Acyl carrier protein OsMTACP2 confers rice cold tolerance at the booting stage.

Low temperatures occurring at the booting stage in rice (Oryza sativa L.) often result in yield loss by impeding male reproductive development. However, the underlying mechanisms by which rice responds to cold at this stage remain largely unknown. Here, we identified MITOCHONDRIAL ACYL CARRIER PROTEIN 2 (OsMTACP2), the encoded protein of which mediates lipid metabolism involved in the cold response at the booting stage. Loss of OsMTACP2 function compromised cold tolerance, hindering anther cuticle and pollen wall development, resulting in abnormal anther morphology, lower pollen fertility, and seed setting. OsMTACP2 was highly expressed in tapetal cells and microspores during anther development, with the encoded protein localizing to both mitochondria and the cytoplasm. Comparative transcriptomic analysis revealed differential expression of genes related to lipid metabolism between the wild type and the Osmtacp2-1 mutant in response to cold. Through a lipidomic analysis, we demonstrated that wax esters, which are the primary lipid components of the anther cuticle and pollen walls, function as cold-responsive lipids. Their levels increased dramatically in the wild type but not in Osmtacp2-1 when exposed to cold. Additionally, mutants of two cold-induced genes of wax ester biosynthesis, ECERIFERUM1 and WAX CRYSTAL-SPARSE LEAF2, showed decreased cold tolerance. These results suggest that OsMTACP2-mediated wax ester biosynthesis is essential for cold tolerance in rice at the booting stage.

Flexible molecular crystals for optoelectronic applications.

The cornerstones of the advancement of flexible optoelectronics are the design, preparation, and utilization of novel materials with favorable mechanical and advanced optoelectronic properties. Molecular crystalline materials have emerged as a class of underexplored yet promising materials due to the reduced grain boundaries and defects anticipated to provide enhanced photoelectric characteristics. An inherent drawback that has precluded wider implementation of molecular crystals thus far, however, has been their brittleness, which renders them incapable of ensuring mechanical compliance required for even simple elastic or plastic deformation of the device. It is perplexing that despite a plethora of reports that have in the meantime become available underpinning the flexibility of molecular crystals, the "discovery" of elastically or plastically deformable crystals remains limited to cases of serendipitous and laborious trial-and-error approaches, a situation that calls for a systematic and thorough assessment of these properties and their correlation with the structure. This review provides a comprehensive and concise overview of the current understanding of the origins of crystal flexibility, the working mechanisms of deformations such as plastic and elastic bending behaviors, and insights into the examples of flexible molecular crystals, specifically concerning photoelectronic changes that occur in deformed crystals. We hope this summary will provide a reference for future experimental and computational efforts with flexible molecular crystals aimed towards improving their mechanical behavior and optoelectronic properties, ultimately intending to advance the flexible optoelectronic technology.

UV-Triggered Drug Release from Mesoporous Titanium Nanoparticles Loaded with Berberine Hydrochloride: Enhanced Antibacterial Activity.

Mesoporous titanium nanoparticles (MTN) have always been a concern and are considered to have great potential for overcoming antibiotic-resistant bacteria. In our study, MTN modified with functionalized UV-responsive ethylene imine polymer (PEI) was synthesized. The characterization of all products was performed by different analyses, including SEM, TEM, FT-IR, TGA, XRD, XPS, and N2 adsorption-desorption isotherms. The typical antibacterial drug berberine hydrochloride (BH) was encapsulated in MTN-PEI. The process exhibited a high drug loading capacity (22.71 ± 1.12%) and encapsulation rate (46.56 ± 0.52%) due to its high specific surface area of 238.43 m2/g. Moreover, UV-controlled drug release was achieved by utilizing the photocatalytic performance of MTN. The antibacterial effect of BH@MTN-PEI was investigated, which showed that it could be controlled to release BH and achieve a corresponding antibacterial effect by UV illumination for different lengths of time, with bacterial lethality reaching 37.76% after only 8 min of irradiation. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the nanoparticles have also been studied. The MIC of BH@MTN-PEI was confirmed as 1 mg/mL against Escherichia coli (E. coli), at which the growth of bacteria was completely inhibited during 24 h and the concentration of 5 mg/mL for BH@MTN-PEI was regarded as MBC against E. coli. Although this proof-of-concept study is far from a real-life application, it provides a possible route to the discovery and application of antimicrobial drugs.

