bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived Self Efficacy in Implementing COVID-19 Preventive Measures Among Residents of Harari Regional State, Eastern Ethiopia: A Community-Based Cross-Sectional Study
Authors: Eyeberu Addis , Debella Adera , Mengistu Dechasa Adare , Arkew Mesay , Hailu Saba , Oljira Amanuel , Yusuf Kebira Jemal , Getachew Tamirat , Nigussie Shamble , Bekele Deribe , Belete Rebuma , Abate Degu , Bekele Habtamu , Tefera Tigist , Alemu Addisu , Dessie Yadeta
Published: April 2022

Background

The COVID-19 outbreak has now become a major international public health concern and a major challenge for the entire world. Poor adherence to COVID-19 prevention measures continues to be a challenge in managing COVID-19 pandemics, including in Ethiopia. As a result, the current study sought to identify the determinants of community adherence to COVID-19 preventive measures among the adult population of Harari Regional State in Eastern Ethiopia.

Methods

A community-based cross-sectional study was conducted in Harari Regional State, Eastern Ethiopia from January 5 to 30, 2021. All adults above the age of 18 who lived in Harari Regional State's selected kebeles were eligible to participate in the study. A systematic random sampling method was used to select the study participants. The study included a total of 1,320 participants. Pre-tested, structured, and self-administered questionnaires were used to collect data, which was then analyzed using STATA version 16 software. The consent was obtained from each individual and concerned body. Binary logistic regression was used to find the correlation between community adherence to COVID-19 preventive measures and sociodemographic, knowledge, self-efficacy, and risk perception. A P-value of 0.05 was used as the statistical significance cut-off point.

Results

One thousand two hundred fifty-five (1,255) people took the survey, yielding a 95.1 % response rate. Adherence to COVID-19 preventive measures resulted in a mean cumulative score of 29.8. Six hundred eight (48.5%) of the participants had good adherence to COVID-19 preventive measures, whereas 647 (51.5%) did not. The researchers also discovered a statistically significant link between participants' residence, educational status, risk perception, income, and adherence to COVID-19 preventive measures.

Conclusion

Appropriate implementation of COVID-19 preventive measures among community members is required to manage or control pandemics and reduce health-related consequences associated with COVID-19 pandemics. The current study, on the other hand, discovered that nearly half of the study participants had poor adherence. As a result, in order to manage this pandemic, the relevant organizations, including the government and non-governmental organizations, must take appropriate and timely measures.
Predicting the Spread of Vector-Borne Diseases in a Warming World
Authors: Endo Andrew , Amarasekare Priyanga
Published: April 2022

Predicting how climate warming affects vector borne diseases is a key research priority. The prevailing approach uses the basic reproductive number (R0) to predict warming effects. However, R0 is derived under assumptions of stationary thermal environments; using it to predict disease spread in non-stationary environments could lead to erroneous predictions. Here, we develop a trait-based mathematical model that can predict disease spread and prevalence for any vector borne disease under any type of non-stationary environment. We parameterize the model with trait response data for the Malaria vector and pathogen to test the latest IPCC predictions on warmer-than-average winters and hotter-than-average summers. We report three key findings. First, the R0 formulation commonly used to investigate warming effects on disease spread violates the assumptions underlying its derivation as the dominant eigenvalue of a linearized host-vector model. As a result, it overestimates disease spread in cooler environments and underestimates it in warmer environments, proving its predictions to be unreliable even in a constant thermal environment. Second, hotter-than-average summers both narrow the thermal limits for disease prevalence, and reduce prevalence within those limits, to a much greater degree than warmer-than-average winters, highlighting the importance of hot extremes in driving disease burden. Third, while warming reduces infected vector populations through the compounding effects of adult mortality, and infected host populations through the interactive effects of mortality and transmission, uninfected vector populations prove surprisingly robust to warming. This suggests that ecological predictions of warming-induced reductions in disease burden should be tempered by the evolutionary possibility of vector adaptation to both cooler and warmer climates.
Identification of a Five-miRNA Signature for Diagnosis of Kidney Renal Clear Cell Carcinoma
Authors: Zhao Enyang , Li Xuedong , You Bosen , Wang Jinpeng , Hou Wenbin , Wu Qiong
Published: April 2022

Motivation: Kidney renal clear cell carcinoma, which is a common type and accounts for 70–80% of renal cell carcinoma, can easily lead to metastasis and even death. A reliable signature for diagnosis of this cancer is in need. Hence, we seek to select miRNAs for identifying kidney renal clear cell carcinoma.

Method: A feature selection strategy is used and improved to identify microRNAs for diagnosis of kidney renal clear cell carcinoma. Samples representing kidney renal clear cell carcinoma and normal tissues are split into training and testing groups. Accumulated scores representing the variable importance of each miRNA are derived from an iteration of resampling, training, and scoring. Those miRNAs with higher scores are selected based on the Gaussian mixture model. The sample split is repeated ten times to get more central miRNAs.

