Full-length transcriptome sequencing reveals extreme incomplete annotation of the goat genome.

Despite recent advances in generating high-quality reference genome assemblies, the genome sequences for most livestock species, including goats, are still poorly annotated. Single-molecule long-read sequencing has greatly facilitated gene annotation by obtaining full-length transcripts. In this study, we generated full-length transcriptome data for samples from abomasum (n = 2) and testicle (n = 1), using PacBio Iso-Seq technology. We further combined these data with published data from abomasum (5ZY, SRR8618141) to evaluate and improve the gene annotation of the goat genome. We identified 14.5-16.3% of novel genes per sample from the four Iso-Seq datasets. At the transcript level, 40.6% of them were novel, including 29.7% novel transcripts from known genes and 10.9% from novel genes. We further verified the expression of novel genes in four additional RNA-seq data and found that the expression level of novel genes was significantly lower than that of known genes, indicating that the lowly expressed genes tend to be missed in the current genome annotation. This study shows the superiority of full-length transcriptome data in gene annotation, and more such data are required to improve the gene annotation for goat genome and other species.

A novel SNP of MYO1A gene associated with heat-tolerance in Chinese cattle.

With the advent of global climate change, heat-tolerance is becoming more and more important to the sustainability of animal husbandry production systems. Previous studies have shown that MYO1A gene associated with pigmentation may be closely related to heat-tolerance in cattle. In this study, a novel missense mutation (NC_037332.1 g.56390345 A > G) was first detected in MYO1A in 891 individuals of 35 cattle breeds, which transformed the amino acid isoleucine into valine. The purpose of this study was to determine the allele frequencies distribution of this locus in Chinese indigenous cattle and to analyze the relationship between this locus and heat-tolerance. Further analysis showed that frequency of wild allele A decreased gradually from northern cattle to southern cattle, whereas frequency of mutant type allele G showed the opposite pattern, which was consistent with the distribution of various climatic conditions of China. Additionally, association analysis was carried out between genotypes and four climatic conditions (annual mean temperature (T), relative humidity (H), temperature-humidity index (THI) and average annual sunshine hours (100-cloudiness) (SR)). Analysis results showed that genotypes were significantly correlated with climatic conditions. Therefore, our results suggest that the novel SNP (rs209559414) is related to heat-tolerance trait of Chinese indigenous cattle.

Development and Validation of a Nomogram for Preoperative Prediction of Perineural Invasion in Colorectal Cancer.

BACKGROUND In colorectal cancer (CRC), perineural invasion (PNI) is usually identified histologically in biopsy or resection specimens and is considered a high-risk feature for recurrence of CRC and is an indicator for adjuvant therapy. Preoperative identification of PNI could help determine the need for adjuvant therapy and the approach to surgical resection. This study aimed to develop and validate a nomogram for the preoperative prediction of PNI in patients with CRC. MATERIAL AND METHODS A total of 664 patients with CRC from a single center were classified into a training dataset (n=468) and a validation dataset (n=196). The least absolute shrinkage and selection operator (LASSO) regression model was used to select potentially relevant features. Multivariate logistic regression analysis was used to develop the nomogram. The performance of the nomogram was assessed based on its calibration, discrimination, and clinical utility. RESULTS The nomogram consisted of five clinical features and provided good calibration and discrimination in the training dataset, with an area under the curve (AUC) of 0.704 (95% CI, 0.657-0.751). Application of the nomogram in the validation cohort showed acceptable discrimination, with the AUC of 0.692 (95% CI, 0.617-0.766) and good calibration. Decision curve analysis (DCA) showed that the nomogram was clinically useful. CONCLUSIONS The nomogram developed in this study might allow clinicians to predict the risk of PNI in patients with CRC preoperatively. The nomogram showed favorable discrimination and calibration values, which may help optimize preoperative treatment decision-making for patients with CRC.

Essential oil of Syzygium aromaticum reverses the deficits of stress-induced behaviors and hippocampal p-ERK/p-CREB/brain-derived neurotrophic factor expression.

