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Objectives: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. Materials and Methods: A conventional ligature‐induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA‐seq) was performed to explore the underlying mechanisms of FoxO1 knockdown‐mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme‐linked immunosorbent assay. Results: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation‐related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA‐seq revealed that the nuclear factor kappa B (NF‐κB) and nucleotide‐binding oligomerization domain‐like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1‐knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. Conclusions: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF‐κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is one of the cancers with the highest mortality rate in China. With the rapid development of high-throughput sequencing technology and the research and application of deep learning methods in recent years, deep neural networks based on gene expression have become a hot research direction in lung cancer diagnosis in recent years, which provide an effective way of early diagnosis for lung cancer. Thus, building a deep neural network model is of great significance for the early diagnosis of lung cancer. However, the main challenges in mining gene expression datasets are the curse of dimensionality and imbalanced data. The existing methods proposed by some researchers can't address the problems of high-dimensionality and imbalanced data, because of the overwhelming number of variables measured (genes) versus the small number of samples, which result in poor performance in early diagnosis for lung cancer. Method: Given the disadvantages of gene expression data sets with small datasets, high-dimensionality and imbalanced data, this paper proposes a gene selection method based on KL divergence, which selects some genes with higher KL divergence as model features. Then build a deep neural network model using Focal Loss as loss function, at the same time, we use k-fold cross validation method to verify and select the best model, we set the value of k is five in this paper. Result: The deep learning model method based on KL divergence gene selection proposed in this paper has an AUC of 0.99 on the validation set. The generalization performance of model is high. Conclusion: The deep neural network model based on KL divergence gene selection proposed in this paper is proved to be an accurate and effective method for lung cancer prediction. [ABSTRACT FROM AUTHOR]

Copyright of Architectural Journal / Jian Zhu Xue Bao is the property of Architectural Journal Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The MYB transcription factor family is one of the largest families of plant transcription factors (TFs), and it plays a vital role in the entire process of a plant's growth and development. Well known in China, Eucommia ulmoides (E. ulmoides) produces a form of natural rubber called Eucommia ulmoides gum (EUG). Nevertheless, there is little research on the evolutionary history and expression patterns of its MYBs, as well as on the regulation of EUG by MYB TFs. This research provides a comprehensive description, classification, and potential functional analysis of the EuMYB gene family. A total of 119 MYB members of E. ulmoides were identified based on the whole genome sequencing data, and their gene structure, phylogenetics, chromosome location, conserved motifs, etc., were analyzed. Based on the phylogenetic tree results, EuMYBs could be divided into 35 sub-groups. In addition, chromosomal localization and collinearity analysis revealed the heterogeneous distribution of the MYB family in the E. ulmoides' genome, indicating the expansion of its gene family. Moreover, promoter cis-acting elements showed that the promoter contained abundant light-responsive elements, anaerobic-induction-responsive elements, and abscisic-acid-responsive elements. A co-expression regulatory network between the EUG biosynthesis genes and the EuMYBs was built. Meanwhile, regarding the six EuMYBs with high expression in the gum-forming tissues selected that correlated with the farnesyl diphosphate synthase (FPS1) structural gene, RT-qPCR experiments showed a possible regulatory relationship between EuMYBs and FPS1, which played an important role in EUG biosynthesis. In conclusion, this paper defines a research gap and lays a foundation for further studies on the biological functions of EuMYBs. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a non-essential, highly phytotoxic metal and damages ramie plant growth and development even at low concentrations. Ramie is one of the most significant crops in China, with excellent fiber quality and immense industrial importance. Planting Cd-tolerant ramie cultivars can prevent yield loss on contaminated soil. Previously, significant efforts have been made to develop Cd tolerance in ramie. However, the Cd tolerance mechanism is still not fully understood; hence, breeding industrial crops is critical to tackling the ongoing challenges. Cd tolerance is a complex genetic mechanism requiring high-level molecular studies to clarify the genes network. Genetic studies have identified several Cd-tolerant genes in ramie, which led to the development of several ramie cultivars suitable to grow on toxic soils; however, due to the continuous rise in Cd toxicity, potent molecular tools are critical in modern-day breeding programs. Genetic engineering, and transcriptome analysis have been used to develop abiotic stress tolerance in ramie, but QTL mapping and clustered regularly interspaced short palindromic repeats (CRISPR) are rarely studied. However, studies are still limited in addressing this issue. This review critically elaborated on using QTL mapping, transcriptomes, transcription factors, CRISPR/Cas9, and genetic engineering to enhance Cd tolerance in ramie. These genes/QTL should be transferred or edited into sensitive cultivars using genetic engineering or CRISPR/Cas9. CRISPR/Cas9 is highly recommended because it provides targeted gene editing in ramie, its use is limited and can address the research gaps, and it would revolutionize the field of agriculture. Limitations, gaps, and future potential are briefly discussed. This review paper presents new clues to help future researchers comprehensively understand Cd tolerance in ramie and develop tolerant cultivars for industrial purposes. [ABSTRACT FROM AUTHOR]

Background and Aims: This study aimed to report nine Charcot–Marie–Tooth disease (CMT) families with six novel IGHMBP2 mutations in our CMT2 cohort and to summarize the genetic and clinical features of all AR‐CMT2S patients reported worldwide. Methods: General information, clinical and neurophysiological data of 275 axonal CMT families were collected. Genetic screening was performed by inherited peripheral neuropathy related genes panel or whole exome sequencing. The published papers reporting AR‐CMT2S from 2014 to 2023 were searched in Pubmed and Wanfang databases. Results: In our CMT2 cohort, we detected 17 AR‐CMT2S families carrying IGHMBP2 mutations and eight were published previously. Among these, c.743 T > A (p.Val248Glu), c.884A > G (p.Asp295Gly), c.1256C > A (p.Ser419*), c.2598_2599delGA (p.Lys868Sfs*16), c.1694_1696delATG (p.Asp565del) and c.2509A > T (p.Arg837*) were firstly reported. These patients prominently presented with early‐onset typical axonal neuropathy and without respiratory dysfunction. So far, 56 AR‐CMT2S patients and 57 different mutations coming from 43 families have been reported in the world. Twenty‐nine of 32 missense mutations were clustered in helicase domain and ATPase region. The age at onset ranged from 0.11to 20 years (Mean ± SD: 3.43 ± 3.88 years) and the majority was infantile‐onset (<2 years). The initial symptoms included weakness of limbs (19, 29.7%), delayed milestones (12, 18.8%), gait disturbance (11, 17.2%), feet deformity (8, 12.5%), feet drop (8, 12.5%), etc. Interpretation: AR‐CMT2S accounted for 6.2% in our CMT2 cohort. We firstly reported six novel IGHMBP2 mutations which expanded the genotypic spectrum of AR‐CMT2S. Furthermore, 17 AR‐CMT2S families could provide more resources for natural history study, drug research and development. [ABSTRACT FROM AUTHOR]

