A type III-A CRISPR-Cas system mediates co-transcriptional DNA cleavage at the transcriptional bubbles in close proximity to active effectors

Many type III CRISPR–Cas systems rely on the cyclic oligoadenylate (cOA) signaling pathway to exert immunization. However, LdCsm, a type III-A lactobacilli immune system mediates efficient plasmid clearance in spite of lacking cOA signaling. Thus, the system provides a good model for detailed characterization of the RNA-activated DNase in vitro and in vivo. We found ATP functions as a ligand to enhance the LdCsm ssDNase, and the ATP enhancement is essential for in vivo plasmid clearance. In vitro assays demonstrated LdCsm cleaved transcriptional bubbles at any positions in non-template strand, suggesting that DNA cleavage may occur for transcribing DNA. Destiny of target plasmid versus nontarget plasmid in Escherichia coli cells was investigated, and this revealed that the LdCsm effectors mediated co-transcriptional DNA cleavage to both target and nontarget plasmids, suggesting LdCsm effectors can mediate DNA cleavage to any transcriptional bubbles in close proximity upon activation. Subcellular locations of active LdCsm effectors were then manipulated by differential expression of LdCsm and CTR, and the data supported the hypothesis. Strikingly, stepwise induction experiments indicated allowing diffusion of LdCsm effector led to massive chromosomal DNA degradation, suggesting this unique IIIA system can facilitate infection abortion to eliminate virus-infected cells.

Polyene-Producing Streptomyces spp. From the Fungus-Growing Termite Macrotermes barneyi Exhibit High Inhibitory Activity Against the Antagonistic Fungus Xylaria

Fungus-growing termites are engaged in a tripartite mutualism with intestinal microbes and a monocultivar (Termitomyces sp.) in the fungus garden. The termites are often plagued by entomopathogen (Metarhizium anisopliae) and fungus garden is always threatened by competitors (Xylaria spp.). Here, we aim to understand the defensive role of intestinal microbes, the actinomycetes which were isolated from the gut of Macrotermes barneyi. We obtained 44 antifungal isolates, which showed moderate to strong inhibition to Xylaria sp. HPLC analysis indicated that different types of polyenes (tetraene, pentene, and heptaene) existed in the metabolites of 10 strong antifungal Streptomyces strains. Two pentene macrolides (pentamycin and 1′14-dihydroxyisochainin) were firstly purified from Streptomyces strain HF10, both exhibiting higher activity against Xylaria sp. and M. anisopliae than cultivar Termitomyces. Subsequently, tetraene and heptaene related gene disruption assay showed that the mutant strains lost the ability to produce corresponding polyenes, and they also had significantly decreased activities against Xylaria sp. and M. anisopliae compared to that of wild type strains. These results indicate that polyene-producing Streptomyces from the guts of M. barneyi have strong inhibition to competitor fungus and polyenes contribute to inhibitory effects on Xylaria sp.

Metabolic syndrome cannot mask the changes of faecal microbiota compositions caused by primary hepatocellular carcinoma

Both hepatocellular carcinoma (HCC) and metabolic syndrome are closely associated with the composition of the gut microbiota (GM). Although it has been proposed that elements of the GM can be used as biomarkers for the early diagnosis of HCC, whether metabolic syndrome results in a misrepresentation of the results of the early diagnosis of HCC using GM remains unclear. We compared the differences in the faecal microbiota of 10 patients with primary HCC, six patients with type 2 diabetes mellitus (T2DM), seven patients with arterial hypertension, six patients with both HCC and T2DM, and 10 patients with both HCC and arterial hypertension, as well as 10 healthy subjects, using high-throughput sequencing of 16S rRNA gene amplicons. Our results revealed a significant difference in the GM between subjects with and without HCC. The 49 bacterial genera out of the 494 detected genera were significantly different between the groups. These results show that changes in the GM can be used to distinguish between subjects with and without HCC, and can resist interference of T2DM and arterial hypertension with the GM. The results of the present study provide an important basis for the clinical auxiliary diagnosis of HCC by detecting the GM.

