bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomics Analysis of Aqueous Humor and Rejected Graft in Pig-to-Non-Human Primate Corneal Xenotransplantation
Authors: Oh Jae Won , Yoon Chang Ho , Ryu Jin Suk , Kim Kwang Pyo , Kim Mee Kum
Published: March 2022

Although pig-to-non-human primate (NHP) corneal xenotransplantation has shown long-term graft survival, xenogeneic antigen-related immune responses are still stronger than allogeneic antigen-associated responses. Therefore, there is an unmet need to investigate major rejection pathways in corneal xenotransplantation, even with immunosuppression. This study aimed to identify biomarkers in aqueous humor for predicting rejection and to investigate rejection-related pathways in grafts from NHPs transplanted with porcine corneas following the administration of steroids combined with tacrolimus/rituximab. NHPs who had received corneas from wild-type (WT) or α-1,3-galactosyltransferase gene-knockout (GTKO) pigs were divided into groups with or without rejection according to clinical examinations. Liquid chromatography-mass spectrometry (LC-MS) was used to analyze the proteomes of corneal tissues or aqueous humor. The biological functions of differentially expressed proteins (DEPs) were assessed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathways and protein–protein interaction network analysis. Among the 66 DEPs in aqueous humor, complement proteins (C3, C5, and C9) and cholesterol metabolic proteins (APOA1 and APOA2) were related to xenogeneic rejection as biomarkers, and alternative pathways of the complement system seemed to be important in xenogeneic graft rejection. Among the 416 DEPs of the cornea, NF-κB1 and proteosomes (PSMD7, PSMA5, and PSMD3) seemed to be related to xenogeneic graft rejection. Additionally, oxidative phosphorylation and leukocyte activation-related pathways are involved in rejection. Overall, our proteomic approach highlights the important role of NF-κB1, proteosomes, oxidative phosphorylation, and leukocyte activation-related inflammation in the cornea and the relevance of complement pathways of the aqueous humor as a predictive biomarker of xenogeneic rejection.
Negative Immune Checkpoint Protein, VISTA, Regulates the CD4+ Treg Population During Sepsis Progression to Promote Acute Sepsis Recovery and Survival
Authors: Gray Chyna C. , Biron-Girard Bethany , Wakeley Michelle E. , Chung Chun-Shiang , Chen Yaping , Quiles-Ramirez Yael , Tolbert Jessica D. , Ayala Alfred
Published: March 2022

Sepsis is a systemic immune response to infection that is responsible for ~35% of in-hospital deaths and over 24 billion dollars in annual treatment costs. Strategic targeting of non-redundant negative immune checkpoint protein pathways can cater therapeutics to the individual septic patient and improve prognosis. B7-CD28 superfamily memberV-domainImmunoglobulinSuppressor ofTcellActivation (VISTA) is an ideal candidate for strategic targeting in sepsis. We hypothesized that immune checkpoint regulator, VISTA, controls T-regulatory cells (Treg), in response to septic challenge, thus playing a protective role/reducing septic morbidity/mortality. Further, we investigated if changes in morbidity/mortality are due to a Treg-mediated effect during the acute response to septic challenge. To test this, we used the cecal ligation and puncture model as a proxy for polymicrobial sepsis and assessed the phenotype of CD4+Tregsin VISTA-gene deficient (VISTA-/-) and wild-type mice. We also measured changes in survival, soluble indices of tissue injury, and circulating cytokines in the VISTA-/-and wild-type mice. We found that in wild-type mice, CD4+Tregsexhibit a significant upregulation of VISTA which correlates with higher Tregabundance in the spleen and small intestine following septic insult. However, VISTA-/-mice have reduced Tregabundance in these compartments met with a higher expression of Foxp3, CTLA4, and CD25 compared to wild-type mice. VISTA-/-mice also have a significant survival deficit, higher levels of soluble indicators of liver injury (i.e., ALT, AST, bilirubin), and increased circulating proinflammatory cytokines (i.e., IL-6, IL-10, TNFα, IL-17F, IL-23, and MCP-1) following septic challenge. To elucidate the role of Tregsin VISTA-/-sepsis mortality, we adoptively transferred VISTA-expressing Tregsinto VISTA-/-mice. This adoptive transfer rescued VISTA-/-survival to wild-type levels. Taken together, we propose a protective Treg-mediated role for VISTA by which inflammation-induced tissue injury is suppressed and improves survival in early-stage murine sepsis. Thus, enhancing VISTA expression or adoptively transferring VISTA+Tregsin early-stage sepsis may provide a novel therapeutic approach to ameliorate inflammation-induced death.
Zebrafish as a Vertebrate Model for Studying Nodavirus Infections
Authors: Lama Raquel , Pereiro Patricia , Figueras Antonio , Novoa Beatriz
Published: March 2022

