Short- and long-term effects of temporary early cow–calf separation or restricted suckling on well-being and performance in zebu cattle

Information on weaning techniques in the tropics is scarce, particularly regarding the long-term effect of temporary early cow–calf separation or restricted suckling. Therefore, we studied the effects of these two handling practices on well-being and performance at 150 days postpartum in fifteen zebu cow–calf pairs randomly assigned to three treatments. Continuous suckling (CS) where calves remained with their dams from birth to weaning; restricted suckling (RS) calves were allowed to suckle 30 min/day from Day 34 until weaning at Day 150 and kept separated the rest of the time; temporary separation (TS) calves were separated for 72 h from their dams from Day 33 to 36 but remained with their dams the rest of the time. Blood samples and behavioral data were collected on Days 32–36 (1st period) and 149–153 (2nd period). In the 1st period, a greater percentage of RS and TS calves were observed close to the fence line (< 10 m) that separated them from their dams (P < 0.0001) and vocalized more than CS calves (P < 0.0001), while in the 2nd period, RS calves had the highest cortisol concentration and vocalization rate (P < 0.05). Similarly, during the 1st period, a greater percentage of RS and TS cows were observed close to the fence line than CS cows (P < 0.0001), with TS cows vocalizing the most (P = 0.001). In the 2nd period, RS cows had greater cortisol concentration than TS (P = 0.037) and CS cows (P = 0.003). More TS and CS cows than RS were observed close to the fence line (P = 0.03 and P = 0.05). On Day 150, TS calves and cows vocalized more than RS and CS animals (P < 0.0001). Before calf–cow separation, 27 out of 45 cows were cycling (CS = 10; RS = 6; TS = 11). After separation, 12 of the remaining 18 cows resumed ovarian activity (CS = 3; RS = 5; TS = 4), and all cows were cycling after estrous synchronization treatment. The pregnancy rate was similar between CS, RS, and TS (60, 53, and 60% respectively). In conclusion, temporary separation increased calf distress response to definitive weaning even four months later, while restricted suckling seemed to reduce it.     

The genome‐scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post‐genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome‐scale metabolic network for E. siliculosus, EctoGEM ( http://ectogem.irisa.fr ). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co‐factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.     

Three‐dimensional genetic networks among seed oil‐related traits,metabolites and genes reveal the genetic foundations of oil synthesis in soybean

Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three‐dimensional genetic networks using six seed oil‐related traits, 52 lipid metabolism‐related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil‐related traits and metabolites by phenotypic and metabolic genome‐wide association studies and multi‐omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil‐related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three‐dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate–GmPDAT–GmFATA2–oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three‐dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.     

Effects of a plant product consisting of green tea and curcuma extract on milk production and the expression of hepatic genes involved in endoplasmic stress response and inflammation in dairy cows

During the periparturient phase, cows are typically in an inflammation-like condition, and it has been proposed that inflammation associated with the induction of stress of the endoplasmic reticulum (ER) in the liver contributes to the development of fatty liver syndrome and ketosis. In the present study, the hypothesis that supplementation of dairy cows with a plant product consisting of green tea (95%) and curcuma extract (5%) rich in polyphenols attenuates inflammation and ER stress in the liver during early lactation was investigated. Twenty-seven cows were assigned to two groups, either a control group (n = 14) or a treatment group (n = 13). Both groups of cows received a total mixed ration, and the ration of the treatment group was supplemented with 0.175 g of the plant product per kg dry matter from week 3 prepartum to week 9 postpartum. Dry matter intake and energy balance during week 2 to week 9 postpartum were not different between the two groups. However, cows supplemented with the plant product had a greater amount of energy-corrected milk during week 2 to week 9 postpartum and lower concentrations of triacylglycerols and cholesterol in the liver in week 1 and week 3 postpartum than cows of the control group (p < 0.05). Cows supplemented with the plant product showed a trend towards a reduced mRNA concentration of haptoglobin (p < 0.10), while relative mRNA concentrations of eight genes of the unfolded protein response considered in the liver were not different between the two groups of cows. Relative hepatic mRNA concentration of fibroblast growth factor, a stress hormone induced by various stress conditions, was reduced at week 1 and week 3 postpartum in cows supplemented with the plant product (p < 0.05). Overall, the data of this study suggest that – although there were only minor effects on the occurrence of ER stress and inflammation – a supplementation of polyphenols might be useful to improve milk yield and prevent fatty liver syndrome in dairy cows.     

