Investigation of bedaquiline resistance and genetic mutations in multi-drug resistant Mycobacterium tuberculosis clinical isolates in Chongqing, China.

BACKGROUND: To investigate the prevalence and molecular characterization of bedaquiline resistance among MDR-TB isolates collected from Chongqing, China. METHODS: A total of 205 MDR-TB isolates were collected from Chongqing Tuberculosis Control Institute between March 2019 and June 2020. The MICs of BDQ were determined by microplate alamarblue assay. All strains were genotyped by melting curve spoligotyping, and were subjected to WGS. RESULTS: Among the 205 MDR isolates, the resistance rate of BDQ was 4.4% (9/205). The 55 (26.8%) were from male patients and 50 (24.4%) were new cases. Furthermore, 81 (39.5%) of these patients exhibited lung cavitation, 13 (6.3%) patients afflicted with diabetes mellitus, and 170 (82.9%) isolates belonged to Beijing family. However, the distribution of BDQ resistant isolates showed no significant difference among these characteristics. Of the 86 OFX resistant isolates, 8 isolates were XDR (9.3%, 8/86). Six BDQ resistant isolates (66.7%, 6/9) and two BDQ susceptible isolates (1.0%, 2/196) carried mutations in Rv0678. A total of 4 mutations types were identified in BDQ resistant isolates, including mutation in A152G (50%, 3/6), T56C (16.7%, 1/6), GA492 insertion (16.7%, 1/6), and A274 insertion (16.7%, 1/6). BDQ showed excellent activity against MDR-TB in Chongqing. CONCLUSIONS: BDQ showed excellent activity against MDR-TB in Chongqing. The resistance rate of BDQ was not related to demographic and clinical characteristics. Mutations in Rv0678 gene were the major mechanism to BDQ resistance, with A152G as the most common mutation type. WGS has a good popularize value and application prospect in the rapid detection of BDQ resistance.

Transcutaneous auricular vagal nerve stimulation releases extrapineal melatonin and reduces thermal hypersensitivity in Zucker diabetic fatty rats.

Type 2 diabetes (T2D) is the most common comorbidity of COVID-19, and both are related to the lack of circulating melatonin. In addition, chronic pain is a common sequela of both COVID-19 and T2D. Using a neuropathic pain model produced by sciatic nerve chronic constriction injury in Zucker diabetic fatty rats, a verified preclinical genetic T2D neuropathy animal model, this study aimed to show that transcutaneous auricular vagal nerve stimulation (taVNS) could elevate plasma melatonin concentration, upregulate the expression of melatonin receptors (MTRs) in the amygdala, and relieve peripheral neuropathic pain. Furthermore, taVNS would restore melatonin levels and relieve pain even in pinealectomized rats. On the contrary, intraperitoneally injected luzindole, a melatonin receptor antagonist, would attenuate the antinociceptive effects of taVNS. In conclusion, the mechanism of the therapeutic effect of taVNS on chronic pain involves the release of extrapineal melatonin and the positive regulation of the expression of central MTRs. This beneficial efficacy should be considered during COVID-19 rehabilitation in individuals with diabetes.

A two-transcript biomarker of host classifier genes for discrimination of bacterial from viral infection in acute febrile illness: a multicentre discovery and validation study.

