bluuebunny/crossref_metadata_2025 huggingface dataset:
PENEMPELAN TERITIP AMPHIBALANUS AMPHITRITE PADA SEMAI MANGROVE RHIZOPORA MUCRONATA DI AREA REHABILITASI MANGROVE DESA BASULE KABUPATEN KONAWE UTARA
Authors: Noer Fachrijal , Ramli Muhammad , Ira .
Published: October 2021

AbstrakTeritip merupakan hama yang melekat pada batang maupun akar. Hal itu dapat merusak kulit batang mangrove dan mengakibatkan kematian mangrove. Penelitian ini bertujuan untuk mengetahui pengaruh parameter kualitas perairan terhadap kepadatan biofouling (teritip), kepadatan dan jenis biofouling (teritip) pada area rehabilitasi mangrove di Desa Basule Kabupaten Konawe Utara. Penentuan stasiun dilakukan secara purposive sampling yang berjumlah 3 stasiun. Pada masing-masing stasiun terdiri dari 3 sub stasiun sepanjang 100 meter dengan interval jarak 10 meter. Pemilihan stasiun ini didasarkan pada perbedaan karakteristik kerapatan mangrove. Penghitungan teritip dilakukan saat air menjelang surut dengan metode plot transek kuadrat. Pada setiap ulangan diletakkan petak ukuran 5x5 meter untuk kategori anakan dan  plot 1 x 1 meter yang ditempatkan dalam petak ukuran 5x 5 meter secara acak. Hasil penelitian menunjukkan bahwa kepadatan tertinggi berada pada stasiun III yang mencapai 17,22 ind/m2 sementara kepadatan terendah terdapat pada stasiun I dengan nilai 12,66 ind/m2 . Hasil penelitian juga menunjukkan bahwa semakin tinggi kerapatan mangrove maka semakin tinggi kepadatan teritip.Kata Kunci: Amphibalanus amphitrite, penempelan, kepadatan, mangrove, Desa Basule
KANDUNGAN LOGAM BERAT Pb PADA SEDIMEN DAN KERANG (POLYMESODA EROSA) DI PERAIRAN KOEONO, KECAMATAN PALANGGA SELATAN, KABUPATEN KONAWE SELATAN
Authors: Mariani Reni Ulfa , Emiyarti . , Haya La Ode Muhammad Yasir
Published: October 2021

Perairan Koeono merupakan pusat aktifitas pertambangan jenis ore nickel. Kondisi perairan tersebut diduga telah tercemar logam berat diantaranya jenis logam berat Timbal (Pb), namun informasi tentang konsentrasi bahan pencemar berbahaya (logam berat Pb) di lokasi penelitian belum tersedia. Tujuan penelitian ini adalah untuk mengetahui kandungan logam berat Pb pada sedimen dan Bivalvia jenis kerang (Polymesoda erosa) di Perairan Koeono. Metode penelitian menggunakan metode purposive sampling. Sampel diambil dengan dua kali pengulangan. Analisa logam berat Pb menggunakan metode Atomic Absorbtion Spectrophotometry (AAS). Berdasarkan hasil penelitian, konsentrasi logam berat Timbal (Pb) pada sedimen berada pada kisaran 0.145-0.345 mg/l dan kerang jenis polymesoda erosa pada kisaran 1.14-2.65 mg/l. Berdasarkan standar baku mutu oleh Kepmen LH No 51 Tahun 2004 dan BPOM dinyatakan kandungan timbal pada sedimen dan kerang (Polymesoda erosa) sudah melewati ambang batas baku mutu dan kerang tidak layak dikonsumsi.Kata kunci: Kerang; Sedimen; logam berat Pb; Perairan Koeono
Investigation on Highway Damages Caused by the Wenchuan Earthquake: Geological Disasters
Authors: Lesheng Chen
Published: October 2021

Starting with introduction to the geologic environment, this book elaborates the theory, cause, and current situation about the highway damages in the Wenchuan Earthquake Stricken Area in simple language on the basis of a great deal of full and accurate investigation data about the Wenchuan Earthquake and post-earthquake geological disasters. These results provide valuable technical support for the reconstruction of post-earthquake highways and prevention of post-earthquake geological disasters. This book, the pictures and their accompanying text are both excellent. This book is divided into fourteen chapters, covering geological disaster review, surface rupture zone and liquefaction, collapses and landslide and post-earthquake secondary debris flow, as well as a large number of precious affected highway examples.
Lean & Green on Industry 4.0 Context – Contribution to Understand L&G Drivers and Design Principles
Authors: John Lenin , Sampayo Manuel , Peças Paulo
Published: October 2021

