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Samples of Crustacea and Annelida (Polychaeta, Sipuncula, and Hirudinea) were collected in the Bering Sea and the northwestern Pacific Ocean during scientific cruise SO-249 BERING in 2016. Biological samples were collected from 32 locations by the team on-board RV Sonne using a chain bag dredge at depths ranging between 330–5,070 m, and preserved in 96% ethanol. Specimens were morphologically identified to the lowest taxonomic level possible using a Leica M60 stereomicroscope. The generated data here comprise taxonomic information as well as annotated bathymetric and biogeographic information from a total of 78 samples (26 Crustacea, 47 Polychaeta, 4 Sipuncula, and 1 Hirudinea). The dataset was prepared following Darwin Core Biodiversity standards for FAIR data sharing based on Ocean Biodiversity Information System (OBIS) and Global Biodiversity Facility (GBIF) guidelines. The standardised digitised data were then mobilised to both OBIS and GBIF under CC BY 4.0 licence to publicly share and adopt the data. As records of these important marine taxa from bathyal and abyssal depths are sparse, especially from the deep Bering Sea, the herein generated and digitised data aid in filling existing knowledge gaps on their diversity and distribution in that region. As part of the “Biogeography of the NW Pacific deep-sea fauna and their possible future invasions into the Arctic Ocean” (BENEFICIAL) project, this dataset thus not only increases our knowledge in re-assessing and uncovering the deep-sea diversity of these taxa, but also serves policy and management sectors by providing first-hand data for global report assessments.
The hepatitis B virus is one of the most common causes of virus-related chronic liver disease and remains a major global health problem affecting 296 million people worldwide. Despite an available and highly effective vaccination, hepatitis B infections lead to an annual mortality rate of approximately 0.8 million people. The global prevalence is heterogeneously distributed and reflects a high infections and chronicity, particularly in low-income countries, due to a lack of vaccination strategies, underdiagnosis and low treatment rates. A complete cure remains undiscovered to this day. Based on their genetic makeup, the virus is categorized into nine genotypes with a genetic difference of more than 8% within the sequence. In addition to their geographical distribution, hepatitis B virus genotypes also differ in terms of their clinical outcome, pathogenesis and treatment response.
The viral protein HBx is known to interact with several cellular signaling pathways and is thereby accounted as the driving force in the development of hepatitis B virus-associated pathogenesis and progression of hepatocellular carcinoma. In particular, HBx interacts with mitochondria and induces profound alterations in the mitochondrial morphology and function with a severe impact on the liver’s physiology and with an emerging role in liver-related disease progression.
This study aims to investigate the genotype-related impact of HBx with regard to their interaction with cellular signaling pathways. A particular focus was placed on mitochondria-dependent interactions and signaling pathways in order to broaden the understanding of the genetic diversity of the genotypes.
Differences between genotypes of HBx were examined and compared through in vitro experiments based on a cell culture-based system. Plasmid DNA encoding the HBx protein of the different genotypes was transiently transfected into Huh7 or HepG2 cells and examined for molecular and protein-biochemical effects on the host cell, usually 72 hours after transfection. This study focused on the most common genotypes A, B, C, D, E and G worldwide.
Based on initial kinome profiling analyses, it was found that HBx differs greatly within their genetic variants and suggests different effects on overall cell function and in particular on mitochondrial kinases. Furthermore, confocal laser scanning microscopy reveals profound HBx-mediated changes in the mitochondrial network structure, however with major differences among the different genotypes. In particular, HBx of genotypes A and G causes enormous fragmentation of mitochondrial structures, accompanied by emergent changes in mitochondrial function. Due to an increased interaction with the voltage-dependent anion channel 3, a significant loss of mitochondrial membrane potential was also observed, together with an increased radial oxygen stress level and an induction of central mitochondria-dependent inflammatory mediators. In contrast, the contribution of HBx-genotype B and E reveals only moderate effects in these regards. Using a pH-sensitive reporter system, HBx genotypes which previously indicated a strong distribution in the mitochondrial morphology and function, also showed an elevated mitophagy through the PINK1/Parkin-mediated pathway. This study provides direct evidence that HBx-mediated changes in host cell signaling pathways, especially in mitochondrial-associated pathways, fundamentally dependent on the different genotypes. In addition, the results also indicate an important role of HBx in the process of genotype-dependent liver pathogenesis and provide insight into the underlying cellular mechanisms and signaling pathways.