High Expression of Complement Components in Omental Adipose Tissue in Obese Men

Objective: Accumulation of visceral fat is recognized as a predictor of obesity‐related metabolic disturbances. Factors that are predominantly expressed in this depot could mediate the link between visceral obesity and associated diseases. Research Methods and Procedures: Paired subcutaneous and omental adipose tissue biopsies were obtained from 10 obese men. Gene expression was analyzed by DNA microarrays in triplicate and by real‐time polymerase chain reaction. Serum C3 and C4 were analyzed by radial immunodiffusion assays in 91 subjects representing a cross section of the general population. Body composition was measured by computerized tomography. Results: Complement components C2, C3, C4, C7, and Factor B had higher expression in omental compared with subcutaneous adipose tissue (～2‐, 4‐, 17‐, 10‐, and 7‐fold, respectively). In addition, adipsin, which belongs to the alternative pathway, and the classical pathway components C1QB, C1R, and C1S were expressed in both depots. Analysis of tissue distribution showed high expression of C2, C3, and C4 in omental adipose tissue, and only liver had higher expression of these genes. Serum C3 levels correlated with both visceral and subcutaneous adipose tissue in both men (r = 0.65 and p < 0.001 and r = 0.52 and p < 0.001, respectively) and women (r = 0.34 and p = 0.023 and r = 0.49 and p < 0.001, respectively), whereas C4 levels correlated with only visceral fat in men (r = 0.36, p = 0.015) and with both depots in women (visceral: r = 0.58, p < 0.001; and subcutaneous: r = 0.51, p < 0.001). Discussion: Recent studies show that the metabolic syndrome is associated with chronically elevated levels of several immune markers, some of which may have metabolic effects. The high expression of complement genes in intra‐abdominal adipose tissue might suggest that the complement system is involved in the development of visceral adiposity and/or contributes to the metabolic complications associated with increased visceral fat mass.     

Natural rubber biosynthesis in plants,the rubber transferase complex,and metabolic engineering progress and prospects

Natural rubber (NR) is a nonfungible and valuable biopolymer, used to manufacture ~50 000 rubber products, including tires and medical gloves. Current production of NR is derived entirely from the para rubber tree (Hevea brasiliensis). The increasing demand for NR, coupled with limitations and vulnerability of H. brasiliensis production systems, has induced increasing interest among scientists and companies in potential alternative NR crops. Genetic/metabolic pathway engineering approaches, to generate NR‐enriched genotypes of alternative NR plants, are of great importance. However, although our knowledge of rubber biochemistry has significantly advanced, our current understanding of NR biosynthesis, the biosynthetic machinery and the molecular mechanisms involved remains incomplete. Two spatially separated metabolic pathways provide precursors for NR biosynthesis in plants and their genes and enzymes/complexes are quite well understood. In contrast, understanding of the proteins and genes involved in the final step(s)—the synthesis of the high molecular weight rubber polymer itself—is only now beginning to emerge. In this review, we provide a critical evaluation of recent research developments in NR biosynthesis, in vitro reconstitution, and the genetic and metabolic pathway engineering advances intended to improve NR content in plants, including H. brasiliensis, two other prospective alternative rubber crops, namely the rubber dandelion and guayule, and model species, such as lettuce. We describe a new model of the rubber transferase complex, which integrates these developments. In addition, we highlight the current challenges in NR biosynthesis research and future perspectives on metabolic pathway engineering of NR to speed alternative rubber crop commercial development.     

Cold effect analysis and screening of SNPs associated with cold‐tolerance in the olive flounder Paralichthys olivaceus

Olive flounder Paralichthys olivaceus is an important mariculture fish and cold stress limits to its growth and survival during winter. In the present study, the cold‐tolerant (CT) and cold‐sensitive (CS) flounder were defined after cold treatment (0.7 ± 0.05°C). Cold effects on histological and physiological and gene expression levels were analyzed. The correlation analyses between single nucleotide polymorphism locus (SNP) in hsp70, yb‐1 and hmgb1 and the trait of cold tolerance were performed. The results showed that flounder gill was obviously damaged after treatment and more serious lesions in some of the epithelial cell layers were observed in the CS group. ATP concentration and pyruvate kinase activity in the CT group were significantly higher than those in the CS group (p < 0.05). Expression levels of hsp70 and yb‐1 were both up‐regulated markedly after cold treatment (p < 0.05). Nine, twenty‐one and ten SNPs were screened from hsp70, yb‐1 and hmgb1 partial sequences, respectively. Among them, 3 SNPs in hsp70 and 2 SNPs in hmgb1 showed significant difference in the two groups. Allele G of the SNP 8 (locus 1797) in hsp70 was only observed in the CT group. In the SNP 7 (locus 725) of hmgb1, genotype TT and allele T, and genotype CC and allele C were associated with cold tolerance and cold sensitive, respectively. Furthermore, one haplotype (TTG) generated from SNPs of hsp70 gene among CT and CS individuals showed significant relationship with cold tolerance (p = 0.031). Two haplotypes (ATG) and (TCT) generated from SNPs of hmgb1 were significantly associated with resistance (p = 0.001) and sensitive (p = 0.002) in cold treatment, respectively. These SNPs, genotype, alleles and haplotypes of hsp70 and hmgb1 may be related to the cold resistance of flounder, and could be candidate markers potentially for further selective breeding.     