Micromelalopha troglodyta (Graeser) is an important pest of poplar in China, and glutathione S -transferase (GST) is an important detoxifying enzyme in M. troglodyta. In this paper, three full-length GST genes from M. troglodyta were cloned and identified. These GST genes all belonged to the epsilon class (MtGSTe1 , MtGSTe2 , and MtGSTe3). Furthermore, the expression of these three MtGSTe genes in different tissues, including midguts and fat bodies, and the MtGSTe expression in association with different concentrations of tannic acid, including 0.001, 0.01, 0.1, 1, and 10 mg ml−1, were analysed in detail. The results showed that the expression levels of MtGSTe1 , MtGSTe2 , and MtGSTe3 were all the highest in the fourth instar larvae; the expression levels of MtGSTe1 and MtGSTe3 were the highest in fat bodies, while the expression level of MtGSTe2 was the highest in midguts. Furthermore, the expression of MtGSTe mRNA was induced by tannic acid in M. troglodyta. These studies were helpful to clarify the interaction between plant secondary substances and herbivorous insects at a deep level and provided a theoretical foundation for controlling M. troglodyta. [ABSTRACT FROM AUTHOR]

Coloured rice has pigments deposited in the grain pericarp; red rice is the most common type of coloured rice. Red rice is rich in essential nutrients and has been grown and consumed in China for a long time. In this study, we report the genetic characterisation and preliminary molecular mapping of a mutant gene encoding red pericarp in rice (Oryza sativa L.). To analyse the genetic basis of the red pericarp mutant, a reciprocal cross between GER-3 (red pericarp, indica cv.) and 898 (white pericarp, indica cv.) was made. The genetic analysis results confirmed that there was only one dominant gene, temporarily designated Rp (Red pericarp) controlling the segregation of the red pericarp in the F2 population. For the molecular mapping of Rp, an F2 population derived from an inter-subspecific cross between Gene Engineering Rice-3 (GER-3) and C418 (japonica cv., white pericarp) was constructed. The genotype of the pericarp colour of the F2 individuals in the mapping population was validated by progeny testing of the F2:3 families. Simple sequence repeat (SSR) markers and the bulked segregation analysis (BSA) method were used; Rp was mapped to the short arm of chromosome 7 between the SSR markers RM21182 and RM21268, with a genetic distance of 3.5 and 12.0 cM, respectively. In this paper, the potential origin of the red pericarp mutant gene Rp was also discussed. [ABSTRACT FROM AUTHOR]

Purpose: The purpose of this paper is to study the correlation between demographic and clinical factors and warfarin dose of patients in Chinese Han population taking warfarin and study gene polymorphisms impact of related gene loci (CYP2C9*3, VKORC1-1639G > A) on warfarin doses, to establish a model to predict initial standard dose and maintenance dose based on CYP2C9*3, VKORC1-1639G > A genotype. Methods: The study collects the data of patients in our hospital and other subcenters which incorporates 2160 patients to establish the initial dose model and 1698 patients for the stable dose model, and sequences 26 multigene sites in 451 patients. Based on the patient's dosage, clinical data, and demographic characteristics, the genetic and non-genetic effects on the initial dose and stable dose of warfarin are calculated by using statistical methods, and the prediction model of initial standard dose and maintenance dose can be established via multiple linear regression. Results: The initial dose of warfarin (mg/day) was calculated as (1.346 + 0.350 × (VKORC1-1639G > A) − 0.273 × (CYP2C9*3) + 0.245 × (body surface area) − 0.003 × (age) − 0.036 × (amine-iodine) + 0.021 × (sex))2. This model incorporated seven factors and explained 55.3% of the individualization differences of the warfarin drug dose. The maintenance dose of warfarin (mg/day) was calculated as (1.336 + 0.299 × (VKORC1-1639G > A) + 0.480 × (body surface area) − 0.214 × (CYP2C9*3) − 0.074 × (amine-iodine) − 0.003 × (age) − 0.077 × (statins) − 0.002 × (height))2. This model incorporated six factors and explained 42.4% of the individualization differences in the warfarin drug dose. Conclusion: The genetic and non-genetic factors affecting warfarin dose in Chinese Han population were studied systematically in this study. The pharmacogenomic dose prediction model constructed in this study can predict anticoagulant efficacy of warfarin and has potential application value in clinical practice. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via the original article. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the safety of clopidogrel in the patients with acute coronary syndrome (ACS) by meta analysis based on ABCB1 C3435 Tgene polymorphism. Methods: The databases, such as Wanfang Data, the Chinese Biomedical Literature Database (CBM), the Chinese Journal Fulltext Database in China National Knowledge Infrastrusture (CNKI), the China Science and Technology Journal Database (VIP), the Science Citation Index (SCI), PubMed and EMBase, were searched from the inception to December 2019. The quality of the collected literature was evaluated, and then meta analysis was performed on the obtained data by using Stata 14.0. Results: Finally, 13 papers were included and 12 970 patients were enrolled for study. Meta analysis showed that there was no significant difference in the incidence of major adverse cardiac events (MACE) among the subgroups based on ABCB1 C3435 T gene polymorphism (P>0.05) ; in the allele gene model OR = 1.11, 95% CI (0.94, 1.30), in the dominant gene model OR = 1.03, 95% CI (0.82, 1.31) and in the recessive gene model OR = 1.13, 95% CI (0.99, 1.30). In the recessive gene model, there was a significant difference in the incidence of MACE of the patients who received a clopidogrel loading dose of 300 mg (P<0.05) and there was also a significant difference in the incidence of MACE in the European population (P<0.05). And in all MACE, there was a significant difference in the incidence of myocardial infarction (P<0.01). Conclusion: There was no correlation between polymorphism of ABCB1 C3435 T gene and MACE incidence, however correlation could be seen in the incidence of MACE and ABCB1 C3435 T gene polymorphism, when the patients received a clopidogrel loading dose of 300 mg and in the European population. [ABSTRACT FROM AUTHOR]

Mythimna separata is a major agricultural pest with seasonal migrating trait in China. Formation and regulation mechanism of migration behavior has resulted in a large number of fundamental researches involving quantitative studies of gene expression in this species. Using appropriate reference gene is critical in RT-qPCR data normalization. A comprehensive study on the reference genes in M. separata is lacking. In this paper, expression stabilities of ten candidate reference genes were evaluated in M. separata under various biotic and abiotic conditions by employing four different software geNorm, NormFinder, BestKeeper, and the comparative ΔCT method. The comprehensive stabilities ranking of these genes were suggested by RefFinder. PKG as a target gene was employed to justify the number of reference genes in four larval tissues and two photoperiod treatments. Results demonstrate that the first three most stable genes were as follows: EF, CypA, and β-TUB for developmental stages; EF, CypA, and RPL12 for larval tissues; EF, TBP, and β-TUB for adult tissues. RPL12, β-TUB, and EF for densities; EF, RPL12, and GAPDH for photoperiod treatments; β-TUB, EF, and ATPase for temperature treatments. Stable reference gene combinations may reduce bias in normalization. This work provides for the first time a comprehensive list of appropriate reference genes and facilitates future studies on gene function of M. separata. [ABSTRACT FROM AUTHOR]