The monophyly of Theraphosinae is supported by both morphological and molecular phylogenies. However, intergeneric relationships often show polytomies and branches with low support. A previous phylogenetic study proposed an intergeneric relationship for the subfamily based on molecular data and divided it into three tribes: Grammostolini, Hapalopini and Theraphosini. However, not all genera of Theraphosinae were sampled, and some relationships were inferred based on morphological similarities. Regarding the Hapalopini from Brazil, the relationships of some genera are still uncertain, such as Kochiana, Catanduba, and Munduruku. In this paper, we describe four new species of Hapalopini from Brazil: Cyriocosmus paresi sp. nov., Hapalopus akroa sp. nov., H. guidonae sp. nov., and K. fukushimae sp. nov. In addition, we propose an updated diagnosis for these three genera and for the species K. brunnipes and M. bicoloratum.
Ophioderma teres (Lyman, 1860), an ophiuroid previously believed to have a wide distribution in the eastern Pacific, has been found to have an unclear taxonomic identity. While considered a well-known species, recent studies have revealed that O. teres lacks a holotype and has vague boundaries with its congeners Ophioderma teres unicolor H.L. Clark, 1940 and Ophioderma sodipallaresi Caso, 1986, as well as with two additional new morphotypes detected in Mexico and Nicaragua, causing continuous misidentifications. This study utilized an integrative taxonomy approach based on morphologic, morphometric, and molecular evidence to clarify the taxonomic status of O. teres, O. sodipallaresi, O. teres unicolor, and the two new morphotypes. Data integration led to the following results: 1) the neotype designation and redescription of O. teres; 2) the proposal of O. sodipallaresi as a junior synonym of O. teres; 3) the status change of O. unicolor stat. nov. from subspecies to species, and 4) the description of the morphotypes as the new species Ophioderma aija sp. nov. and Ophioderma bichi sp. nov. An identification key to the eastern Pacific species of Ophioderma was also developed. This work contributes to the knowledge of Ophioderma in the region, increasing the number of described species and providing resources for their accurate identification.
In this study, we describe two new species of Mesobiotus based on morphological data collected through light and scanning electron microscopy. Descriptions include DNA sequences of four commonly used molecular markers (18S rDNA, 28S rDNA, ITS-2, and COI). Mesobiotus efa sp. nov. was discovered in North-West Russia and belongs to the group of species with smooth cuticle, harmsworthi-type OCA, typical Mesobiotus claws IV with unindented lunules, and egg chorion with reticulated processes in form of ‘sharp wide cones’ or ‘cones with long slender endings’, egg process bases with well-developed crone of dark thickenings without finger-like projections, and egg shell surface between the processes with ridges without reticulation, areolation or semi-areolation. It can be distinguished from all know species of this group by a unique combination of morphological and morphometric characters. Mesobiotus vulpinus sp. nov. was found in the Russian Far East, and is similar to Mesobiotus mauccii by having an egg chorion with polygonal relief. The new species can be distinguished from M. mauccii by having a narrower buccal tube, by details of oral cavity armature, and by longer egg chorion processes. Furthermore, we provide results of the phylogenetic analyses of the genus Mesobiotus conducted in this study.
Although semi-aquatic cockroaches have been known for a long time, these insects remain little studied and their diversity underestimated. While a few species are known from Asia or South America, only a single one is known to be associated with water in Africa. Here, we report two species of semi-aquatic cockroaches of the subfamily Epilamprinae from Cameroon. One of these species is new: Rhabdoblatta fotoi Nyame Mbia, Legendre & Biram à Ngon sp. nov. Africalolampra camerunensis (Borg, 1902) comb. nov. was also found associated to these streams and we provide an extended description of this species, as well as for Africalolampra stipata comb. nov., also known from streams in West Africa. Another species was found in Cameroonian streams and is described here, although only identified at the family level (Blattellidae). The descriptions are based on morpho-anatomic characters, including male genitalia. Because nymphs were found primarily associated with water – more than adults – we provide a description of nymphs whenever possible. We provide molecular data (12S rRNA marker) for two of these water-associated species that we compared with published and unpublished sequences of Epilamprinae in a Maximum Likelihood approach. We also illustrate all but one species from continental Africa in the genera Africalolampra and Rhabdoblatta, including R. punctipennis (Saussure, 1895) which we reinstate. We provide a map and list of localities for Africalolampra and Rhabdoblatta spp. from continental Africa and Madagascar, as well as an identification key for species of Africalolampra. We finally discuss putative adaptations of semi-aquatic cockroaches.
