Analysis Of Molecular Data Research Articles

MycoTWIN Working Group Discussion: A Multi-Actor Perspective on Future Research Directions for Mycotoxins and Toxigenic Fungi Along the Food and Feed Chain

Mycotoxin research is facing unprecedented challenges, starting from the urgent need to cope with the consequences of climate change, the global shortage of grain due to unstable political scenarios, and the major transformation of the supply chains after the COVID-19 pandemic. In this scenario, the mycotoxin contamination of human and animal foods is still unavoidable, thus representing a major challenge to global food security. Next to this, the shift to sustainable and circular food production might be accompanied by an increase in food safety issues involving mycotoxins, e.g., when new technologies are applied to reuse side streams from the food industry, it is not known if and how mycotoxins accumulate in these by-products. MycoTWIN is an EU-funded Horizon 2020 project which fosters knowledge transfer and scientific cooperation within the Mediterranean area, involving worldwide experts, decision makers, and stakeholders in the field of mycotoxigenic fungi and mycotoxins. The MycoTWIN project hosted working group meetings, whose aim was to propose operational plans and/or scientific strategic plans to shape the future research directions to better cope with these challenges. In the working group cycle “Future proof approaches for the management of toxigenic fungi and associated mycotoxins along the food chain”, a multi-actor group was guided in co-creation exercises to elaborate on future research directions and propose relevant actions to be implemented for the present to long-term time periods. The discussion focused on three main topics relevant to the assessment and management of risks associated with mycotoxins and toxigenic fungi: (i) needs for the harmonization of molecular and chemical methods and data analysis, (ii) from lab research to marketable solutions: how to fill the gap, and (iii) gaps in data quality for risk assessment.

Screening of Sugarcane Commercial GMP Varieties Tolerant to Drought Stress Based on Molecular Detection of P5CS Gene

Sugarcane (Saccharum officinarum L.) requires sufficient a water supply to produce optimal productivity. The selection of the superior varieties of sugarcane that are tolerant to drought can be done by molecular detection of the presence of the pyrroline-5-carboxylate synthetase (P5CS) gene. The research is aimed at molecular detection of P5CS gene in a commercial varieties at PT Gunung Madu Plantations (GMP), Indonesia that are potentially drought resistant. Similar research has never been conducted at PT GMP, as evidenced by the absence of official publications. The varieties used are GMP 3, GMP 5, RGM 06-654, PS 864, RGM 08-1026, PSJT 941, RGM 01-1834, GP11, RGM 07-099, and RGM 02-108. The research phases include DNA isolation, quantitative and qualitative DNA amplification, and PCR product visualization. Molecular data analysis is based on DNA band scoring results in the form of binary data which is then used to calculate the level of polimorphism information content (PIC) on the primary data used. The results of the study showed that nine out of ten varieties had P5CS-specific band sizes of ±167 bp, namely GMP 3, GMP 5, RGM 06-654, PS 864, PSJT 941, RGM 01-1834, GP 11, RGM 07-099, and RGM 02-108. A total of four of the nine varieties showed P5CS gene band thicknesses of RGM06-654, PSJT 941, PS864, and RGM 01-1834 which indicates the selected varieties most resistant to drought. The result of the PIC calculation has a value of > 0.25 which indicates the primary P5CS used is quite informative. The molecular detection was continued on one selected variety is PSJT 941, which showed that the relationship analysis of P5CS gene shows close affinity with the isolates from China and Bogor.

Species Diversity, Host Association, and Evolutionary History of Cronartium: An Important Global Fungal Pathogen to Trees.

Pine stem rust, the most damaging and widespread forest disease occurring in pine trees in the Northern Hemisphere, is primarily caused by Cronartium species (Pucciniales, Melampsorineae). While the phylogenetic relationships of major Cronartium species have been largely elucidated, there is limited understanding of their species diversity and the evolutionary processes shaping their distribution patterns. In this work, we performed broad sampling and sequencing of Cronartium taxa in China together with additional sequence data and other accessions in NCBI to investigate the diversification and to estimate the divergence time of major evolutionary events in this genus. Molecular dating analysis suggested that the divergence of the genus Cronartium probably was around 91.78 Ma during the Upper Cretaceous. It is believed that Cronartium species may have originated in Asia and North America, with intercontinental dispersals occurring primarily during the Middle Eocene, Middle Miocene, and Pliocene. These dispersal events likely took place through the North Atlantic Land Bridge, the De Geer Route, and the Bering Land Bridge, and subsequently diverged through sporadic dispersal and vicariance events. Furthermore, our analysis of host associations revealed that the diversification of Cronartium species was correlated with their telial-hosts, and some species may have experienced host jump events, indicating a complex interplay between host specificity and pathogen-host interaction during Cronartium evolution.

Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification.

Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs.

Revisiting the taxonomy of Korean Ischnochiton species (Polyplacophora, Ischnochitonidae) based on a combined analysis of morphological and molecular data.

Chiton species belonging to the genus Ischnochiton J. E. Gray, 1847 are commonly found in intertidal rocky shores worldwide, with the exception of the northern Atlantic and Arctic oceans. Ischnochiton species are characterised by imbricate girdle scales that are uniform in size, rounded, sculpted with striae or occasionally smooth. However, their species-level taxonomy is complicated due to the high variation in their shell microstructures. Despite more than a hundred species reported worldwide, taxonomic studies of this group remain relatively unexplored in Korean waters, with only a few species recorded to date. In this study, we compared the microstructural characteristics of tegmentum sculpture, girdle scales and radula amongst four Korean Ischnochiton species using high-resolution microscopic images and a scanning electron microscope (SEM). Along with mtDNA cox1 sequence comparison, a comprehensive analysis of their morphology revealed that I.hayamii Owada, 2018 was identified for the first time in Korean waters. This species is morphologically distinguished by its small body size of adults, smooth lateral areas on valves and small perinotum scales sculptured with weak longitudinal ribs. Phylogenetic analysis of the mtDNA cox1 sequence provides distinct resolution at the species level, but interrelationships amongst Ischnochiton species remain unresolved. Results from the morphological and molecular analyses presented in this study offer valuable taxonomic information for accurate species identification amongst closely-related Ischnochiton species.

Molecular phylogeny reveals a new genus and species of freshwater mussel (Bivalvia, Unionidae, Gonideinae) from Jiangxi, China

Freshwater mussels of the tribe Gonideini (Bivalvia: Unionidae: Gonideinae) constitute one of the most taxonomically diverse groups and serve as keystone species in riverine and lacustrine ecosystems across East Asia. A new genus and species of Gonideini (Bivalvia: Unionidae) is described from Jiangxi, China, as Pseudopostolata angulagen. et sp. nov. based on an integrative analysis of shell morphology and molecular data. The validity of the new genus and species is supported by distinct conchological features: a short, rounded anterior; a long, wide posterior; a slightly downward-curved dorsal margin; and a distinctly obtuse angle at the center of the posterior margin. The multi-locus (COI + 16S rRNA + 28S rRNA) phylogeny showed that the species formed a monophyletic group in the tribe Gonideini of the subfamily Gonideinae. Pseudopostolata angulagen. et sp. nov. is identified as the sister group to a clade comprising the genera Postolata, Cosmopseudodon, Obovalis, Ptychorhynchus, Parvasolenaia, and Koreosolenaia. We emphasize the significant morphological convergence in freshwater mussels, particularly within Gonideini, highlighting the necessity of an integrated taxonomic approach for accurate generic classification of this group.

Genomic epidemiology and evolutionary dynamics of the Omicron variant of SARS-CoV-2 during the fifth wave of COVID-19 in Pakistan.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed extraordinary challenges to global health systems and economies. The virus's rapid evolution has resulted in several variants of concern (VOCs), including the highly transmissible Omicron variant, characterized by extensive mutations. In this study, we investigated the genetic diversity, population differentiation, and evolutionary dynamics of the Omicron VOC during the fifth wave of COVID-19 in Pakistan. A total of 954 Omicron genomes sequenced during the fifth wave of COVID-19 in Pakistan were analyzed. A Bayesian framework was employed for phylogenetic reconstructions, molecular dating, and population dynamics analysis. Using a population genomics approach, we analyzed Pakistani Omicron samples, revealing low within-population genetic diversity and significant structural variation in the spike (S) protein. Phylogenetic analysis showed that the Omicron variant in Pakistan originated from two distinct lineages, BA.1 and BA.2, which were introduced from South Africa, Thailand, Spain, and Belgium. Omicron-specific mutations, including those in the receptor-binding domain, were identified. The estimated molecular evolutionary rate was 2.562E-3 mutations per site per year (95% HPD interval: 8.8067E-4 to 4.1462E-3). Bayesian skyline plot analysis indicated a significant population expansion at the end of 2021, coinciding with the global Omicron outbreak. Comparative analysis with other VOCs showed Omicron as a highly divergent, monophyletic group, suggesting a unique evolutionary pathway. This study provides a comprehensive overview of Omicron's genetic diversity, genomic epidemiology, and evolutionary dynamics in Pakistan, emphasizing the need for global collaboration in monitoring variants and enhancing pandemic preparedness.

