bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of the Diagnostic Performance of qPCR, Sanger Sequencing, and Whole-Genome Sequencing in Determining Clarithromycin and Levofloxacin Resistance in Helicobacter pylori
Authors: Egli Konrad , Wagner Karoline , Keller Peter M , Risch Lorenz , Risch Martin , Bodmer Thomas
Published: January 2021

Helicobacter pylori antibiotic resistance is increasing worldwide, emphasizing the urgent need for more rapid resistance detection prior to the administration of H. pylori eradication regimens. Macrolides and fluoroquinolones are widely used to treat H. pylori. In this study, we aimed to compare the diagnostic performance of A) 23SrDNA qPCR (with melting curve analysis) and an in-house developed gyrA qPCR followed by Sanger sequencing with a commercial IVD-marked hybridization probe assay (for 23SrDNA and gyrA) using 142 gastric biopsies (skipping culturing) and B) the same two qPCR for 23SrDNA and gyrA (including Sanger sequencing) with whole-genome sequencing (WGS) and phenotypic characterization of clarithromycin and levofloxacin resistance using 76 cultured isolates. The sensitivity of both qPCRs was 100% compared to that of the commercial IVD-marked hybridization probe assay for the detection of H. pylori in gastric biopsies (without resistance testing). The specificity of the qPCR gyrA followed by Sanger sequencing was 100%, indicating that the best sequence identity was always H. pylori. The results show good agreement between molecular tests, especially between qPCR (inclusive Sanger sequencing) and WGS. Discrepancies (concerning mutated or wild type of positive H. pylori gastric biopsies) were observed between Sanger sequencing of the gyrA gene and the corresponding commercial hybridization probe assay, mostly because the high sequence diversity of the gyrA gene even at positions adjacent to the relevant codons of 87 and 91 interfered with obtaining correct results from the hybridization probe assay. Interestingly, we found several mixed sequences, indicating mixed populations in the gastric biopsies (direct detection without culturing). There was a high percentage of both levofloxacin and clarithromycin resistance in gastric biopsies (both between 22% and 29%, direct detection in gastric biopsies). Therefore, we recommend analyzing both targets in parallel. We confirmed that phenotypic resistance is highly correlated with the associated mutations. We concluded that the two qPCR followed by Sanger sequencing of the gyrA gene is a fast, cost-effective and comprehensive method for resistance testing of H. pylori directly in gastric biopsies.
Chlamydia muridarum Can Invade the Central Nervous System via the Olfactory and Trigeminal Nerves and Infect Peripheral Nerve Glial Cells
Authors: Nazareth Lynn , Walkden Heidi , Chacko Anu , Delbaz Ali , Shelper Todd , Armitage Charles W. , Reshamwala Ronak , Trim Logan K. , St John James A. , Beagley Kenneth W. , Ekberg Jenny A. K.
Published: January 2021

Chlamydia pneumoniaecan infect the brain and has been linked to late-onset dementia.Chlamydia muridarum, which infects mice, is often used to model human chlamydial infections. While it has been suggested to be also important for modelling brain infection, nervous system infection byC. muridarumhas not been reported in the literature.C. pneumoniaehas been shown to infect the olfactory bulb in mice after intranasal inoculation, and has therefore been suggested to invade the brainviathe olfactory nerve; however, nerve infection has not been shown to date. Another path by which certain bacteria can reach the brain isviathe trigeminal nerve, but it remains unknown whetherChlamydiaspecies can infect this nerve. Other bacteria that can invade the brainviathe olfactory and/or trigeminal nerve can do so rapidly, however, whetherChlamydiaspp. can reach the brain earlier than one-week post inoculation remains unknown. In the current study, we showed thatC. muridarumcan within 48 h invade the brainviathe olfactory nerve, in addition to infecting the trigeminal nerve. We also cultured the glial cells of the olfactory and trigeminal nerves and showed thatC. muridarumreadily infected the cells, constituting a possible cellular mechanism explaining how the bacteria can invade the nerves without being eliminated by glial immune functions. Further, we demonstrated that olfactory and trigeminal glia differed in their responses toC. muridarum, with olfactory glia showing less infection and stronger immune response than trigeminal glia.
Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes
Authors: Nennig Morgane , Llarena Ann-Katrin , Herold Malte , Mossong Joël , Penny Christian , Losch Serge , Tresse Odile , Ragimbeau Catherine
Published: January 2021

Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasizing the need to investigate their survival strategy in greater depth.
Genomic Epidemiology of Antimalarial Drug Resistance in Plasmodium falciparum in Southern China
Authors: Huang Fang , Jacob Christopher G. , Takala-Harrison Shannon , Adams Matthew , Yang Heng-Lin , Liu Hui , Xia Zhi-Gui , Zhou Shui-Sen , Tang Lin-Hua , Plowe Christopher V.
Published: January 2021

