-finished on concentrates for 146 d-on metabolomic, lipidomic, and fatty acid profiles of striploins (M. longissimus lumborum).

RESULTS

Six hundred and seventy-one (671) out of 1570 profiled compounds (43%) differed between pasture- and pen-finished conditions (n = 20 animals per group) (all, P < 0.05). Relative to pasture-finished animals, the muscle of pen-finished animals displayed elevated glucose metabolites (~ 1.6-fold), triglycerides (~ 2-fold), markers of oxidative stress (~ 1.5-fold), and proteolysis (~ 1.2-fold). In contrast, pasture-finished animals displayed improved mitochondrial (~ 1.3-fold higher levels of various Krebs cycle metabolites) and carnitine metabolism (~ 3-fold higher levels of long-chain acyl carnitines) (all P < 0.05). Pasture-finishing also concentrated higher levels of phenolics (~ 2.3-fold), alpha-tocopherol (~ 5.8-fold), carotene (~ 2.0-fold), and very long-chain fatty acids (~ 1.3-fold) in their meat, while having lower levels of a common advanced lipoxidation (4-hydroxy-nonenal-glutathione; ~ 2-fold) and glycation end-product (N6-carboxymethyllysine; ~ 1.7-fold) (all P < 0.05). In contrast, vitamins B₅, B₆, and C, gamma/beta-tocopherol, and three phenolics commonly found in alfalfa were ~ 2.5-fold higher in pen-finished animals (all P < 0.05); suggesting some concentrate feeding, or grazing plants rich in those compounds, may be beneficial.

CONCLUSIONS

Pasture-finishing (i.e., grass-fed) broadly improves bison metabolic health and accumulates additional potential health-promoting compounds in their meat compared to concentrate finishing in confinement (i.e., pen-finished). Our data, however, does not indicate that meat from pen-finished bison is therefore unhealthy. The studied bison meat-irrespective of finishing practice-contained favorable omega 6:3 ratios (< 3.2), and amino acid and vitamin profiles. Our study represents one of the deepest meat profiling studies to date (> 1500 unique compounds), having revealed previously unrecognized differences in animal metabolic health and nutritional composition because of finishing mode. Whether observed nutritional differences have an appreciable effect on human health remains to be determined.

Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

BACKGROUND

Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.

METHODS

We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.

RESULTS

In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10-6) and AC058822.1 (P = 1.47 × 10-4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.

CONCLUSIONS

Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10-5), demonstrating the importance of diversifying study cohorts.

Analysis and Interpretation of metagenomics data: an approach

Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.

Internal and External Regulatory Elements Controlling Somatic Embryogenesis in Catharanthus: A Model Medicinal Plant

Somatic or in vitro embryogenesis is a unique embryo producing process from vegetative cells observed in plants since 1958. Even over 60 years of research, the transition of somatic cells into embryonic fate is still not elucidated fully. Various networks and signaling elements have been noted to play important role in this "vegetative to reproductive" transition process. The networks include genotypes, explant types, the sugar/carbohydrate sources, cultural/environmental conditions like light quality and intensity, dissolved oxygen (DO) level, cell density, plant growth regulator (PGR) (auxin and cytokinin) signaling, PGR-gene interplay, stresses are important and cause new cellular reprogramming during embryonic acquisition. A wide array of genes, specific to zygotic embryogenesis, also express during somatic embryogenesis. A few embryogenesis-specific genes such as SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE, LEAFY COTYLEDON, AGAMOUS-LIKE 15, and BABY BOOM are crucial and have been discussed. The chapter focuses the importance of these gene products, e.g., proteins, enzymes, and transcription factors in regulating embryogenesis. Many of these encoded proteins act as potential somatic embryogenesis markers. Besides, important elements such as genotype, herbaceous/woody plants' response in culture in inducing embryos have been discussed. All these elements are connected and form network in complex fashion thus difficult to unfold fully; some of the current progress and developments have been presented in this chapter.

Regulation of lipoprotein metabolism by ANGPTL3, ANGPTL4, and ANGPTL8

Triglyceride-rich lipoproteins deliver fatty acids to tissues for oxidation and for storage. Release of fatty acids from circulating lipoprotein triglycerides is carried out by lipoprotein lipase (LPL), thus LPL serves as a critical gatekeeper of fatty acid uptake into tissues. LPL activity is regulated by a number of extracellular proteins including three members of the angiopoietin-like family of proteins. In this review, we discuss our current understanding of how, where, and when ANGPTL3, ANGPTL4, and ANGPTL8 regulate lipoprotein lipase activity, with a particular emphasis on how these proteins interact with each other to coordinate triglyceride metabolism and fat partitioning.

