bluuebunny/crossref_metadata_2025 huggingface dataset:
Codon-Optimized Rhodotorula glutinis PAL Expressed in Escherichia coli With Enhanced Activities
Authors: Xue Feiyan , Liu Zihui , Yu Yue , Wu Yangjie , Jin Yuxin , Yang Mingfeng , Ma Lanqing
Published: February 2021

PAL (phenylalanine ammonia lyase) is important for secondary metabolite production in plants and microorganisms. There is broad interest in engineering PAL for its biocatalytic applications in industry, agriculture, and medicine. The production of quantities of high-activity enzymes has been explored by gene cloning and heterogeneous expression of the corresponding protein. Here, we cloned the cDNA of Rhodotorula glutinis PAL (RgPAL) and introduced codon optimization to improve protein expression in Escherichia coli and enzyme activities in vitro. The RgPAL gene was cloned by reverse transcription and named pal-wt. It had a full-length of 2,121 bp and encoded a 706-amino-acid protein. The pal-wt was inefficiently expressed in E. coli, even when the expression host and physical conditions were optimized. Therefore, codon optimization was used to obtain the corresponding gene sequence, named pal-opt, in order to encode the same amino acid for the RgPAL protein. The recombinant protein encoded by pal-opt, named PAL-opt, was successfully expressed in E. coli and then purified to detect its enzymatic activity in vitro. Consequently, 55.33 ± 0.88 mg/L of PAL-opt protein with a specific activity of 1,219 ± 147 U/mg and Km value of 609 μM for substrate L-phenylalanine was easily obtained. The enzyme protein also displayed tyrosine ammonia lyase (TAL)–specific activity of 80 ± 2 U/mg and Km value of 13.3 μM for substrate L-tyrosine. The bifunctional enzyme RgPAL/TAL (PAL-opt) and its easy expression advantage will provide an important basis for further applications.
Ex situ Synthesis and Characterization of High Strength Multipurpose Bacterial Cellulose-Aloe vera Hydrogels
Authors: Ul-Islam Mazhar , Ahmad Furqan , Fatima Atiya , Shah Nasrullah , Yasir Somayia , Ahmad Md. Wasi , Manan Sehrish , Ullah Muhammad Wajid
Published: February 2021

The innate structural and functional properties of bacterial cellulose (BC) have been greatly improved by developing its composites with other materials for its applications in different fields. In the present study, BC-Aloe vera (BCA) gel composite with high tensile strength was ex situ developed and characterized for its potential applications in environmental and medical fields. FE-SEM micrographs showed the impregnation of Aloe vera gel into the fibril network of BC. The dry weight analysis showed the addition of 40 wt.% Aloe vera contents into the BC matrix. The addition of Aloe vera resulted in a 3-fold increase in the mechanical strength of BCA composite. The critical strain or stress concentration points were accurately identified in the composite using a three-dimensional digital image correlation (3D-DIC) system. The BCA composite retained water for an extended period of up to 70 h. The BCA composite effectively adsorbed Cu, Co, Fe, and Zn metals. Moreover, the BCA composite supported the adhesion and proliferation of MC3T3-E1 cells. The findings of this study suggest that the developed BCA composite could find multipurpose applications in different fields.
Closed Formulas for Some New Degree Based Topological Descriptors Using M-polynomial and Boron Triangular Nanotube
Authors: Shin Dong Yun , Hussain Sabir , Afzal Farkhanda , Park Choonkil , Afzal Deeba , Farahani Mohammad R.
Published: February 2021

In this article, we provide new formulas to compute the reduced reciprocal randić index, Arithmetic geometric1 index, SK index, SK1 index, SK2 index, edge version of the first zagreb index, sum connectivity index, general sum connectivity index, and the forgotten index using the M-polynomial and finding these topological indices for a boron triangular nanotube. We also elaborate the results with graphical representations.
Why Is COVID-19 More Severe in Patients With Diabetes? The Role of Angiotensin-Converting Enzyme 2, Endothelial Dysfunction and the Immunoinflammatory System
Authors: Roberts Jacob , Pritchard Antonia L. , Treweeke Andrew T. , Rossi Adriano G. , Brace Nicole , Cahill Paul , MacRury Sandra M. , Wei Jun , Megson Ian L.
Published: February 2021

Meta-analyses have indicated that individuals with type 1 or type 2 diabetes are at increased risk of suffering a severe form of COVID-19 and have a higher mortality rate than the non-diabetic population. Patients with diabetes have chronic, low-level systemic inflammation, which results in global cellular dysfunction underlying the wide variety of symptoms associated with the disease, including an increased risk of respiratory infection. While the increased severity of COVID-19 amongst patients with diabetes is not yet fully understood, the common features associated with both diseases are dysregulated immune and inflammatory responses. An additional key player in COVID-19 is the enzyme, angiotensin-converting enzyme 2 (ACE2), which is essential for adhesion and uptake of virus into cells prior to replication. Changes to the expression of ACE2 in diabetes have been documented, but they vary across different organs and the importance of such changes on COVID-19 severity are still under investigation. This review will examine and summarise existing data on how immune and inflammatory processes interplay with the pathogenesis of COVID-19, with a particular focus on the impacts that diabetes, endothelial dysfunction and the expression dynamics of ACE2 have on the disease severity.
Effects of Textural Layering on Water Regimes in Sandy Soils in a Desert-Oasis Ecotone, Northwestern China
Authors: Sun Chengpeng , Zhao Wenzhi , Liu Hu , Zhang Yongyong , Zhou Hong
Published: February 2021

