Enterococcus montenegrensis sp. nov., isolated from artisanal Montenegrin dry sausage.

A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22T was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4-50 °C, at pH 5.0-8.0 and with 0-6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as Enterococcus canintestini (log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus Enterococcus. The closest relatives were E. canintestini DSM 21207T and E. dispar ATCC 51266T with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolate CoE-012-22T and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to E. saigonensis JCM 31193T and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to E. malodoratus ATCC 43197T. Two unknown Enterococcus isolates, Enterococcus sp. MJM12 and Enterococcus SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22T and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22T was considered to represent a novel species, for which the name Enterococcus montenegrensis sp. nov. is proposed. The type strain is CoE-012-22T (=DSM 115843T=NCIMB 15468T).

Genome-wide association study identifies genetic variants which predict the response of bone mineral density to teriparatide therapy.

OBJECTIVES: Teriparatide (TPTD) is an effective treatment for osteoporosis but the individual response to therapy is variable for reasons that are unclear. This study aimed to determine whether the response to TPTD might be influenced by genetic factors. METHODS: We searched for predictors of the response of bone mineral density (BMD) to TPTD using a two-stage genome-wide association study in 437 patients with osteoporosis from three referral centres. Demographic and clinical data including the response of BMD to treatment at the lumbar spine and hip were extracted from the medical records of each participant. RESULTS: Allelic variation at rs6430612 on chromosome 2, close to the CXCR4 gene was associated with the response of spine BMD to TPTD at a genome wide significant level (p=9.2×10-9 beta=-0.35 (-0.47 to -0.23)). The increase in BMD was almost twice as great in AA homozygotes at rs6430612 as compared with GG homozygotes with intermediate values in heterozygotes. The same variant was also associated with response of femoral neck and total hip BMD (p=0.007). An additional locus on chromosome 19 tagged by rs73056959 was associated with the response of femoral neck BMD to TPTD (p=3.5×10-9, beta=-1.61 (-2.14 to -1.07)). CONCLUSIONS: Genetic factors influence the response to TPTD at the lumbar spine and hip with a magnitude of effect that is clinically relevant. Further studies are required to identify the causal genetic variants and underlying mechanisms as well as to explore how genetic testing for these variants might be implemented in clinical practice.

IgA vasculitis (Henoch- Schönlein purpura) with gastrointestinal involvement.

We present the case of a patient who was admitted due to jejunitis in the context of an IgA vasculitis, previously known as Schönlein-Henoch vasculitis.

Effects of changes in UV-B radiation levels on biofilm-forming organisms commonly found in cultural heritage surfaces.

Accurate measuring and monitoring methods available since the 1980s have shown that the amount of Ultraviolet B (UV-B) radiation reaching the Earth's surface has increased as a result of degradation of the ozone layer. Since the adoption of the Montreal Protocol in 1987, ozone levels have been recovering successfully. However, in the context of the current climate change, other factors such as changes in cloud patterns and an increased incidence of natural disasters (e.g. fires) may be disrupting this recovery. The present study aimed to investigate the effects of different UV-B radiation levels on biofilms colonising heritage monuments. For this purpose, the effects of current UV-B levels on a biofilm composed of Synechocystis sp. (a cyanobacterium), Bracteacoccus minor (a green alga) and Fusarium sp. (a fungus) were compared at three points along a South-North transect: Portugal, Galicia (NW Spain) and Ireland (from highest to lowest UV-B radiation, respectively). Increased levels of UV-B radiation caused changes in the growth, physiological state and composition of subaerial biofilms, with cyanobacteria being more resistant than green algae to high levels of UV-B. A reduction of fungal growth and extracellular polymer substances (EPS) production was also observed, related to the reduction of biofilm aggregation at high UV-B levels.

Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease.