Results: A total of 611 samples are downloaded from TCGA, each of which contains 1,343 miRNAs. The improved feature selection method is implemented, and five miRNAs are identified as a biomarker for diagnosis of kidney renal clear cell carcinoma. GSE151419 and GSE151423 are selected as the independent testing sets. Experimental results indicate the effectiveness of the selected signature. Both data-driven measurements and knowledge-driven evidence are given to show the effectiveness of our selection results.
m6A Methylation Patterns and Tumor Microenvironment Infiltration Characterization in Clear-Cell Renal Cell Carcinoma
Authors: Ma Tianming , Wang Jiawen , Liu Xiaodong , Zhang Wei , Meng Lingfeng , Zhang Yaoguang
Published: April 2022

Increasing evidence suggests the essential regulation of RNA N6-methyladenosine (m6A) modification in carcinogenesis and immune response. Nevertheless, the potential impacts of these modifications on the tumor microenvironment (TME) immune cell infiltration characteristics in clear-cell renal cell carcinoma (ccRCC) remain unclear. Utilizing a consensus clustering algorithm, we determined three m6A modification patterns and identified three m6A-related gene clusters among 569 ccRCC samples, which were associated with different biological functions and clinical outcomes. Thereafter, the m6A score was constructed using m6A-associated signature genes to accurately exploit the m6A modification patterns within individual tumors. The m6A score was further demonstrated to be noticeably related to ccRCC prognosis. In addition, the m6A score was found to be strongly correlated with tumor mutational burden (TMB), microsatellite instability, immune infiltration, immune checkpoint expression, and immunotherapy response, which was also validated in the pan-cancer analyses. Our findings thoroughly elucidated that m6A modification contributes to tumor microenvironment immune-infiltrating characteristics and prognosis in ccRCC. Assessing the m6A modification patterns of individual patients with ccRCC will offer novel insights into TME infiltration and help develop more effective treatment strategies.
Primary Care Implementation of Genomic Population Health Screening Using a Large Gene Sequencing Panel
Authors: Wildin Robert S. , Giummo Christine A. , Reiter Aaron W. , Peterson Thomas C. , Leonard Debra G. B.
Published: April 2022

To realize the promise of genomic medicine, harness the power of genomic technologies, and capitalize on the extraordinary pace of research linking genomic variation to disease risks, healthcare systems must embrace and integrate genomics into routine healthcare. We have implemented an innovative pilot program for genomic population health screening for any-health-status adults within the largest health system in Vermont, United States. This program draws on key research and technological advances to safely extract clinical value for genomics in routine health care. The program offers no-cost, non-research DNA sequencing to patients by their primary care providers as a preventive health tool. We partnered with a commercial clinical testing company for two next generation sequencing gene panels comprising 431 genes related to both high and low-penetrance common health risks and carrier status for recessive disorders. Only pathogenic or likely pathogenic variants are reported. Routine written clinical consultation is provided with a concise, clinical “action plan” that presents core messages for primary care provider and patient use and supports clinical management and health education beyond the testing laboratory’s reports. Access to genetic counseling is free in most cases. Predefined care pathways and access to genetics experts facilitates the appropriate use of results. This pilot tests the feasibility of routine, ethical, and scalable use of population genomic screening in healthcare despite generally imperfect genomic competency among both the public and health care providers. This article describes the program design, implementation process, guiding philosophies, and insights from 2 years of experience offering testing and returning results in primary care settings. To aid others planning similar programs, we review our barriers, solutions, and perceived gaps in the context of an implementation research framework.
Case Report: Evidence of Migratory Silicone Particles Arising From Cohesive Silicone Breast Implants
Authors: Mustafá Jessica C. R. , Fleury Eduardo de Faria Castro , Dijkman Henry B. P. M.
Published: April 2022

Background

Silicone implants have been used since the 1960s for aesthetic purposes and breast reconstructions. During this period, many women have reported up to 40 similar symptoms, including fatigue, the emergence of autoimmune diseases, Raynaud Phenomenon, arthritis, arthralgias, and hair loss, among others. However, most of the time, these symptoms are neglected by doctors across different specialties and are most often considered a psychosomatic disease. Since 2017, many women suffering from the same complaints have formed social media groups to report their histories and subsequently describe the disease as Breast Implant Illness (BII). The phenomenon of gel bleed and silicone toxicity is known and accepted in literature, but silicone migration into the extracapsular space is still poorly demonstrated, due to the difficulty of monitoring its particles and access to patient data.

Methods

This work demonstrated the presence of silicone through pathological examination in post-explant breast capsules and in the synovial tissue of the right wrist, detected with special Modified Oil Red O (MORO) staining in a patient with a history of BII. The pathological results were compared to the breast MRI imaging files.

Results

The MRI images show the permeability change of the implant shell diagnosed as a water-droplet signal. It was also possible to diagnose the gel bleeding as the silicone-induced granuloma of breast implant capsule (SIGBIC) in both implants. Silicone gel bleed and migration of silicone were detected with MORO staining in and outside the capsule and in the synovial tissue of the right wrist.

