First report of a fish blood fluke from sub-Saharan Africa: Nomasanguinicola dentata (Paperna, 1964) Warren and Bullard, 2023 infecting African sharptooth catfish, Clarias gariepinus (Burchell, 1822) Teugles, 1982 in the Kavango River, Namibia, and a revised phylogeny for Sanguinicolidae Poche, 1926

We herein provide a supplemental description of Nomasanguinicola dentata (Paperna, 1964) Warren and Bullard, 2023 (Digenea: Sanguinicolidae) and provide a revised 28S phylogeny to test relationships among freshwater fish blood flukes. We examined the heart of three African sharptooth catfish, Clarias gariepinus (Burchell, 1822) Teugles, 1982 from the Kavango River (northeastern Namibia) that was infected with adults of N. dentata. This blood fluke differs from N. canthoensis by having a body 5.3-6.7 longer than wide (vs. 3.5-4.6), an anterior esophageal swelling 7-8% (vs. 14-24%) of total esophageal length, a posterior esophageal swelling 3-5% (vs. 8-10%) of total esophageal length, a pre-cecal (vs. wholly post-cecal) testis, and an ovary that does not extend laterally beyond the nerve cords. The 28S sequence for N. dentata differed from that of N. canthoensis by 144 bp (9% difference). The phylogenetic analysis recovered these species as sister taxa and Sanguinicolidae as monophyletic. This is the first report of a fish blood fluke from sub-Saharan Africa, and the first report of a species of Nomasanguinicola from Africa in ∼40 yrs.

Genome constitution and evolution of Elymus atratus (Poaceae: Triticeae) inferred from cytogenetic and phylogenetic analysis

BACKGROUND

Elymus atratus (Nevski) Hand.-Mazz. is perennial hexaploid wheatgrass. It was assigned to the genus Elymus L. sensu stricto based on morphological characters. Its genome constitution has not been disentangled yet.

OBJECTIVE

To identify the genome constitution and origin of E. atratus.

METHODS

In this study, genomic in situ hybridization and fluorescence in situ hybridization, and phylogenetic analysis based on the Acc1, DMC1 and matK sequences were performed.

RESULTS

Genomic in situ hybridization and fluorescence in situ hybridization results reveal that E. atratus 2n = 6x = 42 is composed of 14 St genome chromosomes, 14 H genome chromosomes, and 14 Y genome chromosomes including two H-Y type translocation chromosomes, suggesting that the genome formula of E. atratus is StStYYHH. The phylogenetic analysis based on Acc1 and DMC1 sequences not only shows that the Y genome originated in a separate diploid, but also suggests that Pseudoroegneria (St), Hordeum (H), and a diploid species with Y genome were the potential donors of E. atratus. Data from chloroplast DNA showed that the maternal donor of E. atratus contains the St genome.

CONCLUSION

Elymus atratus is an allohexaploid species with StYH genome, which may have originated through the hybridization between an allotetraploid Roegneria (StY) species as the maternal donor and a diploid Hordeum (H) species as the paternal donor.

Behavioral and phylogenetic correlates of limb length proportions in extant apes and monkeys: Implications for interpreting hominin fossils

The body proportions of extant animals help inform inferences about the behaviors of their extinct relatives, but relationships between body proportions, behavior, and phylogeny in extant primates remain unclear. Advances in behavioral data, molecular phylogenies, and multivariate analytical tools make it an opportune time to perform comprehensive comparative analyses of primate traditional limb length proportions (e.g., intermembral, humerofemoral, brachial, and crural indices), body size-adjusted long bone proportions, and principal components. In this study we used a mix of newly-collected and published data to investigate whether and how the limb length proportions of a diverse sample of primates, including monkeys, apes, and modern humans, are influenced by behavior and phylogeny. We reconfirm that the intermembral index, followed by the first principal component of traditional limb length proportions, is the single most effective variable distinguishing hominoids and other anthropoids. Combined limb length proportions and positional behaviors are strongly correlated in extant anthropoid groups, but phylogeny is a better predictor of limb length proportion variation than of behavior. We confirm convergences between members of the Atelidae and extant apes (especially Pan), members of the Hylobatidae and Pongo, and a potential divergence of Presbytis limb proportions from some other cercopithecoids, which correlate with adaptations for forelimb-dominated behaviors in some colobines. Collectively, these results substantiate hypotheses indicating that extinct hominins and other hominoid taxa can be distinguished by analyzing combinations of their limb length proportions at different taxonomic levels. From these results, we hypothesize that fossil skeletons characterized by notably disparate limb length proportions are unlikely to have exhibited similar behavioral patterns.

Naming Homo erectus: A review

Following the discovery of hominin fossils at Trinil (Java, Indonesia) in 1891 and 1892, Eugène Dubois named a new species, now known as Homo erectus. Although the main historical events are well-known, there appears to be no consensus regarding two important aspects of the naming of the species, including what constitutes the original publication of the name, and what is the name-bearing type specimen. These issues are addressed in this paper with reference to original sources and the International Code of Zoological Nomenclature. Our review confirms earlier studies that cite the published quarterly fieldwork report covering the 3rd quarter of 1892 as the original publication naming the species erectus. However, until recently, the correct publication year of 1893 has consistently been cited as 1892, and it has rarely been recognized that the author of the publication was anonymous, even though the author of the species is specifically named. Importantly, Dubois assigns all three hominin fossils found at Trinil up to that moment to the new species, explicitly stating that they belong to a single individual. The three fossils, a molar, a calotte, and a femur, therefore jointly constitute the original holotype. However, the femur most likely derives from younger strata than the other hominins and shows fully modern human-like morphology, unlike subsequently discovered H. erectus femora. Moreover, there is no consensus over the affinities of the molar, and if it is H. erectus rather than an extinct ape, there is no evidence that it belongs to the same individual as the calotte. Excluding these two fossils from the holotype, the calotte is the appropriate fossil to retain the role as name-bearing specimen.

Can I trust my fake data - A comprehensive quality assessment framework for synthetic tabular data in healthcare

BACKGROUND

Ensuring safe adoption of AI tools in healthcare hinges on access to sufficient data for training, testing and validation. Synthetic data has been suggested in response to privacy concerns and regulatory requirements and can be created by training a generator on real data to produce a dataset with similar statistical properties. Competing metrics with differing taxonomies for quality evaluation have been proposed, resulting in a complex landscape. Optimising quality entails balancing considerations that make the data fit for use, yet relevant dimensions are left out of existing frameworks.

METHOD

We performed a comprehensive literature review on the use of quality evaluation metrics on synthetic data within the scope of synthetic tabular healthcare data using deep generative methods. Based on this and the collective team experiences, we developed a conceptual framework for quality assurance. The applicability was benchmarked against a practical case from the Dutch National Cancer Registry.

CONCLUSION

We present a conceptual framework for quality assuranceof synthetic data for AI applications in healthcare that aligns diverging taxonomies, expands on common quality dimensions to include the dimensions of Fairness and Carbon footprint, and proposes stages necessary to support real-life applications. Building trust in synthetic data by increasing transparency and reducing the safety risk will accelerate the development and uptake of trustworthy AI tools for the benefit of patients.

