bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of semen cryobanks for protecting endangered native salmonids: Advantages and perspectives as outlined by the LIFE Nat.Sal.Mo. project on Mediterranean brown trout (Molise region – Italy)
Authors: Di Iorio Michele , Rusco Giusy , Esposito Stefano , D’Andrea Mariasilvia , Roncarati Alessandra , Iaffaldano Nicolaia
Published: January 2023

The Mediterranean brown trout is one of the most endangered freshwater species. A complicated network of climate and human influences has severely harmed its biodiversity. The introduction of alien trout is one of the most serious threats to native populations’ intraspecific diversity. In Molise region (south-Italy) an important conservation program (LIFE Nat.Sal.Mo project) has recently been proposed to preserve the genetic integrity of native Mediterranean trout. This project, alongside safeguarding and re-establishing the habitats’ usefulness aims to restore the genetic integrity of the autochthonous population. This is one of the major goals, and it is accomplished by employing frozen wild breeder semen in conjunction with proper fertilization techniques to carry out artificial reproduction to enhance genetic diversity in the progeny and maintain fitness within self-sustaining populations. In this regard, the implementation of the first European semen cryobank has played a strategic role for conserving extant genomic diversity of native population. The goal of this review is to outline the procedures developed and guidelines established for the creation of a Mediterranean trout sperm cryobank. Here, we specifically provide an overview of some of the main challenges associated with the implementation of semen cryobank, the results achieved, the prospects for restoring genetic integrity in native populations, and lastly, future views for hatchery management to preserve the wild biodiversity of native salmonid species. During the project timeframe 1,683 semen doses, from 150 native breeders were stored inside the cryobank. Our results clearly showed the efficiency of the freezing procedure used, both in vitro and in vivo. In fact, we recorded satisfactory values of post-thaw sperm motility and viability that ranged from 40% to 80%, and excellent fertilization rate in vivo, which ranged from 64% to 81%.
A long-term ichthyoplankton monitoring program suggests climate-induced environmental variabilities changed fish communities in the Hudson River estuary
Authors: Chang Hsiao-Yun , McKown Kim , Chen Yong
Published: January 2023

Climate change is known to have significant impacts on coastal marine ecosystems. However, a good understanding of the exact impacts requires consistent long-term monitoring programs, which are not available for many coastal marine ecosystems. The Hudson River Estuary (HRE) provides critical habitats for many estuarine, freshwater, and diadromous species. The Longitudinal River Ichthyoplankton Survey and Water Quality Survey in the Hudson River Biological Monitoring Program provided a long-term time series (1974-2017) for examining the changes in salinity and other environmental variables and identifying the temporal variability of fish diversity. In this study, we examined the environmental data and found a 2-phase pattern in the salinity time series data with a change point of 1984. We calculated a Margalef index and a Simpson index to examine species richness and evenness for early and older life stages in the upper and lower HRE, and explored the potential effects of rising sea level and salinity on fish biodiversity. This study reveals that sea level and salinity may play an important part in explaining increased species richness and evenness. The increased occurrence, establishment and range expansion of marine species as well as possible displacement of freshwater species may be associated with sea level-induced salinity change observed in the HRE. This study highlights a need for a long-term consistent monitoring program and a better understanding of climate change effects on the biota in coastal estuary ecosystems such as the HRE in order to enhance management, conservation, and restoration plans.
Can IMTA provide added ecosystem value services in the fish farms of Greece?
Authors: Papageorgiou Nafsika , Dimitriou Panagiotis D. , Chatzivasileiou Dimitra , Tsapakis Manolis , Karakassis Ioannis
Published: January 2023

In addition to food supply, there is a growing recognition of the wider ecosystem benefits of Integrated Multitrophic Aquaculture (IMTA) systems in coastal waters, including regulating services such as carbon sequestration and nutrient remediation. The water trophic status and the co-cultured species combinations affect IMTA productivity. In this study, we examined the ability of different combinations of IMTA organisms to remediate nutrients and the economic/environmental gain for reducing the environmental footprint in potential IMTA systems of the eastern Mediterranean. The results showed that the co-cultivation of organisms can reduce the negative effects on the marine environment of a fish farm both on the water column and the sediment. Meso- and eutrophic water states do not show a high variation in terms of foot print mitigation, with all three of the co-cultivated organisms to perform well. In oligotrophic waters, the obligatory absence of mussels reduces the effectiveness of the IMTA system. As expected, larger-sized IMTA systems have higher production rates and as a result higher percentage of nutrient removal. Finally, bivalve harvesting helps to remove the carbon that is trapped in their shells, contributing to the mitigation of processes related to climate change, such as the acidification of the oceans.
Effect of interval between oocyte retrieval and resuscitation embryo transfer on pregnancy outcomes
Authors: Wan Qi , Chen Ming-Xing , Wang Xuejiao , Tan Li , Yu Hui-Jun , Lv Xing-Yu , Zhong Zhao-Hui , Tang Xiao-Jun , Ding Yu-Bin , Xia Min , Li Yuan
Published: January 2023

