Metagenomic next-generation sequencing of plasma cell-free DNA improves the early diagnosis of suspected infections.

BACKGROUND: Metagenomic next-generation sequencing (mNGS) could improve the diagnosed efficiency of pathogens in bloodstream infections or sepsis. Little is known about the clinical impact of mNGS test when used for the early diagnosis of suspected infections. Herein, our main objective was to assess the clinical efficacy of utilizing blood samples to perform mNGS for early diagnosis of suspected infections, as well as to evaluate its potential in guiding antimicrobial therapy decisions. METHODS: In this study, 212 adult hospitalized patients who underwent blood mNGS test in the early stage of suspected infections were enrolled. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on clinical care was analyzed. RESULTS: In our study, the total detection rate of blood mNGS was significantly higher than that of culture method (74.4% vs. 12.1%, P < 0.001) in the paired mNGS test and blood culture. Blood stream infection (107, 67.3%) comprised the largest component of all the diseases in our patients, and the detection rate of single blood sample subgroup was similar with that of multiple type of samples subgroup. Among the 187 patients complained with fever, there was no difference in the diagnostic efficacy of mNGS when blood specimens or additional other specimens were used in cases presenting only with fever. While, when patients had other symptoms except fever, the performance of mNGS was superior in cases with specimens of suspected infected sites and blood collected at the same time. Guided by mNGS results, therapeutic regimens for 70.3% cases (149/212) were changed, and the average hospitalized days were significantly shortened in cases with the earlier sampling time of admission. CONCLUSION: In this study, we emphasized the importance of blood mNGS in early infectious patients with mild and non-specific symptoms. Blood mNGS can be used as a supplement to conventional laboratory examination, and should be performed as soon as possible to guide clinicians to perform appropriate anti-infection treatment timely and effectively. Additionally, combining the contemporaneous samples from suspected infection sites could improve disease diagnosis and prognoses. Further research needs to be better validated in large-scale clinical trials to optimize diagnostic protocol, and the cost-utility analysis should be performed.

EEF1D facilitates milk lipid synthesis by regulation of PI3K-Akt signaling in mammals.

Mammal's milk is an abundantly foremost source of proteins, lipids, and micronutrients for human nutrition and health. Understanding the molecular mechanisms underlying synthesis of milk components provides practical benefits to improve the milk quality via systematic breeding program in mammals. Through RNAi with EEF1D in primary bovine mammary epithelial cells, we phenotypically observed aberrant formation of cytoplasmic lipid droplets and significantly decreased milk triglyceride level by 37.7%, and exploited the mechanisms by which EEF1D regulated milk lipid synthesis via insulin (PI3K-Akt), AMPK, and PPAR pathways. In the EEF1D CRISPR/Cas9 knockout mice, incompletely developed mammary glands at 9th day postpartum with small or unformed lumens, and significantly decreased triglyceride concentration in milk by 23.4% were observed, as well as the same gene expression alterations in the three pathways. For dairy cattle, we identified a critical regulatory mutation modifying EEF1D transcription activity, which interpreted 7% of the genetic variances of milk lipid yield and percentage. Our findings highlight the significance of EEF1D in mammary gland development and milk lipid synthesis in mammals.

Phoenixin-20 ameliorates brain infarction by promoting microglia M2 polarization in an ischemic stroke model.

