Clinical and molecular characteristics of COVID-19 patients with persistent SARS-CoV-2 infection

AbstractThe characteristics of COVID-19 patients with persistent SARS-CoV-2 infection are not yet well described. Here, we compare the clinical and molecular features of patients with long duration of viral shedding (LDs) with those from patients with short duration patients (SDs), and healthy donors (HDs). We find that several cytokines and chemokines, such as interleukin (IL)-2, tumor necrosis factor (TNF) and lymphotoxin α (LT-α) are present at lower levels in LDs than SDs. Single-cell RNA sequencing shows that natural killer (NK) cells and CD14+ monocytes are reduced, while regulatory T cells are increased in LDs; moreover, T and NK cells in LDs are less activated than in SDs. Importantly, most cells in LDs show reduced expression of ribosomal protein (RP) genes and related pathways, with this inversed correlation between RP levels and infection duration further validated in 103 independent patients. Our results thus indicate that immunosuppression and low RP expression may be related to the persistence of the viral infection in COVID-19 patients.

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Clinical and molecular characteristics of COVID-19 patients with persistent SARS-CoV-2 infection

10.21203/rs.3.rs-86940/v1 ◽

2020 ◽

Author(s):

Chaoyang Sun ◽

Junpeng Fan ◽

Jia Huang ◽

Ensong Guo ◽

Yu Fu ◽

...

Keyword(s):

Nk Cells ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cell ◽

Cell Phenotype ◽

Molecular Characteristics ◽

Clinical Parameters ◽

Sequencing Data ◽

Viral Shedding ◽

Single Cell Rna Sequencing

Abstract The clinical features, molecular characteristics, and immune responses of COVID-19 patients with persistent SARS-CoV-2 infection are not yet well described. In this study, we investigated the differences in clinical parameters, laboratory indexes, plasma cytokines, and peripheral blood mononuclear cell responses, which were assessed using single-cell RNA-sequencing in patients with non-critical COVID-19 with long durations (LDs) and short durations (SDs) of viral shedding. Our results revealed that clinical parameters and laboratory indexes, such as c-reactive protein (CRP) and D-dimer, were comparable between SDs and LDs. Most inflammatory cytokines/chemokines, such as IL-2, IL2R, TNFα/β, IL1β, and CCL5 were present at low levels in LDs. Our single-cell RNA-sequencing revealed a reconfiguration of the peripheral immune cell phenotype in LDs, including decreases in natural killer (NK) cells and CD14+ monocytes and an increase in regulatory T cells (Tregs). Furthermore, most cell subsets in LDs consistently exhibited reduced expression of ribosomal protein (RP) genes, indicating dysfunctions in cytokine/chemokine synthesis, folding, modification, and assembly. Accordingly, the negative correlation between the RP levels and viral shedding duration was validated in an independent cohort of bulk-RNA-sequencing data from 103 non-critical patients, which may help guide clinical management and resource allocation. Moreover, peripheral T and NK cells and memory B cells in LDs likely failed to activate, which contributed to the persistence of viral shedding.

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Insights on Molecular Characteristics of Hydrochars by 13C-NMR and Off-Line TMAH-GC/MS and Assessment of Their Potential Use as Plant Growth Promoters

Molecules ◽

10.3390/molecules26041026 ◽

2021 ◽

Vol 26 (4) ◽

pp. 1026 ◽

Cited By ~ 1

Author(s):

Laís G. Fregolente ◽

João Vitor dos Santos ◽

Giovanni Vinci ◽

Alessandro Piccolo ◽

Altair B. Moreira ◽

...

Keyword(s):

Plant Growth ◽

Phosphoric Acid ◽

13C Nmr ◽

Chemical Properties ◽

Water Soluble ◽

Molecular Characteristics ◽

Initial Growth ◽

Growth Promoters ◽

Molecular Features ◽

Potential Use

Hydrochar is a carbon-based material that can be used as soil amendment. Since the physical-chemical properties of hydrochar are mainly assigned to process parameters, we aimed at evaluating the organic fraction of different hydrochars through 13C-NMR and off-line TMAH-GC/MS. Four hydrochars produced with sugarcane bagasse, vinasse and sulfuric or phosphoric acids were analyzed to elucidate the main molecular features. Germination and initial growth of maize seedlings were assessed using hydrochar water-soluble fraction to evaluate their potential use as growth promoters. The hydrochars prepared with phosphoric acid showed larger amounts of bioavailable lignin-derived structures. Although no differences were shown about the percentage of maize seeds germination, the hydrochar produced with phosphoric acid promoted a better seedling growth. For this sample, the greatest relative percentage of benzene derivatives and phenolic compounds were associated to hormone-like effects, responsible for stimulating shoot and root elongation. The reactions parameters proved to be determinant for the organic composition of hydrochar, exerting a strict influence on molecular features and plant growth response.

