Phenotypic Characteristics Research Articles

Genotypic and phenotypic characterization of some virulence genes of Campylobacter species isolated from fresh meat

Genotypic and phenotypic characterization of some virulence genes of Campylobacter species isolated from fresh meat

Resectable Non-Small Cell Lung Cancer Heterogeneity and Recurrence Assessed by Tissue Next-Generation Sequencing Genotyping and Circulating Tumor Cell EZH2 Characterization

IntroductionNon-small cell lung cancer (NSCLC) is the most common type of lung neoplasm. Despite surgical resection, it has a high relapse rate, accounting for 30–55% of all cases. Next-generation sequencing (NGS) based on a customized gene panel and the analysis of circulating tumor cells (CTCs) can help identify heterogeneity, stratify high-risk patients, and guide treatment decisions. In this descriptive study involving a small prospective cohort, we focus on the phenotypic characterization of CTCs, particularly concerning EZH2 expression (a member of the Polycomb Repression Complex 2), as well as on the mutation profiles of the tissue using a customized gene panel and their association with poor outcomes in NSCLC. MethodsIsolation and characterization of EZH2 on CTCs were evaluated before surgical resection (CTC1) and one month after surgery (CTC2) in resectable NSCLC patients. Targeted NGS was performed using a customized 50-gene panel on tissue samples from a subset of patients. Results76 patients with resectable NSCLC were recruited. The top mutated genes in the cohort included TP53, FLT1, MUC5AC, EGFR, and NLRP3. Pair of genes that had mutually exclusive mutations was TP53-RIN3, and pairs of genes with co-occurring mutations were CD163-TLR4, FGF10-FOXP2, ADAMTSL3-FLT1, ADAMTSL3-MUC5AC and MUC5AC-NLRP3. CTCs decreased significantly between the two time points CTC1 and CTC2 (p<0.0001), and CTCs+ patients with high EZH2 expression had an 87% increased risk of death (p=0.018). ConclusionsIntegrating molecular profiling of tumors and CTC characterization can provide valuable insights into tumor heterogeneity and improve patient stratification for resectable NSCLC.

Phenotypic Characterisation of Obstructive Sleep Apnoea in Acute Coronary Syndrome

Recent neutral randomised clinical trials have created clinical equipoise for treating obstructive sleep apnoea (OSA) for managing cardiovascular risk. The importance of defining the links between OSA and cardiovascular disease is needed with the aim of advancing the robustness of future clinical trials. We aimed to define the clinical correlates and characterise surrogate cardiovascular markers in patients with acute coronary syndrome (ACS) and OSA. Overall, 66 patients diagnosed with ACS were studied. Patients underwent an unattended polysomnogram after hospital discharge (median [interquartile range] 62 [37-132] days). The Epworth Sleepiness Scale, Berlin, and STOP-BANG questionnaires were administered. Surrogate measures of vascular structure and function, and cardiovascular autonomic function were conducted. Pulse wave amplitude drop was derived from the pulse oximetry signals of the overnight polysomnogram. OSA (apnoea-hypopnea index [AHI] ≥5) was diagnosed in 94% of patients. Moderate-to-severe OSA (AHI≥15) was observed in 68% of patients. Daytime sleepiness (Epworth Sleepiness Scale ≥10) was reported in 17% of patients. OSA screening questionnaires were inadequate to identify moderate-to-severe OSA, with an area under the receiver operating characteristic curve of approximately 0.64. Arterial stiffness (carotid-femoral pulse wave velocity, 6.1 [5.2-6.8] vs 7.4 [6.6-8.6] m/s, p=0.002) and carotid intima-media thickness (0.8 [0.7-1.0] vs 0.9 [0.8-1.0] mm, p=0.027) was elevated in patients with moderate-to-severe OSA. After adjusting for age, sex and body mass index, these relationships were not statistically significant. No relationships were observed in other surrogate cardiovascular markers. A high prevalence of OSA in a mostly non-sleepy population with ACS was identified, highlighting a gross underdiagnosis of OSA among cardiovascular patients. The limitations of OSA screening questionnaires highlight the need for new models of OSA screening as part of cardiovascular risk management. A range of inconsistent abnormalities were observed in measures of vascular structure and function, and these appear to be largely explained by confounding factors. Further research is required to elucidate biomarkers for the presence and impact of OSA in ACS patients.