BACKGROUND: Acute febrile illness is one of the main reasons for outpatient hospital visits worldwide. However, differential diagnosis between bacterial and viral causes is challenging and misdiagnosis can result in antimicrobial overuse and hinder prompt treatment. We aimed to build and validate a diagnostic model to discriminate bacterial from viral infection in acute febrile illness by evaluating the expression of potential classifier host genes. METHODS: In this multicentre discovery and validation study, we included patients aged 14-85 years with acute febrile illness (fever for ≤14 days, axillary temperature of ≥38°C, and confirmed bacterial infection, viral infection, or non-infectious inflammatory disease), and healthy control participants (no significant medical history and no fever within the past 90 days) from four hospitals in Shandong province, China. Patients from the first hospital were divided into the screening, discovery, and internal validation groups, and patients from the three other hospitals comprised the external validation group. We measured expression of candidate genes in peripheral blood by RT-PCR, and patients for whom a successful RT-PCT result was recorded were included in the next-step analysis. For patients from the first hospital, those enrolled during the early phase of the study were assigned to the screening group, which was used to identify the optimal transcripts (IFI44L and PI3) for discrimination between bacterial and viral infections by screening four candidate genes (FAM89A, IFI44L, PI3, and ITGB2) by RT-PCR. The remaining patients were then randomly assigned (1:1) to discovery and internal validation groups by time of admission and blood drawing via the equidistant random sampling method. A logistic regression model integrating the mRNA levels of IFI44L and PI3 was built by use of the discovery group, and the diagnostic performance of the model was evaluated in the internal and external validation groups using area under the receiver operating curve (AUC), sensitivity, and specificity. FINDINGS: Between March 1, 2018, and Aug 31, 2019, we assessed 1658 individuals for inclusion in the study. After exclusion of ineligible participants, 458 participants were enrolled (178 patients with acute febrile illness caused by bacterial infection, 212 with acute febrile illness caused by viral infection, 38 with non-infectious inflammatory diseases, and 30 healthy controls). The 390 patients with bacterial or viral infections were assigned to one of four groups: screening (n=64, 33 with bacterial infections and 31 with viral infections), discovery (n=124, 55 with bacterial infections and 69 with viral infections), internal validation (n=124, 55 with bacterial infections and 69 with viral infections), and external validation (n=78, 35 with bacterial infections and 43 with viral infections). Of the four candidate host genes (FAM89A, IFI44L, PI3, and ITGB2), IFI44L and PI3 showed the most discriminative expression pattern and were used to build the logistic regression model. We established the optimal cutoff of the bacterial infection likelihood score to be 0·547598. With the diagnostic result from the gold standard tests (culture and PCR) as the reference, the two-transcript classifier model had an AUC of 0·969 (95% CI 0·937-1·000), sensitivity of 0·891 (0·782-0·949), and specificity of 0·971 (0·900-0·992) to discriminate bacterial and viral infections in the internal validation group. The model showed similar results in the external validation group (AUC 0·986, 95% CI 0·968-1·000; sensitivity 0·857, 0·706-0·937; and specificity 0·954, 0·845-0·987). INTERPRETATION: IFI44L and PI3 transcripts, measured by RT-PCR, are robust classifiers to discriminate bacterial from viral infection in acute febrile illness. This two-transcript biomarker has the potential to be transformed into a commercial panel and applied universally. FUNDING: None.

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population.

BACKGROUND: The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk outer covering the ear. Although several quantitative trait loci (QTL) underlying husk morphology variation have been reported, the genetic basis of husk traits between teosinte and maize remains unclear. RESULTS: A linkage population including 191 BC2F8 inbred lines generated from the maize line Mo17 and the teosinte line X26-4 was used to identify QTL associated with three husk traits: i.e., husk length (HL), husk width (HW) and the number of husk layers (HN). The best linear unbiased predictor (BLUP) depicted wide phenotypic variation and high heritability of all three traits. The HL exhibited greater correlation with HW than HN. A total of 4 QTLs were identified including 1, 1, 2, which are associated with HL, HW and HN, respectively. The proportion of phenotypic variation explained by these QTLs was 9.6, 8.9 and 8.1% for HL, HN and HW, respectively. CONCLUSIONS: The QTLs identified in this study will pave a path to explore candidate genes regulating husk growth and development, and benefit the molecular breeding program based on molecular marker-assisted selection to cultivate maize varieties with an ideal husk morphology.

Detection of QTNs for kernel moisture concentration and kernel dehydration rate before physiological maturity in maize using multi-locus GWAS.