Assessing the burden of submicroscopic Plasmodium infections in a pre-elimination malaria setting in sub-Saharan Africa, Guinea-Bissau.

Submicroscopic Plasmodium infections can be a source of persistent malaria transmission. The aim of this study was to assess their frequency, distribution, morbidity and associated factors in a pre-elimination malaria setting in sub-Saharan Africa, Guinea-Bissau, where the Plasmodium falciparum is the predominant Plasmodium species. Dried fingerprick whole blood samples from 601 participants in the 2017 national, household-based, cross-sectional survey to estimate malaria prevalence were subjected to DNA extraction. The DNA was used in nested end-point PCR assays targeting genus- and species-specific regions of the Plasmodium 18S rRNA genes. Statistical analysis of socio-demographic, clinical and molecular data was carried out using the Statistical Package for the Social Sciences, version 29. Factors associated with submicroscopic P. falciparum infections and their magnitude were sought using Chi-square test and multiple logistic regression models, respectively. Statistically significant level was considered at P-value < 0.05. Nested PCR assays detected submicroscopic P. falciparum infections in 20.3% (95% CI = 16.8-23.8) of individuals microscopically negative for Plasmodium species in the general population and in 21.4% (95% CI = 9.9-36.5) of microscopically negative pregnant women. Submicroscopic Plasmodium malariae infections were also detected as co-infections in 3.0% individuals who were microscopically positive only for P. falciparum. Infections with other Plasmodium species were not detected. Submicroscopic P. falciparum infections were not associated with age, sex, or the presence of fever. A logistic regression model adjusted for ethnicity and health region showed that individuals from the Balanta and Bijagos ethnic groups, most of whom live in the low malaria-transmission areas of Quinara and Bissau, and the Bijagos archipelago, respectively, were less likely to have submicroscopic P. falciparum infections than individuals from the large Fula ethnic group, most of whom live in the high malaria-transmission area of Gabu. Submicroscopic P. falciparum infections were not associated with anaemia in children under 5years of age. The results obtained highlight the contribution of asymptomatic and submicroscopic P. falciparum infections to malaria transmission in high malaria-transmission areas and the need for molecular-based tools to detect submicroscopic Plasmodium species.

First records of Glyphus marsupialis Filhol, 1884 (Decapoda: Pasiphaeidae) in southwestern Atlantic deep waters and extensions of the known distribution of two Pasiphaea species

The Pasiphaeidae Dana, 1852 are a marine shrimp family occurring in both shallow and deeper waters, with its greatest diversity occurring in tropical and subtropical deep seas. This family includes seven genera and 104 species, and is globally distributed. Currently, the genus Pasiphaea Savigny, 1816 includes 73 species, seven of them recorded in the southwestern Atlantic. The genus Glyphus Filhol, 1884 is monotypic and is known from the Indo-Pacific region, the East Pacific Ocean and in the Eastern Atlantic. Herein, we report the first record of the genus in the southwestern Atlantic, completing a cosmopolitan distributional pattern. Further, two new records of Pasiphaea species are commented upon (P. major Hayashi, 2006; P. tarda Kroyer, 1845) along the Northern coastline of the Brazilian coast (Amapá state), also reporting a new host interaction between Thalassomyces sp. and P. major. This is the first record of this Ellobiopsidae genus in the South Atlantic Ocean. The material herein analyzed was sampled by the ReviZEE Program/North, in 1996/2001, during deep-water trawls in the Amazonian slope (Amapá state), at depths from 250 to 1100 m. All material is deposited in the Coleção Carcinológica do Laboratório de Crustáceos (Labcrus)/Universidade Federal Rural da Amazônia (UFRA). The global distribution of Glyphus is commonly observed in deep species and although it has been occasionally contested by the discovery of species complexes (using very detailed morphological and molecular data analyses) with the currently available information, the present material is clearly identifiable as G. marsupialis.

Comparative Molecular Docking of Apigenin and Luteolin versus Conventional Ligands for TP-53, pRb, APOBEC3H, and HPV-16 E6: Potential Clinical Applications in Preventing Gynecological Malignancies.