Emerging artemisinin resistance in Southeast Asia poses a significant risk to malaria control and eradication goals, including China’s plan to eliminate malaria nationwide by 2020. Plasmodium falciparum was endemic in China, especially in Southern China. Parasites from this region have shown decreased susceptibility to artemisinin and delayed parasite clearance after artemisinin treatment. Understanding the genetic basis of artemisinin resistance and identifying specific genetic loci associated with this phenotype is crucial for surveillance and containment of resistance. In this study, parasites were collected from clinical patients from Yunnan province and Hainan island. The parasites were genotyped using a P. falciparum-specific single nucleotide polymorphism (SNP) microarray. The SNP profiles examined included a total of 27 validated and candidate molecular markers of drug resistance. The structure of the parasite population was evaluated by principal component analysis by using the EIGENSOFT program, and ADMIXTURE was used to calculate maximum likelihood estimates for the substructure analysis. Parasites showed a high prevalence of resistance haplotypes of pfdhfr and pfdhps and moderate prevalence of pfcrt. There was no mutation identified on pfmdr1. Candidate SNPs on chromosomes 10, 13, and 14 that were associated with delayed parasite clearance showed a low prevalence of mutants. Parasites from Southern China were clustered and separated from those from Southeast Asia. Parasites from Yunnan province were substructured from parasites from Hainan island. This study provides evidence for a genomic population with drug resistance in Southern China and also illustrates the utility of SNP microarrays for large-scale parasite molecular epidemiology.
The Dynamic Roles of the Inner Membrane Complex in the Multiple Stages of the Malaria Parasite
Authors: Ferreira Josie Liane , Heincke Dorothee , Wichers Jan Stephan , Liffner Benjamin , Wilson Danny W. , Gilberger Tim-Wolf
Published: January 2021

Apicomplexan parasites, such as human malaria parasites, have complex lifecycles encompassing multiple and diverse environmental niches. Invading, replicating, and escaping from different cell types, along with exploiting each intracellular niche, necessitate large and dynamic changes in parasite morphology and cellular architecture. The inner membrane complex (IMC) is a unique structural element that is intricately involved with these distinct morphological changes. The IMC is a double membrane organelle that formsde novoand is located beneath the plasma membrane of these single-celled organisms. InPlasmodiumspp. parasites it has three major purposes: it confers stability and shape to the cell, functions as an important scaffolding compartment during the formation of daughter cells, and plays a major role in motility and invasion. Recent years have revealed greater insights into the architecture, protein composition and function of the IMC. Here, we discuss the multiple roles of the IMC in each parasite lifecycle stage as well as insights into its sub-compartmentalization, biogenesis, disassembly and regulation during stage conversion ofP. falciparum.
Platelet Membrane Receptor Proteolysis: Implications for Platelet Function
Authors: Wu Jiayu , Heemskerk Johan W. M. , Baaten Constance C. F. M. J.
Published: January 2021

The activities of adhesion and signaling receptors in platelets are controlled by several mechanisms. An important way of regulation is provided by proteolytic cleavage of several of these receptors, leading to either a gain or a loss of platelet function. The proteases involved are of different origins and types: (i) present as precursor in plasma, (ii) secreted into the plasma by activated platelets or other blood cells, or (iii) intracellularly activated and cleaving cytosolic receptor domains. We provide a comprehensive overview of the proteases acting on the platelet membrane. We describe how these are activated, which are their target proteins, and how their proteolytic activity modulates platelet functions. The review focuses on coagulation-related proteases, plasmin, matrix metalloproteinases, ADAM(TS) isoforms, cathepsins, caspases, and calpains. We also describe how the proteolytic activities are determined by different platelet populations in a thrombus and conversely how proteolysis contributes to the formation of such populations.
Bathymetry and Shallow Seismic Imaging of the 2018 Flank Collapse of Anak Krakatau
Authors: Priyanto Wisnu S. , Hunt James E. , Hanif Muhammad , Tappin David R. , Permana Haryadi , Susilohadi  , Cassidy Michael , Yulianto Eko
Published: January 2021

