bluuebunny/crossref_metadata_2025 huggingface dataset:
Aberrant signaling of immune cells in Sjögren’s syndrome patient subgroups upon interferon stimulation
Authors: Sarkar Irene , Davies Richard , Aarebrot Anders K. , Solberg Silje M. , Petrovic Aleksandra , Joshi Anagha M. , Bergum Brith , Brun Johan G. , Hammenfors Daniel , Jonsson Roland , Appel Silke
Published: August 2022

Background

Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease, characterized by mononuclear cell infiltrates in the salivary and lacrimal glands, leading to glandular atrophy and dryness. Patient heterogeneity and lack of knowledge regarding its pathogenesis makes pSS a difficult disease to manage.

Methods

An exploratory analysis using mass cytometry was conducted of MAPK/ERK and JAK/STAT signaling pathways in peripheral blood mononuclear cells (PBMC) from 16 female medication free pSS patients (8 anti-Sjögren’s syndrome-related antigen A negative/SSA- and 8 SSA+) and 8 female age-matched healthy donors after stimulation with interferons (IFNs).

Results

We found significant differences in the frequencies of memory B cells, CD8+ T central and effector memory cells and terminally differentiated CD4+ T cells among the healthy donors and patient subgroups. In addition, we observed an upregulation of HLA-DR and CD38 in many cell subsets in the patients. Upon IFNα2b stimulation, slightly increased signaling through pSTAT1 Y701 was observed in most cell types in pSS patients compared to controls, while phosphorylation of STAT3 Y705 and STAT5 Y694 were slightly reduced. IFNγ stimulation resulted in significantly increased pSTAT1 Y701 induction in conventional dendritic cells (cDCs) and classical and non-classical monocytes in the patients. Most of the observed differences were more prominent in the SSA+ subgroup, indicating greater disease severity in them.

Conclusions

Augmented activation status of certain cell types along with potentiated pSTAT1 Y701 signaling and reduced pSTAT3 Y705 and pSTAT5 Y694 induction may predispose pSS patients, especially the SSA+ subgroup, to upregulated expression of IFN-induced genes and production of autoantibodies. These patients may benefit from therapies targeting these pathways.
Strategies to induce natural killer cell tolerance in xenotransplantation
Authors: Lopez Kevin J. , Cross-Najafi Arthur A. , Farag Kristine , Obando Benjamin , Thadasina Deepthi , Isidan Abdulkadir , Park Yujin , Zhang Wenjun , Ekser Burcin , Li Ping
Published: August 2022

Eliminating major xenoantigens in pig cells has drastically reduced human antibody-mediated hyperacute xenograft rejection (HXR). Despite these advancements, acute xenograft rejection (AXR) remains one of the major obstacles to clinical xenotransplantation, mediated by innate immune cells, including macrophages, neutrophils, and natural killer (NK) cells. NK cells play an ‘effector’ role by releasing cytotoxicity granules against xenogeneic cells and an ‘affecter’ role on other immune cells through cytokine secretion. We highlight the key receptor-ligand interactions that determine the NK cell response to target cells, focusing on the regulation of NK cell activating receptor (NKG2D, DNAM1) and inhibitory receptor (KIR2DL1-4, NKG2A, and LIR-1) signaling pathways. Inhibition of NK cell activity may protect xenografts from cytotoxicity. Recent successful approaches to reducing NK cell-mediated HXR and AXR are reviewed, including genetic modifications of porcine xenografts aimed at improving pig-to-human compatibility. Future directions to promote xenograft acceptance are discussed, including NK cell tolerance in pregnancy and NK cell evasion in viral infection.
A score of DNA damage repair pathway with the predictive ability for chemotherapy and immunotherapy is strongly associated with immune signaling pathway in pan-cancer
Authors: Ding Ke , He Youhua , Wei Jinfen , Fu Shuying , Wang Jiajian , Chen Zixi , Zhang Haibo , Qu Yimo , Liang Keying , Gong Xiaocheng , Qiu Li , Chen Dong , Xiao Botao , Du Hongli
Published: August 2022

DNA damage repair (DDR) is critical in maintaining normal cellular function and genome integrity and is associated with cancer risk, progression, and therapeutic response. However, there is still a lack of a thorough understanding of the effects of DDR genes’ expression level in cancer progression and therapeutic resistance. Therefore, we defined a tumor-related DDR score (TR-DDR score), utilizing the expression levels of 20 genes, to quantify the tumor signature of DNA damage repair pathways in tumors and explore the possible function and mechanism for the score among different cancers. The TR-DDR score has remarkably predictive power for tumor tissues. It is a more accurate indicator for the response of chemotherapy or immunotherapy combined with the tumor-infiltrating lymphocyte (TIL) and G2M checkpoint score than the pre-existing predictors (CD8 or PD-L1). This study points out that the TR-DDR score generally has positive correlations with patients of advanced-stage, genome-instability, and cell proliferation signature, while negative correlations with inflammatory response, apoptosis, and p53 pathway signature. In the context of tumor immune response, the TR-DDR score strongly positively correlates with the number of T cells (CD4+ activated memory cells, CD8+ cells, T regs, Tfh) and macrophages M1 polarization. In addition, by difference analysis and correlation analysis, COL2A1, MAGEA4, FCRL4, and ZIC1 are screened out as the potential modulating factors for the TR-DDR score. In summary, we light on a new biomarker for DNA damage repair pathways and explore its possible mechanism to guide therapeutic strategies and drug response prediction.
Combination strategies to optimize the efficacy of chimeric antigen receptor T cell therapy in haematological malignancies
Authors: Xiao Xinyi , Wang Yazhuo , Zou Zhengbang , Yang Yufei , Wang Xinyu , Xin Xin , Tu Sanfang , Li Yuhua
Published: August 2022