DISCUSSION

Despite the growing emphasis on algorithmic fairness and carbon footprint, these metrics were scarce in the literature review. The overwhelming focus was on statistical similarity using distance metrics while sequential logic detection was scarce. A consensus-backed framework that includes all relevant quality dimensions can provide assurance for safe and responsible real-life applications of synthetic data. As the choice of appropriate metrics are highly context dependent, further research is needed on validation studies to guide metric choices and support the development of technical standards.

Linguistic and (micro)cultural differences in the global debate about re-naming 'schizophrenia': A mixed-methods survey from Switzerland

BACKGROUND AND HYPOTHESIS

This survey explores Swiss mental health professionals', users', and relatives' opinions on re-naming schizophrenia exploiting Switzerland's specific multilingualism to examine possible effects of linguistic and microcultural differences on the issue.

STUDY DESIGN

Opinions on 'schizophrenia' were collected using a self-rated online questionnaire incl. Freetext answers available in the three main Swiss languages, German, French and Italian. It was distributed to the main professional and self-help organizations in Switzerland between June and October 2021.

STUDY RESULTS

Overall, 449 persons completed the questionnaire, 263 in German, 172 in French and 14 in Italian. Of the total sample, 339 identified as mental health professionals, 81 as relatives and 29 as users. Considering the whole sample, almost half favored a name-change with a significant difference between stakeholder- and between language groups. Also, the name 'schizophrenia' was evaluated more critically than the diagnostic concept. Qualitative analysis of freetext answers showed a highly heterogenous argumentation, but no difference between language groups.

CONCLUSIONS

Our results suggest the attitude towards re-naming might itself be subject to (micro)cultural difference, and they highlight the nature of 'schizophrenia' as not only a scientific, but also a linguistic and cultural object. Such local factors ought to be taken into consideration in the global debate.

Development and validation of VaxConcerns: A taxonomy of vaccine concerns and misinformation with Crowdsource-Viability

We present VaxConcerns, a taxonomy for vaccine concerns and misinformation. VaxConcerns is an easy-to-teach taxonomy of concerns and misinformation commonly found among online anti-vaccination media and is evaluated to produce high-quality data annotations among crowdsource workers, opening the potential adoption of the framework far beyond just academic or medical communities. The taxonomy shows high agreement among experts and outperforms existing taxonomies for vaccine concerns and misinformation when presented to non-expert users. Our proof-of-concept study on the changes in anti-vaccination content during the COVID-19 pandemic indicate impactful future use cases, such as longitudinal studies of the shift in vaccine concerns over time.

Comparative morphology of eggs of Rhodnius domesticus Neiva & Pinto, Rhodnius neglectus Lent and Rhodnius prolixus Stål (Hemiptera: Reduviidae: Triatominae)

Rhodnius species are potential vectors of the etiological agent of Chagas disease (CD), the protozoan Trypanosoma cruzi. CD impacts around seven million people in Latin America, resulting in approximately fourteen thousand deaths per year. Several species of Rhodnius are notable not only for their epidemiological relevance, but also for the challenging distinction between their species. Rhodnius has twenty species, each with its specific epidemiological importance. Rhodnius neglectus and Rhodnius prolixus are found with colonies in domiciliary environments. The observation of eggs in human dwellings signals the colonization process of these insects, increasing the risk of contamination of the population, since correct identification of eggs is necessary to help more effective vector control programs. Here we highlight diagnostic characters of eggs for these three species.

Fungal diversity present in snow sampled in summer in the north-west Antarctic Peninsula and the South Shetland Islands, Maritime Antarctica, assessed using metabarcoding

We assessed the fungal diversity present in snow sampled during summer in the north-west Antarctic Peninsula and the South Shetland Islands, maritime Antarctica using a metabarcoding approach. A total of 586,693 fungal DNA reads were obtained and assigned to 203 amplicon sequence variants (ASVs). The dominant phylum was Ascomycota, followed by Basidiomycota, Mortierellomycota, Chytridiomycota and Mucoromycota. Penicillium sp., Pseudogymnoascus pannorum, Coniochaeta sp., Aspergillus sp., Antarctomyces sp., Phenoliferia sp., Cryolevonia sp., Camptobasidiaceae sp., Rhodotorula mucilaginosa and Bannozyma yamatoana were assessed as abundant taxa. The snow fungal diversity indices were high but varied across the different locations sampled. Of the fungal ASVs detected, only 28 were present all sampling locations. The 116 fungal genera detected in the snow were dominated by saprotrophic taxa, followed by symbiotrophic and pathotrophic. Our data indicate that, despite the low temperature and oligotrophic conditions, snow can host a richer mycobiome than previously reported through traditional culturing studies. The snow mycobiome includes a complex diversity dominated by cosmopolitan, cold-adapted, psychrophilic and endemic taxa. While saprophytes dominate this community, a range of other functional groups are present.

Morpho-molecular study of entomopathogenic fungi associated with citrus orchard pests in Northern Iran

Entomopathogenic fungi play a significant role in regulating insect populations in nature and have potential applications in pest management strategies in different regions. Citrus spp. are among the important horticultural products in northern Iran, and the orchards are affected by different insect pests, especially mealybugs. This study aimed to isolate and identify entomopathogenic fungi associated with citrus orchard pests in northern Iran, focusing on Akanthomyces and Lecanicillium species on mealybugs. Through the samples collected from different regions within Guilan province, 12 fungal isolates were collected and identified based on the combination of morphological characteristics and molecular data. Akanthomyces lecanii, A. muscarius, Engyodontium rectidentatum, Lecanicillium aphanocladii and Lecanicillium rasoulzarei sp. nov. were identified. Of these, A. muscarius on Lepidosaphes sp., E. rectidentatum on Coccidae, and L. aphanocladii on Tetranychus urticae are reported as new fungal-host records from Iran. Moreover, a new species, Lecanicillium rasoulzarei, is illustrated, described, and compared with closely related species.

Effect of an altitudinal gradient on the morphology, molecular identification and distribution of Rhipicephalus linnaei in Veracruz, Mexico

Studies of morphological and genetic variation in vector populations across environmental gradients can help researchers to estimate species' responses to climate change scenarios and the potential risk of disease-causing pathogen expansion, which impacts negatively on human health. In this study, we analysed the effect of altitudinal gradients on the phenotypic response of the hard tick of medical and veterinary importance, Rhipicephalus sanguineus sensu lato (s.l.). Specimens of R. sanguineus s.l. were collected from host animals in one of Mexico's regions with high climatic heterogeneity (Veracruz), and geometric morphometric theory was employed to assess the response of three morphological characters to the altitudinal gradient. Additionally, genetic similarity data were provided, and ecological niche models were used to project the climatic distribution in the region. Our results demonstrate that the shape and size of ticks respond to altitude. Molecular identification indicate that all analysed samples correspond to the tropical lineage recently named Rhipicephalus linnaei. According to ecological niche models, the mean annual temperature contributes significantly to the spatial distribution of this tick species, with areas of higher suitability in the mountainous region. These changes in morphological structure and the presence of ticks at higher altitudinal gradients suggest that R. linnaei has a high potential for adaptation. Due to the variability of ecosystems in the state of Veracruz, our results could be valuable in assessing the response of this tick in a changing environment, aiding in predicting future scenarios in the distribution and abundance of this species.

