bluuebunny/crossref_metadata_2025 huggingface dataset:
Illumination of Molecular Pathways in Multiple Sclerosis Lesions and the Immune Mechanism of Matrine Treatment in EAE, a Mouse Model of MS
Authors: Dou Mengmeng , Zhou Xueliang , Li Lifeng , Zhang Mingliang , Wang Wenbin , Wang Mengru , Jing Yilei , Ma Rui , Zhao Jie , Zhu Lin
Published: April 2021

The etiology of multiple sclerosis (MS) is not clear, and the treatment of MS presents a great challenge. This study aimed to investigate the pathogenesis and potential therapeutic targets of MS and to define target genes of matrine, a quinolizidine alkaloid component derived from the root of Sophorae flavescens that effectively suppressed experimental autoimmune encephalomyelitis (EAE), an animal model of MS. To this end, the GSE108000 gene data set in the Gene Expression Omnibus Database, which included 7 chronic active MS lesions and 10 control samples of white matter, was analyzed for differentially expressed genes (DEGs). X cell was used to analyze the microenvironmental differences in brain tissue samples of MS patients, including 64 types of immune cells and stromal cells. The biological functions and enriched signaling pathways of DEGs were analyzed by multiple approaches, including GO, KEGG, GSEA, and GSVA. The results by X cell showed significantly increased numbers of immune cell populations in the MS lesions, with decreased erythrocytes, megakaryocytes, adipocytes, keratinocytes, endothelial cells, Th1 cells and Tregs. In GSE108000, there were 637 DEGs, including 428 up-regulated and 209 down-regulated genes. Potential target genes of matrine were then predicted by the network pharmacology method of Traditional Chinese medicine, and 12 key genes were obtained by cross analysis of the target genes of matrine and DEGs in MS lesions. Finally, we confirmed by RT-PCR the predicted expression of these genes in brain tissues of matrine-treated EAE mice. Among these genes, 2 were significantly downregulated and 6 upregulated by matrine treatment, and the significance of this gene regulation was further investigated. In conclusion, our study defined several possible matrine target genes, which can be further elucidated as mechanism(s) of matrine action, and novel targets in the treatment of MS.
Naïve CD4+ T Cell Lymphopenia and Apoptosis in Chronic Hepatitis C Virus Infection Is Driven by the CD31+ Subset and Is Partially Normalized in Direct-Acting Antiviral Treated Persons
Authors: Auma Ann W.N. , Shive Carey L. , Lange Alyssa , Damjanovska Sofi , Kowal Corinne , Zebrowski Elizabeth , Pandiyan Pushpa , Wilson Brigid , Kalayjian Robert C. , Canaday David H. , Anthony Donald D.
Published: April 2021

Background

The mechanisms underlying naïve CD4+ lymphopenia during chronic Hepatitis C Virus (HCV) infection are unclear. Whether direct-acting antiviral (DAA) therapy restores peripheral naïve CD4+ T cell numbers and function is unknown.

Methods

We enumerated frequencies and counts of peripheral naïve CD4+, CD4+CD31+ and CD4+CD31- T cells by flow cytometry in a cross sectional analysis comparing chronic HCV infected (n=34), DAA-treated(n=29), and age-range matched controls (n=25), as well as in a longitudinal cohort of HCV DAA treated persons (n=16). The cross-sectional cohort was stratified by cirrhosis state. Cell apoptosis/survival (AnnexinV+7AAD+/BCL-2 labeling) and cell cycle entry (Ki67 expression) of CD31+ and CD31- naïve CD4+ T cells was analyzed directlyex vivoand following 3 and 5 days ofin vitroculture with media, interleukin (IL) -7 or CD3/CD28 activator.

Results

In the cross-sectional cohort, naïve CD4+ proportions were lower in chronic HCV infected persons compared to controls and DAA-treated persons, an effect in part attributed to cirrhosis. Age was associated with naïve cell counts and proportions in HCV infected and treated persons as well. Naïve CD4+ cell proportions negatively correlated with plasma levels of soluble CD14 following therapy in DAA-treated persons. Naïve CD4+ cells from HCV infected persons exhibited greater directex vivoapoptosis and cell-cycling compared to cells from DAA-treated persons and controls, and this was localized to the CD4+CD31+ subset. On the other hand, no remarkable differences in expression of BCL-2 or IL-7 Receptor (CD127) at baseline or followingin vitromedia or IL7 containing culture were observed. In the longitudinal cohort, naïve CD4+CD31+/CD31- ratio tended to increase 24 weeks after DAA therapy initiation.