Chimeric antigen receptor (CAR) T cell therapy has revolutionized the therapeutic landscape of haematological malignancies. However, resistance and relapse remain prominent limitations, and they are related to the limited persistence and efficacy of CAR T cells, downregulation or loss of tumour antigens, intrinsic resistance of tumours to death signalling, and immune suppressive microenvironment. Rational combined modality treatments are regarded as a promising strategy to further unlock the antitumor potential of CAR T cell therapy, which can be applied before CAR T cell infusion as a conditioning regimen or in ex vivo culture settings as well as concomitant with or after CAR T cell infusion. In this review, we summarize the combinatorial strategies, including chemotherapy, radiotherapy, haematopoietic stem cell transplantation, targeted therapies and other immunotherapies, in an effort to further enhance the effectiveness of this impressive therapy and benefit more patients.
BTLA inhibition has a dominant role in the cis-complex of BTLA and HVEM
Authors: Battin Claire , Leitner Judith , Waidhofer-Söllner Petra , Grabmeier-Pfistershammer Katharina , Olive Daniel , Steinberger Peter
Published: August 2022

The engagement of the herpesvirus entry mediator (HVEM, TNFRSF14) by the B and T lymphocyte attenuator (BTLA) represents a unique interaction between an activating receptor of the TNFR-superfamily and an inhibitory receptor of the Ig-superfamily. BTLA and HVEM have both been implicated in the regulation of human T cell responses, but their role is complex and incompletely understood. Here, we have used T cell reporter systems to dissect the complex interplay of HVEM with BTLA and its additional ligands LIGHT and CD160. Co-expression with LIGHT or CD160, but not with BTLA, induced strong constitutive signalingviaHVEM. In line with earlier reports, we observed thatin cisinteraction of BTLA and HVEM prevented HVEM co-stimulation by ligands on surrounding cells. Intriguingly, our data indicate that BTLA mediated inhibition is not impaired in this heterodimeric complex, suggesting a dominant role of BTLA co-inhibition. Stimulation of primary human T cells in presence of HVEM ligands indicated a weak costimulatory capacity of HVEM potentially owed to itsin cisengagement by BTLA. Furthermore, experiments with T cell reporter cells and primary T cells demonstrate that HVEM antibodies can augment T cell responses by concomitantly acting as checkpoint inhibitors and co-stimulation agonists.
Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective
Authors: Raeisi Hamideh , Azimirad Masoumeh , Nabavi-Rad Ali , Asadzadeh Aghdaei Hamid , Yadegar Abbas , Zali Mohammad Reza
Published: August 2022

Clostridioides difficile (C. difficile), known as the major cause of antibiotic-associated diarrhea, is regarded as one of the most common healthcare-associated bacterial infections worldwide. Due to the emergence of hypervirulent strains, development of new therapeutic methods for C. difficile infection (CDI) has become crucially important. In this context, antibodies have been introduced as valuable tools in the research and clinical environments, as far as the effectiveness of antibody therapy for CDI was reported in several clinical investigations. Hence, production of high-performance antibodies for treatment of CDI would be precious. Traditional approaches of antibody generation are based on hybridoma technology. Today, application of in vitro technologies for generating recombinant antibodies, like phage display, is considered as an appropriate alternative to hybridoma technology. These techniques can circumvent the limitations of the immune system and they can be exploited for production of antibodies against different types of biomolecules in particular active toxins. Additionally, DNA encoding antibodies is directly accessible in in vitro technologies, which enables the application of antibody engineering in order to increase their sensitivity and specificity. Here, we review the application of antibodies for CDI treatment with an emphasis on recombinant fragment antibodies. Also, this review highlights the current and future prospects of the aforementioned approaches for antibody-mediated therapy of CDI.
The development and function of CD11c+ atypical B cells - insights from single cell analysis
Authors: Gao Xin , Cockburn Ian A.
Published: August 2022

CD11c+ T-bet+ atypical B cells (ABCs) have been identified in the context of vaccination, acute and chronic infections and autoimmune disease. However, the origins and functions of ABCs remain elusive. A major obstacle in the study of ABCs, and human MBCs more generally, has been the use of different phenotypic markers in different contexts to identify what appear to be phenotypically similar cells. Advances in single-cell RNA sequencing (scRNA-seq) technology have allowed researchers to accurately identify ABCs in different immune contexts such as diseases and tissues. Notably, recent studies utilizing single cell techniques have demonstrated ABCs are a highly conserved memory B cell lineage. This analysis has also revealed that ABCs are more abundant in ostensibly healthy donors than previously thought. Nonetheless, the normal function of these cells remains elusive. In this review, we will focus on scRNA-seq studies to discuss recent advances in our understanding about the development and functions of ABCs.
FLT3LG and IFITM3P6 consolidate T cell activity in the bone marrow microenvironment and are prognostic factors in acute myelocytic leukemia
Authors: Chen Haiyan , Wu Meng , Xia Hongping , Du Songjie , Zhou Guoren , Long Guangfeng , Zhu Yanan , Huang Xu , Yang Daheng
Published: August 2022