The purpose of this paper is to demonstrate how the implementation of Lean & Green (L&G) in an Industry 4.0 (I4.0) environment can enhance the potential impact of the L&G approach and help manufacturing companies moving towards higher operational and sustainable performances. The research work developed here shows that although a proper definition of L&G is neither exposed worldwide nor explicitly implemented under that name, the current industrial firms are deeply concerned about the demanding challenge of keeping businesses flexible and agile without forgetting strategies to minimize the acceleration of climate change. So, one contribution of this paper is the identification and characterization of L&G drivers and design principles, supporting a robust and well-informed L&G systems implementation. As inferred from the research work, this challenge demands high quality and updated data together with assertive information. Thus, the implementation of L&G in I4.0 contexts is the answer to overcome the identified barriers. Likewise, an L&G system contributes to overcoming the challenges of I4.0 implementation regarding the triple bottom line sustainability concept. Consequently, another contribution of this paper is to depict why an L&G system performs better in the I4.0 context.
Segmentation of Covid-19 Affected X-Ray Image using K-means and DPSO Algorithm
Authors: Kumari Roopa , Gupta Neena , Kumar Narender
Published: October 2021

Covid-19, a disease that originated in the Chinese city of Wuhan, has spread across almost the entire globe. Pneumonia, which infects the lungs, is one of the symptoms of this disease. In the past X-ray images were used to segment various diseases such as pneumonia, tuberculosis, or lung cancer. Recent studies showed that Covid-19 affects the lungs. As a result, an X-ray imaging could help to detect and diagnose Covid-19 infection. This study presents a novel hybrid algorithm (CHDPSOK) for segmenting a Covid-19 infected X-ray image. To find Covid-19 contamination in the lungs, we use a segmentation-based approach using K-means and Dynamic PSO algorithm. In the present paper, segmentation of infected regions in the X-ray image uses a cumulative histogram to initialize the population of the PSO algorithm. In a dynamic PSO algorithm, the velocity of the particle changes dynamically which is useful to avoid the local minima. K-means is used to change the position of the particle dynamically for better convergence. To validate the segmentation performance of our algorithm, we used the Kaggle dataset in our experiments. The performance of the proposed method is analyzed both qualitatively and quantitatively. The results explicitly demonstrate the outperformance of the proposed algorithm.
Exploring the Issues in Policy Deployment Using SAP-LAP and eIRP Approaches: An Empirical Case Study
Authors: Plackal Don , Kumar Sumit , Gupta Pardeep
Published: October 2021

Policy deployment refers to the formulation of policies, their implementations, and reviews. Every organization irrespective of its size and sector involves the process of policy deployment. There exist many factors that affect the process of policy deployment. These factors pose flexibilities that can alter the outcome of a policy. This paper explores the flexibilities in the choice of the factors governing a policy decision. An Indian auto-spare part industry with certain policy issues is selected for theory building. A framework model for solving the policy deployment issues is formulated using an interpretive comparative technique known as situation-actor-process-learnings-actions-performance (SAP-LAP). It is based on the comparative study of contextual relationships within and among its various elements. The contextual relationship within a particular element is presented in the form of a self-interaction matrix and the contextual relationships among the elements are depicted using the cross-interaction matrix. Further, the actors and actions of the framework are ranked using an efficient interpretive ranking process (eIRP) for easy selection and prioritization. The ranks obtained through the efficient IRP model will facilitate the policymakers in the formulation of better decisions and implementation of key policies.
Synthesis of Sitagliptin Intermediate by a Multi-Enzymatic Cascade System Using Lipase and Transaminase With Benzylamine as an Amino Donor
Authors: Khobragade Taresh P. , Sarak Sharad , Pagar Amol D. , Jeon Hyunwoo , Giri Pritam , Yun Hyungdon
Published: October 2021

Herein, we report the development of a multi-enzyme cascade using transaminase (TA), esterase, aldehyde reductase (AHR), and formate dehydrogenase (FDH), using benzylamine as an amino donor to synthesize the industrially important compound sitagliptin intermediate. A panel of 16 TAs was screened using ethyl 3-oxo-4-(2,4,5-trifluorophenyl) butanoate as a substrate (1). Amongst these enzymes, TA from Roseomonas deserti (TARO) was found to be the most suitable, showing the highest activity towards benzylamine (∼70%). The inhibitory effect of benzaldehyde was resolved by using AHR from Synechocystis sp. and FDH from Pseudomonas sp., which catalyzed the conversion of benzaldehyde to benzyl alcohol at the expense of NAD(P)H. Reaction parameters, such as pH, buffer system, and concentration of amino donor, were optimized. A single whole-cell system was developed for co-expressing TARO and esterase, and the promoter engineering strategy was adopted to control the expression level of each biocatalyst. The whole-cell reactions were performed with varying substrate concentrations (10–100 mM), resulting in excellent conversions (ranging from 72 to 91%) into the desired product. Finally, the applicability of this cascade was highlighted on Gram scale, indicating production of 70% of the sitagliptin intermediate with 61% isolated yield. The protocol reported herein may be considered an alternative to existing methods with respect to the use of cheaper amine donors as well as improved synthesis of (R) and (S) enantiomers with the use of non-chiral amino donors.
Extracellular Vesicles in Acute Leukemia: A Mesmerizing Journey With a Focus on Transferred microRNAs
Authors: Izadirad Mehrdad , Huang Zoufang , Jafari Farideh , Hamidieh Amir Ali , Gharehbaghian Ahmad , Li Yi-Dong , Jafari Leila , Chen Zhe-Sheng
Published: October 2021