Conclusions

Activation and apoptosis of peripheral naïve CD4+CD31+ T cells appear to contribute to naïve CD4+ lymphopenia in chronic HCV infection, and this defect is partially reversible with HCV DAA therapy. Age and cirrhosis -associated naïve CD4+ lymphopenia is present both before and after HCV DAA therapy. These findings have implications for restoration of host immune function after DAA therapy.
Taurine Antagonizes Macrophages M1 Polarization by Mitophagy-Glycolysis Switch Blockage via Dragging SAM-PP2Ac Transmethylation
Authors: Meng Ling , Lu Cailing , Wu Bin , Lan Chunhua , Mo Laiming , Chen Chengying , Wang Xinhang , Zhang Ning , Lan Li , Wang Qihui , Zeng Xia , Li Xiyi , Tang Shen
Published: April 2021

The excessive M1 polarization of macrophages drives the occurrence and development of inflammatory diseases. The reprogramming of macrophages from M1 to M2 can be achieved by targeting metabolic events. Taurine promotes for the balance of energy metabolism and the repair of inflammatory injury, preventing chronic diseases and complications. However, little is known about the mechanisms underlying the action of taurine modulating the macrophage polarization phenotype. In this study, we constructed a low-dose LPS/IFN-γ-induced M1 polarization model to simulate a low-grade pro-inflammatory process. Our results indicate that the taurine transporter TauT/SlC6A6 is upregulated at the transcriptional level during M1 macrophage polarization. The nutrient uptake signal on the membrane supports the high abundance of taurine in macrophages after taurine supplementation, which weakens the status of methionine metabolism, resulting in insufficient S-adenosylmethionine (SAM). The low availability of SAM is directly sensed by LCMT-1 and PME-1, hindering PP2Ac methylation. PP2Ac methylation was found to be necessary for M1 polarization, including the positive regulation of VDAC1 and PINK1. Furthermore, its activation was found to promote the elimination of mitochondria by macrophages via the mitophagy pathway for metabolic adaptation. Mechanistically, taurine inhibits SAM-dependent PP2Ac methylation to block PINK1-mediated mitophagy flux, thereby maintaining a high mitochondrial density, which ultimately hinders the conversion of energy metabolism to glycolysis required for M1. Our findings reveal a novel mechanism of taurine-coupled M1 macrophage energy metabolism, providing novel insights into the occurrence and prevention of low-grade inflammation, and propose that the sensing of taurine and SAM availability may allow communication to inflammatory response in macrophages.
Lack of Cell Cycle Inhibitor p21 and Low CD4+ T Cell Suppression in Newborns After Exposure to IFN-β
Authors: Jans Jop , Unger Wendy W. , Raeven Elisabeth A. M. , Simonetti Elles R. , Eleveld Marc J. , de Groot Ronald , de Jonge Marien I. , Ferwerda Gerben
Published: April 2021

Type I IFNs, such as interferon alpha and interferon beta, are key regulators of the adaptive immune response during infectious diseases. Type I IFNs are induced upon infection, bind interferon α/β receptors on T-cells and activate intracellular pathways. The activating and inhibitory consequences of type I IFN-signaling are determined by cell type and cellular environment. The neonatal immune system is associated with increased vulnerability to infectious diseases which could partly be explained by an immature CD4+ T-cell compartment. Here, we show low IFN-β-mediated inhibition of CD4+ T-cell proliferation, phosphorylation of retinoblastoma protein and cytokine production in human newborns compared to adults. In addition, both naïve and total newborn CD4+ T-cells are unable to induce the cell-cycle inhibitor p21 upon exposure to IFN-β in contrast to adults. The distinct IFN-β-signaling in newborns provides novel insights into T cell functionality and regulation of T cell-dependent inflammation during early life immune responses.
Regulatory B Cells Dysregulated T Cell Function in an IL-35-Dependent Way in Patients With Chronic Hepatitis B
Authors: Liu YaYun , Luo Ying , Zhu Tong , Jiang Meng , Tian ZhaoFeng , Tang GuSheng , Liang XueSong
Published: April 2021

Interleukin (IL)-35-secreting B (IL-35+B) cells are critical regulators in autoimmune and infectious diseases and exert suppressive functions in parallel with IL-10-producing B (B10) cells. However, the role of IL-35+B cells in persistent hepatitis B virus (HBV) infection remains unclear. To elucidate the role of IL-35+B cells in the progress of chronic HBV infection, we determined the frequency of IL-35+B cells and their relationship with the classical human regulatory B cell (Breg) subsets, namely, CD19+CD24hiCD38hi and CD19+CD24hiCD27+. Then, the regulatory effect and mechanism of Bregs on effector T cells were investigated in vitro. Here, we found that compared with healthy controls, the frequency of IL-35+B cells was increased in patients with chronic HBV infection and was enriched in human classical Breg subset CD19+CD24hiCD38hi B cells. Moderate correlation was observed between the frequency of IL-35+B cells and alanine aminotransferase levels (Spearman r = 0.401), but only mild correlation was noted between the frequency of IL-35+B cells and HBV DNA level (Spearman r = 0.314). The frequency of IL-35+B cells was negatively correlated with interferon-γ (IFN-γ)-producing CD4+ and CD8+ cells but positively correlated with IL-4-producing T cells. Bregs dysregulated T cell function through an IL-35-dependent mechanism and depended on cell-to-cell contact. In conclusion, IL-35+ B cell was enriched in CD19+CD24hiCD38hi B cell subset during persistent HBV infection and Breg cells exerted dysregulation in T cell function through IL-35 dependent mechanism and depend on cell-to-cell contact.