Acute myelocytic leukemia (AML) is a malignancy of the stem cell precursors of the myeloid lineage. CD4+ and CD8+ T cells play pivotal roles in influencing AML progression but are functionally suppressed in the bone marrow microenvironment. We aimed to find hub genes related to T cell exhaustion and suppression, thereby providing evidence for immunotherapy. In this study, gene transcriptome expression data from TCGA and TARGET databases were utilized to find key genes. Firstly, CIBERSORT immune cell infiltration algorithm and WGCNA method were used to identify CD4+ and CD8+ T cells-related genes. Univariate and multivariate cox regression analyses were then introduced to construct the overall survival prognosis model and included hub genes. The ESTIMATE and ssGSEA scoring methods were used to analyze the correlation between the hub genes and immune activity. Single-cell transcriptome analysis was applied to detect the immune cells expressing hub genes, hence, to detect exact mechanisms. Consequently, FLT3LG and IFITM3P6 were determined to be positively correlated with patients’ overall survival and microenvironment immune activity. Further study suggested FLT3-FLT3LG and IFITM3P6-miR-6748-3p-CBX7 signaling axes were involved in CD4+ and CD8+ T cells activation. This may be one of the mechanisms of T cells suppression in AML.
Repeat controlled human malaria infection of healthy UK adults with blood-stage Plasmodium falciparum: Safety and parasite growth dynamics
Authors: Salkeld Jo , Themistocleous Yrene , Barrett Jordan R. , Mitton Celia H. , Rawlinson Thomas A. , Payne Ruth O. , Hou Mimi M. , Khozoee Baktash , Edwards Nick J. , Nielsen Carolyn M. , Sandoval Diana Muñoz , Bach Florian A. , Nahrendorf Wiebke , Ramon Raquel Lopez , Baker Megan , Ramos-Lopez Fernando , Folegatti Pedro M. , Quinkert Doris , Ellis Katherine J. , Poulton Ian D. , Lawrie Alison M. , Cho Jee-Sun , Nugent Fay L. , Spence Philip J. , Silk Sarah E. , Draper Simon J. , Minassian Angela M.
Published: August 2022

In endemic settings it is known that natural malaria immunity is gradually acquired following repeated exposures. Here we sought to assess whether similar acquisition of blood-stage malaria immunity would occur following repeated parasite exposure by controlled human malaria infection (CHMI). We report the findings of repeat homologous blood-stage Plasmodium falciparum (3D7 clone) CHMI studies VAC063C (ClinicalTrials.gov NCT03906474) and VAC063 (ClinicalTrials.gov NCT02927145). In total, 24 healthy, unvaccinated, malaria-naïve UK adult participants underwent primary CHMI followed by drug treatment. Ten of these then underwent secondary CHMI in the same manner, and then six of these underwent a final tertiary CHMI. As with primary CHMI, malaria symptoms were common following secondary and tertiary infection, however, most resolved within a few days of treatment and there were no long term sequelae or serious adverse events related to CHMI. Despite detectable induction and boosting of anti-merozoite serum IgG antibody responses following each round of CHMI, there was no clear evidence of anti-parasite immunity (manifest as reduced parasite growth in vivo) conferred by repeated challenge with the homologous parasite in the majority of volunteers. However, three volunteers showed some variation in parasite growth dynamics in vivo following repeat CHMI that were either modest or short-lived. We also observed no major differences in clinical symptoms or laboratory markers of infection across the primary, secondary and tertiary challenges. However, there was a trend to more severe pyrexia after primary CHMI and the absence of a detectable transaminitis post-treatment following secondary and tertiary infection. We hypothesize that this could represent the initial induction of clinical immunity. Repeat homologous blood-stage CHMI is thus safe and provides a model with the potential to further the understanding of naturally acquired immunity to blood-stage infection in a highly controlled setting.

Clinical Trial Registration

ClinicalTrials.gov, identifier NCT03906474, NCT02927145.
Long-term adaptive response of an oceanic diatom to copper deficiency
Authors: Kong Liangliang , Price Neil M.
Published: August 2022

