ApoE Mimetic Peptide COG1410 Kills Mycobacterium smegmatis via Directly Interfering ClpC's ATPase Activity.

Antimicrobial peptides (AMPs) hold promise as alternatives to combat bacterial infections, addressing the urgent global threat of antibiotic resistance. COG1410, a synthetic peptide derived from apolipoprotein E, has exhibited potent antimicrobial properties against various bacterial strains, including Mycobacterium smegmatis. However, our study reveals a previously unknown resistance mechanism developed by M. smegmatis against COG1410 involving ClpC. Upon subjecting M. smegmatis to serial passages in the presence of sub-MIC COG1410, resistance emerged. The comparative genomic analysis identified a point mutation in ClpC (S437P), situated within its middle domain, which led to high resistance to COG1410 without compromising bacterial fitness. Complementation of ClpC in mutant restored bacterial sensitivity. In-depth analyses, including transcriptomic profiling and in vitro assays, uncovered that COG1410 interferes with ClpC at both transcriptional and functional levels. COG1410 not only stimulated the ATPase activity of ClpC but also enhanced the proteolytic activity of Clp protease. SPR analysis confirmed that COG1410 directly binds with ClpC. Surprisingly, the identified S437P mutation did not impact their binding affinity. This study sheds light on a unique resistance mechanism against AMPs in mycobacteria, highlighting the pivotal role of ClpC in this process. Unraveling the interplay between COG1410 and ClpC enriches our understanding of AMP-bacterial interactions, offering potential insights for developing innovative strategies to combat antibiotic resistance.

Effect of deep learning image reconstruction with high-definition standard scan mode on image quality of coronary stents and arteries.

Background: The high-definition standard (HD-standard) scan mode has been proven to display stents better than the standard (STND) scan mode but with more image noise. Deep learning image reconstruction (DLIR) is capable of reducing image noise. This study examined the impact of HD-standard scan mode with DLIR algorithms on stent and coronary artery image quality in coronary computed tomography angiography (CCTA) via a comparison with conventional STND scan mode and adaptive statistical iterative reconstruction-Veo (ASIR-V) algorithms. Methods: The data of 121 patients who underwent HD-standard mode scans (group A: N=47, with coronary stent) or STND mode scans (group B: N=74, without coronary stent) were retrospectively collected. All images were reconstructed with ASIR-V at a level of 50% (ASIR-V50%) and a level of 80% (ASIR-V80%) and with DLIR at medium (DLIR-M) and high (DLIR-H) levels. The noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), artifact index (AI), and in-stent diameter were measured as objective evaluation parameters. Subjective assessment involved a 5-point scale for overall image quality, image noise, stent appearance, stent artifacts, vascular sharpness, and diagnostic confidence. Diagnostic confidence was evaluated based on the presence or absence of significant stenosis (≥50% lumen reduction). Both subjective and objective evaluations were conducted by two radiologists independently, with kappa and intraclass correlation statistics being used to test the interobserver agreement. Results: There were 76 evaluable stents in group A, and the DLIR-H algorithm significantly outperformed other algorithms, demonstrating the lowest noise (41.6±7.1/41.3±7.2) and AI (32.4±8.9/31.2±10.1), the highest SNR (14.6±3.5/15.0±3.5) and CNR (13.6±3.8/13.9±3.8), and the largest in-stent diameter (2.18±0.61/2.19±0.61) in representing true stent diameter (all P values <0.01), as well as the highest score in each subjective evaluation parameter. In group B, a total of 296 coronary arteries were evaluated, and the DLIR-H algorithm provided the best objective image quality, with statistically superior noise, SNR, and CNR compared with the other algorithms (all P values <0.05). Moreover, the HD-standard mode scan with DLIR provided better image quality and a lower radiation dose than did the STND mode scan with ASIR-V (P<0.01). Conclusions: HD-standard scan mode with DLIR-H improves image quality of both stents and coronary arteries on CCTA under a lower radiation dose.

Subcytoplasmic location of translation controls protein output.

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.

The FXR1 network acts as signaling scaffold for actomyosin remodeling.

