CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration.

The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

Spatio-temporal pattern and associate factors of intestinal infectious diseases in Zhejiang Province, China, 2008-2021: a Bayesian modeling study.

BACKGROUND: Despite significant progress in sanitation status and public health awareness, intestinal infectious diseases (IID) have caused a serious disease burden in China. Little was known about the spatio-temporal pattern of IID at the county level in Zhejiang. Therefore, a spatio-temporal modelling study to identify high-risk regions of IID incidence and potential risk factors was conducted. METHODS: Reported cases of notifiable IID from 2008 to 2021 were obtained from the China Information System for Disease Control and Prevention. Moran's I index and the local indicators of spatial association (LISA) were calculated using Geoda software to identify the spatial autocorrelation and high-risk areas of IID incidence. Bayesian hierarchical model was used to explore socioeconomic and climate factors affecting IID incidence inequities from spatial and temporal perspectives. RESULTS: From 2008 to 2021, a total of 101 cholera, 55,298 bacterial dysentery, 131 amoebic dysentery, 5297 typhoid, 2102 paratyphoid, 27,947 HEV, 1,695,925 hand, foot and mouth disease (HFMD), and 1,505,797 other infectious diarrhea (OID) cases were reported in Zhejiang Province. The hot spots for bacterial dysentery, OID, and HEV incidence were found mainly in Hangzhou, while high-high cluster regions for incidence of enteric fever and HFMD were mainly located in Ningbo. The Bayesian model showed that Areas with a high proportion of males had a lower risk of BD and enteric fever. People under the age of 18 may have a higher risk of IID. High urbanization rate was a protective factor against HFMD (RR = 0.91, 95% CI: 0.88, 0.94), but was a risk factor for HEV (RR = 1.06, 95% CI: 1.01-1.10). BD risk (RR = 1.14, 95% CI: 1.10-1.18) and enteric fever risk (RR = 1.18, 95% CI:1.10-1.27) seemed higher in areas with high GDP per capita. The greater the population density, the higher the risk of BD (RR = 1.29, 95% CI: 1.23-1.36), enteric fever (RR = 1.12, 95% CI: 1.00-1.25), and HEV (RR = 1.15, 95% CI: 1.09-1.21). Among climate variables, higher temperature was associated with a higher risk of BD (RR = 1.32, 95% CI: 1.23-1.41), enteric fever (RR = 1.41, 95% CI: 1.33-1.50), and HFMD (RR = 1.22, 95% CI: 1.08-1.38), and with lower risk of HEV (RR = 0.83, 95% CI: 0.78-0.89). Precipitation was positively correlated with enteric fever (RR = 1.04, 95% CI: 1.00-1.08), HFMD (RR = 1.03, 95% CI: 1.00-1.06), and HEV (RR = 1.05, 95% CI: 1.03-1.08). Higher HFMD risk was also associated with increasing relative humidity (RR = 1.20, 95% CI: 1.16-1.24) and lower wind velocity (RR = 0.88, 95% CI: 0.84-0.92). CONCLUSIONS: There was significant spatial clustering of IID incidence in Zhejiang Province from 2008 to 2021. Spatio-temporal patterns of IID risk could be largely explained by socioeconomic and meteorological factors. Preventive measures and enhanced monitoring should be taken in some high-risk counties in Hangzhou city and Ningbo city.

Research on the predictive model based on the depth of problem-solving discussion in MOOC forum.

A discussion forum is an indispensable part of a massive open online course (MOOC) environment as it enables knowledge construction through learner-to-learner interaction such as discussion of solutions to assigned problems among learners. In this paper, a machine prediction model is built based on the data from the MOOC forum and the depth of discussion of solutions to assigned problems on the topic among students was analyzed. The data for this study was obtained from Modern educational technology course through Selenium with Python. The course has been offered to a total of 11,184 students from China seven times since February, 2016. The proposed model includes the formula of the depth of problem-solving discussion in MOOC forum and its prediction probability. The efficiency of the prediction model and the most important factor of the depth of problem-solving discussion in MOOC are explained in the paper. Based on the results, useful suggestions for effective teaching in MOOC forums are provided in the article.

