bluuebunny/crossref_metadata_2025 huggingface dataset:
InfersentPPI: Prediction of Protein-Protein Interaction Using Protein Sentence Embedding With Gene Ontology Information
Authors: Li Meijing , Jiang Yingying , Ryu Keun Ho
Published: March 2022

Protein-protein interaction (PPI) prediction is meaningful work for deciphering cellular behaviors. Although many kinds of data and machine learning algorithms have been used in PPI prediction, the performance still needs to be improved. In this paper, we propose InferSentPPI, a sentence embedding based text mining method with gene ontology (GO) information for PPI prediction. First, we design a novel weighting GO term-based protein sentence representation method to generate protein sentences including multi-semantic information in the preprocessing. Gene ontology annotation (GOA) provides the reliability of relationships between proteins and GO terms for PPI prediction. Thus, GO term-based protein sentence can help to improve the prediction performance. Then we also propose an InferSent_PN algorithm based on the protein sentences and InferSent algorithm to extract relations between proteins. In the experiments, we evaluate the effectiveness of InferSentPPI with several benchmarking datasets. The result shows our proposed method has performed better than the state-of-the-art methods for a large PPI dataset.
Case Report: Chanarin-Dorfman Syndrome: A Novel Homozygous Mutation in ABHD5 Gene in a Chinese Case and Genotype-Phenotype Correlation Analysis
Authors: Liang Bo , Huang He , Zhang Jiaxiang , Chen Gang , Kong Xiangsheng , Zhu Mengting , Wang Peiguang , Tang Lili
Published: March 2022

The Chanarin–Dorfman syndrome (CDS) is a rare, autosomal recessively inherited genetic disease, whch is associated with a decrease in the lipolysis activity in multiple tissue cells. The clinical phenotype involves multiple organs and systems, including liver, eyes, ears, skeletal muscle and central nervous system. Mutations in ABHD5/CGI58 gene have been confirmed to be associated with CDS. We performed whole exome sequencing on a Chinese CDS patient with skin ichthyosis features mimicking lamellar ichthyosis, ectropion, sensorineural hearing loss, and lipid storage in peripheral blood neutrophils. A novel homozygous missense mutation (p.L154R) in ABHD5 gene was detected in this patient. Genotype-phenotype analysis in reported CDS patients revealed no particular correlation. Our findings further enrich the reservoir of ABHD5 mutations in CDS.
Therapeutic Potential of Microvesicles in Cell Therapy and Regenerative Medicine of Ocular Diseases With an Especial Focus on Mesenchymal Stem Cells-Derived Microvesicles
Authors: Rad Lina Moallemi , Yumashev Alexey V. , Hussen Bashdar Mahmud , Jamad Hazha Hadayat , Ghafouri-Fard Soudeh , Taheri Mohammad , Rostami Samaneh , Niazi Vahid , Hajiesmaeili Mohammadreza
Published: March 2022

These days, mesenchymal stem cells (MSCs), because of immunomodulatory and pro-angiogenic abilities, are known as inevitable factors in regenerative medicine and cell therapy in different diseases such as ocular disorder. Moreover, researchers have indicated that exosome possess an essential potential in the therapeutic application of ocular disease. MSC-derived exosome (MSC-DE) have been identified as efficient as MSCs for treatment of eye injuries due to their small size and rapid diffusion all over the eye. MSC-DEs easily transfer their ingredients such as miRNAs, proteins, and cytokines to the inner layer in the eye and increase the reconstruction of the injured area. Furthermore, MSC-DEs deliver their immunomodulatory cargos in inflamed sites and inhibit immune cell migration, resulting in improvement of autoimmune uveitis. Interestingly, therapeutic effects were shown only in animal models that received MSC-DE. In this review, we summarized the therapeutic potential of MSCs and MSC-DE in cell therapy and regenerative medicine of ocular diseases.
Identification of Ion Channel-Related Genes and miRNA-mRNA Networks in Mesial Temporal Lobe Epilepsy
Authors: Su Zhengwei , Li Yinchao , Chen Shuda , Liu Xianyue , Zhao Ke , Peng Ying , Zhou Liemin
Published: March 2022

Objective: It aimed to construct the miRNA-mRNA regulatory network related to ion channel genes in mesial temporal lobe epilepsy (mTLE), and further identify the vital node in the network.

Methods: Firstly, we identified ion channel-related differentially expressed genes (DEGs) in mTLE using the IUPHAR/BPS Guide to Pharmacology (GTP) database, neXtProt database, GeneCards database, and the high-throughput sequencing dataset. Then the STRING online database was used to construct a protein-protein interaction (PPI) network of DEGs, and the hub module in the PPI network was identified using the cytoHubba plug-in of Cytoscape software. In addition, the Single Cell Portal database was used to distinguish genes expression in different cell types. Based on the TarBase database, EpimiRBase database and the high-throughput sequencing dataset GSE99455, miRNA-mRNA regulatory network was constructed from selected miRNAs and their corresponding target genes from the identified DEGs. Finally, the rats were selected to construct chronic li-pilocarpine epilepsy model for the next stage experimental verification, and the miR-27a-3p mimic was used to regulate the miRNA expression level in PC12 cells. The relative expression of miR-27a-3p and its targeting mRNAs were determined by RT-qPCR.