Textural layering of soil plays an important role in distributing and regulating resources for plants in many semiarid and arid landscapes. However, the spatial patterns of textural layering and the potential effects on soil hydrology and water regimes are poorly understood, especially in arid sandy soil environments like the desert-oasis ecotones in northwestern China. This work aims to determine the distribution of textural layered soils, analyze the effects of different soil-textural configurations on water regimes, and evaluate which factors affect soil water infiltration and retention characteristics in such a desert-oasis ecotone. We measured soil water content and mineral composition in 87 soil profiles distributed along three transects in the study area. Constant-head infiltration experiments were conducted at 9 of the soil profiles with different texture configurations. The results showed that textural layered soils were patchily but extensively distributed throughout the study area (with a combined surface area percentage of about 84%). Soil water content in the profiles ranged from 0.002 to 0.27 g/cm3 during the investigation period, and significantly and positively correlated with the thickness of a medium-textured (silt or silt loam) layer (p < 0.001). The occurrence of a medium-textured layer increased field capacity and wilting point and decreased available water-holding capacity in soil profiles. Burial depth of the medium-textured layer had no clear effects on water retention properties, but the layer thickness tended to. In textural layered soils, smaller water infiltration rate and cumulative infiltration, and shallower depths of wetting fronts were detected, compared with homogeneous sand profiles. The thickness and burial depth of medium-textured layers had obvious effects on infiltration, but the magnitude of the effects depended on soil texture configuration. The revealed patterns of soil textural layering and the potential effects on water regimes may provide new insight into the sustainable management of rainfed vegetation in the desert-oasis ecotones of arid northwestern China and other regions with similar environments around the world.
17β-Estradiol Induces Mitophagy Upregulation to Protect Chondrocytes via the SIRT1-Mediated AMPK/mTOR Signaling Pathway
Authors: Mei Runhong , Lou Peng , You Guanchao , Jiang Tianlong , Yu Xuefeng , Guo Lei
Published: February 2021

Increasing evidence reveals that estrogen, especially 17β-estradiol (17β-E2), is associated with articular cartilage metabolism disorder and postmenopausal osteoarthritis (OA). SIRT1, AMPK, and mTOR are regarded as critical mitophagy regulators. Recent studies have shown that mitophagy displays a protective effect against OA, but the molecular mechanism is not well known. This study aimed to investigate the effect of 17β-E2 on Sirtuin-1 (SIRT1) expression and the induction of mitophagy upregulation by 17β-E2 via the SIRT1-mediated AMP-activated protein kinase (AMPK)/mammalian target of the rapamycin (mTOR) signaling pathway to protect chondrocytes. ATDC5 chondrocytes were treated with different concentrations of 17β-E2 (0 M, 1 × 10-9 M, 1 × 10-8 M, and 1 × 10-7 M) for 24 h or pretreatment with or without NAM (SIRT1 inhibitor), Compound C (AMPK inhibitor) and S1842 (mTOR inhibitor) for 30 min prior to treatment with 17β-E2 (1 × 10-7 M) for 24 in each groups. Expression of SIRT1 was evaluated by real-time PCR, Western blotting and confocal immunofluorescence staining. Then, the mitophagosomes in cells were observed under a transmission electron microscopy (TEM), and the AMPK/mTOR signaling pathway was detected by Western blotting. The mitophagy-related proteins, p-AMPK, p-mTOR, p-JNK, and p-p38 were also identified by Western blot analysis. The chondrocytes viability and proliferation were determined by MTT and 5-Bromo-2’-deoxyuridine (BrdU) assay. These experiments were independently repeated 3 times The study found that 17β-E2 increased the expression level of SIRT1, p-AMPK, and mitophagy-related proteins but decreased p-mTOR expression, and then induced mitophagy upregulation in chondrocytes. More mitochondrial autophagosomes were observed in 17β-E2-treated chondrocytes under a transmission electron microscope. Also, 17β-E2 improved cell viability and proliferation with the higher expression of SIRT1 and activation of the AMPK/mTOR signaling pathway. However, SIRT1 inhibitor nicotinamide (NAM) and AMPK inhibitor Compound C blocked the beneficial effect of 17β-E2. In summary, this study was novel in demonstrating that 17β-E2 induced mitophagy upregulation to protect chondrocytes via the SIRT1-mediated AMPK/mTOR signaling pathway.
Enhanced Expression of CNTD2/CCNP Predicts Poor Prognosis in Bladder Cancer Based on the GSE13507
Authors: Gong Mancheng , Song Erlin , Huang Guiying , Ni Wenjun , Dong Wenjing , Yuan Runqiang
Published: February 2021

Bladder cancer is one of the most common urogenital malignancies in the world, and there are no adequate prognostic indicators. CNTD2 is one of the atypical cyclins, which may be related to the cell cycle and even the development of cancers. Early studies have shown that CNTD2 is closely related to the occurrence and development of many malignant tumors. However, the mechanism of CNTD2 in bladder cancer has not been reported. In our research, we explored the different expressions of CNTD2 between 411 bladder cancers and 19 normal bladder tissues based on the TCGA dataset. CNTD2-related signaling pathways were identified through the GSEA. We analyzed the associations of CNTD2 expression and bladder cancer progression and survival using GSE13507. Compared with 19 cases of normal bladder tissue, CNTD2 gene expression was increased in 411 cases of bladder cancer. The high expression of CNTD2 strongly correlated with grade (P < 0.0001), T classification (P = 0.0001), N classification (P = 0.00011), M classification (P = 0.044), age (P = 0.027), and gender (P = 0.0012). Bladder cancer patients with high CNTD2 expression had shorter overall survival (P < 0.001). In the meantime, univariate and multivariate analyses showed that the increased expression of CNTD2 was an independent factor for poor prognosis in bladder cancer patients (P < 0.001 and P < 0.001, respectively). CNTD2 expression is closely related to bladder cancer progression, and the high expression of CNTD2 may be an adverse biomarker in bladder cancer patients.
The Shared Use of Extended Phenotypes Increases the Fitness of Simulated Populations
Authors: de Araújo Guilherme F. , Moioli Renan C. , de Souza Sandro J.
Published: February 2021

Extended phenotypes are manifestations of genes that occur outside of the organism that possess those genes. In spite of their widespread occurrence, the role of extended phenotypes in evolutionary biology is still a matter of debate. Here, we explore the indirect effects of extended phenotypes, especially their shared use, in the fitness of simulated individuals and populations. A computer simulation platform was developed in which different populations were compared regarding their ability to produce, use, and share extended phenotypes. Our results show that populations that produce and share extended phenotypes outrun populations that only produce them. A specific parameter in the simulations, a bonus for sharing extended phenotypes among conspecifics, has a more significant impact in defining which population will prevail. All these findings strongly support the view, postulated by the extended fitness hypothesis (EFH) that extended phenotypes play a significant role at the population level and their shared use increases population fitness. Our simulation platform is available at https://github.com/guilherme-araujo/gsop-dist.
Exosomes Derived From Hypertrophic Cardiomyocytes Induce Inflammation in Macrophages via miR-155 Mediated MAPK Pathway
Authors: Yu Hui , Qin Lei , Peng Yunzhi , Bai Wenhui , Wang Zhanli
Published: February 2021

The inflammatory immune microenvironment plays an important role in the development of cardiac hypertrophy. Exosomes have emerged as the potent modulators of inflammatory responses. This study aimed to determine how exosomes derived from angiotensin II (Ang II)-induced hypertrophic cardiomyocytes (HCs) interfere with the inflammatory signal pathways in macrophages. Herein, we showed that increased exosome release was observed in HCs when compared to normal cardiomyocytes (NCs). Incubation of the murine macrophage cell line RAW264.7 in the presence of exosomes isolated from the culture media of HCs triggers the secretion of inflammatory cytokines interleukin (IL)-6 and IL-8. Cytokines release induced by HCs-derived exosomes was prevented by down-regulation of Argonaute2 (AGO2), suggesting that the non-coding RNAs were involved in exosome-induced inflammatory responses in RAW 264.7 macrophages. RNA sequencing assays further demonstrated that a total of seven microRNAs were differentially expressed between NCs-derived and HCs-derived exosomes. Importantly, miR-155 played a crucial role in the initiation of inflammation in macrophages. Further analyses demonstrated that HCs-derived exosomes induced the phosphorylation of extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38 via miR-155. Our results support the concept that exosomal microRNAs have emerged as important inflammatory response modulators regulating cardiac hypertrophy.
Interactions of the Skin Pathogen Haemophilus ducreyi With the Human Host
Authors: Brothwell Julie A. , Griesenauer Brad , Chen Li , Spinola Stanley M.
Published: February 2021

The obligate human pathogen Haemophilus ducreyi causes both cutaneous ulcers in children and sexually transmitted genital ulcers (chancroid) in adults. Pathogenesis is dependent on avoiding phagocytosis and exploiting the suppurative granuloma-like niche, which contains a myriad of innate immune cells and memory T cells. Despite this immune infiltrate, long-lived immune protection does not develop against repeated H. ducreyi infections—even with the same strain. Most of what we know about infectious skin diseases comes from naturally occurring infections and/or animal models; however, for H. ducreyi, this information comes from an experimental model of infection in human volunteers that was developed nearly three decades ago. The model mirrors the progression of natural disease and serves as a valuable tool to determine the composition of the immune cell infiltrate early in disease and to identify host and bacterial factors that are required for the establishment of infection and disease progression. Most recently, holistic investigation of the experimentally infected skin microenvironment using multiple “omics” techniques has revealed that non-canonical bacterial virulence factors, such as genes involved in central metabolism, may be relevant to disease progression. Thus, the immune system not only defends the host against H. ducreyi, but also dictates the nutrient availability for the invading bacteria, which must adapt their gene expression to exploit the inflammatory metabolic niche. These findings have broadened our view of the host-pathogen interaction network from considering only classical, effector-based virulence paradigms to include adaptations to the metabolic environment. How both host and bacterial factors interact to determine infection outcome is a current focus in the field. Here, we review what we have learned from experimental H. ducreyi infection about host-pathogen interactions, make comparisons to what is known for other skin pathogens, and discuss how novel technologies will deepen our understanding of this infection.
The Natural Killer–Dendritic Cell Immune Axis in Anti-Cancer Immunity and Immunotherapy
Authors: Peterson Erin E. , Barry Kevin C.
Published: February 2021