Composition, Color Stability and Antioxidant Properties of Betalain-Based Extracts from Bracts of Bougainvillea.

Betalains in bracts of Bougainvillea are of great application potential as natural food colorants and antioxidants. This study explored the color, spectra, composition, storage stability, and antioxidant properties of betalain-based Bougainvillea bracts extracts (BBEs) to verify their application value. The results showed that Bougainvillea bract color variance is due to varied contents and proportions of betacyanins (Bc) and betaxanthins (Bx). Bc or Bx alone determined hues of purple or yellow, respectively; the co-existence of Bc and Bx would produce varied hues of red. BBEs showed bright color and good antioxidant properties under a wide pH range. The pH range of 5−6 was optimal for the highest color stability, and pHs 3−8 were optimal for stronger antioxidants. Bc mainly underwent color fading during storage, while Bx easily produced dark precipitates or melanism under strong acidic (pH < 4) or alkaline conditions (pH > 8). However, Bougainvillea Bx showed 3−4 times higher antioxidant ability than Bc. Different considerations for Bc and Bx are needed for varied application purposes. The purple bracts containing only Bc would be more suitable as colorant sources, while additional Bx can bring enhancement of antioxidant ability and richness of Bougainvillea extract color.

Comparative analysis of chloroplast genome structure and molecular dating in Myrtales.

BACKGROUND: Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. RESULTS: A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315 bp and exhibit a typical four part structure. The IR region is between 23,901-36,747 bp, with the large single copy region spanning 83,691-91,249 bp and the small single copy region spanning 11,150-19,703 bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88-114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50-118.62 Ma). CONCLUSIONS: The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

Spectral Characteristic, Storage Stability and Antioxidant Properties of Anthocyanin Extracts from Flowers of Butterfly Pea (Clitoria ternatea L.).

Anthocyanins from flowers of the butterfly pea (Clitoria ternatea L.) are promising edible blue food colorants. Food processing often faces extreme pHs and temperatures, which greatly affects the color and nutritional values of anthocyanins. This study explored the color, spectra, storage stability, and antioxidant properties of C. ternatea anthocyanin extract (CTAE) at different pHs. The color and absorption spectra of CTAEs at a pH of 0.5-13 were shown, with their underlying structures analyzed. Then, the storage stability of CTAEs were explored under a combination of pHs and temperatures. The stability of CTAE declines with the increase in temperature, and it can be stored stably for months at 4 °C. CTAEs also bear much resistance to acidic and alkaline conditions but exhibit higher thermal stability at pH 7 (blue) than at pH 0.5 (magenta) or pH 10 (blue-green), which is a great advantage in food making. Antioxidant abilities for flower extracts from the butterfly pea were high at pH 4-7, as assessed by DPPH free radical scavenging assays, and decreased sharply when the pH value exceeded 7. The above results provide a theoretical basis for the application of butterfly pea flowers and imply their great prospect in the food industry.

Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales).

The family Caprifoliaceae s.l. is an asterid angiosperm clade of ca. 960 species, most of which are distributed in temperate regions of the northern hemisphere. Recent studies show that the family comprises seven major clades: Linnaeoideae, Zabelia, Morinoideae, Dipsacoideae, Valerianoideae, Caprifolioideae, and Diervilloideae. However, its phylogeny at the subfamily or genus level remains controversial, and the backbone relationships among subfamilies are incompletely resolved. In this study, we utilized complete plastome sequencing to resolve the relationships among the subfamilies of the Caprifoliaceae s.l. and clarify several long-standing controversies. We generated and analyzed plastomes of 48 accessions of Caprifoliaceae s.l., representing 44 species, six subfamilies and one genus. Combined with available Caprifoliaceae s.l. plastomes on GenBank and 12 outgroups, we analyzed a final dataset of 68 accessions. Genome structure was strongly conserved in general, although the boundaries between the Inverted Repeat were found to have contracted across Caprifoliaceae s.l. to exclude rpl2, rps19, and ycf1, all or parts of which are typically present in the IR of most angiosperms. The ndhF gene was found to have been inverted in all plastomes of Adoxaceae. Phylogenomic analyses of 68 complete plastomes yielded a highly supported topology that strongly supported the monophyly of Zabelia and its sister relationship to Morinoideae. Moreover, a clade of Valerianoideae + Dipsacoideae was recovered as sister to a clade of Linnaeoideae + Zabelia + Morinoideae clade, and Heptacodium was sister to remaining Caprifolioideae. The Diervilloideae and Caprifolioideae were successively sister to all other Caprifoliaceae s.l. Major lineages of Caprifoliaceae s.l. were estimated to have diverged from the Upper Cretaceous to the Eocene (50-100 Ma), whereas within-genus diversification was dated to the Oligocene and later, concomitant with global cooling and drying. Our results demonstrate the power of plastid phylogenomics in improving estimates of phylogeny among genera and subfamilies, and provide new insights into plastome evolution across Caprifoliaceae s.l.

Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation.

Cellular activities such as compound synthesis often require the transcriptional activation of an entire pathway; however, the molecular mechanisms underlying pathway activation have rarely been explained. Here, the cis regulatory architecture of the anthocyanin pathway genes targeted by the transcription factor (TF) complex including MYB, bHLH, and WDR was systematically analysed in one species and the findings extended to others. In Ipomoea purpurea, the IpMYB1-IpbHLH2-IpWDR1 (IpMBW) complex was found to be orthologous to the PAP1-GL3-TTG1 (AtPGT) complex of Arabidopsis thaliana, and interacted with a 7-bp MYB-recognizing element (MRE) and a 6-bp bHLH-recognizing element (BRE) at the proximal promoter region of the pathway genes. There was little transcription of the gene in the absence of the MRE or BRE. The cis elements identified experimentally converged on two syntaxes, ANCNNCC for MREs and CACN(A/C/T)(G/T) for BREs, and our bioinformatic analysis showed that these were present within anthocyanin gene promoters in at least 35 species, including both gymnosperms and angiosperms. For the anthocyanin pathway, IpMBW and AtPGT recognized the interspecific promoters of both early and later genes. In A. thaliana, the seed-specific TF complex (TT2, TT8, and TTG1) may regulate all the anthocyanin pathway genes, in addition to the proanthocyanidin-specific BAN. When multiple TF complexes in the anthocyanin pathway were compared, the cis architecture played a role larger than the TF complex in determining the variation in promoter activity. Collectively, a cis logic common to the pathway gene promoters was found, and this logic is essential for the trans factors to regulate the pathway.

How relations between early reading skills and third-grade mathematics outcomes vary across distribution: A quantile regression approach.

Early reading skills are critical for later academic outcomes, which include mathematics. Yet, these relations may vary by a child's ability level. This study examined how early reading skills relate to different levels of third-grade mathematics. The samples included 105 same-sex twin pairs (210 individuals, 57% female, 43% male) from the ongoing longitudinal Western Reserve Reading and Math Projects, assessed at kindergarten (M = 6.18, SD = 0.44) and third grade (M = 9.07, SD = 0.49). Kindergarten reading measures consisted of the Letter Identification task from the Woodcock Reading Mastery Test-Revised Normative Update, the Deletion subtests from Phonological Awareness Test, and the Letter Naming Fluency task from the Dynamic Indicators of Basic Early Literacy Skills; third-grade math measures included Calculation, Fluency, Applied Problem, and Quantitative Concepts subtests of Woodcock-Johnson III Tests of Achievement. Both linear and quantile regressions were conducted using reading measures as predictors and math measures as the dependent variables. Linear regressions indicated that the Deletion Summary Score was a unique predictor of Applied Problems, and Letter Naming Fluency was a significant and unique predictor of Calculation Fluency and Quantitative Concepts. Quantile regressions provided a more thorough analysis of these relations. It was found that Letter Naming Fluency was significantly associated with Calculation, Calculation Fluency, and Quantitative Concepts at the lower level. The Deletion Summary Score had relatively stable relations with Applied Problems across all levels. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Enhancement of sweetpotato tolerance to chromium stress through melatonin and glutathione: Insights into photosynthetic efficiency, oxidative defense, and growth parameters.

Melatonin (MT) and reduced glutathione (GSH) roles in mitigating chromium (Cr) toxicity in sweetpotato were explored. Plants, pre-treated with varying MT and GSH doses, were exposed to Cr (40 µM). Cr severely hampered growth by disrupting leaf photosynthesis, root system, and oxidative processes and increased Cr absorption. However, the exogenous application of 1 µM of MT and 2 mM of GSH substantially improved growth parameters by enhancing chlorophyll content, gas exchange (Pn, Tr, Gs, and Ci), and chlorophyll fluorescence (Fv/Fm, ETR, qP, and Y(II)). Furthermore, malondialdehyde (MDA), hydrogen peroxide (H2O2), superoxide ion (O2•-), electrolyte leakage (EL), and Cr uptake by roots (21.6 and 27.3%) and its translocation to shoots were markedly reduced by MT and GSH application, protecting the cell membrane from oxidative damage of Cr-toxicity. Microscopic analysis demonstrated that MT and GSH maintained chloroplast structure and integrity of mesophyll cells; they also enhanced stomatal length, width, and density, strengthening the photosynthetic system and plant growth and biomass. MT and GSH improved osmo-protectants (proline and soluble sugars), gene expression, and enzymatic and non-enzymatic antioxidant activities, mitigating osmotic stress and strengthening plant defenses under Cr stress. Importantly, the efficiency of GSH pre-treatment in reducing Cr-toxicity surpassed that of MT. The findings indicate that MT and GSH alleviate Cr detrimental effects by enhancing photosynthetic organ stability, component accumulation, and resistance to oxidative stress. This study is a valuable resource for plants confronting Cr stress in contaminated soils, but further field validation and detailed molecular exploration are necessary.

Harnessing noncanonical crRNA for highly efficient genome editing.

The CRISPR-Cas12a system is more advantageous than the widely used CRISPR-Cas9 system in terms of specificity and multiplexibility. However, its on-target editing efficiency is typically much lower than that of the CRISPR-Cas9 system. Here we improved its on-target editing efficiency by simply incorporating 2-aminoadenine (base Z, which alters canonical Watson-Crick base pairing) into the crRNA to increase the binding affinity between crRNA and its complementary DNA target. The resulting CRISPR-Cas12a (named zCRISPR-Cas12a thereafter) shows an on-target editing efficiency comparable to that of the CRISPR-Cas9 system but with much lower off-target effects than the CRISPR-Cas9 system in mammalian cells. In addition, zCRISPR-Cas12a can be used for precise gene knock-in and highly efficient multiplex genome editing. Overall, the zCRISPR-Cas12a system is superior to the CRISPR-Cas9 system, and our simple crRNA engineering strategy may be extended to other CRISPR-Cas family members as well as their derivatives.

A tailored series of engineered yeasts for the cell-dependent treatment of inflammatory bowel disease by rational butyrate supplementation.

Intestinal microbiota dysbiosis and metabolic disruption are considered essential characteristics in inflammatory bowel disorders (IBD). Reasonable butyrate supplementation can help patients regulate intestinal flora structure and promote mucosal repair. Here, to restore microbiota homeostasis and butyrate levels in the patient's intestines, we modified the genome of Saccharomyces cerevisiae to produce butyrate. We precisely regulated the relevant metabolic pathways to enable the yeast to produce sufficient butyrate in the intestine with uneven oxygen distribution. A series of engineered strains with different butyrate synthesis abilities was constructed to meet the needs of different patients, and the strongest can reach 1.8 g/L title of butyrate. Next, this series of strains was used to co-cultivate with gut microbiota collected from patients with mild-to-moderate ulcerative colitis. After receiving treatment with engineered strains, the gut microbiota and the butyrate content have been regulated to varying degrees depending on the synthetic ability of the strain. The abundance of probiotics such as Bifidobacterium and Lactobacillus increased, while the abundance of harmful bacteria like Candidatus Bacilloplasma decreased. Meanwhile, the series of butyrate-producing yeast significantly improved trinitrobenzene sulfonic acid (TNBS)-induced colitis in mice by restoring butyrate content. Among the series of engineered yeasts, the strain with the second-highest butyrate synthesis ability showed the most significant regulatory and the best therapeutic effect on the gut microbiota from IBD patients and the colitis mouse model. This study confirmed the existence of a therapeutic window for IBD treatment by supplementing butyrate, and it is necessary to restore butyrate levels according to the actual situation of patients to restore intestinal flora.