This study presents a comparative analysis of molecular docking data, focusing on the binding interactions of the natural compounds apigenin and luteolin with the proteins TP-53, pRb, and APOBEC, in comparison to conventional pharmacological ligands. Advanced bioinformatics techniques were employed to evaluate and contrast binding energies, showing that apigenin and luteolin demonstrate significantly higher affinities for TP-53, pRb, and APOBEC, with binding energies of -6.9 kcal/mol and -6.6 kcal/mol, respectively. These values suggest strong potential for therapeutic intervention against HPV-16. Conventional ligands, by comparison, exhibited lower affinities, with energies ranging from -4.5 to -5.5 kcal/mol. Additionally, protein-protein docking simulations were performed to assess the interaction between HPV-16 E6 oncoprotein and tumor suppressors TP-53 and pRb, which revealed high binding energies around -976.7 kcal/mol, indicative of their complex interaction. A conversion formula was applied to translate these protein-protein interaction energies to a comparable scale for non-protein interactions, further underscoring the superior binding potential of apigenin and luteolin. These findings highlight the therapeutic promise of these natural compounds in preventing HPV-16-induced oncogenesis, warranting further experimental validation for clinical applications.

A time-calibrated phylogeny of the diversification of Holoadeninae frogs.

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification. Aiming to fill this gap, we inferred the phylogenetic relationships and divergence times for Holoadeninae using molecular data and calibration information derived from the fossil record of Neobatrachia. Our inferred phylogeny confirmed most genus-level associations, and molecular dating analysis placed the origin of Holoadeninae in the Eocene, with subsequent splits also occurring during this period. The climatic and geological events that occurred during the Oligocene-Miocene transition were crucial to the dynamic biogeographical history of the subfamily. However, the wide highest posterior density intervals in our divergence time estimates are primarily attributed to the absence of Holoadeninae fossil information and, secondarily, to the limited number of sampled nucleotide sites.

A new Oreolalax (Anura: Megophryidae) from the Hoang Lien Range, northwest Vietnam

The megophryid genus Oreolalax is comprised of 19 species, most of which are endemic to China. A single species, Oreolalax sterlingae, is the only member of the genus known from Vietnam. During fieldwork on Mount Po Ma Lung in the Hoang Lien Range of northwest Vietnam, we encountered individuals of both Oreolalax sterlingae and another, morphologically divergent species of Oreolalax. Analyses of morphological and molecular data reveal that these individuals represent a previously undescribed species of Oreolalax which we describe as new to science. The new species, Oreolalax adelphos sp. nov., is sister to Oreolalax xiangchengensis and can be diagnosed from all other congeneric species by the combination of the following characters: (1) SVL of adult male 38.0 mm, N=1; adult female 46.2 mm, N=1; (2) narrow supratympanic fold; (3) no visible tympanum; (4) head longer than wide; (5) vocal sac absent; (6) absence of subarticular tubercles on hands; (7) basal interdigital webbing on hind feet; (8) ventral surface mottled with grey and creamy white; (9) dorsal surface of head and body covered in rounded, evenly spaced and similar sized tubercles; (10) presence of dark bars on limbs; (11) greyish white and creamy white spots on the flanks, and (12) a bicoloured iris. Oreolalax adelphos sp. nov. is only known from a single site of high elevation bamboo forest, where it is sympatric with Oreolalax sterlingae. Both Oreolalax adelphos sp. nov. and O. sterlingae are almost certain to occur in neighbouring Jinping County in Yunnan Province, China. The new species of Oreolalax likely qualifies for being assessed as Data Deficient in accordance with the IUCN Red List of Threatened Species categories and criteria.

Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation.