Metabolites, the biochemical products of the cellular process, can be used to measure alterations in biochemical pathways related to the pathogenesis of Alzheimer's disease (AD). However, the relationships between systemic abnormalities in metabolism and the pathogenesis of AD are poorly understood. In this study, we aim to identify AD-specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework for analyzing genetic, transcriptomic, metabolomic, and proteomic data in AD. Metabolite co-expression network analysis of the blood metabolomic data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) shows short-chain acylcarnitines/amino acids and medium/long-chain acylcarnitines are most associated with AD clinical outcomes, including episodic memory scores and disease severity. Integration of the gene expression data in both the blood from the ADNI and the brain from the Accelerating Medicines Partnership Alzheimer's Disease (AMP-AD) program reveals ABCA1 and CPT1A are involved in the regulation of acylcarnitines and amino acids in AD. Gene co-expression network analysis of the AMP-AD brain RNA-seq data suggests the CPT1A- and ABCA1-centered subnetworks are associated with neuronal system and immune response, respectively. Increased ABCA1 gene expression and adiponectin protein, a regulator of ABCA1, correspond to decreased short-chain acylcarnitines and amines in AD in the ADNI. In summary, our integrated analysis of large-scale multiomics data in AD systematically identifies novel metabolites and their potential regulators in AD and the findings pave a way for not only developing sensitive and specific diagnostic biomarkers for AD but also identifying novel molecular mechanisms of AD pathogenesis.

Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria.

Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.

Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models.

BACKGROUND: For multivariate data analysis involving only two input matrices (e.g., X and Y), the previously published methods for variable influence on projection (e.g., VIPOPLS or VIPO2PLS) are widely used for variable selection purposes, including (i) variable importance assessment, (ii) dimensionality reduction of big data and (iii) interpretation enhancement of PLS, OPLS and O2PLS models. For multiblock analysis, the OnPLS models find relationships among multiple data matrices (more than two blocks) by calculating latent variables; however, a method for improving the interpretation of these latent variables (model components) by assessing the importance of the input variables was not available up to now. RESULTS: A method for variable selection in multiblock analysis, called multiblock variable influence on orthogonal projections (MB-VIOP) is explained in this paper. MB-VIOP is a model based variable selection method that uses the data matrices, the scores and the normalized loadings of an OnPLS model in order to sort the input variables of more than two data matrices according to their importance for both simplification and interpretation of the total multiblock model, and also of the unique, local and global model components separately. MB-VIOP has been tested using three datasets: a synthetic four-block dataset, a real three-block omics dataset related to plant sciences, and a real six-block dataset related to the food industry. CONCLUSIONS: We provide evidence for the usefulness and reliability of MB-VIOP by means of three examples (one synthetic and two real-world cases). MB-VIOP assesses in a trustable and efficient way the importance of both isolated and ranges of variables in any type of data. MB-VIOP connects the input variables of different data matrices according to their relevance for the interpretation of each latent variable, yielding enhanced interpretability for each OnPLS model component. Besides, MB-VIOP can deal with strong overlapping of types of variation, as well as with many data blocks with very different dimensionality. The ability of MB-VIOP for generating dimensionality reduced models with high interpretability makes this method ideal for big data mining, multi-omics data integration and any study that requires exploration and interpretation of large streams of data.

Pattern of SQSTM1 Gene Variants in a Hungarian Cohort of Paget's Disease of Bone.

Paget's disease of bone (PDB) is characterized by focal or multifocal increase in bone turnover. One of the most well-established candidate genes for susceptibility to PDB is Sequestosome 1 (SQSTM1). Mutations in SQSTM1 have been documented among Western-European, British and American patients with PDB. However, there is no information on SQSTM1 mutation status in PDB patients from the Central- and Eastern-European regions. In this study, we conducted a mutation screening for SQSTM1 gene variants in 82 PDB patients and 100 control participants in Hungary. Mutations of SQSTM1 were detected in 18 PDB patients (21.95%); associations between genotype and clinical characteristics were also analyzed. Altogether, six different exonic alterations, including two types of UTR variants in the SQSTM1 gene, were observed in our PDB patients. Similarly, to previous genetic studies on Paget's disease, our most commonly detected variant was the c.1175C > T (p.Pro392Leu) in nine cases (four in monostotic and five in polyostotic form). We have surveyed the germline SQSTM1 variant distribution among Hungarian patients with PDB. We also highlighted that the pattern of the analyzed disease-associated pathophysiological parameters could partially discriminate PDB patients with normal or mutant SQSTM1 genotype. However, our findings also underline and strengthen that not solely SQSTM1 stands in the background of the complex PDB etiology.