Application of Exosomes-Derived Mesenchymal Stem Cells in Treatment of Fungal Diseases: From Basic to Clinical Sciences

Fungal diseases such as candidiasis are some of the deadliest diseases among immunocompromised patients. These fungi naturally exist on human skin and throughout the digestive system. When the microbiota balance becomes upset, these fungi become pathogenic and potentially lethal. At the pathogenesis of fungal diseases, host immune system response is diverse. At the early stages of fungal pathogenesis such as Candida albicans, it was shown that these fungi use the immune cells of the host body and cause malfunction the early induction of proinflammatory cytokines of the host body leading to a reduction in their numbers. However, at some stages of fungal diseases, the immune response is severe. Despite many treatments already being available, it seems that one of the best treatments could be an immune-stimulatory agent. Some of the subsets of MSCs and exosome-derived cells, as a cell-to-cell communicator agent, have many roles in the human body, including anti-inflammatory and immune-modulatory effects. However, the TLR4-primed and IL-17+ subsets of MSCs have been shown to have immune-stimulatory effects. These subsets of the MSCs produce pro-inflammatory cytokines and reduce immunosuppressive cytokines and chemokines. Thus, they could trigger inflammation and stop fungal pathogenesis. As some biological activities and molecules inherit elements of their exosomes from their maternal cells, the exosome-derived TLR4-primed and IL-17+ subsets of MSCs could be a good candidate for fighting against fungal diseases. The applications of exosomes in human diseases are well-known and expanding. It is time to investigate the exosomes application in fungal diseases. In this review, the probable role of exosomes in treating fungal diseases is explored.

Genes, proteins and other networks regulating somatic embryogenesis in plants

Background

Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network.

Main text (observation)

This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation.

Conclusions

The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.

Effect of M2 Macrophages on Injury and Apoptosis of Renal Tubular Epithelial Cells Induced by Calcium Oxalate Crystals

Background: M2 macrophages have important roles in diseases such as tumours, cardiovascular diseases and renal diseases. This study aimed to determine the effects and protective mechanism of M2 macrophages against oxidative stress injury and apoptosis induced by calcium oxalate crystals (CaOx) in renal tubular epithelial cells (HK-2) under coculture conditions. Methods: THP-1 cells were induced to differentiate into M2 macrophages by using phorbol-12-myristate-13-acetate, IL-4 and IL-13. Morphological features were observed by microscopy. Phenotypic markers were identified by reverse transcription-polymerase chain reaction, Western blot and enzyme-linked immunosorbent assay (ELISA). HK-2 cells were treated with 0.5 mg/mL CaOx crystals and co-cultured with M2 macrophages or apocynin. The viability of HK-2 cells was detected by CCK-8 assay. The lactate dehydrogenase (LDH) activity of HK-2 cells was analysed using a microplate reader. The apoptosis of HK-2 cells was examined by flow cytometry and Hoechst 33258 staining. Reactive oxygen species (ROS) expression and mitochondrial membrane potential in HK-2 cells were detected by a fluorescence microplate reader. Western blot analysis was conducted to detect the expression of p47phox, Bcl-2, cleaved caspase-3, cytochrome c, p38 MAPK, phospho-p38 MAPK, Akt and phospho-Akt. Results: The results of morphology, reverse transcription-polymerase chain reaction, Western blot and ELISA showed that THP-1 cells were successfully polarised to M2 macrophages. The results of co-culture suggested that M2 macrophages or apocynin significantly increased the cell viability and decreased the LDH activity and apoptosis rate after HK-2 cells were challenged with CaOx crystals. The expression of the p47phox protein and the concentration of ROS were reduced, the release of mitochondrial membrane potential and the expression of the Bcl-2 protein were upregulated and the protein expression of cleaved caspase-3 and cytochrome c was downregulated. The expression of the phosphorylated form of p38 MAPK increased. Under coculture conditions with M2 macrophages, the Akt protein of HK-2 cells treated with CaOx crystals was dephosphorylated, but the phosphorylated form of Akt was not reduced by apocynin. Conclusions: M2 macrophages reduced the oxidative stress injury and apoptosis of HK-2 cells by downregulating the activation of NADPH oxidase, reducing the production of ROS, inhibiting the phosphorylation of p38 MAPK and enhancing the phosphorylation of Akt. We have revealed one of the possible mechanisms by which M2 macrophages reduce the formation of kidney stones.

Effect of Rhizobium Symbiosis on Low-Temperature Tolerance and Antioxidant Response in Alfalfa (Medicago sativa L.)