Differential expression of genes in milk of dairy cattle during lactation

The milk fat globule (MFG) is one of the most representative of mammary gland tissues and can be utilized to study gene expression of lactating cows during lactation. In this study, RNA‐seq technology was employed to detect differential expression of genes in MFGs at day 10 and day 70 after calving between two groups of cows with extremely high (H group) and low (L group) 305‐day milk yield, milk fat yield and milk protein yield. In total, 1232, 81, 429 and 178 significantly differentially expressed genes (false discovery rate q < 0.05) were detected between H10 and L10, H70 and L70, H10 and H70, and L10 and L70 respectively. Gene Ontology enrichment and pathway analysis revealed that these differentially expressed genes were enriched in biological processes involved in mammary gland development, protein and lipid metabolism process, signal transduction, cellular process, differentiation and immune function. Among these differentially expressed genes, 178 (H10 vs. L10), 4 (H70 vs. L70), 68 (H10 vs. H70) and 22 (L10 vs. L70) were found to be located within previously reported QTL regions for milk production traits. Based on these results, some promising candidate genes for milk production traits in dairy cattle were suggested.     

Differential Proteomic Analysis of Dimethylnitrosamine (DMN)‐Induced Liver Fibrosis

Liver fibrosis is a common pathological feature of many chronic liver diseases. To characterize the entire panorama of proteome changes in dimethylnitrosamine (DMN)‐induced liver fibrosis, isobaric tags for relative and absolute quantitation (iTRAQ)‐based differential proteomic analysis is performed with DMN‐induced liver fibrosis rats. A total of 4155 confidently identified proteins are found, with 365 proteins showing significant changes (fold changes of >1.5 or < 0.67, p < 0.05). In metabolic activation, proteins assigned to drug metabolism enzymes (e.g., CYP2D1) change, suggesting that the liver protection mechanism is activated to relieve DMN toxicity. In addition, the altered proteins of immune response and oxidative stress may activate hepatic stellate cells. Glucose metabolism disorder in DMN model rats is demonstrated by a decrease in key enzymes (e.g., ACSL1) in fatty acid metabolism, a tricabolic acid cycle‐related enzyme (SDH), glycogenolysis enzyme, and gluconeogenesis enzymes (PC, PCKGC) and by an increase in glycolysis enzymes (e.g., HXK1). Meanwhile, alterations in iron and calcium ion homeostasis proteins are observed. Our results also show that mitochondrial dysfunction may be involved in DMN hepatotoxicity. In conclusion, these altered liver proteins in the DMN model and control rats provide data for understanding the functional mechanism of liver fibrosis.     

A critical review of the impacts of cover crops on nitrogen leaching,net greenhouse gas balance and crop productivity

Cover crops play an increasingly important role in improving soil quality, reducing agricultural inputs and improving environmental sustainability. The main objectives of this critical global review and systematic analysis were to assess cover crop practices in the context of their impacts on nitrogen leaching, net greenhouse gas balances (NGHGB) and crop productivity. Only studies that investigated the impacts of cover crops and measured one or a combination of nitrogen leaching, soil organic carbon (SOC), nitrous oxide (N₂O), grain yield and nitrogen in grain of primary crop, and had a control treatment were included in the analysis. Long‐term studies were uncommon, with most data coming from studies lasting 2–3 years. The literature search resulted in 106 studies carried out at 372 sites and covering different countries, climatic zones and management. Our analysis demonstrates that cover crops significantly (p < 0.001) decreased N leaching and significantly (p < 0.001) increased SOC sequestration without having significant (p > 0.05) effects on direct N₂O emissions. Cover crops could mitigate the NGHGB by 2.06 ± 2.10 Mg CO₂‐eq ha^?1 year^?1. One of the potential disadvantages of cover crops identified was the reduction in grain yield of the primary crop by ≈4%, compared to the control treatment. This drawback could be avoided by selecting mixed cover crops with a range of legumes and non‐legumes, which increased the yield by ≈13%. These advantages of cover crops justify their widespread adoption. However, management practices in relation to cover crops will need to be adapted to specific soil, management and regional climatic conditions.     