Recovery Capacity of Subaerial Biofilms Grown on Granite Buildings Subjected to Simulated Drought in a Climate Change Context.

Variations in environmental conditions in the context of climate change are expected to affect biofilm-associated organisms on granite heritage buildings. The number and duration of drought periods should be considered, as these factors will affect the availability of water for the microorganisms. In this study, mature biofilms were exposed to various drying-rewetting cycles, and the effects of water stress on the SAB and their resilience were evaluated in terms of the variation in microbial composition, extracellular polymeric substance production, and photosynthetic efficiency. The structure of the biofilm changed after exposure to drought, becoming more heterogeneous and with an increase in the carbohydrate to protein ratio, especially after the second day of total drought. YMAX and YEF parameters proved to be the most informative, showing that the photosynthetic efficiency and recovery capacity were inversely related to the duration of the drought period. Furthermore, cyanobacteria resisted drought better than algae, giving rise to a decrease in the algae to cyanobacteria ratio.

Gaze and Motor Traces of Language Processing: Evidence from Autism Spectrum Disorders in Comparison to Typical Controls.

We investigated what strategies underlie figurative language processing in two groups of participants distinguished by the presence of a developmental deficit, highly-verbal participants with autism, and control participants without autism in two age ranges each. Individuals with autism spectrum disorder are characterised by impaired social interaction and communication. Even at the high end of the spectrum, where structural language is adequate, difficulties in comprehending non-literal aspects of language are widely attested. The exact causes of these problems are, however, still open to debate. In an interactive sentence-picture matching task participants selected the most suitable image representation of a non-literal figurative expression that matched the target meaning, while their eye-movements and hand movements were being tracked. Our results suggest that individuals with ASD have different processing patterns than typically developing peers when interpreting figurative language, even when they provide the correct answers. Both children with and without autism, and participants with autism display greater uncertainty and competition between alternatives when providing the answer, often reflected in also considering the literal interpretation of the expression against its target figurative meaning. We provide evidence that expression transparency and decomposability play a central role in figurative language processing across all groups.

OnPLS-Based Multi-Block Data Integration: A Multivariate Approach to Interrogating Biological Interactions in Asthma.

Integration of multiomics data remains a key challenge in fulfilling the potential of comprehensive systems biology. Multiple-block orthogonal projections to latent structures (OnPLS) is a projection method that simultaneously models multiple data matrices, reducing feature space without relying on a priori biological knowledge. In order to improve the interpretability of OnPLS models, the associated multi-block variable influence on orthogonal projections (MB-VIOP) method is used to identify variables with the highest contribution to the model. This study combined OnPLS and MB-VIOP with interactive visualization methods to interrogate an exemplar multiomics study, using a subset of 22 individuals from an asthma cohort. Joint data structure in six data blocks was assessed: transcriptomics; metabolomics; targeted assays for sphingolipids, oxylipins, and fatty acids; and a clinical block including lung function, immune cell differentials, and cytokines. The model identified seven components, two of which had contributions from all blocks (globally joint structure) and five that had contributions from two to five blocks (locally joint structure). Components 1 and 2 were the most informative, identifying differences between healthy controls and asthmatics and a disease-sex interaction, respectively. The interactions between features selected by MB-VIOP were visualized using chord plots, yielding putative novel insights into asthma disease pathogenesis, the effects of asthma treatment, and biological roles of uncharacterized genes. For example, the gene ATP6 V1G1, which has been implicated in osteoporosis, correlated with metabolites that are dysregulated by inhaled corticoid steroids (ICS), providing insight into the mechanisms underlying bone density loss in asthma patients taking ICS. These results show the potential for OnPLS, combined with MB-VIOP variable selection and interaction visualization techniques, to generate hypotheses from multiomics studies and inform biology.

