Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo.

Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in a basal diet. After 35 days of supplementation, rumen contents were collected to determine rumen fermentation parameters. The 16S rRNA gene sequencing was performed to elucidate rumen bacteria composition. The obtained taxonomic data were analyzed to explore the rumen bacteriome and predict the associated gene functions and metabolic pathways. Results demonstrated a linear increase (p < 0.01) in rumen acetate, propionate, and total VFAs in the MLF45 group as compared to control. No effect of treatment was observed on rumen pH and butyrate contents. Acetate to propionate ratio in the MLF45 group linearly and quadratically decreased (p = 0.001) as compared to MLF15 and control groups. Similarly, MLF45 linearly increased (p < 0.05) the microbial protein (MCP) and NH3-N as compared to other treatments. Treatment adversely affected (p < 0.01) almost all alpha diversity parameters of rumen bacteria except Simpson index. MLF promoted the abundance of Proteobacteria while reducing the relative abundances of Actinobacteria, Acidobacteria, Chloroflexi, and Patescibacteria. The MLF supplementation tended to substantially reduce (0.05 < p < 0.1) the abundance of Actinobacteria, and Patescibacteria while completely eliminating Acidobacteria (p = 0.029), Chloroflexi (p = 0.059), and Gemmatimonadetes (p = 0.03) indicating the negative effect of flavonoids on the growth of these bacteria. However, MLF45 tended to substantially increase (p = 0.07) the abundance (~21.5%) of Acetobacter. The MLF treatment exhibited negative effect on five genera by significantly reducing (Sphingomonas) or eliminating (Arthobactor, unclassified_c__Actinobacteria, norank_c__Subgroup_6, norank_o__Saccharimonadales, and Nocardioides) them from the rumen microbiota. Pearson correlation analysis revealed 3, 5 and 23 positive correlations of rumen bacteria with milk yield, rumen fermentation and serum antioxidant parameters, respectively. A positive correlation of MCP was observed with three bacterial genera (Acetobacter, Enterobacter, and Klebsiella). The relative abundance of Pseudobutyrivibrio and Empedobacter also showed a positive correlation with the ruminal acetate and propionate. The present study indicated 45 g/d as an appropriate dose of MLF which modulated rumen bacteria and its functional profile in water buffalo.

The role of thermodynamically stable configuration in enhancing crystallographic diffraction quality of flexible MOFs.

Single-crystal X-ray diffraction (SCXRD) is a widely used method for structural characterization. Generally, low temperature is of great significance for improving the crystallographic diffraction quality. Herein we observe that this practice is not always effective for flexible metal-organic frameworks (f-MOFs). An abnormal crystallography, that is, more diffraction spots at a high angle and better resolution of diffraction data as the temperature increases in the f-MOF (1-g), is observed. XRD results reveal that 1-g has a reversible anisotropic thermal expansion behavior with a record-high c-axial positive expansion coefficient of 1,401.8 × 10-6 K-1. Calculation results indicate that the framework of 1-g has a more stable thermodynamic configuration as the temperature increases. Such configuration has lower-frequency vibration and may play a key role in promoting higher Bragg diffraction quality at room temperature. This work is of great significance for how to obtain high-quality SCXRD diffraction data.

Molecular signatures of in vitro produced embryos derived from ovum pick up or slaughterhouse oocytes in buffalo.

This study was performed to investigate the difference in developmental competence of oocytes derived from ovum pick-up (OPU) and slaughterhouse ovaries (SLH), and its underlying mechanisms. The OPU and SLH oocytes were in-vitro maturated and fertilized to produce blastocysts, and these blastoycsts were collected to explore the expression of key genes for developmental potential and telomere (Oct-4, Sox2, Nanog, Cdx2, Gata3, E-cadherin, ß-catenin, TERT, TERF1 and TERF2). The results showed that both the cleavage and blastocyst rates were significantly higher for the OPU group (68.31%, 39.48%, respectively) than SLH group (57.59%, 26.50%, respectively) (P < 0.01). The relative mRNA abundances of Sox2, Oct-4, Nanog and E-cadherin were significantly higher in the OPU blastocysts than the SLH ones (P < 0.01). Protein expression analysis by Western blot and immunofluorescence also revealed that the expression of E-cadherin and Sox2 was significantly higher in OPU blastocysts than SLH ones. However, there was no significant differences between the two groups in the expression of Cdx2, ß-catenin, Gata3, TERT, TERF1, TERF2. These results imply oocyte sources modify the expression of development and adhesion related genes in blastocysts, which may elucidate a possible reasoning for the low development competence of buffalo SLH embryos.

Multi-Neighborhood Learning for Global Alignment in Biological Networks.