Low temperature-induced stress is a major environmental factor limiting the growth and development of plants. Alfalfa (Medicago sativa L.) is a legume well known for its tolerance of extreme environments. In this study, we sought to experimentally investigate the role of rhizobium symbiosis in alfalfa's performance under a low-temperature stress condition. To do this, alfalfa "Ladak+" plants carrying active nodules (AN), inactive nodules (IN), or no nodules (NN) were exposed to an imposed low temperature stress and their survivorship calculated. The antioxidant defense responses, the accumulation of osmotic regulation substances, the cell membrane damage, and the expression of low temperature stress-related genes were determined in both the roots and the shoots of alfalfa plants. We found that more plants with AN survived than those with IN or NN under the same low temperature-stress condition. Greater activity of oxidation protective enzymes was observed in the AN and IN groups, conferring higher tolerance to low temperature in these plants. In addition, rhizobia nodulation also enhanced alfalfa's ability to tolerate low temperature by altering the expression of regulatory and metabolism-associated genes, which resulted in the accumulation of soluble proteins and sugars in the nodulated plants. Taken together, the findings of this study indicate that rhizobium inoculation offers a practical way to promote the persistence and growth potential of alfalfa "Ladak+" in cold areas.

NSAID-induced enteropathy: the current state of the problem

The review analyzes the main etiological and pathogenetic mechanisms of the development of NSAID-enteropathy. Particular attention is paid to the role of intestinal microbiota in the manifestation and progression of NSAID-enteropathy. The special role of probiotics in the prevention and treatment of NSAIDs enteropathy is considered.

Tailoring Thermal Transport Properties of Graphene Paper by Structural Engineering

As a two-dimensional material, graphene has attracted increasing attention as heat dissipation material owing to its excellent thermal transport property. In this work, we fabricated sisal nanocrystalline cellulose/functionalized graphene papers (NPGs) with high thermal conductivity by vacuum-assisted self-assembly method. The papers exhibit in-plane thermal conductivity as high as 21.05 W m⁻¹ K⁻¹ with a thermal conductivity enhancement of 403% from the pure cellulose paper. The good thermal transport properties of NPGs are attributed to the strong hydrogen-bonding interaction between nanocrystalline cellulose and functionalized graphene and the well alignment structure of NPGs.

In Vivo Imaging Markers for Prediction of Radiotherapy Response in Patients with Nasopharyngeal Carcinoma: RESOLVE DWI versus DKI

In this prospective study, we compared the performance of readout segmentation of long variable echo trains of diffusion-weighted imaging (RESOLVE DWI) and diffusion kurtosis imaging (DKI) for the prediction of radiotherapy response in patients with nasopharyngeal carcinoma (NPC). Forty-one patients with NPC were evaluated. All patients underwent conventional MRI, RESOLVE DWI and DKI, before and after radiotherapy. All patients underwent conventional MRI every 3 months until 1 year after radiotherapy. The patients were divided into response group (RG; 36/41 patients) and no-response group (NRG; 5/41 patients) based on follow-up results. DKI (the mean of kurtosis coefficient, Kmean and the mean of diffusion coefficient, Dmean) and RESOLVE DWI (the minimum apparent diffusion coefficient, ADC_min) parameters were calculated. Parameter values at the pre-treatment period, post-treatment period, and the percentage change between these 2 periods were obtained. All parameters differed between the RG and NRG groups except for the pretreatment Dmean and ADC_min. Kmean-post was considered as an independent predictor of local control, with 87.5% sensitivity and 91.3% specificity (optimal threshold = 0.30, AUC: 0.924; 95% CI, 0.83-1.00). Kmean-post values of DKI have the potential to be used as imaging biomarkers for the early evaluation of treatment effects of radiotherapy on NPC.

Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record

The use of metals as biosignatures in the fossil stromatolite record requires understanding of the processes controlling the initial metal(loid) incorporation and diagenetic preservation in living microbialites. Here, we report the distribution of metals and the organic fraction within the lithifying microbialite of the hypersaline Big Pond Lake (Bahamas). Using synchrotron-based X-ray microfluorescence, confocal, and biphoton microscopies at different scales (cm-μm) in combination with traditional geochemical analyses, we show that the initial cation sorption at the surface of an active microbialite is governed by passive binding to the organic matrix, resulting in a homogeneous metal distribution. During early diagenesis, the metabolic activity in deeper microbialite layers slows down and the distribution of the metals becomes progressively heterogeneous, resulting from remobilization and concentration as metal(loid)-enriched sulfides, which are aligned with the lamination of the microbialite. In addition, we were able to identify globules containing significant Mn, Cu, Zn, and As enrichments potentially produced through microbial activity. The similarity of the metal(loid) distributions observed in the Big Pond microbialite to those observed in the Archean stromatolites of Tumbiana provides the foundation for a conceptual model of the evolution of the metal distribution through initial growth, early diagenesis, and fossilization of a microbialite, with a potential application to the fossil record.