Results: 80 mTLE ion channel-related DEGs had been screened. The functional enrichment analysis results of these genes were highly enriched in voltage-gated channel activation and ion transport across membranes. In addition, the hub module, consisting of the Top20 genes in the protein-protein interaction (PPI) network, was identified, which was mainly enriched in excitatory neurons in the CA3 region of the hippocampus. Besides, 14 miRNAs targeting hub module genes were screened, especially the miR-27a-3p deserving particular attention. miR-27a-3p was capable of regulating multiple mTLE ion channel-related DEGs. Moreover, in Li–pilocarpine-induced epilepsy models, the expression level of miR-27a-3p was increased and the mRNAs expression level of KCNB1, SCN1B and KCNQ2 was decreased significantly. The mRNAs expression level of KCNB1 and KCNQ2 was decreased significantly following PC12 cells transfection with miR-27a-3p mimics.

Conclusion: The hub ion channel-related DEGs in mTLE and the miRNA-mRNA regulatory networks had been identified. Moreover, the network of miR-27a-3p regulating ion channel genes will be of great value in mTLE.
Integrated Transcriptome Analysis of Iris Tissues in Experimental Autoimmune Uveitis
Authors: Li Dan , Huang Chang , Han Xiaoyan , Sun Jianguo
Published: March 2022

Uveitis is a severe ocular inflammatory disease that affects the uvea and frequently results in visual impairment, even irreversible blindness. The current treatments for uveitis have exhibited adverse side effects. To find novel targets of this disease, we perform comparative transcriptome analysis using normal (n = 4) and experimental autoimmune uveitis (EAU) (n = 4) rat iris samples. We mainly focus on the expression profiles of mRNAs and long non-coding RNAs, and identify NOD-like receptor signaling pathway as the one that plays a key role in the pathological changes of the EAU irises. Our work demonstrates that the EAU iris transcriptome can be mined to uncover novel targetable pathways for uveitis. The molecules in NOD-like receptor signaling pathway could be novel therapeutic targets for autoimmune uveitis.
The Pathophysiological Link Between Reelin and Autism: Overview and New Insights
Authors: Scala Marcello , Grasso Eleonora A. , Di Cara Giuseppe , Riva Antonella , Striano Pasquale , Verrotti Alberto
Published: March 2022

Reelin is a secreted extracellular matrix protein playing pivotal roles in neuronal migration and cortical stratification during embryonal brain development. In the adult brain, its activity is crucial for synaptic plasticity, memory processing, and cognition. Genetic alterations in RELN have been variably reported as possible contributors to the pathogenesis of autism spectrum disorders (ASD). In particular, GCCs repeats in the 5′UTR, and single nucleotide polymorphysms (SNPs) in RELN have been suggested to affect brain development and predispose to autism. We reviewed pertinent literature on RELN expression and haplotypes transmission in children with ASD, critically analyzing available evidence in support of the pathophysiological association between Reelin deficiency and ASD.
XGEM: Predicting Essential miRNAs by the Ensembles of Various Sequence-Based Classifiers With XGBoost Algorithm
Authors: Min Hui , Xin Xiao-Hong , Gao Chu-Qiao , Wang Likun , Du Pu-Feng
Published: March 2022

MicroRNAs (miRNAs) play vital roles in gene expression regulations. Identification of essential miRNAs is of fundamental importance in understanding their cellular functions. Experimental methods for identifying essential miRNAs are always costly and time-consuming. Therefore, computational methods are considered as alternative approaches. Currently, only a handful of studies are focused on predicting essential miRNAs. In this work, we proposed to predict essential miRNAs using the XGBoost framework with CART (Classification and Regression Trees) on various types of sequence-based features. We named this method as XGEM (XGBoost for essential miRNAs). The prediction performance of XGEM is promising. In comparison with other state-of-the-art methods, XGEM performed the best, indicating its potential in identifying essential miRNAs.
Photorepair of Either CPD or 6-4PP DNA Lesions in Basal Keratinocytes Attenuates Ultraviolet-Induced Skin Effects in Nucleotide Excision Repair Deficient Mice
Authors: Kajitani Gustavo S. , Quayle Carolina , Garcia Camila C. M. , Fotoran Wesley L. , dos Santos Juliana F. R. , van der Horst Gijsbertus T. J. , Hoeijmakers Jan H. J. , Menck Carlos F. M.
Published: March 2022

