bluuebunny/crossref_metadata_2025 huggingface dataset:
Differentiation of Memory CD8 T Cells Unravel Gene Expression Pattern Common to Effector and Memory Precursors
Authors: Neitzke-Montinelli Vanessa , Calôba Carolina , Melo Guilherme , Frade Bianca B. , Caramez Enzo , Mazzoccoli Luciano , Gonçalves André N. A. , Nakaya Helder I. , Pereira Renata M. , Werneck Miriam B. F. , Viola João P. B.
Published: May 2022

Long-term immunological protection relies on the differentiation and maintenance of memory lymphocytes. Since the knowledge of memory generation has been centered on in vivo models of infection, there are obstacles to deep molecular analysis of differentiating subsets. Here we defined a novel in vitro CD8 T cell activation and culture regimen using low TCR engagement and cytokines to generate differentiated cells consistent with central memory-like cells, as shown by surface phenotype, gene expression profile and lack of cytotoxic function after challenge. Our results showed an effector signature expressed by in vitro memory precursors and their plasticity under specific conditions. Moreover, memory CD8 T cells conferred long-term protection against bacterial infection and slowed in vivo tumor growth more efficiently than effector cells. This model may allow further understanding of CD8 T cell memory molecular differentiation subsets and be suited for generating cells to be used for immunotherapy.
A Novel STAT3 Gain-of-Function Mutation in Fatal Infancy-Onset Interstitial Lung Disease
Authors: Deng Mengyue , Li Yue , Li Yulu , Mao Xiaolan , Ke Han , Liang Weiling , Lei Xiaoguang , Lau Yu-Lung , Mao Huawei
Published: May 2022

Signal transducer and activator of transcription 3 (STAT3) gain-of-function (GOF) mutations cause early-onset immune dysregulation syndrome, characterized by multi-organ autoimmunity and lymphoproliferation. Of them, interstitial lung disease (ILD) usually develops after the involvement of other organs, and the onset time is childhood and beyond rather than infancy. Here, we reported a patient who presented with fatal infancy-onset ILD, finally succumbing to death. Next-generation sequencing identified a novel heterozygous mutation in STAT3 (c.989C>G, p.P330R). Functional experiments revealed it was a gain-of-function mutation. Upon interleukin 6 stimulation, this mutation caused a much higher activation of STAT3 than the wild-type control. In addition, the mutation also activated STAT3 under the steady state. The T helper 17 cell level in the patient was significantly higher than that in normal controls, which may contribute to the autoimmune pathology caused by the STAT3P330R mutation. Apart from Janus kinase (JAK) inhibitors, we also provided experimental evidence of a STAT3 selective inhibitor (Stattic) effectively suppressing the activation of mutant STAT3 in vitro. Collectively, our study expanded the clinical spectrum of STAT3 GOF syndrome. STAT3 GOF mutation appears as a new etiology of ILD and should be considered in patients with early-onset ILDs. In addition to JAK inhibitors, the specific STAT3 inhibitor would be an appealing option for the targeted treatment.
MSC-ACE2 Ameliorates Streptococcus uberis-Induced Inflammatory Injury in Mammary Epithelial Cells by Upregulating the IL-10/STAT3/SOCS3 Pathway
Authors: Yan Shuping , Zhang Chonghao , Ji Xiaoxia , Wu Gang , Huang Xinhe , Zhang Yafeng , Zhang Yuanshu
Published: May 2022

In the dairy industry, Streptococcus uberis (S. uberis) is one of the most important pathogenic bacteria associated with mastitis in milk-producing cows, causing vast economic loss. To date, the only real effective method of treating and preventing streptococcal mastitis is antimicrobial therapy. In many inflammatory diseases, mesenchymal stem cells (MSCs) and angiotensin-converting enzyme 2 (ACE2) play an anti-inflammatory and anti-injurious role. Accordingly, we hypothesized that MSCs overexpressing ACE2 (MSC-ACE2) would ameliorate the inflammatory injury caused by S. uberis in mammary epithelial cells more efficiently than MSC alone. By activating the transcription 3/suppressor of cytokine signaling 3 (IL-10/STAT3/SOCS3) signaling pathway, MSC-ACE2 inhibited the NF-κB, MAPKs, apoptosis, and pyroptosis passways. Moreover, MSC-ACE2 overturned the downregulation of Occludin, Zonula occludens 1 (ZO-1), and Claudin-3 expression levels caused by S. uberis, suggesting that MSC-ACE2 promotes the repair of the blood-milk barrier. MSC-ACE2 demonstrated greater effectiveness than MSC alone, as expected. Based on these results, MSC-ACE2 effectively inhibits EpH4-Ev cell’s inflammatory responses induced by S. uberis, and would be an effective therapeutic tool for treating streptococcal mastitis.
Targeting Stress Sensor Kinases in Hepatocellular Carcinoma-Infiltrating Human NK Cells as a Novel Immunotherapeutic Strategy for Liver Cancer
Authors: Zecca Alessandra , Barili Valeria , Olivani Andrea , Biasini Elisabetta , Boni Carolina , Fisicaro Paola , Montali Ilaria , Tiezzi Camilla , Dalla Valle Raffaele , Ferrari Carlo , Cariani Elisabetta , Missale Gabriele
Published: May 2022