Maize is China's largest grain crop. Mechanical grain harvesting is the key technology in maize production, and the kernel moisture concentration (KMC) is the main controlling factor in mechanical maize harvesting in China. The kernel dehydration rate (KDR) is closely related to the KMC. Thus, it is important to conduct genome-wide association studies (GWAS) of the KMC and KDR in maize, detect relevant quantitative trait nucleotides (QTNs), and mine relevant candidate genes. Here, 132 maize inbred lines were used to measure the KMC every 5 days from 10 to 40 days after pollination (DAP) in order to calculate the KDR. These lines were genotyped using a maize 55K single-nucleotide polymorphism array. QTNs for the KMC and KDR were detected based on five methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, and ISIS EM-BLASSO) in the package mrMLM. A total of 334 significant QTNs were found for both the KMC and KDR, including 175 QTNs unique to the KMC and 178 QTNs unique to the KDR; 116 and 58 QTNs were detected among the 334 QTNs by two and more than two methods, respectively; and 9 and 5 QTNs among 58 QTNs were detected in 2 and 3 years, respectively. A significant enrichment in cellular component was revealed by Gene Ontology enrichment analysis of candidate genes in the intervals adjacent to the 14 QTNs and this category contained five genes. The information provided in this study may be useful for further mining of genes associated with the KMC and KDR in maize.

Genotyping and Molecular Characterization of Fluoroquinolone's Resistance Among Multidrug-Resistant Mycobacterium tuberculosis in Southwest of China.

Although fluoroquinolones (FQs) are the backbone drugs for the treatment of multidrug-resistant tuberculosis (MDR-TB), the knowledge about the resistance pattern and molecular characterization of new-generation FQs in Chongqing is limited. This study aimed to investigate the resistance rate and mutation types of later-generation FQs against MDR-TB in Chongqing, and further to explore the relationship between different genotypes and phenotypes. A total of 967 clinical strains were characterized using multilocus sequence typing and drug susceptibility testing, followed by analysis of genotype/phenotype association. The 229 (23.7%, 229/967) isolates were identified as MDR-TB. The most effective agent against MDR-TB was gatifloxacin (GFX) (20.1%, 46/229), and the highest resistant rate was observed in ofloxacin (OFX) (41.0%, 94/229). Of the 190 strains (83.0%) identified as Beijing genotype, 111 isolates were modern Beijing genotype (58.4%) and 79 isolates were ancient Beijing genotype (41.6%). By analyzing 94 OFX-resistant isolates, 13 isolates were clustered with the cumulative clustering rate of 13.8% (13/94). Of the 91 isolates (39.7%, 91/229) with a mutation in gyrA gene, mutation in codon 94 was the most prevalent. Only 15 isolates (6.6%, 15/229) harbored a mutation in gyrB gene. There was no significant difference in the mutation rate of gyrA gene between Beijing and non-Beijing genotype, clustered isolates, and nonclustered isolates (p > 0.05).

QTL mapping and GWAS for field kernel water content and kernel dehydration rate before physiological maturity in maize.

Kernel water content (KWC) and kernel dehydration rate (KDR) are two main factors affecting maize seed quality and have a decisive influence on the mechanical harvest. It is of great importance to map and mine candidate genes related to KWCs and KDRs before physiological maturity in maize. 120 double-haploid (DH) lines constructed from Si287 with low KWC and JiA512 with high KWC were used as the mapping population. KWCs were measured every 5 days from 10 to 40 days after pollination, and KDRs were calculated. A total of 1702 SNP markers were used to construct a linkage map, with a total length of 1,309.02 cM and an average map distance of 0.77 cM. 10 quantitative trait loci (QTLs) and 27 quantitative trait nucleotides (QTNs) were detected by genome-wide composite interval mapping (GCIM) and multi-locus random-SNP-effect mixed linear model (mrMLM), respectively. One and two QTL hotspot regions were found on Chromosome 3 and 7, respectively. Analysis of the Gene Ontology showed that 2 GO terms of biological processes (BP) were significantly enriched (P ≤ 0.05) and 6 candidate genes were obtained. This study provides theoretical support for marker-assisted breeding of mechanical harvest variety in maize.

Noise Enhanced Signal Detection of Variable Detectors under Certain Constraints.

In this paper, a noise enhanced binary hypothesis-testing problem was studied for a variable detector under certain constraints in which the detection probability can be increased and the false-alarm probability can be decreased simultaneously. According to the constraints, three alternative cases are proposed, the first two cases concerned minimization of the false-alarm probability and maximization of the detection probability without deterioration of one by the other, respectively, and the third case was achieved by a randomization of two optimal noise enhanced solutions obtained in the first two limit cases. Furthermore, the noise enhanced solutions that satisfy the three cases were determined whether randomization between different detectors was allowed or not. In addition, the practicality of the third case was proven from the perspective of Bayes risk. Finally, numerous examples and conclusions are presented.