Conclusion

In this case study, we showed that silicone migration is possible via cohesive silicone gel breast implant leakage. The accumulation of silicone in the synovial tissue of the right wrist suggests local silicone toxicity and defects.
Tanreqing Injection Attenuates Macrophage Activation and the Inflammatory Response via the lncRNA-SNHG1/HMGB1 Axis in Lipopolysaccharide-Induced Acute Lung Injury
Authors: Hu Chunling , Li Junlu , Tan Yingshuai , Liu Yang , Bai Chen , Gao Jing , Zhao Shilong , Yao Mengying , Lu Xiaoxiao , Qiu Lingxiao , Xing Lihua
Published: April 2022

The etiology of acute lung injury (ALI) is not clear, and the treatment of ALI presents a great challenge. This study aimed to investigate the pathogenesis and potential therapeutic targets of ALI and to define the target gene of Tanreqing (TRQ), which is a traditional Chinese medicine formula composed of five medicines, scutellaria baicalensis, bear bile powder, goat horn powder, honeysuckle and forsythia. Macrophage activation plays a critical role in many pathophysiological processes, such as inflammation. Although the regulation of macrophage activation has been extensively investigated, there is little knowledge of the role of long noncoding RNAs (lncRNAs) in this process. In this study, we found that lncRNA-SNHG1 expression is distinctly regulated in differently activated macrophages in that it is upregulated in LPS. LncRNA-SNHG1 knockdown attenuates LPS-induced M1 macrophage activation. The SNHG1 promoter was bound by NF-κB subunit p65, indicative of SNHG1 being a direct transcriptional target of LPS-induced NF-κB activation. SNHG1 acts as a proinflammatory driver that leads to the production of inflammatory cytokines and the activation of macrophages and cytokine storms by physically interacting with high-mobility group box 1 (HMGB1) in ALI. TRQ inhibited NF-κB signaling activation and binding of NF-κB to the SNHG1 promoter. In conclusion, this study defined TRQ target genes, which can be further elucidated as mechanism(s) of TRQ action, and provides insight into the molecular pathogenesis of ALI. The lncRNA-SNHG1/HMGB1 axis is an ideal therapeutic for ALI treatment.
DyeVert Contrast Reduction System Use in Patients Undergoing Coronary and/or Peripheral Angiography: A Systematic Literature Review and Meta-Analysis
Authors: Tarantini Giuseppe , Prasad Anand , Rathore Sudhir , Bansal Shweta , Gottfried Regine , Rosenkranz Alexander R. , Briguori Carlo , Yaghoubi Mohsen , Mashayekhi Atefeh , Javanbakht Mehdi , Moloney Eoin
Published: April 2022

Background

Contrast-associated acute kidney injury (CA-AKI) is an important adverse effect associated with injecting iodinated intra-arterial contrast media (CM) during coronary angiography. The DyeVert™ Contrast Reduction System is a medical device intended to reduce the intra-arterial CM volume (CMV) administered. The aim of this study was to assess DyeVert System clinical effectiveness and safety by implementing a systematic review and meta-analysis of existing evidence.

Methods

Systematic electronic literature searches were conducted in MEDLINE, Embase, the Cochrane Database of Systematic Reviews, ClinicalTrials.gov, and the International Clinical Trials Registry Platform database. Relevant data were extracted from included studies and meta-analyses were performed to synthesize evidence across studies.

Results

The review included 17 eligible studies involving 1,731 DyeVert System cases and 1,387 control cases (without the use of DyeVert). Meta-analyses demonstrated use of the DyeVert System reduced CMV delivered to the patient by 39.27% (95% CI, 36.10–42.48%, P < 0.001), reduced CMV/baseline renal function ratios (Hedges’s g, −0.56; 95% CI, −0.70 to −0.42, P < 0.001) and percentage of cases exceeding the maximum CMV threshold (risk difference −0.31, 95% CI, −0.48 to −0.13, P < 0.001) while maintaining adequate image quality in 98% of cases. DyeVert System cases demonstrated lower CA-AKI incidence vs. controls (absolute risk reduction 5.00% (95% CI, 0.40–9.80%; P = 0.03), relative risk 0.60 (95% CI, 0.40–0.90; P = 0.01) with a pooled estimate of the number needed to treat with the DyeVert System to avoid 1 CA-AKI event of 20.

Conclusion

DyeVert System use significantly reduces CMV delivered to the patient, CMV/baseline renal function ratios, and CA-AKI incidence while maintaining image quality. Accordingly, the device may serve as an adjunctive, procedure-based strategy to prevent CA-AKI. Future multi-center studies are needed to further assess effects of minimizing CMV on endpoints such as CA-AKI prevention, incidence of adverse cardiac and renal events, and health care costs.
Use of Phage Cocktail BFC 1.10 in Combination With Ceftazidime-Avibactam in the Treatment of Multidrug-Resistant Pseudomonas aeruginosa Femur Osteomyelitis—A Case Report
Authors: Racenis Karlis , Rezevska Dace , Madelane Monta , Lavrinovics Ervins , Djebara Sarah , Petersons Aivars , Kroica Juta
Published: April 2022