Clinical Trial Registration

www.ClinicalTrials.gov, identifier NCT03734783.
Carbamazepine Induces Focused T Cell Responses in Resolved Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis Cases But Does Not Perturb the Immunopeptidome for T Cell Recognition
Authors: Mifsud Nicole A. , Illing Patricia T. , Lai Jeffrey W. , Fettke Heidi , Hensen Luca , Huang Ziyi , Rossjohn Jamie , Vivian Julian P. , Kwan Patrick , Purcell Anthony W.
Published: April 2021

Antiseizure medications (ASMs) are frequently implicated in T cell-mediated drug hypersensitivity reactions and cause skin tropic pathologies that range in severity from mild rashes to life-threatening systemic syndromes. During the acute stages of the more severe manifestations of these reactions, drug responsive proinflammatory CD8+T cells display classical features of Th1 cytokine production (e.g.IFNγ) and cytolysis (e.g.granzyme B, perforin). These T cells may be found locally at the site of pathology (e.g.blister cells/fluid), as well as systemically (e.g.blood, organs). What is less understood are the long-lived immunological effects of the memory T cell pool following T cell-mediated drug hypersensitivity reactions. In this study, we examine the ASM carbamazepine (CBZ) and the CBZ-reactive memory T cell pool in patients who have a history of either Stevens-Johnson syndrome (SJS) or toxic epidermal necrolysis (TEN) from 3-to-20 years following their initial adverse reaction. We show thatin vitrodrug restimulation of CBZ-reactive CD8+T cells results in a proinflammatory profile and produces a mainly focused, yet private, T cell receptor (TCR) usage amongst human leukocyte antigen (HLA)-B*15:02-positive SJS or TEN patients. Additionally, we show that expression of these CBZ-reactive TCRs in a reporter cell line, lacking endogenous αβTCR, recapitulates the features of TCR activation reported for ASM-treated T cell lines/clones, providing a useful tool for further functional validations. Finally, we conduct a comprehensive evaluation of the HLA-B*15:02 immunopeptidome following ASM (or a metabolite) treatment of a HLA-B*15:02-positive B-lymphoblastoid cell line (C1R.B*15:02) and minor perturbation of the peptide repertoire. Collectively, this study shows that the CBZ-reactive T cells characterized require both the drug and HLA-B*15:02 for activation and that reactivation of memory T cells from blood results in a focusedprivateTCR profile in patients with resolved disease.
Fasciola gigantica–Derived Excretory-Secretory Products Alter the Expression of mRNAs, miRNAs, lncRNAs, and circRNAs Involved in the Immune Response and Metabolism in Goat Peripheral Blood Mononuclear Cells
Authors: Wang Sha-Sha , Chen Dan , He Jun-Jun , Zheng Wen-Bin , Tian Ai-Ling , Zhao Guang-Hui , Elsheikha Hany M. , Zhu Xing-Quan
Published: April 2021

Fasciola gigantica produces excretory-secretory products (ESPs) with immune-modulating effects to promote its own survival. In this study, we performed RNA-seq to gain a comprehensive global understanding of changes in the expression of mRNAs, miRNAs, lncRNAs, and circRNAs in goat peripheral blood mononuclear cells (PBMCs) treated with F. gigantica ESPs. A total of 1,544 differently expressed mRNAs (790 upregulated and 754 downregulated genes), 30 differently expressed miRNAs (24 upregulated and 6 downregulated genes), 136 differently expressed circRNAs (83 upregulated and 53 downregulated genes), and 1,194 differently expressed lncRNAs (215 upregulated and 979 downregulated genes) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that F. gigantica ESPs altered the expression of genes associated with the host immune response, receptor signaling, disease and metabolism. Results from RNA-seq were validated by qRT-PCR. These findings provide an important resource for future investigation of the role of mRNAs and non-coding RNAs in mediating the immune-modulating effects of F. gigantica ESPs.
Spontaneous Differentiation of T Follicular Helper Cells in LATY136F Mutant Mice
Authors: O’Brien Sarah A. , Zhu Minghua , Zhang Weiguo
Published: April 2021

Mice with a mutation at the LAT-PLCγ1 binding site (Y136) have a defect in thymocyte development due to dampened TCR signaling. CD4+ T cells that do reach the periphery are hyper-activated and skewed to Th2. Over time, these mice develop an autoimmune-like syndrome, characterize by overproduction of Th2 cytokines, T cell infiltration into various organs, and B cell activation, isotype switching, and autoantibody production. In this study, we examined IL4 production by CD4+ T cells in the LATY136F mice using the KN2 reporter mice, in which human CD2 expression marks T cells that are actively producing IL4 protein. We showed that these mice had spontaneous Tfh differentiation. Despite the fact that the majority of CD4+ T cells were skewed to Th2 and were GATA3+, only a small subset of them were actively secreting IL4. These T cells were Tfh cells that expressed BCL6 and were localized to B cell-rich germinal centers within the spleen. Interestingly, these Tfh cells expressed high levels of both BCL6 and GATA3. By using LAT conditional knockout mice that inducibly express only the LATY136F allele, we further showed that Tfh cell differentiation was likely the result of defective LAT-PLCγ1 signaling in the periphery. In addition, B cells were required for spontaneous development of Tfh cells and uncontrolled T cell expansion in these mice. Together, these results indicated a novel role for tonic LAT-PLCγ1 signaling in modulating Tfh cell differentiation during development of autoimmune syndrome.
ILC3, a Central Innate Immune Component of the Gut-Brain Axis in Multiple Sclerosis
Authors: Miljković Đorđe , Jevtić Bojan , Stojanović Ivana , Dimitrijević Mirjana
Published: April 2021