Comprehensive analysis unveils altered binding kinetics of 5-/6-methylCytosine/adenine modifications in R2R3-DNA system.

Recent studies have shown that DNA methylation is an important epigenetic marker. Two prominent forms are methylation of the C5 position of cytosine and methylation of the C6 position of adenine. Given the vital significance of DNA methylation, investigating the mechanisms that influence protein binding remains a compelling pursuit. This study used molecular dynamics simulations to investigate the binding patterns of R2R3 protein and four differentially methylated DNAs. The alanine scanning combined with interaction entropy method was used to identify key residues that respond to different methylation patterns. The order of protein binding ability to DNA is as follows: unmethylated DNA > A11 methylation (5'-A6mAC-3') (6m2A system) > A10 methylation (5'-6mAAC-3') (6m1A system) > both A10 and A11 methylation (5'-6mA6mAC-3') (6mAA system) > C12 methylation (5'-AA5mC-3') (5mC system). All methylation systems lead to the sixth α helix (H6) (residues D105 to L116) moving away from the binding interface, and in the 5mC and 6m1A systems, the third α helix (H3) (residues G54 to L65) exhibits a similar trend. When the positively charged amino acids in H3 and H6 move away from the binding interface, their electrostatic and van der Waals interactions with the negatively charged DNA are weakened. Structural changes induced by methylation contributed to the destabilization of the hydrogen bond network near the original binding site, except for the 6m2A system. Moreover, there is a positive correlation between the number of methylated sites and the probability of distorting the DNA structure. Our study explores how different methylation patterns affect binding and structural adaptability, and have implications for drug discovery and understanding diseases related to abnormal methylation.

Risk assessment for biopharmaceutical single-use manufacturing: A case study of upstream continuous processing.

In the current transition to intensified upstream processing, the risks of adopting traditional single-use systems for high-titer, long-duration perfusion cultures, have thus far not been considered. This case study uses the Failure Modes and Effects Analysis (FMEA) method to evaluate the risks associated with implementing upstream single-use technology. The simulated model process was used to compare the risk level of single-use technology for a traditional fed-batch cell culture with that for perfusion culture, under the same annual protein production conditions. To provide a reasonable source of potential risk for FMEA, all single-use upstream operations for both fed-batch and perfusion processes were investigated using an analytical method developed to quantify the impact of process parameters and operating conditions on single-use system specifications and to ensure objectivity. Many of the risks and their levels, were similar in long-duration perfusion cultures and fed-batch cultures. However, differences were observed for high-risk components such as daily sampling and installation. The result of this analysis indicates that the reasons for risk are different for fed-batch cultures and perfusion cultures such as larger bioreactors in fed-batch and longer runs in perfusion, respectively. This risk assessment method could identify additional control measures and be part of a holistic contamination control strategy and help visualize their effectiveness.

The study on the feasibility of dietary supplementation with dimethyl silicone oil to prevent frothy rumen bloat in goats fed with high concentrate diets.

The current study was conducted to investigate the feasibility of high concentration diet (HCD) supplementation with Dimethyl Silicone Oil (DSO) to prevent frothy rumen bloat in goats. The treatments were control group (group C, feeding HCD) and test group (group T, feeding HCD supplemented with 0.1%DSO). The results showed that compared with the group C, the ruminal pH value, Microbial Crude Protein content of group T was extremely significantly higher (p < 0.01), the levels of acetic acid and propionic acid were significantly (p < 0.05) and extremely significantly (p < 0.01) lower in group T, respectively. The foam production and foam strength of the rumen fluid in the group T was extremely significantly lower (p < 0.01), the viscosity was extremely significantly (p < 0.01) higher than those of group C. The total gastrointestinal apparent digestibility of various nutrients, the rumen microbial relative abundance at the phylum level and genus level were not significantly different (p > 0.05). The results indicated that the supplementation of 0.1% DSO in HCD can significantly eliminate foam of the rumen fluid, and didn't disturb the ruminal microorganisms, no negatively affect on digestibility of nutrients in goats, thereby has the application prospect of preventing frothy rumen bloat.