Escherichia coli (E. coli) is closely associated with the occurrence of puerperal metritis in dairy cows. E. coli carries some the virulence and multi-drug resistant genes, which pose a serious threat to the health of postpartum cows. In this study, E. coli was isolated and identified from the uterine contents of postpartum cows with puerperal metritis in the Ningxia region of China, and its phylogenetic subgroups were determined. Meanwhile, virulence and drug resistance genes carried by E. coli and drug sensitivity were detected, and the characteristics of virulence and drug resistance genes distribution in E. coli phylogroups were further analyzed. The results showed that the isolation rate of E. coli in puerperal metritis samples was 95.2%. E. coli was mainly divided into phylogroups B2 and D, followed by groups A and B1, and was more connected to O157:H7, O169:H4, and ECC-1470 type strains. The virulence genes were mainly dominated by ompF (100%), traT (100%), fimH (97%), papC (96%), csgA (95%), Ang43 (93.9%), and ompC (93%), and the resistance genes were dominated by TEM (99%), tetA (71.7%), aac(3)II (66.7%), and cmlA (53.5%). Additionally, it was observed that the virulence and resistance gene phenotypes could be divided into two subgroups, with subgroup B2 and D having the highest distributions. Drug sensitivity tests also revealed that the E. coli was most sensitive to the fluoroquinolones enrofloxacin, followed by macrolides, aminoglycosides, tetracyclines, β-lactams, peptides and sulfonamides, and least sensitive to lincosamides. These results imply that pathogenic E. coli, which induces puerperal metritis of dairy cows in the Ningxia region of China, primarily belongs to the group B2 and D, contains multiple virulence and drug resistance genes, Moreover, E. coli has evolved resistance to several drugs including penicillin, lincomycin, cotrimoxazole, and streptomycin. It will offer specific guidelines reference for the prevention and treatment of puerperal metritis in dairy cows with E. coli infections in the Ningxia region of China. [ABSTRACT FROM AUTHOR]

Background: The relationship between CDH23 gene variants and NIHL is unclear. This study investigates the association between cadherin 23 (CDH23) gene variants and noise-induced hearing loss (NIHL). Methods: This is a case-control study. Workers who were exposed to noise from a steel factory in North China were recruited and divided into two groups: the case group (both ears' high-frequency threshold average [BHFTA] ≥ 40dB) and the control group (BHFTA ≤ 25 dB). This study used the generalised multifactor dimensionality reduction method to analyse the association among 18 single-nucleotide polymorphisms (SNPs) in CDH23 and NIHL. Logistic regression was performed to investigate the main effects of SNPs and the interactions between cumulative noise exposure (CNE) and SNPs. Furthermore, CNE was adjusted for age, gender, smoking, drinking, physical exercise and hypertension. Results: This study recruited 1,117 participants. The results showed that for rs11592462, participants who carried the GG genotype showed an association with NIHL greater than that of those who carried the CC genotype. Accordingly, genetic variation in the CDH23 gene could play an essential role in determining individual susceptibility to NIHL. Conclusion: Genetic variations in the CDH23 gene may play an important role in determining individual susceptibility to NIHL. These results provide new insight into the pathogenesis and early prevention of NIHL. [ABSTRACT FROM AUTHOR]

The increasing importance of computational techniques in post-genomic life science research calls for new forms and combinations of expertise that cut across established disciplinary boundaries between computing and biology. These are most marked in large scale gene sequencing facilities. Here new ways of organising knowledge production, drawing on industrial models, have been perceived as pursuing efficiency and control to the potential detriment of academic autonomy and scientific quality. We explore how these issues are played out in the case of BGI (Beijing Genomics Institute prior to 2008). BGI (in Pinyin, Hua Da Jiyin– Big China Genome) is today the world's largest centre for gene sequencing research. Semi-detached from traditional academic institutions, BGI has developed distinctive models for organising research and for developing expertise, informed by practices in US Information Technology and Life Science Laboratories, that differ from existing models of interdisciplinary research in academic institutions. [ABSTRACT FROM AUTHOR]

Leaf rust caused by Puccinia triticina Eriks. (Pt) is one of the most devastating fungal pathogens affecting wheat (Triticum aestivum L.) production worldwide. Deployment of resistant cultivars is the most environmentally friendly approach to control the disease. In this study, thirty-seven wheat lines from the Hubei and Shaanxi provinces in China were evaluated for seedling resistance in the greenhouse using eighteen Pt races. These lines were also tested for slow rusting resistance in the field in the 2014 to 2018 growing seasons. Eleven molecular markers closely associated with known Lr genes were used as part of the postulation process. Seven known Lr genes, 1, 13, 18, 14a, 26, 34 and 46 either singly or in combination were postulated in twenty-five cultivars. Lr1 and Lr26 were the most commonly identified genes detected in thirteen and ten cultivars, respectively. Lr13 and Lr46 were each found in four and five cultivars. Lr34 was present in three cultivars. Lr18 and Lr14a were identified in cultivar Xi'nong 538. Six cultivars displayed slow rusting resistance in the field tests. The resistant cultivars identified in the present study can be used as resistance parents in crosses aimed at pyramiding and the deployment of leaf rust resistance genes in China. [ABSTRACT FROM AUTHOR]

Mutations affecting flower shape in many plants have been favored by human selection, and various fruit trees are also grown for ornamental purposes. Mei (Prunus mume) is a dual purpose tree originated in China well known in the Western world for its generous early blooms, often bearing double flowers. Building on the knowledge of its genomic location, a candidate gene approach was used to identify a 49 bp deletion encompassing the miR172 target site of the euAP2 gene pmTOE (PmuVar_Ch1_3490) as a prime variant linked to flower doubleness. Searching within a large dataset of genome sequencing data from Eastern germplasm collections demonstrated a tight variant-trait association, further confirmed in a panel of commercial and non-commercial varieties available in Italy. Moreover, two SNP mutations in the miR172 target site of pmPET (PmuVar_Ch1_1333) were identified in some double flower accessions. The mei orthologue of PETALOSA genes already found responsible for the phenotype in other plants suggests that independent variants may have been selected throughout mei domestication history. [ABSTRACT FROM AUTHOR]