It is currently not known that mRNAs fulfill structural roles in the cytoplasm. Here, we report the FXR1 network, an mRNA-protein (mRNP) network present throughout the cytoplasm: FXR1 packages exceptionally long mRNAs that serve as an underlying network scaffold and concentrate FXR1 molecules, which have multiple protein binding sites. The proximity of FXR1 molecules makes the FXR1 network a hub for transient interactions of proteins lacking RNA-binding domains. We show that the FXR1 network is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. A point mutation in FXR1, which is found in its FMR1 homolog and causes Fragile X syndrome, disrupts the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. These findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as organizer of signaling reactions.

Evolutionary game model based on cumulative prospect theory for information management mechanism in SIoT.

As nodes in Social Internet of Things (SIoT) become more intelligent, malicious information occurs more frequently and spreads more widely. This problem can severely affect the trustworthiness of services and applications in SIoT. Methods to effectively control malicious information spreading in SIoT are essential and necessary. Reputation mechanism provides a powerful tool to tackle this challenge. In this paper, we propose a reputation-based mechanism to activate the self-purification capacity of the SIoT network by balancing information conflicts triggered by reporters and supporters. In order to find the best rewarding and punishment strategy, a bilateral cumulative-prospect-based evolutionary game model of SIoT network information conflict is constructed. Using local stability analysis and numerical simulation, the evolutionary trends of the proposed game model under different theoretical application scenarios are analyzed. The findings indicate that the basic income and deposit of both sides, the popularity of information as well as the importance of the conformity effect all have a significant impact on the system's steady state and evolutionary path. The specific conditions that both participating sides of the game tend to treat conflicts relatively rationally are analyzed. Dynamic evolution analysis and sensitivity analysis of selected parameters show that basic income is positively related to smart object's feedback strategies, while deposit is negatively related to that. While weight of conformity effect or the information popularity goes up, the rising of feedback probability is observed. Based on the above results, suggestions on dynamic reward and punishment strategies are given. The proposed model is a helpful attempt to model the evolution of information spreading in SIoT networks, with the ability to simulate several well-known regularities of message dissemination. Proposed model and suggested quantitative strategies can be helpful to build feasible malicious information control facilities in SIoT networks.

High-level production of Aspergillus niger prolyl endopeptidase from agricultural residue and its application in beer brewing.

BACKGROUND: Prolyl endopeptidase from Aspergillus niger (AN-PEP) is a prominent serine proteinase with various potential applications in the food and pharmaceutical industries. However, the availability of efficient and low-cost AN-PEP remains a challenge owing to its low yield and high fermentation cost. RESULTS: Here, AN-PEP was recombinantly expressed in Trichoderma reesei (rAN-PEP) under the control of the cbh1 promoter and its secretion signal. After 4 days of shaking flask cultivation with the model cellulose Avicel PH101 as the sole carbon source, the extracellular prolyl endopeptidase activity reached up to 16.148 U/mL, which is the highest titer reported to date and the secretion of the enzyme is faster in T. reesei than in other eukaryotic expression systems including A. niger and Komagataella phaffii. Most importantly, when cultivated on the low-cost agricultural residue corn cob, the recombinant strain was found to secret a remarkable amount of rAN-PEP (37.125 U/mL) that is twice the activity under the pure cellulose condition. Furthermore, treatment with rAN-PEP during beer brewing lowered the content of gluten below the ELISA kit detection limit (< 10 mg/kg) and thereby, reduced turbidity, which would be beneficial for improving the non-biological stability of beer. CONCLUSION: Our research provides a promising approach for industrial production of AN-PEP and other enzymes (proteins) from renewable lignocellulosic biomass, which provides a new idea with relevant researchers for the utilization of agricultural residues.

The motor domain of the kinesin Kip2 promotes microtubule polymerization at microtubule tips.

Kinesins are microtubule-dependent motor proteins, some of which moonlight as microtubule polymerases, such as the yeast protein Kip2. Here, we show that the CLIP-170 ortholog Bik1 stabilizes Kip2 at microtubule ends where the motor domain of Kip2 promotes microtubule polymerization. Live-cell imaging and mathematical estimation of Kip2 dynamics reveal that disrupting the Kip2-Bik1 interaction aborts Kip2 dwelling at microtubule ends and abrogates its microtubule polymerization activity. Structural modeling and biochemical experiments identify a patch of positively charged residues that enables the motor domain to bind free tubulin dimers alternatively to the microtubule shaft. Neutralizing this patch abolished the ability of Kip2 to promote microtubule growth both in vivo and in vitro without affecting its ability to walk along microtubules. Our studies suggest that Kip2 utilizes Bik1 as a cofactor to track microtubule tips, where its motor domain then recruits free tubulin and catalyzes microtubule assembly.

