Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows

Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH₄) and dry matter intake (DMI) were individually measured over 4–6 weeks to calculate the CH₄ yield (CH₄y = CH₄/DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH₄y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH₄y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH₄y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH₄ emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH₄y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.     

Analysis of respiratory quinones in soil for characterization of microbiota

Method for the analysis of respiratory quinones in soil was developed to characterize soil microbiota. The respiratory quinones were extracted with a mixture of chloroform and methanol using a Wahling blender or a sonicator and cleaned-up by a silicagel column cartridge. The quinone species were determined by reverse-phase high performance liquid chromatography. Spectra of peaks were measured with a photodiode array detector to examine the purity. More than 90% of extractable quinones in soil were recovered by three extractions. The recovery of quinones, added to soil as freeze-dried powder of microorganisms, was higher than 96%. This procedure led to higher representative results as follows. Fluctuations within 95% of cumulative frequency were 13% for the extracted amount of quinones and 20% for the dissimilarity, respectively. The quinone profiles of four soils were determined as follows: a soil from the aerobic layer of a paddy field, an ando soil and two yellow upland soils which had received chemical fertilizers with and without farmyard manure. The quinone profiles displayed clear differences in the microbial composition and in the microbial diversity among the soils. It was demonstrated that the analysis of the respiratory quinone profile was useful to characterize the microbial community structure in soil.     

浅谈定向质谱法验证蛋白质生物标记物

特异性生物标记物的发现有益于疾病的早期诊断,促进靶向治疗的发展,并提供精确的治疗反应监控方法。血浆中候选生物标记物的验证过程中的一个主要问题是血浆中蛋白质浓度的动态范围非常广。本文回顾了当前能够在所预期的血浆浓度范围内(如ng/ml浓度水平)量化候选生物标记物的定向蛋白质组学策略。另外,提供了基于定向质谱法,可对大部分候选生物标记蛋白进行快速验证的技术流程。这些公开数据库中的技术对生物标记的验证研究中的处理量具有极大影响潜力。     

Serum concentration of surfactant protein D in horses with lower airway inflammation

Reasons for performing study: Surfactant protein D (SP‐D), mainly synthesised by alveolar type II cells and nonciliated bronchiolar cells, is one important component of innate pulmonary immunity. In man, circulating concentrations of SP‐D are routinely used as biomarkers for pulmonary injury. To date, serum SP‐D levels have only been investigated in horses in an experimental model of bacterial airway infection. Objectives: To compare serum SP‐D concentrations at rest and after exercise in horses with and without inflammatory airway disease (IAD). Methods: Venous blood samples were collected from 42 Standardbred racehorses at rest and 60 min after performing a standardised treadmill exercise test. Tracheal wash and bronchoalveolar lavage fluid (BALF) samples were collected after exercise. Based on BALF cytology, 22 horses were defined as IAD‐affected and 20 classified as controls. Serum SP‐D concentrations were assessed using a commercially available ELISA kit and statistically compared between groups of horses and sampling times. Results: Serum concentrations of SP‐D in IAD‐affected horses were significantly higher than those of control horses, both at rest and after exercise. Within the IAD‐affected group, no significant correlation was found between serum SP‐D concentrations and BALF cytology. Within each group of horses (IAD and control), no significant influence of exercise was found on serum SP‐D levels. Conclusions: This is the first study determining serum SP‐D concentrations in a noninfectious, naturally occurring form of lower airway inflammation in horses. The results highlight that IAD is associated with a detectable, though moderate, increase of circulating SP‐D levels. Potential relevance: Serum concentration of surfactant protein D could represent a potentially valuable and readily accessible blood biomarker of equine lower airway inflammation.     

湿地匍灯藓（Plagiomnium acutum）对Pb胁迫的生物标志物响应

采用浸没培养实验研究了不同浓度Pb胁迫下湿地匍灯藓(Plagiomnium ac utu)的总叶绿素、丙二醛、可溶性糖、游离脯氨酸含量以及抗氧化酶活性等生理生化生物标志物的变化,以探讨Pb胁迫下湿地匍灯藓的受损和耐受机理.结果表明,湿地匍灯藓外表伤害症状与Pb胁迫浓度存在明显的剂量-效应关系;低浓度(20 mg·L-1)Pb胁迫可以显著地促进湿地匍灯藓的总叶绿素含量增加,而中、高浓度(50 ng ·L-1)Pb胁迫则导致总叶绿素含量显著降低.湿地匍灯藓对Pb具有较强的生物富集能力,且藓体Pb的累积量与环境Pb浓度呈显著正相关.湿地匍灯藓体内MDA和游离脯氨酸含量随Pb胁迫浓度的增加表现为显著升高.可溶性糖含量仅在高浓度Pb胁迫下显著升高.可溶性蛋白含量、过氧化物酶(POD)和过氧化氢酶(CAT)活性均随Pb胁迫浓度的增加而显著下降,其中CAT活性的降幅最大,SOD活性随Pb胁迫浓度的增加逐渐显著增加.在高浓度Pb胁迫下,由于细胞膜脂过氧化和蛋白质变性失活所导致的膜保护体系损伤可能是湿地匍灯藓Pb中毒的主要原因,而渗透调节可能是其缓解Pb毒害的一种主要方式,SOD则在清除Pb胁迫产生的活性氧自由基过程中起重要作用.总叶绿素、丙二醛、游离脯氨酸、可溶性蛋白、CAT和SOD可以作为湿地匍灯藓受Pb胁迫的敏感生物标志物.     

金属硫蛋白作为重金属污染生物标志物的研究进展

金属硫蛋白（MT）是一类普遍存在于生物体内的低分子量、富含半胱氨酸、热稳定性、可诱导型非酶蛋白,具有维持生物体内金属含量动态平衡和重金属解毒作用双重机制。大量研究表明,MT可作为重金属污染的生物标志物,用来预测生物体受重金属暴露的状况和重金属污染的压力,且对制定预防性的管理措施、及时监控环境污染皆具有重要的现实意义。本文根据国内外文献资料查阅及综合分析,主要阐述了金属硫蛋白的基本结构、多态性、生理功能及其作为生物标志物在环境污染检测与诊断方面的研究与应用,并展望其今后研究方向。     

Biologic variability of N-terminal pro-brain natriuretic peptide in healthy dogs and dogs with myxomatous mitral valve disease

Introduction

To determine the biologic variability of N-terminal pro-brain natriuretic peptide (NTproBNP) in healthy dogs and dogs with various stages of myxomatous mitral valve disease (MMVD).