High-energy trauma with severe bone fractures can be complicated by infection, leading to the development of osteomyelitis. Pseudomonas aeruginosa is an important causative agent of such infections because of its high virulence profile and ability to develop resistance against a wide range of antimicrobials quickly. P. aeruginosa biofilms cause treatment failure and relapsing infections. Bacteriophages are viruses that can be used to treat biofilm-associated infections. Moreover, the combination of phages with certain antimicrobials have demonstrated synergistic and additive effects. We present a case of a 21-year-old patient with relapsing multidrug-resistant (MDR) P. aeruginosa femur osteomyelitis that developed after a road accident, with a proximal right femoral Grade III B open fracture and severe soft tissue damage. Despite extensive antimicrobial treatment and multiple surgical interventions with wound debridement, the infection persisted, with subsequent development of femoral osteomyelitis with a fistula. Patient care management included femoral head excision with wound debridement, intravenous (IV) ceftazidime-avibactam, and the local application of the lytic Pseudomonas bacteriophage cocktail BFC 1.10. Nine months after the intervention, the patient did not show any clinical, radiological, or laboratory signs of inflammation; therefore, hip replacement was performed. Nevertheless, recurrent P. aeruginosa infection evolved at the distal side of the femur and was successfully treated with conventional antimicrobials. In this case, wound debridement combined with antibiotics and bacteriophages resulted in bacterial eradication of proximal femoral segment, avoiding leg amputation, but failed to treat osteomyelitis in distal bone segment. An in vitro assessment of the isolated MDR P. aeruginosa strain for biofilm formation and phage susceptibility was performed. Additionally, the antimicrobial effects of ceftazidime-avibactam and BFC 1.10 were determined on planktonic cell growth and bacterial biofilm prevention was evaluated. The isolated bacterial strains were susceptible to the bacteriophage cocktail. Strong biofilm formation was detected 6 h after inoculation. Ceftazidime-avibactam combined with BFC 1.10 was most effective in preventing planktonic cell growth and biofilm formation. In both cases, the required concentration of ceftazidime-avibactam decreased two-fold. This study demonstrates the possible use of bacteriophages and antibiotics in difficult-to-treat bone and soft tissue infections, where the additive effects of phages and antibiotics were observed.
Global Burden of Bacterial Skin Diseases: A Systematic Analysis Combined With Sociodemographic Index, 1990–2019
Authors: Xue Yi , Zhou Jie , Xu Bei-Ni , Li Yue , Bao Wu , Cheng Xia Lin , He Yan , Xu Chun Peng , Ren Jun , Zheng Ya rong , Jia Chi Yu
Published: April 2022

Background

The latest incidence and disability-adjusted life-years (DALYs) of major bacterial skin diseases (BSD) and their relationship with socioeconomic are not readily available.

Objective

Describe the global age-standardized incidence and DALYs rates of BSD and analyze their relationship with socioeconomic.

Methods

All data were obtained from Global Burden of Disease (GBD) 2019 database. The correlation between BSD and socioeconomic development status was analyzed.

Results

The age-standardized incidence and age-standardized DALYs rate of BSD are: 169.72 million [165.28–175.44] and 0.41 million [0.33–0.48]. Of the two main BSD, pyoderma cause significantly much heavier burden than cellulitis. The change of age-standardized incidence (7.38% [7.06–7.67]) and DALYs (−10.27% [−25.65 to 25.45]) rate of BSD presented an upward or downward trend from 1990 to 2019. The highest burden was in the low-middle sociodemographic index (SDI) area while the area with the lowest burden was recorded in the high-middle SDI area in 2019.

Limitations

GBD 2019 data of BSD are derived from estimation and mathematical modeling.

Conclusion

The burden of BSD is related to socioeconomic development status. The results based on GBD2019 data may benefit policymakers in guiding priority-setting decisions for the global burden of BSD.
Synovial Macrophage and Fibroblast Heterogeneity in Joint Homeostasis and Inflammation
Authors: Knab Katharina , Chambers David , Krönke Gerhard
Published: April 2022

The synovial tissue is an immunologically challenging environment where, under homeostatic conditions, highly specialized subsets of immune-regulatory macrophages and fibroblasts constantly prevent synovial inflammation in response to cartilage- and synovial fluid-derived danger signals that accumulate in response to mechanical stress. During inflammatory joint diseases, this immune-regulatory environment becomes perturbed and activated synovial fibroblasts and infiltrating immune cells start to contribute to synovial inflammation and joint destruction. This review summarizes our current understanding of the phenotypic and molecular characteristics of resident synovial macrophages and fibroblasts and highlights their crosstalk during joint homeostasis and joint inflammation, which is increasingly appreciated as vital to understand the molecular basis of prevalent inflammatory joint diseases such as rheumatoid arthritis.
ABO Blood System and COVID-19 Susceptibility: Anti-A and Anti-B Antibodies Are the Key Points
Authors: Tamayo-Velasco Álvaro , Peñarrubia-Ponce María Jesús , Álvarez Francisco Javier , de la Fuente Ignacio , Pérez-González Sonia , Andaluz-Ojeda David
Published: April 2022

The implication of the ABO blood group in COVID-19 disease was formulated early, at the beginning of the COVID-19 pandemic more than 2 years ago. It has now been established that the A blood group is associated with more susceptibility and severe symptoms of COVID-19, while the O blood group shows protection against viral infection. In this review, we summarize the underlying pathophysiology of ABO blood groups and COVID-19 to explain the molecular aspects behind the protective mechanism in the O blood group. A or B antigens are not associated with a different risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than that of other antigens. In this case, the cornerstone is natural anti-A and anti-B antibodies from the ABO system. They are capable of interfering with the S protein (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2; host cell receptor), thereby conferring protection to patients with sufficient antibodies (O blood group). Indeed, the titers of natural antibodies and the IgG isotype (specific to the O blood group) may be determinants of susceptibility and severity. Moreover, older adults are associated with a higher risk of bad outcomes due to the lack of antibodies and the upregulation of ACE2 expression during senescence. A better understanding of the role of the molecular mechanism of ABO blood groups in COVID-19 facilitates better prognostic stratification of the disease. Furthermore, it could represent an opportunity for new therapeutic strategies.
Pars Plana Ahmed Valve Implantation for Vitrectomized Eyes With Refractory Glaucoma
Authors: Xiang Xiaoli , Xiao Pan , Yu Jingjing , Cao Yihong , Jiang Tingwang , Huang Zhengru
Published: April 2022