Natural killer (NK) cells and dendritic cells (DCs) are crucial mediators of productive immune responses to infection and disease. NK cells and a subtype of DCs, the type 1 conventional DCs (cDC1s), are individually important for regulating immune responses to cancer in mice and humans. Recent work has found that NK cells and cDC1s engage in intercellular cross-talk integral to initiating and coordinating adaptive immunity to cancer. This NK cell–cDC1 axis has been linked to increased overall survival and responses to anti-PD-1 immunotherapy in metastatic melanoma patients. Here, we review recent findings on the role of NK cells and cDC1s in protective immune responses to cancer and immunotherapy, as well as current therapies targeting this NK cell–cDC1 axis. Further, we explore the concept that intercellular cross-talk between NK cells and cDC1s may be key for many of the positive prognostic associations seen with NK cells and DCs individually. It is clear that increasing our understanding of the NK cell–cDC1 innate immune cell axis will be critical for the generation of novel therapies that can modulate anti-cancer immunity and increase patient responses to common immunotherapies.
Swine T-Cells and Specific Antibodies Evoked by Peptide Dendrimers Displaying Different FMDV T-Cell Epitopes
Authors: de León Patricia , Cañas-Arranz Rodrigo , Defaus Sira , Torres Elisa , Forner Mar , Bustos María J. , Revilla Concepción , Dominguez Javier , Andreu David , Blanco Esther , Sobrino Francisco
Published: February 2021

Dendrimeric peptide constructs based on a lysine core that comprises both B- and T-cell epitopes of foot-and-mouth disease virus (FMDV) have proven a successful strategy for the development of FMD vaccines. Specifically, B2T dendrimers displaying two copies of the major type O FMDV antigenic B-cell epitope located on the virus capsid [VP1 (140–158)], covalently linked to a heterotypic T-cell epitope from either non-structural protein 3A [3A (21–35)] or 3D [3D (56–70)], named B2T-3A and B2T-3D, respectively, elicit high levels of neutralizing antibodies (nAbs) and IFN-γ-producing cells in pigs. To assess whether the inclusion and orientation of T-3A and T-3D T-cell epitopes in a single molecule could modulate immunogenicity, dendrimers with T epitopes juxtaposed in both possible orientations, i.e., constructs B2TT-3A3D and B2TT-3D3A, were made and tested in pigs. Both dendrimers elicited high nAbs titers that broadly neutralized type O FMDVs, although B2TT-3D3A did not respond to boosting, and induced lower IgGs titers, in particular IgG2, than B2TT-3A3D. Pigs immunized with B2,a control dendrimer displaying two B-cell epitope copies and no T-cell epitope, gave no nABs, confirming T-3A and T-3D as T helper epitopes. The T-3D peptide was found to be an immunodominant, as it produced more IFN-γ expressing cells than T-3A in thein vitrorecall assay. Besides, in pigs immunized with the different dendrimeric peptides, CD4+T-cells were the major subset contributing to IFN-γ expression uponin vitrorecall, and depletion of CD4+cells from PBMCs abolished the production of this cytokine. Most CD4+IFN-γ+cells showed a memory (CD4+2E3−) and a multifunctional phenotype, as they expressed both IFN-γ and TNF-α, suggesting that the peptides induced a potent Th1 pro-inflammatory response. Furthermore, not only the presence, but also the orientation of T-cell epitopes influenced the T-cell response, as B2TT-3D3A and B2groups had fewer cells expressing both cytokines. These results help understand how B2T-type dendrimers triggers T-cell populations, highlighting their potential as next-generation FMD vaccines.
Variation and Change of Upwelling Dynamics Detected in the World’s Eastern Boundary Upwelling Systems
Authors: Abrahams Amieroh , Schlegel Robert W. , Smit Albertus J.
Published: February 2021

Global increases in temperature are altering land-sea temperature gradients. Bakun (1990) hypothesized that changes within these gradients will directly affect atmospheric pressure cells associated with the development of winds and will consequently impact upwelling patterns within ecologically important Eastern Boundary Upwelling Systems (EBUS). In this study we used daily time series of NOAA Optimally Interpolated sea surface temperature (SST) and ERA 5 reanalysis wind products to calculate a series novel of metrics related to upwelling dynamics. We then use these to objectively describe upwelling signals in terms of their frequency, intensity and duration throughout the four EBUS during summer months over the last 37 years (1982–2019). We found that a decrease (increase) in SST is associated with an increase (decrease) in the number of upwelling “events,” a decrease (increase) in the intensity of upwelling, and an increase (decrease) in the cumulative intensity of upwelling, with differences between EBUS and regions within EBUS. The Humboldt Current is the only EBUS that shows a consistent response from north to south with a general intensification of upwelling. However, we could not provide clear evidence for associated changes in the wind dynamics hypothesized to drive the upwelling dynamics.
Preventing SARS-CoV-2 In-Hospital Infections in Cardiovascular Patients and Medical Staff: An Observational Study From the German Heart Center Berlin
Authors: Schöppenthau Doreen , Weiß Karl Jakob , Estepa-Martinez Misael , Hommel Matthias , Miera Oliver , Schoenrath Felix , Hübler Sabine , Obermeier Martin , Pieske Burkert , Stawowy Philipp
Published: February 2021

Objective: COVID-19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Preventing in-hospital infections is crucial to protect patients and hospital staff.

Methods: At the very beginning of the COVID-19 pandemic, the German Heart Center initiated obligatory wearing of surgical face masks for patients and employees, SARS-CoV-2 screening for all patients, and symptom-based testing for employees. In addition, access restriction, closure of outpatient departments, and postponing non-urgent procedures were implemented with community-initiated regulations.

Results: During the observation period (03/16/2020–04/27/2020), 1,128 SARS-CoV-2 tests were performed in 983 persons (1.1 tests/person; 589 in patients and 394 in hospital employees). Up to 60% of the clinical workforce was tested based on symptoms and risk (62.5% symptoms, 19.3% direct or indirect contact to known COVID-19, 4.5% returnee from risk area, 13.7% without specific reason). Patient testing for SARS-CoV-2 was obligatory (100% tested). The overall prevalence of positive tests during the observation period was 0.4% (n = 5 out of 1,128 tests performed). The incidence of new infections with SARS-CoV-2 was 0.5% (n = 5 out of 983 individuals; three healthcare workers, two patients). No nosocominal infections occurred, despite a mean number of 14.8 in-hospital contacts.

Conclusion: Comprehensive SARS-CoV-2 testing and surgical face masks for patients and hospital staff, in addition to others measures, are key factors for the early detection of COVID-19 and to prevent spreading in the vulnerable hospital population.
Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records in the US
Authors: Marić Ivana , Oskotsky Tomiko , Kosti Idit , Le Brian , Wong Ronald J. , Shaw Gary M. , Sirota Marina , Stevenson David K.
Published: February 2021

The severe respiratory illness due to SARS-CoV-2, the virus responsible for coronavirus disease 2019 (COVID-19), is triggered by an intense pro-inflammatory host response. Statins, prescribed primarily for lipid reduction, are known to have anti-inflammatory and immunomodulatory properties and have been associated with a reduced mortality rate among COVID-19 patients taking statins as reported in two recent retrospective studies. However, a meta-analysis that included nine studies showed that statin use did not improve in-hospital outcomes of those with COVID-19. In addition, concerns regarding the use of statins and an increase in COVID-19 infections have been raised, as statins may increase the expression of angiotensin-converting enzyme 2 (ACE2), the primary receptor for the SARS-CoV-2 virus. Our goal was to investigate the effect of statins in COVID-19 patients in a large, diverse patient population across the United States containing nearly 120,000 patients diagnosed with COVID-19. We used propensity score matching of demographics, comorbidities, and medication indication to compare statin-treated patients (N = 2,297) with matched controls (N = 4,594). We observed a small, but statistically significant, decrease in mortality among patients prescribed statins (16.1%) when compared with matched COVID-19-positive controls (18.0 to 20.6%). These results support previous evidence that statins do not increase COVID-19-related mortality and may, in fact, have a mitigating effect on severity of the disease reflected in a slight reduction in mortality. Mixed findings on effects of statins in COVID-19 patients reported in the literature should prompt prospective randomized controlled trials in order to define better who might be advantaged with respect to clinical outcomes.
Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis
Authors: Loh Hui Qi , Hervé Vincent , Brune Andreas
Published: February 2021

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO2 via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C1 carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.
Antibiofilm Activity of Small-Molecule ZY-214-4 Against Staphylococcus aureus
Authors: Yu Jingyi , Rao Lulin , Zhan Lingling , Zhou Yan , Guo Yinjuan , Wu Xiaocui , Song Zengqiang , Yu Fangyou
Published: February 2021

