A Machine Learning-Based Raman Spectroscopic Assay for the Identification of Burkholderia mallei and Related Species

Burkholderia (B.) mallei, the causative agent of glanders, and B. pseudomallei, the causative agent of melioidosis in humans and animals, are genetically closely related. The high infectious potential of both organisms, their serological cross-reactivity, and similar clinical symptoms in human and animals make the differentiation from each other and other Burkholderia species challenging. The increased resistance against many antibiotics implies the need for fast and robust identification methods. The use of Raman microspectroscopy in microbial diagnostic has the potential for rapid and reliable identification. Single bacterial cells are directly probed and a broad range of phenotypic information is recorded, which is subsequently analyzed by machine learning methods. Burkholderia were handled under biosafety level 1 (BSL 1) conditions after heat inactivation. The clusters of the spectral phenotypes and the diagnostic relevance of the Burkholderia spp. were considered for an advanced hierarchical machine learning approach. The strain panel for training involved 12 B. mallei, 13 B. pseudomallei and 11 other Burkholderia spp. type strains. The combination of top- and sub-level classifier identified the mallei-complex with high sensitivities (>95%). The reliable identification of unknown B. mallei and B. pseudomallei strains highlighted the robustness of the machine learning-based Raman spectroscopic assay

Evolution, turnovers and spatial variation of the gastropod fauna of the late Miocene biodiversity hotspot Lake Pannon

AbstractLake Pannon constituted the biggest hotspot of biodiversity in the late Cenozoic of Europe, comprising a total diversity of almost 600 gastropod species. The gastropod fauna of this huge brackish system, which existed over about seven million years from the late Miocene to earliest Pliocene within the Pannonian Basin System, has been well documented by a great many of taxonomic works. In contrast, the faunal development within the lake has not been properly addressed from a statistical point of view. The present investigation demonstrates that species were not homogeneously distributed across space and time, generating uneven and temporally shifting patterns of species richness and degree of point endemism across the lake. The faunal compositions of the time intervals analyzed were highly different, contrasting simple species accumulation as suggested by the overall numbers. Shifting patterns of local diversity within the lake reflect changing paleo-shorelines, resulting from prograding river systems entering and successively diminishing the lake surface area. As mainly herbivorous grazers and predominantly shallow-water inhabitants, the gastropods traced the moving shelf margins and vegetation belts accordingly, producing the observed diversity shifts. In addition, each time interval is characterized by a high degree of provincialism, which is considered to reflect high habitat diversity. This claim is supported by the complex subaqueous topography and the presence of extensive delta plains produced by the incoming river systems. A potential driver for provincialism might be the adaptation of species to distinct water depths (and related parameters). Finally, the notable differences among the faunal compositions of the upper Pannonian strata and the succeeding lower Viviparus beds, especially regarding family-level, indicate an environmental turnover at the transition. Brackish-water species are mostly replaced by typical freshwater elements, indicating strong fluvial influence. Based on our results and latest stratigraphic data, we conclude that the Viviparus beds were deposited in a different environment, replacing Lake Pannon in the southern Pannonian Basin in the early Pliocene

Measurement of liver iron by magnetic resonance imaging in the UK Biobank population

The burden of liver disease continues to increase in the UK, with liver cirrhosis reported to be the third most common cause of premature death. Iron overload, a condition that impacts liver health, was traditionally associated with genetic disorders such as hereditary haemochromatosis, however, it is now increasingly associated with obesity, type-2 diabetes and non-alcoholic fatty liver disease. The aim of this study was to assess the prevalence of elevated levels of liver iron within the UK Biobank imaging study in a cohort of 9108 individuals. Magnetic resonance imaging (MRI) was undertaken at the UK Biobank imaging centre, acquiring a multi-echo spoiled gradient-echo single-breath-hold MRI sequence from the liver. All images were analysed for liver iron and fat (expressed as proton density fat fraction or PDFF) content using LiverMultiScan™. Liver iron was measured in 97.3% of the cohort. The mean liver iron content was 1.32 ± 0.32 mg/g while the median was 1.25 mg/g (min: 0.85 max: 6.44 mg/g). Overall 4.82% of the population were defined as having elevated liver iron, above commonly accepted 1.8 mg/g threshold based on biochemical iron measurements in liver specimens obtained by biopsy. Further analysis using univariate models showed elevated liver iron to be related to male sex (p5.6% PDFF) was associated with a slight increase in prevalence of elevated liver iron (4.4% vs 6.3%, p=0.0007). This study shows that population studies including measurement of liver iron concentration are feasible, which may in future be used to better inform patient stratification and treatment