Nervous necrosis virus (NNV) is a neurotropic pathogenic virus affecting a multitude of marine and freshwater fish species that has a high economic impact on aquaculture farms worldwide. Therefore, the development of new tools and strategies aimed at reducing the mortality caused by this virus is a pivotal need. Although zebrafish is not considered a natural host for NNV, the numerous experimental advantages of this species make zebrafish an attractive model for studying different aspects of the disease caused by NNV, viral encephalopathy and retinopathy (VER). In this work, we established the best way and age to infect zebrafish larvae with NNV, obtaining significant mortalities in 3-day-postfertilization larvae when the virus was inoculated directly into the brain or by intramuscular microinjection. As occurs in naturally susceptible fish species, we confirmed that after intramuscular injection the virus was able to migrate to the central nervous system (CNS). As expected, due to the severe damage that this virus causes to the CNS, alterations in the swimming behavior of the zebrafish larvae were also observed. Taking advantage of the existence of transgenic fluorescent zebrafish lines, we were able to track the migration of different innate immune cells, mainly neutrophils, to the site of infection with NNVviathe brain. However, we did not observe colocalization between the viral particles and neutrophils. RNA-Seq analysis of NNV-infected and uninfected larvae at 1, 3 and 5 days postinfection (dpi) revealed a powerful modulation of the antiviral immune response, especially at 5 dpi. We found that this response was dominated by, though not restricted to, the type I interferon system, the major defence mechanism in the innate immune response against viral pathogens. Therefore, as zebrafish larvae are able to develop the main characteristic of NNV infection and respond with an efficient immune arsenal, we confirmed the suitability of zebrafish larvae for modelling VER disease and studying different aspects of NNV pathogenesis, immune response and screening of antiviral drugs.
MiRAGDB: A Knowledgebase of RAG Regulators
Authors: Desai Sagar Sanjiv , Whadgar Saurabh , Raghavan Sathees C. , Choudhary Bibha
Published: March 2022

RAG1 and RAG2 genes generate diversity in immunoglobulin and TCR genes by initiating the process of V-D-J recombination. RAGs recognize specific sequences (heptamer-nonamer) to generate a diversity of immunoglobulins. RAG expression is limited to early B and T cell developmental stages. Aberrant expression of RAG can lead to double strand breaks and translocations as observed in leukemia and lymphoma. The expression of RAG is tightly regulated at the transcriptional and posttranscriptional levels. MicroRNAs (miRNAs) are small non-coding RNAs that are involved in the post-transcriptional regulation of gene expression. This study aimed to identify and catalog RAG regulation by miRNA during normal development and cancer. NGS data from normal B-cell and T-cell developmental stages and blood cancer samples have been analyzed for the expression of miRNAs against RAG1 (1,173 against human RAG1 and 749 against mouse RAG1). The analyzed data has been organized to retrieve the miRNA and mRNA expression of various RAG regulators (10 transcription factors and interacting partners) in normal and diseased states. The database allows users to navigate through the human and mouse RAG regulators, visualize and plot expression. miRAGDB is freely available and can be accessed at http://52.4.112.252/shiny/miragdb/.
Monoallelic Heb/Tcf12 Deletion Reduces the Requirement for NOTCH1 Hyperactivation in T-Cell Acute Lymphoblastic Leukemia
Authors: Veiga Diogo F. T. , Tremblay Mathieu , Gerby Bastien , Herblot Sabine , Haman André , Gendron Patrick , Lemieux Sébastien , Zúñiga-Pflücker Juan Carlos , Hébert Josée , Cohen Joseph Paul , Hoang Trang
Published: March 2022