ICTV Virus Taxonomy Profile: Fusariviridae 2024

Fusariviridae is a family of mono-segmented, positive-sense RNA viruses with genome sizes of 5.9-10.7 kb. Most genomic RNAs are bicistronic, but exceptions have up to four predicted ORFs. In bicistronic genomes, the 5'-proximal ORF codes for a single protein with both RNA-directed RNA polymerase (RdRP) and RNA helicase (Hel) domains; little is known about the protein encoded by the second ORF. Fusarivirids do not appear to form virions. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Fusariviridae, which is available at ictv.global/report/fusariviridae.

Discovery of a new photosynthetic euglenoid in Poland: Euglena mazurica sp. nov. (Euglenales, Euglenaceae)

Herein we describe a new photosynthetic euglenoid species found in Poland - Euglena mazurica. A large population exists in a small, eutrophic body of water located in a pasture near Mikołajki town inside the Masurian Landscape Park (covering a part of the Masurian Lake District in Poland). The unique cell shape (corkscrew-like) discerns it well from other previously described euglenoid species with metabolic cells. The new species possesses two plate-like chloroplasts each with a pyrenoid accompanied by two paramylon caps placed on either side of it (diplopyrenoids). On the phylogenetic tree, the new species is situated within the Euglena clade. Though it is a sister branch to three clades - one representing the similar Euglena agilis, characterized by its fusiform cells and two chloroplasts with diplopyrenoids, the two species are clearly morphologically and molecularly distinct.

Ontological pluralism and social values

There seems to be an emerging consensus among many philosophers of science that non-epistemic values ought to play a role in the process of scientific reasoning itself. Recently, a number of philosophers have focused on the role of values in scientific classification or taxonomy. Their claim is that a choice of ontology or taxonomic scheme can only be made, or should only be made, by appealing to non-epistemic or social values. In this paper, I take on this "argument from ontological choice," claiming that it equivocates on the notion of choice. An ontological choice can be understood either in terms of determining which taxonomic scheme is valid, or in terms of deciding which taxonomic scheme to deploy in a given context. I try to show that while the latter can be determined in part by social values, the former ought not to be so determined.

A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data

Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.

The genus Perissopalla Brennan and White, 1960 (Trombidiformes: Trombiculidae) in Brazil: Redescriptions, new localities, and host records with the first molecular data for the genus

The genus Perissopalla Brennan and White (Trombidiformes: Trombiculidae) is currently represented by ten species with three from Brazil: Perissopalla barticonycteris Brennan, Perissopalla ipeani Brennan, and Perissopalla tanycera Brennan. In the present study, these three species are redescribed and illustrated based on the types and additional non-type specimens. New host and locality records for P. ipeani and P. tanycera are included. Additionally, a partial sequence for the 18S rRNA gene for P. ipeani was provided.

Genomic analysis of seven mycobacteriophages identifies three novel species with differing phenotypic stabilities

Recently, case studies have been published regarding the application of mycobacteriophage (MP) therapy (MPT) in patients with multi-antibiotic-resistant infections. A major limitation in the development of MPT is the paucity of therapeutically useful MP. As there are approximately 10,000 MP that have yet to be sequenced, it is possible that characterization of this cohort would increase the repertoire of useful MP. This study aims to contribute to such a strategy, by characterizing a cohort of 7 mycobacteriophages. Sequencing analyses revealed that the MP have unique sequences, and subsequent gene annotation revealed differences in gene organization. Notably, MP LOCARD has the largest genome and operons encoding for glycosyltransferases. Taxonomic analysis executed with VIRIDIC, Gegenees and VICTOR revealed that LOCARD belongs to a different genus than the other phages and is the foundational member of one of three novel species identified in this study. LOCARD, LOCV2, and LOCV5 were selected as representative members of their species and subjected to phenotypic analyses to compare their stability under biologically and industrially relevant conditions. Again LOCARD stood out, as it was unaffected by the typical temperatures (37 °C) and salinity (0.9%) experienced in mammals, while the viability of LOCV2 and LOCV5 was significantly reduced. LOCARD was also tolerant to pH 10, low levels of antiviral detergent and was the least impacted by a single freeze-thaw cycle. When all these results are considered, it indicates that LOCARD in particular, has potential therapeutic and/or diagnostics applications, given its resilience towards physiological and storage conditions.

Pacific marine gregarines (Apicomplexa) shed light on biogeographic speciation patterns and novel diversity among early apicomplexans

Gregarines are the most biodiverse group of apicomplexan parasites. This group specializes on invertebrate hosts (e.g., ascidians, crustaceans, and polychaetes). Marine gregarines are of particular interest because they are considered to be the earliest evolving apicomplexan lineage, having subsequently speciated (and radiated) through virtually all existing animal groups. Still, mechanisms governing the broad (global) distribution and speciation patterns of apicomplexans are not well understood. The present study examines Pacific lecudinids, one of the most species-rich and diverse groups of marine gregarines. Here, marine polychaetes were collected from intertidal zones. Single trophozoite cells were isolated for light and electron microscopy, as well as molecular phylogenetic analyses using the partial 18S rRNA gene. The cytochrome c oxidase subunit 1 gene was used to confirm morphology-based host identification. This study introduces Undularius glycerae n. gen., n. sp. and Lecudina kitase n. sp. (Hokkaido, Japan), as well as Difficilina fasoliformis n. sp. (California, USA). Occurrences of Lecudina cf. longissima and Lecudina cf. tuzetae (California, USA) are also reported. Phylogenetic analysis revealed a close relationship between L. pellucida, L. tuzetae, and L. kitase n. sp. Additionally, clustering among North Atlantic and Pacific L. tuzetae formed a species complex, likely influenced by biogeography.

Small intestinal flukes of the genus Metagonimus (Digenea: Heterophyidae) in Europe and the Middle East: A review of parasites with zoonotic potential

The heterophyid trematode Metagonimus romanicus (Ciurea, 1915) (Digenea) is redescribed on the basis of type material from domestic dogs (Canis familiaris) in Romania, vouchers from experimentally infected cats (Felis catus) and adults recovered from golden hamsters (Mesocricetus auratus) infected with metacercariae from scales of chub (Squalius cephalus) and common nase (Chondrostoma nasus) (Cypriniformes: Leuciscidae) in Hungary. This trematode, endemic to Europe and neighbouring regions (northwestern Türkiye), was previously misidentified as M. yokogawai (Katsurada, 1912), a zoonotic parasite of humans in East Asia. However, the two species differ considerably both genetically and morphologically, e.g., in the position of the ventral sucker, the presence of the prepharynx, the anterior extent of the vitelline follicles and the posterior extent of the uterus. Metagonimus ciureanus (Witenberg, 1929) (syn. Dexiogonimus ciureanus Witenberg, 1929), described from domestic cats and dogs in Israel, is a valid species distributed in the Middle East and Transcaucasia, which is also confirmed by molecular data. It differs from all Metagonimus species, including M. romanicus, in having symmetrical testes instead of the oblique testes of the other congeners. The zoonotic significance of M. romanicus and M. ciureanus is unclear, but appears to be low in Europe, mainly because raw or undercooked, whole fish with scales are generally not consumed. Accidental infection of fishermen by metacercariae in the scales when cleaning fish is more likely, but has never been reported. Remains of cyprinoids with scales infected with metacercariae of Metagonimus spp. can be an important natural source of infection for dogs, cats, and other carnivores, which can serve as a reservoir for these parasites.