Introduction: Northeast Merino (NMS) is a breed developed in Northeast China during the 1960s for wool and meat production. It exhibits excellent traits such as high wool yield, superior meat quality, rapid growth rate, robust disease resistance, and adaptability to cold climates. However, no studies have used whole-genome sequencing data to investigate the superior traits of NMS. Methods: In this study, we investigated the population structure, genetic diversity, and selection signals of NMS using whole-genome sequencing data from 20 individuals. Two methods (integrated haplotype score and composite likelihood ratio) were used for selection signal analysis, and the Fixation Index was used to explore the selection signals of NMS and the other two breeds, Mongolian sheep and South African meat Merino. Results: The results showed that NMS had low inbreeding levels, high genomic diversity, and a pedigree of both Merino breeds and Chinese local breeds. A total length of 14.09 Mb genomic region containing 287 genes was detected using the two methods. Further exploration of the functions of these genes revealed that they are mainly concentrated in wool production performance (IRF2BP2, MAP3K7, and WNT3), meat production performance (NDUFA9, SETBP1, ZBTB38, and FTO), cold resistance (DNAJC13, LPGAT1, and PRDM16), and immune response (PRDM2, GALNT8, and HCAR2). The selection signals of NMS and the other two breeds annotated 87 and 23 genes, respectively. These genes were also mainly focused on wool and meat production performance. Conclusion: These results provide a basis for further breeding improvement, comprehensive use of this breed, and a reference for research on other breeds. [ABSTRACT FROM AUTHOR]

Introduction: The moth species Athetis lepigone (Moschler) (Lepidoptera: Noctuidae), which has recently been identified as a pest of summer maize (Zea mays L.) in China, has demonstrated a rapid proliferation with in the Huang-Huai-Hai Plain region since its initial discovery in Hebei Province in 2005. It has become a prevalent pest of corn crops, and its ability to adapt quickly to its surroundings is currently being investigated. One of the key characteristics of its siphoning mouthparts is not only the feeding apparatus itself but also the chemosensory organs that enable the detection of chemical signals from the surrounding environment. However, there is a lack of comprehensive research on the genes responsible for chemosensory and metabolic mechanisms in the proboscises of male and female A. lepigone adults. Methods: In this study, we utilized transcriptome analysis to identify a total of fifty chemosensory genes from six distinct families, including 19 odorant-binding proteins (OBPs), 22 chemosensory proteins (CSPs), one co-receptor (Orco), six odorant receptors (ORs), four ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs) in the proboscis. Notably, seven OBPs, two CSPs, and one OR were discovered for the first time. Additionally, fourteen genes related to metabolism, including cytochrome P450 (CYPs) and carboxylesterases (CXEs), were also identified. Furthermore, a qualitative analysis was conducted on the relative transcript levels of eight related genes. The expression of 21 annotated chemosensory and metabolic genes was compared between A. lepigone adults and larvae using qRT-PCR, revealing tissue specificity. The majority of genes exhibited predominant expression in the antennae and proboscis during the adult stage, while showing slight expression in the combination of sixth-instar larval head oral appendages (maxilla, labium, and antenna) and pheromone gland-ovipositors of female adults. Results/discussion: Our study points to a new pest control strategies that these newly discovered genes have the potential to serve as targets for enhancing future pest control, including mating disruption and the use of food attractants. And it would be advantageous to ascertain the distribution of chemosensory gene expression and gain insights into the functionalities of these genes, thereby establishing a novel theoretical framework for the advancement of eco-friendly pesticides and efficient pest management strategies in the future. [ABSTRACT FROM AUTHOR]

Endemic to the southeast boundary of Tibet plateau, the medicinal alpine shrub Caragana kozlowii is a threatened species. The genetic and molecular data about it is insufficient. In this paper, the complete chloroplast (cp) genome sequence of C. kozlowii was sequenced by the Illumina sequencing platform. The result suggests that C. kozlowii cp genome is relatively short because it lacks an Inverted Repeat (IR) region. It was 131,274 bp in length, containing one large and one small single copy region (SSC and LSC) of 85,281 and 18,919 bp separated by an inverted repeat region (IR) of 27,074 bp, respectively. It contains unique 110 genes, including 76 protein-coding genes, 30 tRNAs, and 4 rRNAs. Similar to the other Inverted Repeat-Lacking Clade (IRLC) plastomes, rpl22 and rps16 are absent. The cp genome has 34.5% GC content. Phylogenetic analysis based on ten chloroplast genomes indicates that C. kozlowii is closely related to C. rosea. [ABSTRACT FROM AUTHOR]

Background: Gonococcal antimicrobial resistance is a global problem. Different resistance plasmids have emerged and spread among the isolates of Neisseria gonorrhoeae worldwide and in China. We conducted this study to monitor the plasmid-mediated penicillin and tetracycline resistance among N. gonorrhoeae isolates in Guangzhou from 2002 to 2012.Methods: Consecutive isolates of N. gonorrhoeae were collected from outpatients with gonorrhea attending the STD clinic in Guangdong Provincial Centre for Skin Diseases and STIs Control and Prevention. Penicillinase-producing N. gonorrhoeae (PPNG) isolates were analyzed by the paper acidometric method. Plasmid-mediated resistance to tetracycline in N. gonorrhoeae (TRNG) isolates was screened by the agar plate dilution method. Plasmid types were determined for TRNG and PPNG isolates using polymerase chain reaction (PCR). Minimum inhibitory concentrations (MICs) to penicillin and tetracycline were detected by the agar plate dilution.Results: Of 1378 consecutive N. gonorrhoeae isolates, 429 PPNG and 639 TRNG isolates were identified. The prevalence of PPNG, TRNG, and PPNG/TRNG increased from 18.3 to 47.1 % (χ (2) = 31.57, p < 0.001), from 29.4 to 52.1 % (χ (2) = 16.28, p < 0.001) and from 10.0 to 26.2 % (χ (2) = 10.46, p < 0.001) between 2002 and 2012, respectively. Genotyping of plasmids among PPNGs showed that the majority (93.7 %) of the isolates were the Asian type plasmids, while the African type plasmid emerged in 2008 and rapidly increased to 14.0 % in 2012 (χ (2) = 25.03, p < 0.001). For TRNGs, all 639 isolates carried the Dutch type plasmid. MICs of penicillin G and tetracycline persisted at high levels and the MIC90s were 32-fold higher than the resistant cutoff point over 11 years. The prevalence rates of penicillin- and tetracycline-resistant N. gonorrhoeae varied from 90.9 to 91.1 % and from 88.3 to 89.3 % during 2002 to 2012, respectively.Conclusions: Resistance to penicillin and tetracycline among N. gonorrhoeae isolates remained at high levels in Guangzhou. The Asian type PPNG continued to spread and Dutch type TRNG was still the dominant strain. The African type PPNG has emerged and is spreading rapidly. [ABSTRACT FROM AUTHOR]