Ultraviolet (UV) radiation is one of the most genotoxic, universal agents present in the environment. UVB (280-315 nm) radiation directly damages DNA, producing cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs). These photolesions interfere with essential cellular processes by blocking transcription and replication polymerases, and may induce skin inflammation, hyperplasia and cell death eventually contributing to skin aging, effects mediated mainly by keratinocytes. Additionally, these lesions may also induce mutations and thereby cause skin cancer. Photolesions are repaired by the Nucleotide Excision Repair (NER) pathway, responsible for repairing bulky DNA lesions. Both types of photolesions can also be repaired by distinct (CPD- or 6-4PP-) photolyases, enzymes that specifically repair their respective photolesion by directly splitting each dimer through a light-dependent process termed photoreactivation. However, as photolyases are absent in placental mammals, these organisms depend solely on NER for the repair of DNA UV lesions. However, the individual contribution of each UV dimer in the skin effects, as well as the role of keratinocytes has remained elusive. In this study, we show that in NER-deficient mice, the transgenic expression and photorepair of CPD-photolyase in basal keratinocytes completely inhibited UVB-induced epidermal thickness and cell proliferation. On the other hand, photorepair by 6-4PP-photolyase in keratinocytes reduced but did not abrogate these UV-induced effects. The photolyase mediated removal of either CPDs or 6-4PPs from basal keratinocytes in the skin also reduced UVB-induced apoptosis, ICAM-1 expression, and myeloperoxidase activation. These findings indicate that, in NER-deficient rodents, both types of photolesions have causal roles in UVB-induced epidermal cell proliferation, hyperplasia, cell death and inflammation. Furthermore, these findings also support the notion that basal keratinocytes, instead of other skin cells, are the major cellular mediators of these UVB-induced effects.
Adult Memory T Cell Responses to the Respiratory Syncytial Virus Fusion Protein During a Single RSV Season (2018–2019)
Authors: Blunck Brittani N. , Angelo Laura S. , Henke David , Avadhanula Vasanthi , Cusick Matthew , Ferlic-Stark Laura , Zechiedrich Lynn , Gilbert Brian E. , Piedra Pedro A.
Published: March 2022

Respiratory Syncytial Virus (RSV) is ubiquitous and re-infection with both subtypes (RSV/A and RSV/B) is common. The fusion (F) protein of RSV is antigenically conserved, induces neutralizing antibodies, and is a primary target of vaccine development. Insight into the breadth and durability of RSV-specific adaptive immune response, particularly to the F protein, may shed light on susceptibility to re-infection. We prospectively enrolled healthy adult subjects (n = 19) and collected serum and peripheral blood mononuclear cells (PBMCs) during the 2018–2019 RSV season. Previously, we described their RSV-specific antibody responses and identified three distinct antibody kinetic profiles associated with infection status: uninfected (n = 12), acutely infected (n = 4), and recently infected (n = 3). In this study, we measured the longevity of RSV-specific memory T cell responses to the F protein following natural RSV infection. We stimulated PBMCs with overlapping 15-mer peptide libraries spanning the F protein derived from either RSV/A or RSV/B and found that memory T cell responses mimic the antibody responses for all three groups. The uninfected group had stable, robust memory T cell responses and polyfunctionality. The acutely infected group had reduced polyfunctionality of memory T cell response at enrollment compared to the uninfected group, but these returned to comparable levels by end-of-season. The recently infected group, who were unable to maintain high levels of RSV-specific antibody following infection, similarly had decreased memory T cell responses and polyfunctionality during the RSV season. We observed subtype-specific differences in memory T cell responses and polyfunctionality, with RSV/A stimulating stronger memory T cell responses with higher polyfunctionality even though RSV/B was the dominant subtype in circulation. A subset of individuals demonstrated an overall deficiency in the generation of a durable RSV-specific adaptive immune response. Because memory T cell polyfunctionality may be associated with protection against re-infection, this latter group would likely be at greater risk of re-infection. Overall, these results expand our understanding of the longevity of the adaptive immune response to the RSV fusion protein and should be considered in future vaccine development efforts.
Discovery of Novel Circulating Immune Complexes in Lupus Nephritis Using Immunoproteomics
Authors: Tang Chenling , Fang Min , Tan Gongjun , Zhang Shu , Yang Bowen , Li Yaxi , Zhang Ting , Saxena Ramesh , Mohan Chandra , Wu Tianfu
Published: March 2022

Objective

The goal is to discover novel circulating immune complexes (ICx) in the serum of lupus nephritis (LN) as potential biomarkers.

Methods

Protein A/G magnetic beads or C1q-coated plates were used to capture ICx in the serum of LN, followed by the identification of immunoglobulin-binding proteins using liquid chromatography and tandem mass spectrometry (LC-MS/MS). Bioinformatic approaches and single-cell RNA sequencing (scRNA Seq) databases were used to select potential candidate ICx markers in LN. The selected ICx markers were further validated using ELISA.

Results

A total of 300 immunoglobulin-binding proteins were discovered in the screening, among which 77 proteins were detectable only in LN samples. Bioinformatics-assisted selection allowed us to further identify 10 potential immunoglobulin-binding proteins, which form ICx as potential biomarkers in LN. In a validation cohort of 62 LN patients and 21 healthy controls (HC), we found that prolyl 3-hydroxylase 1 (P3H1), phosphatase and actin regulator 4 (PHACTR4), and regulator of G-protein signaling 12 (RGS12) ICx exhibited discriminative capability in distinguishing LN from HC, with an area under the curve (AUC) values of 0.82, 0.99, and 0.90, respectively. Furthermore, a biomarker panel comprising CD14, CD34, cystatin A, myocyte enhancer factor 2C (MEF2C), RGS12, and ubiquitin C (UBC) ICx could distinguish active LN from inactive LN with an AUC value of 0.85, which is comparable to or better than pathological parameters such as renal activity index (AI) and renal chronicity index (CI).