Ischemic stroke is one of the most common causes of death worldwide. The transformation of microglia from the classic M1 to the alternative M2 state has been shown to have both deleterious and immunosuppressive roles in neuroinflammation. Microglial polarization toward the M2 phase is currently proposed to be a beneficial phenotype in brain ischemic injury. Phoenixin-20 is a newly identified pleiotropic neuropeptide expressed abundantly in different brain regions. In this study, we found that administration of Phoenixin-20 in ischemic stroke middle cerebral artery occlusion (MCAO) mice significantly reduced the brain infarction area but improved the neurological deficit score. Gene expression analysis showed Phoenixin-20 treatment inhibited pro-inflammatory M1 phase microglial markers: a cluster of differentiation molecule 11b (CD11b), cluster of differentiation molecule 86 (CD86), inducible nitric oxide synthase (iNOS), tumor necrosis factor-alpha (TNF-α), interleukin 6 (IL-6), and increased anti-inflammatory M2 phase markers (found in Inflammatory Zone 1 (FIZZ1), Arginase 1 (Arg-1), Chitinase 3-like 3 (YM1), and interleukin-10 (IL-10)) in the infarcted brain. We further investigated the molecular mechanism of Phoenixin-20 in cultured microglia. We found that treatment with it induced signature genes expression in microglial M2 state, including Fizz1, Arg-1, YM1, and IL-10, indicating the promotion of microglial polarization toward the M2 state. Furthermore, we found that treatment with the M2 phase cytokine interleukin 4 (IL-4) induced the expression of microglial G Protein-Coupled Receptor (GPR173), which is the receptor of Phoenixin-20. Silencing of the microglial signal transducer and activator of transcription 6 (STAT6) partially blocked the effect of IL-4 on GPR173, suggesting that STAT6 is the upstream regulator of GPR173. Finally, we showed that the silencing of GPR173 completely abolished the effect of Phoenixin-20 in microglia, indicating the dependency of its regulatory role on GPR173. Collectively, our study demonstrates that Phoenixin-20 has a protective role in the acute stroke model. Our cell-based study demonstrates Phoenixin-20 promotes microglia toward M2 transformation, which could be the mechanism of its neuroprotection.

GOLM1 and FAM49B: Potential Biomarkers in HNSCC Based on Bioinformatics and Immunohistochemical Analysis.

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide. We aimed to identify potential genetic markers that could predict the prognosis of HNSCC. A total of 44 samples of GSE83519 from Gene Expression Omnibus (GEO) datasets and 546 samples of HNSCC from The Cancer Genome Atlas (TCGA) were adopted. The differently expressed genes (DEGs) of the samples were screened by GEO2R. We integrated the expression information of DEGs with clinical data from GES42743 using the weighted gene co-expression network analysis (WGCNA). A total of 17 hub genes were selected by the module membership (|MM| > 0.8), and the gene significance (|GS| > 0.3) was selected from the turquoise module. GOLM1 and FAM49B genes were chosen based on single-gene analysis results. Survival analysis showed that the higher expression of GOLM1 and FAM49B genes was correlated with a worse prognosis of HNSCC patients. Immunohistochemistry and multiplex immunofluorescence techniques verified that GOLM1 and FAM49B genes were highly expressed in HNSCC cells, and high expressions of GOLM1 were associated with the pathological grades of HNSCC. In conclusion, our study illustrated a new insight that GOLM1 and FAM49B genes might be used as potential biomarkers to determine the development of HNSCC, while GOLM1 and FAM49B have the possibility to be prognostic indicators for HNSCC.

Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages.

BACKGROUND: RNA-sequencing was performed to explore the bovine liver transcriptomes of Holstein cows to detect potential functional genes related to lactation and milk composition traits in dairy cattle. The bovine transcriptomes of the nine liver samples from three Holstein cows during dry period (50-d prepartum), early lactation (10-d postpartum), and peak of lactation (60-d postpartum) were sequenced using the Illumina HiSeq 2500 platform. RESULTS: A total of 204, 147 and 81 differentially expressed genes (DEGs, p < 0.05, false discovery rate q < 0.05) were detected in early lactation vs. dry period, peak of lactation vs. dry period, and peak of lactation vs. early lactation comparison groups, respectively. Gene ontology and KEGG pathway analysis showed that these DEGs were significantly enriched in specific biological processes related to metabolic and biosynthetic and signaling pathways of PPAR, AMPK and p53 (p < 0.05). Ten genes were identified as promising candidates affecting milk yield, milk protein and fat traits in dairy cattle by using an integrated analysis of differential gene expression, previously reported quantitative trait loci (QTL), data from genome-wide association studies (GWAS), and biological function information. These genes were APOC2, PPP1R3B, PKLR, ODC1, DUSP1, LMNA, GALE, ANGPTL4, LPIN1 and CDKN1A. CONCLUSION: This study explored the complexity of the liver transcriptome across three lactation periods in dairy cattle by performing RNA sequencing. Integrated analysis of DEGs and reported QTL and GWAS data allowed us to find ten key candidate genes influencing milk production traits.

Performance Evaluations of LoRa Wireless Communication in Building Environments.

