bluuebunny/crossref_metadata_2025 huggingface dataset:
Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis
Authors: Messager Erwan , Giguet-Covex Charline , Doyen Elise , Etienne David , Gielly Ludovic , Sabatier Pierre , Banjan Mathilde , Develle Anne-Lise , Didier Julien , Poulenard Jérôme , Julien Andréa , Arnaud Fabien
Published: June 2022

Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.
Inference of a Boolean Network From Causal Logic Implications
Authors: Maheshwari Parul , Assmann Sarah M. , Albert Reka
Published: June 2022

Biological systems contain a large number of molecules that have diverse interactions. A fruitful path to understanding these systems is to represent them with interaction networks, and then describe flow processes in the network with a dynamic model. Boolean modeling, the simplest discrete dynamic modeling framework for biological networks, has proven its value in recapitulating experimental results and making predictions. A first step and major roadblock to the widespread use of Boolean networks in biology is the laborious network inference and construction process. Here we present a streamlined network inference method that combines the discovery of a parsimonious network structure and the identification of Boolean functions that determine the dynamics of the system. This inference method is based on a causal logic analysis method that associates a logic type (sufficient or necessary) to node-pair relationships (whether promoting or inhibitory). We use the causal logic framework to assimilate indirect information obtained from perturbation experiments and infer relationships that have not yet been documented experimentally. We apply this inference method to a well-studied process of hormone signaling in plants, the signaling underlying abscisic acid (ABA)—induced stomatal closure. Applying the causal logic inference method significantly reduces the manual work typically required for network and Boolean model construction. The inferred model agrees with the manually curated model. We also test this method by re-inferring a network representing epithelial to mesenchymal transition based on a subset of the information that was initially used to construct the model. We find that the inference method performs well for various likely scenarios of inference input information. We conclude that our method is an effective approach toward inference of biological networks and can become an efficient step in the iterative process between experiments and computations.
SMRT Sequencing Reveals Candidate Genes and Pathways With Medicinal Value in Cipangopaludina chinensis
Authors: Zhou Kangqi , Chen Zhong , Du Xuesong , Huang Yin , Qin Junqi , Wen Luting , Pan Xianhui , Lin Yong
Published: June 2022

Cipangopaludina chinensis is an economically important aquatic snail with high medicinal value. However, molecular biology research on C. chinensis is limited by the lack of a reference genome, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. chinensis. Herein, we conducted the first full-length transcriptome analysis of C. chinensis using PacBio single-molecule real-time (SMRT) sequencing technology. We identified a total of 26,312 unigenes with an average length of 2,572 bp, of which the largest number of zf-c2h2 transcription factor families (120,18.24%) were found, and also observed that the majority of the 8,058 SSRs contained 4-7 repeat units, which provided data for subsequent work on snail genetics Subsequently, 91.86% (24,169) of the genes were successfully annotated to the four major databases, while the highest homology was observed with Pomacea canaliculata. Functional annotation revealed that the majority of transcripts were enriched in metabolism, signal transduction and Immune-related pathways, and several candidate genes involved in drug metabolism and immune response were identified (e.g., CYP1A1, CYP2J, CYP2U1, GST, ,PIK3, PDE3A, PRKAG). This study lays a foundation for future molecular biology research and provides a reference for studying genes associated with the medicinal value of C. chinensis.
Gut Mycobiome in Patients With Chronic Kidney Disease Was Altered and Associated With Immunological Profiles
Authors: Hu Jialin , Wei Shichao , Gu Yifeng , Wang Yang , Feng Yangkun , Sheng Jiayi , Hu Lei , Gu Chaoqun , Jiang Peng , Tian Yu , Guo Wei , Lv Longxian , Liu Fengping , Zou Yeqing , Yan Feng , Feng Ninghan
Published: June 2022

Objectives

Mounting evidence suggests that bacterial dysbiosis and immunity disorder are associated with patients with chronic kidney disease (CKD), but the mycobiome is beginning to gain recognition as a fundamental part of our microbiome. We aim to characterize the profile of the mycobiome in the gut of CKD patients and its correlation to serum immunological profiles.

Methods and materials

Ninety-two CKD patients and sex–age–body mass index (BMI)–matched healthy controls (HCs) were recruited. Fresh samples were collected using sterile containers. ITS transcribed spacer ribosomal RNA gene sequencing was performed on the samples. An immunoturbidimetric test was used to assess the serum levels of immunological features.

Results

The CKD cohort displayed a different microbial community from that in the HC cohort according to principal coordinate analysis (PCoA). (P=0.001). The comparison of the two cohorts showed that the CKD cohort had significantly higher gut microbial richness and diversity (P<0.05). The CKD cohort had lower abundances of Candida, Bjerkandera, Rhodotorula, and Ganoderma compared to the HC cohort, while it had higher Saccharomyces (P<0.05). However, the microbial community alteration was inconsistent with the severity of kidney damage in patients, as only patients in CKD stage 1~3 had differed microbial community concerning for HCs based on PCoA (P<0.05). The serum concentration of the kappa light chain in CKD patients was positively associated with Saccharomyces, whereas the it was negatively associated with Ganoderma (P<0.05).