Genomic and phenotypic characterization of the Oropouche virus strain implicated in the 2022-24 large-scale outbreak in Brazil.

The Orthobunyavirus oropoucheense species encompasses a group of arthropod-borne zoonotic viruses transmitted by biting midges to animals including humans. Several large-scale human outbreaks caused by the prototype member of this species, Oropouche virus (OROV) have been documented since the 1970s and were primarily confined to the Amazon basin. However, since 2022, more widespread OROV outbreaks have been unfolding in Brazil and across South America, with cases exported to Cuba, Italy, Spain, USA and Germany. In Brazil, the virus has reached and established communitary transmission in all geographic areas of the country. We isolated, characterized the cytopathic effect and recovered the full genome of two OROV isolates from the 2022-24 outbreak detected in patients from the Pernambuco state. Phylogenetic data supports a direct introduction from the Amazonas state, the epicenter of the epidemics in the country. As case counts accumulate in the state mounting evidence is supporting the establishiment of sustained transmission chains. Continued studies are critical to understand the transmission cycle in this region, including the most important vectors and reservoirs, to appropriately deploy control measures.

Phenotypic Characterization of Patients with ADPKD with PKD1 and PKD2 Pathogenic Variants Using Advanced Imaging Biomarkers

Phenotypic Characterization of Patients with ADPKD with PKD1 and PKD2 Pathogenic Variants Using Advanced Imaging Biomarkers

Differential Selection for Survival and for Growth in Adaptive Laboratory Evolution Experiments With Benzalkonium Chloride.

Biocides are used to control microorganisms across different applications, but emerging resistance may pose risks for those applications. Resistance to biocides has commonly been studied using adaptive laboratory evolution (ALE) experiments with growth at subinhibitory concentrations linked to serial subculturing. It has been shown recently that Escherichia coli adapts to repeated lethal stress imposed by the biocide benzalkonium chloride (BAC) by increased survival (i.e., tolerance) and not by evolving the ability to grow at increased concentrations (i.e., resistance). Here, we investigate the contributions of evolution for tolerance as opposed to resistance for the outcome of ALE experiments with E. coli exposed to BAC. We find that BAC concentrations close to the half maximal effective concentration (EC50, 4.36 μg mL-1) show initial killing (~40%) before the population resumes growth. This indicates that cells face a two-fold selection pressure: for increased survival and for increased growth. To disentangle the effects of both selection pressures, we conducted two ALE experiments: (i) one with initial killing and continued stress close to the EC50 during growth and (ii) another with initial killing and no stress during growth. Phenotypic characterization of adapted populations showed that growth at higher BAC concentrations was only selected for when BAC was present during growth. Whole genome sequencing revealed distinct differences in mutated genes across treatments. Treatments selecting for survival-only led to mutations in genes for metabolic regulation (cyaA) and cellular structure (flagella fliJ), while treatments selecting for growth and survival led to mutations in genes related to stress response (hslO and tufA). Our results demonstrate that serial subculture ALE experiments with an antimicrobial at subinhibitory concentrations can select for increased growth and survival. This finding has implications for the design of ALE experiments to assess resistance risks of antimicrobials in different scenarios such as disinfection, preservation, and environmental pollution.

Loss of Hdac4 in Osteoprogenitors Impairs Postnatal Trabecular and Cortical Bone Formation, Resulting in a Dwarfism and Osteopenia Phenotype in Mice