Despite their small size, the membrane-bound particles named extracellular vesicles (EVs) seem to play an enormous role in the pathogenesis of acute leukemia. From oncogenic hematopoietic stem cells (HSCs) to become leukemic cells to alter the architecture of bone marrow (BM) microenvironment, EVs are critical components of leukemia development. As a carrier of essential molecules, especially a group of small non-coding RNAs known as miRNA, recently, EVs have attracted tremendous attention as a prognostic factor. Given the importance of miRNAs in the early stages of leukemogenesis and also their critical parts in the development of drug-resistant phenotype, it seems that the importance of EVs in the development of leukemia is more than what is expected. To be familiar with the clinical value of leukemia-derived EVs, this review aimed to briefly shed light on the biology of EVs and to discuss the role of EV-derived miRNAs in the development of acute myeloid leukemia and acute lymphoblastic leukemia. By elaborating the advances and challenges concerning the isolation of EVs, we discuss whether EVs could have a prognostic value in the clinical setting for leukemia.
Protein- and Cell-Resistance of Zwitterionic Peptide-Based Self-Assembled Monolayers: Anti-Biofouling Tests and Surface Force Analysis
Authors: Chang Ryongsok , Quimada Mondarte Evan Angelo , Palai Debabrata , Sekine Taito , Kashiwazaki Aki , Murakami Daiki , Tanaka Masaru , Hayashi Tomohiro
Published: October 2021

Peptide-based self-assembled monolayers (peptide-SAMs) with specific zwitterionic amino acid sequences express an anti-biofouling property. In this work, we performed protein adsorption and cell adhesion tests using peptide-SAMs with repeating units of various zwitterionic pairs of amino acids (EK, DK, ER, and DR). The SAMs with the repeating units of EK and DK (EK and DK SAMs) manifested excellent bioinertness, whereas the SAMs with the repeating units of ER and DR (ER and DR SAMs) adhered proteins and cells. We also performed surface force measurements using atomic force microscopy to elucidate the mechanism underlying the difference in the anti-biofouling property. Our measurements revealed that water-induced repulsion with a range of about 8 nm acts between EK SAMs (immobilized on both probe and substrate) and DK SAMs, whereas such repulsion was not observed for ER and DR SAMs. The strength of the repulsion exhibited a clear correlation with the protein- and cell-resistance of the SAMs, indicating that the interfacial water in the vicinity of EK and DK SAMs is considered as a physical barrier to deter protein and cells from their adsorption or adhesion. The range of the repulsion observed for EK and DK SAMs is longer than 8 nm, indicating that the hydrogen bonding state of the interfacial water with a thickness of 4 nm is modified by EK and DK SAMs, resulting in the expression of the anti-biofouling property.
Novel lncRNA-miRNA-mRNA Competing Endogenous RNA Triple Networks Associated Programmed Cell Death in Heart Failure
Authors: Zheng Yu , Zhang Yingjie , Zhang Xiu , Dang Yini , Cheng Yihui , Hua Wenjie , Teng Meiling , Wang Shenrui , Lu Xiao
Published: October 2021

Objective: Increasing evidence has uncovered the roles of lncRNA-miRNA-mRNA regulatory networks in cardiovascular diseases. However, the crosstalk between ceRNA networks and development of heart failure (HF) remains unclear. This study was to investigate the role of lncRNA-mediated ceRNA networks in the pathophysiological process of HF and its potential regulatory functions on programmed cell death.

Methods: We firstly screened the GSE77399, GSE52601 and GSE57338 datasets in the NCBI GEO database for screening differentially expressed lncRNAs, miRNAs and mRNAs. lncRNA-miRNA-mRNA regulatory networks based on the ceRNA theory were subsequently constructed. GO and KEGG enrichment analysis was conducted to predict potential biological functions of mRNAs in ceRNA networks. Differentially expressed mRNAs were then interacted with programmed cell death related genes. lncRNA-mediated ceRNA regulatory pathways on programmed cell death were validated with qRT-PCR testing.

Results: Based on our bioinformatic analysis, two lncRNAs, eight miRNAs and 65 mRNAs were extracted to construct two lncRNAs-mediated ceRNA networks in HF. Biological processes and pathways were enriched in extracellular matrix. Seven lncRNA-mediated ceRNA regulatory pathways on programmed cell death, GAS5/miR-345-5p/ADAMTS4, GAS5/miR-18b-5p/AQP3, GAS5/miR-18b-5p/SHISA3, GAS5/miR-18b-5p/C1orf105, GAS5/miR-18b-5p/PLIN2, GAS5/miR-185-5p/LPCAT3, and GAS5/miR-29b-3p/STAT3, were finally validated.