Natural killer (NK) cells may become functionally exhausted entering hepatocellular carcinoma (HCC), and this has been associated with tumor progression and poor clinical outcome. Hypoxia, low nutrients, immunosuppressive cells, and soluble mediators characterize the intratumor microenvironment responsible for the metabolic deregulation of infiltrating immune cells such as NK cells. HCC-infiltrating NK cells from patients undergoing liver resection for HCC were sorted, and genome-wide transcriptome profiling was performed. We have identified a marked general upregulation of gene expression profile along with metabolic impairment of glycolysis, OXPHOS, and autophagy as well as functional defects of NK cells. Targeting p38 kinase, a stress-responsive mitogen-activated protein kinase, we could positively modify the metabolic profile of NK cells with functional restoration in terms of TNF-α production and cytotoxicity. We found a metabolic and functional derangement of HCC-infiltrating NK cells that is part of the immune defects associated with tumor progression and recurrence. NK cell exhaustion due to the hostile tumor microenvironment may be restored with p38 inhibitors with a selective mechanism that is specific for tumor-infiltrating—not affecting liver-infiltrating—NK cells. These results may represent the basis for the development of a new immunotherapeutic strategy to integrate and improve the available treatments for HCC.
Toll-Like Receptor 7 Agonist RG7854 Mediates Therapeutic Efficacy and Seroconversion in Woodchucks With Chronic Hepatitis B
Authors: Wildum Steffen , Korolowicz Kyle E. , Suresh Manasa , Steiner Guido , Dai Lue , Li Bin , Yon Changsuek , De Vera Mudry Maria Cristina , Regenass-Lechner Franziska , Huang Xu , Hong Xupeng , Murreddu Marta G. , Kallakury Bhaskar V. , Young John A. T. , Menne Stephan
Published: May 2022

Conventional treatment of chronic hepatitis B (CHB) is rarely curative due to the immunotolerant status of patients. RG7854 is an oral double prodrug of a toll-like receptor 7 (TLR7) agonist that is developed for the treatment of CHB. The therapeutic efficacy, host immune response, and safety of RG7854 were evaluated in the woodchuck model of CHB. Monotreatment with the two highest RG7854 doses and combination treatment with the highest RG7854 dose and entecavir (ETV) suppressed viral replication, led to loss of viral antigens, and induced seroconversion in responder woodchucks. Since viral suppression and high-titer antibodies persisted after treatment ended, this suggested that a sustained antiviral response (SVR) was induced by RG7854 in a subset of animals. The SVR rate, however, was comparable between both treatment regimens, suggesting that the addition of ETV did not enhance the therapeutic efficacy of RG7854 although it augmented the proliferation of blood cells in response to viral antigens and magnitude of antibody titers. The induction of interferon-stimulated genes in blood by RG7854/ETV combination treatment demonstrated on-target activation of TLR7. Together with the virus-specific blood cell proliferation and the transient elevations in liver enzymes and inflammation, this suggested that cytokine-mediated non-cytolytic and T-cell mediated cytolytic mechanisms contributed to the SVR, in addition to the virus-neutralizing effects by antibody-producing plasma cells. Both RG7854 regimens were not associated with treatment-limiting adverse effects but accompanied by dose-dependent, transient neutropenia and thrombocytopenia. The study concluded that finite, oral RG7854 treatment can induce a SVR in woodchucks that is based on the retrieval of antiviral innate and adaptive immune responses. This supports future investigation of the TLR7 agonist as an immunotherapeutic approach for achieving functional cure in patients with CHB.
Recurrence- and Malignant Progression-Associated Biomarkers in Low-Grade Gliomas and Their Roles in Immunotherapy
Authors: Teng Chubei , Zhu Yongwei , Li Yueshuo , Dai Luohuan , Pan Zhouyang , Wanggou Siyi , Li Xuejun
Published: May 2022