The global alignment of biological networks (GABN) aims to find an optimal alignment between proteins across species, such that both the biological structures and the topological structures of the proteins are maximally conserved. The research on GABN has attracted great attention due to its applications on species evolution, orthology detection and genetic analyses. Most of the existing methods for GABN are difficult to obtain a good tradeoff between the conservation of the biological structures and topological structures. In this paper, we propose a multi-neighborhood learning method for solving GABN (called as CLMNA). CLMNA first models GABN as an optimization of a weighted similarity which evaluates the conserved biological and topological similarities of an alignment, and then it combines a first-proximity, second-proximity and individual-aware proximity learning algorithm to solve the modeled problem. Finally, systematic experiments on 10 pairs of biological networks across 5 species show the superiority of CLMNA over the state-of-the-art network alignment algorithms. They also validate the effectiveness of CLMNA as a refinement method on improving the performance of the compared algorithms.

Identification and phylogenetic analysis of the complete mitochondrial genome of Fuzhong buffalo (Artiodactyla: Bovidae).

Fuzhong buffalo (Bubalus bubalis Linnaeus, 1758 breed Fuzhong, FB) is one of the famous indigenous breeds of buffalo in China. It is the first time that the complete mitochondrial genome sequence of the FB was reported. The total length of the mtDNA is 16,363 bp, It contains the typical structure, including 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes and one non-coding control region (D-loop region). The overall composition of the mtDNA was estimated to be 32.98% for A, 26.34% for T, 26.70% for C and 13.98% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 19 ruminantia species are divided into four major clades: Bovidae, Cervidae, Giraffidae and Atilocapridae. In addition, our work confirmed that FB and Murrah buffalo (MB) have a close genetic relationship with fellow tribal members Nili-Ravi buffalo and Mediterranean buffalo. Meanwhile, we also found that FB and MB have a highly similar genetic relationship.

Potential of Mulberry Leaf Biomass and Its Flavonoids to Improve Production and Health in Ruminants: Mechanistic Insights and Prospects.

Leaf biomass from the mulberry plant (genus Morus and family Moraceae) is considered a potential resource for livestock feeding. Mulberry leaves (MLs) contain high protein (14.0-34.2%) and metabolizable energy (1130-2240 kcal/kg) with high dry matter (DM) digestibility (75-85%) and palatability. Flavonoid contents of MLs confer unique antioxidant properties and can potentially help alleviate oxidative stress in animals during stressful periods, such as neonatal, weaning, and periparturient periods. In addition, mulberry leaf flavonoids (MLFs) possess antimicrobial properties and can effectively decrease the population of ruminal methanogens and protozoa to reduce enteric methane (CH4) production. Owing to its rich flavonoid content, feeding MLs increases fiber digestion and utilization leading to enhanced milk production in ruminants. Dietary supplementation with MLFs alters ruminal fermentation kinetics by increasing total volatile fatty acids, propionate, and ammonia concentrations. Furthermore, they can substantially increase the population of specific cellulolytic bacteria in the rumen. Owing to their structural homology with steroid hormones, the MLFs can potentially modulate different metabolic pathways particularly those linked with energy homeostasis. This review aims to highlight the potential of ML and its flavonoids to modulate the ruminal microbiome, fermentation, and metabolic status to enhance productive performance and health in ruminants while reducing CH4 emission.

Effect of season on the in-vitro maturation and developmental competence of buffalo oocytes after somatic cell nuclear transfer.

Somatic cell nuclear transfer (SCNT) is a valuable technology tool with various uses in transgenic animals, regenerative medicine, and stem cell research. However, the efficiency of SCNT embryos appears to have poor developmental competency. Environmental issues may adversely affect SCNT embryos in buffalo. Thereafter, the present study aimed to explore the effect of season on the maturation of buffalo oocytes and subsequent developmental capability after parthenogenetic activation and SCNT in buffalo. Buffalo oocytes (n = 6353) were collected from local slaughterhouse at various seasons; spring (March-April), summer (May-August), autumn (September-November), and winter (December-January). A significant increase (p < 0.05) was recorded in the maturation rate (57.07%) at autumn compared with spring, summer, and winter (50.46, 50.93, and 50.66%, respectively). No significant differences were recorded in the fusion and the cleavage rates among all seasons. Blastocyst development rate was higher (p < 0.05) in autumn and winter (16.52 ± 8.45% and 15.98 ± 7.17%, respectively) than in spring and summer (9.47 ± 6.71% and 10.84 ± 6.58%, respectively) seasons. It could be concluded that the season had a significant effect on oocyte development competence which can be used for SCNT in buffalo.

Effects of laser zona thinning and artificial blastocoel collapse on the cryosurviving and hatching of buffalo (Bubalus bulalis) blastocysts of different ages.