The gas produced by rumen fermentation is wrapped in foam and cannot be discharged is the root cause of frothy bloat induced by a high concentration diet. In the present study, the feasibility of dietary supplementation with Dimethyl Silicone Oil (DSO) to prevent frothy bloat was preliminarily evaluated. The results indicated that DSO can significantly eliminate foam of the rumen fluid, and has not negatively effect on the ruminal microorganisms and the digestibility of nutrients in goats, thereby has the application prospect of preventing frothy bloat.

Effect of dietary concentrate level on digestibility of nutrients in each region of the gastrointestinal tract and rumen fermentation in goats.

This study evaluated the effects of high concentrate diets (HCD) on the rumen fermentation and the digestibility of nutrients in different sites of the gastrointestinal tract (GIT) in goats. Four goats were used in a crossover design. The goats were fitted with a ruminal cannula and flexible T-cannulae proximal duodenum and terminal ileum. Treatments were as follows: low concentrate group (LCG) and high concentrate group (HCG). Duodenal flow and forestomach digestibility of starch were significantly higher in the HCG than those in the LCG (p < 0.05); There was no significant difference in ileum flow and digestibility of starch in the small intestine, large intestine and total GIT (p > 0.05). The digestibility of crude protein (CP) in the forestomach was significantly higher in the HCG than in the LCG (p < 0.05); the flow of the duodenum and ileum of CP, and the CP digestibility of the small intestine, large intestine and total GIT were not significantly different between groups (p > 0.05). The duodenal and ileal flow of neutral detergent fiber (NDF), the NDF digestibility of the different segments and total GIT were not significantly different between groups (p > 0.05). Compared to the LCG, the ruminal pH of the HCG was significantly lower (p < 0.05). The HCG concentrations of microbial crude protein, ammonia nitrogen and isovaleric acid were significantly higher (p < 0.05) than the LCG. The foam strength, foam production and viscosity of the rumen fluid in the HCG were higher than the LCG (p < 0.01). These results showed that when the goats were fed with HCD, the digestibility of nutrients was not significantly impaired, but the risk of frothy rumen bloat increased. ImplicationsDue to a serious shortage of high-quality roughage in China, producers commonly used a high-concentrate diet in ruminants, which can improve animal production performance.Gastrointestinal digestive function plays a vital role in the absorption of nutrients and the healthy growth of animals.Therefore, this research evaluated the digestibility of various nutrients in different segments of the gastrointestinal tract (GIT) under HCD feeding by using three-site cannula goats as experimental animals.The results indicated that the GIT of goats could fully digest nutrients such as starch and protein under HCD feeding conditions.

Effects of uni and bilateral castration on growth performance and lipid metabolism in yellow cattle.

This study was conducted to examine the influence of uni and bilateral castration on growth performance and lipid metabolism in yellow cattle. Eighteen 9-month-old healthy yellow cattle (average body weight 184.03 ± 4.09 kg) were selected and divided into three groups: The uncastrated cattle (C), half castrated cattle (HC) and full castrated cattle (FC). The results showed that the growth rate of FC group was significantly reduced as compared to HC and C group, while the feed to gain ratio exhibited an opposite trend. The concentrations of triglycerides (TG), low-density lipoprotein cholesterol (LDL) and high-density lipoprotein (HDL) were increased significantly in FC group from day 60 to the end of the trial compared to HC and control groups. Serum testosterone concentration of FC group cattle was decreased from day 60 to 120 d of the trial compared to HC and control groups. The concentration of the lauric acid in FC cattle was significantly increased from the HC and control groups. In the FC group, the acetyl-CoA carboxylase alpha (ACACA), ACC and fatty acid synthase (FAS) gene expression levels were significantly higher compared to control and HC groups. Our results of this study suggest that bilateral castration increased the lipid metabolism and fatty acid composition compared to unilateral castrated and un-castrated cattle.HighlightsBilateral castration alters the growth performance in yellow cattle.Bilateral castration alters hormones levels and lipid metabolites levels in serum.Bilateral castration improves the lipid metabolism and fatty acid profile.