Conclusions

Not only was gut mycobiome dysbiosis observed in CKD patients, but the dysbiosis was also associated with the immunological disorder. These findings suggest that therapeutic strategies targeting gut mycobiome might be effective.
Soluble Fc Receptor for IgM in Sera From Subsets of Patients With Chronic Lymphocytic Leukemia as Determined by a New Mouse Monoclonal Antibody
Authors: Mahmoudi Aliabadi Pedram , Teuber Ruth , Jani Peter K. , Wilson Landon , Enghard Philipp , Barnes Stephen , Chiorazzi Nicholas , Radbruch Andreas , Melchers Fritz , Kubagawa Hiromi
Published: June 2022

The FcR for IgM (FcµR) is the newest member of the FcR family, selectively expressed by lymphocytes, and distinct from FcRs for switched Ig isotypes that are expressed by various immune cell types and non-hematopoietic cells. From studies of Fcmr-ablated mice, FcµR was shown to have a regulatory function in B-cell tolerance, as evidenced by high serum titers of autoantibodies of the IgM and IgG isotypes in mutant mice. In our previous studies, both cell-surface and serum FcµR levels were elevated in patients with chronic lymphocytic leukemia (CLL), where antigen-independent self-ligation of BCR is a hallmark of the neoplastic B cells. This was assessed by sandwich ELISA using two different ectodomain-specific mAbs. To determine whether the serum FcµR is derived from cleavage of its cell-surface receptor (shedding) or its alternative splicing to skip the transmembrane exon resulting in a 70-aa unique hydrophilic C-terminus (soluble), we developed a new mouse IgG1κ mAb specific for human soluble FcμR (solFcμR) by taking advantages of the unique nature of transductant stably producing His-tagged solFcµR and of an in vivo differential immunization. His-tagged solFcμR attached to exosomes and plasma membranes, allowing immunization and initial hybridoma screening without purification of solFcμR. Differential immunization with tolerogen (membrane FcμR) and immunogen (solFcμR) also facilitated to generate solFcμR-specific hybridomas. The resultant solFcμR-specific mAb reacted with serum FcµR in subsets of CLL patients. This mAb, along with another ectodomain-specific mAb, will be used for verifying the hypothesis that the production of solFcµR is the consequence of chronic stimulation of BCR.
HBx Mediated Increase of DDX17 Contributes to HBV-Related Hepatocellular Carcinoma Tumorigenesis
Authors: Dong Mei-Ling , Wen Xu , He Xin , Ren Ji-Hua , Yu Hai-Bo , Qin Yi-Ping , Yang Zhen , Yang Min-Li , Zhou Chong-Yang , Zhang Hui , Cheng Sheng-Tao , Chen Juan
Published: June 2022

HBV is strongly associated with HCC development and DEAD-box RNA helicase 17 (DDX17) is a very important member of the DEAD box family that plays key roles in HCC development by promoting cancer metastasis. However, the important role of DDX17 in the pathogenesis of HBV-related HCC remains unclear. In this study, we investigated the role of DDX17 in the replication of HBV and the development of HBV-associated HCC. Based on data from the GEO database and HBV-infected cells, we found that DDX17 was upregulated by the HBV viral protein X (HBx). Mechanistically, increased DDX17 expression promoted HBV replication and transcription by upregulating ZWINT. Further study showed that DDX17 could promote HBx-mediated HCC metastasis. Finally, the promotive effect of DDX17 on HBV and HBV-related HCC was confirmed in vivo. In summary, the results revealed the novel role of DDX17 in the replication of HBV and the metastasis of HBV-associated HCC.
Subsets of Tissue CD4 T Cells Display Different Susceptibilities to HIV Infection and Death: Analysis by CyTOF and Single Cell RNA-seq
Authors: Luo Xiaoyu , Frouard Julie , Zhang Gang , Neidleman Jason , Xie Guorui , Sheedy Emma , Roan Nadia R. , Greene Warner C.
Published: June 2022

CD4 T lymphocytes belong to diverse cellular subsets whose sensitivity or resistance to HIV-associated killing remains to be defined. Working with lymphoid cells from human tonsils, we characterized the HIV-associated depletion of various CD4 T cell subsets using mass cytometry and single-cell RNA-seq. CD4 T cell subsets preferentially killed by HIV are phenotypically distinct from those resistant to HIV-associated cell death, in a manner not fully accounted for by their susceptibility to productive infection. Preferentially-killed subsets express CXCR5 and CXCR4 while preferentially-infected subsets exhibit an activated and exhausted effector memory cell phenotype. Single-cell RNA-seq analysis reveals that the subsets of preferentially-killed cells express genes favoring abortive infection and pyroptosis. These studies emphasize a complex interplay between HIV and distinct tissue-based CD4 T cell subsets, and the important contribution of abortive infection and inflammatory programmed cell death to the overall depletion of CD4 T cells that accompanies untreated HIV infection.
Neuro-Immune Regulation in Inflammation and Airway Remodeling of Allergic Asthma
Authors: Zhang Ning , Xu Jing , Jiang Congshan , Lu Shemin
Published: June 2022

