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BackgroundWHIM syndrome is a rare, autosomal dominant inborn error of immunity characterized by warts, hypogammaglobulinemia, infection, and myelokathexis. It is caused mainly by heterozygous mutations at the C-terminus of the C-X-C chemokine receptor type 4 (CXCR4) gene.MethodsWe described the detailed clinical, genetic, immunological and treatment characteristic of four WHIM patients from a single Chinese family.ResultsHere, we report four patients from a family carrying a variant of CXCR4 (c.1016_1017dupCT), which introduces a frameshift at codon V340, resulting in an extension of 14 amino acids (p.V340L fs*27). We provide and in-depth analysis of their clinical, genetic, immunological and treatment characteristic, noting that these patients exhibited an atypical clinical phenotype when compared to reported CXCR4R334X patients. Additionally, the frameshift variant CXCR4V340fs led to impaired receptor downregulation in patients’ PBMCs, and in HEK293T cells transfected with the variant plasmids.ConclusionsOur study provided detailed clinical features of four CXCR4V340fs WHIM patients from one Chinese family who presented atypical phenotype and enrich the spectrum of WHIM syndrome.

Background and purposeThe systemic immune-inflammation index (SII) is a novel immune inflammatory marker which has been proven to have excellent predictive value for many diseases. The aim of this study was to investigate the predictive value of SII at different time points after admission for functional outcome at discharge in patients with intracerebral hemorrhage (ICH).MethodsThe clinical data of patients with ICH who were treated at a medical center for neurological diseases in China between October 2012 and April 2022 were analyzed in this retrospective study. The SII was calculated based on neutrophil×platelet/lymphocyte counts and collected within the first 14 days after admission to analyze the dynamic changes. Adverse outcome was defined as a modified Rankin Scale (mRS) score of 4–6 at discharge. The correlation between the SII and the outcome was assessed using univariate and multivariate logistic regression analyses. The ability of SII to predict outcome was evaluated by the area under the receiver operating characteristic (ROC) curve (AUC).ResultsA total of 1,569 patients with ICH were included, of whom 790 had adverse outcome (50.35%). The Univariate logistic regression analysis showed that SII at any time point within 14 days after admission was significantly associated with adverse outcome. In the multivariate logistic regression analysis, the SII within 7 days after admission was found to be an independent predictor of adverse functional outcome in ICH patients at discharge. The ROC curve demonstrated that compared to other time points, the SII on day 2 after admission exhibited stronger predictive power for the functional outcome of patients with ICH at discharge (AUC:0.733, 95%CI = 0.679–0.787) (sensitivity 47.09%, specificity 87.02%) (OR 1.074, 95%CI = 1.033–1.126, p = 0.001).ConclusionSII within 7 days after admission, especially on day 2, is independently associated with adverse functional outcome in ICH patients at discharge. This association could be utilized in clinical practice and warrants further investigation.

Pemphigus foliaceus (PF) is a superficial form of pemphigus. Treatment options for PF resemble pemphigus vulgaris, including glucocorticosteroids, immunosuppressive agents and rituximab et al. These treatment approaches can effectively improve the condition but may also be accompanied by high risks of side effects. Therefore, it is crucial to find a safe and effective treatment options for patients with PF. It will not only benefit/be necessary for patients who refuse glucocorticosteroids or immunosuppressive agents treatments, but also for patients who cannot be treated with glucocorticosteroids or immunosuppressive agents. Herein, we reported a case of PF that was treated with apremilast without systemic glucocorticosteroids or immunosuppressive agents. A 54-year-old woman presented with itchy erythema and erosions on the trunk for more than 1 month. The patient applied mometasonefuroate cream without improvement for a duration of two weeks. The past history of diabetes mellitus and atrophic gastritis was reported. Physical examination revealed scattered erythematous macules and erosions on the trunk. No mucosal involvement was observed. The condition was assessed by the pemphigus disease area index and numerical rating scale, with baseline scores of 7 and 8, respectively. Histopathological examination showed acantholysis and intraepithelial blister. Direct immunofluorescence revealed the presence of IgG and Complement 3 deposition between the acanthocytes with the reticular distribution. Based on enzyme-linked immunosorbent assay results, the levels of Dsg1 and Dsg3 antibodies were 28.18 and 0.26 kU/L respectively. The diagnosis of PF was made. This patient was successfully treated with apremilast without systemic glucocorticosteroids or immunosuppressive agents. The patient has continued with apremilast 30mg once daily for maintenance and no adverse events related to apremilast such as gastrointestinal side effects were observed during the 9-month follow-up period. In conclusion, apremilast therapy without systemic glucocorticosteroids nor immunosuppressive agents might provide an effective alternative to management of mild PF without obvious side effect.