Identification of Potential Differentially-Methylated/Expressed Genes in Chronic Obstructive Pulmonary Disease.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease that causes obstructed airflow from the lungs. DNA methylation can regulate gene expression. Understanding the potential molecular mechanism of COPD is of great importance. The aim of this study was to find differentially methylated/expressed genes in COPD. DNA methylation and gene expression profiles in COPD were downloaded from the dataset, followed by functional analysis of differentially-methylated/expressed genes. The potential diagnostic value of these differentially-methylated/expressed genes was determined by receiver operating characteristic (ROC) analysis. Expression validation of differentially-methylated/expressed genes was performed by in vitro experiment and extra online datasets. Totally, 81 hypermethylated-low expression genes and 121 hypomethylated-high expression genes were found in COPD. Among which, 9 core hypermethylated-low expression genes (CD247, CCR7, CD5, IKZF1, SLAMF1, IL2RB, CD3E, CD7 and IL7R) and 8 core hypomethylated-high expression genes (TREM1, AQP9, CD300LF, CLEC12A, NOD2, IRAK3, NLRP3 and LYZ) were identified in the protein-protein interaction (PPI) network. Moreover, these genes had a potential diagnostic utility for COPD. Some signaling pathways were identified in COPD, including T cell receptor signaling pathway, cytokine-cytokine receptor interaction, hematopoietic cell lineage, HTLV-I infection, endocytosis and Jak-STAT signaling pathway. In conclusion, differentially-methylated/expressed genes and involved signaling pathways are likely to be associated with the process of COPD.

Isolation of a Novel QTL, qSCM4, Associated with Strong Culm Affects Lodging Resistance and Panicle Branch Number in Rice.

Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F2 segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC3F2 segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3' UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice.

Synergistic photocatalytic oxidation and adsorption boost arsenic removal by in-situ carbon-doped TiO2 and nitrogen deficiency C3N4 heterojunction.

The efficient removal of arsenic from wastewater is still a challenge. In this paper, a heterojunction consisting of in-situ carbon-doped TiO2 and nitrogen deficiency g-C3N4 (C/TiO2@ND-C3N4) has been constructed, which can completely oxidize As(III) (10,000 µg/L, 40 mL) to As(V) within 12 min under visible light and simultaneously adsorb total As (95.0%) with the pseudo-secondary kinetic equation, superior than in-situ carbon-doped TiO2 (75.0%) and nitrogen deficiency g-C3N4 (50.5%). The good photocatalytic oxidation and adsorption performances of C/TiO2@ND-C3N4 on As(III) removal can be attributed to the successful synthesis of heterojunction. On one hand, the building of C-O-Ti interfacial chemical bonds enable rapid electron transfer and improve the efficiency of photocatalytic oxidation. On the other hand, the decreased As(V) adsorption energy resulted from the synthesized heterojunction boost the adsorption capability of As(V), which was completed by the generation of O-As bonds with oxygen-containing functional groups on the surface of TiO2 and hydrogen bonds with high content pyrrole nitrogen derived from ND-C3N4, respectively. The results manifest that the preparation of bifunctional materials with both photocatalytic oxidation and adsorption properties provides a new strategy to achieve the removal of As.

Tandem expression of Ganoderma sinense sesquiterpene synthase and IDI promotes the production of gleenol in E. coli.

Ganoderma sinense, with more than 2000 years of medicinal history, is a fungus of the basidiomycetes that is rich in polysaccharides and terpenoids. However, the biosynthesis of terpenes, especially sesquiterpenes, has been little studied. The functional identification of sesquiterpene synthases from G. sinense is of great significance to the study of fungal terpenoid biosynthesis and regulation. Our research group has completed the functional characterization of 21 sesquiterpene synthase genes from G. sinense. It was found that gleenol, biosynthesis of which is catalyzed by the sesquiterpene synthase GsSTS26 and GsSTS27, has the functions of killing termites, antihelminth, and plant growth regulation. In the unmodified E. coli Rosetta (DE3) strain, the content of gleenol produced by sesquiterpene synthase from G. sinense is low, which makes it difficult to meet the demand of industrial production and the market. Therefore, it is of great significance to obtain high-yielding strains by means of synthetic biology. In this study, we constructed eight recombinant strains by using tandem gene expression and promoter engineering, and the content of gleenol was increased by up to 23-fold. In this study, we realized the de novo synthesis of gleenol in E. coli and provided a basis for the biosynthesis of terpenoids in basidiomycetes. KEY POINTS: • Eight recombinant expression systems were constructed by using tandem genes and promoter engineering. • The recombinant strain promoted the efficient production of gleenol in E. coli Rosetta (DE3). • The recombinant strain achieved de novo production of gleenol in E. coli.