Allergic asthma is a common chronic inflammation of the airways and causes airway remodeling eventually. For a long time, investigators have been focusing on the immunological mechanism of asthma. However, in recent years, the role of neuro-regulation in the occurrence of asthma has gradually attracted investigators’ attention. In this review, we firstly describe neuro-immune regulation in inflammation of allergic asthma from two aspects: innate immunity and adaptive immunity. Secondly, we introduce neuro-immune regulation in airway remodeling of asthma. Finally, we prospect the role of pulmonary neuroendocrine cells in the development of asthma. In general, the amount of researches is limited. Further researches on the neural regulation during the occurrence of asthma will help us clarify the mechanism of asthma more comprehensively and find more effective ways to prevent and control asthma.
Xenotransplantation of Genetically Modified Neonatal Pig Islets Cures Diabetes in Baboons
Authors: Hawthorne Wayne J. , Salvaris Evelyn J. , Chew Yi Vee , Burns Heather , Hawkes Joanne , Barlow Helen , Hu Min , Lew Andrew M. , Nottle Mark B. , O’Connell Philip J. , Cowan Peter J.
Published: June 2022

Xenotransplantation using porcine donors is rapidly approaching clinical applicability as an alternative therapy for treatment of many end-stage diseases including type 1 diabetes. Porcine neonatal islet cell clusters (NICC) have normalised blood sugar levels for relatively short periods in the preclinical diabetic rhesus model but have met with limited success in the stringent baboon model. Here we report that NICC from genetically modified (GM) pigs deleted for αGal and expressing the human complement regulators CD55 and CD59 can cure diabetes long-term in immunosuppressed baboons, with maximum graft survival exceeding 22 months. Five diabetic baboons were transplanted intraportally with 9,673 – 56,913 islet equivalents (IEQ) per kg recipient weight. Immunosuppression consisted of T cell depletion with an anti-CD2 mAb, tacrolimus for the first 4 months, and maintenance with belatacept and anti-CD154; no anti-inflammatory treatment or cytomegalovirus (CMV) prophylaxis/treatment was given. This protocol was well tolerated, with all recipients maintaining or gaining weight. Recipients became insulin-independent at a mean of 87 ± 43 days post-transplant and remained insulin-independent for 397 ± 174 days. Maximum graft survival was 675 days. Liver biopsies showed functional islets staining for all islet endocrine components, with no evidence of the inflammatory blood-mediated inflammatory reaction (IBMIR) and minimal leukocytic infiltration. The costimulation blockade-based immunosuppressive protocol prevented an anti-pig antibody response in all recipients. In conclusion, we demonstrate that genetic modification of the donor pig enables attenuation of early islet xenograft injury, and in conjunction with judicious immunosuppression provides excellent long-term function and graft survival in the diabetic baboon model.
Contribution of Dysregulated B-Cells and IgE Antibody Responses to Multiple Sclerosis
Authors: Seals Malik R. , Moran Monica M. , Leavenworth Jonathan D. , Leavenworth Jianmei W.
Published: June 2022

Multiple sclerosis (MS), a debilitating autoimmune inflammatory disease that affects the brain and spinal cord, causes demyelination of neurons, axonal damage, and neurodegeneration. MS and the murine experimental autoimmune encephalomyelitis (EAE) model have been viewed mainly as T-cell-mediated diseases. Emerging data have suggested the contribution of B-cells and autoantibodies to the disease progression. However, the underlying mechanisms by which dysregulated B-cells and antibody response promote MS and EAE remain largely unclear. Here, we provide an updated review of this specific subject by including B-cell biology and the role of B-cells in triggering autoimmune neuroinflammation with a focus on the regulation of antibody-producing B-cells. We will then discuss the role of a specific type of antibody, IgE, as it relates to the potential regulation of microglia and macrophage activation, autoimmunity and MS/EAE development. This knowledge can be utilized to develop new and effective therapeutic approaches to MS, which fits the scope of the Research Topic “Immune Mechanism in White Matter Lesions: Clinical and Pathophysiological Implications”.
Pathogenesis of SARS-CoV-2 and Mycobacterium tuberculosis Coinfection
Authors: Shah Taif , Shah Zahir , Yasmeen Nafeesa , Baloch Zulqarnain , Xia Xueshan
Published: June 2022

Coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is an infectious disease that poses severe threats to global public health and significant economic losses. The COVID-19 global burden is rapidly increasing, with over 246.53 million COVID-19 cases and 49.97 million deaths reported in the WHO 2021 report. People with compromised immunity, such as tuberculosis (TB) patients, are highly exposed to severe COVID-19. Both COVID-19 and TB diseases spread primarily through respiratory droplets from an infected person to a healthy person, which may cause pneumonia and cytokine storms, leading to severe respiratory disorders. The COVID-19-TB coinfection could be fatal, exacerbating the current COVID-19 pandemic apart from cellular immune deficiency, coagulation activation, myocardial infarction, and other organ dysfunction. This study aimed to assess the pathogenesis of SARS-CoV-2-Mycobacterium tuberculosis coinfections. We provide a brief overview of COVID19-TB coinfection and discuss SARS-CoV-2 host cellular receptors and pathogenesis. In addition, we discuss M. tuberculosis host cellular receptors and pathogenesis. Moreover, we highlight the impact of SARS-CoV-2 on TB patients and the pathological pathways that connect SARS-CoV-2 and M. tuberculosis infection. Further, we discuss the impact of BCG vaccination on SARS-CoV-2 cases coinfected with M. tuberculosis, as well as the diagnostic challenges associated with the coinfection.
Adaptive Strategies and Evolutionary Responses of Microbial Organisms to Changing Oceans
Authors: Arromrak Bovern Suchart , Li Zhenzhen , Gaitán-Espitia Juan Diego
Published: June 2022