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The m15 Locus of Murine Cytomegalovirus Modulates Natural Killer Cell Responses to Promote Dissemination to the Salivary Glands and Viral Shedding

Pathogens ◽

10.3390/pathogens10070866 ◽

2021 ◽

Vol 10 (7) ◽

pp. 866

Author(s):

Baca Chan ◽

Maja Arapović ◽

Laura Masters ◽

Francois Rwandamuiye ◽

Stipan Jonjić ◽

...

Keyword(s):

Nk Cells ◽

Salivary Glands ◽

Natural Killer ◽

Nk Cell ◽

Acute Infection ◽

Killer Cell ◽

Viral Escape ◽

Murine Cytomegalovirus ◽

Viral Shedding ◽

Cell Responses

As the largest herpesviruses, the 230 kb genomes of cytomegaloviruses (CMVs) have increased our understanding of host immunity and viral escape mechanisms, although many of the annotated genes remain as yet uncharacterised. Here we identify the m15 locus of murine CMV (MCMV) as a viral modulator of natural killer (NK) cell immunity. We show that, rather than discrete transcripts from the m14, m15 and m16 genes as annotated, there are five 3′-coterminal transcripts expressed over this region, all utilising a consensus polyA tail at the end of the m16 gene. Functional inactivation of any one of these genes had no measurable impact on viral replication. However, disruption of all five transcripts led to significantly attenuated dissemination to, and replication in, the salivary glands of multiple strains of mice, but normal growth during acute infection. Disruption of the m15 locus was associated with heightened NK cell responses, including enhanced proliferation and IFNγ production. Depletion of NK cells, but not T cells, rescued salivary gland replication and viral shedding. These data demonstrate the identification of multiple transcripts expressed by a single locus which modulate, perhaps in a concerted fashion, the function of anti-viral NK cells.

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Isolation and characterization of Pseudomonas syringae isolates affecting stone fruits and almond in Montenegro

Journal of Plant Diseases and Protection ◽

10.1007/s41348-020-00417-8 ◽

2021 ◽

Author(s):

Tamara Popović ◽

Jelena Menković ◽

Anđelka Prokić ◽

Nevena Zlatković ◽

Aleksa Obradović

Keyword(s):

Pseudomonas Syringae ◽

Housekeeping Genes ◽

Molecular Characteristics ◽

Biochemical Tests ◽

High Genetic Diversity ◽

Leaf Petiole ◽

Molecular Features ◽

Isolation And Characterization ◽

Genomic Species

AbstractIn Montenegro, stone fruit species are grown on intensive and semi-intensive commercial plantations. However, almond production is mainly organized on family gardens and for household consumption. During two seasons (2017–2018), we surveyed apricot, peach, nectarine, sweet cherry, Japanese plum, and almond orchards for the presence of bacterial diseases at different geographical locations in Montenegro. From leaf, petiole and fruit lesions, branch or twig cankers, and necrotizing buds, a total of 29 isolates were obtained and subjected to identification based on their morphological, pathogenic, biochemical, and molecular characteristics. Pathogenicity of the isolates was confirmed by reproducing the symptoms on leaves, fruits, and twigs of the corresponding host plants. The biochemical tests indicated that the isolates belong to Pseudomonas syringae. However, isolates’ characterization showed variation in their phenotypic and molecular features. The presence of the syrB gene and ice nucleation activity grouped most of the isolates within pathovar syringae. The results of rep-PCR using the BOX primer revealed high genetic diversity of isolates. Multilocus sequence analysis (MLSA), using four housekeeping genes, showed that 27 isolates belong to the genomic species 1, P. syringae sensu stricto, corresponding to P. syringae phylogroup 2. However, isolates from the same phylogroup 2 did not form a monophyletic group. One strain isolated from apricot was most distinct and similar to members of genomic species 2, phylogroup 3. All tested isolates showed significant levels of resistance to copper sulfate and high level of sensitivity to streptomycin sulfate in vitro.

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Molecular Forces Governing the Biological Function of Per-Arnt-Sim-B (PAS-B) Domains: A Comparative Computational Study

Biophysica ◽

10.3390/biophysica1010001 ◽

2021 ◽

Vol 1 (1) ◽

pp. 1-14

Author(s):

João Victor de Souza ◽

Piotr Zaborniak ◽

Sylvia Reznikov ◽

Matthew Kondal ◽

Ruidi Zhu ◽

...