Discoveries of new species often depend on one or a few specimens, leading to delays as researchers wait for additional context, sometimes for decades. There is currently little professional incentive for a single expert to publish a stand-alone species description. Additionally, while many journals accept taxonomic descriptions, even specialist journals expect insights beyond the descriptive work itself. The combination of these factors exacerbates the issue that only a small fraction of marine species are known and new discoveries are described at a slow pace, while they face increasing threats from accelerating global change. To tackle this challenge, this first compilation of Ocean Species Discoveries (OSD) presents a new collaborative framework to accelerate the description and naming of marine invertebrate taxa that can be extended across all phyla. Through a mode of publication that can be speedy, taxonomy-focused and generate higher citation rates, OSD aims to create an attractive home for single species descriptions. This Senckenberg Ocean Species Alliance (SOSA) approach emphasises thorough, but compact species descriptions and diagnoses, with supporting illustrations and with molecular data when available. Even basic species descriptions carry key data for distributions and ecological interactions (e.g., host-parasite relationships) besides universally valid species names; these are essential for downstream uses, such as conservation assessments and communicating biodiversity to the broader public.This paper presents thirteen marine invertebrate taxa, comprising one new genus, eleven new species and one re-description and reinstatement, covering wide taxonomic, geographic, bathymetric and ecological ranges. The taxa addressed herein span three phyla (Mollusca, Arthropoda, Echinodermata), five classes, eight orders and twelve families. Apart from the new genus, an updated generic diagnosis is provided for four other genera. The newly-described species of the phylum Mollusca are Placiphorella methanophila Vončina, sp. nov. (Polyplacophora, Mopaliidae), Lepetodrilus marianae Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Lepetodrilidae), Shinkailepas gigas Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Phenacolepadidae) and Lyonsiella illaesa Machado & Sigwart, sp. nov. (Bivalvia, Lyonsiellidae). The new taxa of the phylum Arthropoda are all members of the subphylum Crustacea: Lepechinella naces Lörz & Engel, sp. nov. (Amphipoda, Lepechinellidae), Cuniculomaera grata Tandberg & Jażdżewska, gen. et sp. nov. (Amphipoda, Maeridae), Pseudionella pumulaensis Williams & Landschoff, sp. nov. (Isopoda, Bopyridae), Mastigoniscus minimus Wenz, Knauber & Riehl, sp. nov. (Isopoda, Haploniscidae), Macrostylis papandreas Jonannsen, Riehl & Brandt, sp. nov. (Isopoda, Macrostylidae), Austroniscus indobathyasellus Kaiser, Kniesz & Kihara, sp. nov. (Isopoda, Nannoniscidae) and Apseudopsis daria Esquete & Tato, sp. nov. (Tanaidacea, Apseudidae). In the phylum Echinodermata, the reinstated species is Psychropotes buglossa E. Perrier, 1886 (Holothuroidea, Psychropotidae).The study areas span the North and Central Atlantic Ocean, the Indian Ocean and the North, East and West Pacific Ocean and depths from 5.2 m to 7081 m. Specimens of eleven free-living and one parasite species were collected from habitats ranging from an estuary to deep-sea trenches. The species were illustrated with photographs, line drawings, micro-computed tomography, confocal laser scanning microscopy and scanning electron microscopy images. Molecular data are included for nine species and four species include a molecular diagnosis in addition to their morphological diagnosis.The five new geographic and bathymetric distribution records comprise Lepechinella naces Lörz & Engel, sp. nov., Cuniculomaera grata Tandberg & Jażdżewska, sp. nov., Pseudionella pumulaensis Williams & Landschoff, sp. nov., Austroniscus indobathyasellus Kaiser, Kniesz & Kihara, sp. nov. and Psychropotes buglossa E. Perrier, 1886, with the novelty spanning from the species to the family level. The new parasite record is Pseudionella pumulaensis Williams & Landschoff, sp. nov., found in association with the hermit crab Pagurus fraserorum Landschoff & Komai, 2018.