A network pharmacology study on the biological action of ginseng in the treatment of colorectal cancer (CRC) by regulating the tumor microenvironment (TME). To investigate the potential mechanism of action of ginseng in the treatment of CRC by regulating TME. This research employed network pharmacology, molecular docking techniques, and bioinformatics validation. Firstly, the active ingredients and the corresponding targets of ginseng were retrieved using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), the Traditional Chinese Medicine Integrated Database (TCMID), and the Traditional Chinese Medicine Database@Taiwan (TCM Database@Taiwan). Secondly, the targets related to CRC were retrieved using Genecards, Therapeutic Target Database (TTD), and Online Mendelian Inheritance in Man (OMIM). Tertiary, the targets related to TME were derived from screening the GeneCards and National Center for Biotechnology Information (NCBI)-Gene. Then the common targets of ginseng, CRC, and TME were obtained by Venn diagram. Afterward, the Protein-protein interaction (PPI) network was constructed in the STRING 11.5 database, intersecting targets identified by PPI analysis were introduced into Cytoscape 3.8.2 software cytoHubba plugin, and the final determination of core targets was based on degree value. The OmicShare Tools platform was used to analyze the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the core targets. Autodock and PyMOL were used for molecular docking verification and visual data analysis of docking results. Finally, we verified the core targets by Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases in bioinformatics. A total of 22 active ingredients and 202 targets were identified to be closely related to the TME of CRC. PPI network mapping identified SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 as possible core targets. Go enrichment analysis showed that it was mainly involved in T cell co-stimulation, lymphocyte co-stimulation, growth hormone response, protein input, and other biological processes; KEGG pathway analysis found 123 related signal pathways, including EGFR tyrosine kinase inhibitor resistance, chemokine signaling pathway, VEGF signaling pathway, ErbB signaling pathway, PD-L1 expression and PD-1 checkpoint pathway in cancer, etc. The molecular docking results showed that the main chemical components of ginseng have a stable binding activity to the core targets. The results of the GEPIA database showed that the mRNA levels of PIK3R1 were significantly lowly expressed and HSP90AA1 was significantly highly expressed in CRC tissues. Analysis of the relationship between core target mRNA levels and the pathological stage of CRC showed that the levels of SRC changed significantly with the pathological stage. The HPA database results showed that the expression levels of SRC were increased in CRC tissues, while the expression of STAT3, PIK3R1, HSP90AA1, and AKT1 were decreased in CRC tissues. Ginseng may act on SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 to regulate T cell costimulation, lymphocyte costimulation, growth hormone response, protein input as a molecular mechanism regulating TME for CRC. It reflects the multi-target and multi-pathway role of ginseng in modulating TME for CRC, which provides new ideas to further reveal its pharmacological basis, mechanism of action and new drug design and development.

Computational modeling of tumor invasion from limited and diverse data in Glioblastoma

For diseases with high morbidity rates such as Glioblastoma Multiforme, the prognostic and treatment planning pipeline requires a comprehensive analysis of imaging, clinical, and molecular data. Many mutations have been shown to correlate strongly with the median survival rate and response to therapy of patients. Studies have demonstrated that these mutations manifest as specific visual biomarkers in tumor imaging modalities such as MRI. To minimize the number of invasive procedures on a patient and for the overall resource optimization for the prognostic and treatment planning process, the correlation of imaging and molecular features has garnered much interest. While the tumor mass is the most significant feature, the impacted tissue surrounding the tumor is also a significant biomarker contributing to the visual manifestation of mutations — which has not been studied as extensively. The pattern of tumor growth impacts the surrounding tissue accordingly, which is a reflection of tumor properties as well. Modeling how the tumor growth impacts the surrounding tissue can reveal important information about the patterns of tumor enhancement, which in turn has significant diagnostic and prognostic value. This paper presents the first work to automate the computational modeling of the impacted tissue surrounding the tumor using generative deep learning. The paper isolates and quantifies the impact of the Tumor Invasion (TI) on surrounding tissue based on change in mutation status, subsequently assessing its prognostic value. Furthermore, a TI Generative Adversarial Network (TI-GAN) is proposed to model the tumor invasion properties. Extensive qualitative and quantitative analyses, cross-dataset testing, and radiologist blind tests are carried out to demonstrate that TI-GAN can realistically model the tumor invasion under practical challenges of medical datasets such as limited data and high intra-class heterogeneity.

Octomacrum spinum (Monogenoidea: Polyopisthocotylea: Octomacridae) from highland stoneroller, Campostoma spidaceum (Cypriniformes: Leuciscidae) from Arkansas and Oklahoma, USA, with a summary of the genus from North American and European fishes.

Octomacrum spinum Dansby & Shoemaker, 1973, is reported for the first time from 23 of 146 (16%) highland stonerollers, Campostoma spadiceum collected from central and western Arkansas and southeastern Oklahoma, USA. Analysis of molecular data revealed that the SSU rRNA gene of specimens of O. spinum from Arkansas was identical to a number of Octomacrum spp. and the LSU rRNA gene was 97.46% similar to Octomacrum europaeum. We also provide a summary of the species of Octomacrum reported from North American and European fishes.

The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.

Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren. Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaBösenberg & Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 andProszynskiaKanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(Bösenberg & Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.