Seven isolates of a putative cytorhabdovirus (family Rhabdoviridae, order Mononegavirales) designated as citrus-associated rhabdovirus CiaRV) were identified in citrus, passion fruit. and paper bush from the same geographical area in China. CiaRV, bean-associated cytorhab-dovirus (Brazil), and papaya virus E (Ecuador) should be taxonomically classified in the species Papaya cytorhabdovirus. Due to natural mutations, the glycoprotein (G) and P4 genes were impaired in citrus-infecting isolates of CiaRV, resulting in an atypical rhabdovirus genome organization of 3' leader-N-P-P3-M-L-5' trailer. The P3 protein of CiaRV shared a common origin with begomoviral movement proteins (family Geminiviridae). Secondary structure analysis and trans-complementation movement-deficient tomato mosaic virus and potato virus X mutants by CiaRV P3 supported its function in viral cell-to-cell trafficking. The wide geographical dispersal of CiaRV and related viruses suggests an efficient transmission mechanism, as well as an underlying risk to global agriculture. Both the natural phenomenon and experimental analyses demonstrated presence of the "degraded" type of CiaRV in citrus, in parallel to "undegraded" types in other host plant species. This case study shows a plant virus losing the function of an important but nonessential gene, likely due to host shift and adaption, which deepened our understanding of course of natural viral diversification. [ABSTRACT FROM AUTHOR]

[ Objective] The secondary flowering ( abnormal) of pears is common in southern China. The interaction between environmental factors and plant genetic factors in this process and the key genetic elements remain to be identified. The present paper aimed to identify SPL ( SQUAMOSA promoter- Binding protein like) gens in the genome of Pyrus bretschneideri and studies its expression changes in secondary flower induction. [ Method] In our previous study, we explored the physiological changes of simulating secondary flowering by leaf defoliation and had determined the transcriptomic changes of the process. Based on the existing genomic data of Pyrus bretschneideri Rehd., the SPLencoding gene was identified from the whole genome scale, and the transcriptome data of the secondary flower induction process was combined to mine the candidate genes involved in the process. [ Result] A total of 34 typical SPL protein family members were obtained, and only three members were arranged in tandem on the current pear reference genome. The phylogenetic analysis classified 34 members into 8 evolutionary groups, in consistence with other species 'SPL classifications. Transcriptional analysis of the secondary flowering induction and uninduced materials of 'Hosui' showed that only two of the 34 SPL protein-coding genes were significantly differentially expressed, of which Pbr038289 was significantly up-regulated, while Pbr002303 was significantly decreased. [Conclusion] These two proteins are expected to become important targets for in-depth study of the flowering regulation in pear. [ABSTRACT FROM AUTHOR]

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Copyright of Genetika (0534-0012) is the property of Serbian Genetics Society and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sika deer is one of the best-known and highly valued animals of China. Despite its economic, cultural, and biological importance, there has not been a large-scale sequencing project for Sika deer to date. With the ultimate goal of sequencing the complete genome of this organism, we first established a bone marrow cDNA library for Sika deer and generated a total of 2,025 reads. After processing the sequences, 2,017 high-quality expressed sequence tags (ESTs) were obtained. These ESTs were assembled into 1,157 unigenes, including 238 contigs and 919 singletons. Comparative analyses indicated that 888 (76.75%) of the unigenes had significant matches to sequences in the non-redundant protein database, In addition to highly expressed genes, such as stearoyl-CoA desaturase, cytochrome c oxidase, adipocyte-type fatty acid-binding protein, adiponectin and thymosin beta-4, we also obtained vascular endothelial growth factor-A and heparin-binding growth-associated molecule, both of which are of great importance for angiogenesis research. There were 244 (21.09%) unigenes with no significant match to any sequence in current protein or nucleotide databases, and these sequences may represent genes with unknown function in Sika deer. Open reading frame analysis of the sequences was performed using the getorf program. In addition, the sequences were functionally classified using the gene ontology hierarchy, clusters of orthologous groups of proteins and Kyoto encyclopedia of genes and genomes databases. Analysis of ESTs described in this paper provides an important resource for the transcriptome exploration of Sika deer, and will also facilitate further studies on functional genomics, gene discovery and genome annotation of Sika deer.

For molecular breeding of future apples, wild apple (Malus sieversii), the primary progenitor of domesticated apples, provides abundant genetic diversity and disease-resistance traits. Valsa canker (caused by the fungal pathogen Valsa mali) poses a major threat to wild apple population as well as to cultivated apple production in China. In the present study, we developed an efficient system for screening disease-resistant genes of M. sieversii in response to V. mali. An optimal agrobacterium-mediated transient transformation of M. sieversii was first used to manipulate in situ the expression of candidate genes. After that, the pathogen V. mali was inoculated on transformed leaves and stems, and 3 additional methods for slower disease courses were developed for V. mali inoculation. To identify the resistant genes, a series of experiments were performed including morphological (incidence, lesion area/length, fungal biomass), physiological (H2O2 content, malondialdehyde content), and molecular (Real-time quantitative Polymerase Chain Reaction) approaches. Using the optimized system, we identified two transcription factors with high resistance to V. mali, MsbHLH41 and MsEIL3. Furthermore, 35 and 45 downstream genes of MsbHLH41 and MsEIL3 were identified by screening the V. mali response gene database in M. sieversii, respectively. Overall, these results indicate that the disease-resistant gene screening system has a wide range of applications for identifying resistant genes and exploring their immune regulatory networks. [ABSTRACT FROM AUTHOR]

Corydalis yanhusuo is a medicinal herb in China that has been widely used to treat various kinds of pain. The tuber is the main organ of C. yanhusuo used for medicinal purposes, but changes in related genes during the development of the tuber have rarely been reported. To identify the differentially expressed genes during tuber development, C. yanhusuo full-length transcriptomic sequencing was performed using single-molecule real-time technology, and tubers at three development stages were selected for comparative transcriptome analysis. A total of 90,496 full-length non-chimeric transcripts were obtained, and 19,341 transcripts were annotated in at least one public database. A total of 9221 differentially expressed genes were identified during the swelling process of C. yanhusuo tuber. A Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes associated with a "starch and sucrose metabolism pathway", "phenylpropanoid biosynthesis pathway", "isoquinoline alkaloid biosynthesis pathway", "zeatin biosynthesis pathway", and "brassinosteroid biosynthesis pathway" were predominantly enriched. In addition, the genes involved in cell wall metabolism were potentially associated with tuber swelling. These processes regulated and were involved in C. yanhusuo tuber development. The results provide a foundation for further research on tuber formation in medicinal plants. [ABSTRACT FROM AUTHOR]