Conclusions: Two novel ceRNA regulatory networks in HF were discovered based on our bioinformatic analysis. Based on the interaction and validation analysis, seven lncRNA GAS5-mediated ceRNA regulatory pathways were hypothesized to impact programmed cell death including seven for apoptosis, three for ferroptosis, and one for pyroptosis. Upon which, we provided novel insights and potential research plots for bridging ceRNA regulatory networks and programmed cell death in HF.
Analysis of Flexural Toppling Failure in Rock Slopes Using Discrete Element Method
Authors: Zheng Yun , Wang Runqing , Chen Congxin , Meng Fei
Published: October 2021

Flexural toppling failure is a common failure mode of natural and artificial rock slopes, which has caused serious damage to human life and property. In this work, an advanced numerical method called the Universal Distinct Element Code (UDEC) was used to study the mechanism of flexural toppling failure. In total, more than twenty slope models were built and analyzed. Two new parameters (displacement discontinuity and transition coefficient of failure surface) were introduced to present a further understanding of flexural toppling. The results show the failure zone of rock slopes subjected to flexural toppling includes two parts: the first-order instability part (FOIP) and the independent toppling zone (ITZ). The FOIP can be further divided into two subzones: the sliding zone (SZ) and the superimposed toppling zone (STZ). The occurrence of surface deformation discontinuities is the precursor to flexural toppling failure. The first displacement discontinuity occurs on the boundary between the FOIP and the ITZ. The angle, spacing, and angle of the joints, the angle of the slope has a significant influence on the stability of anti-dip bedding rock slopes. However, they do not affect the deformation and failure pattern of the slope.
Considering Teachers’ Beliefs, Motivation, and Emotions Regarding Teaching Mathematics With Digital Tools: The Effect of an In-Service Teacher Training
Authors: Reinhold Frank , Strohmaier Anselm , Finger-Collazos Zoraida , Reiss Kristina
Published: October 2021

Mathematics teachers’ motivational and emotional orientations regarding digital tools in mathematics classrooms are key aspects influencingwhetherandhowtechnology is used to teach mathematics—making the support of those characteristics one central goal for teacher education. In this article we investigated if and how a workshop-based in-service teacher training can foster teachers’ perceived value of digital media in mathematics education, their self-efficacy, and their anxiety towards teaching mathematics with digital tools. In an intervention study withN= 83 in-service teachers with varying teaching experience, we used cluster analysis based on their experience, value, self-efficacy, and anxietybeforethe intervention to determine three different teacher orientations regarding teaching mathematics with digital tools. Paired samplet-tests with pretest and posttest data revealed that for two of three clusters these beliefs, motivation, and emotions changed in a positive way during the intervention while for the third no change was found. Our study sheds light on the role of motivational and emotional orientations for the implementation of digital tools in mathematics education: it shows that these orientations can be utilized to cluster teachers on this topic and illustrates that these orientations can be successfully fostered—while individual differences may exist in the effect and success of interventions.
Type 2 Diabetes Modifies Skeletal Muscle Gene Expression Response to Gastric Bypass Surgery
Authors: Barberio Matthew D. , Dohm G. Lynis , Pories Walter J. , Gadaleta Natalie A. , Houmard Joseph A. , Nadler Evan P. , Hubal Monica J.
Published: October 2021

Introduction

Roux-en-Y gastric bypass (RYGB) is an effective treatment for type 2 diabetes mellitus (T2DM) that can result in remission of clinical symptoms, yet mechanisms for improved skeletal muscle health are poorly understood. We sought to define the impact of existing T2DM on RYGB-induced muscle transcriptome changes.

Methods

Vastus lateralis biopsy transcriptomes were generated pre- and 1-year post-RYGB in black adult females with (T2D; n = 5, age = 51 ± 6 years, BMI = 53.0 ± 5.8 kg/m2) and without (CON; n = 7, 43 ± 6 years, 51.0 ± 9.2 kg/m2) T2DM. Insulin, glucose, and HOMA-IR were measured in blood at the same time points. ANCOVA detected differentially expressed genes (p < 0.01, fold change < |1.2|), which were used to identify enriched biological pathways.

Results

Pre-RYGB, 95 probes were downregulated with T2D including subunits of mitochondrial complex I. Post-RYGB, the T2D group had normalized gene expression when compared to their non-diabetic counterparts with only three probes remaining significantly different. In the T2D, we identified 52 probes upregulated from pre- to post-RYGB, including NDFUB7 and NDFUA1.