This study aimed to analyze the surgical outcomes of pars plana Ahmed valve implantation in vitrectomized eyes with refractory glaucoma. We performed a retrospective case review of consecutive patients with refractory glaucoma after undergoing pars plana vitrectomy who underwent pars plana Ahmed valve implantation between July 2019 and December 2020 at the glaucoma unit of the Affiliated Changshu Hospital of Xuzhou Medical University (Changshu, China). All the patients were followed up for ≥12 months postoperatively. We recorded pre- to postoperative changes in best-corrected visual acuity (BCVA), intraocular pressure (IOP), number of anti-glaucoma medication, corneal endothelial count, and surgical complications, if any. There was a significant improvement in the median BCVA from 2.30 (0.87, 2.30) logMAR preoperatively to 1.70 (0.70, 2.30) logMAR at discharge and 1.0 (0.52, 1.85) at final examination (p = 0.011, p = 0.001). Compared with the preoperative IOP level, there was a significant decrease in the postoperative IOP at each postoperative time point (p < 0.001). There was a significant reduction in the median number of anti-glaucoma drugs (including postoperative ocular massage), from 3.00 (2.00, 3.00) preoperatively to 0.00 (0.00, 1.00) at the last follow-up postoperative examination (p < 0.001). A 29-year-old woman with proliferative diabetic retinopathy who underwent surgical treatment at 5 months postoperatively for fibrous wrapping formed around the plate of the Ahmed valve showed an IOP of 14 mmHg at the last follow-up. Our findings indicated that pars plana Ahmed valve implantation can be safely performed for managing vitrectomized eyes with refractory glaucoma.
Trisomy 8 Associated Clonal Cytopenia Featured With Acquired Auto-Inflammation and Its Response to JAK Inhibitors
Authors: Fu Yakai , Wu Wanlong , Chen Zhiwei , Gu Liyang , Wang Xiaodong , Ye Shuang
Published: April 2022

Objects

It has been recognized the nexus between trisomy 8 and auto-inflammatory features in myelodysplasia syndrome (MDS). Recent research about VEXAS syndrome proved clonal hematopoiesis could interfere with innate immune system far before occurrence of hematological malignancies. We reported a case series of clonal cytopenia with auto-inflammatory features in trisomy 8 patients.

Methods

A total of six patients with isolated trisomy 8 excluded from MDS was retrospectively collected from the Department of Rheumatology, Renji Hospital, Shanghai. The clinical presentations and treatment outcomes were presented.

Results

We report patients with trisomy 8 shared the auto-inflammatory features of recurrent fever, arthralgia, gastrointestinal involvement, and elevated inflammatory markers, especially hyperferritinemia, in addition to hematological findings such as macrocytic anemia and cytopenia of other lineages but without myelodysplasia. The symptoms of this disorder responded to the treatment of glucocorticoids but difficult to taper. JAK inhibitors were introduced to four patients with enhanced response along with glucocorticoids sparing effect and good tolerance.

Conclusion

Clonal cytopenia harboring trisomy 8 presenting with auto-inflammatory features was identified. JAK inhibitor may be a promising anti-inflammatory option.
Variation in Bacterial Community Structures and Functions as Indicators of Response to the Restoration of Suaeda salsa: A Case Study of the Restoration in the Beidaihe Coastal Wetland
Authors: He Changfei , Zheng Li , Ding Jinfeng , Gao Wei , Li Qian , Han Bin , Li Jingxi
Published: April 2022

Microbes play an essential role in the restoration of degraded coastal wetlands. However, few studies have focused on the role of key bacteria in the restoration process. Here, Suaeda salsa was planted to recover the biodiversity in the degraded Beidaihe coastal wetland. We monitored omics and soil environmental factors to understand the complex relationship between the bacterial community and wetland health during the restoration period. After planting S. salsa in the degraded area, the soil quality was improved in the later stage of restoration (LPR). Bacterial α-diversity increased with restoration and was positively correlated with TOC. Proteobacteria is the dominant bacterial phylum during the restoration period, and Bacteroidetes, Planctomycetes, Gemmatimonadetes, and Acidobacteria were sensitive to the planting restoration. Random forest analysis picked 30 key OTUs, showing the key bacterial variation of successful restoration. The result indicated that the sum of the relative abundances of key bacterial OTUs was more than 2% in the health wetland. The β-diversity showed that the growth of S. salsa reshaped the soil bacterial community structure and function in the LPR, which recovered to the level in the control area. Putative biogeochemical functions showed that symbionts and aromatic compound degradation were dominant bacterial functions in the growth period of S. salsa. Our study proposed a new indicator to assess wetland health and the planting restoration of S. salsa increased bacteria groups with the ability of symbionts and aromatic compound degradation in the Beidaihe coastal wetland. This study expanded our knowledge of coastal wetland restoration and its ecological contributions.
Isolation, Mutagenesis, and Organic Acid Secretion of a Highly Efficient Phosphate-Solubilizing Fungus
Authors: Yang Tianyou , Li Linbo , Wang Baoshi , Tian Jing , Shi Fanghao , Zhang Shishuang , Wu Zhongqi
Published: April 2022