Despite a generally better prognosis than high-grade glioma (HGG), recurrence and malignant progression are the main causes for the poor prognosis and difficulties in the treatment of low-grade glioma (LGG). It is of great importance to learn about the risk factors and underlying mechanisms of LGG recurrence and progression. In this study, the transcriptome characteristics of four groups, namely, normal brain tissue and recurrent LGG (rLGG), normal brain tissue and secondary glioblastoma (sGBM), primary LGG (pLGG) and rLGG, and pLGG and sGBM, were compared using Chinese Glioma Genome Atlas (CGGA) and Genotype-Tissue Expression Project (GTEx) databases. In this study, 296 downregulated and 396 upregulated differentially expressed genes (DEGs) with high consensus were screened out. Univariate Cox regression analysis of data from The Cancer Genome Atlas (TCGA) yielded 86 prognostically relevant DEGs; a prognostic prediction model based on five key genes (HOXA1, KIF18A, FAM133A, HGF, and MN1) was established using the least absolute shrinkage and selection operator (LASSO) regression dimensionality reduction and multivariate Cox regression analysis. LGG was divided into high- and low-risk groups using this prediction model. Gene Set Enrichment Analysis (GSEA) revealed that signaling pathway differences in the high- and low-risk groups were mainly seen in tumor immune regulation and DNA damage-related cell cycle checkpoints. Furthermore, the infiltration of immune cells in the high- and low-risk groups was analyzed, which indicated a stronger infiltration of immune cells in the high-risk group than that in the low-risk group, suggesting that an immune microenvironment more conducive to tumor growth emerged due to the interaction between tumor and immune cells. The tumor mutational burden and tumor methylation burden in the high- and low-risk groups were also analyzed, which indicated higher gene mutation burden and lower DNA methylation level in the high-risk group, suggesting that with the accumulation of genomic mutations and epigenetic changes, tumor cells continued to evolve and led to the progression of LGG to HGG. Finally, the value of potential therapeutic targets for the five key genes was analyzed, and findings demonstrated that KIF18A was the gene most likely to be a potential therapeutic target. In conclusion, the prediction model based on these five key genes can better identify the high- and low-risk groups of LGG and lay a solid foundation for evaluating the risk of LGG recurrence and malignant progression.
Identification of New Prognostic Markers and Therapeutic Targets for Non-Muscle Invasive Bladder Cancer: HER2 as a Potential Target Antigen
Authors: Chae Han Kyu , Nam Wook , Kim Han Gwun , Lim Sharon , Noh Byeong-Joo , Kim So Won , Kang Gil Hyun , Park Jong Yeon , Eom Dae-Woon , Kim Sung Jin
Published: May 2022

Bacillus Calmette–Guérin (BCG) is the gold standard adjuvant treatment for non-muscle-invasive bladder cancer (NMIBC). However, given the current global shortage of BCG, new treatments are needed. We evaluated tumor microenvironment markers as potential BCG alternatives for NMIBC treatment. Programmed death-ligand 1, human epidermal growth factor receptor-2 (HER2), programmed cell death-1 (PD1), CD8, and Ki67 levels were measured in treatment-naïve NMIBC and MIBC patients (pTa, pT1, and pT2 stages). Univariate and multivariate Cox proportional hazard models were used to determine the impact of these markers and other clinicopathological factors on survival, recurrence, and progression. EP263, IM142, PD1, and Ki67 levels were the highest in the T2 stage, followed by the T1 and Ta stages. HER2 and IM263 expressions were higher in the T1 and T2 stages than in the Ta stage. In NMIBC, the significant prognostic factors for recurrence-free survival were adjuvant therapy, tumor grade, and HER2 positivity, whereas those for progression-free survival included age, T-stage, and IM263. Age, T-stage, EP263, PD1, CD8, and Ki67 levels were significant factors associated with overall survival. IM263 and HER2 are potential biomarkers for progression and recurrence, respectively. Therefore, we propose HER2 as a potential target antigen for intravesical therapeutics as a BCG alternative.
Sirt5 Inhibits BmNPV Replication by Promoting a Relish-Mediated Antiviral Pathway in Bombyx mori
Authors: Zhang Mengmeng , Fei Shigang , Xia Junming , Wang Yeyuan , Wu Hongyun , Li Xian , Guo Yiyao , Swevers Luc , Sun Jingchen , Feng Min
Published: May 2022

Silent information regulators (Sirtuins) belong to the family of nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases (HDACs) that have diverse functions in cells. Mammalian Sirtuins have seven isoforms (Sirt1–7) which have been found to play a role in viral replication. However, Sirtuin members of insects are very different from mammals, and the function of insect Sirtuins in regulating virus replication is unclear. The silkworm, Bombyx mori, as a model species of Lepidoptera, is also an important economical insect. B. mori nucleopolyhedrovirus (BmNPV) is a major pathogen that specifically infects silkworms and causes serious losses in the sericulture industry. Here, we used the infection of the silkworm by BmNPV as a model to explore the effect of Sirtuins on virus replication. We initially knocked down all silkworm Sirtuins, and then infected with BmNPV to analyze its replication. Sirt2 and Sirt5 were found to have potential antiviral functions in the silkworm. We further confirmed the antiviral function of silkworm Sirt5 through its effects on viral titers during both knockdown and overexpression experiments. Additionally, Suramin, a Sirt5 inhibitor, was found to promote BmNPV replication. In terms of molecular mechanism, it was found that silkworm Sirt5 might promote the immune pathway mediated by Relish, thereby enhancing the host antiviral response. This study is the first to explore the role of Sirtuins in insect-virus interactions, providing new insights into the functional role of members of the insect Sirtuin family.
Soil Salinity Estimation Over Coastal Wetlands Based on Random Forest Algorithm and Hydrological Connectivity Metric
Authors: Sui Haochen , Chen Dawei , Yan Jiaguo , Li Bin , Li Wei , Cui Baoshan
Published: May 2022