Laboratory grown subaerial biofilms on granite: application to the study of bioreceptivity.

Simulated environmental colonisation of granite was induced under laboratory conditions in order to develop an experimental protocol for studying bioreceptivity. The experimental set-up proved suitable for producing subaerial biofilms by inoculating granite blocks with planktonic multi-species phototrophic cultures derived from natural biofilms. The ability of four different cultures to form biofilms was monitored over a three-month growth period via colour measurements, quantification of photosynthetic pigments and EPS, and CLSM observations. One of the cultures under study, which comprised several taxa including Bryophyta, Charophyta, Chlorophyta and Cyanobacteria, was particularly suitable as an inoculum, mainly because of its microbial richness, its rapid adaptability to the substratum and its high colonisation capacity. The use of this culture as an inoculum in the proposed experimental set-up to produce subaerial biofilms under laboratory conditions will contribute to standardising the protocols involved, thus enabling more objective assessment of the bioreceptivity of granite in further experiments.

On the dual nature of lichen-induced rock surface weathering in contrasting micro-environments.

Contradictory evidence from biogeomorphological studies has increased the debate on the extent of lichen contribution to differential rock surface weathering in both natural and cultural settings. This study, undertaken in Côa Valley Archaeological Park, aimed at evaluating the effect of rock surface orientation on the weathering ability of dominant lichens. Hyphal penetration and oxalate formation at the lichen-rock interface were evaluated as proxies of physical and chemical weathering, respectively. A new protocol of pixel-based supervised image classification for the analysis of periodic acid-Schiff stained cross-sections of colonized schist revealed that hyphal spread of individual species was not influenced by surface orientation. However, hyphal spread was significantly higher in species dominant on northwest facing surfaces. An apparently opposite effect was noticed in terms of calcium oxalate accumulation at the lichen-rock interface; it was detected by Raman spectroscopy and complementary X-ray microdiffraction on southeast facing surfaces only. These results suggest that lichen-induced physical weathering may be most severe on northwest facing surfaces by means of an indirect effect of surface orientation on species abundance, and thus dependent on the species, whereas lichen-induced chemical weathering is apparently higher on southeast facing surfaces and dependent on micro-environmental conditions, giving only weak support to the hypothesis that lichens are responsible for the currently observed pattern of rock-art distribution in Côa Valley. Assumptions about the drivers of open-air rock-art distribution patterns elsewhere should also consider the micro-environmental controls of lichen-induced weathering, to avoid biased measures of lichen contribution to rock-art deterioration.

Response surface optimization of a method for extracting extracellular polymeric substances (EPS) from subaerial biofilms on rocky substrata.

The aim of the present study was to optimize a protocol for extracting extracellular polymeric substances (EPS) from biofilms on rocky substrata, as the EPS matrix is considered key to understanding the biofilm mode of life. For this purpose, we tested the extraction efficacy of NaOH and H2SO4 at different concentrations, temperatures and times for obtaining EPS from multi-species subaerial biofilms grown on granite blocks under laboratory conditions. Two experimental designs (Box-Behnken design and full factorial design) were used in testing each extractant. The extraction efficiency was determined by analysing the carbohydrate, protein and DNA contents of the extracts obtained. H2SO4 proved unsuitable as an extractant as it caused excessive cell lysis. However, response surface optimization of NaOH-mediated extraction enabled cell lysis to be minimized. Confirmation experiments were performed under the optimal conditions established and a protocol for extracting EPS is proposed, yielding the first quantitative data on EPS extracted from subaerial biofilms developed on rocky substrata. Graphical abstract Development of a method for extracting EPS from subaerial biofilms on rocky substrata.

The susceptibility of weathered versus unweathered schist to biological colonization in the Côa Valley Archaeological Park (north-east Portugal).