Staphylococcus aureus is the most important pathogenic bacteria in humans. As the resistance of S. aureus to existing antibiotics is increasing, there is an urgent need for new anti-infective drugs. S. aureus biofilms cause persistent infections and resist complete eradication with antibiotic therapy. The present study investigated the inhibitory effect of the novel small-molecule ZY-214-4 (C19H11BrNO4) on S. aureus biofilm formation. At a subinhibitory concentration (4 μg/ml), ZY-214-4 had no effect on the growth of S. aureus strains and also showed no cytotoxicity in human normal bronchial epithelial cells (Bease-2B). The results of a semi-quantitative biofilm test showed that ZY-214-4 prevented S. aureus biofilm formation, which was confirmed by scanning electron microscopy and confocal laser scanning microscopy. ZY-214-4 significantly suppressed the production of polysaccharide intercellular adhesion and prevented cell aggregation, and also inhibited the mRNA expression of icaA and other biofilm-related genes (eno, clfA/B, fnbB, fib, ebpS, psmα, and psmβ) in clinical S. aureus isolates. Thus, at a subinhibitory concentration, ZY-214-4 inhibits biofilm formation by preventing cell aggregation, highlighting its clinical potential for preventing or treating S. aureus infections.
Word Entropy-Based Approach to Detect Highly Variable Genetic Markers for Bacterial Genotyping
Authors: Nykrynova Marketa , Barton Vojtech , Sedlar Karel , Bezdicek Matej , Lengerova Martina , Skutkova Helena
Published: February 2021

Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g., local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also non-coding regions are examined.
Acute Traumatic Spinal Cord Injury in Humans, Dogs, and Other Mammals: The Under-appreciated Role of the Dura
Authors: Saadoun Samira , Jeffery Nicolas D.
Published: February 2021

We review human and animal studies to determine whether, after severe spinal cord injury (SCI), the cord swells against the inelastic dura. Evidence from rodent models suggests that the cord swells because of edema and intraparenchymal hemorrhage and because the pia becomes damaged and does not restrict cord expansion. Human cohort studies based on serial MRIs and measurements of elevated intraspinal pressure at the injury site also suggest that the swollen cord is compressed against dura. In dogs, SCI commonly results from intervertebral disc herniation with evidence that durotomy provides additional functional benefit to conventional (extradural) decompressive surgery. Investigations utilizing rodent and pig models of SCI report that the cord swells after injury and that durotomy is beneficial by reducing cord pressure, cord inflammation, and syrinx formation. A human MRI study concluded that, after extensive bony decompression, cord compression against the dura may only occur in a small number of patients. We conclude that the benefit of routinely opening the dura after SCI is only supported by animal and level III human studies. Two randomized, controlled trials, one in humans and one in dogs, are being set up to provide Level I evidence.
A Show of Ewald's Law: I Horizontal Semicircular Canal Benign Paroxysmal Positional Vertigo
Authors: Zhang Xueqing , Bai Yanru , Chen Taisheng , Wang Wei , Han Xi , Li Shanshan , Liu Qiang , Wen Chao
Published: February 2021

Objective: To evaluate horizontal semicircular canal (HSC) effects according to Ewald's law and nystagmus characteristics of horizontal semicircular canal benign paroxysmal positional vertigo (HSC-BPPV) in the supine roll test.

Methods: Patients with HSC-BPPV (n = 72) and healthy subjects (n = 38) were enrolled. Latency, duration, and intensity of nystagmus elicited by supine roll test were recorded using video nystagmography.

Results: In patients with HSC-BPPV, horizontal nystagmus could be elicited by right/left head position (positional nystagmus) and during head-turning (head-turning nystagmus), and nystagmus direction was the same as that of head turning. Mean intensity values of head-turning nystagmus in HSC-BPPV patients were (44.70 ± 18.24)°/s and (44.65 ± 19.27)°/s on the affected and unaffected sides, respectively, which was not a significant difference (p = 0.980), while those for positional nystagmus were (40.81 ± 25.56)°/s and (17.69 ± 9.31)°/s (ratio, 2.59 ± 1.98:1), respectively, representing a significant difference (p < 0.0001). There was no positional nystagmus in 49 HSC-BPPV patients after repositioning treatment, nor in the 38 healthy subjects. No significant difference in head-turning nystagmus was detected in HSC-BPPV patients with or without repositioning.

Conclusions: The direction and intensity of nystagmus elicited by supine roll test in patients with HSC-BPPV, was broadly consistent with the physiological nystagmus associated with a same HSC with single factor stimulus. Our findings suggest that HSC-BPPV can be a show of Ewald's law in human body.
An Intracortical Implantable Brain-Computer Interface for Telemetric Real-Time Recording and Manipulation of Neuronal Circuits for Closed-Loop Intervention
Authors: Zaer Hamed , Deshmukh Ashlesha , Orlowski Dariusz , Fan Wei , Prouvot Pierre-Hugues , Glud Andreas Nørgaard , Jensen Morten Bjørn , Worm Esben Schjødt , Lukacova Slávka , Mikkelsen Trine Werenberg , Fitting Lise Moberg , Adler John R. , Schneider M. Bret , Jensen Martin Snejbjerg , Fu Quanhai , Go Vinson , Morizio James , Sørensen Jens Christian Hedemann , Stroh Albrecht
Published: February 2021