Environmental variability is an intrinsic characteristic of nature. Variability in factors such as temperature, UV, salinity, and nutrient availability can influence structural and functional properties of marine microbial organisms. This influence has profound implications for biochemical cycles and the ecosystem services provided by the oceans. In this review we discuss some of the most relevant mechanisms underpinning adaptive strategies of microbial organisms in variable and dynamic oceans. We assess the extent to which the magnitude and rate of environmental change influence plastic phenotypic adjustments and evolutionary trajectories of microbial populations. This understanding is fundamental for developing better predictions regarding microbial dynamics at ecological and evolutionary time-scales and in response to climate change.
Seasonal and Form-Specific Gene Expression Signatures Uncover Different Generational Strategies of the Pelagic Tunicate Salpa thompsoni During the Southern Ocean Winter
Authors: Müller Svenja J. , Michael Katharina , Urso Ilenia , Sales Gabriele , De Pittà Cristiano , Suberg Lavinia , Wessels Wiebke , Pakhomov Evgeny A. , Meyer Bettina
Published: June 2022

The pelagic tunicateSalpa thompsoniis recognized as a major metazoan grazer in the Southern Ocean. Long term observations show an increase in this species’ biomass and a southward shift in its distribution both of which are positively correlated with ocean warming and winter sea ice decline around the Antarctic Peninsula. However, our understanding on how salps adapt their life cycle to the extreme seasonality of the Southern Ocean and the putative differences between its two reproductive forms (aggregates, solitaries) is rudimentary. In particular, our current knowledge of whether and howS. thompsonioverwinter is limited, largely due to winter sampling constraints. In this study, we investigated the form-specific gene expression profiles ofSalpa thompsoniduring the austral autumn and winter. Between the seasons, genes related to translation showed the biggest difference in gene expression. We found more genes were upregulated in solitaries compared to aggregates, indicating a potentially form-specific overwintering strategy. Our data provide first insights into the seasonal and form-specific physiology of salps by considering their complex life cycle, thereby contributing to a more comprehensive understanding of the response of salps to seasonal changes in their environment and to anthropogenic induced global climate change.
Host Defense Peptides at the Ocular Surface: Roles in Health and Major Diseases, and Therapeutic Potentials
Authors: Ting Darren Shu Jeng , Mohammed Imran , Lakshminarayanan Rajamani , Beuerman Roger W. , Dua Harminder S.
Published: June 2022

Sight is arguably the most important sense in human. Being constantly exposed to the environmental stress, irritants and pathogens, the ocular surface – a specialized functional and anatomical unit composed of tear film, conjunctival and corneal epithelium, lacrimal glands, meibomian glands, and nasolacrimal drainage apparatus – serves as a crucial front-line defense of the eye. Host defense peptides (HDPs), also known as antimicrobial peptides, are evolutionarily conserved molecular components of innate immunity that are found in all classes of life. Since the first discovery of lysozyme in 1922, a wide range of HDPs have been identified at the ocular surface. In addition to their antimicrobial activity, HDPs are increasingly recognized for their wide array of biological functions, including anti-biofilm, immunomodulation, wound healing, and anti-cancer properties. In this review, we provide an updated review on: (1) spectrum and expression of HDPs at the ocular surface; (2) participation of HDPs in ocular surface diseases/conditions such as infectious keratitis, conjunctivitis, dry eye disease, keratoconus, allergic eye disease, rosacea keratitis, and post-ocular surgery; (3) HDPs that are currently in the development pipeline for treatment of ocular diseases and infections; and (4) future potential of HDP-based clinical pharmacotherapy for ocular diseases.
Manipulation of Gut Microbiota as a Key Target for Crohn's Disease
Authors: Rashed Reem , Valcheva Rosica , Dieleman Levinus A.
Published: June 2022

Crohn's disease (CD) is an inflammatory bowel disease (IBD) sub-type characterized by transmural chronic inflammation of the gastrointestinal tract. Research indicates a complex CD etiology involving genetic predisposition and immune dysregulation in response to environmental triggers. The chronic mucosal inflammation has been associated with a dysregulated state, or dysbiosis, of the gut microbiome (bacteria), mycobiome (fungi), virome (bacteriophages and viruses), and archeaome (archaea) further affecting the interkingdom syntrophic relationships and host metabolism. Microbiota dysbiosis in CD is largely described by an increase in facultative anaerobic pathobionts at the expense of strict anaerobic Firmicutes, such as Faecalibacterium prausnitzii. In the mycobiome, reduced fungal diversity and fungal-bacteria interactions, along with a significantly increased abundance of Candida spp. and a decrease in Saccharomyces cerevisiae are well documented. Virome analysis also indicates a significant decrease in phage diversity, but an overall increase in phages infecting bacterial groups associated with intestinal inflammation. Finally, an increase in methanogenic archaea such as Methanosphaera stadtmanae exhibits high immunogenic potential and is associated with CD etiology. Common anti-inflammatory medications used in CD management (amino-salicylates, immunomodulators, and biologics) could also directly or indirectly affect the gut microbiome in CD. Other medications often used concomitantly in IBD, such as antibiotics, antidepressants, oral contraceptives, opioids, and proton pump inhibitors, have shown to alter the gut microbiota and account for increased susceptibility to disease onset or worsening of disease progression. In contrast, some environmental modifications through alternative therapies including fecal microbiota transplant (FMT), diet and dietary supplements with prebiotics, probiotics, and synbiotics have shown potential protective effects by reversing microbiota dysbiosis or by directly promoting beneficial microbes, together with minimal long-term adverse effects. In this review, we discuss the different approaches to modulating the global consortium of bacteria, fungi, viruses, and archaea in patients with CD through therapies that include antibiotics, probiotics, prebiotics, synbiotics, personalized diets, and FMT. We hope to provide evidence to encourage clinicians and researchers to incorporate these therapies into CD treatment options, along with making them aware of the limitations of these therapies, and indicate where more research is needed.
Mini-Review: Gut-Microbiota and the Sex-Bias in Autoimmunity – Lessons Learnt From Animal Models
Authors: Rosser Elizabeth C. , de Gruijter Nina M. , Matei Diana E.
Published: June 2022