Solvent-induced proteome profiling for proteomic quantitation and target discovery of small molecular drugs.

Target identification by modification-free proteomic approaches can potentially reveal the pharmacological mechanism of small molecular compounds. By combining the recent solvent-induced protein precipitation (SIP) method with TMT-labeling quantitative proteomics, we propose solvent-induced proteome profiling (SIPP) approach to identify small molecule-protein interactions. The SIPP approach enables to depict denaturation curves of the target protein by varying concentrations of organic solvents to induce unfolding and precipitation of the cellular proteome. By using this approach, we have successfully identified the known targets of market drugs and natural products and extended the proteome information of SIP for target identification.

MeCIPK10 regulates the transition of the K+ transport activity of MeAKT2 between low- and high-affinity molds in cassava.

AKT1 is an inward-rectifying K+ channel that was originally thought to function only within a low-affinity K+ concentration range. However, the growth of an akt1 mutant of Arabidopsis was shown to be severely inhibited within a high-affinity range. This suggested that AKT1 may also be a high-affinity K+ transporter, but it remains unclear how the two modes of AKT1 coordinate to uptake K+. One gene (MeAKT2) encodes for a putatively inward-rectifying K+ channel and was isolated from cassava. Relative to other tissues, the MeAKT2 gene was expressed mainly in roots, and its transcriptional level was observed to be significantly increased under low-K+ conditions. Functional analyses were performed using a yeast expression system. When MeAKT2 was expressed alone in yeast cells, transgenic yeast could grow only in nutrient media supplied with >0.5 mM potassium. A yeast two-hybrid assay showed that both MeCIPK10 and MeCIPK12 clearly interacted with MeAKT2. Additionally, 0.05 mM K+ was sufficient for the growth of yeast cells co-expressing MeAKT2 with MeCIPK10, but also their co-expression significantly enhanced the growth capacity of yeast cells in the low range of K+ concentrations. Change in K+ uptake rate in co-transgenic yeast cells grown across a wide range of K+ concentrations showed that MeAKT2-mediated K+ uptake displayed a biphasic pattern, but also the switching from low-to high-affinity K+ uptake was regulated by CIPK10. This indicated that MeAKT2 functioned as a dual-affinity transporter to uptake K+ under both low- and high-affinity K+ conditions.

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol.

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in Pogostemon cablin. In this study, the full-length cDNA of the FPP synthase gene from P. cablin (PcFPPS) was cloned and characterized. The expressions of PcFPPS are different among different tissues (highly in P. cablin flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal FPPS deletion mutation in yeast CC25. Transient overexpression of PcFPPS in P. cablin leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of PcFPPS in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of PcFPPS can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of PcWRKY44 in P. cablin upregulated the expression levels of PcFPPS and patchoulol synthase gene (PcPTS), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the PcFPPS and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.

Redistribution of adipose tissue is associated with left atrial remodeling and dysfunction in patients with atrial fibrillation.

Objective: Adipose tissue is recognized as a crucial regulator of atrial fibrillation (AF). However, the effect of epicardial adipose tissue (EAT) on the pathophysiology of AF might be different from that of other adipose tissues. The purpose of this study was to explore the distribution features of different adipose tissues in AF patients and their relationships with left atrial (LA) remodeling and function. Methods: A total of 205 participants (including 112 AF and 93 non-AF patients) were recruited. Color doppler ultrasound was used to measure the thickness of subcutaneous, extraperitoneal, and intra-abdominal adipose tissue. Cardiac CT scan was performed to measure the mean thickness of EAT surrounding the whole heart (total-EAT) and specific regions, including left atrium (LA-EAT), left ventricle, right ventricle, interventricular groove, and atrioventricular groove. LA anatomical remodeling and function were measured by echocardiography, while electrical remodeling was evaluated by P-wave duration and dispersion using Electrocardiography (obtained after cardioversion or ablation in AF patients). Relationship between the thickness of different adipose tissues and LA remodeling and function was analyzed. Results: The thickness of subcutaneous, extraperitoneal, and intra-abdominal adipose tissue was similar between AF and non-AF patients, and had no or only weak association with LA remodeling and dysfunction. However, compared to non-AF participants, total-EAT thickness significantly increased in both paroxysmal and persistent AF patients (non-AF vs. paroxysmal AF vs. persistent AF: 6.31 ± 0.63 mm vs. 6.76 ± 0.79 mm vs. 7.01 ± 1.18 mm, P < 0.001), which was positively correlated with the LA size and P-wave duration and dispersion, and negatively correlated with LA ejection fraction and peak strain rate. More interestingly, EAT thickness in AF patients did not increase uniformly in different regions of the heart. Compared to EAT surrounding the other regions, LA-EAT was found to accumulate more greatly, and had a closer relationship to LA remodeling and dysfunction. Multivariate logistic regression analysis also showed that LA-EAT was significantly correlated with the presence of AF (OR = 4.781; 95% CI 2.589-8.831, P < 0.001). Conclusion: Rather than other adipose tissues, accumulation and redistribution of EAT, especially surrounding the LA, is associated with LA remodeling and dysfunction in AF patients.