Oligocene–Miocene freshwater gastropods from the Oltu-Narman Basin in eastern Turkey

We describe the first record of a late Oligocene or early Miocene freshwater gastropod fauna from the Susuz Formation of the Oltu-Narman Basin in northeastern Anatolia. The assemblage consists of only six species, indicating the presence of a well-oxygenated lake, pond or anabranch rich in vegetation. Only two of the taxa are related to European Oligo-Miocene species. The fauna might be the first indication of a yet undocumented Eastern Anatolian freshwater biogeographic region, characterized by high endemism and minor influence from the coeval Peri-Paratethyan and Aegean–Anatolian regions in the west. The biostratigraphic value of the assemblage is low but might rather point to a Miocene age of the upper part of the Susuz Formation. Theodoxus susuzianus, Bithynia erzurumensis, and Valvata koehleri are described as new species

Early Miocene gastropod and ectothermic vertebrate remains from the Lesvos Petrified Forest (Greece)

The Lesvos Petrified Forest (western Lesvos, Greece) has long been famous for its plant fossils. Recently, one proboscidean (from the Gavathas locality) and seven micromammalian species (from the Lapsarna locality) were described; these were the first animals to be found in the Early Miocene subtropical forest. For the first time, a fauna of gastropods and ectothermic vertebrates from the Lapsarna locality is now available. This fauna derives from lacustrine sediments under the pyroclastic material that contains the petrified plants. Based on fragmented mollusc remains, isolated fish pharyngeal teeth and utricular otoliths (lapilli), fragmented amphibian vertebrae and a tooth-bearing element, and reptile fragmented dentaries, teeth, osteoderms and vertebrae, the presence of eight freshwater and three terrestrial gastropod species, three freshwater cyprinid species, and two amphibian and five reptile taxa has been confirmed. Stratigraphical and radiometric data suggest an age older than 18.4 ± 0.5 Ma (latest Early Miocene), in good agreement with the faunal composition. This paper is the first report of the concurrent presence of three cyprinid fish species in a Greek Early Miocene locality, as well as the first documentation of an Early Miocene proteid amphibian in southeastern Europe. The present findings represent one of the best- documented Early Miocene gastropod and fish faunas in the Aegean/southern Balkans, thus adding to our knowledge of Early Miocene amphibians and reptiles from that region and providing valuable information on the local subtropical ecosystem

Stratigraphic and paleogeographic significance of lacustrine mollusks from the Pliocene Viviparus beds in central Croatia

The mollusk fauna from the Pliocene Viviparus beds of Vukomeričke Gorice hills in central Croatia was investigated at four sites in the region of Kravarsko, S of Zagreb. The region represents a Pleistocene dome-anticline at the southern margin of the Sava depression. Sediments are dominated by clay, bearing some sand, gravel and lignite intercalations. The mollusks, comprising 11 gastropod and 2 bivalve species, prove the studied deposits to derive from the long-lived, highly endemic Lake Slavonia. The taxonomic revisions include the introductions of Viviparus kochanskyae n. sp. for specimens from Lake Slavonia previously identified with V. fuchsi NEUMAYR, 1872 and Prososthenia? praeslavonica n. nom. replacing the primary homonym Hydrobia vitrella BRUSINA, 1897 non Stefanescu, 1896. Recognized as an independent phase in the geodynamic evolution of the Pannonian Basin, the new regional stage Cernikian is introduced for the succession, defined by the complete depositional sequence of the Viviparus beds. Two stratigraphic horizons detected in the studied sites are constrained by the Lower Cernikian Viviparus kochanskyae and the Upper Cernikian Viviparus hoernesi zones and stay in perfect agreement with previous regional data. Timing of the Lake Slavonia history is enabled through several zonal markers calibrated to the Geological Time Scale in the Dacian Basin. Accordingly, the Lower Cernikian transgression dates to c. 4.3 Ma, the Upper Cernikian to c. 3.1 Ma, indicating strong alteration of the lacustrine depositional settings during the Pliocene, most likely related to changes in the regional climate. Interestingly, the second transgression of Lake Slavonia is marked by the evolution of strongly sculptured viviparid shells and coincides with the Pliocene Climate Optimum.</p

Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda.

We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla