bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct Stromal and Immune Features Collectively Contribute to Long-Term Survival in Pancreatic Cancer
Authors: Sadozai Hassan , Acharjee Animesh , Eppenberger-Castori Serenella , Gloor Beat , Gruber Thomas , Schenk Mirjam , Karamitopoulou Eva
Published: February 2021

Background: The aggressive biology and treatment refractory nature of pancreatic ductal adenocarcinoma (PDAC) significantly limits long-term survival. Examining the tumor microenvironment (TME) of long-term survivors (LTS) of PDAC offers the potential of unveiling novel biological insights and therapeutic targets.

Methods: We performed an integrated approach involving immunophenotyping, stromal scoring and histomorphological profiling of a cohort of 112 PDAC-cases, including 25 long-term survivors (LTSs, OS ≥ 60 months). Mutational frequencies were assessed using targeted next generation sequencing. Finally, we validated our findings in silico using an external cohort of microarray data from PDAC patients.

Results: LTS cases exhibit a largely quiescent population of cancer-associated fibroblasts (CAFs). Immune profiling revealed key differences between LTS and NON-LTS cases in the intratumoral and stromal compartments. In both compartments, LTS cases exhibit a T cell inflamed profile with higher density of CD3+ T cells, CD4+ T cells, iNOS+ leukocytes and strikingly diminished numbers of CD68+ total macrophages, CD163+ (M2) macrophages and FOXP3+ Tregs. A large proportion of LTS cases exhibited tertiary lymphoid tissue (TLT) formation, which has been observed to be a positive prognostic marker in a number of tumor types. Using a Random-Forest variable selection approach, we identified the density of stromal iNOS+ cells and CD68+ cells as strong positive and negative prognostic variables, respectively. In an external cohort, computational cell-type deconvolution revealed a higher abundance of T cells, B lymphocytes and dendritic cells (DCs) in patients with long-term OS compared to short-term survivors. Thus, in silico profiling of long-term survivors in an external cohort, strongly corroborated the T cell-inflamed TME observed in our LTS group.

Conclusions: Collectively, our findings highlight the prognostic importance of TME profiles in PDAC, underlining the crucial role of tumor associated macrophages (TAMs) and the potential interdependence between immunosuppressive TAMs and activated CAFs in pancreatic cancer. Additionally, our data has potential for precision medicine and patient stratification. Patients with a T cell inflamed TME might derive benefit from agonistic T cell antibodies (e.g., OX40 or CD137 agonists). Alternately, patients with activated CAFs and high infiltration of immunosuppressive TAMs are highly likely to exhibit therapeutic responses to macrophage targeted drugs (e.g., anti-CSF1R) and anti-CAF agents.
Advances in Human Immune System Mouse Models for Personalized Treg-Based Immunotherapies
Authors: Serr Isabelle , Kral Maria , Scherm Martin G. , Daniel Carolin
Published: February 2021

Immunodeficient mice engrafted with a functional human immune system [Human immune system (HIS) mice] have paved the way to major advances for personalized medicine and translation of immune-based therapies. One prerequisite for advancing personalized medicine is modeling the immune system of individuals or disease groups in a preclinical setting. HIS mice engrafted with peripheral blood mononuclear cells have provided fundamental insights in underlying mechanisms guiding immune activation vs. regulation in several diseases including cancer. However, the development of Graft-vs.-host disease restrains relevant long-term studies in HIS mice. Alternatively, engraftment with hematopoietic stem cells (HSCs) enables mimicking different disease stages, however, low frequencies of HSCs in peripheral blood of adults impede engraftment efficacy. One possibility to overcome those limitations is the use of patient-derived induced pluripotent stem cells (iPSCs) reprogrammed into HSCs, a challenging process which has recently seen major advances. Personalized HIS mice bridge research in mice and human diseases thereby facilitating the translation of immunomodulatory therapies. Regulatory T cells (Tregs) are important mediators of immune suppression and thereby contribute to tumor immune evasion, which has made them a central target for cancer immunotherapies. Importantly, studying Tregs in the human immune systemin vivoin HIS mice will help to determine requirements for efficient Treg-targeting. In this review article, we discuss advances on personalized HIS models using reprogrammed iPSCs and review the use of HIS mice to study requirements for efficient targeting of human Tregs for personalized cancer immunotherapies.
Crab Diets Differ Between Adjacent Estuaries and Habitats Within a Sheltered Marine Embayment
Authors: Campbell Theo I. , Tweedley James R. , Johnston Danielle J. , Loneragan Neil R.
Published: February 2021