Owing to climate warming and human activities (irrigation and reservoirs), sea level rise and runoff reduction have been threatening the coastal ecosystem by increasing the soil salinity. However, short-term sparse in situ observations limit the study on the response of coastal soil salinity to external stressors and thus its effect on coastal ecosystem. In this study, based on hydrological connectivity metric and random forest algorithm (RF), we develop a coastal soil salinity inversion model with in situ observations and satellite-based datasets. Using Landsat images and ancillary as input variables, we produce a 30-m monthly grid dataset of surface soil salinity over the Yellow River Delta. Based on the cross-validation result with in situ observations, the proposed RF model performs higher accuracy and stability with determination coefficient of 0.89, root mean square error of 1.48 g·kg-1, and mean absolute error of 1.05 g·kg-1. The proposed RF model can gain the accuracy improvements of about 11–43% over previous models at different conditions. The spatial distribution and seasonal variabilities of soil salinity is sensitive to the changing signals of runoff, tide, and local precipitation. Combining spatiotemporal collaborative information with the hydrological connectivity metric, we found that the proposed RF model can accurately estimate surface soil salinity, especially in natural reserved regions. The modeling results of surface soil salinity can be significant for exploring the effect of seawater intrusion and runoff reduction to the evolution of coastal salt marsh ecosystems.
Social Network and Environment as Determinants of Disability and Quality of Life in Aging: Results From an Italian Study
Authors: Guastafierro Erika , Toppo Claudia , Corso Barbara , Romano Rosa , Campioni Rino , Brambilla Ersilia , Facchini Carla , Bordoni Sara , Leonardi Matilde
Published: May 2022

Background

The increase in life expectancy is leading to a worldwide increase in chronic diseases and disability, with significant concern about their management and long-term care. Investigating the aging process using a bio-psychosocial perspective is essential to understanding how to reduce disability and improve the quality of life of aging people. This study aims to explore the role of social networks and built environment as predictors of disability and quality of life in the Italian population aged over 50 years.

Materials and Methods

The research protocol is composed of several tools: World Health Organization Disability Assessment Scale 2.0 (WHODAS 2.0), World Health Organization Quality of Life Assessment in Aging (WHOQOL-AGE), Social Network Index (SNI), the Courage Built Environment Self-Reported Questionnaire (CBE-SR), and collection of sociodemographic information and information on health system coverage.

Results

A total of 431 people were administered the protocol, and among them, 209 were males and 222 were females, with a mean age of 70 years. The majority of the sample reported earning a middle or high school diploma, and 60.6% of the sample declared to have a good health status. The results showed that people with a good social support network have higher levels of functioning and quality of life. However, the built environment did not significantly predict either disability or quality of life.

Conclusions

These results could provide elements for dialogue with institutions and policymakers. This is fundamental to develop active policies aimed at the implementation of services and systems to promote healthy aging process.
Overview of Three Proliferation Pathways (Wnt, Notch, and Hippo) in Intestine and Immune System and Their Role in Inflammatory Bowel Diseases (IBDs)
Authors: Khoramjoo Seyed Mobin , Kazemifard Nesa , Baradaran Ghavami Shaghayegh , Farmani Maryam , Shahrokh Shabnam , Asadzadeh Aghdaei Hamid , Sherkat Ghazal , Zali Mohammad Reza
Published: May 2022

Inflammatory bowel disease (IBD) is a disorder, which involves the gastrointestinal (GI) tract consisting Crohn's disease (CD) and ulcerative colitis (UC). The etiology of this disease is not yet clear and, hence, there are numerous medications and treatments for patients with IBD, although a definite and permanent treatment is still missing. Therefore, finding novel therapeutic approaches are vital for curing patients with IBD. In the GI tract, there are various lineages of cells with different roles that their existence is necessary for the barrier function of intestinal epithelial cells (IECs). Therefore, signaling pathways, which manage the hemostasis of cell lineages in intestine, such as Wnt, Notch, and Hippo, could have crucial roles in regulation of barrier function in the intestine. Additionally, these signaling pathways function as a governor of cell growth, tissue homeostasis, and organ size. In patients with IBD, recent studies have revealed that these signaling pathways are dysregulated that it could result in depletion or excess of a cell lineage in the intestine. Moreover, dysregulation of these signaling pathways in different cell lineages of the immune system could lead to dysregulation of the immune system's responses in IBD. In this article, we summarized the components and signaling of Wnt, Notch, and Hippo pathways and their role in the intestine and immune system. Furthermore, we reviewed latest scientific literature on the crosstalk among these three signaling pathways in IBD. An overview of these three signaling pathways and their interactions in IBD could provide a novel insight for prospective study directions into finding efficient medications or treatments.
Simple Death Risk Models to Predict In-hospital Outcomes in Acute Aortic Dissection in Emergency Department
Authors: Xing Lingyu , Zhou Yannan , Han Yi , Chen Chen , Dong Zegang , Zheng Xinde , Chen Dongxu , Yu Yao , Liao Fengqing , Guo Shuai , Yao Chenling , Tang Min , Gu Guorong
Published: May 2022

Objective

We sought to find a bedside prognosis prediction model based on clinical and image parameters to determine the in-hospital outcomes of acute aortic dissection (AAD) in the emergency department.