Recording and manipulating neuronal ensemble activity is a key requirement in advanced neuromodulatory and behavior studies. Devices capable of both recording and manipulating neuronal activity brain-computer interfaces (BCIs) should ideally operate un-tethered and allow chronic longitudinal manipulations in the freely moving animal. In this study, we designed a new intracortical BCI feasible of telemetric recording and stimulating local gray and white matter of visual neural circuit after irradiation exposure. To increase the translational reliance, we put forward a Göttingen minipig model. The animal was stereotactically irradiated at the level of the visual cortex upon defining the target by a fused cerebral MRI and CT scan. A fully implantable neural telemetry system consisting of a 64 channel intracortical multielectrode array, a telemetry capsule, and an inductive rechargeable battery was then implanted into the visual cortex to record and manipulate local field potentials, and multi-unit activity. We achieved a 3-month stability of the functionality of the un-tethered BCI in terms of telemetric radio-communication, inductive battery charging, and device biocompatibility for 3 months. Finally, we could reliably record the local signature of sub- and suprathreshold neuronal activity in the visual cortex with high bandwidth without complications. The ability to wireless induction charging combined with the entirely implantable design, the rather high recording bandwidth, and the ability to record and stimulate simultaneously put forward a wireless BCI capable of long-term un-tethered real-time communication for causal preclinical circuit-based closed-loop interventions.
Cross-Subject EEG-Based Emotion Recognition Through Neural Networks With Stratified Normalization
Authors: Fdez Javier , Guttenberg Nicholas , Witkowski Olaf , Pasquali Antoine
Published: February 2021

Due to a large number of potential applications, a good deal of effort has been recently made toward creating machine learning models that can recognize evoked emotions from one's physiological recordings. In particular, researchers are investigating the use of EEG as a low-cost, non-invasive method. However, the poor homogeneity of the EEG activity across participants hinders the implementation of such a system by a time-consuming calibration stage. In this study, we introduce a new participant-based feature normalization method, named stratified normalization, for training deep neural networks in the task of cross-subject emotion classification from EEG signals. The new method is able to subtract inter-participant variability while maintaining the emotion information in the data. We carried out our analysis on the SEED dataset, which contains 62-channel EEG recordings collected from 15 participants watching film clips. Results demonstrate that networks trained with stratified normalization significantly outperformed standard training with batch normalization. In addition, the highest model performance was achieved when extracting EEG features with the multitaper method, reaching a classification accuracy of 91.6% for two emotion categories (positive and negative) and 79.6% for three (also neutral). This analysis provides us with great insight into the potential benefits that stratified normalization can have when developing any cross-subject model based on EEG.
Down-Regulation of CIDEA Promoted Tumor Growth and Contributed to Cisplatin Resistance by Regulating the JNK-p21/Bad Signaling Pathways in Esophageal Squamous Cell Carcinoma
Authors: Gao Ya-Ping , Li Lei , Yan Jie , Hou Xiao-Xia , Jia Yong-Xu , Chang Zhi-Wei , Guan Xin-Yuan , Qin Yan-Ru
Published: February 2021

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis and lack of effective targeted therapies. In this study, we investigated the tumor suppressive role of the cell death inducing DFF like effector A (CIDEA) in ESCC. Firstly, public datasets and ESCC tissue microarray analysis showed that CIDEA was frequently down-regulated at both the mRNA and protein level. This was significantly associated with low differentiation and TNM stage in ESCC, and indicated poor prognosis for ESCC patients. Bisulfite genomic sequencing (BGS) and methylation-specific PCR (MSP) analysis revealed that the down-regulation of CIDEA was associated with hypermethylation of its promoter, which was also correlated with the poor prognosis in ESCC patients. In vitro and in vivo functional studies demonstrated that CIDEA decreased cell growth, foci formation, DNA replication, and tumorigenesis in nude mice. Further study revealed that, during starvation or cisplatin induced DNA damage, CIDEA facilitated the G1-phase arrest or caspase-dependent mitochondrial apoptosis through the JNK-p21/Bad pathway. Therefore, CIDEA is a novel tumor suppressor gene that plays an important role in the development and progression of ESCC, and may provide a potential therapeutic target for patients with ESCC.
FOXP3 and Tip60 Structural Interactions Relevant to IPEX Development Lead to Potential Therapeutics to Increase FOXP3 Dependent Suppressor T Cell Functions
Authors: Grover Payal , Goel Peeyush N. , Piccirillo Ciriaco A. , Greene Mark I.
Published: February 2021