Introduction: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a growing threat. It is urgent to investigate the multidrug resistance and high virulence of CRPA to provide a basis for infection control and rational use of antibiotics. Methods: A retrospective study of 56 nonduplicated CRPA isolates was conducted. Results: CRPA mainly came from the intensive care unit (ICU) and was mostly isolated from sputum samples. The carbapenem resistance rates of P. aeruginosa were 21.37% (2016), 10.62, 5.88, 10 and 13.87% from 2016 to 2020, respectively. Carbapenem-resistant enzymes and aminoglycoside-modifying enzyme- encoding genes were detected in all isolates, and extended-spectrum β-lactamase and cephalosporin enzyme-encoding genes were present in 96.43 and 80.38% of isolates, respectively. The detection rate of OprM showed a statistically significant difference (p<0.05) between the ICU and other wards. Genes related to biofilms, membrane channel proteins, I integrons and efflux systems were detected in all isolates, with detection rates greater than 90%. CRPA was strongly virulent, and over 80% of isolates carried hypervirulence-associated genes (exoU, exoS, exoT, and exoY). The drug resistance rates of cefepime and piperacillin/tazobactam showed a statistically significant difference (p<0.05) between strains with exoU (+) and exoU (-) (p<0.05). Notably, out of the 7 individuals who died, 4 had extensively drug-resistant P. aeruginosa (57.14%). Discussion: The detection rates of various resistance and virulence genes were high, and the coexistence phenomenon was serious. In clinical practice, antibiotics should be used reasonably based on different drug resistance genes to ensure the rationality and safety of patient medication. [ABSTRACT FROM AUTHOR]

In this paper, we sequenced the complete mitochondrial genome of the Manis pentadactyla (Pholidota: Manidae), which is considered as an endemic species in China. It is listed as a vulnerable species by the International Union for Conservation of Nature and Natural Resources Red List and also an endangered species in China. The genome is 16,578 bp in size. Its gene arrangement pattern was identical with those of Manis tetradactyla. We compared the mitochondrial genome of M. pentadactyla with that of the M. tetradactyla. Nucleotide sequence similarity between the two whole mitochondrial genomes was 79.30%, and the relatively low similarity seems to indicate that the two species are distinctly separated on the species level. The information on the mitochondrial genome comparison of the two species was discussed in detail in this paper. [ABSTRACT FROM AUTHOR]

The repeated transmission to pigs and humans, and the long-term endemicity in terrestrial poultry of H9N2 viruses in China lend urgency to the study of their ecology and pathogenicity. In the present paper, we reported an H9N2 virus sublineage isolated from chickens in northern China from 2007 to 2009 has high lethality for mice. Phylogenetic analysis of the full genome indicated that six representative H9N2 isolates shared high homology to each other, and they clustered in the same sublineage with other H9N2 viruses isolated recently in northern China. The isolates were double-reassortant viruses containing M genes similar to A/Quail/Hong Kong/G1/97 (H9N2) and the other seven gene segments from A/Chicken/ Shanghai/F/98 (H9N2). These six isolates were capable of replicating in the lungs of infected chickens without producing observable clinical signs of disease or death. However, they were highly lethal to mice with mortality rates as high as 100% (14/14) without prior adaptation. The affected mice exhibited severe respiratory syndromes and diffuse lung injury. The H9N2 viruses could be detected in multiple organs of the infected mice, including hearts, livers, spleens, lungs and kidneys. Our findings demonstrated that H9N2 viruses isolated from the chickens in northern China have established a stable sublineage with enhanced pathogenicity to mice, suggesting that urgent attention will need to be paid to the transmission of H9N2 viruses from chickens to mammals. [ABSTRACT FROM AUTHOR]

Based on both morphological and molecular information, two new euplotid genera Apodiophrys n. g. and Heterodiophrys n. g. are described in the present paper. Apodiophrys n. g. is defined as sculptured Diophryinae with bipartite adoral zone; frontoventral cirri arranged in Diophrys-pattern; marginal cirri located in two clearly separated groups. Heterodiophrys n. g. is recognizable by the combination of Diophrys-like frontoventral cirri and the unique structure of several marginal cirri that are arranged in a long row. The type species for both new genera, Apodiophrys ovalis n. sp. and Heterodiophrys zhui n. sp., collected from southern China sea, are described. The small subunit rRNA (SSU rRNA) gene sequences for both new taxa are determined. Phylogenetic analyses based on these data indicate that Apodiophrys is most closely related to Paradiophrys, which then clusters with Uronychia species. Thus, Apodiophrys–Paradiophrys is separated from other typical Diophrys-like genera in the SSU rRNA gene trees. The new genus Heterodiophrys is basal to the sister group of Diophrys–Diophryopsis, hence belongs to the “core” Diophrys-complex. [ABSTRACT FROM AUTHOR]

It is exciting to witness the birth of behavioral genetics in China at a time when the field of genetics is exploding with new discoveries. We begin by discussing the potential for Chinese researchers to sidestep the false starts of previous genetic research on behavior and to become leaders rather than followers in behavioral genetics research. Using learning abilities and disabilities as an example, the rest of the paper considers ways in which quantitative genetic research can go beyond the nature versus nurture question to ask more interesting questions about genetics and psychology. These include the relationship between the normal and abnormal, longitudinal analyses of stability and change, and multivariate analyses of heterogeneity and homogeneity. The most important way to go beyond the rudimentary question about nature versus nurture is to identify the genes responsible for genetic influence on behavior. We briefly describe our quantitative genetic findings and genome-wide association studies of learning ability from the UK Twins Early Development Study (TEDS). It seems a safe prediction that the fast pace of genetic discoveries will continue and will increasingly affect the field of psychology in China and the rest of the world. [ABSTRACT FROM AUTHOR]

Background: Mutations in the GJB2 gene are the most common cause of nonsyndromic recessive hearing loss in China. In about 6% of Chinese patients with severe to profound sensorineural hearing impairment, only monoallelic GJB2 mutations known to be either recessive or of unclear pathogenicity have been identified. This paper reports the prevalence of the GJB2 IVS1+1G>A mutation in a population of Chinese hearing loss patients with monoallelic pathogenic mutation in the coding region of GJB2. Methods: Two hundred and twelve patients, screened from 7133 cases of nonsyndromic hearing loss in China, with monoallelic mutation (mainly frameshift and nonsense mutation) in the coding region of GJB2 were examined for the GJB2 IVS1+1G>A mutation and mutations in the promoter region of this gene. Two hundred and sixty-two nonsyndromic hearing loss patients without GJB2 mutation and 105 controls with normal hearing were also tested for the GJB2 IVS1+1G>A mutation by sequencing. Results: Four patients with monoallelic mutation in the coding region of GJB2 were found carrying the GJB2 IVS1 +1G>A mutation on the opposite allele. One patient with the GJB2 c.235delC mutation carried one variant, -3175 C>T, in exon 1 of GJB2. Neither GJB2 IVS1+1G>A mutation nor any variant in exon 1 of GJB2 was found in the 262 nonsyndromic hearing loss patients without GJB2 mutation or in the 105 normal hearing controls. Conclusion: Testing for the GJB2 IVS 1+1 G to A mutation explained deafness in 1.89% of Chinese GJB2 monoallelic patients, and it should be included in routine testing of patients with GJB2 monoallelic pathogenic mutation. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the diagnostic value of bronchial lavage P16INK4A promoter methylation and lung cancer.Materials and Methods: The databases of PubMed, Medline, China National Knowledge Infrastructure, and Wanfang were electronically searched by two reviewers to find the suitable studies related to the association between P16INK4A promoter methylation and lung cancer. The P16INK4A promoter methylation rate was extracted from each included individual study. The diagnostic sensitivity, specificity, and area under the receiver operating characteristic ROC curve of bronchial lavage P16INK4Aas a biomarker for diagnosis of lung cancer were pooled by stata 11.0 software (Stata Corporation, College Station, TX, USA).Results: At last, 10 publications were included in this meta-analysis. Of the included 10 studies, five are published in English with relatively high quality and other five papers published in Chinese have relatively low quality. The pooled sensitivity and specificity of bronchial lavage P16INK4A promoter methylation for lung cancer diagnosis were 0.61 (95% confidence interval [CI]: 0.57-0.65) and 0.81 (95% CI: 0.78-0.85), respectively, with random effect model. The ROC curve were calculated and drawn according to Bayes' theorem by stata 11.0 software. The systematic area under the ROC was 0.72 (95% CI: 0.68-0.76), which indicated that the diagnostic value of bronchial lavage P16INK4A promoter methylation for lung cancer was relatively high. Moreover, no significant publication bias was existed in this meta-analysis (t = 0.69, P > 0.05).Conclusion: Bronchial lavage P16INK4A promoter methylation can be a potential biomarker for diagnosis of lung cancer. [ABSTRACT FROM AUTHOR]