Methods

Patients who presented with AAD from January 2010 to December 2019 were retrospectively recruited in our derivation cohort. Then we prospectively collected patients with AAD from January 2020 to December 2021 as the validation cohort. We collected the demographics, medical history, treatment options, and in-hospital outcomes. All enrolled patients underwent computed tomography angiography. The image data were systematically reviewed for anatomic criteria in a retrospective fashion by three professional radiologists. A series of radiological parameters, including the extent of dissection, the site of the intimal tear, entry tear diameter, aortic diameter at each level, maximum false lumen diameter, and presence of pericardial effusion were collected.

Results

Of the 449 patients in the derivation cohort, 345 (76.8%) were male, the mean age was 61 years, and 298 (66.4%) had a history of hypertension. Surgical repair was performed in 327 (72.8%) cases in the derivation cohort, and the overall crude in-hospital mortality of AAD was 10.9%. Multivariate logistic regression analysis showed that predictors of in-hospital mortality in AAD included age, Marfan syndrome, type A aortic dissection, surgical repair, and maximum false lumen diameter. A final prognostic model incorporating these five predictors showed good calibration and discrimination in the derivation and validation cohorts. As for type A aortic dissection, 3-level type A aortic dissection clinical prognosis score (3ADPS) including 5 clinical and image variables scored from −2 to 5 was established: (1) moderate risk of death if 3ADPS is <0; (2) high risk of death if 3ADPS is 1–2; (3) very high risk of death if 3ADPS is more than 3. The area under the receiver operator characteristic curves in the validation cohorts was 0.833 (95% CI, 0.700–0.967).

Conclusion

Age, Marfan syndrome, type A aortic dissection, surgical repair, and maximum false lumen diameter can significantly affect the in-hospital outcomes of AAD. And 3ADPS contributes to the prediction of in-hospital prognosis of type A aortic dissection rapidly and effectively. As multivariable risk prediction tools, the risk models were readily available for emergency doctors to predict in-hospital mortality of patients with AAD in extreme clinical risk.
Characterizing the Severity of SARS-CoV-2 Variants at a Single Pediatric Center
Authors: Khan Aslam , Ichura Caroline , Wang Hannah , Rezende Izabela , Sahoo Malaya K. , Huang ChunHong , Solis Daniel , Sibai Mamdouh , Yamamoto Fumiko , Nyathi Sindiso , Bayrau Bethel , Pinsky Benjamin A. , LaBeaud A. Desiree
Published: May 2022

Since March 2020, SARS-CoV-2 has plagued the world with COVID-19 and individuals of all ages have experienced varying symptoms of disease. Older adults were experiencing more severe disease compared to children and were prioritized by vaccination efforts. While biologic therapies and vaccinations were implemented, there were changes in public health restrictions with subsequent surges resulting in more infected children. During these surges there was a rise of different SARS-CoV-2 variants with the dominant variant initially alpha (B.1.1.7 and other Pango lineages) and epsilon (B.1.427/B.1.429) in early 2021 and a dramatic shift to delta (B.1.617.2 and other Pango lineages) by mid-summer 2021. In this study we aimed to characterize the clinical severity and host factors associated with disease by SARS-CoV-2 variant and evaluate if there are differences in disease severity by circulating variant. We retrospectively included all individuals 0–25 years of age who presented to our center and had a positive SARS-CoV-2 RT-PCR, SARS-CoV-2 variant mutation testing, and documented clinical notes from 1 January 2021 through 31 December 2021. We identified 745 individuals who met inclusion criteria and found the delta variant was associated with severe/critical disease compared to the other variants studied. The results of the model showed that underlying respiratory disease and diabetes were risk factors for progression to severe disease. These insights are important when evaluating public health measures and treatment options for children as more variants arise.
Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia
Authors: Vita Madalina M. , Iturbe-Espinoza Paul , Bonte Matthijs , Brandt Bernd W. , Braster Martin , Brown David M. , van Spanning Rob J. M.
Published: May 2022