Objectives

Resuscitation transfer of embryos after elective cryopreservation has been widely applied in in vitro fertilization-embryo transfer (IVF-ET) therapy for human infertility or sterility owing to higher embryo implantation rates. This method separates oocyte retrieval from embryo transfer. The optimal time for frozen embryo transfer (FET) remains unknown. Therefore, this study mainly compares the advantages and disadvantages of delayed FET and immediate FET through retrospective analysis.

Methods

We analyzed real world data of patients who underwent resuscitation transplantation between October 2019 and July 2021 at the Reproductive Center of Chengdu Jinjiang Hospital for Women’s and Children’s Health. Propensity score matching was applied to control potential confounding factors. A total of 5,549 patients who received at least one FET were analyzed. Patients undergoing transplantation within 60 days of oocyte retrieval were included in the immediate FET group (n = 1,265) and those undergoing transplantation > 60 days after retrieval were included in the delayed FET group (n = 4,284).

Results

Live birth rates between the two groups were comparable (45.25% vs. 45.76%, p = 0.757). Moreover, no difference was observed in the rates of biochemical pregnancy (64.50% vs. 66.80%), clinical pregnancy (55.24% vs. 56.83%), ectopic pregnancy (1.47% vs. 1.39%), early miscarriage (14.41% vs. 16.20%), late miscarriage (2.21% vs. 2.09%), singleton premature delivery (16.67% vs. 18.29%), and neonatal deformity (1.97% vs. 1.80%). After stratifying the patients based on the type of embryo transferred, number of embryos transferred, FET protocol, and good prognosis criteria, live birth rates remained comparable between the two groups (p > 0.05).

Conclusion

Pregnancy outcomes were comparable between the immediate and delayed FET groups.
Serum serotonin levels are elevated in patients with increased risk of rheumatoid arthritis
Authors: Wirestam Lina , Martinsson Klara , Kastbom Alf
Published: January 2023

Background

Even though serotonin (5-HT) has been ascribed immunomodulatory features, very little is known about its role in chronic inflammatory diseases. Serotonin is implicated in inflammation and increased levels have been associated with progression of bone erosions in RA.

Objective

To investigate serum serotonin levels in patients with increased risk of rheumatoid arthritis (RA) and patients with recent-onset disease. Moreover, we aimed to determine the prognostic value of serotonin for arthritis development and the disease course.

Methods

Two prospective observational patient cohorts were studied; anti-citrullinated protein antibody (ACPA) -positive patients with musculoskeletal pain without clinical arthritis (n = 82) and patients with early RA (n = 412). Serotonin levels were measured by enzyme-linked immunosorbent assay (ELISA) in baseline serum samples from both cohorts, and longitudinally in at-risk individuals.

Results

Compared to healthy controls (median 65 ng/ml), serotonin levels were significantly higher in both at-risk individuals (median 111 ng/ml, p < 0.0001) and patients with early RA (median 135 ng/ml, p < 0.0001). No significant differences were found between at-risk individuals and patients with early RA. At-risk individuals progressing to arthritis had similar levels as those not progressing, and no significant differences were seen over time. Baseline levels in early RA did not associate with mean 28-joint disease activity scores during 3 years follow-up.

Conclusion

Serum serotonin levels are elevated both at, and prior to, onset of RA. However, increased serotonin is not prognostic for arthritis development or disease course.
Case report: One pediatric liver-transplant recipient with SARS-CoV-2 infection suffering unexplained mixed acidosis
Authors: Yu Lianhu , Zheng Lu , Hu Hui , Wan Ping , Lu Yanming , Wang Libo , Yu Hui , Chen Yiwei , Zhou Jianguo , Xia Qiang , Zhou Wenhao , Zhang Ting
Published: January 2023

Background

The management of LT patients during COVID-19 pandemic is important. Immunosuppressants (IS) are key therapy agents after liver transplant. Different ISs have different side effects. Calcineurin inhibitor (CNI) may lead to metabolic acidosis while mycophenolate mofetil (MMF) showed rare nephrotoxicity. We report a post-liver transplant girl who was infected with SARS-CoV-2, developing a severe mixed acidosis 3 months after the transplantation. Her acidosis was improved after withdrawing of MMF, leading the suspicion that acidosis maybe a rare side effect of MMF.