Keyword(s):

Juvenile Hormone ◽

Hormone Receptor ◽

Redox Regulation ◽

Biological Function ◽

Computational Study ◽

Sequence Similarity ◽

Molecular Characteristics ◽

Drosophila Suzukii ◽

Xenobiotic Stress ◽

Molecular Features

Per-Arnt-Sim (PAS) domains are evolutionarily-conserved regions found in proteins in all living systems, involved in transcriptional regulation and the response to hypoxic and xenobiotic stress. Despite having low primary sequence similarity, they show an impressively high structural conservation. Nonetheless, understanding the underlying mechanisms that drive the biological function of the PAS domains remains elusive. In this work, we used molecular dynamics simulations and bioinformatics tools in order the investigate the molecular characteristics that govern the intrinsic dynamics of five PAS-B domains (human AhR receptor, NCOA1, HIF1α, and HIF2α transcription factors, and Drosophila Suzukii (D. Suzukii) juvenile hormone receptor JHR). First, we investigated the effects of different length of N and C terminal regions of the AhR PAS-B domain, showing that truncation of those segments directly affects structural stability and aggregation propensity of the domain. Secondly, using the recently annotated PAS-B located in the methoprene-tolerant protein/juvenile hormone receptor (JHR) from D. Suzukii, we have shown that the mutation of the highly conserved “gatekeeper” tyrosine to phenylalanine (Y322F) does not affect the stability of the domain. Finally, we investigated possible redox-regulation of the AhR PAS-B domain by focusing on the cysteinome residues within PAS-B domains. The cysteines in AhR PAS-B are directly regulating the dynamics of the small molecule ligand-gating loop (residues 305 to 326). In conclusion, we comprehensibly described several molecular features governing the behaviour of PAS-B domains in solution, which may lead to a better understanding of the forces driving their biological functions.

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Clinical, Pathological and Molecular Characteristics of Chilean Patients with Early-, Intermediate- and Late-Onset Colorectal Cancer

Cells ◽

10.3390/cells10030631 ◽

2021 ◽

Vol 10 (3) ◽

pp. 631

Author(s):

Karin Alvarez ◽

Alessandra Cassana ◽

Marjorie De La Fuente ◽

Tamara Canales ◽

Mario Abedrapo ◽

...

Keyword(s):

Colorectal Cancer ◽

Family History ◽

Age Of Onset ◽

Late Onset ◽

Molecular Characteristics ◽

Family History Of Cancer ◽

Molecular Features ◽

Age Of Diagnosis ◽

History Of ◽

History Of Cancer

Colorectal cancer (CRC) is the second most frequent neoplasm in Chile and its mortality rate is rising in all ages. However, studies characterizing CRC according to the age of onset are still lacking. This study aimed to identify clinical, pathological, and molecular features of CRC in Chilean patients according to the age of diagnosis: early- (≤50 years; EOCRC), intermediate- (51–69 years; IOCRC), and late-onset (≥70 years; LOCRC). The study included 426 CRC patients from Clinica Las Condes, between 2007 and 2019. A chi-square test was applied to explore associations between age of onset and clinicopathological characteristics. Body Mass Index (BMI) differences according to age of diagnosis was evaluated through t-test. Overall (OS) and cancer-specific survival (CSS) were estimated by the Kaplan–Meier method. We found significant differences between the age of onset, and gender, BMI, family history of cancer, TNM Classification of Malignant Tumors stage, OS, and CSS. EOCRC category was characterized by a family history of cancer, left-sided tumors with a more advanced stage of the disease but better survival at 10 years, and lower microsatellite instability (MSI), with predominant germline mutations. IOCRC has shown clinical similarities with the EOCRC and molecular similarities to the LOCRC, which agrees with other reports.

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The effect of HLA–DR on susceptibility to rheumatoid arthritis is influenced by the associated lymphotoxin α–tumor necrosis factor haplotype

Arthritis & Rheumatism ◽

10.1002/art.10719 ◽

2003 ◽

Vol 48 (1) ◽

pp. 90-96 ◽

Cited By ~ 46

Author(s):

Julia Newton ◽

Matthew A. Brown ◽

Anita Milicic ◽

Hans Ackerman ◽

Chris Darke ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Tumor Necrosis Factor ◽

Tumor Necrosis ◽

Hla Dr ◽

Lymphotoxin Α ◽

Necrosis Factor

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NK-dependent DC maturation is mediated by TNFα and IFNγ released upon engagement of the NKp30 triggering receptor

Blood ◽

10.1182/blood-2004-10-4035 ◽

2005 ◽

Vol 106 (2) ◽

pp. 566-571 ◽

Cited By ~ 268

Author(s):

Massimo Vitale ◽

Mariella Della Chiesa ◽

Simona Carlomagno ◽

Daniela Pende ◽

Maurizio Aricò ◽

...