Oil absorbent particles made from surface-modified polypropylene can be used to facilitate the removal of oil from the environment. In this study, we investigated to what extent absorbed oil was biodegraded and how this compared to the biodegradation of oil in water. To do so, we incubated two bacterial communities originating from the Niger Delta, an area subject to frequent oil spills, in the presence and absence of polypropylene particles. One community evolved from untreated soil whereas the second evolved from soil pre-exposed to oil. We observed that the polypropylene particles stimulated the growth of biofilms and enriched species from genera Mycobacterium, Sphingomonas and Parvibaculum. Cultures with polypropylene particles degraded more crude oil than those where the oil was present in suspension regardless of whether they were pre-exposed or not. Moreover, the community pre-exposed to crude oil had a different community structure and degraded more oil than the one from untreated soil. We conclude that the biodegradation rate of crude oil was enhanced by the pre-exposure of the bacterial communities to crude oil and by the use of oil-absorbing polypropylene materials. The data show that bacterial communities in the biofilms growing on the particles have an enhanced degradation capacity for oil.
Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States
Authors: Giddings Lesley-Ann , Kunstman Kevin , Moumen Bouziane , Asiama Laurent , Green Stefan , Delafont Vincent , Brockley Matthew , Samba-Louaka Ascel
Published: May 2022

Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.
Evaluation of Serum Ferritin, Procalcitonin, and C-Reactive Protein for the Prediction of Severity and Mortality in Hemorrhagic Fever With Renal Syndrome
Authors: Che Lihe , Wang Zedong , Du Na , Li Liang , Zhao Yinghua , Zhang Kaiyu , Liu Quan
Published: May 2022

This study aimed to analyze the clinical significance of serum ferritin, procalcitonin (PCT), and C-reactive protein (CRP) in patients with hemorrhagic fever with renal syndrome (HFRS). The demographical, clinical, and laboratory data of 373 patients with HFRS in northeastern China were retrospectively analyzed. The levels of serum ferritin and PCT in severe patients (n = 108) were significantly higher than those in mild patients (n = 265, p < 0.001) and associated with HFRS severity. The area under the receiver operating characteristic curve (AUC) values of serum ferritin and PCT for predicting the severity of HFRS were 0.732 (95% CI 0.678–0.786, p < 0.001) and 0.824 (95% CI 0.773–0.875, p < 0.001), respectively, showing sensitivity and specificity of 0.75 and 0.88 for serum ferritin, and 0.76 and 0.60 for PCT. The CRP level in HFRS with bacterial co-infection (n = 115) was higher than that without bacterial co-infection (n = 258, p < 0.001). The AUC value of CRP for predicting bacterial co-infection was 0.588 (95% CI 0.525–0.652, p < 0.001), showing sensitivity and specificity of 0.43 and 0.76, respectively. The serum ferritin level in non-survivors (n = 14) was significantly higher than in survivors (n = 359, p < 0.001). The AUC value of serum ferritin for predicting mortality was 0.853 (95% CI 0.774–0.933, p < 0.001), showing sensitivity and specificity of 0.933 and 0.739. Serum ferritin and PCT have a robust association with HFRS severity and mortality, which may be promising predictors, and CRP is an effective biomarker to assess bacterial co-infection in HFRS.
High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping
Authors: Cario Anaïs , Larzillière Marina , Nguyen Olivier , Alain Karine , Marre Samuel
Published: May 2022

Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.
DNA/RNA Preservation in Glacial Snow and Ice Samples
Authors: Trivedi Christopher B. , Keuschnig Christoph , Larose Catherine , Rissi Daniel Vasconcelos , Mourot Rey , Bradley James A. , Winkel Matthias , Benning Liane G.
Published: May 2022

The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.
Deep Learning in RNA Structure Studies
Authors: Yu Haopeng , Qi Yiman , Ding Yiliang
Published: May 2022

Deep learning, or artificial neural networks, is a type of machine learning algorithm that can decipher underlying relationships from large volumes of data and has been successfully applied to solve structural biology questions, such as RNA structure. RNA can fold into complex RNA structures by forming hydrogen bonds, thereby playing an essential role in biological processes. While experimental effort has enabled resolving RNA structure at the genome-wide scale, deep learning has been more recently introduced for studying RNA structure and its functionality. Here, we discuss successful applications of deep learning to solve RNA problems, including predictions of RNA structures, non-canonical G-quadruplex, RNA-protein interactions and RNA switches. Following these cases, we give a general guide to deep learning for solving RNA structure problems.
Biochemical Characterization of SARS-CoV-2 Spike RBD Mutations and Their Impact on ACE2 Receptor Binding
Authors: Hoter Abdullah , Naim Hassan Y.
Published: May 2022