Gut immune cells have been increasingly appreciated as important players in the central nervous system (CNS) autoimmunity in animal models of multiple sclerosis (MS). Among the gut immune cells, innate lymphoid cell type 3 (ILC3) is of special interest in MS research, as they represent the innate cell counterpart of the major pathogenic cell population in MS, i.e. T helper (Th)17 cells. Importantly, these cells have been shown to stimulate regulatory T cells (Treg) and to counteract pathogenic Th17 cells in animal models of autoimmune diseases. Besides, they are also well known for their ability to stabilize the intestinal barrier and to shape the immune response to the gut microbiota. Thus, proper maintenance of the intestinal barrier and the establishment of the regulatory milieu in the gut performed by ILC3 may prevent activation of CNS antigen-specific Th17 cells by the molecular mimicry. Recent findings on the role of ILC3 in the gut-CNS axis and their relevance for MS pathogenesis will be discussed in this paper. Possibilities of ILC3 functional modulation for the benefit of MS patients will be addressed, as well.
Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes
Authors: Abbas Hussein A. , Reville Patrick K. , Jiang Xianli , Yang Hui , Reuben Alexandre , Im Jin Seon , Little Latasha , Sinson Jefferson C. , Chen Ken , Futreal Andrew , Garcia-Manero Guillermo
Published: April 2021

Aberrant T-cell function is implicated in the pathogenesis of myelodysplastic syndrome (MDS). Monitoring the T-cell receptor (TCR) repertoire can provide insights into T-cell adaptive immunity. Previous studies found skewed TCR repertoires in MDS compared to healthy patients; however these studies that leverage mRNA-based spectratyping have limitations. Furthermore, evaluating the TCR repertoire in context of hypomethylating agents (HMAs) treatment can provide insights into the dynamics of T-cell mediated responses in MDS. We conducted immunosequencing of the CDR3 regions of TCRβ chains in bone marrows of 11 MDS patients prior to treatment (n=11 bone marrows prior to treatment), and in at least 2 timepoints for each patient following treatment (n=26 bone marrow aspirates post-treatment) with (HMA), alongside analyzing bone marrows from 4 healthy donors as controls. TCR repertoires in MDS patients were more clonal and less diverse than healthy donors. However, unlike previous reports, we did not observe significant skewness in CDR3 length or spectratyping. The global metrics of TCR profiling including richness, clonality, overlaps were not significantly changed in responders or non-responders following treatment with HMAs. However, we found an emergence of novel clonotypes in MDS patients who responded to treatment, while non-responders had a higher frequency of contracted clonotypes following treatment. By applying GLIPH2 for antigen prediction, we found rare TCR specificity clusters shared by TCR clonotypes from different patients at pre- or following treatment. Our data show clear differences in TCR repertoires of MDS compared with healthy patients and that novel TCR clonotype emergence in response to HMA therapy was correlated with response. This suggests that response to HMA therapy may be partially driven by T-cell mediated immunity and that the immune-based therapies, which target the adaptive immune system, may play a significant role in select patients with MDS.
Case Report: Infantile-Onset Fulminant Type 1 Diabetes Mellitus Caused by Novel Compound Heterozygous LRBA Variants
Authors: Totsune Eriko , Nakano Tomohiro , Moriya Kunihiko , Sato Daichi , Suzuki Dai , Miura Akinobu , Katayama Saori , Niizuma Hidetaka , Kanno Junko , van Zelm Menno C. , Imai Kohsuke , Kanegane Hirokazu , Sasahara Yoji , Kure Shigeo
Published: April 2021

Lipopolysaccharide-responsive beige-like anchor (LRBA) deficiency is a subtype of common variable immune deficiency (CVID). Numerous case reports and cohort studies have described a broad spectrum of clinical manifestations and variable disease phenotypes, including immune dysregulation, enteropathy, and recurrent infections. Although LRBA deficiency is an autosomal recessive primary immunodeficiency resulting in a phenotype similar to CVID, it is a monogenic disease and separate from CVID. Recently, in a report of monogenic primary immunodeficiency disorder associated with CVID and autoimmunity, the most common mutated gene was LRBA. We report the case of a girl who presented with fulminant type 1 diabetes at age 7 months. She later experienced recurrent bacterial infections with neutropenia and idiopathic thrombocytopenic purpura. Clinical genome sequencing revealed compound heterozygosity of the LRBA gene, which bore two novel mutations. A genetic basis should be considered in the differential diagnosis for very young patients with fulminant autoimmunity, and the diagnostic work-up should include evaluation of markers of immunodeficiency.
A Rising Tide Does Not Lift All Boats: Intersectional Analysis Reveals Inequitable Impacts of the Seafood Trade in Fishing Communities
Authors: Ferguson Caroline E.
Published: April 2021