Artificial selection on storage protein 1 possibly contributes to increase of hatchability during silkworm domestication.

Like other domesticates, the efficient utilization of nitrogen resources is also important for the only fully domesticated insect, the silkworm. Deciphering the way in which artificial selection acts on the silkworm genome to improve the utilization of nitrogen resources and to advance human-favored domestication traits, will provide clues from a unique insect model for understanding the general rules of Darwin's evolutionary theory on domestication. Storage proteins (SPs), which belong to a hemocyanin superfamily, basically serve as a source of amino acids and nitrogen during metamorphosis and reproduction in insects. In this study, through blast searching on the silkworm genome and further screening of the artificial selection signature on silkworm SPs, we discovered a candidate domestication gene, i.e., the methionine-rich storage protein 1 (SP1), which is clearly divergent from other storage proteins and exhibits increased expression in the ova of domestic silkworms. Knockout of SP1 via the CRISPR/Cas9 technique resulted in a dramatic decrease in egg hatchability, without obvious impact on egg production, which was similar to the effect in the wild silkworm compared with the domestic type. Larval development and metamorphosis were not affected by SP1 knockout. Comprehensive ova comparative transcriptomes indicated significant higher expression of genes encoding vitellogenin, chorions, and structural components in the extracellular matrix (ECM)-interaction pathway, enzymes in folate biosynthesis, and notably hormone synthesis in the domestic silkworm, compared to both the SP1 mutant and the wild silkworm. Moreover, compared with the wild silkworms, the domestic one also showed generally up-regulated expression of genes enriched in the structural constituent of ribosome and amide, as well as peptide biosynthesis. This study exemplified a novel case in which artificial selection could act directly on nitrogen resource proteins, further affecting egg nutrients and eggshell formation possibly through a hormone signaling mediated regulatory network and the activation of ribosomes, resulting in improved biosynthesis and increased hatchability during domestication. These findings shed new light on both the understanding of artificial selection and silkworm breeding from the perspective of nitrogen and amino acid resources.

Effects of dry yeast supplementation on growth performance, rumen fermentation characteristics, slaughter performance and microbial communities in beef cattle.

This study aimed to investigate the effects of active dry yeast (ADY) on growth performance, rumen microbial composition and carcass performance of beef cattle. Thirty-two finishing beef cattle (yak ♂ × cattle-yaks ♀), with an average body weight of 110 ± 12.85 kg, were randomly assigned to one of four treatments: the low plane of nutrition group (control), low plane of nutrition group + ADY 2 g/head daily (ADY2), low plane of nutrition group + ADY 4 g/head daily (ADY4) and the high plane of nutrition group (HPN). Supplementation of ADY increased average daily gain compared to the control group. The neutral detergent fiber and acid detergent fiber apparent digestibility in HPN group was greater than that in control group. The propionic acid concentration in the rumen in ADY2, ADY4, and HPN groups was greater than that in control group. The Simpson and Shannon indexes in control and HPN groups were higher than that in ADY4 group. At the phylum level, the relative abundance of Firmicutes in the HPN group was higher than that in ADY4 group. The relative abundance of Ruminococcaceae UCG-002 in ADY4 group was higher than that in control and HPN groups. In conclusion, supplementation ADY 4 g/head daily shift the rumen microbial composition of beef cattle fed low plane of nutrition to a more similar composition with cattle fed with HPN diet and produce the similar carcass weight with HPN diet.HighlightsThe ADY can improve the utilization of nitrogen and decrease the negative impact on the environment in beef cattle.Cattle fed low plane of nutrition diet supplemented with ADY 4 g/head daily increased growth performance.Supplementation ADY 4 g/head daily in low plane of nutrition diet might be produced comparable carcass weight to HPN diet.

Relationship between the coprecipitation of phosphorus-on-calcite by submerged macrophytes and the phosphorus cycle in water.