Identification of MYH6 as the potential gene for human ischaemic cardiomyopathy

The present study aimed to explore the potential hub genes and pathways of ischaemic cardiomyopathy (ICM) and to investigate the possible associated mechanisms. Two microarray data sets ( GSE5406 and GSE57338 ) were downloaded from the Gene Expression Omnibus (GEO) database. The limma package was used to analyse the differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, Disease Ontology (DO) and Gene Ontology (GO) annotation analyses were performed. A protein-protein interaction (PPI) network was set up using Cytoscape software. Significant modules and hub genes were identified by the Molecular Complex Detection (MCODE) app. Then, further functional validation of hub genes in other microarrays and survival analysis were performed to judge the prognosis. A total of 1065 genes were matched, with an adjusted p < 0.05, and 17 were upregulated and 25 were downregulated with|log₂ (fold change)|≥1.2. After removing the lengthy entries, GO identified 12 items, and 8 pathways were enriched at adjusted p < 0.05 (false discovery rate, FDR set at <0.05). Three modules with a score >8 after MCODE analysis and MYH6 were ultimately identified. When validated in GSE23561 , MYH6 expression was lower in patients with CAD than in healthy controls (p < 0.05). GSE60993 data suggested that MYH6 expression was also lower in AMI patients (p < 0.05). In the GSE59867 data set, MYH6 expression was lower in CAD patients than in AMI patients and lower in heart failure (HF) patients than in non-HF patients. However, there was no difference at different periods within half a year, and HF was increased when MYH6 expression was low (p < 0.05–0.01). We performed an integrated analysis and validation and found that MYH6 expression was closely related to ICM and HF. However, whether this marker can be used as a predictor in blood samples needs further experimental verification.     

Effects of an energy-dense diet and nicotinic acid supplementation on production and metabolic variables of primiparous or multiparous cows in periparturient period

It is well observed that feeding energy-dense diets in dairy cows during the dry period can cause metabolic imbalances after parturition. Especially dairy cows with high body condition score (BCS) and fed an energy-dense diet were prone to develop production diseases due to metabolic disturbances postpartum. An experiment was conducted to determine the effects of an energy-dense diet and nicotinic acid (NA) on production and metabolic variables of primiparous and multiparous cows in late pregnancy and early lactation which were not pre-selected for high BCS. Thirty-six multiparous and 20 primiparous German Holstein cows with equal body conditions were fed with energy-dense (60% concentrate/40% roughage mixture; HC group) or adequate (30% concentrate/70% roughage mixture; LC group) diets prepartum. After parturition, concentrate proportion was dropped to 30% for all HC and LC groups and was increased to 50% within 16 days for LC and within 24 days for HC cows. In addition, half of the cows per group received 24 g NA supplement per day and cow aimed to attenuate the lipid mobilisation postpartum. Feeding energy-dense diets to late-pregnant dairy cows elevated the dry matter (p < 0.001) and energy intake (p < 0.001) as well as the energy balance (p < 0.001) without affecting the BCS (p = 0.265) during this period. However, this did not result in any metabolic deviation postpartum as the effects of prepartum concentrate feeding were not carried over into postpartum period. Multiparous cows responded more profoundly to energy-dense feeding prepartum compared with primiparous cows, and parity-related differences in the transition from late pregnancy to lactation were obvious pre- and postpartum. The supplementation with 24 g NA did not reveal any effect on energy metabolism. This study clearly showed that energy-dense feeding prepartum did not result in metabolic imbalances postpartum in multiparous and primiparous cows not selected for high BCS. A genetic predisposition for an anabolic metabolic status as indicated by high BCS may be crucial for developing production diseases at the onset of lactation.     

Dynamics of lipids and metabolites during the cell cycle of Chlamydomonas reinhardtii

Metabolites and lipids are the final products of enzymatic processes, distinguishing the different cellular functions and activities of single cells or whole tissues. Understanding these cellular functions within a well‐established model system requires a systemic collection of molecular and physiological information. In the current report, the green alga Chlamydomonas reinhardtii was selected to establish a comprehensive workflow for the detailed multi‐omics analysis of a synchronously growing cell culture system. After implementation and benchmarking of the synchronous cell culture, a two‐phase extraction method was adopted for the analysis of proteins, lipids, metabolites and starch from a single sample aliquot of as little as 10–15 million Chlamydomonas cells. In a proof of concept study, primary metabolites and lipids were sampled throughout the diurnal cell cycle. The results of these time‐resolved measurements showed that single compounds were not only coordinated with each other in different pathways, but that these complex metabolic signatures have the potential to be used as biomarkers of various cellular processes. Taken together, the developed workflow, including the synchronized growth of the photoautotrophic cell culture, in combination with comprehensive extraction methods and detailed metabolic phenotyping has the potential for use in in‐depth analysis of complex cellular processes, providing essential information for the understanding of complex biological systems.