HDAC4 is a class II histone deacetylation protein with a well-characterized role in chondrocyte differentiation and skeletal development, and dysregulated expression or haploinsufficiency of Hdac4 leads to skeletal formation and malformation disorders. The early lethality of hdac4 ablation mice hindered further investigation of its role in postnatal bone growth and development. Therefore, this study aims to investigate the significant role of Hdac4 in postnatal endochondral bone development using two mouse models with conditional deletion of Hdac4 in Sp7-expressing osteoprogenitors or chondrocytes and monitored postnatal bone development. The phenotype of Acan-CreERT2; Hdac4fl/fl mice largely resembled that of conventional Hdac4-/- mice. But phenotypic characterizations of mice with Hdac4 inactivation in Sp7-expressing osteoprogenitors (Sp7-Cre; Hdac4fl/fl) showed dwarfism with body and limb shortening and remarkable skeletal defects. Micro-computed tomography analysis of tibias further demonstrated that loss of Hdac4 expression impaired bone formation and microarchitecture, mainly characterized by dysplasia of trabecular and cortical bone in young mice. Our in vivo and in vitro data support a crucial role for Hdac4 in regulating osteoblast proliferation and differentiation, bone matrix protein production, angiogenesis, and ultimately trabecular and cortical bone formation. Moreover, RNA-seq analysis implicated Hdac4 in the regulation of key genes and pathways necessary to affect the accumulation of extracellular matrix, biological processes related to signal transduction, and skeletal growth. Collectively, our data show that postnatal expression of Hdac4 in Sp7-expressing osteoprogenitors provides essential regulatory oversight of endochondral bone formation, bone morphology, and homeostasis.

Cardiac MRI in Duchenne and Becker Muscular Dystrophy.

Cardiovascular magnetic resonance imaging (CMRI) is the noninvasive technique of choice for early detection of cardiac involvement in Duchenne and Becker muscular dystrophy (DMD and BMD, respectively), but is seldom used in routine clinical practice in the Indian context. We sought to determine the prevalence of CMRI abnormalities in patients with DMD and BMD and to compare the CMRI parameters with the phenotypic and genotypic characteristics. A prospective, observational study was conducted on patients genetically diagnosed with DMD and BMD who could complete CMRI between March 2020 and March 2022. Abnormal CMRI was the presence of any late gadolinium enhancement (LGE) that signifies myocardial fibrosis (LGE positivity), regional wall motion abnormality, or reduced left ventricular ejection fraction (LVEF <55%). A total of 46 patients were included: 38 patients with DMD and eight with BMD. Cardiac abnormality was seen in 23 (50%) patients. LGE was more common than impaired LVEF in DMD (16, 42.1%), while impaired LVEF was more common in BMD (5, 62.5%). LGE was most frequently found in lateral wall (18/19) followed by inferior (6/19), septal (5/19), anterior (2/19), and apex (1/19). Among the various clinicodemographic parameters, only age (r = 0.495, P = 0.002) and disease duration (r = 0.407, P = 0.011) were found to significantly correlate with LGE in patients with DMD. No association was found between the various CMRI parameters and the genotype. The current study highlights the differences in myocardial fibrosis and LV dysfunction between DMD and BMD, along with other CMRI parameters. Notably, a genotype-CMRI correlation was not found in the current cohort, which needs to be further explored.

Phenotypic Isolation and Characterization of Bacterial Isolates and Incidence of Multi-Drug-ResistantStrains from Surgical Site Infected Patients of Tertiary Care Hospital, Tamil Nadu

Phenotypic Isolation and Characterization of Bacterial Isolates and Incidence of Multi-Drug-ResistantStrains from Surgical Site Infected Patients of Tertiary Care Hospital, Tamil Nadu

Molecular screening of potential Bacillus species bacteriocin starter cultures isolated from Nigerian fermented condiments

Traditional fermented food condiments in Nigeria are majorly produced by using protein-rich leguminous seeds via spontaneous fermentation or back slopping. However, health risks such as the production of biogenic amines, presence of toxigenic genes and food borne pathogens remains major concerns of public health significance. Hence, the need for the production of safe condiments using non-pathogenic food-grade starter cultures. Isolation and characterization of organisms from spontaneously fermented condiments made from Parkia biglobosa, Ricinus communis, Pentaclethra macrophylla and Prosopis africana was done using standard methods. Phenotypic and biochemical characterizations was down using established protocols while molecular identification was done using 16S rRNA sequencing. Results obtained showed that the microbial load (cfu/ml) recorded from the spontaneously fermented condiments ranged from: 2.1×107-5.2×1012, 15.2×107-4.4×1010, 4.4×1010-4.4×1012 and 6.4×107-1.6×1012 for P. biglobosa, R. communis, P. macrophylla and P. africana respectively. Identification of isolates revealed Bacillus. However, 22.8% of the Bacillus isolates harboured HblA and HblD genes while 40.9 % showed bands for the presence of HblC genes. In addition, the percentage occurrence of 18.1%, 27.2% and 50% was obtained for the presence of NheA, NheB and NheC genes respectively while none of the Bacillus isolates showed bands for the presence of Cytk and EM1 genes. More so, five Bacillus isolates were identified to be non-toxigenic, showing bands only for Bac, Osbo and Spas genes which are bacteriocin producing genes. Put together, the identified non-toxigenic food-grade Bacillus species recorded in this study can be recommended as potential bacteriocin starter cultures for the fermentation of microbiologically safe food products.