The Internet of things presents tremendous opportunities for the energy management and occupant comfort improvement in smart buildings by making data of environmental and equipment parameters more readily and continuously available. Long-range (LoRa) technology provides a comprehensive wireless solution for data acquisition and communication in smart buildings through its superior performance, such as the long-range transmission, low power consumption and strong penetration. Starting with two vital indicators (network transmission delay and packet loss rate), this study explored the coverage and transmission performances of LoRa in buildings in detail. We deployed three LoRa receiver nodes on the same floor and eight LoRa receiver nodes on different floors in a 16-story building, respectively, where data acquisition terminal was located in the center of the whole building. The communication performance of LoRa was evaluated by changing the send power, communication rate, payload length and position of the wireless module. In the current research, the metrics of LoRa were quantified to facilitate its practical application in smart buildings. To the best of our knowledge, this may be the first academic research evaluating RTT performance of LoRa via practical experiments.

[Clinical phenotype and variantal analysis of a pedigree affected with hereditary coagulation factor V deficiency].

OBJECTIVE: To explore the molecular basis for a pedigree affected with coagulation factor V (FV) deficiency. METHODS: Clinical data of the patient and his family members was analyzed. Targeted capture and next-generation sequencing (NGS) and Sanger sequencing were carried out to detect potential variant of the FV gene. RESULTS: The patient presented with jaundice and prolonged prothrombin time (PT) and activated partial thromboplastic time (APTT). V factor activity measured only 0.1% of the normal level, though the patient had no sign of bleeding. A paternal heterozygous variant c.653T>C (p.F218S) and a maternal heterozygous variant c.3642_3643del (p.P1215Rfs*175) were identified in the FV gene of the patient. His elder brother was a heterozygous carrier of the c.653T>C (p.F218S) variant. c.653T>C(p.F218S) was a known pathogenic variant, while the c.3642_3643del (p.P1215Rfs*175) variant was unreported previously. CONCLUSION: Mutations of the FV gene probably underlie the hereditary coagulation factor V deficiency in this patient. NGS combined with Sanger sequencing has detected potential variant with efficiency and provided a reliable basis for clinical and prenatal diagnosis for this family.

Analysis of Liver Proteome and Identification of Critical Proteins Affecting Milk Fat, Protein, and Lactose Metabolism in Dariy Cattle with iTRAQ.

In this study, the proteomes of liver tissues are investigated in three periods of the lactation cycle of Holstein cows by using isobaric tag for relative and absolute quantification (iTRAQ) technique to obtain liver proteome and identify functional proteins/genes involved in milk synthesis in dairy cattle. Based on iTRAQ analysis, 3252 proteins are detected in the liver tissues (false discovery rate ≤0.01). Thirty-two differently expressed proteins (DEPs) are identified during the three periods by p-value <0.05 and fold change (FC) ≥2 or ≤0.5, and 183 DEPs based on p-value <0.05 and FC ≥1.5 or ≤0.67. In addition, 905 DEPs are obtained across the three periods by p-value <0.05 and FC ≥1.2, or ≤0.83, and the subsequent GO and KEGG pathway functional analysis indicate that 73 DEPs are significantly enriched into the metabolic terms and pathways involved in milk synthesis such as citrate cycle, fatty acid, starch and sucrose metabolism, and mTOR and PPAR signaling pathways. Further, 41 out of 73 DEPs are identified near to both the peak locations of the reported quantitative trait locus and significant single nucleotide polymorphisms that associate with milk yield and composition traits. In addition, the 41 DEPs are analyzed with the previous liver transcriptome data that used the same samples as this study, and considered nine proteins/genes-ALDH18A1, APOA4, CYP7A1, HADHB, PRKACA, IDH2, LDHA, LDHB, and MAT2A-to be the promising candidates for milk fat, protein, and lactose synthesis in dairy cattle. This study provides a new vision for identifying the potential critical genes associated with milk synthesis of dairy cattle.

Polyrhachis vicina Roger Alleviates Memory Impairment in a Rat Model of Alzheimer's Disease Through the EGR1/BACE1/APP Axis.