Portunid crabs contribute to significant commercial and recreational fisheries globally and are commonly fished in estuaries and/or marine embayments, which are amongst the most degraded of all aquatic ecosystems. Portunus armatus were collected seasonally between April and February from five locations across three systems in temperate south-western Australia. The dietary composition of crabs was quantified and compared between two estuaries (Peel-Harvey and Swan-Canning) and a sheltered marine embayment (Cockburn Sound) containing three distinct habitats: shallow seagrass, shallow sand and deep sand. Overall, crabs ingested large volumes of bivalves (both live organisms and dead shell), polychaetes, crustaceans (e.g., amphipods, small decapods), and smaller volumes of teleosts, echinoderms and plant material (seagrass, algae). Analysis of Similarities showed that dietary composition varied significantly among the five locations (two estuaries and three habitats within Cockburn Sound) and seasons, with greater location than seasonal differences in the two estuaries. Diets were most distinct in the Cockburn Sound seagrass due to greater volumes of decapods and teleosts and smaller volumes of bivalve shell consumed in this habitat. Crabs from both estuaries consumed greater quantities of bivalves than those from Cockburn Sound. Seasonal differences in both estuaries were greatest between summer and winter, with a more diverse range of prey and large quantities of bivalves ingested in summer, whereas small bivalves and bivalve shell in the Peel-Harvey and polychaetes and other crustaceans in the Swan-Canning, were consumed in greater quantities in winter. The summer diet in the Peel-Harvey Estuary in the current study was compared to that 20 years previous and with documented change in the benthic macroinvertebrate fauna. Currently, crabs consume smaller volumes of high-calorie prey, i.e., polychaetes, small bivalves and teleosts, and instead ingest greater proportions of calcareous material than previously. This marked shift in dietary composition parallels changes in benthic macroinvertebrates in the Peel-Harvey Estuary. Overall, prey availability appears to be the major factor influencing the spatial and temporal differences in P. armatus diets in these three coastal systems.
Warming Iron-Limited Oceans Enhance Nitrogen Fixation and Drive Biogeographic Specialization of the Globally Important Cyanobacterium Crocosphaera
Authors: Yang Nina , Merkel Carlin A. , Lin Yu-An , Levine Naomi M. , Hawco Nicholas J. , Jiang Hai-Bo , Qu Ping-Ping , DeMers Michelle A. , Webb Eric A. , Fu Fei-Xue , Hutchins David A.
Published: February 2021

Primary productivity in the nutrient-poor subtropical ocean gyres depends on new nitrogen inputs from nitrogen fixers that convert inert dinitrogen gas into bioavailable forms. Temperature and iron (Fe) availability constrain marine nitrogen fixation, and both are changing due to anthropogenic ocean warming. We examined the physiological responses of the globally important marine nitrogen fixer, Crocosphaera watsonii across its full thermal range as a function of iron availability. At the lower end of its thermal range, from 22 to 27°C, Crocosphaera growth, nitrogen fixation, and Nitrogen-specific Iron Use Efficiencies (N-IUEs, mol N fixed hour–1 mol Fe–1) increased with temperature. At an optimal growth temperature of 27°C, N-IUEs were 66% higher under iron-limited conditions than iron-replete conditions, indicating that low-iron availability increases metabolic efficiency. However, Crocosphaera growth and function decrease from 27 to 32°C, temperatures that are predicted for an increasing fraction of tropical oceans in the future. Altogether, this suggests that Crocosphaera are well adapted to iron-limited, warm waters, within prescribed limits. A model incorporating these results under the IPCC RCP 8.5 warming scenario predicts that Crocosphaera N-IUEs could increase by a net 47% by 2100, particularly in higher-latitude waters. These results contrast with published responses of another dominant nitrogen fixer (Trichodesmium), with predicted N-IUEs that increase most in low-latitude, tropical waters. These models project that differing responses of Crocosphaera and Trichodesmium N-IUEs to future warming of iron-limited oceans could enhance their current contributions to global marine nitrogen fixation with rates increasing by ∼91 and ∼22%, respectively, thereby shifting their relative importance to marine new production and also intensifying their regional divergence. Thus, interactive temperature and iron effects may profoundly transform existing paradigms of nitrogen biogeochemistry and primary productivity in open ocean regimes.
Tailoring Scaffolds for Orthopedic Application With Anti-Microbial Properties: Current Scenario and Future Prospects
Authors: Preethi A. , Bellare Jayesh R.
Published: February 2021

Research in the orthopedic application has attracted the scientific community to design and develop advanced, engineered synthetic scaffolds that possess all the essential cues properties necessary for successful regeneration and restoration of tissue function. Despite having the best surgical practices, nosocomial infections like surgical site infections can negatively impact the outcome of the scaffolds that are intended only for regenerative purposes. Therefore, there is a need to include anti-microbial properties as one of the parameters while designing a scaffold. There are various methods implemented to tackle microbial colonization such as modifying the scaffold surface that deflects microbes from surface adhesion and modifying the scaffold surface by inactivating microbes upon contact while maintaining the biocompatibility of the scaffold and also maintaining the scaffold viable for new bone formation. This review lists various anti-microbial polymers and compounds available in nature and methods to incorporate them into the scaffold with polymer and ceramics as the base material, without compromising bioactivity. We have reviewed various anti-microbial compounds, biomaterials and have also identified various biomolecules (vitamins, phytochemicals and anti-microbial peptides) that can be utilized for orthopedic application.
Experimental Study of a Variable Stiffness Seat Suspension Installed With a Compact Rotary MR Damper
Authors: Sun Shuaishuai , Yang Jian , Wang Penghui , Nakano Masami , Shen Longjiang , Zhang Shiwu , Li Weihua
Published: February 2021