Regulatory T (Treg) cells play a role in the maintenance of immune homeostasis and are critical mediators of immune tolerance. The Forkhead box P3 (FOXP3) protein acts as a regulator for Treg development and function. Mutations in the FOXP3 gene can lead to autoimmune diseases such as Immunodysregulation, polyendocrinopathy, enteropathy, and X-linked (IPEX) syndrome in humans, often resulting in death within the first 2 years of life and a scurfy like phenotype in Foxp3 mutant mice. We discuss biochemical features of the FOXP3 ensemble including its regulation at various levels (epigenetic, transcriptional, and post-translational modifications) and molecular functions. The studies also highlight the interactions of FOXP3 and Tat-interacting protein 60 (Tip60), a principal histone acetylase enzyme that acetylates FOXP3 and functions as an essential subunit of the FOXP3 repression ensemble complex. Lastly, we have emphasized the role of allosteric modifiers that help stabilize FOXP3:Tip60 interactions and discuss targeting this interaction for the therapeutic manipulation of Treg activity.
Characterization of Mechanical Allodynia and Skin Innervation in a Mouse Model of Type-2 Diabetes Induced by Cafeteria-Style Diet and Low-Doses of Streptozotocin
Authors: Castañeda-Corral Gabriela , Velázquez-Salazar Norma B. , Martínez-Martínez Arisai , Taboada-Serrano Juanita N. , Núñez-Aragón Pablo N. , González-Palomares Laura , Acosta-González Rosa Issel , Petricevich Vera L. , Acevedo-Fernández Juan José , Montes Sergio , Jiménez-Andrade Juan Miguel
Published: February 2021

Background: Painful distal symmetrical polyneuropathy (DPN) is a frequent complication of type-2 diabetes mellitus (T2DM) that commonly presents as neuropathic pain and loss of skin nerve fibers. However, there are limited therapies to effectively treat DPN and many of the current animal models of T2DM-induced DPN do not appear to mirror the human disease. Thus, we validated a DPN mouse model induced by a cafeteria-style diet plus low-doses of streptozotocin (STZ).

Methods: Female C57BL/6J mice were fed either standard (STD) diet or obesogenic cafeteria (CAF) diet for 32 weeks, starting at 8 weeks old. Eight weeks after starting diets, CAF or STD mice received either four low-doses of STZ or vehicle. Changes in body weight, blood glucose and insulin levels, as well as oral glucose- and insulin-tolerance tests (OGTT and ITT) were determined. The development of mechanical hypersensitivity of the hindpaws was determined using von Frey filaments. Moreover, the effect of the most common neuropathic pain drugs was evaluated on T2DM-induced mechanical allodynia. Finally, the density of PGP -9.5+ (a pan-neuronal marker) axons in the epidermis from the hindpaw glabrous skin was quantified.

Results: At 22–24 weeks after STZ injections, CAF + STZ mice had significantly higher glucose and insulin levels compared to CAF + VEH, STD + STZ, and STD + VEH mice, and developed glucose tolerance and insulin resistance. Skin mechanical sensitivity was detected as early as 12 weeks post-STZ injections and it was significantly attenuated by intraperitoneal acute treatment with amitriptyline, gabapentin, tramadol, duloxetine, or carbamazepine but not by diclofenac. The density of PGP-9.5+ nerve fibers was reduced in CAF + STZ mice compared to other groups.

Conclusion: This reverse translational study provides a painful DPN mouse model which may help in developing a better understanding of the factors that generate and maintain neuropathic pain and denervation of skin under T2DM and to identify mechanism-based new treatments.
Cytotoxic and Pro-Apoptotic Effects of a Sub-Toxic Concentration of Fluvastatin on OVCAR3 Ovarian Cancer Cells After its Optimized Formulation to Melittin Nano-Conjugates
Authors: Badr-Eldin Shaimaa M. , Alhakamy Nabil A. , Fahmy Usama A. , Ahmed Osama A. A. , Asfour Hani Z. , Althagafi Abdulhamid A. , Aldawsari Hibah M. , Rizg Waleed Y. , Mahdi Wael A. , Alghaith Adel F. , Alshehri Sultan , Caraci Filippo , Caruso Giuseppe
Published: February 2021

Fluvastatin (FLV) is a hydroxymethylglutaryl coenzyme A (HMG-CoA) reductase inhibitor often used to lower total and low-density lipoprotein (LDL) cholesterol and for the prevention of adverse cardiovascular events. This drug as well as melittin (MEL), the major component of honeybee venom (Apis mellifera), has shown antineoplastic activity, then representing promising approaches for cancer therapy. However, adverse effects related to the use of FLV and MEL have been reported and very few studies have been carried out to obtain an optimized formulation allowing for combining the two drugs and then maximizing the anticancer activity, then minimizing the needed dosage. In the present study, an optimized formulation in terms of minimized particle size and maximized zeta potential was investigated for its cytotoxic potential in human OVCAR3 ovarian cancer cells. FLV-MEL nano-conjugates, containing a sub-toxic concentration of drug, demonstrated an improved cytotoxic potential (IC50 = 2.5 µM), about 18-fold lower, compared to the free drug (IC50 = 45.7 µM). Cell cycle analysis studies demonstrated the significant inhibition of the OVCAR3 cells proliferation exerted by FLV-MEL nano-conjugates compared to all the other treatments, with a higher percentage of cells accumulating on G2/M and pre-G1 phases, paralleled by lower percentage of cells in G0/G1 and S phases. The synergistic antineoplastic activity of FLV and MEL combined in the optimized formula was also showed by the marked pronecrotic and pro-apoptotic activities, the latter mediated by the modulation of BAX/BCL-2 ratio in favor of BAX. Our optimized FLV-MEL formulation might therefore represents a novel path for the development of specific and more effective antineoplastic drugs directed against ovarian cancer.