China reported the first outbreak of foot-and-mouth disease (FMD) serotype Asia 1 in Chinese Hong Kong in March, 2005. Subsequently, this type of the virus was reported from mainland of China in April 2005. Up to September of 2006, it was detected in more than 15 areas of China. In this paper, the complete genomes of two Chinese isolates, Asia 1/HNK/CHA/05 and Asia 1/JS/CHA/05, of foot-and-mouth disease virus (FMDV) were sequenced and compared with some Chinese sequences and reference sequences from other countries. The identities between Asia 1/HNK/CHA/05 and Asia 1/JS/CHA/05 of 5′-UTR, L gene, P1 (VP1) gene, P2 gene, P3 gene, 3′-UTR are 84.8, 87.6, 86.4 (82.3%), 92.5, 92.8 and 95.3%, respectively. The data revealed that these two strains do not belong to the same genotype depending on the analysis of VP1 sequences, and neither of them have deleted bases in 5′UTR and 3A genes compared with the reference sequences. In addition, the secondary structures of their 5′UTR and 3′UTR are discussed. [ABSTRACT FROM AUTHOR]

Paraisometrum mileense is a unique species of Paraisometrum endemic to south-west China, which is a "100-years-lost" plant and was rediscovered in 2006. In this paper, complete plastid genome of P. mileense is firstly assembled and characterized. The length of total plastid genome is 153,259 bp consisting of a large single-copy region (LSC) of 84,293 bp, a small single-copy region (SSC) of 18,162 bp, and two inverted repeat regions (IRs) of 25,402 bp. In total, 113 genes are predicted, including 80 protein-coding genes (PCGs), four rRNA genes and 29 tRNA genes. Phylogenetic analysis indicated that P. mileense with the other eight Gesneriaceae species formed a clade with a 100% bootstrap support. [ABSTRACT FROM AUTHOR]

The case-only design, which requires only diseased subjects, allows for estimation of multiplicative interactions between factors known to be independent in the study population. The design is being used as an alternative to the case-control design to study gene-environment interactions. Estimates of gene-environment interactions have been shown to be very efficient relative to estimates obtained with a case-control study under the assumption of independence between the genetic and environmental factors. In this paper, the authors explore the robustness of this procedure to uncertainty about the independence assumption. By using simulations, they demonstrate that inferences about the multiplicative interaction with the case-only design can be highly distorted when there is departure from the independence assumption. They illustrate their results with a recent study of gene-environment interactions and risk of lung cancer incidence in a cohort of miners from the Yunnan Tin Corporation in southern China. Investigators should be aware that the increased efficiency of the case-only design is a consequence of a strong assumption and that this design can perform poorly if the assumption is violated. [ABSTRACT FROM PUBLISHER]

Background: China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds. Results: We found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33–40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups. Conclusions: Admixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses. [ABSTRACT FROM AUTHOR]

Salinity stress is a great threat to the growth and productivity of crops, and development of salt-tolerant crops is of great necessity to ensure food security. Although a few genes with natural variations that confer salt tolerance at germination and seedling stage in rice have been cloned, effective intragenic markers for these genes are awaited to be developed, which hinder the use of these genes in genetic improvement of salt tolerance in rice. In this study, we first performed haplotype analysis of five rice salt-tolerant-related genes using 38 rice accessions with reference genome and 4,726 rice germplasm accessions with imputed genotypes and classified main haplotype groups and haplotypes. Subsequently, we identified unique variations for elite haplotypes reported in previous studies and developed 11 effective intragenic makers. Finally, we conducted genotyping of 533 of the 4,726 rice accessions from worldwide and 70 approved temperate geng/japonica cultivars in China using the developed markers. These results could provide effective donors and markers of salt-tolerant-related genes and thus could be of great use in genetic improvement of salt tolerance in rice. [ABSTRACT FROM AUTHOR]

With the extensive production and use of antibiotics for medicinal and veterinary purposes, antibiotics and genes that code for antibiotic resistance are now present in various environmental media with higher frequencies of occurrence and at higher concentrations than before. Particularly, China has led the world in the production and consumption of antibiotics, which might lead to higher pollution levels of antibiotic resistance genes and pose a threat to human health. Here, we review the sources of antibiotic resistance genes in China, and their spatial distribution and pollution levels in surface water, e.g., in lakes and rivers, atmosphere, and soil. Statistics indicate that higher levels of antibiotics and related antibiotic resistance genes were detected in eastern China compared with other regions, and that tetracycline and sulfanilamide resistance genes are the most prevalent. The absolute concentrations of antibiotic resistance genes are 102 − 105 copies per milliliter of water, 104–108 copies per gram of soil, and 104–106 copies per cubic meter of atmosphere. We also analyze the pollution status and fate of antibiotic resistance genes in wastewater treatment processes. Then, the biological and abiotic factors affecting the transfer and distribution of antibiotic resistance genes are elucidated. We discuss the risks of antibiotic resistance genes for ecological safety and human health. [ABSTRACT FROM AUTHOR]