It is well appreciated that there is a female preponderance in the development of most autoimmune diseases. Thought to be due to a complex interplay between sex chromosome complement and sex-hormones, however, the exact mechanisms underlying this sex-bias remain unknown. In recent years, there has been a focus on understanding the central pathogenic role of the bacteria that live in the gut, or the gut-microbiota, in the development of autoimmunity. In this review, we discuss evidence from animal models demonstrating that the gut-microbiota is sexually dimorphic, that there is a bidirectional relationship between the production of sex-hormones and the gut-microbiota, and that this sexual dimorphism within the gut-microbiota may influence the sex-bias observed in autoimmune disease development. Collectively, these data underline the importance of considering sex as a variable when investigating biological pathways that contribute to autoimmune disease risk.
Pulmonary Recovery Following Corrective Surgery in Adult Patients With Severe Scoliosis: A Minimum of Five-Year Follow-Up
Authors: Zhou Xin , Zhang Zheng , Yang Yue , Ma Jun , Meng Yichen , Wang Ce , Zhou Xuhui
Published: June 2022

Background

Halo gravity traction (HGT) has been reported to be a safe and effective adjunctive method for the management of scoliosis. However, the direct effects of HGT on the lung recovery of adult patients with scoliosis remain obscure.

Objective

To investigate changes in lung volume and pulmonary function in adult patients with severe scoliosis who underwent posterior spinal fusion concomitant with preoperative halo gravity traction.

Methods

A total of 47 patients with a minimum 5-year follow-up who underwent posterior spinal instrumentation and fusion using preoperative halo–gravity traction were analyzed. Pulmonary function tests and three-dimensional CT were performed to evaluate changes in lung function and lung volume, respectively.

Results

There was significant change in the Cobb angle of the major curve after halo gravity traction (P < 0.0001). Significant improvement in both Cobb angle (P < 0.0001) and thoracic kyphosis (P = 0.034) after corrective surgery was observed. Pulmonary function did not change significantly during traction. However, a significant decline in absolute and percent-predicted pulmonary function values was noted following surgery. The average change in lung volume did not show statistical differences during traction. At 5-year postoperative follow-up, the mean values revealed a significant increase in total lung volume (P < 0.0001) and concave lung volume (P < 0.0001) with surgical correction, but no statistically significant change in lung volume on the convex side (P = 0.57). Postoperative pulmonary complications occurred in nine cases with lower preoperative pulmonary function, indicating the importance of performing spirometry before corrective surgery.

Conclusions

We found that halo gravity traction prior to corrective surgery was less useful in improving pulmonary function in adult patients with severe scoliosis. However, these patients were expected to have increased lung volume after correction of the deformity.
Effect of No Tillage System on Soil Fungal Community Structure of Cropland in Mollisol: A Case Study
Authors: Gao Ming , Li Haiyu , Li Meng
Published: June 2022

Conservation tillage is generally regarded as a sustainable farming system for the future. The fungal community structure has a strong response to conservation tillage. However, how the conservation tillage system affects the soil fungal community structure is little known. Using the high-throughput sequencing technology, the soil fungal community was explored under no tillage (NT) and conventional tillage (CT) in Northeast China Mollisol. The copy number of fungal genes in NT20 was significantly lower than that in other treatments. NT changed the composition of soil fungal communities at the taxonomic level of phylum and genus. The diversity indices of the soil fungal community in no tillage at soil depths of 0–5 cm (NT5) were significantly higher than those in soil depths of 5–20 cm (NT20). The fungal community under NT and CT could form a good cluster distribution and NT5, conventional tillage at soil depths of 0–5 cm (CT5) and 5–20 cm (CT20) had specific indicator species. Most of the potential pathogens were significantly higher in NT5 than in NT20. Tillage and soil depth could explain 64% of the diversity and 95% of the composition of the fungal community, which indirectly changed the diversity and composition of fungi by using soil organic carbon, pH value, and soil bulk density. Furthermore, soil organic carbon (SOC) best explained the soil fungal community, followed by soil pH. The study indicated that the NT system had a comprehensive effect on the soil fungal community and SOC is the most crucial factor in determining this community.
Rotational Mechanism of FO Motor in the F-Type ATP Synthase Driven by the Proton Motive Force
Authors: Kubo Shintaroh , Takada Shoji
Published: June 2022