Efficacy and safety of integrated traditional Chinese and Western medicine for the treatment of infant bronchiolitis: A systematic review, meta-analysis and GRADE evaluation.

BACKGROUND: Infant bronchiolitis has a high death rate in severe cases. In China, traditional Chinese medicine (TCM) is commonly used to treat infant bronchiolitis. However, it has not received enough international attention. OBJECTIVE: We aimed to assess the efficacy and safety of integrated TCM and Western medicine for treating infant bronchiolitis. METHODS: We conducted a systematic review through 7 databases that included randomized controlled trials on integrated TCM and Western medicine for treating bronchiolitis, published in English or Chinese before February 4, 2021. To assess the risk of bias, the Cochrane Collaboration tool was employed to determine the quality of the included studies. We investigated clinical efficacy endpoints, hospitalization time, rates of recurrence, and adverse reactions and meta-analyzed the odds ratio (OR), mean difference (MD), and relative risk (RR), respectively. We assessed the overall certainty of the effect estimates using the GRADE approach. This study is registered with PROSPERO (CRD42021245294). Ethical approval is not required. RESULTS: Forty-six studies (6427 children) were available for inclusion. We used 41 (5490 participants), 11 (1350 participants), 5 (1083 participants), and 11 (1295 participants) studies to analyze clinical efficacy endpoints (OR: 3.31; 95% confidence interval [CI]: 2.93, 3.74; P < .5), hospitalization time (MD: -2.10; 95% CI: -2.87, -1.34; P < .5), recurrence rate (RR: 0·41; 95% CI: 0.30, 0.56; P < .01), and adverse reaction rate (RR: 0.87; 95% CI: 0.55, 1.39; P = .57), respectively. CONCLUSIONS: Integrated TCM and Western medicine is superior to Western medicine alone for treating bronchiolitis in terms of clinical efficacy, hospitalization time, and recurrence rate, with no increase in the adverse reaction rate. TCM is useful as an alternative therapy for viral bronchiolitis. Although further studies are needed to establish specific protocols for the use of TCM in clinical practice, these results may strengthen guideline recommendations regarding the use of TCM.

PatDREB Transcription Factor Activates Patchoulol Synthase Gene Promoter and Positively Regulates Jasmonate-Induced Patchoulol Biosynthesis.

The production of patchoulol in the patchouli (Pogostemon cablin) plant determines its application value, as it is the principal active sesquiterpene of essential oil extracted from this plant. Here, the promoter of patchoulol synthase gene (PatPTSpro) was isolated and found to be methyl jasmonate (MeJA)-induced. A nucleus-localized AP2/ERF transcription factor PatDREB was identified as a transcription activator binding to PatPTSpro, regulating patchoulol biosynthesis through modulating the gene expression. PatDREB also interacts with jasmonate ZIM-domain 4 (JAZ4). Furthermore, PatDREB could physically interact with the MYB-related transcription factor PatSWC4 and synergistically facilitate patchoulol biosynthesis. However, the transcriptional activation activity of the PatDREB-PatSWC4 complex could be inhibited by PatJAZ4, and JA could reverse this interference. Overall, we demonstrated the positive roles of PatDREB and the PatDREB-PatSWC4 complex in regulating patchoulol production, which advance our understanding of the regulatory network of patchoulol biosynthesis.

Toward more efficient ergothioneine production using the fungal ergothioneine biosynthetic pathway.