The flank failure and collapse of Anak Krakatau on December 22nd, 2018 triggered a destructive tsunami. Whether the prior activity of the volcano led to this collapse, or it was triggered by another means, remains a challenge to understand. This study seeks to investigate the recent volcano submarine mass-landslide deposit and emplacement processes, including the seafloor morphology of the flank collapse and the landslide deposit extent. Bathymetry and sparker seismic data were used during this study. Bathymetry data collected in August, 2019 shows the run-out area and the seafloor landslide deposit morphology. Bathymetry data acquired in May, 2017, is used as the base limit of the collapse to estimate the volume of the flank collapse. Comparisons between seismic data acquired in 2017 and 2019 provide an insight into the landslide emplacement processes, the deposit sequence, and structure below the seafloor. From these results we highlight two areas of the submarine-mass landslide deposit, one proximal to Anak Krakatau island (∼1.6 km) and one distal (∼1.4 km). The resulting analysis suggests that the submarine-mass landslide deposit might be produced by a frontally compressional, faulted, landslide, triggered by the critical stability slope, and due to the recent volcanic activity. Blocky seabed features clearly lie to the southwest of Anak Krakatau, and may represent the collapse blocks of the landslide. The seismic analysis of the data acquired in August, 2019 reveals that the blocky facies extends to ∼1.62 km in the width around Anak Krakatau, and the block thicknesses vary up to 70.4 m. The marine data provides a new insight into the landslide run out and extent, together with the landslide deposit morphology and structure that are not available from satellite imagery or subaerial surveys. We conclude that the landslide run out area southwest of the recent collapse, is ∼7.02 ± 0.21 km2.
Toward a Universal Theoretical Framework to Understand Robustness and Resilience: From Cells to Systems
Authors: Davis Jason E. , Kolozsvary Mary Beth , Pajerowska-Mukhtar Karolina M. , Zhang Bo
Published: January 2021

Research across a range of biological subdisciplines and scales, ranging from molecular to ecosystemic, provides ample evidence that living systems generally exhibit both a degree of resistance to disruption and an ability to recover following disturbance. Not only do mechanisms of robustness and resilience exist across and between systems, but those mechanisms exhibit ubiquitous and scalable commonalities in pattern and function. Mechanisms such as redundancy, plasticity, interconnectivity, and coordination of subunits appear to be crucial internal players in the determination of stability. Similarly, factors external to the system such as the amplitude, frequency, and predictability of disruptors, or the prevalence of key limiting resources, may constrain pathways of response. In the face of a rapidly changing environment, there is a pressing need to develop a common framework for describing, assessing, and predicting robustness and resilience within and across living systems.
Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer
Authors: Weng Li , Shen Shanshan , Wu Shaoqiu , Yin Xiang , Liu Bingyan , Shang Mingyi , Zou Xiaoping , Mao Aiwu
Published: January 2021

This study was conducted to explore the potential genes and proteins associated with esophagus benign hyperplasia induced by esophageal stents. Five patients with esophageal cancer subjected to esophageal stent placement were enrolled in this study. Long non-coding RNA (lncRNA) sequencing and tandem mass tag quantitative proteomics analysis were performed by using the collected hyperplastic samples and adjacent non-hyperplastic tissues. Differentially expressed (DE) RNAs and proteins were analyzed, followed by functional enrichment analysis, protein-protein interaction (PPI) network analysis, and competitive endogenous RNA (ceRNA) network construction. Venn analysis was performed to extract the overlaps between DE mRNAs and DE proteins and the expression correlations between DE mRNA and proteins were analyzed. Results showed that total 642 DE RNAs (457 mRNA and 185 lncRNAs) and 256 DE proteins were detected. DE mRNAs (such as MAOB, SDR16C5, and FOSL1) were enriched in oxidation-reduction process-associated functions. PPI network was comprised of 175 nodes and 425 edges. VEGFA was a significant node with the highest degree. LncRNA-mRNA network with three subnetworks (C1, C2, C3) was constructed for lncRNAs with more than 15 gene targets. RP11-58O9.2 was a significant lncRNA with the most target genes and RP11-667F14.1 regulated more than 20 targets. FOSL1 was a common target of the two lncRNAs. Function analysis showed that DE lncRNAs were involved in the HTLV-I infection (RP11-58O9.2 and RP11-667F14.1) and IL-17 signaling pathways (RP11-5O24.1 and RP11-58O9.2). Total 11 DE mRNAs were overlapped with DE proteins, among which MAOB and SDR16C5 showed positive correlations between mRNA and protein expression. Function analysis showed that MAOB was enriched in oxidation-reduction process and its protein was closely related with response to lipopolysaccharide. VEGFA, FOSL1, MAOB, SDR16C5, RP11-58O9.2, RP11-667F14.1, and RP11-288A5.2 may be served as genetic targets for preventing stent restenosis in esophageal cancer.
Identifying Biomarkers to Predict the Progression and Prognosis of Breast Cancer by Weighted Gene Co-expression Network Analysis
Authors: Shi Gengsheng , Shen Zhenru , Liu Yi , Yin Wenqin
Published: January 2021

Breast cancer (BC) is the leading cause of cancer death among women worldwide. The molecular mechanisms of its pathogenesis are still to be investigated. In our study, differentially expressed genes (DEGs) were screened between BC and normal tissues. Based on the DEGs, a weighted gene co-expression network analysis (WGCNA) was performed in 683 BC samples, and eight co-expressed gene modules were identified. In addition, by relating the eight co-expressed modules to clinical information, we found the blue module and pathological stage had a significant correlation (r = 0.24, p = 1e–10). Validated by multiple independent datasets, using one-way ANOVA, survival analysis and expression level revalidation, we finally screened 12 hub genes that can predict BC progression and prognosis. Functional annotation analysis indicated that the hub genes were enriched in cell division and cell cycle regulation. Importantly, higher expression of the 12 hub genes indicated poor overall survival, recurrence-free survival, and disease-free survival in BC patients. In addition, the expression of the 12 hub genes showed a significantly positive correlation with the expression of cell proliferation marker Ki-67 in BC. In summary, our study has identified 12 hub genes associated with the progression and prognosis of BC; these hub genes might lead to poor outcomes by regulating the cell division and cell cycle. These hub genes may serve as a biomarker and help to distinguish different pathological stages for BC patients.
Studying the Interplay Between Apolipoprotein E and Education on Cognitive Decline in Centenarians Using Bayesian Beta Regression
Authors: Xiang Qingyan , Andersen Stacy Lynn , Perls Thomas T. , Sebastiani Paola
Published: January 2021

Apolipoprotein E (APOE) is an important risk factor for cognitive decline and Alzheimer’s disease in aging individuals. Among the 3 known alleles of this gene: e2, e3, and e4, the e4 allele is associated with faster cognitive decline and increased risk for Alzheimer’s and dementia, while the e2 allele has a positive effect on longevity, and possibly on preservation of cognitive function. Education also has an important effect on cognition and longevity but the interplay between APOE and education is not well-characterized. Previous studies of the effect of APOE on cognitive decline often used linear regression with the normality assumption, which may not be appropriate for analyzing bounded and skewed neuropsychological test scores. In this paper, we applied Bayesian beta regression to assess the effect of APOE alleles on cognitive decline in a cohort of centenarians with longitudinal assessment of their cognitive function. The analysis confirmed the negative association between older age and cognition and the beneficial effect of education that persists even at the extreme of human lifespan in carriers of the e3 allele. In addition, the analysis showed an association between APOE and cognition that is modified by education. Surprisingly, an antagonistic interaction existed between higher education and APOE alleles, suggesting that education may reduce the positive effect of APOE e2 and increase the negative effect of APOE e4 at extreme old age.
Impaired Regulation of Histone Methylation and Acetylation Underlies Specific Neurodevelopmental Disorders
Authors: Fallah Merrick S. , Szarics Dora , Robson Clara M. , Eubanks James H.
Published: January 2021

Epigenetic processes are critical for governing the complex spatiotemporal patterns of gene expression in neurodevelopment. One such mechanism is the dynamic network of post-translational histone modifications that facilitate recruitment of transcription factors or even directly alter chromatin structure to modulate gene expression. This is a tightly regulated system, and mutations affecting the function of a single histone-modifying enzyme can shift the normal epigenetic balance and cause detrimental developmental consequences. In this review, we will examine select neurodevelopmental conditions that arise from mutations in genes encoding enzymes that regulate histone methylation and acetylation. The methylation-related conditions discussed include Wiedemann-Steiner, Kabuki, and Sotos syndromes, and the acetylation-related conditions include Rubinstein-Taybi, KAT6A, genitopatellar/Say-Barber-Biesecker-Young-Simpson, and brachydactyly mental retardation syndromes. In particular, we will discuss the clinical/phenotypic and genetic basis of these conditions and the model systems that have been developed to better elucidate cellular and systemic pathological mechanisms.
Rapid GMP-Compliant Expansion of SARS-CoV-2–Specific T Cells From Convalescent Donors for Use as an Allogeneic Cell Therapy for COVID-19
Authors: Cooper Rachel S. , Fraser Alasdair R. , Smith Linda , Burgoyne Paul , Imlach Stuart N. , Jarvis Lisa M. , Turner David M. , Zahra Sharon , Turner Marc L. , Campbell John D. M.
Published: January 2021

COVID-19 disease caused by the SARS-CoV-2 virus is characterized by dysregulation of effector T cells and accumulation of exhausted T cells. T cell responses to viruses can be corrected by adoptive cellular therapy using donor-derived virus-specific T cells. One approach is the establishment of banks of HLA-typed virus-specific T cells for rapid deployment to patients. Here we show that SARS-CoV-2–exposed blood donations contain CD4 and CD8 memory T cells which recognize SARS-CoV-2 spike, nucleocapsid and membrane antigens. Peptides of these antigens can be used to isolate virus-specific T cells in a GMP-compliant process. The isolated T cells can be rapidly expanded using GMP-compliant reagents for use as an allogeneic therapy. Memory and effector phenotypes are present in the selected virus-specific T cells, but our method rapidly expands the desirable central memory phenotype. A manufacturing yield ranging from 1010 to 1011 T cells can be obtained within 21 days culture. Thus, multiple therapeutic doses of virus-specific T cells can be rapidly generated from convalescent donors for potential treatment of COVID-19 patients.
Interleukin-8 as a Biomarker for Disease Prognosis of Coronavirus Disease-2019 Patients
Authors: Li Lili , Li Jie , Gao Meiling , Fan Huimin , Wang Yanan , Xu Xin , Chen Chunfeng , Liu Junxiao , Kim Jocelyn , Aliyari Roghiyh , Zhang Jicai , Jin Yujie , Li Xiaorong , Ma Feng , Shi Minxin , Cheng Genhong , Yang Heng
Published: January 2021

