Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle

The small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate bacterial composition and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the influence of diets on jejunal bacterial communities and examined its relationships with bile acids. Here, we examined the impact of grain- and grass-based diets on jejunal and fecal bacterial communities’ composition and investigated possible association of bacterial features with bile acids. We demonstrated that the influences of diets on intestinal bacteria can be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was documented in feces of grass-fed cattle comparing to grain-fed cattle. Top 20 important genera identified with random forest analysis on fecal bacterial community can be good candidates for microbial biomarkers. Moreover, the jejunal bacteria of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and bacteria signatures predictive of bile acids were identified, indicative of the potential association of bacterial features with bile acids. The findings from this study provided novel insights into the relationships between jejunal bacteria and bile acids under different diets in Angus beef cattle. Our results should help us gain a better understanding of potential health benefits of grass-fed beef.https://doi.org/10.1186/s42523-020-00051-

Function of Chick Subcutaneous Adipose Tissue During the Embryonic and Posthatch Period

Since excess abdominal fat is one of the main problems in the broiler industry for the development of modern broiler and layer industry, the importance of subcutaneous adipose tissue has been neglected. However, chick subcutaneous adipose tissue appeared earlier than abdominal adipose tissue and more than abdominal adipose tissue. Despite a wealth of data, detailed information is lacking about the development and function of chick subcutaneous adipose tissue during the embryonic and posthatch period. Therefore, the objective of the current study was to determine the developmental changes of adipocyte differentiation, lipid synthesis, lipolysis, fatty acid β-oxidation, and lipid contents from E12 to D9.5. The results showed that subcutaneous adipose tissue was another important energy supply tissue during the posthatch period. In this stage, the mitochondrial copy number and fatty acid β-oxidation level significantly increased. It revealed that chick subcutaneous adipose tissue not only has the function of energy supply by lipidolysis but also performs the same function as brown adipose tissue to some extent, despite that the brown adipose tissue does not exist in birds. In addition, this finding improved the theory of energy supply in the embryonic and posthatch period and might provide theoretical basis on physiological characteristics of lipid metabolism in chicks

Dynamic cerebral autoregulation is heterogeneous in different subtypes of acute ischemic stroke.

BACKGROUND AND PURPOSE: Stroke of large-artery atherosclerosis and small-artery occlusion are two main subtypes of stroke according to TOAST classification. The underlying mechanisms of how these two subtypes affect dynamic cerebral autoregulation (dCA) might be heterogeneous, resulting in varied clinical conditions and outcomes. We therefore studied the pattern of dCA in these two subtypes. METHODS: Forty-one patients with acute unilateral middle cerebral artery (MCA) territory stroke (15 with ipsilateral large-artery atherosclerosis and 26 with small-artery occlusion) and 20 healthy volunteers were enrolled. Non-invasive continuous cerebral blood flow velocity and arterial blood pressure were recorded simultaneously from each subject in supine position using transcranial Doppler on MCA bilaterally and servo-controlled plethysmograph on the middle finger, respectively. Transfer function analysis was applied to derive autoregulatory parameters, gain, phase difference (PD), and slope of step response. RESULTS: In the large-artery atherosclerosis group, PD in affected hemisphere was 42.9±18.5 degree, which is significantly lower than the unaffected hemisphere (72.4±29.9 degree, P<0.01), and the healthy group (P<0.01). However, PD is similar in the unaffected hemisphere and healthy group (P>0.1). In the small-artery occlusion group, PD in the affected hemisphere was similar to that in the contralateral hemisphere (33.8±17.9 vs. 32.6±21.1 degree, P>0.1), both sides were significantly lower than the healthy group (all P<0.001).The results of the slope of step response agree with the findings in PD. CONCLUSIONS: DCA in different subtypes of acute ischemic stroke is heterogeneous, which might be attributed to the varied pathologic changes of cerebral blood vessels

Optimized CRISPR/Cas9 system for gene knockout in chicken DF1 cells

ABSTRACT: The editing efficiency primarily hinders the utility of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology in poultry. For a better understanding of the factors that influence the efficiency of gene knockout mediated by CRISPR/Cas9 in chicken DF1 cells, the single or dual single guide RNA (sgRNA) targeted exon regions of genes (taking anti-Müllerian hormone, TGF-beta receptor type-2 and Peroxisome proliferator-activated receptor gamma as examples) were designed. The sgRNA-CRISPR/Cas9 vectors with corresponding reporter vectors were transfected into DF1 cells. T7 endonuclease 1 (T7E1) and amplicon sequencing assay were compared for evaluating genome editing efficiency and the indel profiles were analyzed based on the data of amplicon sequencing. Meanwhile, to evaluate the precision of Cas9 cleavage, we also analyzed the homology of small insertion with the nucleotides of upstream and downstream of cleave sties. The surrogate reporter systems showed strong enrichment function, and the indel percentages were increased after puromycin selection. The indel ratios of T7E1 assay were lower than amplicon sequencing assay, which indicated T7E1 isn't fit to be used as the sole evaluation criterion for the targeting efficiency of CRISPR/Cas9. Based on the amplicon sequencing analysis, the editing efficiency showed noticeable differences among cells treated with different sgRNAs. However, the variety of indel efficiencies was not related to the GC content of sgRNA or chromosome types of targeted genes. The results showed that the dual sgRNA might not raise the indel ratios compared with individual sgRNA, but they could increase the ratios of the fragment deletions. The present study suggested that the surrogate reporter was an effective method to promote the editing efficiencies of CRISPR/Cas9 in chicken cells. The dual sgRNA could increase the fragment deletions, and the sensitivity of amplicon sequencing to detect cleavage was higher than the T7 endonuclease 1 assay. These results are essential to improve the application of CRISPR/Cas9 technology in chicken cells

Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats

The development of hair follicle in cashmere goats shows significant periodic change, as with mice and humans. However, for cashmere goat with double-coat, the periodic change may be due to other regulatory molecules and signal pathways. To understand the mechanism of periodic development of hair follicle, we performed a weighted gene coexpression network analysis (WGCNA) to mine key genes and establish an interaction network by utilizing the NCBI public dataset. Ten coexpression modules, including 7689 protein-coding genes, were constructed by WGCNA, six of which are considered to be significantly related to the development of the hair follicle cycle. A functional enrichment analysis for each model showed that they are closely related to ECM- receptor interaction, focal adhesion, PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. Combined with the analysis of differential expressed genes, 12 hub genes from coexpression modules were selected as candidate markers, i.e., COL1A1, C1QTNF6, COL1A2, AQP3, KRTAP3-1, KRTAP11-1, FA2H, NDUFS5, DERL2, MRPL14, ANTKMT and XAB2, which might be applied to improve cashmere production

Three autoregulatory parameters, A) phase difference, B) gain, and C) step response, derived from the transfer function are plotted.

<p>H (: right side and : left side), L (: affected side and : unaffected side), and S (same legends as L) denote healthy controls, large-artery atherosclerosis group, and small-artery occlusion group, respectively. The first column shows that all parameters in the healthy group from both sides indicate that autoregulation is intact. There is evident positive phase difference. The shape of high-pass filter can also be speculated. The step response, H-C), shows that cerebral blood flow velocity quickly returns to the baseline level within approximately 4 seconds if a unit step change of arterial blood pressure is induced. In the second column, the parameters changes asymmetrically. Dynamic cerebral autoregulation on the affected side is substantially reduced than the unaffected side with decreased phase difference, flattened gain, and slower return of cerebral blood flow velocity in response to a step change of arterial blood pressure. In the last column, this series of subplots show that autoregulation is worsen bilaterally when comparing with the healthy controls.</p

Statistical distributions of the autoregulatory parameters for each category are shown above.

<p>A) Phase difference (PD) from the affected side in the large-artery atherosclerosis group is significantly lower than the contralateral side as well the healthy group. PD from the small-artery occlusion group is bilaterally lower than those in the healthy group but there is no difference within the group. B) No statistical difference is detected using gain. C) The results of the slope of step response agree with the findings in PD. Flatter slope (the value of the slope of step response is closer to zero) is observed within the affected side in large-artery atherosclerosis group than in other conditions. The slope in the small-artery occlusion group is also flatter than the healthy controls only. H, L, and S denote the three groups as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093213#pone-0093213-g001" target="_blank">Figure 1</a>. Rt and Lt stand for right and left side, respectively, for the healthy controls. U and A denote unaffected and affected sides, respectively, for the patients. For each box plot, the central mark is the median and the edges of the box are the 25th and 75th percentiles, the whiskers extend to the most extreme data points which are not outliers, and the outliers are plotted individually as ‘○’. <b>^*</b>denotes <i>P</i><0.05 for comparing between two sides within the same group. <b>^†</b>denotes <i>P</i><0.05 for comparing with the overall of healthy group.</p

Baseline characteristics.

<p>Baseline characteristics.</p

Phase difference (PD), gain and slope of step response in patients and controls.

<p><b>*</b>and <b>^†</b>denote the same statistical meaning as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093213#pone-0093213-g002" target="_blank">Figure 2</a>.</p

Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig

<div><p>Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude. A total of 3,066 DEGs were identified and this list was over-represented for the ontology terms including metabolic process, catalytic activity, and KEGG pathway including metabolic pathway and PI3K-Akt signaling pathway. The regulatory (RIF) and phenotypic (PIF) impact factor analysis identified several known and several potentially novel regulators of hypoxia adaption, including: <i>IKBKG</i>, <i>KLF6</i> and <i>RBPJ</i> (RIF1), <i>SF3B1</i>, <i>EFEMP1</i>, <i>HOXB6</i> and <i>ATF6</i> (RIF2). These findings provide new details of the regulatory architecture of hypoxia-adaptive genes and also insight into which genes may undergo epigenetic modification for further study in the high-altitude adaptation.</p></div