The objectives of this study were to investigate whether blastocoel collapse before vitrification induced by laser improves the cryo-survivability of buffalo in-vitro-fertilized (IVF) blastocysts and whether laser assisted hatching (LAH) promotes hatchability of fresh and frozen-thawed IVF blastocysts. The expanded blastocysts were harvested on Days 6-9 and randomly allocated into five groups as follows: (1) blastocysts were vitrified and thawed without any treatment; (2) blastocysts were vitrified after 15-20 µm zona pellucida (ZP) thinning opposite to the inner cell mass, and blastocoels were also blotted in order to outflow the blastocoelic fluid before vitrification; (3) ZP thinning was made immediately after thawing; (4) fresh blastocysts underwent LAH; and (5) as a control, fresh blastocysts without treatment. Results of the present study showed that the cryosurvival rates of vitrified Day 8 and Day 9 blastocysts in Group 2 were significantly (P < 0.01) higher in Group 2 than Group 1. The hatching rates of Day 8 and Day 9 blastocysts in Group 2 and Group 3 were also significantly (P < 0.01) higher compared with Group 1. Moreover, the hatching rate of Day 9 blastocysts in Group 4 was notably (P < 0.05) higher than Group 5. In conclusion, LAH promotes the hatching rates of Day 9 fresh and Days 8-9 vitrified blastocysts, and artificial blastocoel collapse before vitrification improves the cryosurvival rate of Days 8-9 IVF buffalo blastocysts.

Vitrification alters cell adhesion related genes in pre-implantation buffalo embryos: Protective role of ß-mercaptoethanol.

The objectives of the present study were to investigate the effect of vitrification on the expression of the key genes associated with blastocyst developmental potential (ß-catenin, E-cadherin, Oct-4, Cdx2, Gata3), and whether the presence of ß-mercaptoethanol (ß-ME, 100 µM) in in vitro culture (IVC) media will affect the expression of these genes. Buffalo pre-implantation embryos were divided into three groups: (1) fresh non-vitrified embryos were used as control, (2) vitrified embryos cultured with ß-ME (+), and (3) vitrified embryos cultured without (-) ß-ME. The results showed that all genes were affected by vitrification, however, the presence of ß-ME in IVC media significantly (P < 0.05) modified the expression level of ß-catenin, E-cadherin and Oct-4 in vitrified blastocyst compared to those cultured without ß-ME. Protein expression analysis by immunofluorescence and western blot also revealed that the expression level of ß-catenin and E-cadherin was significantly higher in vitrified embryos cultured with ß-ME than those cultured without ß-ME, which, in turn, was lower than fresh control group. However, there was no significant difference between vitrified groups in the expression level of Cdx2 and Gata3. Furthermore, the reduced rate of apoptosis in embryos cultured with ß-ME confirms its role in protecting vitrified blastocyst against stress. In summary, vitrification alters the expression of the adhesion related genes in vitrified blastocyst, which may explain, at least in part, the reason for the low pregnancy rate following transfer of such embryos into recipient animal, and the supplementation of IVC media with ß-ME significantly improved the quality of vitrified blastocyst evidenced by the modulation of the expression of blastocyst important genes, ß-catenin, E-cadherin and Oct-4, and the ability to protect vitrified blastocyst against apoptosis.

Developmental competence of buffalo (Bubalus bubalis) denuded oocytes cocultured with cumulus cells: Protective role of cumulus cells.

The objectives of the present study were to evaluate the developmental competence of buffalo denuded oocytes (DOs) cocultured with cumulus cells (CCs) during in vitro maturation, and to investigate the mechanisms by which CCs promote oocyte maturation and development. Buffalo oocytes were matured in vitro for 24 h in three groups: (1) intact cumulus-oocyte complexes (COCs) (2) DOs cocultured with CCs (DOsCC), and (3) DOs cultured alone (DOs). Matured oocytes were used to determine the relative mRNA abundance of Gdf-9, Bmp15, Zar1, Caspase-3, Bcl-2, Zp2, Zp3, Cd9 and Pde3a by Rt-qPCR and CASPASE-3 protein expression by immunofluorescence. The intracellular content of cGMP, cAMP and MPF activity and the rate of embryonic development were also assessed. Results of the present study showed that in DOs, the relative mRNA abundance of Gdf-9, Bmp15, and Cd9 significantly (P < 0.05) decreased, whereas Caspase-3 (mRNA and protein levels), Bcl-2, and Pde3a exhibited higher expression than DOsCC and COCs. However, there was no significant difference among the groups in the expression level of Zar-1, Zp2, and Zp3. The intracellular content of cAMP and MPF activity was notably higher (P < 0.05) in DOs compared to COCs and DOsCC. There was no significant difference between COCs and DOsCC in cGMP content, which was significantly lower (P < 0.05) in DOs. Moreover, the cleavage and blastocyst rates were 58.4 ±â€¯1.8%, 43.7 ±â€¯1.1%, 18.4 ±â€¯0.9% and 18.0 ±â€¯1.3%, 11.0 ±â€¯0.9% and 4.5 ±â€¯0.6% in COCs, DOsCC and DOs groups, respectively. In conclusion, the presence of CCs protects buffalo DOs from apoptosis and promotes maturation through regulation of the intracellular content of cAMP and MPF activity and improves the fertilizing capacity of oocytes through modulation of the gamete fusion gene, Cd9.