The widespread prevalence of coronavirus disease-2019 (COVID-19) which is caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has resulted in a severe global public health emergency. However, there are no sensitive biomarkers to predict the disease prognosis of COVID-19 patients. Here, we have identified interleukin-8 (IL-8) as a biomarker candidate to predict different disease severity and prognosis of COVID-19 patients. While serum IL-6 become obviously elevated in severe COVID-19 patients, serum IL-8 was easily detectible in COVID-19 patients with mild syndromes. Furthermore, lL-8 levels correlated better than IL-6 levels with the overall clinical disease scores at different stages of the same COVID-19 patients. Thus, our studies suggest that IL-6 and IL-8 can be respectively used as biomarkers for severe COVID-19 patients and for COVID-19 disease prognosis.
Nanoparticle-Induced Complement Activation: Implications for Cancer Nanomedicine
Authors: La-Beck Ninh M. , Islam Md. Rakibul , Markiewski Maciej M.
Published: January 2021

Nanoparticle-based anticancer medications were first approved for cancer treatment almost 2 decades ago. Patients benefit from these approaches because of the targeted-drug delivery and reduced toxicity, however, like other therapies, adverse reactions often limit their use. These reactions are linked to the interactions of nanoparticles with the immune system, including the activation of complement. This activation can cause well-characterized acute inflammatory reactions mediated by complement effectors. However, the long-term implications of chronic complement activation on the efficacy of drugs carried by nanoparticles remain obscured. The recent discovery of protumor roles of complement raises the possibility that nanoparticle-induced complement activation may actually reduce antitumor efficacy of drugs carried by nanoparticles. We discuss here the initial evidence supporting this notion. Better understanding of the complex interactions between nanoparticles, complement, and the tumor microenvironment appears to be critical for development of nanoparticle-based anticancer therapies that are safer and more efficacious.
IL-33/Vitamin D Crosstalk in Psoriasis-Associated Osteoporosis
Authors: De Martinis Massimo , Ginaldi Lia , Sirufo Maria Maddalena , Bassino Enrica Maria , De Pietro Francesca , Pioggia Giovanni , Gangemi Sebastiano
Published: January 2021

Patients with psoriasis (Pso) and, in particular, psoriatic arthritis (PsoA) have an increased risk of developing osteoporosis (OP). It has been shown that OP is among the more common pathologies associated with Pso, mainly due to the well-known osteopenizing conditions coexisting in these patients. Pso and OP share common risk factors, such as vitamin D deficiency and chronic inflammation. Interestingly, the interleukin (IL)-33/ST2 axis, together with vitamin D, is closely related to both Pso and OP. Vitamin D and the IL-33/ST2 signaling pathways are closely involved in bone remodeling, as well as in skin barrier pathophysiology. The production of anti-osteoclastogenic cytokines, e.g., IL-4 and IL-10, is promoted by IL-33 and vitamin D, which are stimulators of both regulatory and Th2 cells. IL-33, together with other Th2 cytokines, shifts osteoclast precursor differentiation towards macrophage and dendritic cells and inhibits receptor activator of nuclear factor kappa-B ligand (RANKL)-induced osteoclastogenesis by regulating the expression of anti-osteoclastic genes. However, while the vitamin D protective functions in OP and Pso have been definitively ascertained, the overall effect of IL-33 on bone and skin homeostasis, because of its pleiotropic action, is still controversial. Emerging evidence suggests a functional link between vitamin D and the IL-33/ST2 axis, which acts through hormonal influences and immune-mediated effects, as well as cellular and metabolic functions. Based on the actions of vitamin D and IL-33 in Pso and OP, here, we hypothesize the role of their crosstalk in the pathogenesis of both these pathologies.
PD-L1/PD-1 Pattern of Expression Within the Bone Marrow Immune Microenvironment in Smoldering Myeloma and Active Multiple Myeloma Patients
Authors: Costa Federica , Vescovini Rosanna , Marchica Valentina , Storti Paola , Notarfranchi Laura , Dalla Palma Benedetta , Toscani Denise , Burroughs-Garcia Jessica , Catarozzo Maria Teresa , Sammarelli Gabriella , Giuliani Nicola
Published: January 2021

Background

The PD-1/PD-L1 axis has recently emerged as an immune checkpoint that controls antitumor immune responses also in hematological malignancies. However, the use of anti-PD-L1/PD-1 antibodies in multiple myeloma (MM) patients still remains debated, at least in part because of discordant literature data on PD-L1/PD-1 expression by MM cells and bone marrow (BM) microenvironment cells. The unmet need to identify patients which could benefit from this therapeutic approach prompts us to evaluate the BM expression profile of PD-L1/PD-1 axis across the different stages of the monoclonal gammopathies.

