The presence of (NRPS) and (PKS) genes at the deepsea hydrothermal field in the Aegean Sea

Deep-sea hydrothermal vents are characterized by extremely high concentrations of microorganisms in stark contrast to the surrounding sea bottom. Nevertheless, deepsea consumers do not rapidly remove the high biomass of prey from these communities maybe due to vent microbes’ chemical defenses which still remain largely unknown. Meanwhile, the detection of genes responsible for antimicrobial and cytotoxic activity such as non-ribosomal peptide synthases (NRPS) and polyketide (PKS) of deep-sea vent bacteria has not so far been attempted

The Kolumbo submarine volcano of Santorini island is a large pool of bacterial strains with antimicrobial activity

Microbes in hydrothermal vents with their unique secondary metabolism may represent an untapped potential source of new natural products. In this study, samples were collected from the hydrothermal field of Kolumbo submarine volcano in the Aegean Sea, in order to isolate bacteria with antimicrobial activity. Eight hundred and thirty-two aerobic heterotrophic bacteria were isolated and then differentiated through BOX-PCR analysis at the strain level into 230 genomic fingerprints, which were screened against 13 different type strains (pathogenic and nonpathogenic) of Gram-positive, Gram-negative bacteria and fungi. Forty-two out of 176 bioactive-producing genotypes (76 %) exhibited antimicrobial activity against at least four different type strains and were selected for 16S rDNA sequencing and screening for nonribosomal peptide (NRPS) and polyketide (PKS) synthases genes. The isolates were assigned to genus Bacillus and Proteobacteria, and 20 strains harbored either NRPS, PKS type I or both genes. This is the first report on the diversity of culturable mesophilic bacteria associated with antimicrobial activity from Kolumbo area; the extremely high proportion of antimicrobial-producing strains suggested that this unique environment may represent a potential reservoir of novel bioactive compounds

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

The Kolumbo submarine volcano of Santorini island is a large pool of bacterial strains with antimicrobial activity

Microbes in hydrothermal vents with their unique secondary metabolism may represent an untapped potential source of new natural products. In this study, samples were collected from the hydrothermal field of Kolumbo submarine volcano in the Aegean Sea, in order to isolate bacteria with antimicrobial activity. Eight hundred and thirty-two aerobic heterotrophic bacteria were isolated and then differentiated through BOX-PCR analysis at the strain level into 230 genomic fingerprints, which were screened against 13 different type strains (pathogenic and nonpathogenic) of Gram-positive, Gram-negative bacteria and fungi. Forty-two out of 176 bioactive-producing genotypes (76 %) exhibited antimicrobial activity against at least four different type strains and were selected for 16S rDNA sequencing and screening for nonribosomal peptide (NRPS) and polyketide (PKS) synthases genes. The isolates were assigned to genus Bacillus and Proteobacteria, and 20 strains harbored either NRPS, PKS type I or both genes. This is the first report on the diversity of culturable mesophilic bacteria associated with antimicrobial activity from Kolumbo area; the extremely high proportion of antimicrobial-producing strains suggested that this unique environment may represent a potential reservoir of novel bioactive compounds. © 2015, Springer-Verlag Berlin Heidelberg

In vivo Prevalence of Alzheimer Biomarkers in Dementia with Lewy Bodies

Background: Neuropathological studies indicate concomitant Alzheimer's disease (AD) pathology in patients with dementia with Lewy bodies (DLB). Objectives: To measure cerebrospinal fluid (CSF) levels of β-amyloid peptide with 42 amino acids (Aβ42), total tau protein (τT), and tau phosphorylated at threonine 181 (τP-181) in 38 patients fulfilling the diagnostic criteria of probable DLB according to the most recent (4th consensus) report. Methods: Double-sandwich commercial ELISAs (Innotest; Fujirebio, Gent, Belgium) were used for measurements. Results: According to the current cutoff values of our laboratory, 4 biomarker profiles were noted: abnormal levels of Aβ42 only (44.7%), full AD profile (39.5%), abnormal levels of τT only (5.3%), and normal levels of all 3 biomarkers (10.5%). AD profile was associated with female sex, older age, lower education, and lower MMSE scores. Conclusions: Reduction in Î'β42 in DLB may be more common (>80% of patients) than previously thought, and ∼40% may have the typical CSF AD biomarker profile. AD biochemistry in DLB may be an evolving process showing increasing frequency with disease progression. © 2019 S. Karger AG, Basel. All rights reserved

Endothelial Tpl2 regulates vascular barrier function via JNK-mediated degradation of claudin-5 promoting neuroinflammation or tumor metastasis

Increased vascular permeability and leakage are hallmarks of several pathologies and determine disease progression and severity by facilitating inflammatory/metastatic cell infiltration. Using tissue-specific genetic ablation in endothelial cells, we have investigated in vivo the role of Tumor progression locus 2 (Tpl2), a mitogen-activated protein kinase kinase kinase (MAP3K) member with pleiotropic effects in inflammation and cancer. In response to proinflammatory stimuli, endothelial Tpl2 deletion alters tight junction claudin-5 protein expression through inhibition of JNK signaling and lysosomal degradation activation, resulting in reduced vascular permeability and immune cell infiltration. This results in significantly attenuated disease scores in experimental autoimmune encephalomyelitis and fewer tumor nodules in a hematogenic lung cancer metastasis model. Accordingly, pharmacologic inhibition of Tpl2 or small interfering RNA (siRNA)-mediated Tpl2 knockdown recapitulates our findings and reduces lung metastatic tumor invasions. These results establish an endothelial-specific role for Tpl2 and highlight the therapeutic potential of blocking the endothelial-specific Tpl2 pathway in chronic inflammatory and metastatic diseases. © 2021 The Author(s