Pre-Treatment, Extraction Solvent, and Color Stability of Anthocyanins from Purple Sweetpotato.

Purple sweetpotato anthocyanins (PSPA) exhibit significant potential as food colorants with associated health benefits. However, challenges related to browning and instability have hindered the application of PSPA. In this study, various pre-treatments and solvents for PSPA extraction were evaluated based on color, anthocyanin yields, antioxidant capabilities, and brown index. Browning markedly influenced the color and reduced the antioxidant capacity. Optimal results were obtained with the pre-treatment of "steaming of unpeeled whole sweetpotato" and the solvent "1% citric acid-ddH2O". Furthermore, the color stability of purified PSPA solutions was evaluated under pH levels from 1 to 13 at 25 °C and 65 °C. The PSPA solutions showed a color spectrum from magenta, blue/green, and then to yellow across the pH range. The blue/green hues at pH 10-12 rapidly degraded, while the magenta hue at lower pH showed higher color stability. Elevated temperatures significantly accelerated the PSPA degradation. However, PSPA solutions at pH 1-2 exhibited remarkable color stability, with no spectral decay at either 65 °C for 12 h or 25 °C for 32 days. These results provide valid guidance for the extraction, preservation, and application of PSPA in the food industry.

To Cut or not to Cut: Next-generation Genome Editors for Precision Genome Engineering.

Since the original report of repurposing the CRISPR/Cas9 system for genome engineering, the past decade has witnessed profound improvement in our ability to efficiently manipulate the mammalian genome. However, significant challenges lie ahead that hinder the translation of CRISPR-based gene editing technologies into safe and effective therapeutics. The CRISPR systems often have a limited target scope due to PAM restrictions, and the off-target activity also poses serious risks for therapeutic applications. Moreover, the first-generation genome editors typically achieve desired genomic modifications by inducing double-strand breaks (DSBs) at target site(s). Despite being highly efficient, this "cut and fix" strategy is less favorable in clinical settings due to drawbacks associated with the nuclease-induced DSBs. In this review, we focus on recent advances that help address these challenges, including the engineering and discovery of novel CRISPR/Cas systems with improved functionalities and the development of DSB-free genome editors.

ROS-responsive 18ß-glycyrrhetic acid-conjugated polymeric nanoparticles mediate neuroprotection in ischemic stroke through HMGB1 inhibition and microglia polarization regulation.

Ischemic stroke is an acute and serious cerebral vascular disease, which greatly affects people's health and brings huge economic burden to society. Microglia, as important innate immune components in central nervous system (CNS), are double-edged swords in the battle of nerve injury, considering their polarization between pro-inflammatory M1 or anti-inflammatory M2 phenotypes. High mobility group box 1 (HMGB1) is one of the potent pro-inflammatory mediators that promotes the M1 polarization of microglia. 18ß-glycyrrhetinic acid (GA) is an effective intracellular inhibitor of HMGB1, but of poor water solubility and dose-dependent toxicity. To overcome the shortcomings of GA delivery and to improve the efficacy of cerebral ischemia therapy, herein, we designed reactive oxygen species (ROS) responsive polymer-drug conjugate nanoparticles (DGA) to manipulate microglia polarization by suppressing the translocation of nuclear HMGB1. DGA presented excellent therapeutic efficacy in stroke mice, as evidenced by the reduction of infarct volume, recovery of motor function, suppressed of M1 microglia activation and enhanced M2 activation, and induction of neurogenesis. Altogether, our work demonstrates a close association between HMGB1 and microglia polarization, suggesting potential strategies for coping with inflammatory microglia-related diseases.

Predicting the potential suitable distribution area of Emeia pseudosauteri in Zhejiang Province based on the MaxEnt model.