Curtobacterium salicis sp. nov., isolated from willow tree stems in Washington state

Curtobacterium sp. strain WW7 is a Gram-positive, non-motile, orange rod-shaped bacterium isolated from branches of wild willow (Salix sitchensis) trees. The WW7T strain has optimum growth in the temperature range between 25 and 30 °C, a pH range of 6-7.7, and tolerates up to 5.5% (w/v) of NaCl. The genome sequencing of strain WW7T revealed a genome size of approximately 3.8 Mbp and a G + C content of 71.3 mol%. The phylogenomic analyses support the WW7T affiliation to a novel Curtobacterium lineage, with Curtobacterium herbarum being the closest type-strain. Chemotaxonomic analysis indicates that the carbon sources assimilation profile of strain WW7T was similar to the type strains, i.e. Curtobacterium luteum, Curtobacterium albidum, and Curtobacterium flaccumfaciens, while no assimilation of the organic acids succinate, alpha-ketobutyrate, mono methyl-succinate, and lactate was observed. Finally, fatty acid methyl ester analysis identifies anteiso-C15:0 and anteiso-C17:0 as major cellular fatty acids which is a common feature for members of the Curtobacterium genus. Based on the results of phylogenomic and chemotaxonomic analyses, strain WW7T represents a novel Curtobacterium lineage, for which the name Curtobacterium salicis sp. nov. is proposed. The type strain is WW7T (DSM 34805T-NRRL B-68078T).

Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples

BACKGROUND

Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. DNA from saliva, oral biofilms (subgingival plaque) and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively.

RESULTS

With both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such as Streptococcus tended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in subgingival plaque biofilm samples) none of the differences were statistically significant when correcting for multiple testing.

CONCLUSIONS

The results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.

Lepocreadiidae (Trematoda) associated with gelatinous zooplankton (Cnidaria and Ctenophora) and fishes in Australian and Japanese waters

We examined gelatinous zooplankton from off eastern Australia for lepocreadiid trematode metacercariae. From 221 specimens of 17 species of cnidarian medusae and 218 specimens of four species of ctenophores, infections were found in seven cnidarian and two ctenophore species. Metacercariae were distinguished using cox1 mtDNA, ITS2 rDNA and morphology. We identified three species of Prodistomum Linton, 1910 [P. keyam Bray & Cribb, 1996, P. orientale (Layman, 1930), and Prodistomum Type 3], two species of Opechona Looss, 1907 [O. kahawai Bray & Cribb, 2003 and O. cf. olssoni], and Cephalolepidapedon saba Yamaguti, 1970. Two species were found in cnidarians and ctenophores, three only in cnidarians, and one only in a ctenophore. Three Australian fishes were identified as definitive hosts; four species were collected from Scomber australasicus and one each from Arripis trutta and Monodactylus argenteus. Transmission of trematodes to these fishes by ingestion of gelatinous zooplankton is plausible given their mid-water feeding habits, although such predation is rarely reported. Combined morphological and molecular analyses of adult trematodes identified two cox1 types for C. saba, three cox1 types and species of Opechona, and six cox1 types and five species of Prodistomum of which only two are identified to species. All three genera are widely distributed geographically and have unresolved taxonomic issues. Levels of distinction between the recognised species varied dramatically for morphology, the three molecular markers, and host distribution. Phylogenetic analysis of 28S rDNA data extends previous findings that species of Opechona and Prodistomum do not form monophyletic clades.

Glochidionyangchunense (Phyllanthaceae), a new species with discoid flowers from Guangdong Province, China

Phyllanthodendron can be readily morphologically distinguished from Glochidion, but recent molecular evidence showed that Phyllanthodendron is paraphyletic due to Glochidion being nested within it. In this study, a new species of the former Phyllanthodendron is described and illustrated as Glochidionyangchunense Z.Q. Song & Gang Yao from the limestone areas of South China. This is a peculiar new species and morphologically distinguished by its discoid flowers, T-shaped disc segments, and glabrous flowering branches. A key to Glochidionyangchunense and related species in China is provided here.

Foveavelia, a new South American genus of Veliinae (Hemiptera: Heteroptera: Veliidae)

Background

Semiaquatic bugs (Hemiptera: Heteroptera: Gerromorpha) are distributed worldwide and play fundamental roles in limnic ecosystems. They are the most successful group of organisms to occupy the air-water interface, are important models to study ecology and evolution, and can be relevant tools in biomonitoring. Veliidae is the second most speciose family of semiaquatic bugs, but its internal classification, including subfamilies and genera, is artificial and based on symplesiomorphies. One of these non-monophyletic entities is Paravelia Breddin, 1898, the largest genus in the subfamily Veliinae.

Results

In an effort to better classify the Veliinae, we describe Foveavelia to hold five South American species previously placed in Paravelia. The new genus is characterized by the following combination of features: unusual coarse cuticular punctures throughout the thorax and abdomen; a pair of small, frosty, pubescent areas formed by a very dense layer of short setae on the anterior lobe of the pronotum; fore tibial grasping comb present only in males; middle tibia with a row of elongate dark-brown trichobothria-like setae on the distal third, decreasing in size distally; macropterous specimens with the apical macula of the forewings elongate and constricted at mid-length, reaching the wing apex; and the male proctiger with a pair of anterodorsal projections. Besides the description, a key to the species of Foveavelia is provided, accompanied by illustrations and a species distribution map.

Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution

Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.

Diversity and enzymatic, biosurfactant and phytotoxic activities of culturable Ascomycota fungi present in marine sediments obtained near the South Shetland Islands, maritime Antarctica

We studied the culturable fungal community recovered from deep marine sediments in the maritime Antarctic, and assessed their capabilities to produce exoenzymes, emulsifiers and metabolites with phytotoxic activity. Sixty-eight Ascomycota fungal isolates were recovered and identified. The most abundant taxon recovered was the yeast Meyerozyma guilliermondii, followed by the filamentous fungi Penicillium chrysogenum, P. cf. palitans, Pseudeurotium cf. bakeri, Thelebolus balaustiformis, Antarctomyces psychrotrophicus and Cladosporium sp. Diversity indices displayed low values overall, with the highest values obtained at shallow depth, decreasing to the deepest location sampled. Only M. guilliermondii and P. cf. palitans were detected in the sediments at all depths sampled, and were the most abundant taxa at all sample sites. The most abundant enzymes detected were proteases, followed by invertases, cellulases, lipases, carrageenases, agarases, pectinases and esterases. Four isolates showed good biosurfactant activity, particularly the endemic species A. psychrotrophicus. Twenty-four isolates of P. cf. palitans displayed strong phytotoxic activities against the models Lactuca sativa and Allium schoenoprasum. The cultivable fungi recovered demonstrated good biosynthetic activity in the production of hydrolytic exoenzymes, biosurfactant molecules and metabolites with phytotoxic activity, reinforcing the importance of documenting the taxonomic, ecological and biotechnological properties of fungi present in deep oceanic sediments of the Southern Ocean.

