Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation.

BACKGROUND: Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS: In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS: The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.

Impact of overexpressing NADH kinase on glucoamylase production in Aspergillus niger.

Glucoamylase has a wide range of applications in the production of glucose, antibiotics, amino acids, and other fermentation industries. Fungal glucoamylase, in particular, has attracted much attention because of its wide application in different industries, among which Aspergillus niger is the most popular strain producing glucoamylase. The low availability of NADPH was found to be one of the limiting factors for the overproduction of glucoamylase. In this study, 3 NADH kinases (AN03, AN14, and AN17) and malic enzyme (maeA) were overexpressed in aconidial A. niger by CRISPR/Cas9 technology, significantly increasing the size of the NADPH pool, resulting in the activity of glucoamylase was improved by about 70%, 50%, 90%, and 70%, respectively; the total secreted protein was increased by about 25%, 22%, 52%, and 26%, respectively. Furthermore, the combination of the mitochondrial NADH kinase (AN17) and the malic enzyme (maeA) increased glucoamylase activity by a further 19%. This study provided an effective strategy for enhancing glucoamylase production of A. niger.

A Special Phenotype of Aconidial Aspergillus niger SH2 and Its Mechanism of Formation via CRISPRi.

The complex morphological structure of Aspergillus niger influences its production of proteins, metabolites, etc., making the genetic manipulation and clonal purification of this species increasingly difficult, especially in aconidial Aspergillus niger. In this study, we found that N-acetyl-D-glucosamine (GlcNAc) could induce the formation of spore-like propagules in the aconidial Aspergillus niger SH2 strain. The spore-like propagules possessed life activities such as drug resistance, genetic transformation, and germination. Transcriptomic analysis indicated that the spore-like propagules were resting conidia entering dormancy and becoming more tolerant to environmental stresses. The Dac1 gene and the metabolic pathway of GlcNAc converted to glycolysis are related to the formation of the spore-like propagules, as evidenced by the CRISPRi system, qPCR, and semi-quantitative RT-PCR. Moreover, a method based on the CRISPR-Cas9 tool to rapidly recycle screening tags and recover genes was suitable for Aspergillus niger SH2. To sum up, this suggests that the spore-like propagules are resting conidia and the mechanism of their formation is the metabolic pathway of GlcNAc converted to glycolysis, particularly the Dac1 gene. This study can improve our understanding of the critical factors involved in mechanisms of phenotypic change and provides a good model for researching phenotypic change in filamentous fungi.

[Interaction between exposure to environmental smoke and the family history of chronic bronchitis (CB) on the risk of CB in rural females in Liuyang city, Hunan province].

OBJECTIVE: To explore the relationships and interaction among the exposure to environmental smoke, family history of chronic bronchitis (CB) and CB, in rural women. METHODS: A population-based case-control study chi(2) was used to analyze the relationship between environmental smoke exposure, CB family history and CB. Additive effects model was used to analyze the interaction. RESULTS: In the first stage, 157 CB patients were screened from 24 268 women residents (prevalence rate is 6.47 per thousand), then 92 patients (case group) and 114 healthy women (control group) were investigated in the second stage. Results showed that: coal/firewood for heating (OR = 36.21) and CB family history (OR = 6.41) might serve as the risk factors of CB in rural women (P < 0.05). Factors as frequent cooking and using coal/firewood for heating had a positive interaction with family history of CB in rural women, CB with S as 5.39 and 9.02, attributable proportions of interaction (API) as 72% and 88%, relative excess risk of interaction (RERI) as 6.50 and 225.99, respectively. CONCLUSION: Using coal/firewood for heating and CB family history might be the risk factors of CB for rural women. A positive interaction between cooking frequently, heating model and CB family history was also seen.

[Study on risk factors and predictive model for lumbar intervertebral disc herniation in the rural population].

OBJECTIVE: To explore the risk factors on the symptoms of lumbar intervertebral disc herniation so as to develop a predictive model for the disease. METHODS: With a population-based case-control study, 303 of 50 123 residents were diagnosed as having lumbar intervertebral disc herniation symptoms. 152 cases and 167 healthy controls, matched by gender and age, were randomly chosen as case and control groups. Questionnaires were used to collect information on the exposure to risk factors and logistic predictive model was then established. RESULTS: Through non-conditional logistic regression analysis, data showed that the positive family history of lumbar vertebra disorder, lumbar treatment or surgery, mental stress, acute low back injury, permanent work pose, and body mass index >/= 23.0 kg/m(2) were the risk factors among residents from the countryside. The area under the receiver operator characteristic curve of logistic predictive model was 0.809. When 0.4 was set as the classification cutoff, the total predictive correct rate, sensitivity, and specificity were 74.0%, 73.7%, and 74.3% respectively. CONCLUSION: The occurrence of lumbar disk herniation can in countryside population was affected by multi-variables including genetic and environmental, and could be predicted with the logistic regression model established by our group. The positive predictive results could be used to alarm the patients and doctors for prevention and treatment of the disease.