Evolution of Strigamia centipedes (Chilopoda): a first molecular assessment of phylogeny and divergence times

We present a first phylogenetic and temporal framework, with biogeographical insights, for the centipedes of the genus Strigamia, which are widespread predators in the forest soils of the Northern Hemisphere and comprise the evo-devo model species Strigamia maritima. The phylogeny was estimated by different methods of maximum likelihood and Bayesian inference from sequences of two mitochondrial (16S, COI) and two nuclear (18S, 28S) genes, obtained from 16 species from all major areas of the global range of the genus and encompassing most of the overall morphological and ecological diversity. Divergence times were estimated after calibration upon the fossil record of centipedes. We found that major lineages of extant species of Strigamia separated most probably around 60 million years (Ma) ago. The two most diverse lineages diversified during the last 30 Ma and are today segregated geographically, one in Europe and another in Eastern Asia. This latter region hosts a hitherto underestimated richness and anatomical diversity of species, including three still unknown, yet morphologically well distinct species, which are here described as new: Strigamia inthanoni sp. n. from Thailand, Strigamia korsosi sp. n. from the Ryukyu Islands and Strigamia nana sp. n. from Taiwan. The northern European model species S. maritima is more strictly related to the Eastern Asian lineage, from which it most probably separated around 35 Ma ago before the major diversification of the latter

Collagen-an important fish allergen for improved diagnosis

Background Fish collagen is widely used in medicine, cosmetics, and the food industry. However, its clinical relevance as an allergen is not fully appreciated. This is likely due to collagen insolubility in neutral aqueous solutions, leading to low abundance in commercially available in vitro and skin prick tests for fish allergy. Objective To investigate the relevance of fish collagen as an allergen in a large patient population (n = 101). Methods Acid-soluble collagen type I was extracted from muscle and skin of Atlantic salmon, barramundi, and yellowfin tuna. IgE binding to collagen was analyzed by ELISA for 101 fish-allergic patients. Collagen-sensitized patients' sera were tested for IgE binding to parvalbumin from the same fish species. IgE cross-linking was analyzed by rat basophil leukemia assay and basophil activation test. Protein identities were confirmed by mass spectrometry. Results Purified fish collagen contained type I α1 and α2 chains and their multimers. Twenty-one of 101 patients (21%) were sensitized to collagen. Eight collagen-sensitized patients demonstrated absence of parvalbumin-specific IgE to some fish species. Collagen induced functional IgE cross-linking, as shown by rat basophil leukemia assay performed using 6 patients' sera, and basophil activation test using fresh blood from 1 patient. Collagen type I α chains from barramundi and Atlantic salmon were registered at www.allergen.org as Lat c 6 and Sal s 6, respectively. Conclusions IgE sensitization and IgE cross-linking capacity of fish collagen were demonstrated in fish-allergic patients. Inclusion of relevant collagen allergens in routine diagnosis is indicated to improve the capacity to accurately diagnose fish allergy

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Abstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here,as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA

Morphology and phylogeny of Dicellophilus, a centipede genus with highly disjunct distribution (Chilopoda, Mecistocephalidae)

The centipede genus Dicellophilus Cook, 1896 (Chilopoda: Geophilomorpha: Mecistocephalidae) has been revised by means of a comparative examination of representative specimens of all the species: morphological variation has been documented by means of both light and scanning electronic microscopy, the geographical distribution has been reassessed and updated based on published and new records, and the phyletic relations between the species have been analysed based on morphological evidence. Dicellophilus is confirmed as a highly distinct lineage, supported by synapomorphies in the labrum and in the pattern of coxal organs. Four species are morphologically recognized, each of them occurring in one of three limited, highly disjunct areas in a restricted boreal temperate belt: Dicellophilus carniolensis (C.L. Koch, 1847) is limited to central Europe (central\u2013eastern Alps, Dinarids, Carpathians, and Dobrogea), Dicellophilus pulcher (Kishida, 1928) occurs in Japan (Honshu), and Dicellophilus anomalus (Chamberlin, 1904) and Dicellophilus limatus (Wood, 1862) both occur in the south-western part of North America (California and Oregon). High support has been found for the following phyletic relationships: (D. carniolensis (D. pulcher (D. anomalus + D. limatus))). Dicellophilus carniolensis is strongly distinct in some autapomorphic traits, including enlarged clypeus and fewer mandibular lamellae, whereas the sister species D. anomalus and D. limatus share some derived features, including an elongated head and associated appendages, longer antennal setae, and stronger forcipular tubercles. The peculiar geographical distribution of Dicellophilus and the historical scenario suggested by the phylogeny are very unusual in respect to the biogeographical patterns known in all other major groups of terrestrial animals