Designing and developing photocatalysts with excellent performance in order to achieve efficient hydrogen production is an important strategy for addressing future energy and environmental challenges. Traditional single-phase photocatalytic materials either have a large bandgap and low visible light response or experience rapid recombination of the photogenerated carriers with low quantum efficiency, seriously hindering their photocatalytic applications. To solve these issues, an important solution is to construct well-matched heterojunctions with highly efficient charge separation capabilities. To this end, an in situ sulfurization reaction was adopted after the deposition of Bi3+ supramolecular complex on a layered supramolecular precursor of tubular carbon nitride (TCN). X-ray diffraction (XRD) patterns confirmed that the as-prepared sample has a good crystalline structure without any other impurities, while high-resolution transmission electron microscopy (HR-TEM) revealed that the heterojunction possesses a 2D structure with a layer of nano-array on its surface. Combined Fourier-transform infrared (FT-IR) spectra and energy-dispersive X-ray spectroscopy (EDX) revealed the interfacial interactions. Owing to the formation of the Z-scheme heterojunction, the visible light adsorption and the separation efficiency of the photo-generated carriers are both obviously enhanced, leaving the high energy electrons and high oxidative holes to participate in the photocatalytic reactions. As a result, the photocatalytic hydrogen evolution rate of Bi2S3-TCN achieves 65.2 μmol g-1·h-1. This proposed green and environmentally benign route can also be applied to construct other sulfides with 2D TCN, providing some important information for the design and optimization of novel carbon-nitride-based semiconductors.

IntroductionA series of significant ecological construction projects in the southern hilly region have brought about substantial changes to the ecological status and comprehensive zoning of the region. Hunan Province, with its strategic significance, was chosen as a representative research subject in the southern hilly region.MethodsWe conducted a dynamic evaluation of the ecological status change and comprehensive zoning of Hunan Province from a structure–function perspective by applying the transfer matrix, Theil-Sen, Mann-Kendall, and ecosystem service trade-offs or synergies methods. The research goal was to integrate and harmonize structural complexity and functional diversification, providing valuable insights for optimizing both ecological background and territorial background.ResultsThe main results are as follows: (1) The structural changes of ecosystems were mainly concentrated in settlement and Cropland ecosystems. While the area of bulti-up ecosystems has increased significantly, from 1.34% in 2000 to 2.72% in 2020. Cropland ecosystems marking a decrease of 1.39%, with a continued conversion of Cropland into construction land ecosystems. (2) Ecosystem function changes have introduced instability. Over time, NPP exhibited an oscillating trend of increase followed by a decrease. Spatially, there was a sharp decline in peripheral building land, and the regions of declining NPP displayed a lateral U-shaped distribution. (3) The overall trend in ecosystem service changes was positive. Quantitatively, GP and CS experienced an ascending-then-decreasing pattern, while HQ showed a weak decline and WY increased annually. At the county scale, there was noticeable spatial heterogeneity. Human socio-economic activities and environmental protection policies exert a significant impact on the ecological conditions within the study area. (4) Regarding the national territory space function partition, urban functional zones have primarily catered to residential functions and were mainly distributed in the Changsha-Zhuzhou-Xiangtan area.DiscussionEcological functional zones were mainly centered on ecological functions, and most were located in the mountainous areas of western and southern Hunan Province. The agricultural function areas were mainly to serve production functions and were mainly located in the Dongting Lake Plain, the nearshore plain of the mainstream and tributary systems of the rivers of Xiang, Zi, Yuan, and Li. In general, the changes in ecosystem structure and function in the study area reflect changes in ecological conditions. In the future, ecosystem diversity, stability, and sustainability should be improved from an integrated structure–function perspective.

Background/ObjectiveSilage characteristics of grass materials directly affect their silage qualities. To expand the source of silage raw materials and develop mixed silages underlined by exploring the positive interactions between forage grasses and legumes, three gramineous grasses, Napier grass (Pennisetum purpureum), king grass (Pennisetum sinese), and forage maize (Zea mays) were separately mixed ensiled with a combination of four forage legumes including Medicago sativa, Vicia villosa, Vicia sativa, and Trifolium repens.MethodsThe chemical composition and fermentation quality of the mixed silages were analyzed and compared with those of the sole silages of these three grasses, as well as the diversity of microbial communities, through the 16S/ITS full-length sequencing.ResultsThe results showed that the inclusion of forage legumes could somewhat improve the fermentation quality, as indicated by significantly (p < 0.05) higher crude protein and lactic acid contents while lower neutral detergent fiber, acid detergent fiber contents and pH values, compared with the sole silages. Among the three types of mixed silages, the mixed king grass had the highest dry matter and crude protein content as well as lowest neutral detergent fiber and acid detergent fiber content. Meanwhile, the bacterial and fungal communities in the mixed silages were influenced by increased the relative abundance of lactic acid bacteria, which inhibited the proliferation of undesirable bacteria, such as Hafnia alvei, Enterobacter cloacae, and Serratia proteamaculanss. Co-occurrence networks identified 32 nodes with 164 positive and 18 negative correlations in bacteria and 80 nodes with two negative and 76 positive correlations in fungi during fermentation.ConclusionInclusion of forage legume to grasses can improve the fermentation quality and optimize the structure of microbial community, which appears to be a feasible strategy to enhance the forage resource utilization.