Infection of mammalian cells by SARS-CoV-2 coronavirus requires primary interaction between the receptor binding domain (RBD) of the viral spike protein and the host cell surface receptor angiotensin-converting enzyme 2 (ACE2) glycoprotein. Several mutations in the RBD of SARS-CoV-2 spike protein have been reported for several variants and resulted in wide spread of the COVID pandemic. For instance, the double mutations L452R and E484Q present in the Indian B.1.617 variant have been suggested to cause evasion of the host immune response. The common RBD mutations N501Y and E484K were found to enhance the interaction with the ACE2 receptor. In the current study, we analyzed the biosynthesis and secretion of the RBD double mutants L452R and E484Q in comparison to the wild-type RBD and the individual mutations N501 and E484K in mammalian cells. Moreover, we evaluated the interaction of these variants with ACE2 by means of expression of the S protein and co-immunoprecipitation with ACE2. Our results revealed that the double RBD mutations L452R and E484Q resulted in a higher expression level and secretion of spike S1 protein than other mutations. In addition, an increased interaction of these mutant forms with ACE2 in Calu3 cells was observed. Altogether, our findings highlight the impact of continuous S1 mutations on the pathogenicity of SARS-CoV-2 and provide further biochemical evidence for the dominance and high transmissibility of the double Indian mutations.
Diospyros malabarica Fruit Extract Derived Silver Nanoparticles: A Biocompatible Antibacterial Agent
Authors: Polash Shakil Ahmed , Hamza Amir , Hossain Md. Monir , Tushar Mehedi Hasan , Takikawa Masato , Shubhra Razib Datta , Saiara Noshin , Saha Tanushree , Takeoka Shinji , Sarker Satya Ranjan
Published: May 2022

Biogenic silver nanoparticles demonstrate excellent antibacterial activity against a broad range of bacteria. Herein, aqueous biogenic silver nanoparticles (Aq@bAgNPs) and ethanolic biogenic silver nanoparticles (Et@bAgNPs) were synthesized using aqueous as well as ethanolic extracts of Diospyros malabarica fruit, respectively. The as-prepared biogenic silver nanoparticles (bAgNPs) were characterized using UV-Vis, FTIR as well as energy dispersive X-ray (EDS) spectroscopy, electron microscopy, dynamic light scattering spectroscopy (DLS), and zetasizer. The zeta potentials of Aq@bAgNPs and Et@bAgNPs were −9.8 ± 2.6, and −12.2 ± 1.9 mV, respectively. The antibacterial activity of bAgNPs was investigated against seven bacterial strains (i.e., pathogenic and nonpathogenic) and Et@bAgNPs exhibited the highest antibacterial propensity (i.e., 20 nm in diameter) against Bacillus subtillis through disk diffusion assay. The trypan blue dye exclusion assay also confirmed the antibacterial propensity of as-prepared bAgNPs. Furthermore, both Aq@bAgNPs and Et@bAgNPs oxidize bacterial membrane fatty acids and generate lipid peroxides which eventually form complexes with thiobarbituric acid (i.e., malondialdehyde-thiobarbituric acid adduct) to bring about bacterial death. Both the nanoparticles demonstrated good hemocompatibility against human as well as rat red blood cells (RBCs). In addition, they exhibited excellent biocompatibility in vivo in terms of rat liver (i.e., serum ALT, AST, and γ-GT) and kidneys (i.e., serum creatinine) function biomarkers.
Sex Differences in Blood–Brain Barrier Transport of Psychotropic Drugs
Authors: Dalla Christina , Pavlidi Pavlina , Sakelliadou Danai-Georgia , Grammatikopoulou Tatiana , Kokras Nikolaos
Published: May 2022

Treatment of neuropsychiatric disorders relies on the effective delivery of therapeutic molecules to the target organ, the brain. The blood–brain barrier (BBB) hinders such delivery and proteins acting as transporters actively regulate the influx and importantly the efflux of both endo- and xeno-biotics (including medicines). Neuropsychiatric disorders are also characterized by important sex differences, and accumulating evidence supports sex differences in the pharmacokinetics and pharmacodynamics of many drugs that act on the brain. In this minireview we gather preclinical and clinical findings on how sex and sex hormones can influence the activity of those BBB transporter systems and affect the brain pharmacokinetics of psychotropic medicines. It emerges that it is not well understood which psychotropics are substrates for each of the many and not well-studied brain transporters. Indeed, most evidence originates from studies performed in peripheral tissues, such as the liver and the kidneys. None withstanding, accumulated evidence supports the existence of several sex differences in expression and activity of transport proteins, and a further modulating role of gonadal hormones. It is proposed that a closer study of sex differences in the active influx and efflux of psychotropics from the brain may provide a better understanding of sex-dependent brain pharmacokinetics and pharmacodynamics of psychotropic medicines.
Salivary Cortisol, but Not Oxytocin, Varies With Social Challenges in Domestic Pigs: Implications for Measuring Emotions
Authors: Moscovice Liza R. , Gimsa Ulrike , Otten Winfried , Eggert Anja
Published: May 2022