Integrated Bioprocessing for the pH-Dependent Production of 4- Levulinate in Pseudomonas putida KT2440

Enzymes are powerful biocatalysts capable of performing specific chemical transformations under mild conditions, yet as catalysts they remain subject to the laws of thermodynamics, namely, that they cannot catalyze chemical reactions beyond equilibrium. Here we report the phenomenon and application of using extracytosolic enzymes and medium conditions, such as pH, to catalyze metabolic pathways beyond their intracellular catalytic limitations. This methodology, termed “integrated bioprocessing” because it integrates intracellular and extracytosolic catalysis, was applied to a lactonization reaction in Pseudomonas putida for the economical and high-titer biosynthesis of 4-valerolactone from the inexpensive and renewable source levulinic acid. Mutant paraoxonase I (PON1) was expressed in P. putida, shown to export from the cytosol in Escherichia coli and P. putida using an N-terminal sequence, and demonstrated to catalyze the extracytosolic and pH-dependent lactonization of 4-hydroxyvalerate to 4-valerolactone. With this production system, the titer of 4-valerolactone was enhanced substantially in acidic medium using extracytosolically expressed lactonase versus an intracellular lactonase: from <0.2 g liter−1 to 2.1 ± 0.4 g liter−1 at the shake flask scale. Based on these results, the production of 4-hydroxyvalerate and 4-valerolactone was examined in a 2-liter bioreactor, and titers of 27.1 g liter−1 and 8.2 g liter−1 for the two respective compounds were achieved. These results illustrate the utility of integrated bioprocessing as a strategy for enabling production from novel metabolic pathways and enhancing product titers.Synthetic Biology Engineering Research CenterNational Science Foundation (Grant Number EEC-0540879

Trends of Tropical Cyclone Translation Speed over the Western North Pacific during 1980&minus;2018

Tropical cyclone (TC) translation speed often affects the time of strong wind attacks and precipitation accumulation in the areas that TCs pass through. Therefore, the trend of TC translation speed has important implications for TC-related risks in the current and future climate. In this paper, the trends of TC translation speed over the Western North Pacific (WNP) from 1980 to 2018 are analyzed, and TC lifetime maximum intensity (LMI) is proposed as a factor related to the interdecadal change of translation speed. During the periods with accurate data, 1980&ndash;1997 shows a decreasing trend in TC translation speed while an increasing trend was found in 1998&ndash;2018. The main lifetime period contributing to a TC translation speed change is before the occurrence of the LMI. The change in the trend is related to both the TC&rsquo;s characteristics itself and the environmental factors. For the period 1998&ndash;2018, an increasing trend of TC intensity has a significant influence on the trend of translation speed. For the environmental factors, a trend of east wind enhancement at and above 500 hPa as the steering flow is found mostly correlated in the active TC region of the WNP with westward translation before reaching LMI, accompanied by a weakening trend of 200&ndash;850 hPa vertical wind shear, and an increasing trend of potential intensity

Trends of Tropical Cyclone Translation Speed over the Western North Pacific during 1980−2018

Tropical cyclone (TC) translation speed often affects the time of strong wind attacks and precipitation accumulation in the areas that TCs pass through. Therefore, the trend of TC translation speed has important implications for TC-related risks in the current and future climate. In this paper, the trends of TC translation speed over the Western North Pacific (WNP) from 1980 to 2018 are analyzed, and TC lifetime maximum intensity (LMI) is proposed as a factor related to the interdecadal change of translation speed. During the periods with accurate data, 1980–1997 shows a decreasing trend in TC translation speed while an increasing trend was found in 1998–2018. The main lifetime period contributing to a TC translation speed change is before the occurrence of the LMI. The change in the trend is related to both the TC’s characteristics itself and the environmental factors. For the period 1998–2018, an increasing trend of TC intensity has a significant influence on the trend of translation speed. For the environmental factors, a trend of east wind enhancement at and above 500 hPa as the steering flow is found mostly correlated in the active TC region of the WNP with westward translation before reaching LMI, accompanied by a weakening trend of 200–850 hPa vertical wind shear, and an increasing trend of potential intensity