Early T-cell development is precisely controlled by E proteins, that indistinguishably include HEB/TCF12 and E2A/TCF3 transcription factors, together with NOTCH1 and pre-T cell receptor (TCR) signalling. Importantly, perturbations of early T-cell regulatory networks are implicated in leukemogenesis. NOTCH1 gain of function mutations invariably lead to T-cell acute lymphoblastic leukemia (T-ALL), whereas inhibition of E proteins accelerates leukemogenesis. Thus, NOTCH1, pre-TCR, E2A and HEB functions are intertwined, but how these pathways contribute individually or synergistically to leukemogenesis remain to be documented. To directly address these questions, we leveragedCd3e-deficient mice in which pre-TCR signaling and progression through β-selection is abrogated to dissect and decouple the roles of pre-TCR, NOTCH1, E2A and HEB in SCL/TAL1-induced T-ALL,viathe use ofNotch1gain of function transgenic (Notch1ICtg) andTcf12+/-orTcf3+/-heterozygote mice. As a result, we now provide evidence that both HEB and E2A restrain cell proliferation at the β-selection checkpoint while the clonal expansion of SCL-LMO1-induced pre-leukemic stem cells in T-ALL is uniquely dependent onTcf12gene dosage. At the molecular level, HEB protein levels are decreasedviaproteasomal degradation at the leukemic stage, pointing to a reversible loss of function mechanism. Moreover, inSCL-LMO1-induced T-ALL, loss of oneTcf12allele is sufficient to bypass pre-TCR signaling which is required forNotch1gain of function mutations and for progression to T-ALL. In contrast,Tcf12monoallelic deletion does not accelerateNotch1IC-induced T-ALL, indicating thatTcf12andNotch1operate in the same pathway. Finally, we identify a tumor suppressor gene set downstream of HEB, exhibiting significantly lower expression levels in pediatric T-ALL compared to B-ALL and brain cancer samples, the three most frequent pediatric cancers. In summary, our results indicate a tumor suppressor function of HEB/TCF12 in T-ALL to mitigate cell proliferation controlled by NOTCH1 in pre-leukemic stem cells and prevent NOTCH1-driven progression to T-ALL.
Radiological Investigation of Gas Embolism in the East Asian Finless Porpoise (Neophocaena asiaeorientalis sunameri)
Authors: Yuen Adams Hei Long , Kim Sang Wha , Lee Sung Bin , Lee Seyoung , Lee Young Ran , Kim Sun Min , Poon Cherry Tsz Ching , Kwon Jun , Jung Won Joon , Giri Sib Sankar , Kim Sang Guen , Kang Jeong Woo , Lee Young Min , Seo Jong-pil , Kim Byung Yeop , Park Se Chang
Published: March 2022

Cetaceans have long been considered biologically adapted to suffer no adverse effects from diving-related tissue gas tension. However, increasing reports of gas embolism in cetaceans inhabiting European, Mediterranean and American waters have challenged the conventional understanding of marine mammal diving physiology. In human hyperbaric medicine, virtopsy techniques such as post-mortem computed tomography (PMCT) facilitate the visualization of gas embolism and could be performed adjunct to conventional autopsy. This research presents the first case of gas embolism identified in an East Asian finless porpoise inhabiting Asian waters. Massive gas embolic lesions were found in the liver, which had been compressing both the lungs and abdominal organs, and signs of pneumonia and parasitic infection were observed in both lungs. It is hypothesized that this porpoise might have been unable to expelin vivogas bubbles from its circulation due to pulmonary dysfunction. Consequently, gas bubbles agglomerated in the liver, resulting in the development of gas embolic lesions. The findings of the present study provide insights into the occurrence of gas embolism in the East Asian finless porpoise, highlighting the potential of PMCT as a promising tool for the diagnosis of gas embolism in stranded cetaceans.
Environmental Change at Deep-Sea Sponge Habitats Over the Last Half Century: A Model Hindcast Study for the Age of Anthropogenic Climate Change
Authors: Samuelsen Annette , Schrum Corinna , Yumruktepe Veli Çağlar , Daewel Ute , Roberts Emyr Martyn
Published: March 2022