Seafood is the world’s most traded food commodity, and the international trade in seafood is promoted as a development strategy in low-income coastal communities across the globe. However, the seafood trade can drive negative social and environmental impacts in fishing communities, and whether the benefits of trade actually reach fishers is a subject of ongoing scholarship. Furthermore, scholars and policymakers have tended to treat fishing communities as homogeneous, assuming that trade policies will impact all members equally. Yet individual community members have different roles, statuses, and entitlements according to their intersecting identities, meaning that different fishers will be differently impacted by the seafood trade. In particular, women occupy different positions than men in seafood value chains and in fishing communities. There are also important within-group differences among men and among women depending on their nationality, marital status, and other identity markers. Through 205 surveys, 54 interviews, and ethnographic field methods conducted in fifteen rural Palauan fishing communities between November 2019 and March 2020, this case study of the sea cucumber trade in Palau brings together theories of gender, intersectionality, and access to answer the question, “How are the harms and benefits of the seafood trade distributed in fishing communities?” In this case, men benefited more than women from the export of sea cucumbers by leveraging access to technology; knowledge; and authority, and the trade depleted resources relied on primarily by women for their food security and livelihoods. An intersectional analysis revealed that marital status and nationality determined access among women, with married women having greater access than unmarried women and immigrant women having greater access than immigrant men, demonstrating the importance of intersectionality as an analytical tool.
How Can Information Contribute to Management? Value of Information (VOI) Analysis on Indian Ocean Striped Marlin (Kajikia audax)
Authors: Xia Meng , Carruthers Tom , Kindong Richard , Dai Libin , Geng Zhe , Dai Xiaojie , Wu Feng
Published: April 2021

Fisheries researchers have focused on the value of information (VOI) in fisheries management and trade-offs since scientists and managers realized that information from different resources has different contribution in the management process. We picked seven indicators, which are log-normal annual catch observation error (Cobs), annual catch observation bias (Cbias), log-normal annual index observation error (Iobs), maximum length observation bias (Linfbias), observed natural mortality rate bias (Mbias), observed von Bertalanffy growth parameter K bias (Kbias), and catch-at-age sample size (CAA_nsamp), and built operating models (OMs) to simulate fisheries dynamics, and then applied management strategy evaluation (MSE). Relative yield is chosen as the result to evaluate the contribution of the seven indicators. Within the parameter range, there was not much information value reflected from fisheries-dependent parameters including Cobs, Cbias, and Iobs. On the other hand, for fisheries-independent parameters such as Kbias, Mbias, and Linfbias, similar tendency of the information value was showed in the results, in which the relative yield goes down from the upper bound to the lower bound of the interval. CAA_nsamp had no impact on the yield after over 134 individuals. The VOI analysis contributes to the trade-offs in the decision-making process. Information with more value is more worthy to collect in case of waste of time and money so that we could make the best use of scientific effort. But we still need to improve the simulation process such as enhancing the diversity and predictability in an OM. More parameters are on the way to be tested in order to collect optimum information for management and decision-making.
Development of a Phase Field Tool Coupling With Thermodynamic Data for Microstructure Evolution Simulation of Alloys in Nuclear Reactors
Authors: Guo Yaolin , Li Yifan , Liu Zhen , Shi Diwei , Song Jiexi , Zhang Biao , Bu Moran , Du Shiyu
Published: April 2021

We have developed a new phase field tool PHAFIS to automatically incorporate the thermodynamic data for both of WBM and KKS phase field simulations, which are widely used in the simulation of microstructure evolution of nuclear materials. Based on the generic C/C++ programming language, PHAFIS is capable of automatically parsing the standard TDB files, extracting the free energy and diffusion potential varying with the composition in an analytical way. Based on the two diffrerent TDB files of Fe-Cr binary system and the interpolated data, the phase morphologies during spinodal decomposition at 700 K and liquid-solid transition at high temperatures above 1800 K are reproduced and compared with each other by WBM and KKS model, respectively. Specifically, both of interface-controlled and diffusion-controlled phase transition mechanisms are successfully revealed for solidification through our KKS simulation, consistent with classic phase transition theories. It can be concluded that even slight differences in thermodynamic data will cause significant changes in the microstructure evolution. The integrity of our software tool will facilitate the coupling of phase field methods with thermodynamic data for other materials, paving a fundamental step for coupling more factors required in microstructure simulation.
Evaluation of Donor and Recipient Characteristics Involved in Descemet Stripping Automated Endothelial Keratoplasty Outcomes
Authors: Lanza Michele , Boccia Rosa , Ruggiero Adriano , Melillo Paolo , Bifani Sconocchia Mario , Simonelli Francesca , Sbordone Sandro
Published: April 2021

Aims: To evaluate both donor and recipient features involved in visual acuity restoring and complication insurgence in eyes that have undergone Descemet stripping automated endothelial keratoplasty (DSAEK).

Methods: In this retrospective study, charts of 111 eyes of 96 patients (mean age 70.25 ± 8.58 years) that underwent DSAEK were evaluated. Only Fuch's Distrophy (FD) or Bullous Keratopathy (BK) due to cataract surgery eyes were included. A complete ophthalmic check with endothelial cell density (ECD) and central corneal thickness (CCT) measurement was performed before surgery and at 1, 3, 6, and 12 months follow-up. Each DSAEK was performed by the same well-trained surgeon; only pre-cut lenticules, provided by same Eye Bank, were implanted.