Isolation and characterization of a spotted leaf 32 mutant with early leaf senescence and enhanced defense response in rice

Leaf senescence is a complex biological process and defense responses play vital role for rice development, their molecular mechanisms, however, remain elusive in rice. We herein reported a rice mutant spotted leaf 32 (spl32) derived from a rice cultivar 9311 by radiation. The spl32 plants displayed early leaf senescence, identified by disintegration of chloroplasts as cellular evidence, dramatically decreased contents of chlorophyll, up-regulation of superoxide dismutase enzyme activity and malondialdehyde, as physiological characteristic, and both up-regulation of senescence-induced STAY GREEN gene and senescence-associated transcription factors, and down-regulation of photosynthesis-associated genes, as molecular indicators. Positional cloning revealed that SPL32 encodes a ferredoxin-dependent glutamate synthase (Fd-GOGAT). Compared to wild type, enzyme activity of GOGAT was significantly decreased, and free amino acid contents, particularly for glutamate and glutamine, were altered in spl32 leaves. Moreover, the mutant was subjected to uncontrolled oxidative stress due to over-produced reactive oxygen species and damaged scavenging pathways, in accordance with decreased photorespiration rate. Besides, the mutant showed higher resistance to Xanthomonas oryzae pv. Oryzae than its wild type, coupled with up-regulation of four pathogenesis-related marker genes. Taken together, our results highlight Fd-GOGAT is associated with the regulation of leaf senescence and defense responses in rice.

X-ray induced singlet oxygen generation by nanoparticle-photosensitizer conjugates for photodynamic therapy: determination of singlet oxygen quantum yield

Singlet oxygen is a primary cytotoxic agent in photodynamic therapy. We show that CeF₃ nanoparticles, pure as well as conjugated through electrostatic interaction with the photosensitizer verteporfin, are able to generate singlet oxygen as a result of UV light and 8 keV X-ray irradiation. The X-ray stimulated singlet oxygen quantum yield was determined to be 0.79 ± 0.05 for the conjugate with 31 verteporfin molecules per CeF₃ nanoparticle, the highest conjugation level used. From this result we estimate the singlet oxygen dose generated from CeF₃-verteporfin conjugates for a therapeutic dose of 60 Gy of ionizing radiation at energies of 6 MeV and 30 keV to be (1.2 ± 0.7) × 10⁸ and (2.0 ± 0.1) × 10⁹ singlet oxygen molecules per cell, respectively. These are comparable with cytotoxic doses of 5 × 10⁷–2 × 10⁹ singlet oxygen molecules per cell reported in the literature for photodynamic therapy using light activation. We confirmed that the CeF3-VP conjugates enhanced cell killing with 6 MeV radiation. This work confirms the feasibility of using X- or γ- ray activated nanoparticle-photosensitizer conjugates, either to supplement the radiation treatment of cancer, or as an independent treatment modality.

A fully roll-to-roll gravure-printed carbon nanotube-based active matrix for multi-touch sensors

Roll-to-roll (R2R) printing has been pursued as a commercially viable high-throughput technology to manufacture flexible, disposable, and inexpensive printed electronic devices. However, in recent years, pessimism has prevailed because of the barriers faced when attempting to fabricate and integrate thin film transistors (TFTs) using an R2R printing method. In this paper, we report 20 × 20 active matrices (AMs) based on single-walled carbon nanotubes (SWCNTs) with a resolution of 9.3 points per inch (ppi) resolution, obtained using a fully R2R gravure printing process. By using SWCNTs as the semiconducting layer and poly(ethylene terephthalate) (PET) as the substrate, we have obtained a device yield above 98%, and extracted the key scalability factors required for a feasible R2R gravure manufacturing process. Multi-touch sensor arrays were achieved by laminating a pressure sensitive rubber onto the SWCNT-TFT AM. This R2R gravure printing system overcomes the barriers associated with the registration accuracy of printing each layer and the variation of the threshold voltage (Vth). By overcoming these barriers, the R2R gravure printing method can be viable as an advanced manufacturing technology, thus enabling the high-throughput production of flexible, disposable, and human-interactive cutting-edge electronic devices based on SWCNT-TFT AMs.