Deep-sea sponges inhabit multiple areas of the deep North Atlantic at depths below 250 m. Living in the deep ocean, where environmental properties below the permanent thermocline generally change slowly, they may not easily acclimatize to abrupt changes in the environment. Until now consistent monitoring timeseries of the environment at deep sea sponge habitats are missing. Therefore, long-term simulation with coupled bio-physical models can shed light on the changes in environmental conditions sponges are exposed to. To investigate the variability of North Atlantic sponge habitats for the past half century, the deep-sea conditions have been simulated with a 67-year model hindcast from 1948 to 2014. The hindcast was generated using the ocean general circulation model HYCOM, coupled to the biogeochemical model ECOSMO. The model was validated at known sponge habitats with available observations of hydrography and nutrients from the deep ocean to evaluate the biases, errors, and drift in the model. Knowing the biases and uncertainties we proceed to study the longer-term (monthly to multi-decadal) environmental variability at selected sponge habitats in the North Atlantic and Arctic Ocean. On these timescales, these deep sponge habitats generally exhibit small variability in the water-mass properties. Three of the sponge habitats, the Flemish Cap, East Greenland Shelf and North Norwegian Shelf, had fluctuations of temperature and salinity in 4–6 year periods that indicate the dominance of different water masses during these periods. The fourth sponge habitat, the Reykjanes Ridge, showed a gradual warming of about 0.4°C over the simulation period. The flux of organic matter to the sea floor had a large interannual variability, that, compared to the 67-year mean, was larger than the variability of primary production in the surface waters. Lateral circulation is therefore likely an important control mechanism for the influx of organic material to the sponge habitats. Simulated oxygen varies interannually by less than 1.5 ml/l and none of the sponge habitats studied had oxygen concentrations below hypoxic levels. The present study establishes a baseline for the recent past deep conditions that future changes in deep sea conditions from observations and climate models can be evaluated against.
Effect of Grain Structure on the Failure Mechanism of Cu/Cu3Sn Investigated Via Molecular Dynamic Simulations
Authors: Zhang Jicheng , Jiang Zhitao , Zhang Yuanxiang
Published: March 2022

The grain structure has a great influence on the mechanical reliability of miniaturized interconnect circuits. Under the working conditions, Cu3Sn will be the main intermetallic compound that forms during electromigration and the thermal ageing process, which can easily induce cracks between Cu3Sn and the copper pad. This paper investigated the effect of the Cu grain structure on the Cu3Sn/Cu interface reliability via molecular dynamic simulations. Single-crystal Cu, twin-crystal Cu, and polycrystalline Cu models were implemented to form the interface structure, and uniaxial tension simulations were performed at strain rates of 0.01, 0.1, and 0.5% ps−1 to evaluate the interfacial strength and interface failure mechanism. Results show that the polycrystalline Cu models always exhibits a lower degree of stress and shows a great ductile character. The existence of twin grain boundaries makes Cu layer more stable, and their failure processes are dominated by stair-rod type dislocations with a Burgers vector of 1/6 [110] instead of Shockley dislocations with a Burgers vector of 1/6 [112], which induce their interface models fail in Cu3Sn layer near the interface. The strain rate dependence mechanical character of both interface and grains would be the main reason of phenomenon for the difference failure character affected by grain structure and strain rate.
Impact of Isolation Time of COVID-19 Patients in Intensive Care Unit on Healthcare Workers Contamination and Nursing Care Intensity
Authors: Doyen Denis , Morand Lucas , Jozwiak Mathieu , Aurenche Mateu Didac , Saccheri Clément , Hyvernat Hervé , Cremoni Marion , Brglez Vesna , Bèle Nicolas , Bernardin Gilles , Seitz-Polski Barbara , Dellamonica Jean
Published: March 2022

Background

The optimal isolation time of COVID-19 patients in intensive care unit (ICU) is debated. We investigated the impact of two different COVID-19 patient isolation time strategies on healthcare workers (HCW) contamination, intensity of nursing care and potential associated adverse events.

Methods

We prospectively included all consecutive COVID-19 patients and HCW in our ICU in the first two pandemic waves (March to May 2020 and August to November 2020). Specific isolation measures for COVID-19 patients were released after two negative RT-PCR assays in the first wave and 14 days after the onset of symptoms in the second wave. Contamination of HCW was assessed at the end of each pandemic wave by combining both a RT-PCR assay and a serological test.

Results

Overall, 117 COVID-19 patients and 73 HCW were included. Despite an earlier release from isolation after ICU admission in the second than in the first wave [6 (4–8) vs. 15 (11–19) days, p < 0.01], the proportion of HCW with a positive serological test (16 vs. 17%, p = 0.94) or with a positive RT-PCR assay (3 vs. 5%, p = 0.58) was not different between the two waves. Although a lower nurse-to-bed ratio, the intensity of nursing care was higher in the second than in the first wave. A longer isolation time was associated with accidental extubation (OR = 1.18, 95%CI:1.07–1.35, p = 0.005) but neither with ventilator-associated pneumonia nor with dysglycemia.

Conclusion

A shorter isolation time of COVID-19 patients in ICU was not associated with higher HCW contamination, while a longer isolation time seemed to be associated with higher accidental extubation.
Human Amnion Epithelial Cells and Their Derived Exosomes Alleviate Sepsis-Associated Acute Kidney Injury via Mitigating Endothelial Dysfunction
Authors: Chi Dongxuan , Chen Ying , Xiang Chengang , Yao Weijian , Wang Hui , Zheng Xizi , Xu Damin , Li Nan , Xie Min , Wang Suxia , Liu Gang , Li Shuangling , Yang Li
Published: March 2022

Background

Sepsis is characterized by organ dysfunction resulting from a patient’s dysregulated response to infection. Sepsis-associated acute kidney injury (S-AKI) is the most frequent complication contributing to the morbidity and mortality of sepsis. The prevention and treatment of S-AKI remains a significant challenge worldwide. In the recent years, human amnion epithelial cells (hAECs) have drawn much attention in regenerative medicine, yet the therapeutic efficiency of hAECs in S-AKI has not been evaluated.

Methods

Septic mice were induced by cecal ligation and puncture (CLP) operation. hAECs and their derived exosomes (EXOs) were injected into the mice via tail vein right after CLP surgery. The 7-day survival rate was observed. Serum creatinine level was measured and H&E staining of tissue sections were performed 16 h after CLP. Transmission electron microscopy was used to examine the renal endothelial integrity in CLP mice. Human umbilical vein endothelial cells (HUVECs) were treated with lipopolysaccharide (LPS) and EXOs. Zonula occludens-1 (ZO-1) localization was observed by immunofluorescence staining. Expression of phosphor-p65 (p-p65), p65, vascular cell adhesion molecule-1 (VCAM-1), and ZO-1 in the kidney were determined by Western blot.

Results

hAECs decreased the mortality of CLP mice, ameliorated septic injury in the kidney, and improved kidney function. More precisely, hAECs suppressed systemic inflammation and maintained the renal endothelial integrity in septic animals. EXOs from hAECs exhibited similar renal protective effects as their parental cells. EXOs maintained endothelial cell adhesion junction in vitro and inhibited endothelial cell hyperactivation in vivo. Mechanistically, EXOs suppressed proinflammatory nuclear factor kappa B (NF-κB) pathway activation in LPS-treated HUVECs and in CLP mice kidneys.

Conclusion

Our results indicate that hAECs and their derived EXOs may ameliorate S-AKI via the prevention of endothelial dysfunction in the early stage of sepsis in mice. Stem cell or exosome-based therapy targeting endothelial disorders may be a promising alternative for treatment of S-AKI.
The Role of Surgery in High-Grade Neuroendocrine Cancer: Indications for Clinical Practice
Authors: Petrella Francesco , Bardoni Claudia , Casiraghi Monica , Spaggiari Lorenzo
Published: March 2022

Pulmonary neuroendocrine tumors (pNET) represent a particular type of malignant lung cancers and can be divided into well-differentiated low-grade NET and poorly-differentiated high-grade NET. Typical and atypical carcinoids belong to the first group while large cell neuroendocrine carcinomas (LCNEC) and small-cell lung cancers (SCLC) belong to the second one. The aim of this mini-review is to focus on the role of surgical therapy for high grade neuroendocrine tumors. SCLC has the worst prognosis among all lung cancer neoplasms: in fact, the two-year survival rate is about 5% and median survival usually ranges between 15 and 20 months. The surgical treatment of SCLC has thus infrequently been judged as a valuable aspect of the therapeutic approach, the gold standard treatment being a combination of platinum-based chemotherapy and radiotherapy. As LCNEC are rare, there is a lack of extensive literature and randomized clinical trials, therefore the curative approach is still controversial. Current treatment guidelines suggest treating LCNEC by surgical resection in non-metastatic stages and recommend adjuvant chemotherapy according to SCLC protocol. Upfront surgery is suggested in early stages (from I to IIB), a multimodality approach is recommended in locally advanced stages (III) while surgery is not recommended in stage IV LCNEC. The rate of surgical resection is quite low, particularly for SCLC, ranging from 1 to 6% in limited diseases; lobectomy with radical lymphadenectomy is considered the gold standard surgical procedure in the case of limited disease SCLC and resectable LCNEC; pneumonectomy, although reported as an effective tool, should be avoided in the light of local and distant recurrence rates.
The Characteristics of the HIV-1 Env Glycoprotein Are Linked With Viral Pathogenesis
Authors: Pérez-Yanes Silvia , Pernas María , Marfil Silvia , Cabrera-Rodríguez Romina , Ortiz Raquel , Urrea Víctor , Rovirosa Carla , Estévez-Herrera Judith , Olivares Isabel , Casado Concepción , Lopez-Galindez Cecilio , Blanco Julià , Valenzuela-Fernández Agustín
Published: March 2022