Syzygium aromaticum has been widely used in traditional medicine. Our study investigated the safety and antidepressant-like effects of the essential oil of S. aromaticum after acute or long-term treatment. Using GC-MS, a total of eight volatile constituents were identified in the essential oil of S. aromaticum. The single LD50 was approximately 4500 mg/kg based on a 24-h acute oral toxicity study. In a long-term repeated toxicity study of this essential oil (100, 200, and 400 mg/kg, p. o.), only 400 mg/kg induced a significant decrease in body weight. In addition, no significant changes in relative organ weights and histopathological analysis were observed in all doses of essential oil-treated mice compared with the control group. Furthermore, acute S. aromaticum essential oil administration by gavage exerted antidepressant-like effects in the forced swimming test (200 mg/kg, p < 0.05) and tail suspension test (100 and 200 mg/kg, p < 0.05). Long-term S. aromaticum essential oil treatment via gavage significantly increased sucrose preference (50 mg/kg, p < 0.05; 100 and 200 mg/kg, p < 0.01) as well as elevated the protein levels of hippocampal p-ERK, p-CREB, and brain-derived neurotrophic factor in mice exposed to chronic unpredictable mild stress. These results confirmed the safety of the essential oil of S. aromaticum and suggested that its potent antidepressant-like property might be attributed to the improvement in the hippocampal pERK1/2-pCREB-BDNF pathway in rats exposed to chronic unpredictable mild stress.

The multi-kingdom microbiome of the goat gastrointestinal tract.

BACKGROUND: Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS: We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS: Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.

A new prediction model for overall survival of elderly patients with solitary bone plasmacytoma: A population-based study.

Background: Comprehensive studies on the prognosis of solitary bone plasmacytoma (SPB) are lacking, especially in elderly patients with SPB. This study aims to establish a novel nomogram and risk stratification system to predict the overall survival (OS) of elderly patients with SPB. Methods: The data of elderly patients with SPB from 2000 to 2017 were identified in the SEER database. SPB patients were randomly assigned to the training set (n = 825) and validation set (n = 354). The Cox regression analysis was used to determine the independent risk factors for OS in elderly SPB patients. The nomogram was established and assessed by the area under the receiver operating curve (AUC), the consistency index (C-index), and the calibration plot. Patients were divided into low-, medium-, and high-risk groups based on the score of the nomogram. The Kaplan-Meier (K-M) curve was used to verify the differences in overall survival among the three groups. Result: A total of 1,179 elderly patients with SPB were included in the study. Age at diagnosis, prior cancer before SPB, marital status, radiotherapy, and chemotherapy were independent risk factors of OS. The AUC of the 3, 5, and 8-year OS in the training and validation sets were between 0.707 and 0.860. The C-index and calibration plot also indicated that the nomogram has great predictive accuracy and robustness. After risk stratification, patients in the high-risk group had the worst OS. Conclusion: A novel nomogram was built to predict the OS of elderly patients with SPB. It will help clinicians formulate more reasonable and personalized treatment strategies.

Effects of coconut water on blood sugar and retina of rats with diabetes.

BACKGROUND: This study aimed to evaluate the effects of coconut water on the general condition (fasting blood sugar and body weight) and retina of diabetic rats. METHODS: Forty-eight Sprague-Dawley male rats were divided into normal controls (NC), diabetes mellitus (DM), diabetes+coconut water (DM+CW), and diabetes+glibenclamide (DM+Gli) groups. After 4 weeks of normal feeding, coconut water was given to group III-DM+CW and 0.6 mg/kg glibenclamide to group IV-DM+Gli. The blood sugar, body weight, total retinal thickness, pathological changes, and VEGF expression in the retina were analyzed at different time points. RESULTS: The fasting blood sugar was 4-6 mmol/L in group I-NC and continuously increased in group II-DM, whereas gradually decreased after the 4th experiment week in the remaining two groups. The rats, except in group I-NC, have lost weight. In group II-DM, the total retinal thickness was significantly increased after the 8th and 12th experiment week, and the pathological changes in retina were observed. VEGF was almost fully expressed in the ganglion cell layer and inner granular layer and partially expressed in the outer granular layer in group II-DM, and mainly expressed in the ganglion cell layer and inner layer in group I-NC, with a lighter color. Group III-DM + CW and group IV-DM + Gli demonstrated similar VEGF expression as in group I-NC. CONCLUSIONS: Coconut water has the potential to reduce blood sugar and diabetic retinal damage, serving as a candidate drug or nutrient for treating diabetes and its complications.