Cerebrospinal fluid biomarker profiling in corticobasal degeneration: Application of the AT(N) and other classification systems

Introduction: Total tau (τT), phosphorylated tau (τP-181) and amyloid beta (Aβ42) are cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD). There is no consensus on the interpretation criteria of these biomarkers. The aim of this study was to apply three different sets of criteria for CSF AD biomarker interpretation in a cohort of corticobasal degeneration (CBD) patients. Method: SForty patients fulfilling diagnostic criteria for “probable CBD” were included. The AT(N), BIOMARKAPD/ABSI and the τP-181/Aβ42 ratio criteria were applied. Results: The AT(N) criteria categorized 50% of “probable CBD” patients as AD, and 62.5% as harboring amyloid pathology. The BIOMARKAPD/ABSI and τP- 181/Aβ42 criteria categorized ~40% of “probable CBD” patients as AD. Discussion: Use of different interpretation criteria for CSF AD biomarkers produces diverse results. AD pathology is common in patients fulfilling “probable” CBD criteria. CBD diagnostic criteria may have suboptimal positive predictive value. A consensus regarding interpretation criteria of CSF AD biomarkers is pivotal. © 202

Cerebrospinal Fluid TAR DNA-Binding Protein 43 Combined with Tau Proteins as a Candidate Biomarker for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Spectrum Disorders

Background: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are nowadays recognized as spectrum disorders with a molecular link, the TAR DNA-binding protein 43 (TDP-43), rendering it a surrogate biomarker for these disorders. Methods: We measured cerebrospinal fluid (CSF) levels of TDP-43, beta-amyloid peptide with 42 amino acids (Aβ42), total tau protein (τT), and tau protein phosphorylated at threonine 181 (τP-181) in 32 patients with ALS, 51 patients with FTD, and 17 healthy controls. Double-sandwich commercial enzyme-linked immunosorbent assays were used for measurements. Results: Both ALS and FTD patients presented with higher TDP-43 and τT levels compared to the control group. The combination of biomarkers in the form of the TDP-43 × τT / τP-181 formula achieved the best discrimination between ALS or FTD and controls, with sensitivities and specificities >0.8. Conclusion: Combined analysis of TDP-43, τT, and τP-181 in CSF may be useful for the antemortem diagnosis of ALS and FTD. © 2017 S. Karger AG, Basel

TARDBP pathogenic variants in patients with amyotrophic lateral sclerosis, frontotemporal dementia and Alzheimer's disease phenotypes

BACKGROUND: Genetic, cerebrospinal fluid and histopathological studies have highlighted the importance of TDP-43 (the protein product of the TARDBP gene) in the pathophysiology of neurodegeneration. Specifically, TDP-43 pathology has been associated with Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS) and, lately, Alzheimer's Disease (AD). Here we searched for TARDBP pathogenic variants in a cohort of Greek patients with AD, FTD, ALS or FTD/ALS. METHOD: A total of 192 patients were included in the study. These participants were 1) referred for testing to the Neurology/Neurogenetics Laboratory of the University of Crete, 2) identified through the Cretan Aging Cohort (CAC), 3) referred to the 1st Department of Neurology of the National and Kapodistrian University of Athens at Eginition Hospital, Athens, Greece. Of these, 95 were clinically characterized as AD, 45 as FTD, 44 as ALS and 8 as FTD-ALS. Patients' DNA samples were analyzed through Whole Exome Sequencing (WES). Subsequently, we analyzed WES data for the presence of TARDBP pathogenic variants. All TARDBP pathogenic variants identified were verified by Sanger sequencing. RESULT: We found three different TARDBP pathogenic variants in five apparently unrelated patients, two of whom had a family history of dementia or ALS. Two of the five patients, an 80-year-old male and a 82-year-old female, members of the CAC, were initially diagnosed as suffering from late-onset AD on the basis of their clinical presentation. Both were found to harbor the p.Ile383Val (c.1147A>G) TARDBP variant. The same variant had been found in another patient, also from Crete, presenting with a combined FTD/ALS phenotype. In addition, in 2 patients with pure ALS, we found the p.Met337Val (c.1009A>G) and the p.Asn352Ser (c.1055A>G) TARDBP pathogenic variants, respectively. CONCLUSION: Our analyses unraveled five patients with pathogenic TARDBP variants presenting with heterogeneous phenotypes, namely apparent late-onset AD, FTD/ALS and pure ALS phenotypes. Our findings further expand the phenotypic variability of the TARDBP gene variants and draw attention to the possibility that patients diagnosed with possible typical AD could harbor pathogenic TARDBP variants. Furthermore, our study showed that TARDBP pathogenic variants are a rather frequent cause of dementia in the Greek population. © 2021 the Alzheimer's Association