To assess potential phosphorus removal, we utilized Potamogeton crispus to determine the effects of calcium addition on phosphorus removal. Plastic film was used to block material exchange between the overlying water and the sediment, and we compared the experimental results with long-term monitoring results of Yimeng Lake, which contained a dense population of P. crispus. The results revealed that the first 10-40 days constituted a period of rapid P decrease, as P. crispus could effectively remove the phosphorus in the water through coprecipitation of CaCO3-P. The treatment groups indicated that P. crispus released calcium into the overlying water, and after the addition of calcium ions, P. crispus showed increased phosphorus removal efficiency in the water. Total phosphorus (TP) and P/Ca content increased with increasing pH in the treatment groups, and the TP and pH declined as the calcium content increased in the treatment groups. Long-term field observations showed that the calcium-to-phosphorus ratio in the coprecipitates was dependent on the pH during the crystallization process. Thus, water calcium driven by P. crispus plays an important role in the phosphorus cycle of water, due to P. crispus assisted precipitation. This study revealed the effect of P. crispus on the water purification, the migration and transformation of Ca and P in sediment and overlying water under the condition of sediment calcium addition, so as to provide a theoretical basis for the ecological restoration of shallow lakes eutrophication.

Reduction of peripheral regulatory T cells in active rheumatoid arthritis patients with coronary artery disease.

OBJECTIVE: To identify lymphocyte and CD4 + T cell subset characteristics, particularly regulatory T cells (Tregs), in active rheumatoid arthritis (RA) patients with coronary artery disease (CAD). METHODS: A total of 54 RA patients with CAD (RA-CAD group), 43 RA patients without CAD (pure RA group), and 43 healthy controls (HC group) were enrolled. The absolute number and frequency of lymphocyte subpopulations and CD4 + T cell subsets were analyzed by flow cytometry. Serum levels of cytokines were analyzed using a cytometric bead array. Clinical and laboratory data were collected retrospectively and their correlation with CD4 + T subsets were analyzed. RESULTS: There was a significant decrease in the absolute number of Treg cells (CD4 + CD25 + Foxp3 + T cells) in the RA-CAD group compared to the pure RA group (p < 0.001). Similarly, both the absolute number (p = 0.001) and frequency (p = 0.011) of Tregs in the RA-CAD group were decreased compared to the HCs, causing a Th17/Treg imbalance (p = 0.044). No difference was found in the absolute number and frequency of Treg cells between the pure RA and HC groups. However, the absolute Th17 cell count was increased in the pure RA group (p = 0.032). The serum level of cytokine IL-17 was lower in the RA-CAD group than in the pure RA group (p = 0.023). In the RA-CAD group, the Treg number was negatively correlated with the RA disease activity score and ESR value, and LDL and ApoB100 levels were negatively correlated with the number of Th17 cells. CONCLUSIONS: Active RA patients with CAD sustain more severe immune tolerance damage and Th17/Treg disorder. Monitoring of lymphocyte and CD4 + T cell subsets, particularly Treg cells, is crucial to understanding immune status in this group. Focusing on RA activity and CAD risk control, immune-regulatory therapy based on the Treg level may be more beneficial for RA patients with CAD.

Comparative study of the bacterial communities throughout the gastrointestinal tract in two beef cattle breeds.

Investigation of the compositional and functional characteristics of the gastrointestinal bacterial community in beef cattle breeds can improve our understanding of the influence of gastrointestinal tract (GIT) regions and host breeds on the bacterial community. In this study, 16S ribosomal RNA (16S rRNA) gene amplicon sequencing was used to characterize the bacterial communities in the rumen, duodenum, jejunum, ileum, caecum, and colon of Xuanhan yellow cattle (XHC) and Simmental crossbred cattle (SXC). The results showed that the diversity of the bacterial population was different in GIT regions of XHC and SXC (P < 0.05). In total, ten bacterial phyla, sixteen bacterial genera, and nine metabolic pathways were identified in the core bacteria. The phyla Firmicutes, Bacteroidetes, and Proteobacteria were predominant, but their proportions were different in GIT regions (P < 0.05). The diversity, structure, and composition of the bacteria in the rumen were similar between the breeds (P > 0.05), and the indices in the intestine showed significant differences (P < 0.05). Moreover, the composition and structure of the bacterial communities in the rumen, small intestine, and large intestine were different regardless of the breed. Thus, the bacterial communities were different among the gastrointestinal regions in each breed, and the bacterial community in the rumen had more stable characteristics than that in the intestine between two breeds. Further studies may focus on the minor microbial communities and the functions of GIT bacteria to better understand gut-microbe interactions. KEY POINTS: • Differences in bacteria among gastrointestinal regions differ in cattle breeds. • Differences between the breeds in the ruminal bacteria are less pronounced than differences in the intestinal bacteria.