200 years of taxonomic confusion: Sporendonema and allies

The genus Sporendonema (Gymnoascaceae, Onygenales) was introduced in 1827 with the type species S. casei for a red mould on cheese. Cheese is a consistent niche for this species. Sphaerosporium equinum is another species classified in Gymnoascaceae and has also been reported from cheese. Recently, other habitats have been reported for both Sporendonema casei and Sphaerosporium equinum. The present study aimed to investigate the taxonomy of Sporendonema and Sphaerosporium, as well as a close neighbour, Arachniotus. Two strains of Hormiscium aurantiacum, another related cheese-associated species were also included in the analyses. Strains were evaluated in terms of macro- and micromorphology, physiology including salt tolerance, growth rate at different temperatures, casein degradation, cellulase activity, lipolytic activity, and multi-locus phylogeny with sequences of the nuclear ribosomal internal transcribed spacer region, the D1-D2 region of the large subunit and partial β-tubulin locus sequences. The results showed that the analysed species were congeneric, and the generic names Arachniotus and Sphaerosporium should be reduced to the synonymy of Sporendonema. Therefore, four new combinations as well as one lectotype and one epitype were designated in Sporendonema. Two strains attributed to Sphaerosporium equinum from substrates other than cheese were found to be phylogenetically and morphologically deviant and were introduced as a new species named Sporendonema isthmoides.

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes

BACKGROUND

By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems.

RESULTS

Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria.

CONCLUSIONS

Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.

Digital skull anatomy of the Oligocene North American tortoise Stylemys nebrascensis with taxonomic comments on the species and comparisons with extant testudinids of the Gopherus-Manouria clade

The anatomy of North American tortoises is poorly understood, despite a rich fossil record from the Eocene and younger strata. Stylemys nebrascensis is a particularly noteworthy turtle in this regard, as hundreds of specimens are known from Oligocene deposits, and as this species is one of the earliest fossil turtles to have been described in the scientific literature. Since its initial description based on a shell, many specimens with more complete material have been referred to Stylemys nebrascensis. Here, we review and confirm the referral of an important historic specimen to Stylemys nebrascensis, which includes shell, non-shell postcranial, and skull material. This allows us to document unique skull features of Stylemys nebrascensis (e.g., an unusual 'poststapedial canal' that connects the posterior skull surface with the cavum acustico-jugulare) and to refer another well-preserved skull to the species. Based on computed-tomography scanning of these two skulls, we provide a detailed description of the cranial and mandibular osteology of Stylemys nebrascensis. Stylemys nebrascensis has a combination of plesiomorphic skull characteristics (e.g., retention of a medial jugal process) and derived traits shared with extant gopher tortoises (e.g., median premaxillary ridge) that suggest it may be a stem-representative of the gopher tortoise lineage. This supports the hypothesis that extant and fossil tortoises from North America form a geographically restricted clade that split from Asian relatives during the Paleogene.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Solibacillus ferritrahens sp. nov., a novel siderophore-producing bacterium isolated from Wumeng Mountain National Nature Reserve in Yunnan Province

A gram-stain-positive, aerobic, rod-shaped bacterial strain capable of producing siderophores, named YIM B08730T, was isolated from a soil sample collected from Wumeng Mountain National Nature Reserve, Zhaotong City, Yunnan Province. Growth occurred at 10-45 °C (optimum, 35-40 ℃), pH 7.0-9.0 (optimum, 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 0-1 %, w/v). A comparative analysis of the 16S rRNA gene sequence (1558 bp) of strain YIM B08730T showed the highest similarity to Solibacillus isronensis JCM 13838T (96.2 %), followed by Solibacillus silvestris DSM 12223T (96.0 %) and Solibacillus kalamii ISSFR-015T (95.4 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unidentified lipid. The main respiratory quinone of strain YIM B08730T was menaquinone 7 (MK-7). The major fatty acids were iso-C15:0 and C16:1ω7c alcohol. The digital DNA-DNA hybridization and average nucleotide identity values between strain YIM B08730T and the reference strain S. isronensis JCM 13838T were 24.8 % and 81.2 %, respectively. The G + C content of the genomic DNA was 37.1 mol%. The genome of the novel strain contained genes associated with the production of siderophores, and it also revealed other functional gene clusters involved in plant growth promotion and soil bioremediation. Based on these phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM B08730T is considered to be a novel species of the genus Solibacillus, for which the name Solibacillus ferritrahens sp. nov. is proposed. The type strain is YIM B08730T (= NBRC 116268T = CGMCC 1.60169T).

ChatGPT in healthcare: A taxonomy and systematic review

The recent release of ChatGPT, a chat bot research project/product of natural language processing (NLP) by OpenAI, stirs up a sensation among both the general public and medical professionals, amassing a phenomenally large user base in a short time. This is a typical example of the 'productization' of cutting-edge technologies, which allows the general public without a technical background to gain firsthand experience in artificial intelligence (AI), similar to the AI hype created by AlphaGo (DeepMind Technologies, UK) and self-driving cars (Google, Tesla, etc.). However, it is crucial, especially for healthcare researchers, to remain prudent amidst the hype. This work provides a systematic review of existing publications on the use of ChatGPT in healthcare, elucidating the 'status quo' of ChatGPT in medical applications, for general readers, healthcare professionals as well as NLP scientists. The large biomedical literature database PubMed is used to retrieve published works on this topic using the keyword 'ChatGPT'. An inclusion criterion and a taxonomy are further proposed to filter the search results and categorize the selected publications, respectively. It is found through the review that the current release of ChatGPT has achieved only moderate or 'passing' performance in a variety of tests, and is unreliable for actual clinical deployment, since it is not intended for clinical applications by design. We conclude that specialized NLP models trained on (bio)medical datasets still represent the right direction to pursue for critical clinical applications.