Enhanced vertical stratification brought about by warming of the ocean surface is expected to reduce vertical circulation and nutrient input with knock-on effects for phytoplankton. Increased nutrient limitation is one predicted outcome, but how that will impact phytoplankton is uncertain because we do not know how they will adapt. We used copper (Cu) as a model catalytic nutrient to explore the adaptive response of an oceanic diatom to continuous nutrient deprivation in laboratory experiments. Populations of Thalassiosira oceanica maintained under Cu-limiting and sufficient conditions for ~380 generations differed significantly in their abilities to grow in medium containing 1 nM Cu. Continued selection for more than 2000 generations increased Cu use efficiency (CuUE) of a low Cu-adapted (LCuA) population by more than 2-fold compared to the control and ancestral populations. The increase in CuUE resulted from a decrease in the amount of cellular Cu required for growth and an increase in the net carbon assimilation rate. Redistribution of cellular Cu and increased efficiency of photosynthetic reactions are hypothesized to explain the fast rates of maximum electron transport of low Cu-adapted cells despite containing less Cu. The results show that adaptation increased resource use efficiency in phytoplankton, which could reduce the impact of increased nutrient deficiency in the future ocean.
Application of modified clay in intensive mariculture pond: Impacts on nutrients and phytoplankton
Authors: Chi Lianbao , Ding Yu , He Liyan , Wu Zaixing , Yuan Yongquan , Cao Xihua , Song Xiuxian , Yu Zhiming
Published: August 2022

Nutrients and phytoplankton associated with mariculture development are important concerns globally, as they can significantly impact water quality and aquaculture yield. Currently, there is still insufficient information regarding the variations in nutrients and phytoplankton community of intensive mariculture systems, and effective treatment is lacking. Here, based on consecutive daily monitoring of two Litopenaeus vannamei ponds from July to October, the dynamic variations in nutrients and phytoplankton were elucidated. In addition, modified clay (MC) method was adopted to regulate the nutrients and phytoplankton community. The temporal variations in organic and inorganic nutrients presented fluctuating upward trends. Notably, organic nutrients were the dominant species, with average proportions of TON/P in TN/P were as high as 75.29% and 87.36%, respectively. Furthermore, a marked increase in the ratios of dinoflagellates to diatoms abundance were also observed in the control pond, concurrently with dominant organic nutrients, ascending N/P ratio and decreasing Si/N and Si/P ratios. In the MC-regulated pond, MC reduced the contents of both organic and inorganic nutrients. Furthermore, a distinct change pattern of dominant phytoplankton community occurred, with green algae becoming the most abundant phytoplankton in the MC-regulated pond. This study can provide new insights into an effective treatment for managing water quality and maintaining sustainable mariculture development.
Development and validation of an interpretable 3 day intensive care unit readmission prediction model using explainable boosting machines
Authors: Hegselmann Stefan , Ertmer Christian , Volkert Thomas , Gottschalk Antje , Dugas Martin , Varghese Julian
Published: August 2022

Background

Intensive care unit (ICU) readmissions are associated with mortality and poor outcomes. To improve discharge decisions, machine learning (ML) could help to identify patients at risk of ICU readmission. However, as many models are black boxes, dangerous properties may remain unnoticed. Widely used post hoc explanation methods also have inherent limitations. Few studies are evaluating inherently interpretable ML models for health care and involve clinicians in inspecting the trained model.

Methods

An inherently interpretable model for the prediction of 3 day ICU readmission was developed. We used explainable boosting machines that learn modular risk functions and which have already been shown to be suitable for the health care domain. We created a retrospective cohort of 15,589 ICU stays and 169 variables collected between 2006 and 2019 from the University Hospital Münster. A team of physicians inspected the model, checked the plausibility of each risk function, and removed problematic ones. We collected qualitative feedback during this process and analyzed the reasons for removing risk functions. The performance of the final explainable boosting machine was compared with a validated clinical score and three commonly used ML models. External validation was performed on the widely used Medical Information Mart for Intensive Care version IV database.

Results

The developed explainable boosting machine used 67 features and showed an area under the precision-recall curve of 0.119 ± 0.020 and an area under the receiver operating characteristic curve of 0.680 ± 0.025. It performed on par with state-of-the-art gradient boosting machines (0.123 ± 0.016, 0.665 ± 0.036) and outperformed the Simplified Acute Physiology Score II (0.084 ± 0.025, 0.607 ± 0.019), logistic regression (0.092 ± 0.026, 0.587 ± 0.016), and recurrent neural networks (0.095 ± 0.008, 0.594 ± 0.027). External validation confirmed that explainable boosting machines (0.221 ± 0.023, 0.760 ± 0.010) performed similarly to gradient boosting machines (0.232 ± 0.029, 0.772 ± 0.018). Evaluation of the model inspection showed that explainable boosting machines can be useful to detect and remove problematic risk functions.

Conclusions

We developed an inherently interpretable ML model for 3 day ICU readmission prediction that reached the state-of-the-art performance of black box models. Our results suggest that for low- to medium-dimensional datasets that are common in health care, it is feasible to develop ML models that allow a high level of human control without sacrificing performance.
A study protocol for an observational cohort investigating cardiac transthyretin amyloidosis flow reserve before and after Tafamidis treatment: The AMYTRE study
Authors: Vançon Bastien , Bisson Arnaud , Courtehoux Maxime , Bernard Anne , Bailly Matthieu
Published: August 2022

Introduction

Anginal symptoms and signs of ischemia have been reported in some patients with cardiac transthyretin amyloidosis (ATTR) without obstructive epicardial coronary artery disease (CAD). Few studies found that coronary microvascular dysfunction was highly prevalent in subjects with cardiac amyloidosis, even in the absence of epicardial CAD. The purpose of this study is to confirm the coronary microvascular dysfunction, and to go further with evaluation of the effect of Tafamidis on microvascular dysfunction after 24 months of treatment.