Memory deficits and loss are the earliest and most prominent features of Alzheimer's disease (AD). This study was aimed to clarify the mechanistic basis of an active fraction of Polyrhachis vicina Roger (AFPR) on the memory abilities of AD rat models, which involves early growth response 1 (EGR1) expression and ß-secretase 1 (BACE1)-mediated deposition of amyloid ß peptide (Aß). An AD rat model was developed by Aß25-35, which was further treated with AFPR alone or in combination with lentiviral EGR1. The Morris water maze test and HE and Fluoro-Jade C staining were adopted to observe the memory behaviors, hippocampus neuron morphology, and Aß deposition. Aß25-35-induced SK-N-SH and HT22 neurons were subjected to AFPR for in vitro experiments on neuronal viability and apoptosis. AFPR improved the impaired memory function, preserved the neuron structure, and suppressed Aß deposition in AD rat models. Further, the expression of APP pathway-related proteins was downregulated by AFPR in both rat and cellular models. Moreover, AFPR inhibited the Aß25-35-induced neuronal apoptosis. AFPR suppressed the expression of EGR1, downregulated the BACE1 expression via impeding the binding of EGR1 to the BACE1 promoter, and thus blocked the activation of the APP signaling, ultimately protecting neurons. Notably, the aforementioned effects of AFPR were in a concentration-dependent manner; among three doses, 3.65, 15.6, and 30 mg/(kg·d), high-dose AFPR exhibited the most appreciable effects. In conclusion, AFPR inhibited the BACE1 expression by repressing the binding of EGR1 to the promoter of BACE1, thereby suppressing the Aß deposition and improving the memory function of AD rats.

Age and episode-associated occurrence of Cryptosporidium species and subtypes in a birth-cohort of dairy calves.

The role of species-specific immunity in infection patterns of Cryptosporidium spp. in humans and farm animals is not well understood. In the present study, the dynamics of Cryptosporidium infections in a natural cryptosporidiosis model was examined using genotyping, subtyping and whole genome sequencing tools. In a cross-sectional survey of Cryptosporidium spp. in 934 dairy cattle on one farm, marked age-associated differences in the distribution of Cryptosporidium species and C. bovis subtypes were observed. In a closely followed longitudinal birth cohort study of 81 calves over a 9-month period, shedding of C. parvum oocysts by the IIdA19G1 subtype started at 4 days, peaked at 2 weeks and ended mostly by 4 weeks. In contrast, the shedding of C. bovis oocysts started at 2 weeks, peaked initially at 6 weeks and had a second wave during 15th to 23rd weeks. For C. ryanae, calves had mostly only one episode of infection by one subtype, with accumulative infection increasing much slower than C. parvum and C. bovis. Overall, the accumulative infection rates and mean duration of oocyst shedding for calves in the cohort were 97.4% (76/78) and 2.3 weeks, 100.0% (80/80) and 3.9 weeks, and 78.7% (63/80) and 3.2 weeks for C. parvum, C. bovis and C. ryanae, respectively. The oocyst shedding intensity was much lower in C. bovis and C. ryanae infections compared with C. parvum infection, and in the second episode of C. bovis infection compared with the first episode. The two episodes of C. bovis infections were caused by different genome types that differed mostly in nine genes. Cryptosporidium parvum infection was associated with the occurrence of watery diarrhoea. Data from the natural history study of cryptosporidiosis indicate that despite the existence of acquired immunity against homologous pathogens, neonatal animals experience waves of Cryptosporidium infections by different species and genome types.

Cryptosporidiosis outbreak caused by Cryptosporidium parvum subtype IIdA20G1 in neonatal calves.

Cryptosporidium parvum is a major zoonotic pathogen responsible for outbreaks of severe diarrhoea in humans and calves. Almost all investigations of cryptosporidiosis outbreaks caused by C. parvum have focused on its IIa subtype family in industrialized nations. From December 2018 to April 2019, approximately 200 neonatal calves on a large cattle farm in Hebei Province, China, were diagnosed with watery diarrhoea and over 40 died. To investigate the cause of the outbreak, faecal samples were taken during and after the outbreak from neonatal calves of ≤4 weeks of age (n = 40 and n = 56) and older calves of 4-24 weeks of age (n = 79 and n = 38). A total of 18 faecal samples collected from ill calves at the peak of the outbreak were analysed for four common enteric pathogens using an enzymatic immunoassay (EIA). In addition, 75 samples from neonatal calves were tested for rotavirus by EIA. All samples were analysed for Cryptosporidium spp. using PCR and sequencing techniques. Of the initial 18 samples from sick calves, ten were positive for C. parvum, five for rotavirus, and one for coronavirus. The overall prevalence of rotavirus in neonatal calves was 20.0% (15/75), with no significant differences during and after the outbreak. In contrast, Cryptosporidium parvum infections were significantly higher during the outbreak (60.0%, 24/40) than after the outbreak (30.4%, 17/56; p = .004). Cryptosporidium parvum infection was associated with the presence of watery diarrhoea in neonatal calves (OR = 11.19), while no association was observed between C. bovis infection and diarrhoea. All C. parvum isolates were identified as subtype IIdA20G1. This is one of the few reports of outbreaks of severe diarrhoea caused by C. parvum IId subtypes in calves. More attention should be directed towards the dissemination of C. parvum in China.