Conclusion

Black females with T2DM show extensive downregulation of genes across aerobic metabolism pathways prior to RYGB, which resolves 1 year post-RYGB and is related to improvements in clinical markers. These data support efficacy of RYGB for improving skeletal muscle health, especially in patients with T2DM.
Interaction of Severe Acute Respiratory Syndrome Coronavirus 2 and Diabetes
Authors: Shao Shiying , Yang Qin , Pan Ruping , Yu Xuefeng , Chen Yong
Published: October 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a worldwide epidemic. It spreads very fast and hits people of all ages, especially patients with underlying diseases such as diabetes. In this review, we focus on the influences of diabetes on the outcome of SARS-CoV-2 infection and the involved mechanisms including lung dysfunction, immune disorder, abnormal expression of angiotensin-converting enzyme 2 (ACE2), overactivation of mechanistic target of rapamycin (mTOR) signaling pathway, and increased furin level. On the other hand, SARS-CoV-2 may trigger the development of diabetes. It causes the damage of pancreatic β cells, which is probably mediated by ACE2 protein in the islets. Furthermore, SARS-CoV-2 may aggravate insulin resistance through attacking other metabolic organs. Of note, certain anti-diabetic drugs (OADs), such as peroxisome proliferator-activated receptor γ (PPARγ) activator and glucagon-like peptide 1 receptor (GLP-1R) agonist, have been shown to upregulate ACE2 in animal models, which may increase the risk of SARS-CoV-2 infection. However, Metformin, as a first-line medicine for the treatment of type 2 diabetes mellitus (T2DM), may be a potential drug benefiting diabetic patients with SARS-CoV-2 infection, probably via a suppression of mTOR signaling together with its anti-inflammatory and anti-fibrosis function in lung. Remarkably, another kind of OADs, dipeptidyl Peptidase 4 (DPP4) inhibitor, may also exert beneficial effects in this respect, probably via a prevention of SARS-CoV-2 binding to cells. Thus, it is of significant to identify appropriate OADs for the treatment of diabetes in the context of SARS-CoV-2 infections.
Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs
Authors: Guevara Elaine E. , Greene Lydia K. , Blanco Marina B. , Farmer Casey , Ranaivonasy Jeannin , Ratsirarson Joelisoa , Mahefarisoa Karine L. , Rajaonarivelo Tsiky , Rakotondrainibe Hajanirina H. , Junge Randall E. , Williams Cathy V. , Rambeloson Elodi , Rasoanaivo Hoby A. , Rahalinarivo Vololonirina , Andrianandrianina Laza H. , Clayton Jonathan B. , Rothman Ryan S. , Lawler Richard R. , Bradley Brenda J. , Yoder Anne D.
Published: October 2021

The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
Omics and Computational Modeling Approaches for the Effective Treatment of Drug-Resistant Cancer Cells
Authors: Jung Hae Deok , Sung Yoo Jin , Kim Hyun Uk
Published: October 2021

Chemotherapy is a mainstream cancer treatment, but has a constant challenge of drug resistance, which consequently leads to poor prognosis in cancer treatment. For better understanding and effective treatment of drug-resistant cancer cells, omics approaches have been widely conducted in various forms. A notable use of omics data beyond routine data mining is to use them for computational modeling that allows generating useful predictions, such as drug responses and prognostic biomarkers. In particular, an increasing volume of omics data has facilitated the development of machine learning models. In this mini review, we highlight recent studies on the use of multi-omics data for studying drug-resistant cancer cells. We put a particular focus on studies that use computational models to characterize drug-resistant cancer cells, and to predict biomarkers and/or drug responses. Computational models covered in this mini review include network-based models, machine learning models and genome-scale metabolic models. We also provide perspectives on future research opportunities for combating drug-resistant cancer cells.
Tracking the Evolutionary Trends Among Small-Size Fishes of the Genus Pyrrhulina (Characiforme, Lebiasinidae): New Insights From a Molecular Cytogenetic Perspective
Authors: de Moraes Renata Luiza Rosa , Sassi Francisco de Menezes Cavalcante , Bertollo Luiz Antonio Carlos , Marinho Manoela Maria Ferreira , Viana Patrik Ferreira , Feldberg Eliana , Oliveira Vanessa Cristina Sales , Deon Geize Aparecida , Al-Rikabi Ahmed B. H. , Liehr Thomas , Cioffi Marcelo de Bello
Published: October 2021

Miniature fishes have always been a challenge for cytogenetic studies due to the difficulty in obtaining chromosomal preparations, making them virtually unexplored. An example of this scenario relies on members of the family Lebiasinidae which include miniature to medium-sized, poorly known species, until very recently. The present study is part of undergoing major cytogenetic advances seeking to elucidate the evolutionary history of lebiasinids. Aiming to examine the karyotype diversification more deeply in Pyrrhulina, here we combined classical and molecular cytogenetic analyses, including Giemsa staining, C-banding, repetitive DNA mapping, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) to perform the first analyses in five Pyrrhulina species (Pyrrhulina aff. marilynae, Pyrrhulina sp., P. obermulleri, P. marilynae and Pyrrhulina cf. laeta). The diploid number (2n) ranged from 40 to 42 chromosomes among all analyzed species, but P. marilynae is strikingly differentiated by having 2n = 32 chromosomes and a karyotype composed of large meta/submetacentric chromosomes, whose plesiomorphic status is discussed. The distribution of microsatellites does not markedly differ among species, but the number and position of the rDNA sites underwent significant changes among them. Interspecific comparative genome hybridization (CGH) found a moderate divergence in the repetitive DNA content among the species’ genomes. Noteworthy, the WCP reinforced our previous hypothesis on the origin of the X1X2Y multiple sex chromosome system in P. semifasciata. In summary, our data suggest that the karyotype differentiation in Pyrrhulina has been driven by major structural rearrangements, accompanied by high dynamics of repetitive DNAs.
Suppression of Transmembrane Tumor Necrosis Factor Alpha Processing by a Specific Antibody Protects Against Colitis-Associated Cancer
Authors: Ba Hongping , Jiang Rui , Zhang Meng , Yin Bingjiao , Wang Jing , Li Zhuoya , Li Baihua , Zhou Xiaoxi
Published: October 2021