Methods and analysis

This study is a multicentric, prospective, observational cohort study. Adult patients with confirmed ATTR cardiomyopathy seen in the nuclear medicine departments of three large referral centers and treated with Tafamidis will be included. At baseline, patients will have a clinical and echocardiography evaluation. They will undergo a dynamic rest/stress cardiac scintigraphy with flow and reserve measurements before and 24 months after Tafamidis introduction. The primary outcome of this study will be the variation of stress and rest myocardial blood flow and flow reserve between baseline and 24 months after treatment. The effect of Tafamidis will be assessed by an intention to treat analysis.

Ethics and dissemination

The study has received the following approvals: Orleans Hospital Research Committee (CHRO-2021-05) and Sud-Mediterranée IV Regional Ethics Committee (21 06 02). Results will be made available to physicians, the funders, and other researchers.

Clinical trial registration

[https://clinicaltrials.gov/ct2/show/NCT05103943], identifier [NCT05103943].
Dry eye disease in patients with type II diabetes mellitus: A retrospective, population-based cohort study in Taiwan
Authors: Pan Li-Yen , Kuo Yu-Kai , Chen Tien-Hsing , Sun Chi-Chin
Published: August 2022

Purpose

To investigate the risk and protective factors of dry eye disease (DED) in patients with type II diabetes mellitus (DM).

Design

A retrospective cohort study using Chang- Gung research database collecting data from 2005 to 2020.

Methods

Patients with type II DM were included, and those with previous ocular diseases were excluded. Ten thousand twenty nine developed DED (DED group), and 142,491 didn't (non-DED group). The possible risk and protective factors were compared and analyzed using the logistic regression model.

Results

A majority of the DED group were female with significantly higher initial and average glycated hemoglobin levels, and higher incidence of diabetic neuropathy and retinopathy. In conditional logistic regression model, advanced age was a risk factor. After adjusting for sex, age, and DM duration; average glycated hemoglobin level, diabetic neuropathy, retinopathy, and nephropathy with eGFR 30 ~ 59 and intravitreal injection, vitrectomy, pan-retinal photocoagulation, and cataract surgery were contributing factors of DED. Considering antihyperglycemic agents, DPP4 inhibitor, SGLT2 inhibitor, GLP-1 agonist, and insulin monotherapy and dual medications combining any two of the aforementioned agents were protective factors against DED compared with metformin alone. In the monotherapy group, SLGT2 inhibitor had the lowest odds ratio, followed by GLP1 agonist, DPP4 inhibitor, and insulin.

Conclusions

DED in patients with DM is associated with female sex, advanced age, poor diabetic control, microvascular complications and receiving ocular procedures. GLP-1 agonist, SGLT-2 inhibitor, DPP4 inhibitor, and insulin are superior to metformin alone in preventing DM-related DED. A prospective randomized control trial is warranted to clarify our results.
Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1
Authors: Li Yang , Han Leilei , Wang Yanglan , Wang Xiaolin , Jia Lei , Li Jingyun , Han Jingwan , Zhao Jin , Li Hanping , Li Lin
Published: August 2022

In the latest HIV-1 global drug resistance report released by WHO, countries are advised to strengthen pre-treatment monitoring of drug resistance in AIDS patients. In this study, we established an NGS-based segmented amplification HIV-1 drug resistance mutation detection method. The pol region of HIV-1 was divided into three short fragments for NGS. The entire amplification and sequencing panel were more cost-effective and batched by using the barcode sequence corresponding to the sample. Each parameter was evaluated using samples with known resistance variants frequencies. The nucleotide sequence error rate, amino acid error rate, and noise value of the NGS-based segmented amplification method were both less than 1%. When the threshold was 2%, the consensus sequences of the HIV-1 NL4-3 strain were completely consistent with the Sanger sequences. This method can detect the minimum viral load of the sample at 102 copies/ml, and the input frequency and detection frequency of HIV-1 resistance mutations within the range of 1%–100% had good conformity (R2 = 0.9963; R2 = 0.9955). This method had no non-specific amplification for Hepatitis B and C. Under the 2% threshold, the incidence of surveillance drug resistance mutations in ART-naive HIV-infected patients was 20.69%, among which NRTIs class resistance mutations were mainly.
Isolation of a diazinon-degrading strain Sphingobium sp. DI-6 and its novel biodegradation pathway
Authors: Wang Guangli , Li Xiang , Zheng Jiaxin , Li Xuedong , Bai Lingling , Yue Wenlong , Jiang Li
Published: August 2022