Case presentation

A girl was admitted to our hospital due to SARS-CoV-2 infection, 3 months before admission the patient received LT due to Niemann-Pick disease (NPD). During hospitalization, blood gas analysis showed severe mixed acidosis. To relieve mixed acidosis, the patient was given oral rehydration salt and liquid replacement therapy. Considering that immunosuppressants may cause metabolic acidosis, dose of CsA was decreased and MMF was discontinued.

Results

However, liquid replacement therapy and decreased CsA dose cannot improve the condition. As an attempt, MMF was discontinued, and 3 days later, the girl’s acidosis was relieved, the latest blood gas analysis was normal with the original dose of CsA and no use of MMF or other IS. In addition, we used Naranjo Scale to see if adverse drug reactions (ADRs) existed. The final score was 6 which means MMF contributes to acidosis probably.

Conclusion

The girl’s mixed acidosis cannot be explained by Niemann-Pick disease and SARS-CoV-2 infection. CNIs could cause metabolic acidosis but declining the dose of CsA didn’t improve her acidosis while withdrawing MMF showed a good effect. Together with the Naranjo Scale result, we suspect that acidosis maybe a rare side effect of MMF.
Chinese medicine for residual symptoms of COVID-19 recovered patients (long COVID)—A double-blind, randomized, and placebo-controlled clinical trial protocol
Authors: Sum Chi Him , Ching Jessica Yuet Ling , Song Tianhe , Cheong Pui Kuan , Lo Cho Wing , Lai Mei Kwan , Chia Chon Pin , Chan Kam Leung , Mak Wing Yan , Leung Ka Chun , Leung Sin Bond , Zhang Hongwei , Lin Zhixiu
Published: January 2023

Introduction

Coronavirus disease 2019 (COVID-19) is the current global pandemic of which residual symptoms exhibited by post-acute, rehabilitating patients include fatigue, dyspnoea, and insomnia. Chinese medicine (CM) has been widely used in China to treat different stages of COVID-19. While there are a significant number of clinical studies suggesting its efficacy and safety in its use during acute stage, there are very few randomized controlled trials focusing on the rehabilitation stage. Liujunzhi Decoction and Shashen Maidong Decoction are frequently recommended by official clinical guidelines in China to treat COVID-19 patients in rehabilitation stage. This double-blind, randomized, placebo controlled study aims to evaluate the efficacy and safety of the combination of the two formulae [named “COVID-19 Rehab Formula (CRF)”] in treating COVID-19 residual symptoms (long COVID).

Methods

Eligible subjects will be randomly divided into treatment group and control group in 1:1 ratio. Treatment group will receive CRF along with certain pre-defined CM according to symptoms for 8 weeks, while control group will receive equivalent packs of placebo for 8 weeks. Data in terms of Fatigue Severity Score (FSS), self-reported COVID-19 long term symptom assessment, the modified British Medical Research Council (mMRC) Dyspnoea Scale, EuroQol Five-Dimension Five-Level (EQ-5D-5L) Questionnaire, pulmonary function test and adverse events will be collected and analyzed by SPSS 24. Blood test on liver and renal functions will also be conducted as safety measures.

Conclusion

This study will evaluate the efficacy and safety of CRF in the treatment COVID-19 residual symptoms in a scientifically rigorous design.

Clinical trial registration

[ClinicalTrials.gov], identifier [NCT04924881].
Comparative survey study of the use of a low cost exoscope vs. microscope for anterior cervical discectomy and fusion (ACDF)
Authors: Encarnacion Ramirez Manuel , Peralta Baez Ismael , Nurmukhametov Renat , Goncharov Efgeni , Efe Ibrahim E. , Sufianov Albert , Ramirez Pena Issael
Published: January 2023

Background

Anterior cervical discectomy and fusion (ACDF) is an often performed procedure in spine neurosurgery. These are often performed using an operating microscope (OM) for better illumination and visualization. But its use is limited to the surgeon and the assistant. There is difficulty in maneuvering long surgical instruments due to the limited space available. Exoscope (EX) has been used as an alternative to microscopes and endoscopes. We used an EX in patients undergoing ACDF for cervical spondylotic myelopathy.

Methods

A prospective comparative trial was conducted to test the safety and usability of a low-cost EX compared to a conventional surgical binocular OM in ACDF. Twenty-six patients with degenerative cervical myelopathy symptoms were operated by ACDF assisted by the EX and OM between December 2021 and June 2022. The authors collected and compared data on operative time, intraoperative hemorrhage, hospital admission, and complications in the two groups.