BACKGROUND: Ergothioneine (ERG) is a potent histidine-derived antioxidant that confers health-promoting effects. Only certain bacteria and fungi can biosynthesize ERG, but the ERG productivity in natural producers is low. ERG overproduction through genetic engineering represents an efficient and cost-effective manufacturing strategy. RESULTS: Here, we showed that Trichoderma reesei can synthesize ERG during conidiogenesis and hyphal growth. Co-expression of two ERG biosynthesis genes (tregt1 and tregt2) from T. reesei enabled E. coli to generate 70.59 mg/L ERG at the shaking flask level after 48 h of whole-cell biocatalysis, whereas minor amounts of ERG were synthesized by the recombinant E. coli strain bearing only the tregt1 gene. By fed-batch fermentation, the extracellular ERG production reached 4.34 g/L after 143 h of cultivation in a 2-L jar fermenter, which is the highest level of ERG production reported thus far. Similarly, ERG synthesis also occurred in the E. coli strain engineered with the two well-characterized genes from N. crassa and the ERG productivity was up to 4.22 g/L after 143 h of cultivation under the above-mentioned conditions. CONCLUSIONS: Our results showed that the overproduction of ERG in E. coli could be achieved through two-enzymatic steps, demonstrating high efficiency of the fungal ERG biosynthetic pathway. Meanwhile, this work offers a more promising approach for the industrial production of ERG.

Overcoming peri- and ortho-selectivity in C-H methylation of 1-naphthaldehydes by a tunable transient ligand strategy.

Methyl groups widely exist in bioactive molecules, and site-specific methylation has become a valuable strategy for their structural functionalization. Aiming to introduce this smallest alkyl handle, a highly regioselective peri- and ortho-C-H methylation of 1-naphthaldehyde by using a transient ligand strategy has been developed. A series of methyl-substituted naphthalene frameworks have been prepared in moderate to excellent yields. Mechanistic studies demonstrate that peri-methylation is controlled by the higher electronic density of the peri-position of 1-naphthaldehyde as well as the formation of intermediary 5,6-fused bicyclic palladacycles, whereas experimental studies and theoretical calculations inferred that a 5-membered iridacycle at the ortho-position of 1-naphthaldehyde leads to energetically favorable ortho-methylation via an interconversion between the peri-iridacycle and ortho-iridacycle. Importantly, to demonstrate the synthetic utility of this method, we show that this strategy can serve as a platform for the synthesis of multi-substituted naphthalene-based bioactive molecules and natural products.

Clinical Application Value of Multimedia Education and Nursing Intervention in a Coronary Computed Tomography Angiography.

To explore the application value of multimedia education and nursing intervention in a coronary computed tomography angiography (CCTA). A total of 120 patients who underwent a 256-slice spiral CCTA examination in our hospital from April 2019 to April 2020 were selected. Patients were divided into two groups of 60 patients each, that is, the control group and the observation group, using a random number table method. The control group received traditional education before an examination, and patients were given routine breathing training. The observation group was given multimedia education and nursing intervention. The heart rate (HR), diastolic blood pressure (DBP), systolic blood pressure (SBP), and respiratory rate in the two groups were observed. The psychological status, imaging quality, and incidence of adverse reactions were compared between the two groups. The HR, DBP, SBP, and respiratory rate of the observation group were all lower compared to those in control group, and the differences were statistically significant (p < 0.05). Following multimedia education and nursing intervention, the anxiety and depression scores of patients in the observation group were considerably lower compared with those in the control group, and the differences were statistically significant (p < 0.05). Observation group image quality I level higher than the control group, and the proportion of patients with the difference was statistically significant (p < 0.05). The proportion of grade II to IV patients was lower in the observation group than in the control group; however, the difference was not statistically significant (p > 0.05). There was a significant difference in the incidence of adverse reactions between the two groups (χ2, p = .031). For patients undergoing a CCTA examination, multimedia education and nursing intervention can effectively improve their immediate psychological state, control their heart rate, and blood pressure before the examination, reduce the incidence of adverse reactions and improve imaging quality, thereby improving the overall reliability of a clinical diagnosis.

A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly.

Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.

Understanding the Role of Trichoderma reesei Vib1 in Gene Expression during Cellulose Degradation.