Diazinon is one of the most widely used organophosphate insecticides, one that is frequently detected in the environment. In this study, a diazinon-degrading bacterium, DI-6, previously isolated from diazinon-contaminated soil in China has been subsequently identified as Sphingobium sp. on the basis of its physiological and biochemical characteristics, as well as by virtue of a comparative analysis of 16S rRNA gene sequences. This strain is capable of using diazinon as its sole carbon source for growth and was able to degrade 91.8% of 100 mg L–1 diazinon over a 60-h interval. During the degradation of diazinon, the following seven metabolites were captured and identified by gas chromatography/mass spectrometry (GC–MS) analysis: diazoxon, diazinon aldehyde, isopropenyl derivative of diazinon, hydroxyethyl derivative of diazinon, diazinon methyl ketone, O-[2-(1-hydroxyethyl)-6-methylpyrimidin-4-yl] O-methyl O-hydrogen phosphorothioate, and O-(6-methyl pyrimidin-4-yl) O,O-dihydrogen phosphorothioate. Based on these metabolites, a novel microbial biodegradation pathway of diazinon by Sphingobium sp. DI-6 is proposed. This research provides potentially useful information for the application of the DI-6 strain in bioremediation of diazinon-contaminated environments.
A consolidated review of commercial-scale high-value products from lignocellulosic biomass
Authors: Zheng Bo , Yu Shengzhu , Chen Zhenya , Huo Yi-Xin
Published: August 2022

For decades, lignocellulosic biomass has been introduced to the public as the most important raw material for the environmentally and economically sustainable production of high-valued bioproducts by microorganisms. However, due to the strong recalcitrant structure, the lignocellulosic materials have major limitations to obtain fermentable sugars for transformation into value-added products, e.g., bioethanol, biobutanol, biohydrogen, etc. In this review, we analyzed the recent trends in bioenergy production from pretreated lignocellulose, with special attention to the new strategies for overcoming pretreatment barriers. In addition, persistent challenges in developing for low-cost advanced processing technologies are also pointed out, illustrating new approaches to addressing the global energy crisis and climate change caused by the use of fossil fuels. The insights given in this study will enable a better understanding of current processes and facilitate further development on lignocellulosic bioenergy production.
F1FO ATP synthase molecular motor mechanisms
Authors: Frasch Wayne D. , Bukhari Zain A. , Yanagisawa Seiga
Published: August 2022

The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.
Genome editing in the edible fungus Poria cocos using CRISPR-Cas9 system integrating genome-wide off-target prediction and detection
Authors: Xie Zhenni , Zhong Can , Liu Xiaoliu , Wang Ziling , Zhou Rongrong , Xie Jing , Zhang Shuihan , Jin Jian
Published: August 2022

Poria cocos is an important edible and medicinal fungus with a long history. However, the lack of adequate genetic tools has hindered molecular genetic research and the genetic modification of this species. In this study, the endogenous U6 promoters were identified by mining data from the P. cocos genome, and the promoter sequence was used to construct a sgRNA expression vector pFC332-PcU6. Then, the protoplast isolation protocol was developed, and the sgRNA-Cas9 vector was successfully transformed into the cells of P. cocos via PEG/CaCl2-mediated transformation approach. Off-target sites were genome-widely predicted and detected. As a result, the target marker gene ura3 was successfully disrupted by the CRISPR-Cas9 system. This is the first report of genome editing in P. cocos using CRISPR-Cas9 system integrating genome-wide off-target prediction and detection. These data will open up new avenues for the investigation of genetic breeding and commercial production of edible and medicinal fungus.
Peptide profile of Parmigiano Reggiano cheese after simulated gastrointestinal digestion: From quality drivers to functional compounds
Authors: Castellone Vincenzo , Prandi Barbara , Bancalari Elena , Tedeschi Tullia , Gatti Monica , Bottari Benedetta
Published: August 2022

Time of ripening has a strong impact on shaping the valuable and recognizable characteristics of long-ripened types of cheese such as Parmigiano Reggiano (PR) due to the interrelationship between microbiota and proteolysis that occurs during ripening. The derived peptide profile is linked to cheese quality and represents the canvas for enzymes upon digestion, which could be responsible for the release of potentially bioactive peptides (BPs). In this study, we aimed at investigating the presence of BP in 72 PR cheese samples of different ripening times, from curd to 24 months of ripening, produced in six different dairies, and following their fate after simulated gastrointestinal digestion. A small number of peptide sequences sharing 100% similarity with known antimicrobial, antioxidant, and ACE-inhibitor sequences were found in PR cheeses, while a higher number of potential BPs were found after their simulated gastrointestinal digestion, in different amounts according to ripening time. Taking advantage of the complex organization of the sampling plan, we were able to follow the fate of peptides considered quality drivers during cheese ripening to their release as functional compounds upon digestion.
Alginate oligosaccharides increase boar semen quality by affecting gut microbiota and metabolites in blood and sperm
Authors: Han Hui , Zhou Yexun , Xiong Bohui , Zhong Ruqing , Jiang Yue , Sun Haiqing , Tan Jiajian , Zhang Bin , Guan Chang , Schroyen Martine , Chen Liang , Zhao Yong , Zhang Hongfu
Published: August 2022