Methods

The PD-L1/PD-1 axis was evaluated by flow cytometry in the BM samples of a total cohort of 141 patients with monoclonal gammopathies including 24 patients with Monoclonal Gammopathy of Undetermined Significance (MGUS), 38 patients with smoldering MM (SMM), and 79 patients with active MM, including either newly diagnosed or relapsed-refractory patients. Then, data were correlated with the main immunological and clinical features of the patients.

Results

First, we did not find any significant difference between MM and SMM patients in terms of PD-L1/PD-1 expression, on both BM myeloid (CD14+) and lymphoid subsets. On the other hand, PD-L1 expression by CD138+ MM cells was higher in both SMM and MM as compared to MGUS patients. Second, the analysis on the total cohort of MM and SMM patients revealed that PD-L1 is expressed at higher level in CD14+CD16+ non-classical monocytes compared with classical CD14+CD16− cells, independently from the stage of disease. Moreover, PD-L1 expression on CD14+ cells was inversely correlated with BM serum levels of the anti-tumoral cytokine, IL-27. Interestingly, relapsed MM patients showed an inverted CD4+/CD8+ ratio along with high levels of pro-tumoral IL-6 and a positive correlation between %CD14+PD-L1+ and %CD8+PD-1+ cells as compared to both SMM and newly diagnosed MM patients suggesting a highly compromised immune-compartment with low amount of CD4+ effector cells.

Conclusions

Our data indicate that SMM and active MM patients share a similar PD-L1/PD-1 BM immune profile, suggesting that SMM patients could be an interesting target for PD-L1/PD-1 inhibition therapy, in light of their less compromised and more responsive immune-compartment.
Spatial Management Measures Alter Vessel Behavior in the Aleutian Archipelago
Authors: Sullender Benjamin K. , Kapsar Kelly , Poe Aaron , Robards Martin
Published: January 2021

The Aleutian Archipelago and surrounding waters have enormous ecological, cultural, and commercial significance. As one of the shortest routes between North American and Asian ports, the North Pacific Great Circle Route, which crosses through the Aleutian Archipelago, is traveled by thousands of large cargo ships and tanker vessels every year. To reduce maritime risks and enhance navigational safety, the International Maritime Organization built upon earlier offshore routing efforts by designating five Areas To Be Avoided (ATBAs) in the Aleutian Islands in 2016. The ATBAs are designed to keep large vessels at least 50 nautical miles (93 km) from shore unless calling at a local port or transiting an authorized pass between islands. However, very few studies have examined the effectiveness of ATBAs as a mechanism for changing vessel behavior and thereby reducing the ecological impacts of maritime commerce. In this study, we use 4 years of satellite-based vessel tracking data to assess the effectiveness of the Aleutian ATBAs since their implementation in 2016. We determined whether vessels transiting the North Pacific Great Circle Route changed behavior after ATBA implementation, both in terms of overall route selection and in terms of compliance with each ATBA boundary. We found a total of 2,252 unique tankers and cargo vessels >400 gross tons transited the study region, completing a total of 8,794 voyages. To quantify routing changes of individual vessels, we analyzed the 767 vessels that transited the study region both before and after implementation. The percentage of voyages transiting through the boundaries of what would become ATBAs decreased from 76.3% in 2014–2015 (prior to ATBA designation) to 11.8% in 2016–2017 (after implementation). All five Aleutian ATBAs had significant increases in compliance, with the West ATBA showing the most dramatic increase, from 32.1% to 95.0%. We discuss the framework for ATBA enforcement and highlight the value of local institutional capacity for real-time monitoring. Overall, our results indicate that ATBAs represent a viable strategy for risk mitigation in sensitive ecological areas and that through monitoring, spatial protections influence vessel route decisions on multiple spatial scales.
Temporal and Spatial Variations in Particle Fluxes on the Chukchi Sea and East Siberian Sea Slopes From 2017 to 2018
Authors: Kim Ho-Jung , Kim Hyung Jeek , Yang Eun-Jin , Cho Kyoung-Ho , Jung Jinyoung , Kang Sung-Ho , Lee Kyung-Eun , Cho Sosul , Kim Dongseon ,   on behalf of the Collaborative Working Group
Published: January 2021