[The role of Artificial intelligent-based FFRCT in assessing the hemodynamic relevance of deep myocardial bridge of the left anterior descending coronary artery]

Objective: To investigate the role of artificial intelligence-based coronary CT blood flow reserve score (FFR_CT) in assessing hemodynamic relevance in patients with deep myocardial bridge (MB) of the left anterior descending coronary artery. Methods: A total of 113 patients diagnosed with deep MB of the left anterior descending coronary artery by coronary CT angiography (CCTA) at the Department of Radiology of Tongji Hospital Affiliated to Tongji University from January 2017 to December 2019 were retrospectively analyzed. The location, length, depth, and degree of systolic compression of the MB were measured. The artificial intelligence-based coronary FFR_CT software was employed to calculate the FFR_CT value of the deep MB of the left anterior descending coronary artery. With the boundary of 0.80, all patients were divided into FFR_CT normal group (FFR_CT>0.80) and FFR_CT abnormal group (FFR_CT≤0.80), and the relationship between FFR_CT abnormality and the location, length, depth, and degree of systolic stenosis of the deep MB of the left anterior descending branch was analyzed. The effectiveness of the receiver operating characteristic (ROC) curve in predicting FFR_CT abnormalities was measured by using ROC curve to analyze the length, depth, and degree of systolic stenosis of MB. Results: There were no significant differences in age, gender and high-risk factors between FFR_CT normal group (n=79) and FFR_CT abnormal group (n=34) (P>0.05). In terms of clinical symptoms, unstable angina, asymptomatic myocardial ischemia, stable angina in the FFR_CT normal group were 15.2%, 41.8%, 32.9%,respectively, while 32.4%, 23.5%, 35.3% in the FFR_CT abnormal group,respectively. Except for unstable angina (χ²=4.32,P=0.038), there were no significant differences in asymptomatic myocardial ischemia and stable angina between the two groups (χ²=3.42, 0.06, P>0.05). The length of deep MB was about (36±5) mm in the FFR_CT normal group and (44±5) mm in the FFR_CT abnormal group, respectively. The difference between the two groups was statistically significant (t=-7.703, P<0.001). The ROC curve showed that the optimal critical value of the length of the deep MB was 39.7 mm, the area under the curve was 0.88 (95%CI:0.81-0.95, P<0.001), and the accuracy rate of diagnosing FFR_CT ≤0.80 was 82.3%. Conclusion: FFR_CT value is of great value in the evaluation of hemodynamics in patients with deep myocardial bridge of left anterior descending coronary artery, and the length of deep myocardial bridge is an important factor affecting FFR_CT value.

[Present and future: artificial intelligence in medical imaging]

Artificial intelligence (AI) is a hot point in clinical medicine research. In recent years, AI has played an important role in recognizing the lesion, improving the diagnostic accuracy and assessing the diagnostic efficacy. To accelerate the pace of AI industry, it should be a first thing to improve relevant industrial policies and regulations and to build a transformation platform for industry-university-research. All these will contribute to the standardization in further development of medical imaging AI industry.

First record of gregarine protists (Apicomplexa: Sporozoa) in Asian fungus-growing termite Macrotermes barneyi (Blattaria: Termitidae)

Macrotermes barneyi, widely distributed in southern China, is the major fungus-growing termite in the subfamily Macrotermitinae. It has no flagellated protists in the guts. Here, we report occurrence of gregarine, a protozoan parasite in the digestive tract of M. barneyi. The general morphology and ultrastructure of the gregarine gamonts and syzygies by light micrograph and scanning electron micrograph are presented. SSU rDNA sequence analysis showed that the termite gregarine has the highest identity (90.10%) to that of Gregarina blattarum from cockroaches. Phylogenetic analysis based on the SSU rDNA sequences from diverse insect eugregarines indicated that the gregarine from M. barneyi is phylogenetically close to G. blattarus, L. erratica and G. tropica from Gregarinidae and Leidyanidae families, and may represent a novel species. This study expands our knowledge about the diversity of terrestrial eugregarines parasitizing in termites.

Predictive Value of Serum Creatinine/Cystatin C in Acute Ischemic Stroke Patients under Nutritional Intervention

BACKGROUND AND PURPOSE

As a very common risk of adverse outcomes of the ischemic stroke patients, sarcopenia is associated with infectious complications and higher mortality. The goal of this retrospective study is to explore the predictive value of serum Cr/CysC ratio in acute ischemic stroke patients receiving nutritional intervention.

METHODS

We reviewed adult patients with AIS from December 2019 to February 2020. Patients with acute kidney injury were excluded and all patients received nutritional intervention during a 3-month follow-up period. We collected baseline data at admission including creatinine and cystatin C. The primary poor outcome was major disability (modified Rankin Scale score ≥ 4) at 3 months after AIS.