Soluble tumor necrosis factor-α (sTNF-α) plays an important role in colitis-associated cancer (CAC); however, little is known about transmembrane TNF-α (tmTNF-α). Here, we observed an increase in sTNF-α mainly in colitis tissues from an azoxymethane/dextran sodium sulfate (DSS)-induced CAC mouse model whereas tmTNF-α levels were chiefly increased on epithelial cells at the tumor stage. The ratio of intracolonic tmTNF-α/sTNF-α was negatively correlated with the levels of pro-inflammatory mediators (IL-1β, IL-6, and NO) and M1 macrophages but positively correlated with the infiltration of myeloid-derived suppressor cells, regulatory T cells, and the level of the anti-inflammatory cytokine IL-10, suggesting an anti-inflammatory effect of tmTNF-α. This effect of tmTNF-α was confirmed again by the induction of resistance to LPS in colonic epithelial cell lines NCM460 and HCoEpiC through the addition of exogenous tmTNF-α or transfection of the tmTNF-α leading sequence that lacks the extracellular segment but retains the intracellular domain of tmTNF-α. A tmTNF-α antibody was used to block tmTNF-α shedding after the first or second round of inflammation induction by DSS drinking to shift the time window of tmTNF-α expression ahead to the inflammation stage. Antibody treatment significantly alleviated inflammation and suppressed subsequent adenoma formation, accompanied by increased apoptosis. An antitumor effect was also observed when the antibody was administered at the malignant phase of CAC. Our results reveal tmTNF-α as a novel molecular marker for malignant transformation in CAC and provide a new insight into blocking the pathological process by targeting tmTNF-α processing.
A Comprehensive Review on the Role of Genetic Factors in Neuromyelitis Optica Spectrum Disorder
Authors: Ghafouri-Fard Soudeh , Azimi Tahereh , Taheri Mohammad
Published: October 2021

Neuromyelitis optica spectrum disorders (NMOSD) comprise a variety of disorders being described by optic neuritis and myelitis. This disorder is mostly observed in sporadic form, yet 3% of cases are familial NMO. Different series of familial NMO cases have been reported up to now, with some of them being associated with certain HLA haplotypes. Assessment of HLA allele and haplotypes has also revealed association between some alleles within HLA-DRB1 or other loci and sporadic NMO. More recently, genome-wide SNP arrays have shown some susceptibility loci for NMO. In the current manuscript, we review available information about the role of genetic factors in NMO.
Methyltransferase-Deficient Avian Flaviviruses Are Attenuated Due to Suppression of Viral RNA Translation and Induction of a Higher Innate Immunity
Authors: Wu Xuedong , Zhang Yuetian , Wang Mingshu , Chen Shun , Liu Mafeng , Zhu Dekang , Zhao Xinxin , Wu Ying , Yang Qiao , Zhang Shaqiu , Huang Juan , Ou Xumin , Zhang Ling , Liu Yunya , Yu Yanling , Gao Qun , Mao Sai , Sun Di , Tian Bin , Yin Zhongqiong , Jing Bo , Cheng Anchun , Jia Renyong
Published: October 2021

The 5’ end of the flavivirus genome contains a type 1 cap structure formed by sequential N-7 and 2’-O methylations by viral methyltransferase (MTase). Cap methylation of flavivirus genome is an essential structural modification to ensure the normal proliferation of the virus. Tembusu virus (TMUV) (genus Flavivirus) is a causative agent of duck egg drop syndrome and has zoonotic potential. Here, we identified the in vitro activity of TMUV MTase and determined the effect of K61-D146-K182-E218 enzymatic tetrad on N-7 and 2’-O methylation. The entire K61-D146-K182-E218 motif is essential for 2’-O MTase activity, whereas N-7 MTase activity requires only D146. To investigate its phenotype, the single point mutation (K61A, D146A, K182A or E218A) was introduced into TMUV replicon (pCMV-Rep-NanoLuc) and TMUV infectious cDNA clone (pACYC-TMUV). K-D-K-E mutations reduced the replication ability of replicon. K61A, K182A and E218A viruses were genetically stable, whereas D146A virus was unstable and reverted to WT virus. Mutant viruses were replication and virulence impaired, showing reduced growth and attenuated cytopathic effects and reduced mortality of duck embryos. Molecular mechanism studies showed that the translation efficiency of mutant viruses was inhibited and a higher host innate immunity was induced. Furthermore, we found that the translation inhibition of MTase-deficient viruses was caused by a defect in N-7 methylation, whereas the absence of 2’-O methylation did not affect viral translation. Taken together, our data validate the debilitating mechanism of MTase-deficient avian flavivirus and reveal an important role for cap-methylation in viral translation, proliferation, and escape from innate immunity.
Similarities and Differences in the Acute-Phase Response to SARS-CoV-2 in Rhesus Macaques and African Green Monkeys
Authors: Coleman Celeste , Doyle-Meyers Lara A. , Russell-Lodrigue Kasi E. , Golden Nadia , Threeton Breanna , Song Kejing , Pierre Genevieve , Baribault Carl , Bohm Rudolf P. , Maness Nicholas J. , Kolls Jay K. , Rappaport Jay , Mudd Joseph C.
Published: October 2021