Results: A total of 48 (43%) complications have been observed (most of them were 22 partial graft detachments and 17 IOP spikes). At the last follow-up (mean: 8.58 ± 4.09 months), a significant increase (p < 0.05) of best corrected visual acuity (BCVA) was detected. Overall mean BCVA of the eyes evaluated was 0.40 ± 0.43 LogMAR with BK eyes showing a significantly higher improvement (p < 0.05) compared to FD eyes. The only factor showing a significant correlation (p < 0.05) with visual acuity enhancement was the implant of a lenticule thinner than 100 μm. Recipient features significantly (p < 0.05) associated with complications observed after surgery were glaucoma and diabetes mellitus.

Conclusion: The use of a graft thinner than 100 μm can provide better visual acuity recovery while recipients affected by glaucoma or diabetes mellitus are more prone to develop complications after surgery.
Neutrophil Extracellular Traps in Systemic Lupus Erythematosus Stimulate IgG2 Production From B Lymphocytes
Authors: Bertelli Roberta , Schena Francesca , Antonini Francesca , Reverberi Daniele , Signa Sara , Pedemonte Nicoletta , Consolaro Alessandro , Gattorno Marco , Negrini Simone , Pupo Francesca , Volpi Stefano , Ghiggeri Gian Marco
Published: April 2021

Circulating autoantibodies of IgG2 isotype predominate in Systemic Lupus Erythematosus (SLE) and concur to the development of the renal lesions characteristic of Lupus Nephritis (LN). Anti-dsDNA and anti-histones IgG2, together with anti-podocyte proteins (i.e., α-enolase) are the major autoantibodies in serum and renal glomeruli of LN patients. The mechanisms underlying autoantibody formation and isotype switching in SLE and LN are unknown. A major issue is how DNA/histones are externalized from cell nucleus, driving the autoimmune response. Neutrophil Extracellular Traps (NETs) have been recently identified as crucial players in this context, representing the main source of DNA and nucleosome proteins. A second key point is what regulates IgG2 isotype switching: in mouse models, T-bet transcription factor has been described as essential for IgG2a class switch. We hypothesized that, in SLE, NET formation is the key mechanism responsible for externalization of autoantigens (i.e., dsDNA, histones 2,3, and α-enolase) and that T-bet is upregulated by NETs, driving, in this way, immunoglobulin class switch recombination (CSR), with production of IgG2 autoantibodies. The data here presented show that NETs, purified from SLE patients, stimulate ex vivo IgG2 isotype class switch possibly through the induction of T-bet. Of note, we observed a prominent effect of NETs on the release of soluble IgG2 in SLE patients', but not in healthy donors' B cells. Our results add important knowledge on the mechanisms of IgG2 class switch in SLE and contribute to further elucidate the role of NETs in LN pathogenesis.
Dengue Virus and Vaccines: How Can DNA Immunization Contribute to This Challenge?
Authors: Alves Ada Maria Barcelos , Costa Simone Morais , Pinto Paolla Beatriz Almeida
Published: April 2021

Dengue infections still have a tremendous impact on public health systems in most countries in tropical and subtropical regions. The disease is systemic and dynamic with broad range of manifestations, varying from mild symptoms to severe dengue (Dengue Hemorrhagic Fever and Dengue Shock Syndrome). The only licensed tetravalent dengue vaccine, Dengvaxia, is a chimeric yellow fever virus with prM and E genes from the different dengue serotypes. However, recent results indicated that seronegative individuals became more susceptible to develop severe dengue when infected after vaccination, and now WHO recommends vaccination only to dengue seropositive people. One possibility to explain these data is the lack of robust T-cell responses and antibody-dependent enhancement of virus replication in vaccinated people. On the other hand, DNA vaccines are excellent inducers of T-cell responses in experimental animals and it can also elicit antibody production. Clinical trials with DNA vaccines have improved and shown promising results regarding the use of this approach for human vaccination. Therefore, in this paper we review preclinical and clinical tests with DNA vaccines against the dengue virus. Most of the studies are based on the E protein since this antigen is the main target for neutralizing antibody production. Yet, there are other reports with DNA vaccines based on non-structural dengue proteins with protective results, as well. Combining structural and non-structural genes may be a solution for inducing immune responses aging in different infection moments. Furthermore, DNA immunizations are also a very good approach in combining strategies for vaccines against dengue, in heterologous prime/boost regimen or even administering different vaccines at the same time, in order to induce efficient humoral and cellular immune responses.
Effects of Hydrothermal Pretreatment and Hydrochar Addition on the Performance of Pig Carcass Anaerobic Digestion
Authors: Xu Jie , Lin Hongjian , Sheng Kuichuan
Published: April 2021