Traditional MR seat suspension without stiffness control is not able to avoid the resonance between the excitation and the seat, though it can dampen the vibration energy. To solve this problem, this paper proposed a variable stiffness (VS) magnetorheological (MR) damper to implement an advanced seat suspension. Its natural frequency can be shifted away from the excitation frequency through the variations of stiffness, thereby realizing the non-resonance control. The new seat suspension is designed and prototyped first, and then its dynamic property under different energizing current, excitation amplitude, and excitation frequency was tested using an MTS machine. The testing results verified its stiffness controllability. The vibration attenuation performance of the seat suspension was also evaluated on a vibration shaking table. The vibration reduction performance of the seat suspension was evaluated under two kinds of excitations, i.e., harmonic excitation and random excitation; the experimental results indicate that the new seat suspension outperforms passive seat suspensions regarding their ride comfort.
Texturing of Glass Surface using Micro-slurry Jet Machining Process
Authors: Yamaguchi Hajime , Sakata Koshi , Kasamura Keiji , Nakashima Yuta , Nakanishi Yoshitaka
Published: February 2021

Existing methods for the microfabrication of convex structures on a glass surface require a complex and expensive masking process. In this study, a simple microfabrication method that combines the masking process using polyimide tapes and a micro-slurry jet (MSJ) process was developed. The masking process was performed using a CO₂ laser machine, and the surface of the processed glass was observed using a three-dimensional laser microscope. Although the geometric shape of the mask was not a perfect circle, convex structures with a diameter of approximately 1.0 mm and heights of more than 1.5 μm were formed on soda-lime glass surfaces. The deepest structures were observed to create convex structures with a height of 19 µm. The effects of the travel speed of the nozzle and number of repetitions of the MSJ process on the height of the convex structures on the glass surface were also investigated. It was found that the masking process combining polyimide tapes and the MSJ process could form high-convexity structures on the glass surface. The proposed method is expected to enable the fabrication of devices with various functional properties for materials that cannot be processed using existing methods.
Adjunctive Immunotherapy With Polyclonal Ig-M Enriched Immunoglobulins for Septic Shock: From Bench to Bedside. The Rationale for a Personalized Treatment Protocol
Authors: Busani Stefano , Roat Erika , Tosi Martina , Biagioni Emanuela , Coloretti Irene , Meschiari Marianna , Gelmini Roberta , Brugioni Lucio , De Biasi Sara , Girardis Massimo
Published: February 2021

Septic shock still has a high mortality rate which has not hinted at decreasing in recent years. Unfortunately, randomized trials failed mainly because the septic patient was considered as a homogeneous entity. All this creates a sort of therapeutic impotence in everyday clinical practice in treating patients with septic shock. The need to customize therapy on each patient with sepsis has now become an established necessity. In this scenario, adjuvant therapies can help if interpreted as modulators of the immune system. Indeed, the host's immune response differs from patient to patient based on the virulence of the pathogen, comorbidity, infection site, and prolonged hospitalization. In this review, we summarize the rationale for using immunoglobulins as an adjunctive treatment. Furthermore, we would like to suggest a possible protocol to personalize treatment in the different clinical scenarios of the host's response to serious infectious events.
Visualization and Analysis in the Field of Pan-Cancer Studies and Its Application in Breast Cancer Treatment
Authors: Zhang Xianwen , Lai Han , Zhang Fan , Wang Yixi , Zhang Li , Yang Ni , Wang Chunrong , Liang Zheng , Zeng Jieping , Yang Jinrong
Published: February 2021

Although all cancers are molecularly distinct, many share common driver mutations. Pan-cancer analysis, utilizes next-generation sequencing (NGS), pan-cancer model systems, and pan-cancer projects such as The Cancer Genome Atlas (TCGA), to assess frequently mutated genes and other genomic abnormalities that are common among many cancer types, regardless of the tumor origin, providing new directions for tumor biology research. However, there is currently no study that has objectively analyzed the results of pan-cancer studies on cancer biology. For this study, 999 articles on pan-cancer published from 2006 to 2020 were obtained from the Scopus database, and bibliometric methods were used to analyze citations, international cooperation, co-authorship and keyword co-occurrence clusters. Furthermore, we also focused on and summarized the application of pan-cancer in breast cancer. Our result shows that the pan-cancer studies were first published in 2006 and entered a period of rapid development after 2013. So far, 86 countries have carried out international cooperation in sharing research. Researchers form the United States and Canada have published the most articles and have made the most extensive contribution to this field, respectively. Through author keyword analysis of the 999 articles, TCGA, biomarkers, NGS, immunotherapy, DNA methylation, prognosis, and several other keywords appear frequently, and these terms are hot spots in pan-cancer studies. There are four subtypes of breast cancer (luminalA, luminalB, HER2, and basal-like) according to pan-cancer analysis of breast cancer. Meanwhile, it was found that breast cancer has genetic similarity to pan-gynecological cancers, such as ovarian cancer, which indicates related etiology and possibly similar treatments. Collectively, with the emergence of new detection methods, new cancer databases, and the involvement of more researchers, pan-cancer analyses will play a greater role in cancer biology research.
Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean
Authors: Wang Yayu , Liao Shuilin , Gai Yingbao , Liu Guilin , Jin Tao , Liu Huan , Gram Lone , Strube Mikael Lenz , Fan Guangyi , Sahu Sunil Kumar , Liu Shanshan , Gan Shuheng , Xie Zhangxian , Kong Lingfen , Zhang Pengfan , Liu Xin , Wang Da-Zhi
Published: February 2021

Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.85 and 23.56% of relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%), Firmicutes (0.76%), Verrucomicrobia (0.36%), and Planctomycetes (0.31%). Overall, only 24.3% of functional genes were common among all sampling stations indicating a high level of gene diversity. However, the presence of 82.6% common KEGG Orthology (KOs) in all samples showed high functional redundancy across the Indian Ocean. Temperature, phosphate, silicate and pH were important environmental factors regulating the microbial distribution in the Indian Ocean. The cyanobacterial genus Prochlorococcus was abundant with an average 17.4% of relative abundance in the surface waters, and while 54 Prochlorococcus genomes were detected, 53 were grouped mainly within HLII clade. In total, 179 of 234 Prochlorococcus sequences extracted from the global ocean dataset were clustered into HL clades and exhibited less divergence, but 55 sequences of LL clades presented more divergence exhibiting different branch length. The genes encoding enzymes related to ammonia metabolism, such as urease, glutamate dehydrogenase, ammonia transporter, and nitrilase presented higher abundances than the genes involved in inorganic N assimilation in both microbial community and metagenomic Prochlorococcus population. Furthermore, genes associated with dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification and anammox were absent in metagenome Prochlorococcus population, i.e., nitrogenase and nitrate reductase. Notably, the de novo biosynthesis pathways of six different amino acids were incomplete in the metagenomic Prochlorococcus population and Prochlorococcus genomes, suggesting compensatory uptake of these amino acids from the environment. These results reveal the features of the taxonomic and functional structure of the Indian Ocean microbiome and their adaptive strategies to ambient N deficiency in the oligotrophic ocean.
Estimation of the Prevalence of Antimicrobial Resistance in Badgers (Meles meles) and Foxes (Vulpes vulpes) in Northern Ireland
Authors: O’Hagan Maria J. H. , Pascual-Linaza Ana V. , Couzens Catherine , Holmes Clare , Bell Colin , Spence Nessie , Huey Robert J. , Murphy Julie A. , Devaney Ryan , Lahuerta-Marin Angela
Published: February 2021

Antimicrobial resistant (AMR) bacteria can be shared between humans and animals, through food, water, and the environment. Wild animals are not only potential reservoirs of AMR, but are also sentinels mirroring the presence of AMR zoonotic bacteria in the environment. In Northern Ireland, little is known about levels of AMR in bacteria in wildlife, thus the current study aimed to estimate the prevalence of AMR bacteria in wildlife using wildlife species from two ongoing surveys as a proxy. Nasopharyngeal swabs and faecal samples from European badgers (Meles meles) (146 faecal samples; 118 nasal samples) and red foxes (Vulpes vulpes) (321 faecal samples; 279 nasal samples) were collected throughout Northern Ireland and were used to survey for the presence of extended spectrum beta lactamase resistant and AmpC-type beta lactamases Escherichia coli (ESBL/AmpC), Salmonella spp. (only in badgers) and methicillin resistant Staphylococcus aureus (MRSA). ESBLs were detected in 13 out of 146 badger faecal samples (8.90%) and 37 out of 321 of fox faecal samples (11.53%), all of them presenting multi-drug resistance (MDR). Fourteen out of 146 (9.59%) badger faecal samples carried Salmonella spp. [S. Agama (n = 9), S. Newport (n = 4) and S. enterica subsp. arizonae (n = 1)]. Overall, AMR was found only in the S. enterica subsp. arizonae isolate (1/14, 7.14%). No MRSA were detected in nasopharyngeal swabs from badgers (n = 118) and foxes (n = 279). This is the first attempt to explore the prevalence of AMR in the two common wildlife species in Northern Ireland. These findings are important as they can be used as a base line for further research exploring the origin of the found resistance. These results should encourage similar surveys where environmental samples are included to bring better understanding of AMR dynamics, and the impact on wildlife, domestic livestock and humans.
Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas
Authors: Pereira Higor Sette , Tagliaferri Thaysa Leite , Mendes Tiago Antônio de Oliveira
Published: February 2021

In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.
The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch
Authors: Maraci Öncü , Antonatou-Papaioannou Anna , Jünemann Sebastian , Castillo-Gutiérrez Omar , Busche Tobias , Kalinowski Jörn , Caspers Barbara A.
Published: February 2021

Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
Parametarhizium (Clavicipitaceae) gen. nov. With Two New Species as a Potential Biocontrol Agent Isolated From Forest Litters in Northeast China
Authors: Gao Siyu , Meng Wei , Zhang Lixiang , Yue Qun , Zheng Xu , Xu Lijian
Published: February 2021