Hydroxychloroquine-Mediated Autophagy Inhibition Shifts Monocyte-Derived Dendritic Cells Toward Immunogenic Phenotype In Vitro

Dendritic cells (DCs) are recognized as the most potent antigen-presenting cells (APCs) and act as intermediaries between the innate and adaptive immune systems. The maturation and function of DCs are significantly influenced by autophagy. Hence, the current research evaluated the effect of hydroxychloroquine (HCQ), an autophagy inhibitor, on the maturation and activation of monocyte-derived DCs. Monocytes were cultured and induced to differentiate into monocyte-derived DCs by the addition of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4) cytokines. After five days, the immature DCs were exposed to HCQ and Lipopolysaccharides (LPS), followed by a 24-hour incubation period. On the sixth day, the flow cytometry technique was employed to assess the impact of HCQ on the phenotypic characteristics of the DCs. Finally, the expression of both pro- and anti-inflammatory genes in the HCQ-treated and untreated DCs groups was examined using the real-time PCR method. DCs that were subjected to treatment with HCQ exhibited a notable augmentation in the expression of CD11c, CD86, and HLA-DR, which are markers associated with maturation and antigen presentation. Furthermore, the DCs treated with HCQ demonstrated a significant reduction in the expression of IL-10, TGF-β, and IDO genes, while displaying an increase in the expression of TNF-α and IL-12 when compared to the control group. These findings indicate that targeting autophagy can induce a shift in DCs towards an immunogenic state. However, further investigations are necessary to assess the impact of HCQ-treated DCs on T cell responses both in vitro and in vivo in tumor-bearing animal models.

Joint self-supervised and supervised contrastive learning for multimodal MRI data: Towards predicting abnormal neurodevelopment

The integration of different imaging modalities, such as structural, diffusion tensor, and functional magnetic resonance imaging, with deep learning models has yielded promising outcomes in discerning phenotypic characteristics and enhancing disease diagnosis. The development of such a technique hinges on the efficient fusion of heterogeneous multimodal features, which initially reside within distinct representation spaces. Naively fusing the multimodal features does not adequately capture the complementary information and could even produce redundancy. In this work, we present a novel joint self-supervised and supervised contrastive learning method to learn the robust latent feature representation from multimodal MRI data, allowing the projection of heterogeneous features into a shared common space, and thereby amalgamating both complementary and analogous information across various modalities and among similar subjects. We performed a comparative analysis between our proposed method and alternative deep multimodal learning approaches. Through extensive experiments on two independent datasets, the results demonstrated that our method is significantly superior to several other deep multimodal learning methods in predicting abnormal neurodevelopment. Our method has the capability to facilitate computer-aided diagnosis within clinical practice, harnessing the power of multimodal data. The source code of the proposed model is publicly accessible on GitHub: https://github.com/leonzyzy/Contrastive-Network.

Prevalence of viviparous germination as a function of seasonal conditions and seed phenotypic characteristics in the bottle gourd Lagenaria siceraria (Molina) Standley (Cucurbitaceae)