Effects of Coconut Water on Retina in Diabetic Rats.

Coconut water (CW) is a natural aseptic nutritious beverage, containing several biologically active compounds. This study aimed to determine the antiretinopathy effects of CW on diabetic Sprague Dawley (SD) rats using streptozotocin (STZ) and explore its potential mechanism. After allowing the rats to acclimatize for 7 days, 48 healthy adult male SD rats were selected and randomly divided into 4 groups, involving control (Ctrl), diabetic rats (DM), diabetic rats treated with CW (DM-CW), and diabetic rats treated with glibenclamide (DM-Gli). The diabetic models were established by an intraperitoneal injection of STZ (60 mg/kg). The Ctrl group was injected with an equal volume of sodium citrate solution. The experiment was totally conducted during 20 weeks, and then, all rats were sacrificed. The serum levels of superoxide dismutase (SOD), malondialdehyde (MDA), and glutathione peroxidase (GSH-Px) were measured; additionally, the activities of interleukin-6 (IL-6) and intercellular adhesion molecule-1 (ICAM-1) in the retina were investigated using biochemical assays. Hematoxylin and eosin (H&E) staining was performed to observe pathological changes of retinal tissues. In presence of treatment with CW, serum level of MDA was decreased, while serum levels of SOD and GSH-Px were increased; besides, the activities of IL-6 and ICAM-1 in the retina were reduced compared with the DM group. The antiretinopathy feature of CW was confirmed by the increased number of neurons in the ganglion cell layer (GCL), total retina thickness (TRT), and thickness of the retinal nuclear layer (RNL) in diabetic rats. CW can be protective against diabetic retinopathy (DR), and its effects are comparable to Gli. The possible underlying mechanism may be partly explained by decreasing oxidative stress and anti-inflammatory activities in the retina. However, further research should be conducted to reveal the exact mechanism.

Nomogram for predicting overall survival in stage II-III colorectal cancer.

PURPOSE: The overall survival (OS) of patients diagnosed with stage II-III colorectal cancer (CRC) can vary greatly, even between patients with the same tumor stage. We aimed to design a nomogram to predict OS in resected, stage II-III CRC and stratify patients with CRC into different risk groups. PATIENTS AND METHODS: Based on data from 873 patients with CRC, we used univariate Cox regression analysis to select the significant prognostic features, which were subjected to the least absolute shrinkage and selection operator (LASSO) regression algorithm for feature selection. Cross-validation was used to confirm suitable tuning parameters (λ) for LASSO logistic regression. Then, the nomogram was used to estimate 3- and 5-year OS based on the multivariable Cox regression model. The survival curves of the two groups were produced using the Kaplan-Meier method. Risk group stratification was performed to assess the predictive capacity of the nomogram. RESULTS: Preoperative mean platelet volume, preoperative platelet distribution width, monocytes, and postoperative adjuvant chemotherapy were identified as independent prognostic factors by LASSO regression and integrated for the construction of the nomogram. The nomogram provided good discrimination, with C-indices of 0.67 and 0.69 for the training and validation sets, respectively. Calibration plots illustrated excellent agreement between the nomogram predictions and actual observations for 3- and 5-year OS. Moreover, a significant difference in OS was shown between patients stratified into different risk groups (P < .001). CONCLUSION: We constructed and validated an original predictive nomogram for OS in patients with CRC after surgery, facilitating physicians to appraise the individual survival of postoperative patients accurately and identify high-risk patients who need more aggressive treatment and follow-up strategies.

A nomogram for preoperative prediction of lymphatic infiltration in colorectal cancer: A personalized approach to clinical decision making.