The understanding of HIV-1 pathogenesis and clinical progression is incomplete due to the variable contribution of host, immune, and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has been concentrated on in many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controller individuals contemporary to LTNPs or recent, named Old and Modern progressors. We studied the Env expression, the fusion and cell-to-cell transfer capacities, as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4, and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs from virus of patients presenting viremic control and the non-progressor clinical phenotype showed poor viral functions and shorter sequences, whereas functional Envs were associated with virus of patients lacking virological control and with progressor clinical phenotypes. These correlations support the role of Env genotypic and phenotypic characteristics in thein vivoHIV-1 infection and pathogenesis.
Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field
Authors: Dookie Navisha , Khan Azraa , Padayatchi Nesri , Naidoo Kogieleum
Published: March 2022

The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
Microbial Community Changes in 26,500-Year-Old Thawing Permafrost
Authors: Scheel Maria , Zervas Athanasios , Jacobsen Carsten S. , Christensen Torben R.
Published: March 2022

Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.
Spread of Respiratory Pathogens During the COVID-19 Pandemic Among Children in the Northeast of Italy
Authors: Cason Carolina , Zamagni Giulia , Cozzi Giorgio , Tonegutto Davide , Ronfani Luca , Oretti Chiara , De Manzini Andrea , Barbi Egidio , Comar Manola , Amaddeo Alessandro
Published: March 2022

The social distancing measures adopted during the coronavirus disease 2019 (COVID-19) pandemic led to a profound change in the behavioral habits of the population. This study analyzes the impact of restriction measures on the shaping of the epidemiology of common winter respiratory pathogens in the pediatric population of northeast of Italy. From August 2020 to March 2021, a total of 1,227 nasopharyngeal swabs from symptomatic pediatric patients were tested for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B, adenovirus, other coronaviruses, parainfluenza virus 1–4, enterovirus, bocavirus, metapneumovirus, respiratory syncytial virus, rhinovirus, Bordetella pertussis, Bordetella parapertussis, and Mycoplasma pneumoniae. To relate virus positivity with the clinic characteristics of the subjects enrolled, multinomial logistic models were estimated. SARS-CoV-2 was detected in 5.2% of the children; fever resulted as risk factor for infection [relative risk ratio (RRR) = 2.88, p = 0.034]. Rhinovirus was detected in the 40.7% of the subjects, with cough and rhinitis as risk factors (respectively, RRR = 1.79, p = 0.001 and RRR = 1.53, p = 0.018). Other coronaviruses were found in 10.8% of children and were associated to pharyngodynia (RRR = 4.94, p < 0.001). Adenovirus, observed in 11.6% of subjects, showed to have fever as risk factor (RRR = 6.44, p < 0.001). Bocavirus was detected in 3.2% of children. In conclusion, our results showed that social isolation measures had an impact on the circulation of RSV and influenza, although children under the age of 2 were most affected by the other respiratory infections. Therefore, this study highlights the need for continuing surveillance for a delayed spread of RSV and other respiratory pathogens.
A Cationic Amphipathic Tilapia Piscidin 4 Peptide-Based Antimicrobial Formulation Promotes Eradication of Bacterial Vaginosis-Associated Bacterial Biofilms
Authors: Lin Wen-Chun , Chen Yun-Ru , Chuang Chi-Mu , Chen Jyh-Yih
Published: March 2022

Bacterial vaginosis (BV) is prevalent among women of reproductive age and has a high rate of recurrence, which can be largely attributed to ineffective BV biofilm eradication by current first-line antibiotics. In this study, we report that the Nile tilapia piscidin 4 (TP4) exhibits broad-spectrum antimicrobial and antibiofilm activity against BV-associated bacteria, but not beneficial lactobacilli. In addition, BV-associated Gardnerella vaginalis remains susceptible to TP4 even after continual exposure to the peptide for up to 22 passages. Gardnerella vaginalis and Streptococcus anginosus are both biofilm-forming BV-associated bacteria, and we found that combining TP4 peptide and disodium EDTA with the biofilm-disrupting agent, chitosan, can eradicate biofilms formed by single or mixed G. vaginalis and S. anginosus. In addition, long-term storage of TP4 peptide in chitosan did not diminish its bactericidal activity toward G. vaginalis. Preformulation studies were performed using High performance liquid chromatography (HPLC) and Circular Dichroism (CD). The long-term stability of TP4 peptide was assessed under various conditions, such as different temperatures and ionic strengths, and in the presence of H2O2 and lactic acid. When exposed to sodium dodecyl sulfate (SDS), TP4 maintained its secondary structure at various temperatures, salt and disodium EDTA concentrations. Furthermore, the TP4 microbicide formulation significantly reduced the colonization density of BV-associated bacteria in mice infected with single or mixed bacteria (G. vaginalis and S. anginosus). The TP4 microbicide formulation showed biocompatibility with beneficial human vaginal lactobacilli and female reproductive tissues in C57BL/6 mice. These results suggest that the TP4 microbicide formulation could be a promising topical microbicide agent for BV treatment.
The Chemical Relationship Among Beta-Lactam Antibiotics and Potential Impacts on Reactivity and Decomposition
Authors: Turner Jonathan , Muraoka Alyssa , Bedenbaugh Michael , Childress Blaine , Pernot Lauren , Wiencek Mark , Peterson Yuri K.
Published: March 2022