Results

There were no statistically significant differences between the two groups in mean operative time, hospital stay, or postoperative complications. The average intraoperative blood loss was significantly more in the OM group. There were no surgical complications related to the use of the EX or OM. The comfort level, preoperative setup and intraoperative adjustment of position and angle of the EX were rated higher than the OM group. The image quality, depth perception, and illumination were rated as inferior to that of the OM. The low-cost EX was rated to be superior to that of the OM with regard to education and training purposes.

Conclusion

Our study showed that the low-cost EX appears to be a safe and effective alternative for OM-assisted ACDF with great comfort and ergonomics and serves as an essential tool for education and training purposes. However, some limitations of our EX included slightly inferior image quality and illumination when compared with the OM.
Exploration of the potential mechanism of Baicalin for hepatic fibrosis based on network pharmacology, gut microbiota, and experimental validation
Authors: Liu Sujie , Chen Pingping , Mohammed Shadi A. D. , Li Zihui , Jiang Xin , Wu Juan , Liu Shumin
Published: January 2023

Baicalin (BA) is among the most effective and abundant flavonoids extracted from Scutellaria baicalensis that may be utilized to treat diseases associated with hepatic fibrosis (HF). Through network pharmacology, gut microbiota, and experimental validation, this research intends to elucidate the multi-target mechanism of BA on HF. BA targets were screened using databases and literature. As a result, In the anti-HF mechanism, the BA and 191 HF-associated targets interact, with 9 specific targets indicating that the BA’s anti-HF mechanism is closely linked to gut microbiota. Consequently, rat intestinal content samples were obtained and examined using 16S rRNA sequencing. In the BA-treated group, the gut microbiota was positively regulated at the phylum,and genus levels, with Lactobacillus performing significantly. The study concluded that BA has a multi-targeted anti-HF effect and has changed the gut microbial ecosystem.
Diversification of Sinorhizobium populations associated with Medicago polymorpha and Medicago lupulina in purple soil of China
Authors: Tang Mingxing , Wang Haoyu , Qi Xin , He Teng , Zhang Bin , Wang Entao , Yu Miao , Wang Beinan , Wang Fang , Liu Zhongkuan , Liu Xiaoyun
Published: January 2023

The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S–23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.
Enhancing the ethanol production by exploiting a novel metagenomic-derived bifunctional xylanase/β-glucosidase enzyme with improved β-glucosidase activity by a nanocellulose carrier
Authors: Ariaeenejad Shohreh , Motamedi Elaheh , Kavousi Kaveh , Ghasemitabesh Rezvaneh , Goudarzi Razieh , Salekdeh Ghasem Hosseini , Zolfaghari Behrouz , Roy Swapnoneel
Published: January 2023

Some enzymes can catalyze more than one chemical conversion for which they are physiologically specialized. This secondary function, which is called underground, promiscuous, metabolism, or cross activity, is recognized as a valuable feature and has received much attention for developing new catalytic functions in industrial applications. In this study, a novel bifunctional xylanase/β-glucosidase metagenomic-derived enzyme, PersiBGLXyn1, with underground β-glucosidase activity was mined by in-silico screening. Then, the corresponding gene was cloned, expressed and purified. The PersiBGLXyn1 improved the degradation efficiency of organic solvent pretreated coffee residue waste (CRW), and subsequently the production of bioethanol during a separate enzymatic hydrolysis and fermentation (SHF) process. After characterization, the enzyme was immobilized on a nanocellulose (NC) carrier generated from sugar beet pulp (SBP), which remarkably improved the underground activity of the enzyme up to four-fold at 80°C and up to two-fold at pH 4.0 compared to the free one. The immobilized PersiBGLXyn1 demonstrated 12 to 13-fold rise in half-life at 70 and 80°C for its underground activity. The amount of reducing sugar produced from enzymatic saccharification of the CRW was also enhanced from 12.97 g/l to 19.69 g/l by immobilization of the enzyme. Bioethanol production was 29.31 g/l for free enzyme after 72 h fermentation, while the immobilized PersiBGLXyn1 showed 51.47 g/l production titre. Overall, this study presented a cost-effective in-silico metagenomic approach to identify novel bifunctional xylanase/β-glucosidase enzyme with underground β-glucosidase activity. It also demonstrated the improved efficacy of the underground activities of the bifunctional enzyme as a promising alternative for fermentable sugars production and subsequent value-added products.
Conjugation of plasmid harboring blaNDM-1 in a clinical Providencia rettgeri strain through the formation of a fusion plasmid
Authors: Zhang Meng , Yu Yanhua , Wang Qian , Chen Ran , Wang Yueling , Bai Yuanyuan , Song Zhen , Lu Xinglun , Hao Yingying
Published: January 2023