Time-series sediment traps were deployed on the Chukchi Sea and East Siberian Sea slopes from August 2017 to August 2018 with the aim of elucidating the temporal and spatial variations in particle fluxes and identifying the main processes affecting those variations. Particle fluxes showed a typical seasonal pattern, with high values in summer and low values in other seasons, and a large inter-annual variation was observed only on the East Siberian Sea slope, where particle fluxes were one order of magnitude higher in early August 2018 than in late August 2017. This large inter-annual variation in particle flux resulted from the episodic intrusion of nutrient-enriched shelf water in the East Siberian Sea, which enhanced biological production at the surface and particle fluxes. The Chukchi Sea slope was influenced by the inflow of Anadyr Water, with high salinity and high nutrient concentrations, which had little annual variability. Therefore, particle flux showed little inter-annual variation on the Chukchi Sea slope. Under-ice phytoplankton blooms were observed in both the Chukchi Sea and East Siberian Sea slopes, and increases in particulate organic carbon (POC) flux and the C:N ratio under the sea ice were related to transparent exopolymer (TEP) production by ice algae. On the East Siberian Sea slope, particle fluxes increased slightly from 115 to 335 m, indicating lateral transport of suspended particulate matter; POC and lithogenic particles may be laterally transported to the slope as nutrient-rich shelf waters flowed from the East Siberian Sea to the Makarov Basin. Annual POC fluxes were 2.3 and 2.0 g C m–2 year–1 at 115 and 335 m, respectively, on the East Siberian Sea slope and was 2.1 g C m–2 year–1 at 325 m on the Chukchi Sea slope. Annual POC fluxes were higher on the Chukchi Sea and East Siberian Sea slopes than in Arctic basins, lower than on Arctic shelves, and generally similar to those on western Arctic slopes.
Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains
Authors: Carvalho Rodrigo , Aburjaile Flavia , Canario Marcus , Nascimento Andréa M. A. , Chartone-Souza Edmar , de Jesus Luis , Zamyatnin Andrey A. , Brenig Bertram , Barh Debmalya , Ghosh Preetam , Goes-Neto Aristoteles , Figueiredo Henrique C. P. , Soares Siomar , Ramos Rommel , Pinto Anne , Azevedo Vasco
Published: January 2021

The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.
Correlation of Salmonella enterica and Listeria monocytogenes in Irrigation Water to Environmental Factors, Fecal Indicators, and Bacterial Communities
Authors: Gu Ganyu , Strawn Laura K. , Ottesen Andrea R. , Ramachandran Padmini , Reed Elizabeth A. , Zheng Jie , Boyer Renee R. , Rideout Steven L.
Published: January 2021

Outbreaks of foodborne illnesses linked to fresh fruits and vegetables have been key drivers behind a wide breadth of research aiming to fill data gaps in our understanding of the total ecology of agricultural water sources such as ponds and wells and the relationship of this ecology to foodborne pathogens such as Salmonella enterica and Listeria monocytogenes. Both S. enterica and L. monocytogenes can persist in irrigation water and have been linked to produce contamination events. Data describing the abundance of these organisms in specific agricultural water sources are valuable to guide water treatment measures. Here, we profiled the culture independent water microbiota of four farm ponds and wells correlated with microbiological recovery of S. enterica (prevalence: pond, 19.4%; well, 3.3%), L. monocytogenes (pond, 27.1%; well, 4.2%) and fecal indicator testing. Correlation between abiotic factors, including water parameters (temperature, pH, conductivity, dissolved oxygen percentage, oxidation reduction potential, and turbidity) and weather (temperature and rainfall), and foodborne pathogens were also evaluated. Although abiotic factors did not correlate with recovery of S. enterica or L. monocytogenes (p > 0.05), fecal indicators were positively correlated with incidence of S. enterica in well water. Bacterial taxa such as Sphingomonadaceae and Hymenobacter were positively correlated with the prevalence and population of S. enterica, and recovery of L. monocytogenes was positively correlated with the abundance of Rhizobacter and Comamonadaceae (p < 0.03). These data will support evolving mitigation strategies to reduce the risk of produce contamination by foodborne pathogens through irrigation.
Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region
Authors: Sváb Domonkos , Falgenhauer Linda , Horváth Balázs , Maróti Gergely , Falgenhauer Jane , Chakraborty Trinad , Tóth István
Published: January 2021

Shigella dysenteriae are significant agents of bacillary dysentery, accounting for a considerable number of illnesses with high morbidity worldwide. The Shiga toxin (Stx) encoded by a defective prophage is the key virulence factor of S. dysenteriae type 1 (SD1) strains. Here we present the full genome sequence of an SD1 strain HNCMB 20080 isolated in 1954, compare it to other sequenced SD1 genomes, and assess the diversity of Stx-prophages harbored by previously sequenced SD1 strains. The genome of HNCMB 20080 consists of a chromosome sized 4,393,622 bp containing 5,183 CDSs, as well as two small plasmids. Comparative genomic analysis revealed a high degree of uniformity among SD1 genomes, including the structure of Stx prophage regions, which we found to form two subgroups termed PT-I and PT-II. All PT-I strains are members of the sequence type (ST) 146 or ST260, while the only PT-II harboring strain, Sd1617 proved to be ST untypeable. In accordance with data from previous reports, the Stx1 prophage could not be induced from HNCMB 20080. Our cumulative data do not support the notion that stx-harboring phages in STEC are derived from historical SD1 isolates.
NusG, an Ancient Yet Rapidly Evolving Transcription Factor
Authors: Wang Bing , Artsimovitch Irina
Published: January 2021