Animals respond to inherently rewarding or punishing stimuli with changes in core affective states, which can be investigated with the aid of appropriate biomarkers. In this study we evaluate salivary cortisol (sCORT) and salivary oxytocin (sOXT) concentrations under baseline conditions and in response to two negatively- and two positively-valenced social challenges in 75 young pigs (Sus scrofa domesticus), housed and tested in eight social groups. We predicted that: (1) Relative to baseline, weaning and brief social isolation would be associated with increases in sCORT, due to psychosocial stress, and reductions in sOXT, due to a lack of opportunities for social support; and (2) Opportunities for social play, and reunions with group members after a separation would be associated with weaker sCORT responses, and increases in sOXT concentrations compared to baseline and to negative social challenges. Testing and sample collection occurred between 28 and 65 days of age and involved a within-subject design, in which every subject was sampled multiple times in neutral (baseline), negative and positive social contexts. We also recorded behavioral data and measured rates of agonism, play and affiliative interactions in the different contexts, prior to saliva sampling. As expected, negative social challenges were associated with robust cortisol responses. Relative to baseline, pigs also had higher sCORT responses to positive social challenges, although these differences were only significant during reunions. Salivary oxytocin concentrations did not differ between the different social conditions, although sOXT was lowest during the brief social isolation. Behavioral analyses confirmed predictions about the expected changes in social interactions in different social contexts, with increases in agonism following weaning, increases in coordinated locomotor play in the play context and high rates of affiliative interactions during reunions. Relative sCORT reactivity to different contexts may reflect the intensity of emotional responses, with greater increases occurring in response to challenges that involve more psychosocial stress. Our results suggest that sOXT is not a reliable indicator of emotional valence in pigs, although more research is needed to characterize sOXT responses to various challenges with and without access to social support.
Characterization of Parkinson's Disease Subtypes and Related Attributes
Authors: Shakya Shamatree , Prevett Julia , Hu Xiao , Xiao Ran
Published: May 2022

Parkinson's disease is a progressive neurodegenerative disease with complex, heterogeneous motor and non-motor symptoms. The current evidence shows that there is still a marked heterogeneity in the subtyping of Parkinson's disease using both clinical and data-driven approaches. Another challenge posed in PD subtyping is the reproducibility of previously identified PD subtypes. These issues require additional results to confirm previous findings and help reconcile discrepancies, as well as establish a standardized application of cluster analysis to facilitate comparison and reproducibility of identified PD subtypes. Our study aimed to address this gap by investigating subtypes of Parkinson's disease using comprehensive clinical (motor and non-motor features) data retrieved from 408 de novo Parkinson's disease patients with the complete clinical data in the Parkinson's Progressive Marker Initiative database. A standardized k-means cluster analysis approach was developed by taking into consideration of common practice and recommendations from previous studies. All data analysis codes were made available online to promote data comparison and validation of reproducibility across research groups. We identified two distinct PD subtypes, termed the severe motor-non-motor subtype (SMNS) and the mild motor- non-motor subtype (MMNS). SMNS experienced symptom onset at an older age and manifested more intense motor and non-motor symptoms than MMNS, who experienced symptom onset at a younger age and manifested milder forms of Parkinson's symptoms. The SPECT imaging makers supported clinical findings such that the severe motor-non-motor subtype showed lower binding values than the mild motor- non-motor subtype, indicating more significant neural damage at the nigral pathway. In addition, SMNS and MMNS show distinct motor (ANCOVA test: F = 47.35, p< 0.001) and cognitive functioning (F = 33.93, p< 0.001) progression trends. Such contrast between SMNS and MMNS in both motor and cognitive functioning can be consistently observed up to 3 years following the baseline visit, demonstrating the potential prognostic value of identified PD subtypes.
Auto-Selection of an Optimal Sparse Matrix Format in the Neuro-Simulator ANNarchy
Authors: Dinkelbach Helge Ülo , Bouhlal Badr-Eddine , Vitay Julien , Hamker Fred H.
Published: May 2022

Modern neuro-simulators provide efficient implementations of simulation kernels on various parallel hardware (multi-core CPUs, distributed CPUs, GPUs), thereby supporting the simulation of increasingly large and complex biologically realistic networks. However, the optimal configuration of the parallel hardware and computational kernels depends on the exact structure of the network to be simulated. For example, the computation time of rate-coded neural networks is generally limited by the available memory bandwidth, and consequently, the organization of the data in memory will strongly influence the performance for different connectivity matrices. We pinpoint the role of sparse matrix formats implemented in the neuro-simulator ANNarchy with respect to computation time. Rather than asking the user to identify the best data structures required for a given network and platform, such a decision could also be carried out by the neuro-simulator. However, it requires heuristics that need to be adapted over time for the available hardware. The present study investigates how machine learning methods can be used to identify appropriate implementations for a specific network. We employ an artificial neural network to develop a predictive model to help the developer select the optimal sparse matrix format. The model is first trained offline using a set of training examples on a particular hardware platform. The learned model can then predict the execution time of different matrix formats and decide on the best option for a specific network. Our experimental results show that using up to 3,000 examples of random network configurations (i.e., different population sizes as well as variable connectivity), our approach effectively selects the appropriate configuration, providing over 93% accuracy in predicting the suitable format on three different NVIDIA devices.