Generation and characterization of caprine chymosin in corn seed.

Chymosin is widely used in the dairy industry, and much is produced through recombinant DNA in organisms such as bacteria and tobacco. In this study, we used a new transgenic method to express caprine chymosin in corn seeds with lower cost and better storage capability. The recombinant chymosin protein was successfully expressed at an average level of 0.37 mg/g dry weight, which is 0.27% of the total soluble protein in the corn seed. Prochymosin can be activated to produce a chymosin protein with the ability to induce clotting in milk, similar to the commercial protein. The activity of the purified recombinant chymosin was as high as 178.5 U/mg. These results indicate that we have successfully established a technology for generating corn seed-derived caprine chymosin for potential use in the dairy industry.

Crossover replantation after bilateral traumatic lower limb amputations: a case report.

INTRODUCTION: Replantation of a limb to the contralateral stump after bilateral traumatic amputations is rare. To the best of our knowledge, there are only a few reports of crossover lower limb replantation in the literature. CASE PRESENTATION: We treated a 37-year-old Chinese woman with bilateral lower limb crush injuries sustained in a traffic accident. Her lower limb injuries were at different anatomic levels. We performed emergency bilateral amputations followed by crossover replantation. Five years later, the woman had recovered well, and had perfect movement and stability in her replanted leg. After reviewing the literature, we thought that presentation of our patient's case might provide useful information for clinicians. CONCLUSIONS: Crossover replantation should be considered when evaluating a patient with bilateral lower limb injuries, thus allowing the patient to touch the ground and stand using their own foot.

[One family investigation and risk factors analysis of developmental dysplasia of the hip].

OBJECTIVE: To investigate the clinical manifestations and risk factors of the patients from developmental dysplasia of the hip(DDH) family. METHODS: Detailed epidemiology investigation, physical examination, functional movement assessment, lab test and X-ray examination were applied to the whole members of a DDH family. RESULTS: In the family with 9 generations and 218 persons, the incidence of DDH was 31.03% in 145 survivors. Patients mainly manifested bilateral knee and hip joint pain, flexion contracture of hip, limitation in internal and external rotation of hip; a few had arthritic functional disorder, deformation, and limp. The radiography illustrated shallow acetabulum with increased inclination, which encompassed the femoral head badly. Deformation of the femoral head, narrow joint space and osteophyte were also found by X-ray examination. The main risk factors of DDH were genetic factors, gender, birth season etc. The son or daughter with one or two DDH parents had a higher risk for developing DDH than those with no DDH parents. Furthermore, first-degree relatives of the DDH patients also had a greater chance to develop DDH than second-degree relatives and third-degree relatives. The incidence among females was higher than males, and the family member who was given birth in winter had a highest risk for developing DDH. However, there was no difference between incidence of DDH in children and youths and in adults; the incidence of DDH in the immigrants with no blood relationship also did not differ from the incidence of DDH in the family member. CONCLUSION: The genetic factors play an important role in the development of DDH, so do the environmental factors.

Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes.

MOTIVATION: For the purpose of identifying evolutionary reticulation events in flowering plants, we determine a large number of paired, conserved DNA oligomers that may be used as primers to amplify orthologous DNA regions using the polymerase chain reaction (PCR). RESULTS: We develop an initial candidate set by comparing the Arabidopsis and rice genomes using MoBIoS (Molecular Biological Information System). MoBIoS is a metric-space database management system targeting life science data. Through the use of metric-space indexing techniques, two genomes can be compared in O(mlog n), where m and n are the lengths of the genomes, versus O(mn) for BLAST-based analysis. The filtering of low-complexity regions may also be accomplished by directly assessing the uniqueness of the region. We describe mSQL, a SQL extension being developed for MoBIoS that encapsulates the algorithmic details in a common database programming language, shielding end-users from esoteric programming. AVAILABILITY: Available upon request from authors.