This study addresses the primary and secondary bioreceptivity of schist used as a support for prehistoric rock art in the Côa Valley Archaeological Park (north-east Portugal) and provides some parameters that can be related to the risk of biologically induced schist weathering. Samples of freshly quarried and naturally weathered schist were characterized in terms of their intrinsic properties and maintained in controlled environmental conditions after inoculation with biofilm-forming cyanobacteria. The physical properties of the studied schist, as well as its abrasion pH, all varied according to the weathering degree of the samples and so did its susceptibility to colonization by biofilm-forming cyanobacteria. Complete separation between weathered and unweathered schist samples in terms of laboratory-induced photosynthetic biomass was obtained by measuring total colour change in the CIE (International Commission on Illumination) L*a*b* colour space. Weathered schist was more bioreceptive than unweathered schist, associated with increased open porosity, water saturation, capillary water and capillarity coefficient and decreased abrasion pH. In the future, it might be possible to determine the susceptibility of schist surfaces to biological colonization through evaluation of colour differences associated with the different weathering degrees presented by those surfaces prior to colonization.

Complete genome of a multiresistant Pasteurella multocida isolated from a diseased Austrian bovine calf.

Pasteurella multocida (P. multocida) plays an important role in bovine respiratory diseases. Here we describe the complete genome of a multiresistant P. multocida. The strain was isolated from the lung of a diseased, 4-month old, male Fleckvieh calf with a clinical history of bronchopneumonia in Upper Austria.

Complete genome of Microbacterium plantarum CoE-159-22, isolated from traditionally produced Montenegrin cheese.

Microbacterium plantarum (M. plantarum) was recently described as a new species isolated from copper globemallow (Sphaeralcea angustifolia). Here, we report the complete genome of M. plantarum CoE-159-22, which was obtained from traditionally produced Montenegrin cheese.

Complete genome sequence of Bordetella parapertussis strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023.

Here, we report the complete genome of Bordetella parapertussis strain 400431-b isolated from a nasopharyngeal swab from a 4-year-old patient presenting with a protracted course of whooping cough, vaccinated with three doses of diphtheria-tetanus-acellular pertussis-hepatitis B-poliomyelitis-Haemophilus influenzae type b vaccine.

Philippine retinoblastoma initiative multi-eye center study 2010-2020.

AIM: To provide a comprehensive and more representative national data on the disease, especially on treatment options and outcomes, and to determine access of retinoblastoma patients from Luzon, Visayas and Mindanao to eye care, and determine if access is associated with delay in consultation, staging and outcomes. METHODS: Cohort study of retinoblastoma patients seen in eleven institutions located in the three major areas of the Philippines namely Luzon, Vizayas and Mindanao from 2010-2020. RESULTS: Totally 636 patients, involving 821 eyes, were included. Majority (57%) were from Luzon and were seen in institutions in Luzon (72%). Annually, 58±10 new cases were seen with 71% having unilateral disease. Median delay of consultation remained long at 9 (3, 17)mo, longest in patients with unilateral disease (P<0.02) and those from the Visayas (P<0.003). Based on the International Retinoblastoma Staging System, only 35% of patients had Stage 1 while 47% already had extraocular disease. Enucleation was the most common treatment received by 484 patients while intravenous chemotherapy was received by 469. There were 250 (39%) patients alive, 195 (31%) dead, 85 (13%) abandoned, 17 (3%) refused and 89 (14%) with no data. CONCLUSION: This study presents the largest cohort of retinoblastoma patients in the Philippines in terms of patients' and participating institutions' number and geographical location and type of institution (private and public). It also presents more comprehensive data on the treatments used and outcomes (survival, globe salvage, and vision retention rates). Delay in consultation was still long among patients leading to advanced disease stage and lower survival rate. Despite increasing capacity to diagnose and manage retinoblastoma in the country, the delay of consultation remains long primarily due to accessibility issues to eye care institutions especially in the Visayas and financial concerns. The delay was still significant that overall survival rate remain low.

Draft Genome Sequence of Enterococcus dispar CoE-457-22, Isolated from Traditionally Produced Montenegrin Dry Sausage.

Enterococcus dispar was isolated for the first time from synovial fluid and stool cultures and described as a new species in 1991. Here, we report the genome of E. dispar CoE-457-22, which was obtained from traditionally produced Montenegrin dry sausage (sudzuk).