Selection for resistance to viviparous germination is an important step and one of the most effective strategies for solving the problem of vivipary in orthodox seed species. Vivipary generally occurs when mature fruits are exposed to rain. To understand the existing relationships between seed phenotypic characteristics, seasonal conditions and the prevalence of vivipary in Lagenaria siceraria, experiments were carried out under natural conditions during the short and long rainy seasons of 2014 and 2015. Three main conclusions were drawn from the results. Firstly, yellowish seeds with a soft seed coat without a cap and yellowish seeds with a soft seed coat with a thin cap were more susceptible to vivipary with prevalences of 37.64% and 29.75% respectively. The whitish seeds with a hard seed coat and no cap, the brown seeds with a hard seed coat and no cap, the yellowish seeds with a soft seed coat and a thick cap and the seeds with a soft seed coat and a brown cap did not show vivipary whatever the intensity of the rain preceding harvest. Secondly, although the prevalence of vivipary was affected by the interaction of phenotype and rainy seasons, it explained only 7.57% of the variation. Most of the variation in vivipary prevalence was related to seed phenotype (68.33%) indicating that seed phenotype is the main factor influencing vivipary prevalence in L. siceraria. Finally, vivipary prevalence was strongly and positively correlated with rainfall and humidity in viviparous genotypes, whereas non-viviparous genotypes were not affected by climatic parameters.

Crop Improvement of Moringa oleifera L. through Genotype Screening for the Development of Clonal Propagation Techniques of High-Yielding Clones in Malaysia.

Moringa oleifera L. is a valuable multipurpose tree species widely planted for centuries due to its high medicinal value and antifungal, antiviral, antidepressant, and anti-inflammatory properties in the food industry. However, its cultivation is hindered by production constraints such as the unavailability of planting material and the inadequate number of high-yielding clones. Thus, a study was initiated to select high-yielding clones in terms of growth and chemical content for the mass propagation of superior moringa trees. Screening on high-yielding clones with high astragalin content was conducted through the high-performance liquid chromatography (HPLC) analysis of moringa leaf extract. Selected genotypes were evaluated for their anti-inflammatory potential through in vitro bioactivity assays of leaf methanol extract. The effects of the rooting hormone, rooting substrates, and size of the cutting on the rooting response of branch cuttings of moringa were investigated. Results found that samples collected from different ecological zones of Peninsular Malaysia show significant variation in terms of astragalin content. The extracts were observed to show considerable variation in biological activity against the pro-inflammatory enzymes. The size of the cuttings had significant effects on the rooting of the cuttings as longer cuttings with bigger diameters rooted better than shorter cuttings with smaller diameters. Several genotypes of M. oleifera with superior phenotypic characteristics and bioactive compounds have been identified. Factors affecting the rooting efficiency and optimal conditions of rooting are suggested, which provides valuable information for the propagation of the superior planting material of moringa. This effort will ensure the sustainable production and supply of good quality raw materials for the production of quality end-products for the food and pharmaceutical industry.

Phenotypic variations in knee osteoarthritis: insights from MRI and radiographic comparisons.

To investigate the correlation between MRI-based phenotypes (cartilage-meniscus, subchondral bone, and inflammatory) and radiography-based atrophic and hypertrophic phenotypes, aiming to demonstrate MRI's diagnostic capability in identifying complex osteoarthritis phenotypes that radiography cannot fully capture. This single-center retrospective study examined knee radiographs and MRIs of patients from November 2021 to April 2023 to identify osteoarthritis phenotypes. Radiographs were staged by the Kellgren-Lawrence system, and both modalities were classified into atrophic or hypertrophic phenotypes. MRIs were further classified into three phenotypes: cartilage-meniscus, subchondral bone, and inflammatory. Associations between phenotypes, Kellgren-Lawrence stage, age, and gender were analyzed with Pearson chi-square test and student T-test. Reliability measurements were evaluated using kappa statistic. A total of 214 knees from 187 individuals (73.3% women, 26.7% men; mean age 57.1 ± 9.1years) were included. The hypertrophic MRI phenotype was significantly associated with cartilage-meniscus and subchondral bone phenotypes (p < 0.001). Cartilage-meniscus and subchondral bone phenotypes were less prevalent in Kellgren-Lawrence stage 2 than in stages 3 and 4 (p < 0.001 and p = 0.004, respectively). The subchondral bone phenotype was more common in men (p = 0.022), and the cartilage-meniscus phenotype in the elderly (p < 0.001). Radiography and MRI had substantial agreement (Kappa = 0.637, p < 0.001) in diagnosing hypertrophic and atrophic phenotypes. The hypertrophic phenotype was associated with cartilage-meniscus and subchondral bone phenotypes, with lower prevalences in Kellgren-Lawrence stage 2 knees. MRI offers enhanced phenotypic characterization, which facilitates more precise and individualized management in osteoarthritis care. Despite limitations compared to MRI, radiography remains valuable for the evaluation of hypertrophic and atrophic phenotypes.