Providencia rettgeri has recently gained increased importance owing to the New Delhi metallo-β-lactamase (NDM) and other β-lactamases produced by its clinical isolates. These enzymes reduce the efficiency of antimicrobial therapy. Herein, we reported the findings of whole-genome sequence analysis and a comprehensive pan-genome analysis performed on a multidrug-resistant P. rettgeri 18004577 clinical strain recovered from the urine of a hospitalized patient in Shandong, China, in 2018. Providencia rettgeri 18004577 was found to have a genome assembly size of 4.6 Mb with a G + C content of 41%; a circular plasmid p18004577_NDM of 273.3 Kb, harboring an accessory multidrug-resistant region; and a circular, stable IncT plasmid p18004577_Rts of 146.2 Kb. Additionally, various resistance genes were identified in its genome, including blaNDM-1, blaOXA-10, blaPER-4, aph(3′)-VI, ant(2′′)-Ia, ant(3′)-Ia, sul1, catB8, catA1, mph(E), and tet. Conjugation experiments and whole-genome sequencing revealed that the blaNDM-1 gene could be transferred to the transconjugant via the formation of pJ18004577_NDM, a novel hybrid plasmid. Based on the genetic comparison, the main possible formation process for pJ18004577_NDM was the insertion of the [ΔISKox2-IS26-ΔISKox2]-aph(3′)-VI-blaNDM-1 translocatable unit module from p18004577_NDM into plasmid p18004577_Rts in the Russian doll insertion structure (ΔISKox2-IS26-ΔISKox2), which played a role similar to that of IS26 using the “copy-in” route in the mobilization of [aph(3′)-VI]-blaNDM-1. The array, multiplicity, and diversity of the resistance and virulence genes in this strain necessitate stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of the resistance genes. Roary analysis based on 30 P. rettgeri strains pan genome identified 415 core, 756 soft core, 5,744 shell, and 12,967 cloud genes, highlighting the “close” nature of P. rettgeri pan-genome. After a comprehensive pan-genome analysis, representative biological information was revealed that included phylogenetic distances, presence or absence of genes across the P. rettgeri bacteria clade, and functional distribution of proteins. Moreover, pan-genome analysis has been shown to be an effective approach to better understand P. rettgeri bacteria because it helps develop various tailored therapeutic strategies based on their biological similarities and differences.
Sources of nitrous oxide emissions from hydroponic tomato cultivation: Evidence from stable isotope analyses
Authors: Karlowsky Stefan , Buchen-Tschiskale Caroline , Odasso Luca , Schwarz Dietmar , Well Reinhard
Published: January 2023

Introduction

Hydroponic vegetable cultivation is characterized by high intensity and frequent nitrogen fertilizer application, which is related to greenhouse gas emissions, especially in the form of nitrous oxide (N2O). So far, there is little knowledge about the sources of N2O emissions from hydroponic systems, with the few studies indicating that denitrification could play a major role.

Methods

Here, we use evidence from an experiment with tomato plants (Solanum lycopersicum) grown in a hydroponic greenhouse setup to further shed light into the process of N2O production based on the N2O isotopocule method and the 15N tracing approach. Gas samples from the headspace of rock wool substrate were collected prior to and after 15N labeling at two occasions using the closed chamber method and analyzed by gas chromatography and stable isotope ratio mass spectrometry.

Results

The isotopocule analyses revealed that either heterotrophic bacterial denitrification (bD) or nitrifier denitrification (nD) was the major source of N2O emissions, when a typical nutrient solution with a low ammonium concentration (1–6 mg L−1) was applied. Furthermore, the isotopic shift in 15N site preference and in δ18O values indicated that approximately 80–90% of the N2O produced were already reduced to N2 by denitrifiers inside the rock wool substrate. Despite higher concentrations of ammonium present during the 15N labeling (30–60 mg L−1), results from the 15N tracing approach showed that N2O mainly originated from bD. Both, 15N label supplied in the form of ammonium and 15N label supplied in the form of nitrate, increased the 15N enrichment of N2O. This pointed to the contribution of other processes than bD. Nitrification activity was indicated by the conversion of small amounts of 15N-labeled ammonium into nitrate.

Discussion/Conclusion

Comparing the results from N2O isotopocule analyses and the 15N tracing approach, likely a combination of bD, nD, and coupled nitrification and denitrification (cND) was responsible for the vast part of N2O emissions observed in this study. Overall, our findings help to better understand the processes underlying N2O and N2 emissions from hydroponic tomato cultivation, and thereby facilitate the development of targeted N2O mitigation measures.
Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco
Authors: Sun Meili , Shi Caihua , Huang Yang , Wang Hancheng , Li Jianjun , Cai Liuti , Luo Fei , Xiang Ligang , Wang Feng
Published: January 2023

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.
Intercropping enhances microbial community diversity and ecosystem functioning in maize fields
Authors: Xiao Xiwen , Han Lei , Chen Hongri , Wang Jianjun , Zhang Yuping , Hu Ang
Published: January 2023

Background and aims:

Intercropping, a widely used planting pattern, could affect soil physicochemical properties, microbial community diversity, and further crop yields. However, its impacts on soil microbial diversity and ecosystem functioning and further soil sustainability are poorly understood.