Comparison of carcass characteristics and meat quality between Simmental crossbred cattle, cattle-yaks and Xuanhan yellow cattle.

BACKGROUND: The study compared the growth performance, carcass characteristics and meat quality of steers of Xuanhan yellow cattle, Simmental crossbreed cattle (Simmental × Xuanhan yellow cattle) and cattle-yak (Jersey × yak). All steers were feed with the same diet from 6 months until slaughter at 30 months. The longissimus dorsi muscle was used to compare the meat quality traits. RESULTS: By comparison, Simmental crossbreed cattle had higher growth performance (P < 0.05) and carcass characteristics (P < 0.05); cattle-yak had higher value of a*, b* of meat color (P < 0.05) and higher protein contents of meat (P < 0.05); Xuanhan yellow cattle had higher water holding capacity (P < 0.05) and lower shear force (P < 0.05). CONCLUSIONS: The results show that Simmental crossbred cattle had better meat performance and provided low-fat meat with a beneficial fatty acid composition, but with lower meat quality; cattle-yaks provided greater meat color and higher protein content; Xuanhan yellow cattle provided meat with preferable tenderness. © 2020 Society of Chemical Industry.

New algorithms for detecting multi-effect and multi-way epistatic interactions.

MOTIVATION: Epistasis, which is the phenomenon of genetic interactions, plays a central role in many scientific discoveries. However, due to the combinatorial nature of the problem, it is extremely challenging to decipher the exact combinations of genes that trigger the epistatic effects. Many existing methods only focus on two-way interactions. Some of the most effective methods used machine learning techniques, but many were designed for special case-and-control studies or suffer from overfitting. We propose three new algorithms for multi-effect and multi-way epistases detection, with one guaranteeing global optimality and the other two being local optimization oriented heuristics. RESULTS: The computational performance of the proposed heuristic algorithm was compared with several state-of-the-art methods using a yeast dataset. Results suggested that searching for the global optimal solution could be extremely time consuming, but the proposed heuristic algorithm was much more effective and efficient than others at finding a close-to-optimal solution. Moreover, it was able to provide biological insight on the exact configurations of epistases, besides achieving a higher prediction accuracy than the state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: Data source was publicly available and details are provided in the text.

High light efficiency snapshot spectral imaging via spatial multiplexing and spectral mixing.

Computational photography has been striving to capture the spectral information of the dynamic world in the last few decades. However, due to the curse of dimensionality between the 3D spectral images and the 2D imaging sensors, light-blocking components, e.g., bandpass filters or coded apertures, have to be used in spectral imaging systems to project the 3D signal into 2D measurements selectively. Accordingly, computational reconstruction is integrated to recover the underlying 3D signal. Thus, these systems suffer from low light efficiency and high computational burden, both of which cannot afford dynamic spectral imaging. In this paper, we propose a novel snapshot spectral imaging system that can dynamically capture the spectral images. The system is composed of a lens array, a notch filter array, and a monochrome camera in principle. Incoming light beams from the scene are spatially multiplexed by the lens array, spectrally mixed by the notch filter array, and captured by the monochrome camera. The two distinct characteristics, i.e., spatial multiplexing and spectral mixing, guarantee the advantages of low computational burden and high light efficiency, respectively. We further build a prototype system according to the imaging principles. The system can record two kinds of images in a single snapshot: bandstop multispectral images and a panchromatic image, which are used jointly to recover the bandpass multispectral images at few computational costs. Moreover, the proposed system is friendly with spectral super-resolution, for which we develop a theoretical demonstration. Both simulations and experiments are conducted to verify the effectiveness of the proposed system.