Objectives of this study are to determine the differences in clonality, virulence gene (VG) content and phylogenetic group between non extended-spectrum beta-lactamase-producing E. coli (non-ESBL-EC) and ESBL-EC isolates from urine.Patients and Methods: This study characterized a total of 100 clinical E. coli isolates consecutively obtained from the inpatients hospitalized in The First Affiliated Hospital of Ningbo University in China by polymerase-chain reaction (PCR).Results: Phylogenetic group B2 was found to be the most prevalent in both ESBL-EC and non-ESBL-EC group. Among 100 clinical isolates, the count of acquired virulence genes in group B2 was found to be significantly higher than that in group A, B1, and D (p < 0.001). Additionally, the presence of content within virulence genes (the total number of virulence genes detected per isolate) in B2 of non-ESBL-EC and ESBL-EC showed a significant difference (p< 0.001). ST131 was detected exclusively in ESBL-EC, while ST95 and ST73 were the main sequence types in non-ESBL-EC.Conclusion: Our study demonstrated the different distribution of MLST, phylogenetic group in ESBL-EC and non-ESBL-EC group. The inverse association between beta-lactamase resistance and VG content performed in this study should get a lot more attention. At the same time, we should also be wary of the appearance of non-ESBL-EC isolates of group B2 harboring more virulence genes which will lead to high pathogenicity. [ABSTRACT FROM AUTHOR]

Rice, a major food crop in China, contributes significantly to international food stability. Advances in rice genome sequencing, bioinformatics, and transgenic techniques have catalyzed Chinese researchers' discovery of novel genes that control rice yield. These breakthroughs in research also encompass the analysis of genetic regulatory networks and the establishment of a new framework for molecular design breeding, leading to numerous transformative findings in this field. In this review, some breakthroughs in rice yield traits and a series of achievements in molecular design breeding in China in recent years are presented; the identification and cloning of functional genes related to yield traits and the development of molecular markers of rice functional genes are summarized, with the intention of playing a reference role in the following molecular design breeding work and how to further improve rice yield. [ABSTRACT FROM AUTHOR]

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990–2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept. [Display omitted] • Antibiotic resistant bacteria (ARB) are major public health concerns globally. • The diversity and distribution of antibiotic resistance genes (ARGs) are presented. • Factors that affect ARB and ARGs in different environments are discussed. • Different 'omics' tools used to study resistome development are also presented. [ABSTRACT FROM AUTHOR]

In the secondary constriction region of the short arm of human group D and group G acrocentric chromosomes there are tandemly repeated sequences of transcriptable segments and non-transcriptable spacers of rRNA genes. In the non-transcriptable spacer segments there is a polymorphic region with length variation. This paper reports the results obtained when the BamHI digested products of genomic DNA from 36 cases of Han nationality and those from 40 cases of Yi nationality were probed with a cDNA subprobe, pA(BE), which corresponds to the downstream one third of the 28S rRNA gene and is 1.6kb long with BamHI and EcoRI restriction sites at its two terminal respectively, using Southern blotting and molecular hybridization techniques. A total of 10 different restriction fragments were detected. Four fragments (7.9, 4.9, 4.0 and 1.2 kb) were seen in all subjects tested and the frequencies of six other polymorphic fragments in Hans and Yis (10.0, 9.4, 8.5, 6.7 6.0 and 3.0 kb) showed no significant difference when compared to each other. From the 10 different patterns of combination of restriction fragments four of them (1HY, 2HY, 3HY and 4HY) were detected in both Hans and Yis with no significant difference between their respective frequencies. Four other patterns (5H, 6H, 7H and 8H) were only seen in Hans with individual frequencies not high enough to be statistically significant. However, the statistical test for the combined frequencies of these four patterns showed highly significant difference between Hans and Yis (P < 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)

Simple Summary: The purpose of this paper was to determine which genes in Aquatica leii, an endemic Chinese firefly, are suitable for use as reference genes in future RT-qPCR studies. This is the first example of an effective knockdown in fireflies and an important methodological advance for continuing research in A. leii. The results of this study will help improve accuracy and reliability to normalize RT-qPCR data in A. leii for further molecular analysis. Since luciferase is very abundant in the adult light organ of fireflies generally, this is an encouraging result and of interest not just for A. leii researchers but other researchers who plan to perform RNAi or RT-qPCR in fireflies, or other nonmodel insects, as well. Aquatica leii Fu and Ballantyne is a species of rare aquatic firefly and endemic in China. It is considered good material to study the molecular mechanism of sexual flash communication systems. To improve conservation and behavioral research strategies, large-scale genetic studies involving gene-expression analysis are required and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the most commonly used method. However, there have been very few reports on appropriate reference genes in any species of firefly. Here, we evaluated eight widely utilized reference genes including 18S, Actin, Reep5, Odc1, Tub, Gapdh, Ef1a and S27Ae for their expression stabilities in A. leii under three different conditions, i.e., life stage, tissue and dsRNA injection. Based on the gene stability ranking calculated by RefFinder, which integrates four algorithms (geNorm, delta Ct method, NormFinder, and BestKeeper), we recommend S27Ae and Reep5 as the most appropriate reference genes for molecular studies in different life stages; Ef1a and Odc1 for different tissues; Tub and Odc1 for RNAi studies. The most appropriate reference genes in all treatments are S27Ae and Tub. The results of this study will help improve accuracy and reliability to normalize RT-qPCR data in A. leii for further molecular analysis. [ABSTRACT FROM AUTHOR]

The Formosania is only distributed in a narrow area in Southeast China, and differentiation of the species of this genus may be helpful in understanding the formation process of the water system on both sides of the Taiwan Strait. The complete mitochondrial genome of Formosania chenyiyui is sequenced in this paper. The results show that the full length of the complete mitochondrial genome is 16,572 bp, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Overall base composition is 30.35% A, 26.68% T, 15.86% G, and 27.11% C. The result of phylogenetic analysis suggests that F. chenyiyui is close to that of F. lacustre and Vanmanenia stenosoma, and accords with the evolutionary viewpoint of Formosaniini group based on morphological characteristics. [ABSTRACT FROM AUTHOR]

Drought is one of the major abiotic stresses seriously affecting cotton yield. At present, the main cotton-producing areas in China are primarily arid and semiarid regions. Therefore, the identification of molecular markers and genes associated with cotton yield traits under drought conditions is of great importance for stabilize cotton yield under such conditions. In this study, resequencing data were used to conduct a genome-wide association study (GWAS) on 8 traits of 150 cotton germplasms. Under drought stress, 18 SNPs were significantly correlated with yield traits (single-boll weight (SBW) and seed (SC)), and 8 SNPs were identified as significantly correlated with effective fruit shoot number (EFBN) traits (a trait that is positively correlated with yield). Finally, a total of 15 candidate genes were screened. The combined results of the GWAS and transcriptome data analysis showed that four genes were highly expressed after drought stress, and these genes had significantly increased expression at 10, 15 and 25 DPA of fiber development. qRT-PCR was performed on two samples with drought tolerance extremes (drought-resistant Xinluzao 45 and droughtsensitive Xinluzao 26), revealing that three of the genes had the same differential expression pattern. This study provides a theoretical basis for the genetic analysis of cotton yield traits under drought stress, and provides gene resources for improved breeding of cotton yield traits under drought stress. [ABSTRACT FROM AUTHOR]