Conclusion

Immunoproteomics-based discovery studies have enabled us to identify circulating immune complexes as potential biomarkers of LN.
Platelets in Viral Infections – Brave Soldiers or Trojan Horses
Authors: Schrottmaier Waltraud C. , Schmuckenschlager Anna , Pirabe Anita , Assinger Alice
Published: March 2022

Viral infections are often associated with platelet activation and haemostatic complications. In line, low platelet counts represent a hallmark for poor prognosis in many infectious diseases. The underlying cause of platelet dysfunction in viral infections is multifaceted and complex. While some viruses directly interact with platelets and/or megakaryocytes to modulate their function, also immune and inflammatory responses directly and indirectly favour platelet activation. Platelet activation results in increased platelet consumption and degradation, which contributes to thrombocytopenia in these patients. The role of platelets is often bi-phasic. Initial platelet hyper-activation is followed by a state of platelet exhaustion and/or hypo-responsiveness, which together with low platelet counts promotes bleeding events. Thereby infectious diseases not only increase the thrombotic but also the bleeding risk or both, which represents a most dreaded clinical complication. Treatment options in these patients are limited and new therapeutic strategies are urgently needed to prevent adverse outcome. This review summarizes the current literature on platelet-virus interactions and their impact on viral pathologies and discusses potential intervention strategies. As pandemics and concomitant haemostatic dysregulations will remain a recurrent threat, understanding the role of platelets in viral infections represents a timely and pivotal challenge.
B-Cell Epitope Mapping of TprC and TprD Variants of Treponema pallidum Subspecies Informs Vaccine Development for Human Treponematoses
Authors: Molini Barbara , Fernandez Mark C. , Godornes Charmie , Vorobieva Anastassia , Lukehart Sheila A. , Giacani Lorenzo
Published: March 2022

Several recent studies have focused on the identification, functional analysis, and structural characterization of outer membrane proteins (OMPs) ofTreponema pallidum(Tp). TheTpspecies encompasses the highly relatedpallidum,pertenue, andendemicumsubspecies of this pathogen, known to be the causative agents of syphilis, yaws, and bejel, respectively. These studies highlighted the importance of identifying surface-exposed OMP regions and the identification of B-cell epitopes that could be protective and used in vaccine development efforts. We previously reported that the TprC and TprD OMPs ofTpare predicted to contain external loops scattered throughout the entire length of the proteins, several of which show a low degree of sequence variability among strains and subspecies. In this study, these models were corroborated using AlphaFold2, a state-of-the-art protein structure modeling software. Here, we identified B-cell epitopes across the full-length TprC and TprD variants using the Geysan pepscan mapping approach with antisera from rabbits infected with syphilis, yaws, and bejel strains and from animals immunized with refolded recombinant TprC proteins from three syphilis strains. Our results show that the humoral response is primarily directed to sequences predicted to be on surface-exposed loops of TprC and TprD proteins, and that the magnitude of the humoral response to individual epitopes differs among animals infected with various syphilis strains andTpsubspecies. Rather than exhibiting strain-specificity, antisera showed various degrees of cross-reactivity with variant sequences from other strains. The data support the further exploration of TprC and TprD as vaccine candidates.
CRISPR/Cas9 Approach to Generate an Auxotrophic BCG Strain for Unmarked Expression of LTAK63 Adjuvant: A Tuberculosis Vaccine Candidate
Authors: Moraes Luana , Trentini Monalisa Martins , Fousteris Dimitrios , Eto Silas Fernandes , Chudzinski-Tavassi Ana Marisa , Leite Luciana Cezar de Cerqueira , Kanno Alex Issamu
Published: March 2022

Tuberculosis is one of the deadliest infectious diseases and a huge healthcare burden in many countries. New vaccines, including recombinant BCG-based candidates, are currently under evaluation in clinical trials. Our group previously showed that a recombinant BCG expressing LTAK63 (rBCG-LTAK63), a genetically detoxified subunit A of heat-labile toxin (LT) from Escherichia coli, induces improved protection against Mycobacterium tuberculosis (Mtb) in mouse models. This construct uses a traditional antibiotic resistance marker to enable heterologous expression. In order to avoid the use of these markers, not appropriate for human vaccines, we used CRISPR/Cas9 to generate unmarked mutations in the lysA gene, thus obtaining a lysine auxotrophic BCG strain. A mycobacterial vector carrying lysA and ltak63 gene was used to complement the auxotrophic BCG which co-expressed the LTAK63 antigen (rBCGΔ-LTAK63) at comparable levels to the original construct. The intranasal challenge with Mtb confirmed the superior protection induced by rBCGΔ-LTAK63 compared to wild-type BCG. Furthermore, mice immunized with rBCGΔ-LTAK63 showed improved lung function. In this work we showed the practical application of CRISPR/Cas9 in the tuberculosis vaccine development field.
Scallop IKK1 Responds to Bacterial and Virus-Related Pathogen Stimulation and Interacts With MyD88 Adaptor of Toll-Like Receptor Pathway Signaling
Authors: Li Lingling , Liu Wenjuan , Fan Nini , Li Fangshu , Huang Baoyu , Liu Qian , Wang Xiaomei , Zheng Yanxin , Sang Xiuxiu , Dong Juan , Wang Xiaona , Wei Lei , Liu Yaqiong , Zhang Meiwei , Ma Jilv , Chen Jiwen , Qi Yitao , Wang Xiaotong
Published: March 2022