Understanding SARS-CoV-2 immune pathology is critical for the development of effective vaccines and treatments. Here, we employed unbiased serial whole-blood transcriptome profiling by weighted gene network correlation analysis (WGCNA) at pre-specified timepoints of infection to understand SARS-CoV-2-related immune alterations in a cohort of rhesus macaques (RMs) and African green monkeys (AGMs) presenting with varying degrees of pulmonary pathology. We found that the bulk of transcriptional changes occurred at day 3 post-infection and normalized to pre-infection levels by 3 weeks. There was evidence of coordination of transcriptional networks in blood (defined by WGCNA) and the nasopharyngeal SARS-CoV-2 burden as well as the absolute monocyte count. Pathway analysis of gene modules revealed prominent regulation of type I and type II interferon stimulated genes (ISGs) in both RMs and AGMs, with the latter species exhibiting a greater breadth of ISG upregulation. Notably, pathways relating to neutrophil degranulation were enriched in blood of SARS-CoV-2 infected AGMs, but not RMs. Our results elude to hallmark similarities as well as differences in the RM and AGM acute response to SARS-CoV-2 infection, and may help guide the selection of particular NHP species in modeling aspects of COVID-19 disease outcome.
TNF Patterns and Tumor Microenvironment Characterization in Head and Neck Squamous Cell Carcinoma
Authors: Long Qian , Huang Chunyu , Meng Qi , Peng Jin , Yao Fan , Du Dingfu , Wang Xiaonan , Zhu Wancui , Shi Dingbo , Xu Xiangdong , Qi Xiang , Deng Wuguo , Chen Miao , Li Yizhuo , Yang Ankui
Published: October 2021

Background

HNSCC is a heterogeneous disease, which arises from distinct anatomic subsites, associates with various risk factors and possesses diverse molecular pathological features. Generally, HNSCC is considered as an immunosuppressive disease, characterized by abnormal tumor immune microenvironment. The TNF family plays a crucial role in the survival, proliferation, differentiation, and effector functions in both immune and non-immune cells. However, the expression patterns of TNF in HNSCC remains to be systematically analyzed.

Methods

We downloaded transcriptional profile data of HNSCC from TCGA and GEO datasets. Unsupervised clustering methods were used to identify different TNF patterns and classify patients for further analysis. PCA was conducted to construct a TNF relevant score, which we called risk score.

Results

In this study, we systematically evaluated the patterns of TNF family and tumor immune microenvironment characteristics of HNSCC patients by clustering the expression of 46 members of TNF family. We identified two subtypes with distinct clinical and immune characteristics in HNSCC and constructed a risk scoring system based on the expression profile of TNF family genes.

Conclusion

Risk score serves as a reliable predictor of overall survival, clinical characteristics, and immune cell infiltration, which has the potential to be applied as a valuable biomarker for HNSCC immunotherapy.
Expression Regulation and Function of T-Bet in NK Cells
Authors: Huang Chen , Bi Jiacheng
Published: October 2021

Natural killer (NK) cells are cytotoxic innate lymphocytes that play an important role in immune surveillance. The development, maturation and effector functions of NK cells are orchestrated by the T-box transcription factor T-bet, whose expression is induced by cytokines such as IFN-γ, IL-12, IL-15 and IL-21 through the respective cytokine receptors and downstream JAK/STATs or PI3K-AKT-mTORC1 signaling pathways. In this review, we aim to discuss the expression and regulation of T-bet in NK cells, the role of T-bet in mouse NK cell development, maturation, and function, as well as the role of T-bet in acute, chronic infection, inflammation, autoimmune diseases and tumors.
Species That Fly at a Higher Game: Patterns of Deep–Water Emergence Along the Chilean Coast, Including a Global Review of the Phenomenon
Authors: Häussermann Vreni , Ballyram Stacy Anushka , Försterra Günter , Cornejo Claudio , Ibáñez Christian M. , Sellanes Javier , Thomasberger Aris , Espinoza Juan Pablo , Beaujot Francine
Published: October 2021