Lymphatic infiltration (LI) is a key factor affecting the treatment of patients with colorectal cancer (CRC). Thus, the aim of this study was to develop and validate a nomogram for individual preoperative prediction of LI in patients with CRC.We conducted a retrospective analysis of 664 patients who received their initial diagnosis of CRC at our center. Those patients were allocated to a training dataset (n = 468) and a validation dataset (n = 196). The least absolute shrinkage and selection operator regression model was used for data dimension reduction and feature selection. The nomogram was constructed from the training dataset and internally verified using the concordance index (C-index), calibration, area under the receiver operating characteristic curve and decision curve analysis (DCA).The enhancement computed tomography reported N1/N2 classification, preoperative tumor differentiation, elevated carcinoembryonic antigen, and carbohydrate antigen19-9 level were selected as variables for the prediction nomogram. Encouragingly, the nomogram showed favorable calibration with C-index 0.757 in the training cohort and 0.725 in validation cohort. The DCA signified that the nomogram was clinically useful. The Kaplan-Meier survival curve showed that patients with LI had a worse prognosis and could benefit from postoperative adjuvant chemotherapy.Use common clinicopathologic factors, a non-invasive scale for individualized preoperative forecasting of LI was established conveniently. LI prediction has great significance for risk stratification of prognosis and treatment of resectable CRC.

A nomogram to predict vascular invasion before resection of colorectal cancer.

Vascular invasion (VI) is an important feature for systemic recurrence and an indicator for the application of adjuvant therapy in colorectal cancer (CRC). Preoperative knowledge of VI is important in determining whether adjuvant therapy is necessary, as well as the adequacy of surgical resection. In the present study, a predictive nomogram for VI in patients with CRC was constructed. The prediction model consisted of 664 eligible patients with CRC, who were divided into a training set (n=468) and a validation set (n=196). Data were collected between August 2013 and April 2018. The feature selection model was established using the least absolute shrinkage and selection operator regression model. Multivariable logistic regression analysis was used to construct the predictive nomogram. The performance of the nomogram was evaluated by calibration, discrimination and clinical usefulness. Differentiation, computed tomography (CT)-based on N stage (CT N stage), hemameba and tumor distance from the anus (cm) were integrated into the nomogram. The nomogram exhibited good discrimination, with an area under the curve (AUC) of 0.731 and good calibration. Application of the nomogram in the validation cohort showed acceptable discrimination, with an AUC of 0.710 and good calibration. Decision curve analysis revealed that the nomogram was clinically useful. These findings suggests, to the best of our knowledge, that this may be the first nomogram for individual preoperative prediction of VI in patients with CRC, which may promote preoperative optimization strategies for this selected group of patients.

Evaluation of the toxicological properties and anti-inflammatory mechanism of Hemerocallis citrina in LPS-induced depressive-like mice.

Hemerocallis citrina Baroni (Liliaceae), a Liliaceae plant, has been widely used in food and traditional medicine. This study investigated the safety of ethanol extracts from Hemerocallis citrina (HCE) after oral treatment (p.o.) and evaluating the anti-inflammatory mechanism of HCE in a lipopolysaccharide (LPS)-induced depressive-like model. First, in an 8-week experimental procedure, blood and tissue samples collected from mice were used for biochemical and histopathological analysis every two weeks. Neither the body weight nor relative organ weights were affected by HCE administration. Only the total cholesterol levels were decreased by HCE administration. Histopathological analysis showed no significant liver and kidney changes caused by HCE. In addition, in an LPS-induced mouse depressive-like model, HCE significantly reversed the reduction of sucrose preference with LPS. The results also indicated that LPS activated the nuclear factor-κB (NF-κB), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) expression in the prefrontal cortex. In contrast, these activations were normalized by HCE pretreatment. In summary, our study provided essential evidence for the safety of Hemerocallis citrina in both food and medicine. The results also demonstrated that HCE exhibited antidepressant-like effects that might be related to inhibition of the NF-κB signaling pathway.

Antidepressant-like effects of standardized gypenosides: involvement of brain-derived neurotrophic factor signaling in hippocampus.