Ciceribacter sichuanensis sp. nov., a plant growth promoting rhizobacterium isolated from root nodules of soybean in Sichuan, China

The fast-growing rhizobia-like strains S101T and S153, isolated from root nodules of soybean (Glycine max) in Sichuan, People's Republic of China, underwent characterization using a polyphasic taxonomy approach. The strains exhibited growth at 20-40 °C (optimum, 28 °C), pH 4.0-10.0 (optimum, pH 7.0) and up to 2.0% (w/v) NaCl (optimum, 0.01%) on Yeast Mannitol Agar plates. The 16S rRNA gene of strain S101T showed 98.4% sequence similarity to the closest type strain, Ciceribacter daejeonense L61T. Major cellular fatty acids in strain S101T included summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant quinone was ubiquinone-10. The polar lipids of strain S101T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethyl ethanolamine, phosphatidyl ethanolamine, amino phospholipid, unidentified phosphoglycolipid and unidentified amino-containing lipids. The DNA G + C contents of S101T and S153 were 61.1 and 61.3 mol%, respectively. Digital DNA-DNA hybridization relatedness and average nucleotide identity values between S101T and C. daejeonense L61T were 46.2% and 91.4-92.2%, respectively. In addition, strain S101T promoted the growth of soybean and carried nitrogen fixation genes in its genome, hinting at potential applications in sustainable agriculture. We propose that strains S101T and S153 represent a novel species, named Ciceribacter sichuanensis sp. nov., with strain S101T as the type strain (= CGMCC 1.61309 T = JCM 35649 T).

CHARACTERIZATION OF EIMERIA LANCASTERENSIS AND EIMERIA ONTARIOENSIS (APICOMPLEXA: EIMERIIDAE) FOUND IN EASTERN GRAY SQUIRRELS, SCIURUS CAROLINENSIS (RODENTIA: SCIURIDAE), FROM ARKANSAS AND OKLAHOMA

We report the morphological characteristics of oocysts of Eimeria lancasterensisJoseph, 1969, collected from 6 of 6 (100%) eastern gray squirrels, Sciurus carolinensis, collected in Arkansas (n = 3) and Oklahoma (n = 3), and Eimeria ontarioensisLee and Dorney, 1971, recovered from an individual of S. carolinensis from Arkansas. Oocysts of E. lancasterensis were ovoidal to ellipsoidal, measuring (L × W) 24.0 × 14.6 (18-29 × 12-16) µm; shape index (L/W) was 1.6 (1.3-1.8). A micropyle and an oocyst residuum were absent, but up to 2 polar granules were present. Oocysts of E. ontarioensis were piriform and measured 40.6 × 26.0 (37-44 × 23-28); L/W was 1.6 (1.5-1.7). These oocysts possessed a distinct micropyle and rarely a polar granule but lacked an oocyst residuum. The DNA was isolated from both eimerians, and the 18S rDNA genetic markers were PCR-amplified, cloned, sequenced, and analyzed. To our knowledge, this study represents the first time 18S DNA sequence data have been generated from E. lancasterensis and E. ontarioensis found in North American sciurid hosts, as well as new geographic distribution records for these coccidians. In addition, we also include a tabular summary of these 2 species of Eimeria from Sciurus spp. worldwide, with information on their hosts, distribution, and taxonomically important morphological characteristics, including key measurements of oocysts and sporocysts.

Relictithismia kimotsukiensis, a new genus and species of Thismiaceae from southern Japan with discussions on its phylogenetic relationship

The family Thismiaceae, known as "fairy lanterns" for their urn- or bell-shaped flowers with basally fused tepals, consists of non-photosynthetic flowering monocots mainly in tropical regions, extending into subtropical and temperate areas. Here, we propose a new mycoheterotrophic genus, Relictithismia Suetsugu & Tagane (Thismiaceae), with its monotypic species Relictithismia kimotsukiensis Suetsugu, Yas.Nakam. & Tagane from Kimotsuki Mountains in the Osumi Peninsula, Kagoshima Prefecture, Kyushu Island, southern Japan. Relictithismia resembles Haplothismia Airy Shaw in having a cluster of tuberous roots, a feature previously observed only in this genus within the family Thismiaceae. However, it differs in having solitary flowers (vs. 2-6-flowered pseudo-raceme in Haplothismia), anther thecae largely separated (vs. connate), and the presence of an annulus (vs. absent). Additionally, Relictithismia differs from the geographically overlapping genus Thismia Griff. in its stamen structure and the position of the annulus. In Relictithismia, the stamens lack connectives, and its free filaments arise from the annulus located inside the perianth mouth, while in Thismia, the stamens typically have connate connectives, forming a staminal tube pendulous from the annulus located at the mouth of the floral tube. Our morphological and phylogenetic data indicated that R. kimotsukiensis holds an early-diverging position within the family, situated outside the Old World Thismia clade. This paper offers an extensive description and color photographs of R. kimotsukiensis, complemented by notes on its phylogenetic relationship and evolutionary history.

Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae)

A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.

Description of two new species of dactylogirids (Monogenoidea: Dactylogyridae) from Mylossoma albiscopum (Cope, 1872) (Characiformes: Serrasalmidae) from the Peruvian Amazonia

INTRODUCTION

Two new dactylogyrid monogeneans, Anacanthorus cultro n. sp. and Notozothecium palometae n. sp., are described based on specimens collected from the gill filaments of Mylossoma albiscopum (Cope, 1872) (Characiformes: Serrasalmidae), a pelagic and herbivore teleost collected in the Tigre river, Loreto, Peru.

MATERIALS AND METHODS

Some monogeneans were stained with Gomori's trichrome and mounted in Canada Balsam to determine internal soft structures. Others were cleared in Hoyer's medium for the study of sclerotized structures. Drawings were made using a drawing tube and a microprojector.

RESULTS

Anacanthorus cultro n. sp. is characterized by the presence of a rod-shaped male copulatory organ (MCO) lacking featherlike structures, and a knife-shaped accessory piece with a submedial knob. Notozothecium palometae n. sp. can be distinguished from all congeners by its MCO with a subbasal spur and an accessory piece with inverted hammer shaped.

CONCLUSIONS

This is the first data on the parasites of M. albiscopum, a popular fish in local markets. Anacanthorus cultro n. sp. is the twenty-fifth documented species of the genus in Peru, while N. palometae n. sp. represents the seventh species of the genus known to infect freshwater fish species in Peru.

Sphingomonas flavescens sp. nov., isolated from soil

An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).

Decision support framework for IT project manager recruitment

Information technology project managers (IT PM) have a critical influence on IT project success while attracting and selecting the right IT PM is challenging. We followed a four-level research design and firstly developed a taxonomy as an input for a cluster analysis to identify patterns in IT PM job advertisements. Based hereon, we developed a decision support framework for IT PM recruitment. We evaluated our findings in an online survey. We identified multiple design elements for IT PM job advertisements within five perspectives and deduced five IT PM archetypes. The decision support framework uses five questions to assist IT PM recruitment. We expand the knowledge base and consider not only IT PM requirements but also benefits. Our decision support framework is the first to holistically support IT PM recruitment, supports recruitment managers in structuring job interviews, identifies potential matches between applicants and recruiters, and assists in the final selection.

The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis

BACKGROUND

The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia. Despite many previous taxonomic insights into it, phylogenetic studies of the genus are still lacking. And the establishment of a robust phylogenetic framework remains elusive, impeding advancements and revisions in the taxonomic system for this genus. Plastomes with greater variability in their genetic characteristics hold promise for building a more robust Libanotis phylogeny.