Characterization of Vitronectin Effect in 3D Ewing Sarcoma Models: A Digital Microscopic Analysis of Two Cell Lines.

Ewing sarcoma (ES) is an aggressive bone and soft-tissue pediatric cancer. High vitronectin (VN) expression has been associated with poor prognosis in other cancers, and we aimed to determine the utility of this extracellular matrix glycoprotein as a biomarker of aggressiveness in ES. Silk fibroin plus gelatin-tyramine hydrogels (HGs) were fabricated with and without cross-linked VN and cultivated with A673 and PDX73 ES cell lines for two and three weeks. VN secretion to culture media was assessed using ELISA. Morphometric analysis was applied for phenotypic characterization. VN release to culture media was higher in 3D models than in monolayer cultures, and intracellular, intercellular, and pericluster presence was also observed. A673-HGs showed lower density of clusters but a proportion of larger clusters than PDX73-HGs, which presented low cluster circularity. The cluster density of A673-HGs without added VN was higher than with added VN and slightly lower in the case of PDX73-HGs. Furthermore, a culture time of three weeks provided no benefits in cluster growth compared to two weeks, especially in A673-HGs. These advances in 3D modeling and digital quantification pave the way for future studies in ES and other cancers to deepen understanding about intra- and intercellular heterogeneity and anti-adhesion VN therapies.

SARS-CoV-2-Specific T-Cell as a Potent Therapeutic Strategy against Immune Evasion of Emerging COVID-19 Variants.

Despite advances in vaccination and therapies for coronavirus disease, challenges remain due to reduced antibody longevity and the emergence of virulent variants like Omicron (BA.1) and its subvariants (BA.1.1, BA.2, BA.3, and BA.5). This study explored the potential of adoptive immunotherapy and harnessing the protective abilities using virus-specific T cells (VSTs). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) VSTs were generated by stimulating donor-derived peripheral blood mononuclear cells with spike, nucleocapsid, and membrane protein peptide mixtures. Phenotypic characterization, including T-cell receptor (TCR) vβ and pentamer analyses, was performed on the ex vivo-expanded cells. We infected human leukocyte antigen (HLA)-partially matched human Calu-3 cells with various authentic SARS-CoV-2 strains in a Biosafety Level 3 facility and co-cultured them with VSTs. VSTs exhibited a diverse TCR vβ repertoire, confirming their ability to target a broad range of SARS-CoV-2 antigens from both the ancestral and mutant strains, including Omicron BA.1 and BA.5. These ex vivo-expanded cells exhibited robust cytotoxicity and low alloreactivity against HLA-partially matched SARS-CoV-2-infected cells. Their cytotoxic effects were consistent across variants, targeting conserved spike and nucleocapsid epitopes. Our findings suggest that third-party partial HLA-matching VSTs could counter immune-escape mechanisms posed by emerging variants of concern.

Extracellular Vesicle-Based Characterization of Stem Cell Phenotype in Glioblastomas.

Glioblastoma (GB) is the most common brain malignancy occurring in adult patients having an extremely low overall survival. Therefore, it is paramount to establish reliable and accurate diagnostic and prognostic markers to guide a personalized and more effective treatment. Molecular characterization of the tumor is the ultimate goal in GB management and comprises, among others, the study of the extracellular vesicles (EVs). Not only do they carry within their cargo molecules involved in shaping a favorable microenvironment for GB development, but EVs also present surface markers mirroring the phenotype of the donor cells. Our study aims to assess the dynamic evolution of EV-positive surface biomarkers and EV-derived proteins involved in maintaining and transferring a stem cell phenotype to the cells from GB surroundings. We performed a prospective observational study on GB patients operated on in the Neurosurgery Clinic of the Emergency Clinical County Hospital of Târgu Mureș, Romania. GB-derived EVs were isolated from the patients' plasma using a density gradient ultracentrifugation protocol. The expression of EVs positive to four epitopes specific to stem cells (CD44, CD133, CD326/EpCAM, and SSEA4) was followed in three moments in time, preoperatively, seven days, and three months postoperatively, respectively, and quantified by a bead-based multiple analysis using flow cytometry. Moreover, NANOGP8, a protein within GB cargo capable of promoting a stem cell phenotype, was dynamically evaluated using the Western blot technique. Our study showed a statistically significant decrease of all surface markers and NANOGP8 immediately after tumor ablation. Nonetheless, the long-term follow-up of the patients revealed an extremely variable evolutionary pattern reflecting the high heterogeneity of GB. Further studies are necessary to either confirm or infirm the accuracy of these markers in early diagnosing GB, in predicting the outcome of this disease, and in guiding an individualized therapy.