Beta-lactam antibiotics remain one of the most commonly prescribed drug classes, but they are limited by their propensity to cause hypersensitivity reactions (e.g., from allergy to anaphylaxis) as well as by the emergence of bacteria with a myriad of resistance mechanisms such as β-lactamases. While development efforts continue to focus on overcoming resistance, there are ongoing concerns regarding cross-contamination of β-lactams during manufacturing and compounding of these drugs. Additionally, there is a need to reduce levels of drugs such as β-lactam antibiotics in waste-water to mitigate the risk of environmental exposure. To help address future development of effective remediation chemistries and processes, it is desired to better understand the structural relationship among the most common β-lactams. This study includes the creation of a class-wide structural ordering of the entire β-lactam series, including both United States Food and Drug Association (US-FDA)-approved drugs and experimental therapies. The result is a structural relational map: the “Lactamome,” which positions each substance according to architecture and chemical end-group. We utilized a novel method to compare the structural relationships of β-lactam antibiotics among the radial cladogram and describe the positioning with respect to efficacy, resistance to hydrolysis, reported hypersensitivity, and Woodward height. The resulting classification scheme may help with the development of broad-spectrum treatments that reduce the risk of occupational exposure and negative environmental impacts, assist practitioners with avoiding adverse patient reactions, and help direct future drug research.
Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid
Authors: Hernández Ruth , Chaib De Mares Maryam , Jimenez Hugo , Reyes Alejandro , Caro-Quintero Alejandro
Published: March 2022

Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
Surface Ammonia-Oxidizer Abundance During the Late Summer in the West Antarctic Coastal System
Authors: Alcamán-Arias María E. , Cifuentes-Anticevic Jerónimo , Díez Beatriz , Testa Giovanni , Troncoso Macarena , Bello Estrella , Farías Laura
Published: March 2022

Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation rates, abundance and identity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were evaluated in the marine surface layer (to 30 m depth) in Chile Bay (Greenwich Island, WAP) over three consecutive late-summer periods (2017, 2018, and 2019). Ammonia-oxidation rates of 68.31 nmol N L−1 day−1 (2018) and 37.28 nmol N L−1 day−1 (2019) were detected from illuminated 2 m seawater incubations. However, high ammonia-oxidation rates between 267.75 and 109.38 nmol N L−1 day−1 were obtained under the dark condition at 30 m in 2018 and 2019, respectively. During the late-summer sampling periods both stratifying and mixing events occurring in the water column over short timescales (February–March). Metagenomic analysis of seven nitrogen cycle modules revealed the presence of ammonia-oxidizers, such as the Archaea Nitrosopumilus and the Bacteria Nitrosomonas and Nitrosospira, with AOA often being more abundant than AOB. However, quantification of specific amoA gene transcripts showed number of AOB being two orders of magnitude higher than AOA, with Nitrosomonas representing the most transcriptionally active AOB in the surface waters. Additionally, Candidatus Nitrosopelagicus and Nitrosopumilus, phylogenetically related to surface members of the NP-ε and NP-γ clades respectively, were the predominant AOA. Our findings expand the known distribution of ammonium-oxidizers to the marine surface layer, exposing their potential ecological role in supporting the marine Antarctic system during the productive summer periods.
Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening
Authors: Li Xiaoqiong , Zhu Liying , Wang Xin , Li Jinjun , Tang Biao
Published: March 2022

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.
Multi-Omics Analyses Characterize the Gut Microbiome and Metabolome Signatures of Soldiers Under Sustained Military Training
Authors: Shi Yifan , Wang Peng , Zhou Da , Huang Longchang , Zhang Li , Gao Xuejin , Maitiabula Gulisudumu , Wang Siwen , Wang Xinying
Published: March 2022