Deep-water emergence (DWE) is the phenomenon where marine species normally found at great depths (i.e., below 200 m), can be found locally occurring in significantly shallower depths (i.e., euphotic zone, usually shallower than 50 m). Although this phenomenon has been previously mentioned and deep-water emergent species have been described from the fjord regions of North America, Scandinavia, and New Zealand, local or global hypotheses to explain this phenomenon have rarely been tested. This publication includes the first literature review on DWE. Our knowledge of distribution patterns of Chilean marine invertebrates is still very scarce, especially from habitats below SCUBA diving depth. In our databases, we have been gathering occurrence data of more than 1000 invertebrate species along the Chilean coast, both from our research and from the literature. We also distributed a list of 50 common and easilyin situ-identifiable species among biologically experienced sport divers along the Chilean coast and recorded their sighting reports. Among other findings, the analysis of the data revealed patterns from 28 species and six genera with similar longitudinal and bathymetric distribution along the entire Chilean coast: along the Chilean coast these species are typically restricted to deep water (>200 m) but only in some parts of Chilean Patagonia (>39°S–56°S), the same species are also common to locally abundant at diving depths (<30 m). We found 28 of these ‘deep’ species present in shallow-water of North Patagonia, 32 in Central Patagonia and 12 in South Patagonia. The species belong to the phyla Cnidaria (six species), Mollusca (four species), Arthropoda (two species) and Echinodermata (16 species). We ran several analyses comparing depth distribution between biogeographic regions (two-way ANOVA) and comparing abiotic parameters of shallow and deep sites to search for correlations of distribution with environmental variables (Generalized Linear Models). For the analyses, we used a total of 3328 presence points and 10635 absence points. The results of the statistical analysis of the parameters used, however, did not reveal conclusive results. We summarize cases from other fjord regions and discuss hypotheses of DWE from the literature for Chilean Patagonia.
New Arsenite Oxidase Gene (aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing
Authors: Hu Min , Li Fangbai , Qiao Jiangtao , Yuan Chaolei , Yu Huanyun , Zhuang Li
Published: October 2021

Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5′-ATC TGG GGB AAY RAC AAY TA−3′) and 1548R (5′-TTC ATB GAS GTS AGR TTC AT−3′), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.
A High-Throughput Assay for Quantifying Phenotypic Traits of Microalgae
Authors: Argyle Phoebe A. , Hinners Jana , Walworth Nathan G. , Collins Sinead , Levine Naomi M. , Doblin Martina A.
Published: October 2021

High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell size, granularity, chlorophyll a, neutral lipid content, silicification, reactive oxygen species accumulation, and photophysiology parameters: ETRmax, Ik, and alpha) into one workflow. We demonstrate the utility of the QPA onThalassiosiraspp., a cosmopolitan marine diatom, phenotyping six strains in a standard nutrient rich environment (f/2 media) using the full 10-trait assay. The multivariate phenotypes of strains can be simplified into two dimensions using principal component analysis, generating a trait-scape. We determine that traits show a consistent pattern when grown in small volume compared to more typical large volumes. The QPA can thus be used for quantifying traits across different growth environments without requiring exhaustive large-scale culturing experiments, which facilitates experiments on trait plasticity. We confirm that this assay can be used to phenotype newly isolated diatom strains within 4 weeks of isolation. The QPA described here is highly amenable to customisation for other traits or unicellular taxa and provides a framework for designing high-throughput experiments. This method will have applications in experimental evolution, modelling, and for commercial applications where screening of phytoplankton traits is of high importance.
Lactiplantibacillus plantarum–Nomad and Ideal Probiotic
Authors: Fidanza Mario , Panigrahi Pinaki , Kollmann Tobias R.
Published: October 2021

Probiotics are increasingly recognized as capable of positively modulating several aspects of human health. There are numerous attributes that make an ideal probiotic. Lactiplantibacillus plantarum (Lp) exhibits an ecological and metabolic flexibility that allows it to thrive in a variety of environments. The present review will highlight the genetic and functional characteristics of Lp that make it an ideal probiotic and summarizes the current knowledge about its potential application as a prophylactic or therapeutic intervention.
The Antiviral Effect of Novel Steroidal Derivatives on Flaviviruses
Authors: Zhang Luping , Zhou Dengyuan , Li Qiuyan , Zhu Shuo , Imran Muhammad , Duan Hongyu , Cao Shengbo , Ke Shaoyong , Ye Jing
Published: October 2021

Flaviviruses are the major emerging arthropod-borne pathogens globally. However, there is still no practical anti-flavivirus approach. Therefore, existing and emerging flaviviruses desperately need active broad-spectrum drugs. In the present study, the antiviral effect of steroidal dehydroepiandrosterone (DHEA) and 23 synthetic derivatives against flaviviruses such as Japanese encephalitis virus (JEV), Zika virus (ZIKV), and Dengue virus (DENV) were appraised by examining the characteristics of virus infection both in vitro and in vivo. Our results revealed that AV1003, AV1004 and AV1017 were the most potent inhibitors of flavivirus propagation in cells. They mainly suppress the viral infection in the post-invasion stage in a dose-dependent manner. Furthermore, orally administered compound AV1004 protected mice from lethal JEV infection by increasing the survival rate and reducing the viral load in the brain of infected mice. These results indicate that the compound AV1004 might be a potential therapeutic drug against JEV infection. These DHEA derivatives may provide lead scaffolds for further design and synthesis of potential anti-flavivirus potential drugs.