Lelliottia wanjuensis sp. nov. Isolated from Korean Lettuce in Wanju, South Korea

Ten Gram stain-negative, oxidase-negative, catalase-positive, rod-shaped strains were isolated from lettuce in the city Wanju in South Korea. Comparative 16S rRNA gene analysis and multilocus sequence analysis indicated that the strains grouped closely together with all other Lelliottia (L.)-type strains. The average nucleotide identity (ANI) comparisons of the isolates showed a high relationship between the strains, as the ANI values of all strains ranged from 91.01 to 91.31% when compared to the L. jeotgali-type strain PFL01T. All isolates showed the highest genomic DNA sequence similarity to the L. jeotgali PFL01T strain at 43.3% when compared with digital DNA–DNA hybridization (dDDH). Strain V104_15T of the proposed novel Lelliottia species showed 91.2% and 43.3% similarity with the most closely related L. jeotgali PFL01T-type strain in the ANI and dDDH comparisons, respectively. Strain V104_15T could not grow at 45 °C and 7% NaCl, while L. jeotgali PFL01T strain could grow at both these conditions. Strain V104_15T showed ß-glucosidase activity but not α-glucosidase activity, while the L. jeotgali PFL01T strain was α-glucosidase positive but ß-glucosidase negative. The major cellular fatty acids of strain V104_15T were C16:0 and cyclo-C17:0 including summed features. The mol % G + C content of the genomic DNA of strain V104_15T was 55.74%. Phenotypic and biochemical characteristics, as well as the phylogenomic analysis indicated that the strain V104_15T represents a novel species of the genus Lelliottia, for which the name Lelliottia wanjuensis sp. nov. is proposed. The type strain is V104_15T (= LMG 32996 T = DSM 115585 T).

Novel endothelial progenitor cells populations as biomarkers of damage and remission in systemic lupus erythematosus

IntroductionEndothelial progenitor cells (EPCs) are essential for maintenance of vascular homeostasis and stability, key processes in the pathogenesis of systemic lupus erythematosus (SLE). However, the role and phenotypic characterization of EPCs populations in SLE have not been completely elucidated.ObjectiveTo identify EPCs specific subpopulations in patients with SLE using a novel flow cytometry tool.MethodsPeripheral blood mononuclear cells (PBMCs) were isolated from patients with SLE and healthy controls (HC). mRNA and surface protein expression were determined by quantitative PCR (qPCR) and flow cytometry. Clusters identification and characterization were performed using tSNE-CUDA dimensionality reduction algorithms.ResultstSNE-CUDA analysis identified eight different clusters in PBMCs from HC and patients with SLE. Three of these clusters had EPC-like phenotype and the expression was elevated in patients with SLE. Moreover, four SLE-associated subclusters were found mainly expressed in patients with SLE, being only present in patients in remission with SLE and significantly associated with the 2021 Definition of Remission in SLE. Importantly, we also identified specific clusters in SLE patients with organ damage, according to the Systemic Lupus International Collaborating Clinics (SLICC)/American College of Rheumatology damage index (SDI). These clusters showed an EPC-like phenotype, but the expression of angiogenic markers was lower compared to HC or patients without organ damage, suggesting an impaired angiogenic function.ConclusionOur novel approach identified clusters of EPCs in patients with SLE that are associated with remission and damage. Therefore, these clusters might be useful biomarkers to predict disease progression and severity in SLE pathogenesis.