RESULTS

A total of 217 patients with AIS were identified for this study. Serum Cr/CysC ratio was significantly correlated with NIHSS at discharge, 1-month modified Rankin Scale score, and 3-month modified Rankin Scale score. During 3 months, 34 (15.70%) patients had a poor outcome after AIS and 11 (5.10%) patients died within 30 days. In multivariable logistic regression analyses, serum Cr/CysC ratio at admission was independently associated with 3-month poor outcomes (OR: 0.953, 95% CI: 0.921-0.986, p = .006) and 30-day mortality (OR: 0.953, 95% CI: 0.921-0.986, p = .006).

CONCLUSION

As a blood biochemical indexes reflecting the muscle mass and aiding in risk stratification, Cr/CysC ratio at admission could be used as a predictor of 30-day mortality and long-term poor prognosis in AIS patients.

Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A

DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.

Functional Analysis of the NucS/EndoMS of the Hyperthermophilic Archaeon Sulfolobus islandicus REY15A

EndoMS is a recently identified mismatch specific endonuclease in Thermococcales of Archaea and Mycobacteria of Bacteria. The homologs of EndoMS are conserved in Archaea and Actinobacteria, where classic MutS-MutL-mediated DNA mismatch repair pathway is absent or non-functional. Here, we report a study on the in vitro mismatch cleavage activity and in vivo function of an EndoMS homolog (SisEndoMS) from Sulfolobus islandicus REY15A, the model archaeon belonging to Crenarchaeota. SisEndoMS is highly active on duplex DNA containing G/T, G/G, and T/T mismatches. Interestingly, the cleavage activity of SisEndoMS is stimulated by the heterotrimeric PCNAs, and when Mn²⁺ was used as the co-factor instead of Mg²⁺, SisEndoMS was also active on DNA substrates containing C/T or A/G mismatches, suggesting that the endonuclease activity can be regulated by ion co-factors and accessory proteins. We compared the spontaneous mutation rate of the wild type strain REY15A and ∆endoMS by counter selection against 5-fluoroorotic acid (5-FOA). The endoMS knockout mutant had much higher spontaneous mutation rate (5.06 × 10⁻³) than that of the wild type (4.6 × 10⁻⁶). A mutation accumulation analysis also showed that the deletion mutant had a higher mutation occurrence than the wild type, with transition mutation being the dominant, suggesting that SisEndoMS is responsible for mutation avoidance in this hyperthermophilic archaeon. Overexpression of the wild type SisEndoMS in S. islandicus resulted in retarded growth and abnormal cell morphology, similar to strains overexpressing Hje and Hjc, the Holliday junction endonucleases. Transcriptomic analysis revealed that SisEndoMS overexpression led to upregulation of distinct gene including the CRISPR-Cas IIIB system, methyltransferases, and glycosyltransferases, which are mainly localized to specific regions in the chromosome. Collectively, our results support that EndoMS proteins represent a noncanonical DNA repair pathway in Archaea. The mechanism of the mismatch repair pathway in Sulfolobus which have a single chromosome is discussed.

Yeast cell wall product enhanced intestinal IgA response and changed cecum microflora species after oral vaccination in chickens

The study was designed to explore the effect of a commercial yeast cell wall product (YP) on chicken intestinal IgA response and cecum microbiome after oral vaccination. Chickens were fed with YP during the experiments and orally immunized with live Newcastle disease virus (NDV) vaccine at 2 wk of age. Then, the animals were sacrificed, and samples were collected to measure the indicators of hemagglutination inhibition (HI), IgA response, IgA + cells, and cecum microbiome populations. The results showed that supplement of YP significantly enhanced serum NDV HI titer, intestinal NDV-specific secretory IgA, and intestinal IgA + cells. The sequencing results revealed that obviously increased relative abundance of Ruminococcaceae and decreased population of Bacteroidaceae in cecum were found in YP group. In summary, YP supplementation in diet enhanced intestinal IgA response to NDV vaccination by oral route and modulated the cecum microbiota to the advantage of the host in chickens.

Cerebral Microbleeds Are Associated with Loss of White Matter Integrity

BACKGROUND AND PURPOSE

Previous studies have shown that diffusion tensor imaging suggests a diffuse loss of white matter integrity in people with white matter hyperintensities or lacunes. The purpose of this study was to investigate whether the presence of cerebral microbleeds and their distribution are related to the integrity of white matter microstructures.