Proper disposal and utilization of dead pig carcasses are problems of public concern. The combination of hydrothermal pretreatment (HTP) and anaerobic digestion is a promising method to treat these wastes, provided that digestion inhibition is reduced. For this reason, the aim of this work was to investigate the optimal HTP temperature (140–180°C) for biogas production during anaerobic digestion of dead pigs in batch systems. In addition, the effects of hydrochar addition (6 g/L) on anaerobic digestion of pork products after HTP in continuous stirred tank reactors (CSTR) were determined. According to the results, 90% of lipids and 10% of proteins present in the pork were decomposed by HTP. In addition, the highest chemical oxygen demand (COD) concentration in liquid products (LP) reached 192.6 g/L, and it was obtained after 170°C HTP. The biogas potential from the solid residue (SR) and LP was up to 478 mL/g-VS and 398 mL/g-COD, respectively. A temperature of 170°C was suitable for pork HTP, which promoted the practical biogas yield because of the synergistic effect between proteins and lipids. Ammonia inhibition was reduced by the addition of hydrochar to the CSTR during co-digestion of SR and LP, maximum ammonia concentration tolerated by methanogens increased from 2.68 to 3.38 g/L. This improved total biogas yield and degradation rate of substrates, reaching values of 28.62 and 36.06%, respectively. The acetate content in volatile fatty acids (VFA) may be used as an index that reflects the degree of methanogenesis of the system. The results of the present work may also provide guidance for the digestion of feedstock with high protein and lipid content.
High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.
Authors: Seferbekova Zaira , Zabelkin Alexey , Yakovleva Yulia , Afasizhev Robert , Dranenko Natalia O. , Alexeev Nikita , Gelfand Mikhail S. , Bochkareva Olga O.
Published: April 2021

Shigellaare pathogens originating within theEscherichialineage but frequently classified as a separate genus.Shigellagenomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes ofE. coliandShigellastrains to assess the contribution of genomic rearrangements toShigellaevolution. We found thatShigellaexperienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenicE. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in differentShigellalineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by allShigellastrains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasiveE. coli(EIEC) strain, which is a pathogenicE. coliwith a phenotype intermediate betweenShigellaand non-pathogenicE. coli, we found a rate of genome rearrangements comparable to those in otherE. coliand no functional copies of the twoShigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.
Ecophysiological and Cell Biological Traits of Benthic Diatoms From Coastal Wetlands of the Southern Baltic Sea
Authors: Prelle Lara R. , Albrecht Martin , Karsten Ulf , Damer Pauline , Giese Tabea , Jähns Jessica , Müller Simon , Schulz Louisa , Viertel Lennard , Glaser Karin
Published: April 2021

The German Baltic Sea coastline is characterized by sea-land transitions zones, specifically coastal peatlands. Such transition zones exhibit highly fluctuating environmental parameters and dynamic gradients that affect physiological processes of inhabiting organisms such as microphytobenthic communities. In the present study four representative and abundant benthic diatom strains [Melosira nummuloides, Nitzschia filiformis, Planothidium sp. (st. 1) and Planothidium sp. (st.2)] were isolated from a Baltic Sea beach and three peatlands that are irregularly affected by Baltic Sea water intrusion. Ecophysiological and cell biological traits of the strains were investigated for the first time as function of light, temperature and salinity. The four strains exhibited euryhaline growth over a range of 1–39 SA, surpassing in situ salinity of the respective brackish habitats. Furthermore, they showed eurythermal growth over a temperature range from 5 to 30°C with an optimum temperature between 15 and 20°C. Growth rates did not exhibit any differences between the peatland and Baltic Sea strains. The photosynthetic temperature optimum of the peatland diatom isolates, however, was much higher (20–35°C) compared to the Baltic Sea one (10°C). All strains exhibited light saturation points ranging between 29.8 and 72.6 μmol photons m–2 s–1. The lipid content did not change in response to the tested abiotic factors. All data point to wide physiological tolerances in these benthic diatoms along the respective sea-land transitions zones. This study could serve as a baseline for future studies on microphytobenthic communities and their key functions, like primary production, under fluctuating environmental stressors along terrestrial-marine gradients.
Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model
Authors: Zhang Chengwei , Huang Jing
Published: April 2021

The organization of genomes in space and time dimension plays an important role in gene expression and regulation. Chromatin folding occurs in a dynamic, structured way that is subject to biophysical rules and biological processes. Nucleosomes are the basic unit of chromatin in living cells, and here we report on the effective interactions between two nucleosomes in physiological conditions using explicit-solvent all-atom simulations. Free energy landscapes derived from umbrella sampling simulations agree well with recent experimental and simulation results. Our simulations reveal the atomistic details of the interactions between nucleosomes in solution and can be used for constructing the coarse-grained model for chromatin in a bottom-up manner.
Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too
Authors: Baumgartner Jackson T. , Habeeb Mohammad Thahani S. , Czub Mateusz P. , Majorek Karolina A. , Arolli Xhulio , Variot Cillian , Anonick Madison , Minor Wladek , Ballicora Miguel A. , Becker Daniel P. , Kuhn Misty L.
Published: April 2021

Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme’s kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions.
Interplay Between Receptor-Ligand Binding and Lipid Domain Formation Depends on the Mobility of Ligands in Cell-Substrate Adhesion
Authors: Li Long , Wang Xiaohuan , Wu Helong , Shao Yingfeng , Wu Huaping , Song Fan
Published: April 2021