Timely and accurate RNA synthesis depends on accessory proteins that instruct RNA polymerase (RNAP) where and when to start and stop transcription. Among thousands of transcription factors, NusG/Spt5 stand out as the only universally conserved family of regulators. These proteins interact with RNAP to promote uninterrupted RNA synthesis and with diverse cellular partners to couple transcription to RNA processing, modification or translation, or to trigger premature termination of aberrant transcription. NusG homologs are present in all cells that utilize bacterial-type RNAP, from endosymbionts to plants, underscoring their ancient and essential function. Yet, in stark contrast to other core RNAP components, NusG family is actively evolving: horizontal gene transfer and sub-functionalization drive emergence of NusG paralogs, such as bacterial LoaP, RfaH, and UpxY. These specialized regulators activate a few (or just one) operons required for expression of antibiotics, capsules, secretion systems, toxins, and other niche-specific macromolecules. Despite their common origin and binding site on the RNAP, NusG homologs differ in their target selection, interacting partners and effects on RNA synthesis. Even among housekeeping NusGs from diverse bacteria, some factors promote pause-free transcription while others slow the RNAP down. Here, we discuss structure, function, and evolution of NusG proteins, focusing on unique mechanisms that determine their effects on gene expression and enable bacterial adaptation to diverse ecological niches.
Comparison of Cerebrospinal Fluid Amyloidogenic Nanoplaques With Core Biomarkers of Alzheimer’s Disease
Authors: Aksnes Mari , Tiiman Ann , Edwin Trine Holt , Terenius Lars , Bogdanović Nenad , Vukojević Vladana , Knapskog Anne-Brita
Published: January 2021

Accurate biomarkers of Alzheimer’s disease (AD) are essential for early diagnosis and intervention. Available biomarkers are not sufficient to permit the monitoring of AD progression over time, and additional biomarkers are required. Measures of aggregated amyloid-β (Aβ) could be useful biomarkers for AD. Here, we investigate whether levels of Thioflavin-T (ThT) positive amyloid aggregates, i.e., nanoplaques, in cerebrospinal fluid (CSF) could serve as useful biomarkers for AD. One-hundred and eighteen memory clinic patients were AT(N) classified, and CSF nanoplaque concentrations were compared between patients on the “Alzheimer’s continuum” (A+ patients) and patients with “Normal AD biomarkers” or “Non-AD pathologic change” (A− patients). CSF nanoplaque concentrations and sizes were quantified using the novel ThT-Fluorescence Correlation Spectroscopy (ThT-FCS) assay, and core biomarkers (Aβ42, total tau and phosphorylated tau) were determined by enzyme-linked immunosorbent assays. We investigated the association between nanoplaque concentrations and core biomarkers, and the diagnostic value of nanoplaque levels. Nanoplaque levels were increased in A+ patients compared to A− patients. Nanoplaque concentrations were negatively associated with Aβ42, but not related to total tau or phosphorylated tau measures. Quantification of nanoplaques did not improve the classification of patients on the Alzheimer’s continuum compared to the core biomarkers alone. Dynamic changes in nanoplaques concentration and size throughout AD stages should be explored in longitudinal studies.
Characterization of Feedback Neurons in the High-Level Visual Cortical Areas That Project Directly to the Primary Visual Cortex in the Cat
Authors: Pan Huijun , Zhang Shen , Pan Deng , Ye Zheng , Yu Hao , Ding Jian , Wang Qin , Sun Qingyan , Hua Tianmiao
Published: January 2021

Previous studies indicate that top-down influence plays a critical role in visual information processing and perceptual detection. However, the substrate that carries top-down influence remains poorly understood. Using a combined technique of retrograde neuronal tracing and immunofluorescent double labeling, we characterized the distribution and cell type of feedback neurons in cat’s high-level visual cortical areas that send direct connections to the primary visual cortex (V1: area 17). Our results showed: (1) the high-level visual cortex of area 21a at the ventral stream and PMLS area at the dorsal stream have a similar proportion of feedback neurons back projecting to the V1 area, (2) the distribution of feedback neurons in the higher-order visual area 21a and PMLS was significantly denser than in the intermediate visual cortex of area 19 and 18, (3) feedback neurons in all observed high-level visual cortex were found in layer II–III, IV, V, and VI, with a higher proportion in layer II–III, V, and VI than in layer IV, and (4) most feedback neurons were CaMKII-positive excitatory neurons, and few of them were identified as inhibitory GABAergic neurons. These results may argue against the segregation of ventral and dorsal streams during visual information processing, and support “reverse hierarchy theory” or interactive model proposing that recurrent connections between V1 and higher-order visual areas constitute the functional circuits that mediate visual perception. Also, the corticocortical feedback neurons from high-level visual cortical areas to the V1 area are mostly excitatory in nature.