MATERIALS AND METHODS

The study comprised 982 participants who underwent brain MR imaging to determine microbleed status. The cross-sectional relation between microbleeds and the microstructural integrity of the white matter was assessed by 2 statistical methods: a multilinear regression model based on the average DTI parameters of normal-appearing white matter and Tract-Based Spatial Statistics analysis, a tract-based voxelwise analysis. Fiber tractography was used to spatially describe the microstructural abnormalities along WM tracts containing a cerebral microbleed.

RESULTS

The presence of cerebral microbleeds was associated with lower mean fractional anisotropy and higher mean diffusivity, axial diffusivity, and radial diffusivity, and the association remained when cardiovascular risk factors and cerebral small-vessel disease markers were further adjusted. Tract-Based Spatial Statistics analysis indicated strictly lobar cerebral microbleeds associated with lower fractional anisotropy, higher mean diffusivity, and higher radial diffusivity in the internal capsule and corpus callosum after adjusting other cerebral small-vessel disease markers, while only a few voxels remained associated with deep cerebral microbleeds. Diffusion abnormalities gradients along WM tracts containing a cerebral microbleed were not found in fiber tractography analysis.

CONCLUSIONS

Cerebral microbleeds are associated with widely distributed changes in white matter, despite their focal appearance on SWI.

A Novel Digestive GH16 β-1,3(4)-Glucanase from the Fungus-Growing Termite Macrotermes barneyi

β-1,3-glucanases are the main digestive enzymes of plant and fungal cell wall. Transcriptomic analysis of the fungus-growing termite Macrotermes barneyi revealed a high expression of a predicted β-1,3(4)-glucanase (Mbbgl) transcript in termite gut. Here, we described the cDNA cloning, heterologous expression, and enzyme characterization of Mbbgl. Sequence analysis and RT-PCR results showed that Mbbgl is a termite-origin GH16 β-1,3(4)-glucanase. The recombinant enzyme showed the highest activity towards laminarin and was active optimally at 50 °C, pH 5.5. The enzyme displayed endo/exo β-1,3(4)-glucanase activities. Moreover, Mbbgl had weak transglycosylation activity. The results indicate that Mbbgl is an endogenous digestive β-1,3(4)-glucanase, which contributes to the decomposition of plant biomass and fungal hyphae. Additionally, the multiple activities, pH, and ion stabilities make Mbbgl a potential candidate for application in the food industry.

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments

AIMS

This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors.

METHODS AND RESULTS

We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables.

CONCLUSIONS

Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

Roles of UGT2B7 C802T gene polymorphism on the efficacy of morphine treatment on cancer pain among the Chinese han population

Background

Morphine is a common analgesic often used to manage chronic pain, especially for patients with pain due to malignancies. Since UGT2B7 plays an important role in the metabolism of morphine, UGT2B7 gene mutation may influence the efficacy of morphine in patients with cancer being treated by this medication.

Aims

The aim of this study is to investigate the relationship between the polymorphisms of UGT2B7 and the efficacy of morphine treatment on cancer pain among the Chinese Han population.

Materials and Methods

A total of 120 patients with cancer pain were enrolled in this study. Morphine was administrated through patient-controlled analgesia infusion pump, and the visual analog score (VAS) was used for pain assessment at 0.5, 4, 6, 12, 24, 48, and 72-h post morphine treatment, respectively. The plasma concentration of morphine and genetic polymorphism of UGT2B7 C802T and G221T was analyzed, respectively.

Results

The frequencies of UGT2B7 C802T were CC: 13.33%, CT: 45% and TT: 41.67%, and the frequencies of UGT2B7 G221T were GG: 76.67%, GT: 22.5% and TT: 0.83%. Moreover, the VAS score of patients with either C802T CT or TT was significantly higher than that in patients with C802T CC. However, no difference of VAS scores was observed between patients carrying G221T GG and patients carrying G221T GT. The plasma concentration of morphine for patients with the C802T CC was significantly lower than that in patients carrying C802T CT or TT, while there was no significant difference in the level of morphine between patients with G221T GG and G221T GT.

Conclusion

The polymorphism of UGT2B7 C802T, but not UGT2B7 G221T, has been associated with the efficacy of morphine treatment on cancer pain among Chinese Han population.