Human activities, including urbanization, industrialization, agricultural pollution, and land use, have contributed to the increased fragmentation of natural habitats and decreased biodiversity in Zhejiang Province as a result of socioeconomic development. Numerous studies have demonstrated that the protection of ecologically significant species can play a crucial role in restoring biodiversity. Emeia pseudosauteri is regarded as an excellent environmental indicator, umbrella and flagship species because of its unique ecological attributes and strong public appeal. Assessing and predicting the potential suitable distribution area of this species in Zhejiang Province can help in the widespread conservation of biodiversity. We used the MaxEnt ecological niche model to evaluate the habitat suitability of E. pseudosauteri in Zhejiang Province to understand the potential distribution pattern and environmental characteristics of suitable habitats for this species, and used the AUC (area under the receiver operating characteristic curve) and TSS (true skill statistics) to evaluate the model performance. The results showed that the mean AUC value was 0.985, the standard deviation was 0.011, the TSS average value was 0.81, and the model prediction results were excellent. Among the 11 environmental variables used for modeling, temperature seasonality (Bio_4), altitude (Alt) and distance to rivers (Riv_dis) were the key variables affecting the distribution area of E. pseudosauteri, with contributions of 33.5%, 30% and 15.9%, respectively. Its main suitable distribution area is in southern Zhejiang Province and near rivers, at an altitude of 50-300 m, with a seasonal variation in temperature of 7.7-8 °C. Examples include the Ou River, Nanxi River, Wuxi River, and their tributary watersheds. This study can provide a theoretical basis for determining the scope of E. pseudosauteri habitat protection, population restoration, resource management and industrial development in local areas.

Association of tea and its extracts with colorectal adenomas: meta-analysis and systematic review.

Background: There are many studies on the association of tea and its extracts with colorectal adenomas, but the results have varied. The study aims to investigate the effect of tea and its extracts on colorectal adenomas using meta analysis and systematic review. Methods: Literature was obtained through PubMed, Cochrane Library, Embase and Chinese BioMedical Literature Service System since the establishment of the database until April 31, 2023. Search terms include adenomas, polyps, colorectal, rectal, rectum, tea, epigallocatechin, drinking and beverages. Meta-regression analysis was used to infer the source of heterogeneity. Heterogeneity was assessed using I2 statistics and Q test. The effect measures were odds ratio (OR) and 95% confidence interval (95% CI). Stata17.0 software was used for data processing. Results: The findings indicated that study design (t = 0.78, P = 0.454), types of tea intake (t = 1.35, P = 0.205), occurrences (t = -0.19, P = 0.852), regions (t = 1.13, P = 0.281) and grades of adenomas (t = 0.06, P = 0.952) were statistical homogeneity. Tea and its extracts were negatively correlated with the risk of colorectal adenomas (OR = 0.81, 95% CI: 0.66-0.98). No publication bias was found in this study (t = -0.22, P = 0.828) and the results are robust. Conclusion: This study suggests that tea and its extracts have a certain protective effect on colorectal adenomas, which provides scientific evidence for preventive strategies for colorectal adenomas. As for the causal relationship between tea and its extracts on colorectal adenomas, further prospective studies are needed.

Synthetic bacterial therapies for intestinal diseases based on quorum-sensing circuits.

Bacterial therapy has become a key strategy against intestinal infectious diseases in recent years. Moreover, regulating the gut microbiota through traditional fecal microbiota transplantation and supplementation of probiotics faces controllability, efficacy, and safety challenges. The infiltration and emergence of synthetic biology and microbiome provide an operational and safe treatment platform for live bacterial biotherapies. Synthetic bacterial therapy can artificially manipulate bacteria to produce and deliver therapeutic drug molecules. This method has the advantages of solid controllability, low toxicity, strong therapeutic effects, and easy operation. As an essential tool for dynamic regulation in synthetic biology, quorum sensing (QS) has been widely used for designing complex genetic circuits to control the behavior of bacterial populations and achieve predefined goals. Therefore, QS-based synthetic bacterial therapy might become a new direction for the treatment of diseases. The pre-programmed QS genetic circuit can achieve a controllable production of therapeutic drugs on particular ecological niches by sensing specific signals released from the digestive system in pathological conditions, thereby realizing the integration of diagnosis and treatment. Based on this as well as the modular idea of synthetic biology, QS-based synthetic bacterial therapies are divided into an environmental signal sensing module (senses gut disease physiological signals), a therapeutic molecule producing module (plays a therapeutic role against diseases), and a population behavior regulating module (QS system). This review article summarized the structure and function of these three modules and discussed the rational design of QS gene circuits as a novel intervention strategy for intestinal diseases. Moreover, the application prospects of QS-based synthetic bacterial therapy were summarized. Finally, the challenges faced by these methods were analyzed to make the targeted recommendations for developing a successful therapeutic strategy for intestinal diseases.