Assembly of the Non-Canonical Myo9a-RhoGAP and RhoA·GDP Transition State Complex in the Presence of MgF3.

Myo9a is an actin-based molecular motor with a RhoGAP domain in its C-terminal tail. It plays a role in a variety of biological processes, such as in regulating the immune response, neuron development, and cancer progression, and its deregulation can lead to the development of disease conditions. Myo9a acts mainly via its RhoGAP domain. In the current study, we used a pET32a vector with an N-terminal Trx-His6 tag to express Myo9a-RhoGAP in a soluble form. High-purity Myo9a-RhoGAP protein was obtained after two rounds of Ni2+ affinity and size-exclusion chromatography. We mixed Myo9a-RhoGAP and RhoA in equimolar ratios in the presence of 5 mM MgCl2 and 20 mM NaF to achieve a stable RhoA GTP hydrolysis transition state complex. Analytical gel filtration and SDS-PAGE were used to verify complex formation. ITC and GAP assays suggested that Myo9a-RhoGAP could bind to RhoA and accelerate RhoA GTP hydrolysis in vitro. We purified the soluble Myo9a-RhoGAP protein with GAP activity and achieved the Myo9a-RhoGAP/RhoA·GDP/MgF3- complex assembly in vitro for the first time. The data may provide novel insights into Myo9a structure and function.

Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China.

: Cryptosporidium felis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Effect of methamphetamine on potassium and L-type calcium currents in rat ventricular myocytes.

The mechanisms of cardiac toxicity caused by methamphetamine (MA) are poorly understood at present. This study was designed to investigate the effects of MA on ionic currents in myocardial cells. The effects of MA on transient outward potassium current (I(to)), inward rectifying potassium current (I(K1)), and L-type calcium current (I(Ca-L)) in isolated rat ventricular myocytes were studied using the whole-cell patch clamp technique. It was demonstrated that MA inhibited the I(to), I(K1), and I(Ca-L) in the rat ventricular myocytes concentration-dependently. MA shifted left the I(to) steady-state inactivation curve and shifted down the recovery curve, but had no influence on the steady-state activation curve. MA did not affect the I(Ca-L) steady-state activation curve or steady-state inactivation curve, but shifted down the recovery curve. We concluded that MA had inhibitory effects on the I(to), I(K1), and I(Ca-L) in ventricular myocytes, which might be one of the possible electrophysiological mechanisms of cardiac damage caused by MA.

SOCS3 protects against neonatal necrotizing enterocolitis via suppressing NLRP3 and AIM2 inflammasome activation and p65 nuclear translocation.

BACKGROUND: Necrotizing enterocolitis (NEC) is an acquired disorder of mucosal damage characterized by the diffuse or local necrosis of the intestine. The suppressor of cytokine signaling 3 (SOCS3) has been demonstrated to possess anti-inflammatory action in gastritis, ulcerative colitis and other inflammatory diseases. The present study aims to explore the effects of SOCS3 on LPS-induced colonic cell model of NEC, and investigate the underlying mechanisms. METHODS: Expression of SOCS3 in tissue samples of NEC and LPS-induced enterocytes were evaluated by real-time quantitative PCR (RT-qPCR). Western blotting and enzyme-linked immunosorbent assay (ELISA) were applied to examine the effect of SOCS3 on inflammatory molecules. Co-immunoprecipitation assay were devoted to explore the relation between SOCS3 and TLR4. RESULTS: We proved that SOCS3 was expressed at a low level in tissue samples of NEC and LPS-induced enterocytes, and LPS inhibited SOCS3 expression via JAK2/STAT3 pathway. Overexpression of SOCS3 weaken the LPS-induced inflammatory response in FHC and CACO2 cells. Moreover, SOCS3 downregulates proinflammatory cytokines by targeting TLR4, thus mediating the p65 nuclear translocation, and the activation of NLR family pyrin domain containing 3/absent in melanoma-2 (NLRP3/AIM2) inflammasome, ultimately reveals its anti-inflammatory effects. CONCLUSIONS: Taken together, our data revealed that LPS inhibited SOCS3 expression via JAK2/STAT3 pathway, and SOCS3 protects enterocytes against NEC through mediating p65 nuclear translocation and NLRP3/AIM2 inflammasome activation in a TLR4 dependent manner.