Buffalo oocyte-secreted factors promote cumulus cells apoptosis and the rate of cGMP production but not steroidogenesis.

The objectives of this study were to investigate the effect of buffalo oocyte-secreted factors (OSFs) on cumulus cells (CCs) functions, apoptosis and cGMP generation, and whether the direct contact between oocyte and CCs is essential for oocyte-mediated regulation of CCs functions. Buffalo CCs were cultured during IVM within three groups: (a) intact cumulus-oocyte complexes (COCs), (b) CCs cocultured with denuded oocytes (DOs) (CCs + DOs) and (c) CCs monolayer cultured alone (CCsM). After 24 hr of IVM, CCs were harvested for evaluation of the relative mRNA abundance of the genes encoding gap junction (GJA1), glycolysis (PFKP and LDHA), apoptosis (CASPASE-3 and BCL-2) and steroidogenesis (ER-ß and PGR) by QRT-PCR, and CASPASE-3 proteins, using western blot. Intracellular cGMP content was also assessed by ELISA. Results showed that the relative abundance of LDHA, PFKP and BCL-2 significantly increased (p < 0.05) in COCs, whereas GJA1 and CASPASE-3 exhibited lower expression (p < 0.05) compared to CCs + DOs and CCsM groups. However, the expression levels of CASPASE-3, both mRNA and protein, were significantly (p < 0.05) downregulated in CCs + DOs compared to CCsM. There was no significant difference in the expression level of PGR and ER-ß between the groups. The intracellular content of cGMP was notably (p < 0.05) higher in COCs compared to CCs + DOs and CCsM groups. In conclusion, this study demonstrated, for the first time, that buffalo OSFs protect CCs against apoptosis and stimulate their cGMP production; however, the regulation of cumulus glycolysis and gap junction is confined to those in close contact with the oocyte. Neither OSFs from COCs nor those from DOs have any effect on CCs steroidogenesis.

A Global Network Alignment Method Using Discrete Particle Swarm Optimization.

Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyze the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations. The particle statuses and status updating rules are redefined in a discrete form by using permutation. A seed-and-extend strategy is employed to guide the searching for the superior alignment. The proposed initialization method "seeds" matches with high sequence similarity into the alignment, which guarantees the functional coherence of the mapping nodes. A greedy local search method is designed as the "extension" procedure to iteratively optimize the edge conservations. PSONA is compared with several state-of-art methods on ten network pairs combined by five species. The experimental results demonstrate that the proposed aligner can map the proteins with high functional coherence and can be used as a booster to effectively refine the well-studied aligners.

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling.

The castor plant (Ricinus communis L.) is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P) and monoecious (JXBM0705M) lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3000 of differentially expressed genes (DEGs) were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, such as auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage) of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that of down-regulation in the small raceme of the mutant. In this study, a large number of DEGs and some suggestions involved in sex expression and reproduction were discovered using DGE analysis, which provides large information and valuable hints for next insights into the molecular mechanism of sex determination. It is useful for other further studies in Ricinus.

Outbreak of carbapenemase-producing Klebsiella pneumoniae neurosurgical site infections associated with a contaminated shaving razor used for preoperative scalp shaving.

Between July 5 and 21, 2011, an outbreak of neurosurgical site infections with carbapenemase-producing Klebsiella pneumonia occurred in a tertiary care hospital. The outbreak affected 7 patients. The subsequent investigation revealed that a barber's contaminated shaving razor may have caused the carbapenemase-producing Klebsiella pneumonia outbreak. Standardized skin preparation performed by registered nurses using sterilized instruments should be emphasized.

[Topological match method in 3D reconstruction of heart vessel].

This paper presents a novel matching method of vessels in 3D reconstruction of heart vessel. The directed binary tree was used to describe the topological structure of heart vessel tree's skeleton. Based on topological property and epipolar property, the branch-points and end-points of each branch level could be automatically matched along the direction of blood stream. Thereupon it is easy to couple the corresponding vessels segments of two angiograms projected in different directions. The 3D heart vessel tree was successfully reconstructed from clinic coronary angiograms, which validates the presented method.