At onset of milk production and in early lactation highly producing dairy cows are most susceptible for inflammatory diseases due to functional suppression of immune cells. Intensive supervision of the animals is essential and implementation of new technologies to on-farm routines will be the next step to provide automation and improvement of herd health monitoring programs. Objective of our study was to identify and validate immunological biomarkers in milk that indicate extra-mammary inflammatory diseases to characterize the general health status of highly-producing dairy cows. In total 89 healthy and 75 diseased animals (German Holstein cows) were included. Diseases were distinguished by either systemic (extra-mammary) occurrence or those affecting the mammary gland (mastitis) and further classified by their severity. For protein biomarker discovery we used a top-down approach to narrow down a broad range of secreted gene products of the milk cell transcriptome (microarray) and proteome to a few promising candidates which were validated using real-time PCR and ELISA. The most promising biomarker candidates were statistically evaluated. Receiver operating characteristic analysis revealed haptoglobin, secretory component, lactoferrin and vascular endothelial growth factor showing the highest discriminatory capability for diseased vs. healthy cows. Values for sensitivity at a specificity of 94% were 82% for haptoglobin, 59% for secretory component, 55% for lactoferrin and 67% for vascular endothelial growth factor. Statistical evaluation by multinomial logistic regression and k-nearest neighbor method confirmed haptoglobin as the best single-use biomarker. In combination with secretory component or lactoferrin an increase in overall sensitivity or specificity, depending on the classification method, could be achieved. The application of the validated health biomarkers in combination with an easy high-throughput detection system would offer a solution to adapt dairy herd management to changing requirements on animal welfare, farming efficiency, milk supply, and food safety in modern agriculture.

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primeror polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). segemehl now supports the SAM format, reads gzip’ed queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

Retinopathy of prematurity (ROP) is a severe retinal dysfunction in prematurely born babies. The relationship between non-coding RNAs and retinopathy of prematurity (ROP) remain unclear. Microarray analysis of lncRNAs, miRNAs, and mRNAs was conducted in a mouse model of ROP. A competing endogenous RNA (ceRNA) network was constructed. The relationship among MALAT1, miR-124–3p, and Early growth response protein 1 (EGR1) was assessed in hypoxia-induced primary human umbilical vein endothelial cells (HUVECs) and ROP mouse model. In the study, we found 2252 lncRNAs, 1239 mRNAs, and 36 miRNAs were differentially regulated. ceRNA network consisting of 21 lncRNAs, 10 miRNAs, and 19 mRNAs was established. Of the most down-regulated miRNAs, miR-124–3p was selected for additional study. miR-124–3p ceased the migration and proliferation of primary HUVECs in hypoxic conditions, and directly suppressed EGR1. Additionally, MALAT1 directly sponged miR-124–3p. Knockdown of MALAT1 decreased EGR1 expression and inhibited the migration and proliferation of primary HUVECs in hypoxia. Furthermore, these changes were rescued by depletion of miR-124–3p. In vivo, intravitreal injection of miR-124–3p, shMALAT1 decreased EGR1 expression and markedly suppressed retinal neovascularization in OIR models. Intravitreal injection of shMALAT1 and miR-124–3p antagomir at the same time can promote retinal neovascularization, which reversed the suppression of retinal neovascularization functioned by shMALAT1. In conclusion, the expression profiles of lncRNAs and miRNAs and the ceRNA network in a mouse model of ROP may be indicative of the underlying mechanisms of retinal angiogenesis and neural activity. The MALAT1/miR-124–3p/EGR1 regulatory axis is partly responsible for retinal neovascularization, which may provide a novel theoretical basis for the pathogenesis of ROP.