A novel genus Parametarhizium with two new entomopathogenic species, Parametarhizium changbaiense and Parametarhizium hingganense, was introduced based on their morphological characteristics and a multigene phylogenetic analysis, which were isolated from the forest litters collected in Northeast China. To infer their phylogenetic relationships, a six-gene dataset consisting of DNA fragments of [nuclear small subunit rDNA (SSU) + LSU + TUB + TEF + RPB1 + RPB2] was used for phylogenetic analysis, including 105 related fungi. The new genus Parametarhizium formed a monophyletic clade basal to Metarhizium and its related genera (formerly Metarhizium sensu lato). Parametarhizium can be morphologically distinguished from related genera by the combination of the following characteristics: formation of white to yellow colonies on different media, candelabrum-like arrangement of cylindrical or obpyriform phialides, and small subglobose to ellipsoidal conidia. Both P. hingganense and P. changbaiense exhibited anti-insect activities against three farmland pests Monolepta hieroglyphica, Callosobruchus chinensis, and Rhopalosiphum maidis. This is the first report of entomopathogenic fungi exhibiting the anti-insect activity against Mo. hieroglyphica.
Identification of a Putative Sensor Protein Involved in Regulation of Vesicle Production by a Hypervesiculating Bacterium, Shewanella vesiculosa HM13
Authors: Yokoyama Fumiaki , Imai Tomoya , Aoki Wataru , Ueda Mitsuyoshi , Kawamoto Jun , Kurihara Tatsuo
Published: February 2021

Bacteria secrete and utilize nanoparticles, called extracellular membrane vesicles (EMVs), for survival in their growing environments. Therefore, the amount and components of EMVs should be tuned in response to the environment. However, how bacteria regulate vesiculation in response to the extracellular environment remains largely unknown. In this study, we identified a putative sensor protein, HM1275, involved in the induction of vesicle production at high lysine concentration in a hypervesiculating Gram-negative bacterium, Shewanella vesiculosa HM13. This protein was predicted to possess typical sensing and signaling domains of sensor proteins, such as methyl-accepting chemotaxis proteins. Comparison of vesicle production between the hm1275-disrupted mutant and the parent strain revealed that HM1275 is involved in lysine-induced hypervesiculation. Moreover, HM1275 has sequence similarity to a biofilm dispersion protein, BdlA, of Pseudomonas aeruginosa PAO1, and hm1275 disruption increased the amount of biofilm. Thus, this study showed that the induction of vesicle production and suppression of biofilm formation in response to lysine concentration are under the control of the same putative sensor protein.
Synthesis of Cordyceps fumosorosea-Biochar Nanoparticles and Their Effects on Growth and Survival of Bemisia tabaci (Gennadius)
Authors: Wang Xingmin , Xu Jing , Sun Tingfei , Ali Shaukat
Published: February 2021

Nanotechnology can offer an environmentally sustainable alternative to synthetic chemicals for pest management. Nano-formulations of different microbial pest control agents have been effective against several insect pests. Synthesis of Cordyceps fumosorosea-biochar (BC) nanoparticles and their bio-efficacy against Bemisia tabaci was observed during this study. The characterization of C. fumosorosea-BC nanoparticles through different analytical techniques showed successful synthesis of nanoparticles. UV spectroscopy showed a characteristic band of surface plasmon between 350 and 400 nm; SEM images confirmed the synthesis of spherical shaped nanoparticles; X-ray diffractogram showed strong peaks between 2θ values of 20°–25°; and atomic force microscopy (AFM) analysis revealed particle size of 49.151 nm. The bioassay studies demonstrated that different concentrations of C. fumosorosea-BC nanoparticles caused significant reduction in hatchability of B. tabaci eggs as well as survival of immatures emerging from treated eggs when compared with controls. The results also revealed that C. fumosorosea-BC nanoparticles were highly pathogenic against 2nd and 3rd instar nymphs and pupae of B. tabaci having LC50 values of 6.80, 7.45, and 8.64 ppm, respectively. The LT50 values for 20 ppm concentration of C. fumosorosea-BC nanoparticles against 2nd and 3rd instar nymphs, and pupae of B. tabaci were 3.25 ± 0.29, 3.69 ± 0.52, and 4.07 ± 0.51 days, respectively. These findings suggest that C. fumosorosea-BC nanoparticles can potentially be used in biorational B. tabaci management programs.
Rotavirus Induces Epithelial–Mesenchymal Transition Markers by Transcriptional Suppression of miRNA-29b
Authors: Mukhopadhyay Urbi , Banerjee Anwesha , Chawla-Sarkar Mamta , Mukherjee Anupam
Published: February 2021