IKK proteins are key signaling molecules in the innate immune system of animals, and act downstream of pattern recognition receptors. However, research on IKKs in invertebrates, especially marine mollusks, remains scarce. In this study, we cloned CfIKK1 gene from the Zhikong scallop (Chlamys farreri) and studied its function and the signaling it mediates. The open reading frame of CfIKK1 was 2190 bp and encoded 729 amino acids. Phylogenetic analysis showed that CfIKK1 belonged to the invertebrate IKKα/IKKβ family. Quantitative real-time PCR analysis revealed the ubiquitous expression of CfIKK1 mRNA in all scallop tissues and challenge with lipopolysaccharide, peptidoglycan, or poly(I:C) significantly upregulated the expression of CfIKK1. Co-immunoprecipitation assays confirmed the interaction of CfIKK1 with scallop MyD88 (Myeloid differentiation actor 88, the key adaptor of the TLR signaling pathway) via its N-terminal kinase domain. Additionally, CfIKK1 protein could form homodimers and even oligomers, with N-terminal kinase domain and C-terminal scaffold dimerization domain playing key roles in this process. Finally, the results of RNAi experiments showed that when the scallop IKK1 gene was suppressed, the expression of IRF genes also decreased significantly. In conclusion, CfIKK1 could respond to PAMPs challenge and interact with MyD88 protein of scallop TLR signaling, with the formation of CfIKK1 dimers or oligomers. At the same time, the results of RNAi experiments revealed the close regulatory relationship between IKK1 and IRF genes of scallop. Therefore, as a key signal transduction molecule and immune activity regulator, CfIKK1 plays important roles in the innate immune system of scallops.
Cancer Cell Phenotype Plasticity as a Driver of Immune Escape in Melanoma
Authors: Benboubker Valentin , Boivin Félix , Dalle Stéphane , Caramel Julie
Published: March 2022

Immunotherapies blocking negative immune checkpoints are now approved for the treatment of a growing number of cancers. However, even in metastatic melanoma, where sustained responses are observed, a significant number of patients still do not respond or display resistance. Increasing evidence indicates that non-genetic cancer cell-intrinsic alterations play a key role in resistance to therapies and immune evasion. Cancer cell plasticity, mainly associated with the epithelial-to-mesenchymal transition in carcinoma, relies on transcriptional, epigenetic or translational reprogramming. In melanoma, an EMT-like dedifferentiation process is characterized by the acquisition of invasive or neural crest stem cell-like features. Herein, we discuss recent findings on the specific roles of phenotypic reprogramming of melanoma cells in driving immune evasion and resistance to immunotherapies. The mechanisms by which dedifferentiated melanoma cells escape T cell lysis, mediate T cell exclusion or remodel the immune microenvironment will be detailed. The expanded knowledge on tumor cell plasticity in melanoma should contribute to the development of novel therapeutic combination strategies to further improve outcomes in this deadly metastatic cancer.
Perspectives of JAK Inhibitors for Large Vessel Vasculitis
Authors: Watanabe Ryu , Hashimoto Motomu
Published: March 2022

Vasculitis is an inflammation of the blood vessels caused by autoimmunity and/or autoinflammation, and recent advances in research have led to a better understanding of its pathogenesis. Glucocorticoids and cyclophosphamide have long been the standard of care. However, B-cell depletion therapy with rituximab has become available for treating antineutrophil cytoplasmic antibody-associated vasculitis (AAV). More recently, avacopan, an inhibitor of the complement 5a receptor, was shown to have high efficacy in remission induction against AAV. Thus, treatment options for AAV have been expanded. In contrast, in large vessel vasculitis (LVV), including giant cell arteritis and Takayasu arteritis, tocilizumab, an IL-6 receptor antagonist, was shown to be effective in suppressing relapse and has steroid-sparing effects. However, the relapse rate remains high, and other therapeutic options have long been awaited. In the last decade, Janus kinase (JAK) inhibitors have emerged as therapeutic options for rheumatoid arthritis (RA). Their efficacy has been proven in multiple studies; thus, JAK inhibitors are expected to be promising agents for treating other rheumatic diseases, including LVV. This mini-review briefly introduces the mechanism of action of JAK inhibitors and their efficacy in patients with RA. Then, the pathophysiology of LVV is updated, and a rationale for treating LVV with JAK inhibitors is provided with a brief introduction of our preliminary results using a mouse model. Finally, we discuss the newly raised safety concerns regarding JAK inhibitors and future perspectives for treating LVV.
Anchor Forces on Coir-Based Artificial Seagrass Mats: Dependence on Wave Dynamics and Their Potential Use in Seagrass Restoration
Authors: Villanueva Raúl , Paul Maike , Schlurmann Torsten
Published: March 2022