Alginate oligosaccharides (AOS), natural polymers from brown seaweeds (such as Laminaria japonica, Undaria pinnatifida, and Sargassum fusiforme), have been reported to possess many beneficial advantages for health. In the current study, after 9 weeks of dietary supplementation, AOS 10 mg/kg group (AOS 10) group increased boar sperm motility from 87.8% to 93.5%, p < 0.05. Moreover, AOS10 increased the relative abundances of Bifidobacterium, Coprococcus, Butyricicoccus (1.3–2.3-fold; p < 0.05) to increase the beneficial blood and sperm metabolites (1.2–1.6-fold; p < 0.05), and important sperm proteins such as gelsolin, Zn-alpha2 glycoprotein, Cation Channel Sperm-Associated Protein, outer dense fiber of sperm tails, etc. (1.5–2.2-fold; p < 0.05). AOS had a long-term beneficial advantage on boar semen quality by the increase in semen volume (175 vs. 160 ml/ejaculation, p < 0.05). AOS may be used as dietary additives for improving semen quality.
Molecular epidemiology and carbapenem resistance characteristics of Acinetobacter baumannii causing bloodstream infection from 2009 to 2018 in northwest China
Authors: Gu Yihai , Zhang Wei , Lei Jine , Zhang Lixia , Hou Xuan , Tao Junqi , Wang Hui , Deng Minghui , Zhou Mengrong , Weng Rui , Xu Jiru
Published: August 2022

Bloodstream infection (BSI) caused by Acinetobacter baumannii poses a serious threat to health and is correlated with high mortality in patients with hospital-acquired infections, so the molecular epidemiology and antimicrobial resistance characteristics of this pathogen urgently need to be explored. A. baumannii isolates from BSI patients were collected in three tertiary hospitals in northwest China from 2009 to 2018. Antimicrobial susceptibility testing was used to determine the MICs of the A. baumannii isolates. Whole-genome sequencing based on the Illumina platform was performed for molecular epidemiological analyses and acquired resistance gene screening. The efflux pump phenotype was detected by examining the influence of an efflux pump inhibitor. The expression of efflux pump genes was evaluated by RT-PCR. In total, 47 A. baumannii isolates causing BSI were collected and they presented multidrug resistance, including resistance to carbapenems. Clone complex (CC) 92 was the most prevalent with 30 isolates, among which a cluster was observed in the phylogenetic tree based on the core genome multi-locus sequence type, indicating the dissemination of a dominant clone. BSI-related A. baumannii isolates normally harbour multiple resistance determinants, of which oxacillinase genes are most common. Except for the intrinsic blaOXA-51 family, there are some carbapenem-resistant determinants in these A. baumannii isolates, including blaOXA-23, which is encoded within the Tn2006, Tn2008 or Tn2009 transposon structures and blaOXA-72. The transfer of blaOXA-72 was suggested by XerC/D site-specific recombination. The AdeABC efflux pump system contributed to carbapenem resistance in A. baumannii isolates, as evidenced by the high expression of some of its encoding genes. Both the clone dissemination and carbapenem resistance mediated by oxacillinase or efflux pumps suggest an effective strategy for hospital infection control.
PTBPs: An immunomodulatory-related prognostic biomarker in pan-cancer
Authors: Chen Chen , Shang Anquan , Gao Yuting , Huang Jingjuan , Liu Gege , Cho William C. , Li Dong
Published: August 2022

Background: The polypyrimidine tract-binding protein (PTBP) nuclear ribonucleoprotein family of proteins, including PTBP1, PTBP2 and PTBP3, regulate the process of cell proliferation, differentiation, apoptosis and carcinogenesis. PTBPs exhibit oncogenic effects in certain tumors. However, the role of PTBPs in pan-cancer remains unclear. Our study examined the clinical significance and mechanism of PTBPs in pan-cancer.

Methods: We compared the expression of PTBPs in paired and unpaired tissue samples from the Cancer Genome Atlas (TCGA) database. Univariate and multivariate Cox regression, Kaplan–Meier curves, and time-dependent receiver operating characteristic (ROC) curves were used to assess the prognostic significance of PTBPs in pan-cancer. The cBioPortal database also identified genomic abnormalities in PTBPs. TISIDB, TCGA, and Cellminer were used to investigate the relationship between PTBP expression and immune subtypes, immune checkpoint (ICP) genes, tumor mutational burden (TMB), microsatellite instability (MSI), tumor-infiltrating immune cells, and chemosensitivity. cBioPortal was used to search for PTBP co-expressing genes in pan-cancer, and GO and KEGG enrichment analyses were performed to search for PTBP-related signaling pathways.

Results:PTBPs were shown to be widely upregulated in human tumor tissues. PTBP1 showed good prognostic value in ACC, KIRP, and LGG; PTBP2 in ACC and KICH; and PTBP3 in ACC, LGG, and PAAD, with AUC >0.7. PTBPs were differentially expressed in tumor immune subtypes and had a strong correlation with tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment (TME). In addition, PTBP expressions were related to ICP, TMB, and MSI, suggesting that these three PTBPs may be potential tumor immunotherapeutic targets and predict the efficacy of immunotherapy. Enrichment analysis of co-expressed genes of PTBPs showed that they may be involved in alternative splicing, cell cycle, cellular senescence, and protein modification.