IntroductionInfluenza A virus (IAV)-induced dysbiosis may predispose to severe bacterial superinfections. Most studies have focused on the microbiota of single mucosal surfaces; consequently, the relationships between microbiota at different anatomic sites in IAV-infected mice have not been fully studied.MethodsWe characterized respiratory and gut microbiota using full-length 16S rRNA gene sequencing by Nanopore sequencers and compared the nasopharyngeal, oropharyngeal, lung and gut microbiomes in healthy and IAV-infected mice.ResultsThe oropharyngeal, lung and gut microbiota of healthy mice were dominated by Lactobacillus spp., while nasopharyngeal microbiota were comprised primarily of Streptococcus spp. However, the oropharyngeal, nasopharyngeal, lung, and gut microbiota of IAV-infected mice were dominated by Pseudomonas, Escherichia, Streptococcus, and Muribaculum spp., respectively. Lactobacillus murinus was identified as a biomarker and was reduced at all sites in IAV-infected mice. The microbiota composition of lung was more similar to that of the nasopharynx than the oropharynx in healthy mice.DiscussionThese findings suggest that the main source of lung microbiota in mice differs from that of adults. Moreover, the similarity between the nasopharyngeal and lung microbiota was increased in IAV-infected mice. We found that IAV infection reduced the similarity between the gut and oropharyngeal microbiota. L. murinus was identified as a biomarker of IAV infection and may be an important target for intervention in post-influenza bacterial superinfections.

IntroductionNanopore sequencing has been widely used in clinical metagenomic sequencing for pathogen detection with high portability and real-time sequencing. Oxford Nanopore Technologies has recently launched an adaptive sequencing function, which can enrich on-target reads through real-time alignment and eject uninteresting reads by reversing the voltage across the nanopore. Here we evaluated the utility of adaptive sequencing in clinical pathogen detection.MethodsNanopore adaptive sequencing and standard sequencing was performed on a same flow cell with a bronchoalveolar lavage fluid sample from a patient with Chlamydia psittacosis infection, and was compared with the previous mNGS results.ResultsNanopore adaptive sequencing identified 648 on-target stop receiving reads with the longest median read length(688bp), which account for 72.4% of all Chlamydia psittaci reads and 0.03% of total reads in enriched group. The read proportion matched to C. psittaci in the stop receiving group was 99.85%, which was much higher than that of the unblock (

PurposeIn football, attacking has seen evolving for decades and attacking pattern detection is an important topic in this sport. The purpose of this study was to identify the general and threatening attacking patterns of different playing styles in world top football matches, which represented the latest evolvement of soccer attacking.MethodsAttacking sequence data of the top three teams from 21 matches in the 2018 World Cup were collected. The three teams were classified into two playing styles according to a previous study, France was a direct-play team, and Croatia and Belgium were possession-play teams. The football field was divided into 12 zones and Markov transition matrix-based zone models were applied to assess the attacking pattern in the 21 matches. Both descriptive analysis and simulative analysis were conducted using this model.ResultsThe results revealed that (1) flanker attacks were frequently taken among all three teams, and possession playing teams (Croatia and Belgium) played more often than direct playing teams (France) in their center of the midfield zone and (2) forward passes across/through zones toward the middle of attacking quarter (A1/4) have a positive impact of creating a chance of a goal.ConclusionUsing Markov transition matrix, general and threatening attacking patterns were found. The combination of possession play and counterattack was a new trend that emerged in the 2018 World Cup. These findings can help coaches to develop corresponding strategies when facing opponents of different playing styles.