Seagrasses represent an essential part of the coastal environment and are hence the target of many coastal restoration projects. Artificial seagrass (ASG) mats may facilitate seagrass growth, making them a captivating option for restoration projects. However, little is known about the forces occurring on mats deployed in marine environments and especially on how these forces are transmitted to the anchoring points. Here, we present a study of prototype biodegradable coconut-mesh mats as base layer for ASG meadows and investigate the forces that occur at the anchors. We test the performance of three mesh types under wave forcing using two different anchor configurations without ASG and subsequently test ASG mats of one mesh type under wave forcing and a 4-anchor configuration to assess the effect of the ASG on anchor loading as a function of incident orbital velocities. We found that the mat composition plays a more important role than the number of anchors in anchor load reduction. The anchor forces were 2–4 times higher at front anchors compared to rear anchors, relative to wave propagation direction, and were also considerably higher in that direction compared to the opposite direction. With ASG, the forces increased compared to the highest measured forces without ASG. The forces on the anchors were almost fully dominated by the drag on the ASG based on material properties, ASG reconfiguration and flow conditions. We derive a relation between horizontal orbital velocities and expected forcing on the anchor based on ASG properties and the corresponding area of each anchor and discuss relevant criteria for the design of ASG mats. This should help to assess the loading on anchors deployed for restoration under specific site conditions and chosen materials.
Marine Environmental Change Induced by Anthropogenic Activities – From a Viewpoint of Aquatic Palynomorph Assemblages Preserved in Sediment Cores of Beppu Bay, West Japan
Authors: Matsuoka Kazumi , Kojima Natsuhiko , Kuwae Michinobu
Published: March 2022

Stratigraphic cluster analysis using aquatic palynomorphs preserved in the core sediments revealed a rapid eutrophication due to anthropogenic activities from the mid 1960s in Beppu Bay, East Kyushu, Japan. These assemblages were divided into three major units: BP-I, BP-II and BP-III, and also only dinoflagellate cyst assemblages were divided into the following four units in Beppu Bay: BP-A, BP-B, BP-C, and BP-D. Unit boundaries based on aquatic palynomorphs and dinoflagellate cysts were different except in the upper part, BP-III and BP-D, both of which clearly indicated anthropogenic eutrophication in both sea water and bottom sediments. On the other hand, in dinoflagellate cyst assemblages, Unit BP-A was characterized by stable occurrence of Spiniferites bulloideus and Spiniferites hyperacanthus, Lingulodinium machaerophorum of Gonyaulacales, and reduction of heterotrophic Peridinioid Brigantedinium spp. In Unit BP-C there was a clear decrease of L. machaerophorum. Unit BP-B was characterized by decreases of S. bulloideus, S. hyperacanthus, and L. machaerophorum, and little increase of Spniferites bentori. Unit BP-C was characterized by an increase in S. bulloideus and heterotrophic Peridinioid Echinidinium spp. Unit BP-D was subdivided into Subunit BP-D1 where dinoflagellate cysts showed a marked increase in S. bulloideus accompanied by the appearance of L. machaerophorum and Tuberculodinium vancampoae, and Subunit PB-D2 where there was a decrease of total dinoflagellate cysts. From the dinoflagellate cyst assemblages, the marine environment of the period of BP-A Unit was suggested to be warm and stable. However, L. machaerophorum started to decrease in BP-B. The clear decrease of L. machaerophorum suggest that the marine environment became cooler than that of Unit BP-A. Significant increases of S. bulloideus, S. hypearcanthus, L. machaerophorum, T. vancampoae, Brigantedinium spp., and Polykrikos kofoidii were characteristic of Unit BP-D. The increase in total dinoflagellate cyst density and the increase of the ratio of heterotrophic dinoflagellate cysts in Subunit BP-D1 are manifestations of the Oslo fjord Signal and Heterotroph Signal, respectively. In addition, the decrease in microforaminiferal lining that continued from Unit BP-C to Unit BP-D might indicate deterioration of the bottom sediment environment.
Remote Sensing of the Tautra Ridge: An Overview of the World’s Shallowest Cold-Water Coral Reefs
Authors: Mogstad Aksel Alstad , Løvås Håvard Snefjellå , Sture Øystein , Johnsen Geir , Ludvigsen Martin
Published: March 2022

On the Tautra Ridge – a 39-100 m deep morainic sill located in the middle of the Trondheimsfjord, Norway – some of the world’s shallowest known occurrences of the scleractinian cold-water coral (CWC) Desmophyllum pertusum can be found. The earliest D. pertusum records from the Tautra Ridge date back to the 18th century, and since then, the location has provided easy access to physical coral specimens for numerous scientific studies. In 2013, the ridge was declared a marine protected area by the Norwegian Government due to its unique CWC reefs. However, few attempts have to our knowledge yet been made to characterize the distribution, extent and condition of these reefs extensively. The aim of the current study was therefore to add geospatial context to the Tautra CWC reef complex. In the study, data from multibeam echo sounding, synthetic aperture sonar imaging and underwater hyperspectral imaging are used to assess CWC reef occurrences from multiple perspectives. The study demonstrates how complementary remote sensing techniques can be used to increase knowledge generation during seafloor mapping efforts. Ultimately, predictive modeling based on seafloor geomorphometry is used to estimate both distribution and areal coverage of D. pertusum reefs along the majority of the Tautra Ridge. Our findings suggest that D. pertusum reef distribution on the Tautra Ridge is affected by several geomorphometric seafloor properties, and that the total reef extent in the area likely is close to 0.64 km2. Better description of current patterns across the Tautra Ridge will improve our understanding of the interaction between hydrography and geomorphology at the Tautra CWC reef complex in the future.
The Association of Urine Creatinine With Kidney Stone Prevalence in US Adults: Data From NHANES 2009–2018
Authors: Shen Xudong , Chen Yan , Zhang Yangyang , Xia Kaiguo , Chen Yang , Hao Zongyao
Published: March 2022

Background

The primary objective of this project is to explore the association of urine creatinine (UCR) with the prevalence rate of kidney stones.