Conclusion: PTBPs are involved in the malignant progression of tumors. PTBP1, PTBP2 and PTBP3 may be potential biomarkers for prognosis and immunotherapy in pan-cancer and may be novel immunotherapeutic targets.
TRPM4 and TRPV2 are two novel prognostic biomarkers and promising targeted therapy in UVM
Authors: Wang Jiong , Qiao Sen , Liang Shenzhi , Qian Cheng , Dong Yi , Pei Minghang , Wang Hongmei , Wan Guangming
Published: August 2022

Uveal melanoma (UVM) is the most common primary intraocular malignancy tumor in adults. Almost 50% of UVM patients develop metastatic disease, and is usually fatal within 1 year. However, the mechanism of etiology remains unclear. The lack of prognostic, diagnostic and therapeutic biomarkers is a main limitation for clinical diagnosis and treatment. The transient receptor potential (TRP) channels play important roles in the occurrence and development of tumors, which may have the potential as a therapeutic target for UVM. This current study aimed to identify the potential effect and function of the TRPs that could provide survival prediction and new insight into therapy for UVM. Based on the transcriptome data and potential key genes of UVM were screened using the Cancer Genome Atlas (TCGA) databases, Gene expression analysis showed the expression of TRPM4, TRPV2 and other TRPs was high levels in UVM. Using survival analysis, we screened out that the high expression of TRPM4 and TRPV2 was negatively correlated with the prognosis of UVM patients. Cox regression analysis and functional enrichment analysis further indicated that TRPM4 and TRPV2 were the most convincing therapeutic targets of UVM, and the majority of genes involved in ferroptosis pathways in UVM showed positively correlated with the expression levels of TRPM4 and TRPV2. In conclusion, TRPM4 and TRPV2 were considered as two novel prognostic biomarkers and a promising targeted therapy in UVM.
Trimethylamine N-oxide promotes demyelination in spontaneous hypertension rats through enhancing pyroptosis of oligodendrocytes
Authors: Ji Xiaotan , Tian Long , Niu Shenna , Yao Shumei , Qu Chuanqiang
Published: August 2022

Background

Hypertension is a leading risk factor for cerebral small vessel disease (CSVD), a brain microvessels dysfunction accompanied by white matter lesions (WML). Trimethylamine N-oxide (TMAO), a metabolite of intestinal flora, is correlated with cardiovascular and aging diseases. Here, we explored the effect of TMAO on the demyelination of WML.

Methods

Spontaneous hypertension rats (SHRs) and primary oligodendrocytes were used to explore the effect of TMAO on demyelination in vivo and in vitro. T2-weighted magnetic resonance imaging (MRI) was applied to characterize the white matter hyperintensities (WMH) in rats. TMAO level was evaluated using LC-MS/MS assay. The histopathological changes of corpus callosum were measured by hematoxylin-eosin and luxol fast blue staining. And the related markers were detected by IHC, IF and western blot assay. Mito Tracker Red probe, DCFH-DA assay, flow cytometry based on JC-1 staining and Annexin V-FITC/PI double staining were conducted to evaluate the mitochondrial function, intracellular ROS levels and cell apoptosis.

Results

SHRs exhibited stronger WMH signals and a higher TMAO level than age-matched normotensive Wistar-kyoto rats (WKY). The corpus callosum region of SHR showed decreased volumes and enhanced demyelination when treated with TMAO. Furthermore, TMAO significantly elevated ROS production and induced NLRP3 inflammasome and impairment of mitochondrial function of oligodendrocytes. More importantly, TMAO enhanced the pyroptosis-related inflammatory death of oligodendrocytes.

Conclusion

TMAO could cross the blood-brain barrier (BBB) and promote oligodendrocytes pyroptosis via ROS/NLRP3 inflammasome signaling and mitochondrial dysfunction to promote demyelination, revealing a new diagnostic marker for WML under hypertension.
Early life stress exacerbates behavioural and neuronal alterations in adolescent male mice lacking methyl-CpG binding protein 2 (Mecp2)
Authors: Torres-Pérez Jose Vicente , Martínez-Rodríguez Elena , Forte Anabel , Blanco-Gómez Carlos , Stork Oliver , Lanuza Enrique , Santos Mónica , Agustín-Pavón Carmen
Published: August 2022

The methyl-CpG binding protein 2 gene (MECP2) encodes an epigenetic transcriptional regulator implicated in neuronal plasticity. Loss-of-function mutations in this gene are the primary cause of Rett syndrome and, to a lesser degree, of other neurodevelopmental disorders. Recently, we demonstrated that both Mecp2 haploinsuficiency and mild early life stress decrease anxiety-like behaviours and neuronal activation in brain areas controlling these responses in adolescent female mice. Here, we extend this work to males by using Mecp2-null and wild type adolescent mice subjected to maternal separation and their non-stressed controls. We assessed their behavioural responses in a battery of anxiety-provoking tests. Upon exposure to an elevated plus maze in aversive conditions, we evaluated changes in c-FOS expression in stress- and anxiety-related brain regions. In addition, we assessed the impact of maternal separation in neuronal maturation using doublecortin and reelin as surrogate markers. Mutant males showed reduced motor abilities, increased activation of the olfactory bulbs, probably due to breathing abnormalities, and decreased activation of the paraventricular thalamic nucleus, when compared to wild type mice. In addition, maternal separation increased the number of immature doublecortin-like neurons found in Mecp2-null animals. Moreover, this work shows for the first time that reelin is decreased in the mutant animals at the olfactory tubercle, piriform cortex and hippocampal dentate gyrus, an effect also associated to maternal separation. Taken together, our results suggest that maternal separation exacerbates some phenotypical alterations associated with lack of MeCP2 in adolescent males.