Acute gastroenteritis (AGE) is a serious global health problem and has been known to cause millions of infant deaths every year. Rotavirus (RV), a member of the Reoviridae family, still majorly accounts for the AGE in children below 5 years of age in India and worldwide. The involvement of miRNAs in the pathogenesis of RV has been suggested to be of the proviral as well as the anti-viral nature. miRNAs that promote the RV pathogenesis are capable of targeting the cellular components to evade the host anti-viral strategies. On the other hand, miRNAs with anti-rotaviral properties are themselves incapacitated during the progression of the infection. The exploitation of the epithelial–mesenchymal transition (EMT) as a pro-rotaviral strategy has already been identified. Thus, miRNAs that proficiently target the intermediates of the EMT pathway may serve as anti-viral counterparts in the RV–host interactions. The role of microRNA-29b (miR-29b) in the majority of human cancers has been well demonstrated, but its significance in viral infections is yet to be elaborated. In this study, we have assessed the role of miR-29b in RV-induced EMT and RV replication. Our study on miR-29b provides evidence for the recruitment of RV non-structural protein NSP1 to control the trans-repression of miR-29b in a p53-dependent manner. The trans-repression of miR-29b modulates the EMT pathway by targeting tripartite motif-containing protein 44 (TRIM44) and cyclin E1 (CCNE1). SLUG and SNAIL transcription repressors (downstream of TRIM44 and CCNE1) regulate the expression of E-cadherin, an important marker of the EMT. Also, it is established that ectopic expression of miR-29b not only constrains the EMT pathway but also restricts RV replication. Therefore, miR-29b repression is a crucial event in the RV pathogenesis. Ectopic expression of miR-29b displays potential anti-viral properties against RV propagation.
The Roles of Envelope Glycoprotein M in the Life Cycle of Some Alphaherpesviruses
Authors: Li Chunmei , Wang Mingshu , Cheng Anchun , Jia Renyong , Yang Qiao , Wu Ying , Zhu Dekang , Zhao Xinxin , Chen Shun , Liu Mafeng , Zhang Shaqiu , Ou Xumin , Mao Sai , Gao Qun , Sun Di , Wen Xingjian , Tian Bin
Published: February 2021

The envelope glycoprotein M (gM), a surface virion component conserved among alphaherpesviruses, is a multiple-transmembrane domain-containing glycoprotein with a complex N-linked oligosaccharide. The gM mediates a diverse range of functions during the viral life cycle. In this review, we summarize the biological features of gM, including its characterization and function in some specicial alphaherpesviruses. gM modulates the virus-induced membrane fusion during virus invasion, transports other proteins to the appropriate intracellular membranes for primary and secondary envelopment during virion assembly, and promotes egress of the virus. The gM can interact with various viral and cellular components, and the focus of recent research has also been on interactions related to gM. And we will discuss how gM participates in the life cycle of alphaherpesviruses.
Structural and Signaling Events Driving Aspergillus fumigatus-Induced Human Eosinophil Extracellular Trap Release
Authors: Barroso Marina Valente , Gropillo Isabella , Detoni Marcella A. A. , Thompson-Souza Glaucia A. , Muniz Valdirene S. , Vasconcelos Claudia Regina Isaías , Figueiredo Rodrigo T. , Melo Rossana C. N. , Neves Josiane S.
Published: February 2021

Eosinophils are granulocytes classically involved in allergic diseases and in the host immune responses to helminths, fungi, bacteria and viruses. The release of extracellular DNA traps by leukocytes is an important mechanism of the innate immune response to pathogens in various infectious conditions, including fungal infections.Aspergillus fumigatusis an opportunistic fungus responsible for allergic bronchopulmonary aspergillosis (ABPA), a pulmonary disease marked by prominent eosinophilic inflammation. Previously, we demonstrated that isolated human eosinophils release extracellular DNA traps (eosinophil extracellular traps; EETs) when stimulated byA. fumigatus in vitro. This release occurs through a lytic non-oxidative mechanism that involves CD11b and Syk tyrosine kinase. In this work, we unraveled different intracellular mechanisms that drive the release of extracellular DNA traps byA. fumigatus-stimulated eosinophils. Ultrastructurally, we originally observed thatA. fumigatus-stimulated eosinophils present typical signs of extracellular DNA trap cell death (ETosis) with the nuclei losing both their shape (delobulation) and the euchromatin/heterochromatin distinction, followed by rupture of the nuclear envelope and EETs release. We also found that by targeting class I PI3K, and more specifically PI3Kδ, the release of extracellular DNA traps induced byA. fumigatusis inhibited. We also demonstrated thatA. fumigatus-induced EETs release depends on the Src family, Akt, calcium and p38 MAPK signaling pathways in a process in which fungal viability is dispensable. Interestingly, we showed thatA. fumigatus-induced EETs release occurs in a mechanism independent of PAD4 histone citrullination. These findings may contribute to a better understanding of the mechanisms that underlie EETs release in response toA. fumigatus, which may lead to better knowledge of ABPA pathophysiology and treatment.
The Cysteine Protease MaOC1, a Prokaryotic Caspase Homolog, Cleaves the Antitoxin of a Type II Toxin-Antitoxin System
Authors: Klemenčič Marina , Halužan Vasle Ana , Dolinar Marko
Published: February 2021