Nanopore sequencing has been widely used for the real-time detection and surveillance of pathogens with portable MinION. Nanopore adaptive sequencing can enrich on-target sequences without additional pretreatment. In this study, the performance of adaptive sequencing was evaluated for viral genome enrichment of clinical respiratory samples. Ligation-based nanopore adaptive sequencing (LNAS) and rapid PCR-based nanopore adaptive sequencing (RPNAS) workflows were performed to assess the effects of enrichment on nasopharyngeal swab samples from human adenovirus (HAdV) outbreaks. RPNAS was further applied for the enrichment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples to evaluate sensitivity and timeliness. The RPNAS increased both the relative abundance (7.87–12.86-fold) and data yield (1.27–2.15-fold) of HAdV samples, whereas the LNAS increased only the relative abundance but had no obvious enrichment on the data yield. Compared with standard nanopore sequencing, RPNAS detected the SARS-CoV-2 reads from two low-abundance samples, increased the coverage of SARS-CoV-2 by 36.68–98.92%, and reduced the time to achieve the same coverage. Our study highlights the utility of RPNAS for virus enrichment directly from clinical samples, with more on-target data and a shorter sequencing time to recover viral genomes. These findings promise to improve the sensitivity and timeliness of rapid identification and genomic surveillance of infectious diseases.

Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato–S. endobioticum pathosystem.

Viral disease in potatoes has been a major problem in potato production worldwide. In addition to the potential risk of introducing new diseases in new areas, viral-disease epidemics/pandemics can be initiated by “spillover” of indigenous viruses from infected alternative hosts into introduced cultivars. To investigate the tendency of potential viral infection/resistance, we analyzed the viromes of introduced and indigenous varieties of potatoes among different tissues using RNA-seq libraries. Bioinformatics analyses revealed that potato viruses PVM, PVY, and PVS were dominant and the most frequently identified viruses infecting potato virus-free plants in the field, and showed an infection bias between introduced and indigenous cultivars. PVY and PVS were the major viruses in introduced varieties, whereas PVM showed an extraordinarily high percentage in the indigenous variety. Other three common viruses, PVH, potato mop-top virus, and potato leafroll virus were identified specifically in the indigenous variety. There was a tendency for tissue-specific infection and sequence variation in viruses: underground parts (tubers, roots) harbored more unusual viruses, and tubers harbored relatively more variation with a high frequency of single nucleotide polymorphisms than other tissues. Taken together, our study provides a comprehensive overview of the composition, distribution, and sequence variation of viruses between introduced and indigenous varieties of potatoes.

ObjectiveThe study aims to investigate if a relationship exists between vaginal doses and vaginal stenosis (VS) using posterior–inferior border of symphysis (PIBS) points and the International Commission on Radiation Units-Rectum (ICRU-R) point evaluation system for definitive radio(chemo)therapy in locally advanced cervical cancer.Methods and MaterialsFrom a vaginal dose study in China, 351 patients were prospectively assessed. For every reference point of the PIBS system and ICRU-R point was calculated for all BT and summed with EBRT. Pearson’s chi-square test and Student’s unpaired t-test compared variables with and without vaginal stenosis (VS) G ≥2. The risk factors were assessed for VS G ≥2 in multi- and univariate analyses through Cox proportional hazards model followed by a dose–effect curve construction. The VS morbidity rate was compared via the log-rank test using the median vaginal reference length (VRL).ResultsThe patients (38-month median follow-up) had 21.3% three-year actuarial estimate for VS G ≥2. Compared to G 4.6 cm, the 3-year actuarial estimate was 12.8% vs. 29.6% for VRL ≤4.6 cm. According to the model curve, the risks were 21, 30, and 39% at 75, 85, and 95 Gy, respectively (ICRU-R point dose).ConclusionsPIBS system point doses correlated with late vaginal toxicity. VRL combined with both EBRT and BT dose to the ICRU-R point contribute to VS risk.

The domesticated silkworm, Bombyx mori, is an economically important insect that synthesizes large amounts of silk proteins in its silk gland to make cocoons. In recent years, germline transformation strategies advanced the bioengineering of the silk gland as an ideal bioreactor for mass production of recombinant proteins. However, the yield of exogenous proteins varied largely due to the random insertion and gene drift caused by canonical transposon-based transformation, calling for site-specific and stable expression systems. In the current study, we established a targeted in-fusion expression system by using the transcription activator-like effector nuclease (TALEN)-mediated targeted insertion to target genomic locus of sericin, one of the major silk proteins. We successfully generated chimeric Sericin1-EGFP (Ser-2A-EGFP) transformant, producing up to 3.1% (w/w) of EGFP protein in the cocoon shell. With this strategy, we further expressed the medically important human epidermal growth factor (hEGF) and the protein yield in both middle silk glands, and cocoon shells reached to more than 15-fold higher than the canonical piggyBac-based transgenesis. This natural Sericin1 expression system provides a new strategy for producing recombinant proteins by using the silkworm silk gland as the bioreactor.