Multi-site-mediated entwining of the linear WIR-motif around WIPI ß-propellers for autophagy.

WIPI proteins (WIPI1-4) are mammalian PROPPIN family phosphoinositide effectors essential for autophagosome biogenesis. In addition to phosphoinositides, WIPI proteins can recognize a linear WIPI-interacting-region (WIR)-motif, but the underlying mechanism is poorly understood. Here, we determine the structure of WIPI3 in complex with the WIR-peptide from ATG2A. Unexpectedly, the WIR-peptide entwines around the WIPI3 seven-bladed ß-propeller and binds to three sites in blades 1-3. The N-terminal part of the WIR-peptide forms a short strand that augments the periphery of blade 2, the middle segment anchors into an inter-blade hydrophobic pocket between blades 2-3, and the C-terminal aromatic tail wedges into another tailored pocket between blades 1-2. Mutations in three peptide-binding sites disrupt the interactions between WIPI3/4 and ATG2A and impair the ATG2A-mediated autophagic process. Thus, WIPI proteins recognize the WIR-motif by multi-sites in multi-blades and this multi-site-mediated peptide-recognition mechanism could be applicable to other PROPPIN proteins.

Structural Conservation of the Two Phosphoinositide-Binding Sites in WIPI Proteins.

WIPI proteins are mammalian PROPPIN family members that bind to phosphoinositides and play prominent roles in autophagosome biogenesis. Two phosphoinositide-binding sites were previously described in yeast PROPPIN Hsv2 but remain to be determined in mammalian WIPI proteins. Here, we characterized four human WIPI proteins (WIPI1-4) and solved the structure of WIPI3. WIPI proteins can bind to PI(3)P and PI(3,5)P2 and adopt a conventional seven-bladed ß-propeller fold. The structure of WIPI3 revealed that WIPI proteins also contain two sites embedded in blades 5 and 6 for recognizing phosphoinositides, resembling that in Hsv2. Structural comparison further demonstrated that the two conserved phosphoinositide-binding sites in PROPPIN proteins are not identical but intrinsically tend to recognize different types of phosphoinositides. This work provides the structural evidence to support the conservation of the two phosphoinositide-binding sites in WIPI proteins and also uncovers the potential phosphoinositide-binding selectivity for each site.

Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle.

Our initial RNA sequencing work identified that lipin 1 (LPIN1) was differentially expressed during dry period, early lactation, and peak of lactation in dairy cows, and it was enriched into the fat metabolic Gene Ontology (GO) terms and pathways, thus we considered LPIN1 as the candidate gene for milk production traits. In this study, we detected the polymorphisms of LPIN1 and verified their genetic effects on milk yield and composition in a Chinese Holstein cow population. We found seven SNPs by re-sequencing the entire coding region and partial flanking region of LPIN1, including one in 5' flanking region, four in exons, and two in 3' flanking region. Of these, four SNPs, c.637T > C, c.708A > G, c.1521C > T, and c.1555A > C, in the exons were predicted to result in the amino acid replacements. With the Haploview 4.2, we found that seven SNPs in LPIN1 formed two haplotype blocks (D' = 0.98-1.00). Single-SNP association analyses showed that SNPs were significantly associated with milk yield, fat yield, fat percentage, or protein yield in the first or second lactation (p = < 0.0001-0.0457), and only g.86049389C > T was strongly associated with protein percentage in both lactations (p = 0.0144 and 0.0237). The haplotype-based association analyses showed that the two haplotype blocks were significantly associated with milk yield, fat yield, protein yield, or protein percentage (p = < 0.0001-0.0383). By quantitative real-time PCR (qRT-PCR), we found that LPIN1 had relatively high expression in mammary gland and liver tissues. Furthermore, we predicted three SNPs, c.637T > C, c.708A > G, and c.1521C > T, using SOPMA software, changing the LPIN1 protein structure that might be potential functional mutations. In summary, we demonstrated the significant genetic effects of LPIN1 on milk production traits, and the identified SNPs could serve as genetic markers for dairy breeding.

Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver.

RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.