The bloom-forming cyanobacterium Microcystis aeruginosa is known for its global distribution and for the production of toxic compounds. In the genome of M. aeruginosa PCC 7806, we discovered that the gene coding for MaOC1, a caspase homolog protease, is followed by a toxin-antitoxin module, flanked on each side by a direct repeat. We therefore investigated their possible interaction at the protein level. Our results suggest that this module belongs to the ParE/ParD-like superfamily of type II toxin-antitoxin systems. In solution, the antitoxin is predominantly alpha-helical and dimeric. When coexpressed with its cognate toxin and isolated from Escherichia coli, it forms a complex, as revealed by light scattering and affinity purification. The active site of the toxin is restricted to the C-terminus of the molecule. Its truncation led to normal cell growth, while the wild-type form prevented bacterial growth in liquid medium. The orthocaspase MaOC1 was able to cleave the antitoxin so that it could no longer block the toxin activity. The most likely target of the protease was the C-terminus of the antitoxin with two sections of basic amino acid residues. E. coli cells in which MaOC1 was expressed simultaneously with the toxin-antitoxin pair were unable to grow. In contrast, no effect on cell growth was found when using a proteolytically inactive MaOC1 mutant. We thus present the first case of a cysteine protease that regulates the activity of a toxin-antitoxin module, since all currently known activating proteases are of the serine type.
Functional Expression of the Human Glucose Transporters GLUT2 and GLUT3 in Yeast Offers Novel Screening Systems for GLUT-Targeting Drugs
Authors: Schmidl Sina , Tamayo Rojas Sebastian A. , Iancu Cristina V. , Choe Jun-Yong , Oreb Mislav
Published: February 2021

Human GLUT2 and GLUT3, members of the GLUT/SLC2 gene family, facilitate glucose transport in specific tissues. Their malfunction or misregulation is associated with serious diseases, including diabetes, metabolic syndrome, and cancer. Despite being promising drug targets, GLUTs have only a few specific inhibitors. To identify and characterize potential GLUT2 and GLUT3 ligands, we developed a whole-cell system based on a yeast strain deficient in hexose uptake, whose growth defect on glucose can be rescued by the functional expression of human transporters. The simplicity of handling yeast cells makes this platform convenient for screening potential GLUT2 and GLUT3 inhibitors in a growth-based manner, amenable to high-throughput approaches. Moreover, our expression system is less laborious for detailed kinetic characterization of inhibitors than alternative methods such as the preparation of proteoliposomes or uptake assays inXenopusoocytes. We show that functional expression of GLUT2 in yeast requires the deletion of the extended extracellular loop connecting transmembrane domains TM1 and TM2, which appears to negatively affect the trafficking of the transporter in the heterologous expression system. Furthermore, single amino acid substitutions at specific positions of the transporter sequence appear to positively affect the functionality of both GLUT2 and GLUT3 in yeast. We show that these variants are sensitive to known inhibitors phloretin and quercetin, demonstrating the potential of our expression systems to significantly accelerate the discovery of compounds that modulate the hexose transport activity of GLUT2 and GLUT3.
Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection
Authors: Chyży Piotr , Kulik Marta , Re Suyong , Sugita Yuji , Trylska Joanna
Published: February 2021

Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. One switch, called riboswitch N1, is regulated by aminoglycosides such as neomycin. Nucleobase mutations in the apical loop, although distant from the binding pocket, significantly affect neomycin affinity and riboswitch regulatory efficiency. To explain this influence, we conducted molecular dynamics simulations using generalized replica exchange with solute tempering (gREST). Translation assay of a reporter protein in a yeast system shows that mutating A17 to G in the riboswitch apical loop reduces 6-fold the translation regulation efficiency of the mutant. Indeed, simulations of the unbound riboswitch show that G17 frequently stacks with base 7, while base 8 is stabilized towards the binding site in a way that it may interfere with the conformational selection mechanism and decrease riboswitch regulatory activity. In the riboswitch complexes, this single-point A to G mutation disrupts a strong hydrogen bond between nucleotides 5 and 17 and, instead, a new hydrogen bond between residue 17 and neomycin is created. This change forces neomycin to occupy a slightly shifted position in the binding pocket, which increases neomycin flexibility. Our simulations of the U14C mutation suggest that the riboswitch complex with neomycin is more stable if cytosine 14 is protonated. A hydrogen bond between the RNA phosphate and protonated cytosine appears as the stabilizing factor. Also, based on the cell-free translation assay and isothermal titration calorimetry experiments, mutations of nucleotides 14 and 15 affect only slightly the riboswitch ability to bind the ligand and its activity. Indeed, the simulation of the unbound U15A mutant suggests conformations preformed for ligand binding, which may explain slightly higher regulatory activity of this mutant. Overall, our results corroborate the in vivo and in vitro experiments on the N1 riboswitch-neomycin system, detail the relationship between nucleobase mutations and RNA dynamics, and reveal the conformations playing the major role in the conformational selection mechanism.
Extracellular Vesicles From 3xTg-AD Mouse and Alzheimer’s Disease Patient Astrocytes Impair Neuroglial and Vascular Components
Authors: González-Molina Luis Alfonso , Villar-Vesga Juan , Henao-Restrepo Julián , Villegas Andrés , Lopera Francisco , Cardona-Gómez Gloria Patricia , Posada-Duque Rafael
Published: February 2021