The highly effective phosphate-solubilizing microorganisms are significant for making full use of the potential phosphorus resources in the soil and alleviating the shortage of phosphorus resources. In this study, a phosphate-solubilizing fungus was isolated from wheat and cotton rhizosphere soils in the lower reaches of the Yellow River in China and was identified asPenicillium oxalicumby morphological and ITS sequencing analysis. In order to obtain a fungus with more efficient phosphorus solubilization ability, we tested three positive mutant strains (P1, P2, and P3) and three negative mutant strains (N1, N2, and N3) through low-energy nitrogen ion implantation mutagenesis. Compared with the parental strain, the phosphate-solubilizing capacity of P1, P2, and P3 was enhanced by 56.88%, 42.26%, and 32.15%, respectively, and that of N1, N2, and N3 was weakened by 47.53%, 35.27%, and 30.86%, respectively. Compared with the parental strain, the total amount of organic acids secreted significantly increased in the three positive mutant strains and decreased in the negative mutant strains; the pH of culture medium was significantly lower in the positive mutant strains and higher in the negative mutant strains. The capacity of phosphate-solubilizing fungus to secrete organic acids and reduce the growth-medium pH was closely related to its phosphate-solubilizing ability. The changes in the amount of organic acids secreted by mutants can alter their acidification and phosphate-solubilizing capacity. In conclusion, this study offers a theoretical basis and strain materials for the exploration and application of phosphate-solubilizing fungi.
Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations
Authors: Marsh Kirsty J. , Raulo Aura M. , Brouard Marc , Troitsky Tanya , English Holly M. , Allen Bryony , Raval Rohan , Venkatesan Saudamini , Pedersen Amy B. , Webster Joanne P. , Knowles Sarah C. L.
Published: April 2022

The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
A Synthesis of Viral Contribution to Marine Nitrogen Cycling
Authors: Wang Shuai , Yang Yu , Jing Jiaojiao
Published: April 2022

Nitrogen is an essential component of major cellular macromolecules, such as DNA and proteins. Its bioavailability has a fundamental influence on the primary production of both terrestrial and oceanic ecosystems. Diverse marine microbes consume nitrogen, while only a limited taxon could replenish it, leaving nitrogen one of the most deficient nutrients in the ocean. A variety of microbes are involved in complex biogeochemical transformations of nitrogen compounds, and their ecological functions might be regulated by viruses in different manners. First and foremost, viruses drive marine nitrogen flowviahost cell lysis, releasing abundant organic nitrogen into the surrounding environment. Secondly, viruses can also participate in the marine nitrogen cycle by expressing auxiliary metabolic genes (AMGs) to modulate host nitrogen metabolic pathways, such as nitrification, denitrification, anammox, and nitrogen transmembrane transport. Additionally, viruses also serve as a considerable reservoir of nitrogen element. The efficient turnover of viruses fundamentally promotes nitrogen flow in the oceans. In this review, we summarize viral contributions in the marine nitrogen cycling in different aspects and discuss challenges and issues based on recent discoveries of novel viruses involved in different processes of nitrogen biotransformation.
Conjugation of a Hybrid Plasmid Encoding Hypervirulence and Carbapenem Resistance in Klebsiella pneumoniae of Sequence Type 592
Authors: Zhao Qian , Feng Yu , Zong Zhiyong
Published: April 2022

Klebsiella pneumoniae simultaneously carrying genes encoding carbapenem resistance and hypervirulence causes fatal infections, representing a severe threat to human health. These carbapenem-resistant and hypervirulent K. pneumoniae (hvCRKP) strains are increasingly reported worldwide and have been found to belong to a variety of sequence types (STs). In this study, we report and characterized an hvCRKP strain of ST592, an uncommon ST, which caused a fatal infection in intensive care unit (ICU) in China and represents a novel type of hvCRKP. We demonstrated that this novel hvCRKP type emerged from the carbapenem-susceptible hypervirulent K. pneumoniae (hvKP) lineage of the K57 capsular type. K57 hvKP contains a pLVPK-like virulence plasmid and then acquired a conjugative blaKPC–2-carrying plasmid to form hvCRKP. The pLVPK-like virulence plasmid contains no complete conjugation module but was able to be transferred by fusion with the conjugative blaKPC–2-carrying plasmid during conjugation. This represents a new mechanism of simultaneous transfer genetic determinants of carbapenem resistance and virulence and highlights the undergoing expansion of hvCRKP, which requires rigorous monitoring and novel countermeasures to curb plasmid-mediated transmission.
Interactive Effects of Epichloë Endophytes and Arbuscular Mycorrhizal Fungi on Saline-Alkali Stress Tolerance in Tall Fescue
Authors: Liu Hui , Tang Huimin , Ni Xiaozhen , Zhang Yajie , Wang Yingchao
Published: April 2022