In FOF1 ATP synthase, driven by the proton motive force across the membrane, the FO motor rotates the central rotor and induces conformational changes in the F1 motor, resulting in ATP synthesis. Recently, many near-atomic resolution structural models have been obtained using cryo-electron microscopy. Despite high resolution, however, static information alone cannot elucidate how and where the protons pass through the FO and how proton passage is coupled to FO rotation. Here, we review theoretical and computational studies based on FO structure models. All-atom molecular dynamics (MD) simulations elucidated changes in the protonation/deprotonation of glutamate—the protein-carrier residue—during rotation and revealed the protonation states that form the “water wire” required for long-range proton hopping. Coarse-grained MD simulations unveiled a free energy surface based on the protonation state and rotational angle of the rotor. Hybrid Monte Carlo and MD simulations showed how proton transfer is coupled to rotation.
Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes
Authors: Paul Shyam Sundar , Rama Rao Savaram Venkata , Hegde Nagendra , Williams Nicola J. , Chatterjee Rudra Nath , Raju Mantena Venkata Lakshmi Narasimha , Reddy Godumagadda Narender , Kumar Vikas , Phani Kumar Prakki Santosh , Mallick Sathi , Gargi Madhuranjana
Published: June 2022

Antimicrobial growth promoters (AGPs) are commonly used in broiler production. There is a huge societal concern around their use and their contribution to the proliferation of antimicrobial resistance (AMR) in food-producing animals and dissemination to humans or the environment. However, there is a paucity of comprehensive experimental data on their impact on poultry production and the AMR resistome. Here, we investigated the effect of five antimicrobial growth promoters (virginiamycin, chlortetracycline, bacitracin methyl disalicylate, lincomycin, and tylosin) used in the commercial broiler production in the Indian subcontinent and in the different parts of the world for three consecutive production cycles on performance variables and also the impact on gut bacteria, bacteriophage, and resistome profile using culture-independent approaches. There was no significant effect of AGPs on the cumulative growth or feed efficiency parameters at the end of the production cycles and cumulative mortality rates were also similar across groups. Many antibiotic resistance genes (ARGs) were ubiquitous in the chicken gut irrespective of AGP supplementation. In total, 62 ARGs from 15 antimicrobial classes were detected. Supplementation of AGPs influenced the selection of several classes of ARGs; however, this was not correlated necessarily with genes relevant to the AGP drug class; some AGPs favored the selection of ARGs related to antimicrobials not structurally related to the AGP. AGPs did not impact the gut bacterial community structure, including alpha or beta diversity significantly, with only 16–20 operational taxonomic units (OTUs) of bacteria being altered significantly. However, several AGPs significantly reduced the population density of some of the potential pathogenic genera of bacteria, such as Escherichia coli. Chlortetracycline increased the abundance of Escherichia phage, whereas other AGPs did not influence the abundance of bacteriophage significantly. Considering the evidence that AGPs used in poultry production can select for resistance to more than one class of antimicrobial resistance, and the fact that their effect on performance is not significant, their use needs to be reduced and there is a need to monitor the spread of ARGs in broiler chicken farms.
Boric Acid Solution Inhibits Candida albicans Infections in Mouse Skin via the IL-23/Th17 Axis
Authors: Liu Zhao , Liu Qing , Xu Yanyan , Han Zhao , Zhang Ling , Li Xiaojing
Published: June 2022

The purpose of this study was to investigate the effect and mechanism of 3% boric acid solution (BAS) against Candida albicans (CA) infection via the interleukin-23 (IL-23)/T helper 17 cell (Th17) axis. 36 female mice were randomly divided into 3 groups, and 2 injection sites on the back of the mice were chosen at random. Group N was injected with sterile water for injection (SWFI), and Group M and Group B were injected with CA mycelium suspension. After successful model verification, the remaining mice entered the following treatments 5 days later. Group B was treated with 3% BAS, Group M was treated with SWFI, and Group N was not treated. Levels of interleukin-17 (IL-17), IL-22, and IL-23 in mouse blood were measured on days 1, 3, 5, and 7 of treatment. On day 7, IL-17, IL-22, and IL-23 in mouse skin were detected. Serum levels of IL-17, IL-22, and IL-23 in Group M were higher than in Group N on the first day of treatment (p < 0.05). Expression levels of IL-17, IL-22, and IL-23 in the epidermis of the skin lesions in Group M were higher than in Group N on day 7 (p < 0.05). The serum level of IL-17 in Group B was higher than in Group M on days 5 and 7 (p < 0.05). Serum levels of IL-22 in Group B on days 1, 5, and 7 were higher than in Group M (p < 0.05). Serum levels of IL-23 in Group B were higher than in Group M on days 3, 5, and 7 (p < 0.05). IL-17 and IL-23 in Group B reached a peak on day 5, significantly different on days 1, 3, and 7 (p < 0.05). The expression intensity of IL-17, IL-22, and IL-23 in the skin lesions of Group B was higher than that of Group M on day 7 (p < 0.05). We conclude that IL-17, IL-22, and IL-23 are involved in the anti-CA activity in mouse skin, and 3% BAS increased IL-17, IL-22, and IL-23 to mediate these effects.
The Role of Exopolysaccharides in Direct Interspecies Electron Transfer
Authors: Zhuang Zheng , Xia Xue , Yang Guiqin , Zhuang Li
Published: June 2022