Cell-cell adhesion and the adhesion of cells to extracellular matrix are mediated by the specific binding of receptors on the cell membrane to their cognate ligands on the opposing surface. The adhesion receptors can exhibit affinity for nanoscale lipid clusters that form in the cell membrane. Experimental studies of such adhesion systems often involve a cell adhering either to a solid surface with immobile ligands or a supported lipid bilayer with mobile ligands. A central question in these cell-substrate adhesions is how the mobility of the ligands physically affects their binding to the adhesion receptors and thereby the behavior of the nanoscale lipid clusters associated with the receptors. Using a statistical mechanical model and Monte Carlo simulations for the adhesion of cells to substrates with ligands, we find that, for mobile ligands, binding to adhesion receptors can promote the formation of mesoscale lipid domains, which in turn enhances the receptor-ligand binding. However, in the case of immobile ligands, the receptor-ligand binding and the tendency for the nanoscale lipid clusters to further coalesce depend on the distribution of the ligands on the substrate. Our findings help to explain why different adhesion experiments for identifying the interplay between receptor-ligand binding and heterogeneities in cell membranes led to contradictory results.
A Comprehensive Analysis of the Role of hnRNP A1 Function and Dysfunction in the Pathogenesis of Neurodegenerative Disease
Authors: Clarke Joseph P. , Thibault Patricia A. , Salapa Hannah E. , Levin Michael C.
Published: April 2021

Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a member of the hnRNP family of conserved proteins that is involved in RNA transcription, pre-mRNA splicing, mRNA transport, protein translation, microRNA processing, telomere maintenance and the regulation of transcription factor activity. HnRNP A1 is ubiquitously, yet differentially, expressed in many cell types, and due to post-translational modifications, can vary in its molecular function. While a plethora of knowledge is known about the function and dysfunction of hnRNP A1 in diseases other than neurodegenerative disease (e.g., cancer), numerous studies in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, multiple sclerosis, spinal muscular atrophy, Alzheimer’s disease, and Huntington’s disease have found that the dysregulation of hnRNP A1 may contribute to disease pathogenesis. How hnRNP A1 mechanistically contributes to these diseases, and whether mutations and/or altered post-translational modifications contribute to pathogenesis, however, is currently under investigation. The aim of this comprehensive review is to first describe the background of hnRNP A1, including its structure, biological functions in RNA metabolism and the post-translational modifications known to modify its function. With this knowledge, the review then describes the influence of hnRNP A1 in neurodegenerative disease, and how its dysfunction may contribute the pathogenesis.
Quantitative Analysis of Synthetic Magnetic Resonance Imaging in Alzheimer’s Disease
Authors: Lou Baohui , Jiang Yuwei , Li Chunmei , Wu Pu-Yeh , Li Shuhua , Qin Bin , Chen Haibo , Wang Rui , Wu Bing , Chen Min
Published: April 2021

Objectives: The purpose of this study was to evaluate the feasibility and whether synthetic MRI can benefit diagnosis of Alzheimer’s disease (AD).

Materials and Methods: Eighteen patients and eighteen age-matched normal controls (NCs) underwent MR examination. The mini-mental state examination (MMSE) scores were obtained from all patients. The whole brain volumetric characteristics, T1, T2, and proton density (PD) values of different cortical and subcortical regions were obtained. The volumetric characteristics and brain regional relaxation values between AD patients and NCs were compared using independent-samples t-test. The correlations between these quantitative parameters and MMSE score were assessed by the Pearson correlation in AD patients.

Results: Although the larger volume of cerebrospinal fluid (CSF), lower brain parenchymal volume (BPV), and the ratio of brain parenchymal volume to intracranial volume (BPV/ICV) were found in AD patients compared with NCs, there were no significant differences (p > 0.05). T1 values of right insula cortex and T2 values of left hippocampus and right insula cortex were significantly higher in AD patients than in NCs, but T1 values of left caudate showed a reverse trend (p < 0.05). As the MMSE score decreased in AD patients, the BPV and BPV/ICV decreased, while the volume of CSF and T1 values of bilateral insula cortex and bilateral hippocampus as well as T2 values of bilateral hippocampus increased (p < 0.05).

Conclusion: Synthetic MRI not only provides more information to differentiate AD patients from normal controls, but also reflects the disease severity of AD.
Older Adults Show Reduced Spatial Precision but Preserved Strategy-Use During Spatial Navigation Involving Body-Based Cues
Authors: McAvan Andrew S. , Du Yu Karen , Oyao Alexis , Doner Stephanie , Grilli Matthew D. , Ekstrom Arne
Published: April 2021

Older adults typically perform worse on spatial navigation tasks, although whether this is due to degradation of memory or an impairment in using specific strategies has yet to be determined. An issue with some past studies is that older adults are tested on desktop-based virtual reality: a technology many report lacking familiarity with. Even when controlling for familiarity, these paradigms reduce the information-rich, three-dimensional experience of navigating to a simple two-dimensional task that utilizes a mouse and keyboard (or joystick) as means for ambulation. Here, we utilize a wireless head-mounted display and free ambulation to create a fully immersive virtual Morris water maze in which we compare the navigation of older and younger adults. Older and younger adults learned the locations of hidden targets from same and different start points. Across different conditions tested, older adults remembered target locations less precisely compared to younger adults. Importantly, however, they performed comparably from the same viewpoint as a switched viewpoint, suggesting that they could generalize their memory for the location of a hidden target given a new point of view. When we implicitly moved one of the distal cues to determine whether older adults used an allocentric (multiple landmarks) or beaconing (single landmark) strategy to remember the hidden target, both older and younger adults showed comparable degrees of reliance on allocentric and beacon cues. These findings support the hypothesis that while older adults have less precise spatial memories, they maintain the ability to utilize various strategies when navigating.