Epichloë endophytes and arbuscular mycorrhizal fungi (AMFs) are two important symbiotic microorganisms of tall fescue (Lolium arundinaceum). Our research explores the combined effects of endophytes and AMF on saline-alkali stress. The finding revealed that a significant interaction between Epichloë endophytes and AMF, and saline-alkali stress occurred in the growth and physiological parameters of tall fescue. Endophyte infection significantly enhanced tall fescue resistance to saline-alkali stress by increasing shoot and root biomass and nutrient uptake (organic carbon, total nitrogen, and total phosphorus concentration), and accumulating K+ while decreasing Na+ concentration. Furthermore, the beneficial effect of endophytes was enhanced by the beneficial AMF, Claroideoglomus etunicatum (CE) but was reduced by the detrimental AMF, Funneliformis mosseae (FM). Our findings highlight the importance of interactions among multiple microorganisms for plant performance under saline-alkali stress.
Six New Species of Tomentella (Thelephorales, Basidiomycota) From Tropical Pine Forests in Central Vietnam
Authors: Lu Xu , Cao Ting , Nguyễn Trang Thị Thu , Yuan Hai-Sheng
Published: April 2022

Up to this point, studies on the taxonomy and phylogeny of the basidiomycetous genus Tomentella stemmed mainly from the temperate to boreal zones of the Northern hemisphere but were scarce in tropical Asia. In this study, six new species—T. bidoupensis, T. brevisterigmata, T. cinereobrunnea, T. longiechinula, T. stipitobasidia, and T. verruculata from central Vietnam in Southeast Asia—are described and illustrated on the basis of morphological characteristics and molecular phylogenetic analyses of the nuclear ribosomal ITS (internal transcribed spacer: ITS1-5.8S-ITS2) and LSU (large subunit: 28S) markers. Maximum likelihood and Bayesian analyses were used to confirm the phylogenetic positions of these new species and all of them can be well recognized by the macroscopical and anatomical characteristics. The new species and closely related species in the phylogenetic tree, and the new species and morphologically similar species are discussed, whereas the host plant for these new species were speculated on the basis of the phylogenetic analyses and the tree species information of the investigated forests.
Exploiting Information and Control Theory for Directing Gene Expression in Cell Populations
Authors: Henrion Lucas , Delvenne Mathéo , Bajoul Kakahi Fatemeh , Moreno-Avitia Fabian , Delvigne Frank
Published: April 2022

Microbial populations can adapt to adverse environmental conditions either by appropriately sensing and responding to the changes in their surroundings or by stochastically switching to an alternative phenotypic state. Recent data point out that these two strategies can be exhibited by the same cellular system, depending on the amplitude/frequency of the environmental perturbations and on the architecture of the genetic circuits involved in the adaptation process. Accordingly, several mitigation strategies have been designed for the effective control of microbial populations in different contexts, ranging from biomedicine to bioprocess engineering. Technically, such control strategies have been made possible by the advances made at the level of computational and synthetic biology combined with control theory. However, these control strategies have been applied mostly to synthetic gene circuits, impairing the applicability of the approach to natural circuits. In this review, we argue that it is possible to expand these control strategies to any cellular system and gene circuits based on a metric derived from this information theory, i.e., mutual information (MI). Indeed, based on this metric, it should be possible to characterize the natural frequency of any gene circuits and use it for controlling gene circuits within a population of cells.
Cyanobacterial Community Structure and Isolates From Representative Hot Springs of Yunnan Province, China Using an Integrative Approach
Authors: Keshari Nitin , Zhao Yang , Das Sudipta Kumar , Zhu Tao , Lu Xuefeng
Published: April 2022

Cyanobacteria from the representative hot springs of Yunnan Province, China are explored for their diversity and community composition following an integrative approach of cultivation-independent and -dependent studies and further isolation of potential taxa for future biotechnological perspective. 16S rRNA amplicon sequencing of microbial mats in these hot springs with temperature ranging from 38 to 90°C revealed Cyanobacteria and Proteobacteria constituting a bounteous portion of the bacterial community. The combined approach of 16S rRNA amplicon sequencing and phenotypic analysis revealed the diversity of cyanobacteria (a total of 45 genera). Out of these, a total of 19 cyanobacterial taxa belonging to 6 genera and 10 species were isolated as individuals with the possibility of biotechnological utilization. These isolates were subjected to a thorough morphological study and molecular characterization using 16S rRNA gene sequencing for identification and understanding their phylogeny. The identity and phenotypic and genotypic characteristics of 7 cyanobacterial isolates are not identical to any known cyanobacterial species, generating scope for future taxonomic novelties. Preliminary experiments based on high-temperature (50°C) cultivation showed that most of the isolates were thermotolerant and suggested for their high biotechnological usage potential.
Epigallocatechin-3-Gallate Ameliorates Acute Lung Damage by Inhibiting Quorum-Sensing-Related Virulence Factors of Pseudomonas aeruginosa
Authors: Tang Huaqiao , Hao Suqi , Khan Muhammad Faraz , Zhao Ling , Shi Fei , Li Yinglun , Guo Hongrui , Zou Yuanfeng , Lv Cheng , Luo Jie , Zeng Ze , Wu Qiang , Ye Gang
Published: April 2022