Methods:

We conducted field experiments by intercropping maize with four important crops (i.e., sesame, peanut, soybean, and sweet potato), and examined soil microbial community diversity and ecosystem functioning such as microbial biomass and enzyme activities under monocropping and intercropping. We quantified their intercropping effects on microbial diversity and ecosystem functions with effect size metric Cohen d by comparing to the monocropping of maize.

Results:

We found that the four intercropping systems significantly increased soil aggregates in respective of the 2–0.25 mm grain size. Intercropping consistently elevated ecosystem functioning, such as soil enzyme activities of urease, phosphatase, and catalase, soil microbial biomass carbon and soil microbial biomass nitrogen. The Cohen d of bacterial richness also increased from 0.39 to 2.36, the latter of which was significant for maize/peanut intercropping. Notably, these ecosystem functions were strongly associated with the diversity of bacteria and fungi and the relative abundance of their ecological clusters identified with network analysis.

Conclusion:

Together, our findings indicate that intercropping generally affected soil physicochemical properties, ecosystem functions, and promoted microbial community diversity. More importantly, our findings highlight the important roles of microbial diversity of ecological clusters (that is, network modules) in maintaining ecosystem functioning after intercropping. These results will help to better understand the microbial diversity and ecosystem function in intercropping systems and guide agricultural practice.
Rapid biodegradation of atrazine by a novel Paenarthrobacter ureafaciens ZY and its effects on soil native microbial community dynamic
Authors: Zhao Yue , Li Xin , Li Yunyang , Bao Huanyu , Nan Jun , Xu Guoren
Published: January 2023

An atrazine-utilizing bacterium, designated as ZY, was isolated from agricultural soil and identified as Paenarthrobacter ureafaciens. The P. ureafaciens ZY demonstrated a significant degradation capacity of atrazine, with the degradation efficiency of 12.5 mg L−1 h−1 in liquid media (at pH 7, 30°C, and the atrazine level of 100 mg L−1). The P. ureafaciens ZY contained three atrazine-degrading genes (i.e., trzN, atzB, and atzC) could metabolize atrazine to form cyanuric acid, which showed lower biotoxicity than the parent atrazine as predicted by Ecological Structure Activity Relationships model. A laboratory-scale pot experiment was performed to examine the degradation of atrazine by P. ureafaciens ZY inoculation and investigate its effects on the native microbial communities. The results exhibited that the P. ureafaciens ZY was conductive to the degradation of atrazine, increased the total soil phospholipid fatty acids at the atrazine level of 50, 70, and 100 mg kg−1. By using high-throughput sequencing analysis, Frateuria, Dyella, Burkholderia-Caballeronia-Paraburkholderia were considered as the most important indigenous atrazine-degrading microorganisms due to their relative abundances were positively correlated with the atrazine degradation rate. In addition, P. ureafaciens ZY also increased the abundance of atrazine-degrading genus Streptomyces and Bacillus, indicating that there may be a synergic relationship between them in the process of atrazine degradation. Our work provides a new insight between inoculums and native microorganisms on the degradation of atrazine.
New and traditional methods for antibiotic resistance genes removal: Constructed wetland technology and photocatalysis technology
Authors: Chen Pingping , Yu Xiaofei , Zhang Jingyao , Wang Yiqi
Published: January 2023

Antibiotic resistance genes (ARGs) are a new environmental contaminant that poses a major hazard to humans and the environment. This research discusses the methods and drawbacks of two ARG removal approaches, constructed wetlands (CWs) and photocatalysis. CWs primarily rely on the synergistic effects of substrate adsorption, plant uptake, and microbial processes to remove ARGs. The removal of ARGs can be influenced by wetland plants, substrate type, wetland type, and hydraulic conditions. The absolute abundance of ARGs in effluent decreased, but their relative abundance increased. Photocatalysis deactivates ARGs predominantly through reactive oxygen species, with removal effectiveness determined by catalyst type, radiation type, and radiation intensity. The drawback is that it exposes intracellular resistance genes, perhaps increasing the risk of ARG spread. To address the current shortcomings, this paper proposes the feasibility of combining a constructed wetland with photocatalysis technology, which provides a novel strategy for ARG removal.
The power of the smallest: The inhibitory activity of microbial volatile organic compounds against phytopathogens
Authors: Almeida Octávio Augusto Costa , de Araujo Natália Oliveira , Dias Bruno Henrique Silva , de Sant’Anna Freitas Carla , Coerini Luciane Fender , Ryu Choong-Min , de Castro Oliveira Juliana Velasco
Published: January 2023