Analysis on the factors associated with COVID-19 infection among Chinese residents after the implementation of the 10 new rules to optimize COVID-19 response: a cross-sectional study.

Introduction: This study aimed to investigate the status of COVID-19 infection and the associated factors among Chinese residents after the implementation of the 10 New Rules to optimize COVID response. Methods: Participants were recruited using convenience sampling. The study used self-filled questionnaires to examine COVID-19 infection and associated factors among Chinese residents, from December 29, 2022, to January 2, 2023. For the statistical analysis, descriptive and quantitative analyses were used. The potential risk factors for COVID-19 infection were identified by multivariable logistic regression analysis. Results: After the adjustments in control strategies against COVID-19, the infection rate of COVID-19 was high among respondents, and 98.4% of individuals who tested positive showed symptoms including cough, fever, fatigue, headache, sore throat, nasal congestion, sputum production, muscle and joint pain, and runny nose. The main problems respondents reported were the shortage of drugs and medical supplies, the increased burden on families, and the unreliable information source of COVID-19 infection. Logistic regression showed that isolating patients with COVID-19 at home was associated with a lower risk of COVID-19 infection (OR = 0.58, 95%CI: 0.42-0.81). Conclusion: COVID-19 infection among residents is closely related to age, gender, and epidemic prevention measures. The government needs to strengthen education for individuals and centrally manage and properly address difficulties that may arise during COVID-19.

Association between dietary factors and colorectal serrated polyps: a systematic review and meta-analysis.

Background: Dietary factors may affect the incidence of colorectal serrated polyps (SP). However, its effects on SP are unclear as epidemiological studies on this topic have showed inconsistent results. The present systematic review and meta-analysis sought to evaluate the effects of dietary factors on SPs. Methods: Studies regarding the association between dietary factors and SPs were identified by searching PubMed, Cochrane library, Embase and Chinese Biomedical Literature database from inception until 27 February 2023. Search terms include serrated, hyperplastic, adenoma, polyps, colorectal, rectal, rectum and risk. Heterogeneity was assessed using I2 statistics. The meta-analysis was conducted by using a random-effects model, and the pooled effects were expressed with odds ratios (OR) and 95% confidence intervals (95% CI). Probable sources of heterogeneity were identified through meta-regression. Subgroup analysis were based on lesion types, study designs, countries, and so on. Results: 28 studies were ultimately eligible after scanning, and five dietary factors including vitamin D, calcium, folate, fiber and red or processed meat were excerpted. Higher intakes of vitamin D (OR = 0.95, 95%CI:0.90-1.02), calcium (OR = 0.97, 95%CI: 0.91-1.03) and folate (OR = 0.82, 95% CI: 0.6-1.13) were not significantly associated with SP. Fiber intake (OR = 0.90, 95% CI: 0.82-0.99) was a protective factor against SPs. Red meat intake increased the risk of SPs by 30% for the highest versus lowest intakes (OR = 1.30, 95% CI: 1.13-1.51). For different lesion types, higher folate intake was associated with a decreased risk of HPs (OR = 0.59, 95%CI: 0.44-0.79), and higher vitamin D intake decreased the risk of SPs including SSA/P (OR = 0.93, 95%CI: 0.88-0.98). Conclusions: Higher dietary fiber intake plays an effective role in preventing SP, while red meat intake is associated with an increased risk of SP. This evidence provides guidance for us to prevent SP from a dietary perspective. Systematic review registration: https://www.crd.york.ac.uk/prospero/display_record.php?, RecordID=340750.