Method

The National Health and Nutrition Examination Survey (NHANES) database was employed to conduct a cross-sectional study. The analysis samples included adults aged ≥20 years from five consecutive cycles of the NHANES 2009–2018. The association between UCR and kidney stones was detected using univariate and multivariate logistic regression analyses. Further, subgroup analyses were performed to evaluate the subgroup effects.

Results

After adjustment for all confounders, multiple logistic regression analysis revealed a weak positive relationship between UCR and kidney stone (OR = 1.015, 95% CI: 1.008–1.021). In the subgroup analysis stratified by sex, age, or race, the risk further increased in men (OR = 1.014, 95% CI: 1.005–1.023), women (OR = 1.015, 95% CI: 1.005–1.025), white race (OR = 1.022, 95% CI: 1.013–1.030), aged 40–59 years (OR = 1.017, 95% CI: 1.006–1.028), and aged 60–80 years (OR = 1.017, 95% CI: 1.006–1.028).

Conclusions

Our results confirmed a moderately increased risk of kidney stone formation attributed to high levels of UCR, especially in middle-aged and older adults and the white race. However, because of the cross-sectional design of the study, causal inferences cannot be made.
DNA Methylation - and Telomere - Based Biological Age Estimation as Markers of Biological Aging in Donors Kidneys
Authors: Pavanello Sofia , Campisi Manuela , Rigotti Paolo , Bello Marianna Di , Nuzzolese Erica , Neri Flavia , Furian Lucrezia
Published: March 2022

The biological age of an organ may represent a valuable tool for assessing its quality, especially in the elder. We examined the biological age of the kidneys [right (RK) and left kidney (LK)] and blood leukocytes in the same subject and compared these to assess whether blood mirrors kidney biological aging. Biological age was studied in n = 36 donors (median age: 72 years, range: 19–92; male: 42%) by exploring mitotic and non-mitotic pathways, using telomere length (TL) and age-methylation changes (DNAmAge) and its acceleration (AgeAcc). RK and LK DNAmAge are older than blood DNAmAge (RK vs. Blood, p = 0.0271 and LK vs. Blood, p = 0.0245) and RK and LK AgeAcc present higher score (this mean the AgeAcc is faster) than that of blood leukocytes (p = 0.0271 and p = 0.0245) in the same donor. TL of RK and LK are instead longer than that of blood (p = 0.0011 and p = 0.0098) and the increase in Remuzzi-Karpinski score is strongly correlated with kidney TL attrition (p = 0.0046). Finally, blood and kidney TL (p < 0.01) and DNAmAge (p < 0.001) were correlated. These markers can be evaluated in further studies as indicators of biological age of donor organ quality and increase the usage of organs from donors of advanced age therefore offering a potential translational research inkidney transplantation.
Microbial Degradation of Aldrin and Dieldrin: Mechanisms and Biochemical Pathways
Authors: Pang Shimei , Lin Ziqiu , Li Jiayi , Zhang Yuming , Mishra Sandhya , Bhatt Pankaj , Chen Shaohua
Published: March 2022

As members of the organochlorine group of insecticides, aldrin and dieldrin are effective at protecting agriculture from insect pests. However, because of excessive use and a long half-life, they have contributed to the major pollution of the water/soil environments. Aldrin and dieldrin have been reported to be highly toxic to humans and other non-target organisms, and so their use has gradually been banned worldwide. Various methods have been tried to remove them from the environment, including xenon lamps, combustion, ion conversion, and microbial degradation. Microbial degradation is considered the most promising treatment method because of its advantages of economy, environmental protection, and convenience. To date, a few aldrin/dieldrin-degrading microorganisms have been isolated and identified, including Pseudomonas fluorescens, Trichoderma viride, Pleurotus ostreatus, Mucor racemosus, Burkholderia sp., Cupriavidus sp., Pseudonocardia sp., and a community of anaerobic microorganisms. Many aldrin/dieldrin resistance genes have been identified from insects and microorganisms, such as Rdl, bph, HCo-LGC-38, S2-RDLA302S, CSRDL1A, CSRDL2S, HaRdl-1, and HaRdl-2. Aldrin degradation includes three pathways: the oxidation pathway, the reduction pathway, and the hydroxylation pathway, with dieldrin as a major metabolite. Degradation of dieldrin includes four pathways: oxidation, reduction, hydroxylation, and hydrolysis, with 9-hydroxydieldrin and dihydroxydieldrin as major products. Many studies have investigated the toxicity and degradation of aldrin/dieldrin. However, few reviews have focused on the microbial degradation and biochemical mechanisms of aldrin/dieldrin. In this review paper, the microbial degradation and degradation mechanisms of aldrin/dieldrin are summarized in order to provide a theoretical and practical basis for the bioremediation of aldrin/dieldrin-polluted environment.
Biodiversity and Biogeography of Abundant and Rare Microbial Assemblages in the Western Subtropical Pacific Ocean
Authors: Shao Qianwen , Sun Dong , Fang Chen , Feng Yunzhi , Wang Chunsheng
Published: March 2022

The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance–decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.
Methanethiol Consumption and Hydrogen Sulfide Production by the Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum SolV
Authors: Schmitz Rob A. , Mohammadi Sepehr S. , van Erven Timo , Berben Tom , Jetten Mike S. M. , Pol Arjan , Op den Camp Huub J. M.
Published: March 2022