Direct interspecies electron transfer (DIET) is an effective mechanism for microbial species to exchange electrons cooperatively during syntrophic metabolism. It is generally accepted that DIET is mainly mediated by electrically conductive pili and outer surface c-type cytochromes (c-Cyts). However, as an extracellular matrix is ubiquitous and abundant on the surface of microorganisms, the effect and mechanism of exopolysaccharides on DIET are still unclear. This study constructed a co-culture of exopolysaccharides-deficient Geobacter sulfurreducens with Geobacter metallireducens to explore the role of exopolysaccharides in DIET. Results revealed that the deficiency of exopolysaccharides extended the metabolic period of the co-culture by 44.4% and changed the proportions of each species in the co-culture. The exopolysaccharides-deficient co-culture failed to form large, tight spherical aggregates and the expression of c-Cyts and pili was decreased. The addition of magnetite and granular activated carbon (GAC), respectively, might compensate for the functions of c-Cyts and pili in the first generation of co-culture, but the stimulatory effect on the metabolic stable period co-culture was fairly limited. These findings demonstrate that non-conductive exopolysaccharides are an important component of DIET aggregates and an extracellular matrix for DIET-required c-Cyts.
Preparation of Photo-Bioelectrochemical Cells With the RC-LH Complex From Roseiflexus castenholzii
Authors: Du Jinsong , Xin Jiyu , Liu Menghua , Zhang Xin , He Huimin , Wu Jingyi , Xu Xiaoling
Published: June 2022

Roseiflexus castenholzii is an ancient green non-sulfur bacteria that absorbs the solar energy through bacteriochlorophylls (BChls) bound in the only light harvesting (LH) complex, and transfers to the reaction center (RC), wherein primary charge separation occurs and transforms the energy into electrochemical potentials. In contrast to purple bacteria, R. castenholzii RC-LH (rcRC-LH) does not contain an H subunit. Instead, a tightly bound tetraheme cytochrome c subunit is exposed on the P-side of the RC, which contains three BChls, three bacteriopheophytins (BPheos), two menaquinones, and one iron for electron transfer. These novel structural features of the rcRC-LH are advantageous for enhancing the electron transfer efficiency and subsequent photo-oxidation of the c-type hemes. However, the photochemical properties of rcRC-LH and its applications in developing the photo-bioelectrochemical cells (PBECs) have not been characterized. Here, we prepared a PBEC using overlapped fluorine-doped tin oxide (FTO) glass and Pt-coated glass as electrodes, and rcRC-LH mixed with varying mediators as the electrolyte. Absence of the H subunit allows rcRC-LH to be selectively adhered onto the hydrophilic surface of the front electrode with its Q-side. Upon illumination, the photogenerated electrons directly enter the front electrode and transfer to the counter electrode, wherein the accepted electrons pass through the exposed c-type hemes to reduce the excited P+, generating a steady-state current of up to 320 nA/cm2 when using 1-Methoxy-5-methylphenazinium methyl sulfate (PMS) as mediator. This study demonstrated the novel photoelectric properties of rcRC-LH and its advantages in preparing effective PBECs, showcasing a potential of this complex in developing new type PBECs.
Genomic Analysis of KPC-2-Producing Klebsiella pneumoniae ST11 Isolates at the Respiratory Department of a Tertiary Care Hospital in Beijing, China
Authors: Guo Ling , Wang Lifeng , Zhao Qiang , Ye Liyan , Ye Kun , Ma Yanning , Shen Dingxia , Yang Jiyong
Published: June 2022

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important pathogen causing hospital-associated outbreaks worldwide. The spread of K. pneumoniae carbapenemase-2 (KPC-2)-producing CRKP is primarily associated with sequence type (ST) 11.

Methods

A total of 152 KPC-2-producing K. pneumoniae ST11 isolates were collected from the respiratory department of a tertiary care hospital in Beijing, China between 2009 and 2018. The genome sequencing of these isolates was performed on the HiSeq X Ten sequencer. Multilocus sequence typing (MLST), capsular type, plasmid replicon types and resistance genes were identified. Fifteen isolates were selected for the subsequent single-molecule real-time (SMRT) sequencing on the PacBio RS II. Alignment of the complete sequences of the plasmids carrying blaKPC–2 and/or virulence genes was performed by using BRIG and Easyfig.

Results

From 2012 to 2018, the detection rate of the blaKPC–2-carrying CRKP rose rapidly from 3.3 to 28.1%. KPC-2-producing K. pneumoniae ST11 isolates were dominant in CRKP, which emerged in 2012 and caused several outbreaks. Most isolates exhibited multidrug-resistant to commonly used antibiotics, while all the isolates remained susceptible to tigecycline and polymyxin B. The single nucleotide polymorphism (SNP) analysis showed that all these 152 KPC-2-producing K. pneumoniae ST11 isolates could be divided into three genetically distinct clades (A, B, and C) and eleven subclades (A1–A9 and B1–B2). The majority belonged to clade A with KL47 serotype (n = 117, 77.0%), while KL64 and KL16 were identified in clades B and C, respectively. The blaKPC–2-carrying plasmids exhibited diverse types, namely, IncFII (pHN7A8)/IncR(6/15), IncFII (pHN7A8)/IncpA1763–KPC (5/15), IncFII (pHN7A8) (1/15), IncR (1/15), and IncpA1763–KPC (1/15). The genetic environment of blaKPC–2 showed nine IS26-based composite transposons, which had a basic core structure ISKpn27-blaKPC–2-ΔISKpn6. About 27.6% (42/152) isolates co-carried 2 to 4 virulence marker genes (namely, peg344, iucA, iroB, rmpA, and rmpA2) for hvKp strains. At least three isolates were identified to harbor virulence gene-carrying plasmids.