Exercise can directly alter the gut microbiome at the compositional and functional metabolic levels, which in turn may beneficially influence physical performance. However, data how the gut microbiome and fecal metabolome change, and how they interact in soldiers who commonly undergo sustained military training are limited. To address this issue, we first performed 16S rRNA sequencing to assess the gut microbial community patterns in a cohort of 80 soldiers separated into elite soldiers (ES, n = 40) and non-elite soldiers (N-ES, n = 40). We observed that the α-diversities of the ES group were higher than those of the N-ES group. As for both taxonomical structure and phenotypic compositions, elite soldiers were mainly characterized by an increased abundance of bacteria producing short-chain fatty acids (SCFAs), including Ruminococcaceae_UCG-005, Prevotella_9, and Veillonella, as well as a higher proportion of oxidative stress tolerant microbiota. The taxonomical signatures of the gut microbiome were significantly correlated with soldier performance. To further investigate the metabolic activities of the gut microbiome, using an untargeted metabolomic method, we found that the ES and N-ES groups displayed significantly different metabolic profiles and differential metabolites were primarily involved in the metabolic network of carbohydrates, energy, and amino acids, which might contribute to an enhanced exercise phenotype. Furthermore, these differences in metabolites were strongly correlated with the altered abundance of specific microbes. Finally, by integrating multi-omics data, we identified a shortlist of bacteria-metabolites associated with physical performance, following which a random forest classifier was established based on the combinatorial biomarkers capable of distinguishing between elite and non-elite soldiers with high accuracy. Our findings suggest possible future modalities for improving physical performance through targeting specific bacteria associated with more energetically efficient metabolic patterns.
Evaluation of the QIAstat-Dx RP2.0 and the BioFire FilmArray RP2.1 for the Rapid Detection of Respiratory Pathogens Including SARS-CoV-2
Authors: Cassidy Hayley , van Genne Mart , Lizarazo-Forero Erley , Niesters Hubert G. M. , Gard Lilli
Published: March 2022

Point-of-care syndromic panels allow for simultaneous and rapid detection of respiratory pathogens from nasopharyngeal swabs. The clinical performance of the QIAstat-Dx Respiratory SARS-CoV-2 panel RP2.0 (QIAstat-Dx RP2.0) and the BioFire FilmArray Respiratory panel RP2.1 (BioFire RP2.1) was evaluated for the detection of SARS-CoV-2 and other common respiratory pathogens. A total of 137 patient samples were retrospectively selected based on emergency department admission, along with 33 SARS-CoV-2 positive samples tested using a WHO laboratory developed test. The limit of detection for SARS-CoV-2 was initially evaluated for both platforms. The QIAstat-Dx RP2.0 detected SARS-CoV-2 at 500 copies/mL and had a positive percent agreement (PPA) of 85%. The BioFire RP2.1 detected SARS-CoV-2 at 50 copies/mL and had a PPA of 97%. Both platforms showed a negative percent agreement of 100% for SARS-CoV-2. Evaluation of analytical specificity from a range of common respiratory targets showed a similar performance between each platform. The QIAstat-Dx RP2.0 had an overall PPA of 82% (67–100%) in clinical samples, with differences in sensitivity depending on the respiratory target. Both platforms can be used to detect acute cases of SARS-CoV-2. While the QIAstat-Dx RP2.0 is suitable for detecting respiratory viruses within a clinical range, it has less analytical and clinical sensitivity for SARS-CoV-2 compared to the BioFire RP2.1.
Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing
Authors: Liu Yancheng , Takagi Yuko , Sugijanto Milyadi , Nguyen Kieu Duong My , Hirata Akira , Hori Hiroyuki , Ho C. Kiong
Published: March 2022

RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon Thermococcus kodakarensis to identify its biological targets. A comparative analysis of circular RNA reveals that the Rnl-knockout strain represses circularization of C/D box sRNAs without affecting the circularization of tRNA and rRNA processing intermediates. Recombinant archaeal Rnl could circularize C/D box sRNAs with a mutation in the conserved C/D box sequence element but not when the terminal stem structures were disrupted, suggesting that proximity of the two ends could be critical for intramolecular ligation. Furthermore, T. kodakarensis accumulates aberrant RNA fragments derived from ribosomal RNA in the absence of Rnl. These results suggest that Rnl is responsible for C/D box sRNA circularization and may also play a role in ribosomal RNA processing.