The superbug Pseudomonas aeruginosa is among the most formidable antibiotic-resistant pathogens. With declining options for antibiotic-resistant infections, new medicines are of utmost importance to combat with P. aeruginosa. In our previous study, we demonstrated that Epigallocatechin-3-gallate (EGCG) can inhibit the production of quorum sensing (QS)-regulated virulence factors in vitro. Accordingly, the protective effect and molecular mechanisms of EGCG against P. aeruginosa-induced pneumonia were studied in a mouse model. The results indicated that EGCG significantly lessened histopathological changes and increased the survival rates of mice infected with P. aeruginosa. EGCG effectively alleviated lung injury by reducing the expression of virulence factors and bacterial burden. In addition, EGCG downregulated the production of pro-inflammatory cytokines, such as TNF-α, IL-1, IL-6, and IL-17, and increased the expression of anti-inflammatory cytokines IL-4 and IL-10. Thus, the experimental results supported for the first time that EGCG improved lung damage in P. aeruginosa infection by inhibiting the production of QS-related virulence factors in vivo.
The Enterococcus faecalis FabT Transcription Factor Regulates Fatty Acid Biosynthesis in Response to Exogeneous Fatty Acids
Authors: Zou Qi , Dong Huijuan , Zhu Lei , Cronan John E.
Published: April 2022

The phospholipid acyl chains of Enterococcus faecalis can be derived either by de novo synthesis or by incorporation of exogenous fatty acids through the fatty acid kinase complex (Fak)-phosphate acyltransferase (PlsX) pathway. Exogenous fatty acids suppress fatty acid synthesis through the transcriptional repressor FabT, the loss of which eliminated regulation of de novo fatty acid biosynthesis and resulted in decreased incorporation of exogenous unsaturated fatty acids. Purified FabT bound to the promoters of several fatty acid synthesis genes that contain a specific palindromic sequence and binding was enhanced by acylated derivatives of acyl carrier protein B (acyl-AcpB). The loss of the PlsX pathway blocked FabT-dependent transcriptional repression in the presence of oleic acid. Transcriptional repression was partially retained in a E. faecalis ΔacpB strain which showed decreased fatty acid biosynthesis in the presence of exogenous unsaturated fatty acids. The FabT-dependent activity remaining in the ΔacpB strain indicates that acylated derivatives of AcpA were weak enhancers of FabT binding although AcpA is believed to primarily function in de novo fatty acid synthesis.
Non-homologous End Joining-Mediated Insertional Mutagenesis Reveals a Novel Target for Enhancing Fatty Alcohols Production in Yarrowia lipolytica
Authors: Li Mengxu , Zhang Jinlai , Bai Qiuyan , Fang Lixia , Song Hao , Cao Yingxiu
Published: April 2022

Non-homologous end joining (NHEJ)-mediated integration is effective in generating random mutagenesis to identify beneficial gene targets in the whole genome, which can significantly promote the performance of the strains. Here, a novel target leading to higher protein synthesis was identified by NHEJ-mediated integration that seriously improved fatty alcohols biosynthesis in Yarrowia lipolytica. One batch of strains transformed with fatty acyl-CoA reductase gene (FAR) showed significant differences (up to 70.53-fold) in fatty alcohol production. Whole-genome sequencing of the high-yield strain demonstrated that a new target YALI0_A00913g (“A1 gene”) was disrupted by NHEJ-mediated integration of partial carrier DNA, and reverse engineering of the A1 gene disruption (YlΔA1-FAR) recovered the fatty alcohol overproduction phenotype. Transcriptome analysis of YlΔA1-FAR strain revealed A1 disruption led to strengthened protein synthesis process that was confirmed by sfGFP gene expression, which may account for enhanced cell viability and improved biosynthesis of fatty alcohols. This study identified a novel target that facilitated synthesis capacity and provided new insights into unlocking biosynthetic potential for future genetic engineering in Y. lipolytica.
The Emerging Role of Central and Peripheral Immune Systems in Neurodegenerative Diseases
Authors: Zang Xin , Chen Si , Zhu JunYao , Ma Junwen , Zhai Yongzhen
Published: April 2022

For decades, it has been widely believed that the blood–brain barrier (BBB) provides an immune privileged environment in the central nervous system (CNS) by blocking peripheral immune cells and humoral immune factors. This view has been revised in recent years, with increasing evidence revealing that the peripheral immune system plays a critical role in regulating CNS homeostasis and disease. Neurodegenerative diseases are characterized by progressive dysfunction and the loss of neurons in the CNS. An increasing number of studies have focused on the role of the connection between the peripheral immune system and the CNS in neurodegenerative diseases. On the one hand, peripherally released cytokines can cross the BBB, cause direct neurotoxicity and contribute to the activation of microglia and astrocytes. On the other hand, peripheral immune cells can also infiltrate the brain and participate in the progression of neuroinflammatory and neurodegenerative diseases. Neurodegenerative diseases have a high morbidity and disability rate, yet there are no effective therapies to stop or reverse their progression. In recent years, neuroinflammation has received much attention as a therapeutic target for many neurodegenerative diseases. In this review, we highlight the emerging role of the peripheral and central immune systems in neurodegenerative diseases, as well as their interactions. A better understanding of the emerging role of the immune systems may improve therapeutic strategies for neurodegenerative diseases.