The role of artificial intelligence in revolutionizing personalized medicine: A comprehensive review of techniques and applications

This comprehensive review explores the transformative role of Artificial Intelligence (AI) in revolutionizing personalized medicine, focusing on techniques, applications, and future directions. Personalized medicine, which tailors medical interventions to individual characteristics, has significantly advanced through the integration of AI technologies. AI's capabilities in data integration, genomic and molecular data analysis, predictive modeling, and personalized treatment development are highlighted. The review also addresses the challenges and limitations of AI in personalized medicine, such as data privacy, bias, and the need for seamless clinical integration. Furthermore, it discusses future trends, including advances in AI technologies, the integration of multi-omics data, and the importance of ethical and regulatory considerations. The historical evolution of personalized medicine is traced, emphasizing key milestones that have led to current innovations. This review underscores AI's pivotal role in enhancing the precision and effectiveness of personalized healthcare, offering insights into how AI-driven approaches can shape the future of medicine.

YELLOW RoUTIne prospective cohort study protocol: insight in the dynamics of bacteria in the elderly bladder

BackgroundAsymptomatic bacteriuria (ASB) – the presence of bacteria in urine without urinary tract infection (UTI) related signs & symptoms (S&S) – is common in the elderly bladder and is not considered pathogenic for UTI. We hypothesise that colonisation with non-uropathogenic bacteria could protect the bladder from invasion of more harmful bacteria. The exact role and dynamics of bacteriuria in the relation to the development of a UTI is still unknown. We aim to provide insight into the course of bacteriuria in the elderly bladder and its relation to UTI in frail older adults.Methods and analysisA prospective observational cohort study is being conducted in Dutch nursing homes (NHs) between February 2024 and December 2025. Urine samples and case report forms (CRF) on UTI-related S&S will be collected from each consenting NH resident every 3 months for a follow-up period of 18 months. Whenever a UTI-suspicion occurs in between the 3 monthly time points, additional data and a urine sample will be collected. Urine samples undergo several urinalyses (e.g. dipstick and bacterial culture). Additional molecular analysis will be conducted on a selection of cultured Escherichia coli (E. coli) for virulence genes.Primary analyses will be conducted between residents with and without ASB at each time point. The primary outcome is UTI incidence during follow-up. In secondary analyses we will also take into account the low versus high presence of virulence genes of the E. coli.DiscussionThe combination of high ASB prevalence and a reduced ability of frail older adults to express UTI-related S&S may lead to UTI misdiagnosis and inappropriate antibiotic use. To our knowledge, this is the first study to investigate the dynamics and role of bacteriuria in the elderly bladder and their potential protective effect on the development of UTI.The study findings with comprehensive analysis of epidemiological, clinical and molecular data could set the fundamental base for future guidelines and studies, and contribute to improving prevention, diagnosis and treatment of UTI in frail older adults, in addition to contributing to antibiotic stewardship in NHs.

Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics would not be expected to capture dynamic clusters of transmission. We, therefore, sought to evaluate the performance of existing and adapted phylogeny-based cluster identification tools on simulated transmission clusters exhibiting dynamic transmission behavior over time. Despite the complementarity of the tools, we provide strong evidence that novel cluster identification methods are needed for reliable detection of epidemiologically linked individuals, particularly those exhibiting changing transmission dynamics during dynamic outbreak scenarios.

FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology.

Spatial -OMICS technologies facilitate the interrogation of molecular profiles in the context of the underlying histopathology and tissue microenvironment. Paired analysis of histopathology and molecular data can provide pathologists with otherwise unobtainable insights into biological mechanisms. To connect the disparate molecular and histopathologic features into a single workspace, we developed FUSION (Functional Unit State IdentificatiON in WSIs [Whole Slide Images]), a web-based tool that provides users with a broad array of visualization and analytical tools including deep learning-based algorithms for in-depth interrogation of spatial -OMICS datasets and their associated high-resolution histology images. FUSION enables end-to-end analysis of functional tissue units (FTUs), automatically aggregating underlying molecular data to provide a histopathology-based medium for analyzing healthy and altered cell states and driving new discoveries using "pathomic" features. We demonstrate FUSION using 10x Visium spatial transcriptomics (ST) data from both formalin-fixed paraffin embedded (FFPE) and frozen prepared datasets consisting of healthy and diseased tissue. Through several use-cases, we demonstrate how users can identify spatial linkages between quantitative pathomics, qualitative image characteristics, and spatial --omics.