Conclusion

KPC-2-producing K. pneumoniae ST11 was highly heterogeneous in our hospital. Transmission of these strains was mainly mediated by twelve high-risk clones. The blaKPC–2-carrying plasmids and genetic environment of blaKPC–2 genes exhibited active evolution in K. pneumoniae ST11. More attention should be paid to the tendency of KPC-2-ST11 to acquire hypervirulent plasmids.
Design of Multi-Functional Superhydrophobic Coating via Bacterium-Induced Hierarchically Structured Minerals on Steel Surface
Authors: Zhang Yiwen , Liu Tao , Kang Jian , Guo Na , Guo Zhangwei , Chen Jinghao , Yin Yansheng
Published: June 2022

The fabrication of an eco-friendly, multi-functional, and mechanically robust superhydrophobic coating using a simple method has many practical applications. Here, inspired by shell nacre, the micro- or nano-scale surface roughness that is necessary for superhydrophobic coatings was formed via Bacillus subtilis–induced mineralization. The biomineralized film coated with hexadecyltrimethoxysilane (HDTMS) exhibited superhydrophobicity with water contact angles of 156°. The biomimetic HDTMS/calcite-coating showed excellent self-cleaning, anti-icing, and anti-corrosion performances. Furthermore, mechanically robust superhydrophobicity could be realized by hierarchically structured biomineralized surfaces at two different length scales, with a nano-structure roughness to provide water repellency and a micro-structure roughness to provide durability. Our design strategy may guide the development of “green” superhydrophobic coatings that need to retain effective multi-functional abilities in harsh marine environments.
Risk Factors Affecting Cognitive Impairment of the Elderly Aged 65 and Over: A Cross-Sectional Study
Authors: Han Fengyue , Luo Changjiang , Lv Duojiao , Tian Long , Qu Chuanqiang
Published: June 2022

Objectives

Elderly population with cognitive impairment has been accelerating in China. This study aimed to explore the relationship between each risk factor and each cognitive domain to provide evidence for risk prevention of controlling impaired cognitive function in elderly.

Methods

This cross-sectional study analyzed the cognitive status of the elderly aged 65 and above in three communities in Shizhong District of Jinan City. Cognitive status was assessed by MMSE. The influencing factors of cognitive impairment were analyzed by chi square test, correlation analysis and regression analysis.

Results

Among 1,171 participants, 643 were defined as cognitive impairment with an incidence of 54.9%. And we found that there were significant differences in the incidence of cognitive impairment among residents with different gender, age, education level, hypertension and LDL-C (P< 0.05). However, BMI, marital status, smoking, physical exercise, T2DM, TC, TG and HDL-C had no significant differences in the incidence of cognitive impairment. In addition, education level (b= 1.194,P<0.001), age (b= −0.040,P= 0.001), LDL-C (b= 0.169,P= 0.018) had statistical significance on the total score of MMSE according to binary logistic regression analysis.

Conclusion

Gender, age, education level, hypertension and LDL-C had significant differences in the incidence of cognitive impairment. And these risk factors could provide a basis for the early screening and intervention of cognitive impairment in the elderly.
A New Instrument Combines Cognitive and Social Functioning Items for Detecting Mild Cognitive Impairment and Dementia in Parkinson’s Disease
Authors: Yu Ya-Wen , Tan Chun-Hsiang , Su Hui-Chen , Chien Chung-Yao , Sung Pi-Shan , Lin Tien-Yu , Lee Tsung-Lin , Yu Rwei-Ling
Published: June 2022

Background

The commonly used screening tests for Parkinson’s disease (PD) are the Montreal Cognitive Assessment (MoCA) and Mini-Mental State Examination (MMSE), both of which only focus on cognitive function. A composite assessment that considers both cognitive and social dysfunction in PD would be helpful in detecting mild cognitive impairment (MCI) and PD dementia (PDD).

Objective

We aimed to simplify the commonly used tools and combine cognitive and social functioning tests to detect early MCI and PDD.

Materials and Methods

A total of 166 participants (84 PD patients and 82 healthy) were recruited who completed the MMSE, MoCA, PD social functioning scale (PDSFS), clock drawing test, activities of daily living, comprehensive neuropsychological assessment (e.g., executive, attention, language, memory, and visuospatial functions), and movement disorder society (MDS)-unified PD rating scale. According to the MDS diagnostic criteria, the patients were grouped into PD-nonMCI, PD-MCI, or PDD.

Results

To detect PD-MCI, the optimal cut-off scores for the simplified MoCA and the combined test were 9 and 35. The discrimination values measured by the area under the receiver operating characteristic curve (AUC) of the two tests were 0.767 (p < 0.001) and 0.790 (p < 0.001). When the simplified MoCA was 7 or the combined test 30, the patients would be classified as having PDD. The AUCs of the two tests were 0.846 (p < 0.001) and 0.794 (p = 0.003).

Conclusion

We suggest considering both cognitive and social functions when detecting PD-MCI and PDD.