RESULTS

During our research, we sequenced, assembled, and annotated complete plastomes for twelve Libanotis species belong to three sections and two closely related taxa. We conducted a comprehensive comparative analysis through totally thirteen Libanotis plastomes for the genus, including an additional plastome that had been published. Our results suggested that Libanotis plastome was highly conserved between different subclades, while the coding regions were more conserved than the non-coding regions, and the IR regions were more conserved than the single copy regions. Nevertheless, eight mutation hotspot regions were identified among plastomes, which can be considered as candidate DNA barcodes for accurate species identification in Libanotis. The phylogenetic analyses generated a robustly framework for Libanotis and revealed that Libanotis was not a monophyletic group and their all three sections were polygenetic. Libanotis schrenkiana was sister to L. sibirica, type species of this genus, but the remainders scattered within Selineae.

CONCLUSION

The plastomes of Libanotis exhibited a high degree of conservation and was effective in enhancing the support and resolution of phylogenetic analyses within this genus. Based on evidence from both phylogeny and morphology, we propose the recognition of "Libanotis sensu stricto" and provide taxonomic recommendations for other taxa that previously belonged to Libanotis. In conclusion, our study not only revealed the phylogenetic position and plastid evolution of Libanotis, but also provided new insights into the phylogeny of the family Apiaceae and phylogenetic relationships within the tribe Selineae.

Isospora juruviarae n. sp. (Apicomplexa: Eimeriidae) from chivi vireos Vireo chivi (Vieillot, 1817) (Passeriformes: Vireonidae) in South America

Chivi vireos Vireo chivi (Vieillot, 1817) are passerine birds widely distributed throughout Brazil, but mainly observed in the Atlantic Forest of the South and Southeast regions of the country. In this context, the current study identifies a new species of Isospora Schneider, 1881 from V. chivi captured in the Marambaia Island, on the coast of the State of Rio de Janeiro, Southeastern Brazil. The oocysts of Isospora juruviarae Andrade & Berto n. sp. are subspheroidal to ovoidal, measuring on average 26 by 24 μm. Micropyle is absent or inconspicuous. Oocyst residuum absent, but polar granules are present. Sporocysts are ellipsoidal with pointed posterior end, measuring on average 17 by × 11 μm. Stieda and Sub-Stieda bodies are present. Sporocyst residuum is present among the vermiform sporozoites, which have refractile bodies and nucleus. This morphology was different from the other Isospora spp. recorded in the same family, superfamily and parvorder as the host. Molecular identification was targeted by the amplification and sequencing of two different loci of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and one locus of the 18S small subunit ribosomal RNA (18S) gene. Phylogenetic analyses were not very efficient in forming monophyletic groups associated with host taxon, zoogeographical region or taxonomic character; however, they confirmed the identification as a new species through comparison with sequences from Isospora spp. of wild passerines. Finally, based on the morphological and molecular analyses of the oocysts recovered from the chivi vireo V. chivi in the current work, I. juruviarae is considered new to science, being the second species recorded in the host family Vireonidae and the first to have a supplementation by molecular identification.

Phocaeicola acetigenes sp. nov., producing acetic acid and iso-butyric acid, isolated faeces from a healthy human

An obligately anaerobic, non-motile, Gram-stain-negative, and rod-shaped strain KGMB11183T was isolated from the feces of healthy Koreans. The growth of strain KGMB11183T occurred at 30-45 °C (optimum 37 °C), at pH 6-9 (optimum pH 7), and in the presence of 0-0.5% NaCl (optimum 0%). Strain KGMB11183T showed 16S rRNA gene sequence similarities of 95.4% and 94.2% to the closest recognized species, Phocaeicola plebeius M12T, and Phocaeicola faecicola AGMB03916T. Phylogenetic analysis showed that strain KGMB11183T is a member of the genus Phocaeiocla. The major end products of fermentation are acetic acid and isobutyric acid. The major cellular fatty acids (> 10%) of this isolate were C18:1 cis 9, anteiso-C15:0, and summed feature 11 (iso-C17:0 3-OH and/or C18:2 DMA). The assembled draft genome sequences of strain KGMB11183T consisted of 3,215,271 bp with a DNA G + C content of 41.4%. According to genomic analysis, strain KGMB11183T has a number of genes that produce acetic acid. The genome of strain KGMB11183T encoded the starch utilization system (Sus) operon, SusCDEF suggesting that strain uses many complex polysaccharides that cannot be digested by humans. Based on the physiological, chemotaxonomic, phenotypic, and phylogenetic data, strain KGMB11183T is regarded a novel species of the genus Phocaeicola. The type strain is KGMB11183T (= KCTC 25284T = JCM 35696T).

A New Eyeless Species of Micranops Cameron 1913 from Bolivia (Coleoptera: Staphylinidae: Paederinae)

This work adds a new eyeless species of the genus Micranops Cameron, 1913 (Staphylinidae, Paederinae, Scopaeina) to the endogean Coleoptera of the Bolivian fauna. The loss of eyes is usually associated with adaptations to subterranean habitats, although M. bolivianus Guzman & Żyła sp. nov. was collected from leaf litter. We also report new occurrences for the genus west of the Andes mountain range. Our work increases the number of known Neotropical Micranops species to seven and extends the known distribution range for the genus in South America.

Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic

The iconic mountains of the Pantepui biogeographical region host many early-diverging endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient "Lost World". While this is the case of several frog lineages, others appear to have more recent origins, adding to the controversy around the diversification processes in this region. Due to its remoteness, Pantepui is challenging for biological surveys, and only a glimpse of its biodiversity has been described, which hampers comprehensive evolutionary studies in many groups. During a recent expedition to the Neblina massif on the Brazil-Venezuela border, we sampled two new frog species that could not be assigned to any known genus. Here, we perform phylogenetic analyses of mitogenomic and nuclear loci to infer the evolutionary relationships of the new taxa and support their description. We find that both species represent single lineages deeply nested within Brachycephaloidea, a major Neotropical clade of direct-developing frogs. Both species diverged >45 Ma from their closest relatives: the first is sister to all other Brachycephaloidea except for Ceuthomantis, another Pantepui endemic, and the second is sister to Brachycephalidae, endemic to the Brazilian Atlantic Forest. In addition to these considerable phylogenetic and biogeographic divergences, external morphology and osteological features support the proposition of two new family and genus-level taxa to accommodate these new branches of the amphibian tree of life. These findings add to other recently described ancient vertebrate lineages from the Neblina massif, providing a bewildering reminder that our perception of the Pantepui's biodiversity remains vastly incomplete. It also provides insights into how these mountains acted as "museums" during the diversification of Brachycephaloidea and of Neotropical biotas more broadly, in line with the influential "Plateau theory". Finally, these discoveries point at the yet unknown branches of the tree of life that may go extinct, due to global climate change and zoonotic diseases, before we even learn about their existence, amphibians living at higher elevations being particularly at risk.