Methanotrophs aerobically oxidize methane to carbon dioxide to make a living and are known to degrade various other short chain carbon compounds as well. Volatile organic sulfur compounds such as methanethiol (CH3SH) are important intermediates in the sulfur cycle. Although volatile organic sulfur compounds co-occur with methane in various environments, little is known about how these compounds affect methanotrophy. The enzyme methanethiol oxidase catalyzing the oxidation of methanethiol has been known for decades, but only recently the mtoX gene encoding this enzyme was identified in a methylotrophic bacterium. The presence of a homologous gene in verrucomicrobial methanotrophs prompted us to examine how methanotrophs cope with methanethiol. Here, we show that the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV consumes methanethiol and produces H2S, which is concurrently oxidized. Consumption of methanethiol is required since methanethiol inhibits methane oxidation. Cells incubated with ∼15 μM methanethiol from the start clearly showed inhibition of growth. After depletion of methanethiol, growth resumed within 1 day. Genes encoding a putative methanethiol oxidase were found in a variety of methanotrophs. Therefore, we hypothesize that methanethiol degradation is a widespread detoxification mechanism in methanotrophs in a range of environments.
Improvement of Direct Interspecies Electron Transfer via Adding Conductive Materials in Anaerobic Digestion: Mechanisms, Performances, and Challenges
Authors: Chen Le , Fang Wei , Chang Jianning , Liang Jinsong , Zhang Panyue , Zhang Guangming
Published: March 2022

Anaerobic digestion is an effective and sustainable technology for resource utilization of organic wastes. Recently, adding conductive materials in anaerobic digestion to promote direct interspecies electron transfer (DIET) has become a hot topic, which enhances the syntrophic conversion of various organics to methane. This review comprehensively summarizes the recent findings of DIET mechanisms with different mediating ways. Meanwhile, the influence of DIET on anaerobic digestion performance and the underlying mechanisms of how DIET mediated by conductive materials influences the lag phase, methane production, and system stability are systematically explored. Furthermore, current challenges such as the unclear biological mechanisms, influences of non-DIET mechanisms, limitations of organic matters syntrophically oxidized by way of DIET, and problems in practical application of DIET mediated by conductive materials are discussed in detail. Finally, the future research directions for practical application of DIET are outlined.
Interrelated Oncogenic Viruses and Breast Cancer
Authors: Afzal Samia , Fiaz Khadija , Noor Afifa , Sindhu Amira Saleem , Hanif Asma , Bibi Ayesha , Asad Muhammad , Nawaz Saba , Zafar Saba , Ayub Sidra , Hasnain Syeda Bariyyah , Shahid Muhammad
Published: March 2022

Breast Cancer is a multifactorial disease and recent evidence that viruses have a greater role in its aetiology and pathophysiology than previously hypothesized, has garnered a lot of attention in the past couple of years. After the role of Mouse Mammary Tumour Virus (MMTV) in the oncogenesis of breast cancer has been proved in mice, search for similar viruses found quite a plausible relation of Human Papilloma Virus (HPV), Epstein–Barr virus (EBV), and Bovine Leukaemia Virus (BLV) with breast cancer. However, despite practical efforts to provide some clarity in this issue, the evidence that viruses cause breast cancer still remains inconclusive. Therefore, this article aims to clarify some ambiguity and elucidate the correlation of breast cancer and those particular viruses which are found to bring about the development of tumorigenesis by a previous infection or by their own oncogenic ability to manipulate the molecular mechanisms and bypass the immune system of the human body. Although many studies have reported, both, the individual and co-existing presence of HPV, EBV, MMTV, and BLV in patient sample tissues, particularly in Western women, and proposed oncogenic mechanisms, majority of the collective survey of literature fails to provide a delineated and strong conclusive evidence that viruses do, in fact, cause breast cancer. Measures to prevent these viral infections may curb breast cancer cases, especially in the West. More studies are needed to provide a definite conclusion.
Ionic Liquid Co-Catalyst Assisted Biodiesel Production From Waste Cooking Oil Using Heterogeneous Nanocatalyst: Optimization and Characterization
Authors: Baskar Gurunathan , Anita Nalathamalar T. , Jeehoon Han , Naveenkumar Rajendran
Published: March 2022

In the present work, the biodiesel was produced from waste cooking oil (WCO) using heterogeneous zinc doped iron nanocatalyst and tetrabutylammonium iodide (TBAI) as co-catalyst. The heterogeneous zinc doped iron nanocatalyst was synthesized and characterized. The functional group in the heterogeneous nanocatalyst was confirmed using FTIR analysis, the crystalline nature was studied by XRD analysis, and the size and structure of the nanocatalyst were analyzed by SEM. The optimization of transesterification parameters like oil to methanol molar ratio, zinc doped iron concentration, TBAI concentration, temperature, and time were carried out for the maximum conversion of biodiesel from WCO. At 50 min the maximum biodiesel conversion of 90% was achieved at 55°C with 12% catalyst, 30% co-catalyst, and 1:11 WCO to methanol ratio. The presence of functional groups and the methyl ester composition of the biodiesel from WCO were confirmed by FTIR and GC-MS analysis. The use of zinc doped iron nanocatalyst with TBAI showed good catalytic activity to produce biodiesel from WCO.