Plant diseases caused by phytopathogens result in huge economic losses in agriculture. In addition, the use of chemical products to control such diseases causes many problems to the environment and to human health. However, some bacteria and fungi have a mutualistic relationship with plants in nature, mainly exchanging nutrients and protection. Thus, exploring those beneficial microorganisms has been an interesting and promising alternative for mitigating the use of agrochemicals and, consequently, achieving a more sustainable agriculture. Microorganisms are able to produce and excrete several metabolites, but volatile organic compounds (VOCs) have huge biotechnology potential. Microbial VOCs are small molecules from different chemical classes, such as alkenes, alcohols, ketones, organic acids, terpenes, benzenoids and pyrazines. Interestingly, volatilomes are species-specific and also change according to microbial growth conditions. The interaction of VOCs with other organisms, such as plants, insects, and other bacteria and fungi, can cause a wide range of effects. In this review, we show that a large variety of plant pathogens are inhibited by microbial VOCs with a focus on the in vitro and in vivo inhibition of phytopathogens of greater scientific and economic importance in agriculture, such as Ralstonia solanacearum, Botrytis cinerea, Xanthomonas and Fusarium species. In this scenario, some genera of VOC-producing microorganisms stand out as antagonists, including Bacillus, Pseudomonas, Serratia and Streptomyces. We also highlight the known molecular and physiological mechanisms by which VOCs inhibit the growth of phytopathogens. Microbial VOCs can provoke many changes in these microorganisms, such as vacuolization, fungal hyphal rupture, loss of intracellular components, regulation of metabolism and pathogenicity genes, plus the expression of proteins important in the host response. Furthermore, we demonstrate that there are aspects to investigate by discussing questions that are still not very clear in this research area, especially those that are essential for the future use of such beneficial microorganisms as biocontrol products in field crops. Therefore, we bring to light the great biotechnological potential of VOCs to help make agriculture more sustainable.
Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals
Authors: Bitar Ibrahim , Papagiannitsis Costas C. , Kraftova Lucie , Marchetti Vittoria Mattioni , Petinaki Efthymia , Finianos Marc , Chudejova Katerina , Zemlickova Helena , Hrabak Jaroslav
Published: January 2023

Background

VIM metallo-β-lactamases are enzymes characterized by the ability to hydrolyze all β-lactams. Usually, blaVIM-like genes are carried by class 1 integrons. In the Czech Republic, only sporadic cases of VIM-producing Enterobacterales have been reported in which those isolates carried the VIM-1 carbapenemase-encoding integron In110. However, during 2019–2020, an increased number was reported. Therefore, the aim of the current study was to characterize the genetic elements involved in the increased spread of blaVIM genes.

Materials and methods

32 VIM-producing Enterobacterales collected between 2019 and 2020 were subjected to: antimicrobial susceptibility testing, integron analysis, and short reads sequencing. Based on the results, 19 isolates were selected as representative and sequenced using Sequel I platform.

Results

The 32 VIM-producing isolates exhibited variations in the MICs of carbapenems. Based on short-read data, 26 of the 32 sequenced isolates harbored the blaVIM-1 allele while six isolates carried the blaVIM-4 gene. The most prevalent was the In110 integron (n = 24) and two isolates carried the In4873 class 1 integron. The blaVIM-4 allele was identified in class 1 integrons In1174 (n = 3), In416 (n = 1), In2143 (n = 1) and In2150. Long reads sequencing revealed that the blaVIM was carried by: pKPC-CAV1193-like (n = 6), HI1 (pNDM-CIT; n = 4), HI2 (n = 3), FIB (pECLA; n = 2) and N (n = 1) incompatibility groups. Two blaVIM-carrying plasmids could not be typed by the database, while another one was integrated into the chromosome.