NDM-1-producing multidrug-resistant Proteus mirabilis brings formidable clinical challenges. We report a nosocomial outbreak of carbapenem-resistant P. mirabilis in China. Six P. mirabilis strains collected in the same ward showed close phylogenetic relatedness, indicating clonal expansion. Illumina and MinION sequencing revealed that three isolates harbored a novel Salmonella genomic island 1 carrying a blaNDM–1 gene (SGI1-1NDM), while three other isolates showed elevated carbapenem resistance and carried a similar SGI1 but with two blaNDM–1 gene copies (SGI1-2NDM). Four new single nucleotide mutations were present in the genomes of the two-blaNDM–1-harboring isolates, indicating later emergence of the SGI1-2NDM structure. Passage experiments indicated that both SGI variants were stably persistent in this clone without blaNDM–1 copy number changes. This study characterizes two novel blaNDM–1-harboring SGI1 variants in P. mirabilis and provides a new insight into resistance gene copy number variation in bacteria.

This is the second of two manuscripts that presents a computationally efficient full-field deterministic model for laser powder bed fusion (LPBF). The Hybrid Line (HL) thermal model developed in part I is extended to predict the in-process residual stresses due to laser processing of a nickel-based superalloy, RENÉ 65. The computational efficiency and accuracy of the HL thermo-mechanical model is first compared to the exponential decaying heat input model on a single-track simulation. LPBF thin-wall builds with three different laser powers and four printing patterns are evaluated in this study and compared with part-scale simulations. The simulations show good agreements with the experimental X-Ray diffraction measured residual stresses. Compared to the laser power, the scanning pattern is demonstrated to have significant effects on residual stresses. Laser scan patterns utilizing short laser paths generate lower tensile stress along the longitudinal direction of the part and higher compressive stress along the build direction.

This is the first of two manuscripts that presents a computationally efficient full field deterministic model for laser powder bed fusion (LPBF). A new Hybrid Line (HL) heat input model integrates an exponentially decaying (ED) heat input over a portion of a laser path to significantly reduce the computational time. Experimentally measured properties of the high gamma prime nickel-based superalloy RENÉ 65 are implemented in the model to predict the in-process temperature distribution, stresses, and distortions. The model accounts for specific properties of the material as different phases. The first manuscript presents the HL heat transfer model, which is compared with the beam-scale exponentially decaying model, along with the melt pool geometry obtained experimentally by varying the laser parameters. The predicted melt pool geometry of the beam-scale ED model is shown to have good agreement with experimental measurements. While the proposed HL model exhibits lesser accuracy in predicting the melt pool geometries, it can predict the cooling rates and nodal temperatures as accurately as to the ED model. Moreover, under large time integration steps, the HL model becomes more than 1,500 times faster than the ED model.

Psoriasis is characterized by keratinocyte proliferation and immune cell infiltration. M2 isoform of pyruvate kinase (PKM2) was reported to have an important role in cell proliferation, which is a rate-limiting enzyme that regulates the final step of glycolysis. However, how PKM2 regulates cell metabolism and proliferation in psoriatic keratinocytes is still poorly understood. Interestingly, we found that PKM2 was highly expressed in psoriatic epidermis from patients and mouse models. PKM2 overexpression promoted keratinocyte glycolytic metabolism while knockdown inhibited keratinocyte proliferation and glycolysis. Mice lacking PKM2 specifically in keratinocytes, pharmacological inhibition of PKM2 or glycolysis inhibited keratinocyte proliferation and showed obvious remission in an imiquimod-induced psoriatic mouse model. Moreover, the inhibitor of the EGF-receptor blocked EGF-stimulated PKM2 expression and glycolysis in keratinocytes. We identify PKM2 as an upregulated gene in psoriasis. PKM2 is essential in keratinocyte over-proliferation and may represent a therapeutic target for psoriasis.

The purpose of this study was to investigate the impact of high (HPBPT) and low percentage ball possession teams (LPBPT) on physical and technical-tactical performance indicators in the Chinese Football Super League (CSL). Eight physical performance indicators and 26 technical-tactical performance indicators from all 240 matches from season 2018 were analyzed, as well as three contextual variables (team strength, quality of opposition, and match location). Players were divided according to five positions: fullbacks, central defenders, wide midfielders, central midfielders, and attackers. A k-means cluster analysis was conducted to classify all match observations into two groups: HPBPT (n = 229) and LPBPT (n = 251). A mixed linear model was fitted with contextual variables as covariates. When significant interactions or main effects were detected, a post hoc comparison was used to compare physical and technical/tactical differences between HPBPT and LPBPT. Results showed that central defenders and fullbacks covered more high-intensity and sprint running distance in the high possession teams, while wide midfielders and forward covered more high-intensity and sprint running distance in the low possession teams. Meanwhile, players from high ball possession teams were strong in technical indicators, especially in attacking organization. These results may help coaches to understand current football development trends and develop suitable training plans and tests for elite football players.

Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.

Long-term continuous monocropping negatively influences the physicochemical and biological characteristics of cultivated soil, especially for the economically important crop of flue-cured tobacco that is intolerant to continuous monocropping. The underlying mechanism of soil sickness under continuous monoculture and the temporal dynamic changes over the tobacco life cycle among different monoculture time spans remain poorly characterized. In this study, high-throughput sequencing targeting the 16S rRNA gene phylogenetic marker was performed on 60 soil samples of rhizosphere soil from flue−cured tobacco in the replanting, growth and harvest period across 5, 10, and 20 years of a continuous monocropping system. Bacterial community diversity decreased with the increase in duration of continuous monocropping, and the rhizosphere microbiota was highly dynamic in the harvest period. The random forests algorithm identified 17 taxa as biomarkers and a model was established to correlate root microbiota with continuous monocropping time of flue-cured tobacco. Molecular ecological network analysis elaborated the differences and interactions in bacterial co-occurrence patterns under different monocropping systems. The co-occurrence microbial network was larger in size but there were fewer interactions among microbial communities with the increase in continuous monocropping duration. These results provide insights into the changes of flue−cured tobacco root microbiome diversity in response to continuous monocropping and suggest a model for successional dynamics of the root-associated microbiota over continuous monocropping time and development stage. This study may help elucidate the theoretical basis underlying obstacles to continuous monocropping and could contribute to improving guidance for tobacco production.

Platinum-based regimens have been routinely used in the clinical treatment of patients with esophageal squamous cell carcinoma (ESCC). However, administration of these drugs is frequently accompanied by drug resistance. Revealing the underlying mechanisms of the drug resistance and developing agents that enhance the sensitivity to platinum may provide new therapeutic strategies for the patients. In the present study, we found that the poor outcome of ESCC patients receiving platinum-based regimens was associated with co-expression of Shh and Sox2. The sensitivity of ESCC cell lines to cisplatin was related to their activity of Shh signaling. Manipulating of Shh expression markedly changed the sensitivity of ESCC cells to platinum. Continuous treatment with cisplatin resulted in the activation of Shh signaling and enhanced cancer stem cell-like phenotypes in ESCC cells. Dihydroartemisinin (DHA), a classic antimalarial drug, was identified as a novel inhibitor of Shh pathway. Treatment with DHA attenuated the cisplatin-induced activation of the Shh pathway in ESCC cells and synergized the inhibitory effect of cisplatin on proliferation, sphere and colony formation of ALDH-positive ESCC cells in vitro and growth of ESCC cell-derived xenograft tumors in vivo. Taken together, these results demonstrate that the Shh pathway is an important player in cisplatin-resistant ESCC and DHA acts as a promising therapeutic agent to sensitize ESCC to cisplatin treatment.

CRISPR/Cas9 gene editing technology has been very effective in editing genes in many plant species including rice. Here we further improve the current CRISPR/Cas9 gene editing technology in both efficiency and time needed for isolation of transgene-free and target gene-edited plants. We coupled the CRISPR/Cas9 cassette with a unit that activates anthocyanin biosynthesis, providing a visible marker for detecting the presence of transgenes. The anthocyanin-marker assisted CRISPR (AAC) technology enables us to identify transgenic events even at calli stage, to select transformants with elevated Cas9 expression, and to identify transgene-free plants in the field. We used the AAC technology to edit LAZY1 and G1 and successfully generated many transgene-free and target gene-edited plants at T1 generation. The AAC technology greatly reduced the labor, time, and costs needed for editing target genes in rice.

BackgroundEnterobacter cloacae is an opportunistic pathogen which is responsible for serious nosocomial infections. A gene which plays an important role in resistance to carbapenems is the New Delhi metallo-β-lactamase 1 (NDM-1). Currently, the spread of NDM-1-producing E. cloacae strains is a serious public threat.MethodsA multidrug-resistant E. cloacae ssp. dissolvens strain CBG15936 was recovered in 2017 in Guangzhou, China. PCR, S1-pulsed-field gel electrophoresis, and Southern blotting were performed to locate the blaNDM–1 gene. Susceptibility testing and conjugation experiments were also performed. Illumina HiSeq and Nanopore sequencers were used to perform whole-genome sequencing.ResultsStrain CBG15936 belongs to ST932 and is resistant to carbapenems. The blaNDM–1 gene was found on a ∼62-kb plasmid, which has a conjugation frequency of 1.68 × 10–3 events per donor cell. Genome sequencing and analysis revealed that the NDM-1-carrying IncN1 plasmid contained a new transposon Tn6696, which consists of an intact qnrS1-carrying Tn6292 element, an inverted 8.3-kb Tn3000 remnant, ISkpn19, ΔtnpA, and IS26.ConclusionA new transposon, Tn6696, has been detected on a blaNDM–1-carrying plasmid recovered from multidrug-resistant E. cloacae ssp. dissolvens CBG15936 from China. This finding provides a new perspective regarding the potential for blaNDM–1 to undergo horizontal transfer among drug-resistant bacteria.

Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified Klebsiella pneumoniae by an 823 bp specific sequence within 1 min. Genomic analysis further identified blaSHV-12, blaKPC-2, blaTEM-1, blaCTX-M-65, and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.

The emergence of carbapenem-resistant Enterobacteriaceae poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant Escherichia coli strain with two different blaNDM–5-carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one blaNDM–5 gene together with mphA was located on a 55-kb IncX3 plasmid, while the other blaNDM–5 gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of blaNDM–5 than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes (blaCTX–M–15 and blaOXA–1) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two blaNDM–5-carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.

Considering the predicted rising temperatures under current climate change and heat wave scenarios, organisms are expected to suffer more intense and frequent thermal stress. Induced heat is accumulated by organisms and can cause a variety of physiological stress responses. Ophraella communa is an effective biological control agent of common ragweed, Ambrosia artemisiifolia, but the responses of this biocontrol agent to heat stress have not been fully elucidated and, therefore, its potential responses to climate change are uncertain. We investigated the physiological metabolism of subsequent O. communa adults after: (1) different developmental stages (egg, larval, pupal, and adult) were exposed to thermal stress for 3 h each day for 3, 5, 5, and 5 days, respectively (by stage); and (2) individuals were exposed to thermal stress throughout the egg-to-adult period for 3 h each day. The high temperatures of 40, 42, and 44°C were used to induce thermal stress. A control group was reared at 28 ± 2°C. The results showed that short- or long-term exposure to daily phasic high temperatures significantly decreased water and lipid contents and significantly increased glycogen and glycerol contents in all adults (i.e., after exposure of different stages or throughout the egg-to-adult period). However, the total sugar content significantly increased in adults after the eggs and larvae were exposed to brief short-term thermal stress. Compared to the control, the total sugar content was also significantly higher in the adults and pupae exposed to 44°C. Total sugar content in females increased significantly in response to long-term phasic thermal stress at 40°C. However, sugar content of males exposed to 44°C decreased significantly. After long-term phasic thermal stress, water and glycogen contents in males were significantly higher than in females; however, females had higher total sugar and lipid contents. Therefore, our study provides a basic understanding of the metabolic responses of O. communa to thermal stress and offers insights into its potential as a natural biocontrol agent against A. artemisiifolia during the summer season and under predicted climate change scenarios.

Shigellosis, caused by Shigella, is a major global health concern, with nearly 164.7 million cases and over a million deaths occurring annually worldwide. Shigella flexneri is one of the most common subgroups of Shigella with a high incidence of multidrug-resistance. The phage therapy approach is an effective method for controlling multidrug-resistant bacteria. However, only a few Shigella phages have been described to date. In this study, a novel lytic bacteriophage SFPH2 was isolated from a sewage sample obtained from a hospital in Beijing, China, using a multidrug-resistant S. flexneri 2a strain (SF2) isolated from the fecal sample of a dysentery patient. SFPH2 is a member of the Podoviridae virus family with an icosahedral capsid and a short, non-contractile tail. It was found to be stable over a wide range of temperatures (4–50°C) and pH values (pH 3–11). Moreover, SFPH2 could infect two other S. flexneri serotypes (serotypes 2 variant and Y). High-throughput sequencing revealed that SFPH2 has a linear double-stranded DNA genome of 40,387 bp with 50 open reading frames. No tRNA genes were identified in the genome. Comparative analysis of the genome revealed that the SFPH2 belongs to the subfamily Autographivirinae and genus T7virus. The genome shows high similarity with other enterobacterial T7virus bacteriophages such as Citrobacter phage SH4 (95% identity and 89% coverage) and Cronobacter phage Dev2 (94% identity and 92% coverage). A comparison of the fiber proteins showed that minor differences in the amino acid residues might specify different protein binding regions and determine host species. In conclusion, this is the first report of a T7virus that can infect Shigella; SFPH2 has a functional stability under a wide range of temperatures and pH values, showing the potential to be widely applied to control Shigella–associated clinical infections and reduce the transmission rates of S. flexneri serotype 2a and its variants in the environment.