Astrocytes are specialized glial cells that are essential components of the neurovascular unit (NVU) and are involved in neurodevelopment, brain maintenance and repair, and neurodegeneration. Astrocytes mediate these processes by releasing cellular mediators such as extracellular vesicles (EVs). EVs are vehicles of cell-cell communication and have been proposed as mediators of damage in AD. However, the transcellular mechanism by which Alzheimer disease (AD) astrocytes impair the function of NVU components is poorly understood. Therefore, we evaluated the effects of adult PS1-KI and 3xTg-AD astrocyte conditioned media (CM) and EVs on NVU components (neuroglia and endothelium) in vitro. Additionally, SAD and FAD astrocyte-derived EVs (A-EVs) were characterized, and we evaluated their effects on NVU in cocultured cells in vitro and on intrahippocampal CA1 cells in vivo. Surprisingly, cultured 3xTg-AD astrocytes showed increased glial fibrillary acidic protein (GFAP) reactivity compared to PS1-KI astrocytes, which denotes astrocytic hyperreactivity. CM from adult mice 3xTg-AD astrocytes increased cell-cell gaps between endothelial cells, filopodia-like dendritic protrusions in neurons and neuronal and endothelial cell death. 3xTg-AD A-EVs induced neurotoxicity and increased astrocyte GFAP reactivity. Cultured human postmortem astrocytes from AD patients also increased GFAP reactivity and EVs release. No differences in the size or number of A-EVs were detected between AD and control samples; however, both SAD and FAD A-EVs showed increased expression of the surface marker aquaporin 4. A-EVs induced cytotoxicity and astrocyte hyperactivation: specifically, FAD A-EVs induced neuroglial cytotoxicity and increased gaps between the endothelium, while SAD A-EVs mainly altered the endothelium. Similarly, both AD A-EVs increased astrocyte GS reactivity and vascular deterioration in vivo. We associated this finding with perivascular reactive astrocytes and vascular deterioration in the human AD brain. In summary, these results suggest that AD A-EVs impair neuroglial and vascular components.
Loss of Integrity of Corpus Callosum White Matter Hyperintensity Penumbra Predicts Cognitive Decline in Patients With Subcortical Vascular Mild Cognitive Impairment
Authors: Qiu Yage , Yu Ling , Ge Xin , Sun Yawen , Wang Yao , Wu Xiaowei , Xu Qun , Zhou Yan , Xu Jianrong
Published: February 2021

Loss of white matter (WM) integrity contributes to subcortical vascular mild cognitive impairment (svMCI). Diffusion tensor imaging (DTI) has revealed damage beyond the area of WM hyperintensity (WMH) including in normal-appearing WM (NAWM); however, the functional significance of this observation is unclear. To answer this question, in this study we investigated the relationship between microstructural changes in the WMH penumbra (WMH-P) and cognitive function in patients with svMCI by regional tract-based analysis. A total of 111 patients with svMCI and 72 patients with subcortical ischemic vascular disease (SIVD) without cognitive impairment (controls) underwent DTI and neuropsychological assessment. WMH burden was determined before computing mean values of fractional anisotropy (FA) and mean diffusivity (MD) within WMHs and WMH-Ps. Pearson’s partial correlations were used to assess the relationship between measurements showing significant intergroup differences and composite Z-scores representing global cognitive function. Multiple linear regression analysis was carried out to determine the best model for predicting composite Z-scores. We found that WMH burden in the genu, body, and splenium of the corpus callosum (GCC, BCC, and SCC respectively); bilateral anterior, superior, and posterior corona radiata; left sagittal stratum was significantly higher in the svMCI group than in the control group (p < 0.05). The WMH burden of the GCC, BCC, SCC, and bilateral anterior corona radiata was negatively correlated with composite Z-scores. Among diffusion parameters showing significant differences across the 10 WM regions, mean FA values of WMH and WMH-P of the BCC were correlated with composite Z-scores in svMCI patients. The results of the multiple linear regression analysis showed that the FA of WMH-P of the BCC and WMH burden of the SCC and GCC were independent predictors of composite Z-score, with the FA of WMH-P of the BCC making the largest contribution. These findings indicate that disruption of the CC microstructure—especially the WMH-P of the BCC—may contribute to the cognitive deficits associated with SIVD.
Neuroimaging, Behavioral, and Gait Correlates of Fall Profile in Older Adults
Authors: Kirby Krystal M. , Pillai Sreekrishna , Brouillette Robert M. , Keller Jeffrey N. , De Vito Alyssa N. , Bernstein John P. , Van Gemmert Arend W. A. , Carmichael Owen T.
Published: February 2021

Prior research has suggested that measurements of brain functioning and performance on dual tasks (tasks which require simultaneous performance) are promising candidate predictors of fall risk among older adults. However, no prior study has investigated whether brain function measurements during dual task performance could improve prediction of fall risks and whether the type of subtasks used in the dual task paradigm affects the strength of the association between fall characteristics and dual task performance. In this study, 31 cognitively normal, community-dwelling older adults provided a self-reported fall profile (number of falls and fear of falling), completed a gait dual task (spell a word backward while walking on a GaitRite mat), and completed a supine dual task (rhythmic finger tapping with one hand while completing the AX continuous performance task (AX-CPT) with the other hand) during functional magnetic resonance imaging (fMRI). Gait performance, AX-CPT reaction time and accuracy, finger tapping cadence, and brain functioning in finger-tapping-related and AX-CPT-related brain regions all showed declines in the dual task condition compared to the single task condition. Dual-task gait, AX-CPT and finger tapping performance, and brain functioning were all independent predictors of fall profile. No particular measurement domain stood out as being the most strongly associated measure with fall variables. Fall characteristics are determined by multiple factors; brain functioning, motor task, and cognitive task performance in challenging dual-task conditions all contribute to the risk of falling.