RATIONALE: Gypenosides have been reported to produce neuroprotective effects and increase monoamine neurotransmitter levels in the brain. OBJECTIVE: Considering that depression is involved in monoamine reduction, this study evaluated the antidepressant-like effects of gypenosides in mice exposed to chronic unpredictable mild stress (CUMS). METHODS: The sucrose preference test and forced swimming test were performed after administration of gypenosides (at 25, 50, or 100 mg/kg) for 4 weeks. Hippocampal brain-derived neurotrophic factor (BDNF) and its downstream targets were analyzed by western blot. Additionally, hippocampal neuronal proliferation was measured by immunohistochemistry. RESULTS: Four-week treatment with fluoxetine (20 mg/kg) and gypenosides (at either 50 or 100 mg/kg) increased sucrose preference and decreased the immobility time in mice exposed to CUMS. In addition, gypenosides (at either 50 or 100 mg/kg) also increased BDNF expression and neuronal proliferation in the hippocampus of CUMS animals. Further, we showed that treating CUMS mice with K252a, which is an inhibitor of the BDNF receptor TrkB, blocked the effects of gypenosides (100 mg/kg), including behavioral improvements, neuronal proliferation, and up-regulation of p-TrkB, p-ERK, and p-Akt proteins. CONCLUSIONS: This study demonstrates that gypenosides exhibit antidepressant-like effects in mice, which may be mediated by activation of the BDNF-ERK/Akt signaling pathway in the hippocampus.

ERK-dependent brain-derived neurotrophic factor regulation by hesperidin in mice exposed to chronic mild stress.

A previous study found that the antidepressant-like effects of ethanolic extracts from Hemerocallis citrina are predominantly related to the flavonoid, hesperidin. The study herein aimed to explore the antidepressant-like mechanism of hesperidin in mice induced by chronic mild stress (CMS). The results indicated that hesperidin reversed the reduction of sucrose preference and the elevation of immobility time in mice induced by CMS. In addition, the increase in serum corticosterone levels and decrease in hippocampal extracellular signal-regulated kinase (ERK) phosphorylation and brain-derived neurotrophic factor (BDNF) levels in CMS mice were also ameliorated by hesperidin treatment. In contrast, improvement by hesperidin was suppressed by pretreatment with ERK inhibitor SL327. Taken together, our findings confirmed the antidepressant-like effect of hesperidin and indicated that hesperidin-induced BDNF up-regulation was mediated in an ERK-dependent manner.

Activation of hippocampal BDNF signaling is involved in the antidepressant-like effect of the NMDA receptor antagonist 7-chlorokynurenic acid.

Previous studies showed that acute 7-chlorokynurenic acid treatment produced a rapid antidepressant-like action in depression-like animal models. However, the underlying mechanism involved in neurotrophin system about 7-chlorokynurenic acid is unclear. Our present study aimed to verify whether chronic 7-chlorokynurenic acid treatment produced an antidepressant-like effect through the activation of brain-derived neurotrophic factor (BDNF) signaling in mice exposed to chronic unpredictable mild stress (CUMS). In addition, we performed an oral toxicological evaluation of chronic 7-chlorokynurenic acid administration in mice. The results showed that a two-week administration with 7-chlorokynurenic acid reversed the decreased sucrose preference and prolonged first feeding latency. In addition, 7-chlorokynurenic acid significantly reversed the CUMS-induced down-regulation of BDNF, p-ERK, p-Akt, PSD-95, synapsin I and cell proliferation in the hippocampus. In contrast, K252a, an inhibitor of BDNF receptor tropomyosin-related kinase receptor B (TrkB), blocked the antidepressant-like effect and the improvement of 7-chlorokynurenic acid. Furthermore, we found that 7-chlorokynurenic acid did not produce any toxicological effect in mice. In conclusion, our findings suggest that the antidepressant-like effect of 7-chlorokynurenic acid may be mediated, at least in part, by activating BDNF signaling in the hippocampus.

[Postmenopausal osteoporosis and blood stasis].

OBJECTIVE: To investigate whether blood stasis is one of the main causes in the pathogenesis of postmenopausal osteoporosis. METHODS: The clinical manifestation of blood stasis syndrome were comprehensively scored in sixty postmenopausal osteoporosis patients, their vascular endothelial function and platelet activating capacity were also detected, and compared with those in 30 healthy women as control. RESULTS: The molecular indexes as vascular endothelial function and platelet activating capacity, as well as comprehensive scores of clinical manifestation of blood stasis syndrome in postmenopausal osteoporosis patients were significantly different to those of healthy women (P < 0.05, P < 0.01). CONCLUSION: There is objective molecular pathologic change of blood stasis syndrome in postmenopausal osteoporosis. Blood stasis plays an important role in pathogenesis of postmenopausal osteoporosis.