The chronic production of hepatitis B viral (HBV) antigens could cause inflammation and necrosis, leading to elevation of liver enzymes from necrotic hepatocytes, hepatitis, cirrhosis, hepatocellular carcinoma, and liver failure. However, no current treatment is capable of significantly reducing HBsAg expression in patients. Our previous studies had confirmed the ability of CRISPR-Cas9 in disrupting HBV cccDNA. Here, to inhibit HBV expression efficiently in the mouse model of chronic HBV infection, the miniaturized CRISPR-SaCas9 system compatible with a HBV core region derived guide-RNA had been packaged in recombinant adeno-associated virus (AAV) type 8, which lowered the levels of serum HBsAg, HBeAg, and HBV DNA efficiently in HBV transgenic mice during 58 days continuous observation after vein injection. It further confirms the potential of the CRISPR-Cas9 technique for use in hepatitis B gene therapy.

A well-developed root system in rice and other crops can ensure plants to efficiently absorb nutrients and water. Auxin is a key regulator for various aspect of root development, but the detailed molecular mechanisms by which auxin controls crown root development in rice are not understood. We show that overexpression of a YUC gene, which encodes the rate-limiting enzyme in auxin biosynthesis, causes massive proliferation of crown roots. On the other hand, we find that disruption of TAA1, which functions upstream of YUC genes, greatly reduces crown root development. We find that YUC overexpression-induced crown root proliferation requires the presence of the transcription factor WOX11. Moreover, the crown rootless phenotype of taa1 mutants was partially rescued by overexpression of WOX11. Furthermore, we show that WOX11 expression is induced in OsYUC1 overexpression lines, but is repressed in the taa1 mutants. Our results indicate that auxin synthesized by the TAA/YUC pathway is necessary and sufficient for crown root development in rice. Auxin activates WOX11 transcription, which subsequently drives crown root initiation and development, establishing the YUC-Auxin-WOX11 module for crown root development in rice.

In this study, we discovered a novel mobilized colistin resistance (mcr-1) gene variant, named mcr-1.9, which was identified in a colistin-resistant enterotoxigenic Escherichia coli (ETEC) strain from a clinical diarrhea case. The mcr-1.9 gene differs from mcr-1 at position 1036 due to a single nucleotide polymorphism (G→A), which results in an aspartic acid residue being replaced by an asparagine residue (Asp346→Asn) in the MCR-1 protein sequence. Antimicrobial susceptibility testing showed that the mcr-1.9-harboring ETEC strain is resistant to colistin at a minimum inhibitory concentration of 4 μg/ml. Plasmid profiling and conjugation experiments also suggest that the mcr-1.9 variant can be successfully transferred into the E. coli strain J53, indicating that the gene is located on a transferable plasmid. Bioinformatics analysis of data obtained from genome sequencing indicates that the mcr-1.9 gene is located on a 64,005 bp plasmid which has been named pEC26. This plasmid was found to have high similarity to the mcr-1-bearing IncI2-type plasmids pWF-5-19C (99% identity and 99% coverage) and pmcr1-IncI2 (99% identity and 98% coverage). The mcr-1.9-harboring ETEC also shows multidrug resistance to nine classes of antibiotics, and contains several virulence and antimicrobial-resistance genes suggested by the genome sequence analysis. Our report is the first to identify a new mcr-1 variant in an ETEC isolated from a human fecal sample, raising concerns about the existence of more such variants in human intestinal flora. Therefore, we believe that an undertaking to identify new mcr-1 variants in the bacterial communities of human intestines is of utmost importance, and that measures need to be taken to control the spread of mcr-1 and its variants in human intestinal microflora.

Leucine-rich repeat kinase 2 (LRRK2) is a Ser/Thr kinase having mixed lineage kinase-like and GTPase domains, controlling neurite outgrowth and neuronal cell death. Evidence suggests that LRRK2 is involved in innate immune response signaling, but the underlying mechanism is yet unknown. A novel protein inhibitor of phosphatase 3B, RCAN1, is known to positively regulate inflammatory signaling through modulation of several intracellular targets of interleukins in immune cells. In the present study, we report that LRRK2 phosphorylates RCAN1 (RCAN1-1S) and is markedly up-regulated during interleukin-1β (IL-1β) treatment. During IL-1β treatment, LRRK2-mediated phosphorylation of RCAN1 promoted the formation of protein complexes, including that between Tollip and RCAN1. LRRK2 decreased binding between Tollip and IRAK1, which was accompanied by increased formation of the IRAK1-TRAF6 complex. TAK1 activity was significantly enhanced by LRRK2. Furthermore, LRRK2 enhanced transcriptional activity of NF-κB and cytokine IL-8 production. These findings suggest that LRRK2 might be important in positively modulating IL-1β-mediated signaling through selective phosphorylation of RCAN1.