Keyword(s):

Nk Cells ◽

Tumor Necrosis ◽

Tumor Necrosis Factor Α ◽

Nk Cell ◽

Interferon Γ ◽

Cell Functions ◽

Relevant Role ◽

Factor Α ◽

Necrosis Factor ◽

Dc Maturation

Abstract Natural killer (NK) cells were recently shown to play a relevant role in the process of dendritic cell (DC) maturation. This function is exerted either by direct DC stimulation or through killing those DCs that did not properly acquire a mature phenotype. While killing of immature DCs is dependent on the function of the NKp30 triggering receptor, the mechanism by which NK cells induce DC maturation is still unclear. In this study, we show that also the NK-mediated induction of DC maturation is dependent on NKp30. Upon NK/DC interaction, resulting in NKp30 engagement, NK cells produced tumor necrosis factor α (TNFα) (and interferon γ [IFNγ]) that, in turn, promoted DC maturation. Masking of NKp30 with specific monoclonal antibodies (mAbs) strongly reduced maturation of DCs cocultured with NK cells. In addition, supernatant from NK cells stimulated via NKp30 induced DC maturation, and this effect was neutralized by anti-TNFα antibodies (Abs). This NKp30 function is controlled by the HLA-specific inhibitory NK receptors. Accordingly, the ability to promote maturation was essentially confined to NK cells expressing the killer immunoglobulin-like receptor–negative (KIR–) NKG2Adull phenotype. Finally, the analysis of perforin-deficient NK cells allowed the dissection of the 2 NKp30-mediated NK-cell functions, since NKp30 could induce cytokine-dependent DC maturation in the absence of NK-mediated DC killing.

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Involvement of fractalkine and macrophage inflammatory protein-1 alpha in moderate-severe depression

Mediators of Inflammation ◽

10.1080/09511920410001713484 ◽

2004 ◽

Vol 13 (3) ◽

pp. 205-207 ◽

Cited By ~ 21

Author(s):

Rosaria Alba Merendino ◽

Giuseppe Di Pasquale ◽

Filippo De Luca ◽

Laura Di Pasquale ◽

Edoardo Ferlazzo ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Immune Therapy ◽

Severe Depression ◽

Mononuclear Phagocytes ◽

Cytokines And Chemokines ◽

Inflammatory Protein ◽

Healthy Donors ◽

The Central Nervous System ◽

Macrophage Inflammatory Protein

MODERATE-severe depression (MSD) is linked to overexpression of proinflammatory cytokines and chemokines. Fractalkine (FKN) and macrophage inflammatory protein-1 alpha (MIP-1α) are, respectively, members of CX3C and C-C chemokines, and both are involved in recruiting and activating mononuclear phagocytes in the central nervous system. We analysed the presence of FKN and MIP-1α in sera of untreated MSD patients and healthy donors. High FKN levels were observed in all MSD patients as compared with values only detectable in 26% of healthy donors. MIP-1α was measurable in 20% of patients, while no healthy donors showed detectable chemokine levels. In conclusion, we describe a previously unknown involvement of FKN in the pathogenesis of MSD, suggesting that FKN may represent a target for a specific immune therapy of this disease.

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Functional domains of HSP70 stimulate generation of cytokines and chemokines, maturation of dendritic cells and adjuvanticity

Biochemical Society Transactions ◽

10.1042/bst0320629 ◽

2004 ◽

Vol 32 (4) ◽

pp. 629-632 ◽

Cited By ~ 65

Author(s):

T. Lehner ◽

Y. Wang ◽

T. Whittall ◽

E. McGowan ◽

C.G. Kelly ◽

...

Keyword(s):

Amino Acids ◽

Dendritic Cells ◽

Immune Responses ◽

Cd40 Ligand ◽

Interleukin 12 ◽

Cytokines And Chemokines ◽

Cc Chemokines ◽

Factor Α ◽

Antigen Presenting ◽

Necrosis Factor

Microbial HSP70 (heat-shock protein 70) consists of three functionally distinct domains: an N-terminal 44 kDa ATPase portion (amino acids 1–358), followed by an 18 kDa peptide-binding domain (amino acids 359–494) and a C-terminal 10 kDa fragment (amino acids 495–609). Immunological functions of these three different domains in stimulating monocytes and dendritic cells have not been fully defined. However, the C-terminal portion (amino acids 359–610) stimulates the production of CC chemokines, IL-12 (interleukin-12), TNFα(tumour necrosis factor α), NO and maturation of dendritic cells and also functions as an adjuvant in the induction of immune responses. In contrast, the ATPase domain of microbial HSP70 mostly lacks these functions. Since the receptor for HSP70 is CD40, which with its CD40 ligand constitutes a major co-stimulatory pathway in the interaction between antigen-presenting cells and T-cells, HSP70 may function as an alternative ligand to CD40L. HSP70–CD40 interaction has been demonstrated in non-human primates to play a role in HIV infection, in protection against Mycobacterium tuberculosis and in conversion of tolerance to immunity.

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