Conclusion

We observed the spread of VIM-encoding integrons, mainly of In110, among Enterobacterales isolated from Czech hospitals, but also an increased number of novel elements underlining the ongoing evolution.
Assessing the role of membrane lipids in the action of ruthenium(III) anticancer compounds
Authors: Starosta Radoslaw , Santos Telma C. , Dinis de Sousa Andreia F. , Santos Maria Soledade , Corvo M. Luisa , Tomaz Ana Isabel , de Almeida Rodrigo F. M.
Published: January 2023

This work addresses the possible role of the cell membrane in the molecular mechanism of action of two salan-type ruthenium complexes that were previously shown to be active against human tumor cells, namely [Ru(III)(L1)(PPh3)Cl] and [Ru(III)(L2)(PPh3)Cl] (where L1 is 6,6′-(1R,2R)-cyclohexane-1,2-diylbis(azanediyl)bis(methylene)bis(3-methoxyphenol); and L2 is 2,2′-(1R,2R)-cyclohexane-1,2-diylbis(azanediyl)bis(methylene)bis(4-methoxyphenol)). One-component membrane models were first used, a disordered fluid bilayer of dioleoylphosphatodylcholine (DOPC), and an ordered rigid gel bilayer of dipalmitoylphosphatidylcholine. In addition, two quaternary mixtures of phosphatidylcholine, phosphatidylethanolamine, sphingomyelin and cholesterol were used to mimic the lipid composition either of mammalian plasma membrane (1:1:1:1 mol ratio) or of a cancer cell line membrane (36.2:23.6:6.8:33.4 mol ratio). The results show that both salan ligands L1 and L2 bind relatively strongly to DOPC bilayers, but without significantly affecting their structure. The ruthenium complexes have moderate affinity for DOPC. However, their impact on the membranes was notable, leading to a significant increase in the permeability of the lipid vesicles. None of the compounds compromised liposome integrity, as revealed by dynamic light scattering. Fluorescence spectroscopy studies revealed changes in the biophysical properties of all membrane models analyzed in the presence of the two complexes, which promoted an increased fluidity and water penetration into the lipid bilayer in the one-component systems. In the quaternary mixtures, one of the complexes had an analogous effect (increasing water penetration), whereas the other complex reorganized the liquid ordered and liquid disordered domains. Thus, small structural differences in the metal ligands may lead to different outcomes. To better understand the effect of these complexes in cancer cells, the membrane dipole potential was also measured. For both Ru complexes, an increase in the dipole potential was observed for the cancer cell membrane model, while no alteration was detected on the non-cancer plasma membrane model. Our results show that the action of the Ru(III) complexes tested involves changes in the biophysical properties of the plasma membrane, and that it also depends on membrane lipid composition, which is frequently altered in cancer cells when compared to their normal counterparts.
Ending a bad start: Triggers and mechanisms of co-translational protein degradation
Authors: Eisenack Tom Joshua , Trentini Débora Broch
Published: January 2023

Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis–the state of proteome balance–cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
Balanced activities of Hsp70 and the ubiquitin proteasome system underlie cellular protein homeostasis
Authors: Jawed Areeb , Ho Chi-Ting , Grousl Tomas , Shrivastava Aseem , Ruppert Thomas , Bukau Bernd , Mogk Axel
Published: January 2023

To counteract proteotoxic stress and cellular aging, protein quality control (PQC) systems rely on the refolding, degradation and sequestration of misfolded proteins. In Saccharomyces cerevisiae the Hsp70 chaperone system plays a central role in protein refolding, while degradation is predominantly executed by the ubiquitin proteasome system (UPS). The sequestrases Hsp42 and Btn2 deposit misfolded proteins in cytosolic and nuclear inclusions, thereby restricting the accessibility of misfolded proteins to Hsp70 and preventing the exhaustion of limited Hsp70 resources. Therefore, in yeast, sequestrase mutants show negative genetic interactions with double mutants lacking the Hsp70 co-chaperone Fes1 and the Hsp104 disaggregase (fes1Δ hsp104Δ, ΔΔ) and suffering from low Hsp70 capacity. Growth of ΔΔbtn2Δ mutants is highly temperature-sensitive and results in proteostasis breakdown at non-permissive temperatures. Here, we probed for the role of the ubiquitin proteasome system in maintaining protein homeostasis in ΔΔbtn2Δ cells, which are affected in two major protein quality control branches. We show that ΔΔbtn2Δ cells induce expression of diverse stress-related pathways including the ubiquitin proteasome system to counteract the proteostasis defects. Ubiquitin proteasome system dependent degradation of the stringent Hsp70 substrate firefly Luciferase in the mutant cells mirrors such compensatory activities of the protein quality control system. Surprisingly however, the enhanced ubiquitin proteasome system activity does not improve but aggravates the growth defects of ΔΔbtn2Δ cells. Reducing ubiquitin proteasome system activity in the mutant by lowering the levels of functional 26S proteasomes improved growth, increased refolding yield of the Luciferase reporter and attenuated global stress responses. Our findings indicate that an imbalance between Hsp70-dependent refolding, sequestration and ubiquitin proteasome system-mediated degradation activities strongly affects protein homeostasis of Hsp70 capacity mutants and contributes to their severe growth phenotypes.