GREGARINA LUTESCENS N. SP. INFECTING THE HARLEQUIN LADYBIRD HARMONIA AXYRIDIS (COLEOPTERA: COCCINELLIDAE)

Gregarina lutescens n. sp. is described from the alimentary canal of the harlequin ladybird or multicolored Asian lady beetle, Harmonia axyridis (Coleoptera: Coccinellidae) collected from prairie fleabane, Erigeron strigosus, at Peru State College, Peru, Nemaha Co., Nebraska. Our specimens differ from all 11 known species of Gregarina infecting coccinellid beetles worldwide by differences in size and relative shape, color, and association structure. Gregarina lutescens n. sp. is smaller than 7 known species infecting coccinellid beetles but larger than the other 4 known species based on confidence interval exclusion of means. Our specimens are unique among known species of interest in their quince-yellow cytoplasm and precocious but ephemeral serial associations of up to 5 satellites. Nucleotide sequence (18S) phylogenetic analyses place the new species basal to a member of an internal clade of Gregarina that comprises gregarines parasitizing chrysomelid beetles. Phylogenetically, the analysis recovered 3 major lineages within the gregarines, representing the superfamilies Gregarinoidea, Stenophoroidea, and Stylocephaloidea and indicating the propensity of gregarines to track host lineages and environments through evolutionary time. These findings confirm the polyphyletic nature of Gregarina, which currently comprises over 300 described species, only a handful of which have documented genetic sequences suitable for phylogenetic analysis. Recollection, redescription, and molecular clarification of gregarine species infecting coccinellids would likely result in identification of a unique clade that would be an excellent system for studying the effect of intraguild host competition on parasite diversification and community structure. Ecologically, patterns of prevalence in this study indicate that G. lutescens reproduces primarily in larval hosts but depends on infections in adult beetles to overwinter, reflecting the differential vagility and frost tolerance of larval and adult host life cycle stages.

Comparative metagenomics and microbial dynamics of jute retting environment

Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.

Description of Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. (Ciliophora, Hypotricha) from northern China

The morphology and morphogenesis of a new urostylid, Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. were analyzed. The new subspecies differs from the nominotypical subspecies H. (Extraholostichides) eastensis eastensis Wang et al., 2022 by the relatively long frontoterminal row (about 60% vs. 30% of body length), colorless cortical granules (vs. dark brown), two (vs. one) parabuccal cirri, and usually an extra cirrus behind the first midventral pair (vs. lacking). Based on the difference in the frontal ciliature, we split Holostichides into two subgenera: H. (Extraholostichides) subgen. nov. (type species Holostichides eastensis Wang et al., 2022; with a short cirral row behind the middle frontal cirrus) and H. (Holostichides) Foissner, 1987 (type species Holostichides chardezi Foissner, 1987; lacking this short row). The main morphogenetic characters of the new subspecies are very similar to those of H. (Extraholostichides) eastensis eastensis except for some minor differences. Phylogenetic analyses based on SSU rDNA sequences indicate that H. (Extraholostichides) subgen. nov. is monophyletic and nested within the monophyletic genus Holostichides, which is sister to Eschaneustyla lugeri.

Micrometer insights into Nepeta genus: Pollen micromorphology unveiled

This study provides a comprehensive pollen micromorphology within the Nepeta genus, revealing intricate details about the pollen grains' structure and characteristics. The findings shed light on the evolutionary and taxonomical aspects of this plant genus, offering valuable insights for botanists and researchers studying Nepeta species. The pollen grains of 18 Nepeta species were studied using scanning electron microscopy (SEM) and light microscopy (LM) in Northern Pakistan. At the microscale, pollen quantitative measurements, qualitative traits, and diverse sculpturing patterns were reported and compared. Significant differences in pollen size, shape, ornamentation, and sculpturing patterns were discovered among the Nepeta species. Our data show that exine sculpturing is quite diverse, with most species exhibiting a reticulate perforate pollen pattern. Nepeta connata, Nepeta discolor, Nepeta elliptica, revealed a distinct bireticulate perforate exine stratification. Hexazonocolpate pollen is the most common. Furthermore, the surface membrane attributes of the colpus varied greatly, ranging from rough, scabrate, psilate, to sinuate patterns. Principal Component Analysis (PCA) was used to discover the key factors influencing pollen diversity. PCA results showed that polar and equatorial diameters, colpi size, and exine thickness were the most influential pollen features between Nepeta species. This study adds to our understanding of pollen morphology in the Nepeta genus, offering information on the vast range of characteristics found in this economically important group. The extensive characterization of pollen features provides useful insights for the categorization and differentiation of Nepeta species, adding to the Lamiaceae micromorphology.

Morphogenesis of an anaerobic ciliate Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 (Ciliophora, Armophorea) with notes on its morphological and molecular characterization

The morphology, morphogenesis, and molecular phylogeny of Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 were studied using microscopical observations on live and protargol-stained specimens as well SSU rRNA gene sequencing. The morphogenetic data for the genus are presented for the first time. Compared to other metopids, the morphogenesis of H. palaeformis is distinct since its (1) perizonal stripe rows 4 and 5 are involved in the formation of the opisthe's adoral polykinetids; (2) perizonal stripe rows 3-5 and two adjacent preoral dome kineties contribute to most of the opisthe's paroral membrane while perizonal stripe rows 1 and 2 contribute very little; (3) four kinety rows are formed to the left of the opisthe's adoral zone of polykinetids. The Chinese population resembles the original and neotype populations well in terms of general morphology - characterized by a life size of 55-120 × 10-20 μm, an elongate ellipsoidal body with a hardly spiralized flat preoral dome, about 18 somatic kineties and 20 adoral polykinetids. The SSU rDNA sequence of the present population exhibits a disparity of 1.33%-2.22% divergence from sequences of other populations. Nevertheless, phylogenetic analysis reveals that populations of H. palaeformis form a separate, stable cluster within the paraphyletic Metopidae clade.

Linkage facilitation services for opioid use disorder: Taxonomy of facilitation practitioners, goals, and activities

INTRODUCTION

This article proposes a taxonomy of linkage facilitation services used to help persons with opioid use disorder access treatment and recovery resources. Linkage facilitation may be especially valuable for persons receiving medication for opioid use disorder (MOUD) given the considerable barriers to treatment access and initiation that have been identified. The science of linkage facilitation currently lacks both consistent communication about linkage facilitation practices and a conceptual framework for guiding research.

METHODS

To address this gap, this article presents a taxonomy derived from expert consensus that organizes the array of practitioners, goals, and activities associated with linkage services for OUD and related needs. Expert panelists first independently reviewed research reports and policy guidelines summarizing the science and practice of linkage facilitation for substance use disorders generally and OUD specifically, then met several times to vet the conceptual scheme and content of the taxonomy until they reached a final consensus.

RESULTS

The derived taxonomy contains eight domains: facilitator identity, facilitator lived experience, linkage client, facilitator-client relationship, linkage activity, linkage method, linkage connectivity, and linkage goal. For each domain, the article defines basic domain categories, highlights research and practice themes in substance use and OUD care, and introduces innovations in linkage facilitation being tested in one of two NIDA-funded research networks: Justice Community Opioid Innovation Network (JCOIN) or Consortium on Addiction Recovery Science (CoARS).

CONCLUSIONS

To accelerate consistent application of this taxonomy to diverse research and practice settings, the article concludes by naming several considerations for linkage facilitation workforce training and implementation.