Vib1, a member of the Ndt80/PhoG-like transcription factor family, has been shown to be essential for cellulase production of Trichoderma reesei. Here, we combined transcriptomic and genetic analyses to gain mechanistic insights into the roles of Vib1 during cellulose degradation. Our transcriptome analysis showed that the vib1 deletion caused 586 genes with decreased expression and 431 genes with increased expression on cellulose. The downregulated genes were enriched for Gene Ontology terms associated with carbohydrate metabolism, transmembrane transport, oxidoreductase activity, and transcription factor activity. Of the 258 genes induced by cellulose, 229 showed no or decreased expression in Δvib1 on cellulose, including almost all (hemi)cellulase genes, crucial sugar transporter genes (IDs:69957, 3405), and the genes encoding main transcriptional activators Xyr1 and Ace3. Additionally, Vib1 also regulated the expression of genes involved in secondary metabolism. Further comparison of the transcriptomes of Δvib1 and Δxyr1 in cellulose revealed that the genes regulated by Vib1 had much overlap with Xyr1 targets especially for the gene set induced by cellulose, presumably whose expression requires the cooperativity between Vib1 and Xyr1. Genetic evidence indicated that Vib1 regulates cellulase gene expression partially via Xyr1. Our results will provide new clues for strain improvement.

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices.

BACKGROUND: Changes of soil microbial communities are one of the main factors of continuous cropping problem. Andrographis paniculata has been reported to have replant problem in cultivation. However, little is known about the variations of rhizosphere soil microbial communities of A. paniculata under a continuous cropping system. Here, Illumina MiSeq was used to investigate the shifts of rhizospheric bacterial and fungal communities after continuous cropping of A. paniculata. RESULTS: The bacterial diversity increased whereas the fungal diversity decreased in rhizosphere soil after consecutive A. paniculata monoculture; and the soil microbial community structure differed between newly plant soil and continuous cropped soil. Taxonomic analyses further revealed that the bacterial phyla Proteobacteria, Acidobacteria and Bacteroidetes and the fungal phyla Zygomycota, Ascomycota and Cercozoa were the dominant phyla across all soil samples. The relative abundance of phyla Acidobacteria and Zygomycota were significantly increased after continuous cropping. Additionally, the most abundant bacterial genus Pseudolabrys significantly decreased, while the predominant fungal genus Mortierella increased considerably in abundance after continuous cropping. CONCLUSIONS: Our results revealed the changes on diversity and composition of bacterial and fungal communities in rhizospheric soil under continuous cropping of A. paniculata. These data contributed to the understanding of soil micro-ecological environments in the rhizosphere of A. paniculata.

Chest CT-based differential diagnosis of 28 patients with suspected corona virus disease 2019 (COVID-19).

OBJECTIVES: The chest CT findings that can distinguish patients with corona virus disease 2019 (COVID-19) from those with clinically suspected COVID-19 but subsequently found to be COVID-19 negative have not previously been described in detail. The purpose of this study was to determine the distinctions among patients with COVID-19 by comparing the imaging findings of patients with suspected confirmed COVID-19 and those of patients initially suspected to have COVID-19 who were ultimately negative for the disease. METHODS: 28 isolated suspected in-patients with COVID-19 were enrolled in this retrospective study from January 22, 2020 to February 6, 2020. 12 patients were confirmed to have positive severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) RNA results, and 16 patients had negative results. The thin-section CT imaging findings and clinical and laboratory data of all the patients were evaluated. RESULTS: There were no significant differences between the 12 confirmed COVID-19 (SARS-Cov-2-positive) patients and 16 SARS-CoV-2-negative patients in epidemiology and most of the clinical features or laboratory data. The CT images showed that the incidence of pure/mixed ground-glass opacities (GGOs) was not different between COVID-19 and SARS-CoV-2-negative patients [9/12 (75.0%) vs 10/16 (62.5%), p = 0.687], but pure/mixed GGOs in the peripheral were more common in patients with COVID-19 [11/12 (91.7%) vs 6/16 (37.5%), p = 0.006]. There were no significant differences in the number of lesions, bilateral lung involvement, large irregular/patchy opacities, rounded opacities, linear opacities, crazy-paving patterns, halo signs, interlobular septal thickening or air bronchograms. CONCLUSIONS: Although peripheral pure/mixed GGOs on CT may help distinguish patients with COVID-19 from clinically suspected but negative patients, CT cannot replace RT-PCR testing. ADVANCES IN KNOWLEDGE: Peripheral pure/mixed GGOs on-chest CT findings can be helpful in distinguishing patients with COVID-19 from those with clinically suspected COVID-19 but subsequently found to be COVID-19 negative.