Using e+e− annihilation data sets corresponding to an integrated luminosity of 4.5 fb−1, collected with the BESIII detector at center-of-mass energies between 4.600 and 4.699 GeV, we report the first measurements of the absolute branching fractions B(Λ+c→pK0L)=(1.67±0.06±0.04)%, B(Λ+c→pK0Lπ+π−)=(1.69±0.10±0.05)%, and B(Λ+c→pK0Lπ0)=(2.02±0.13±0.05)%, where the first uncertainties are statistical and the second systematic. Combining with the known branching fractions of Λ+c→pK0S, Λ+c→pK0Sπ+π−, and Λ+c→pK0Sπ0, we present the first measurements of the K0S-K0L asymmetries R(Λ+c,K0S,LX)=B(Λ+c→K0SX)−B(Λ+c→K0LX)B(Λ+c→K0SX)+B(Λ+c→K0LX) in charmed baryon decays: R(Λ+c,pK0S,L)=−0.025±0.031, R(Λ+c,pK0S,Lπ+π−)=−0.027±0.048, and R(Λ+c,pK0S,Lπ0)=−0.015±0.046. No significant asymmetries within the uncertainties are observed.
Purpose: To assess the diagnostic precision of three different workstations for measuring thoracic aortic aneurysms (TAAs) in vivo and ex vivo using either pre-interventional computed tomography angiography scans (CTA) or a specifically designed phantom model.
Methods: This retrospective study included 23 patients with confirmed TAA on routinely performed CTAs. In addition to phantom tube diameters, one experienced blinded radiologist evaluated the dimensions of TAAs on three different workstations in two separate rounds. Precision was assessed by calculating measurement errors. In addition, correlation analysis was performed using Pearson correlation.
Results: Measurements acquired at the Siemens workstation deviated by 3.54% (range, 2.78–4.03%; p = 0.14) from the true size, those at General Electric by 4.05% (range, 1.46–7.09%; p < 0.0001), and at TeraRecon by 4.86% (range, 3.22–6.45%; p < 0.0001). Accordingly, Siemens provided the most precise workstation at simultaneously most fluctuating values (scattering of 4.46%). TeraRecon had the smallest fluctuation (scattering of 2.83%), but the largest deviation from the true size of the phantom. The workstation from General Electric showed a scattering of 2.94%. The highest overall correlation between the 1st and 2nd rounds was observed with measurements from Siemens (r = 0.898), followed by TeraRecon (r = 0.799), and General Electric (r = 0.703). Repetition of measurements reduced processing times by 40% when using General Electric, by 20% with Siemens, and by 18% with TeraRecon.
Conclusions: In conclusion, all three workstations facilitated precise assessment of dimensions in the majority of cases at simultaneously high reproducibility, ensuring accurate pre-interventional planning of thoracic endovascular aortic repair.
This study evaluates whether the short version of the German LITMUS quasi-universal nonword repetition task (LITMUS-QU-NWR) can be used as an index test for monolingual and early second language learners (eL2) of German aged 8 to 10 years. The NWR taps into quasi-universal phonological knowledge via the so-called language-independent part and into language-specific phonological knowledge via the language-dependent part. Thirty-six monolingual and thirty-three eL2 learners of German, typically developing (TD) and diagnosed as language-impaired (DLD), participated in the study. The effects of the language group (Mo vs. eL2) and the clinical status (TD vs. DLD) on repetition accuracy are investigated by a logistic mixed-model analysis. Receiver operating characteristics (ROC) and likelihood ratios are calculated to determine the diagnostic accuracy of the two parts. The group comparisons showed significant effects of the clinical status but not of the language group. The ROC analyses and the likelihood ratios reveal better diagnostic values for the language-dependent compared to the language-independent part and almost similar diagnostic values for the monolingual and the eL2 group. The results indicate that the LITMUS-QU-NWR helps to disentangle DLD and DLD in monolingual children and eL2 learners aged 8 to 10 years.
Background: Opsoclonus-myoclonus syndrome (OMS) is a rare, immune-mediated neurological disorder. In adults, the pathogenesis can be idiopathic, post-infectious or paraneoplastic, the latter etiology belonging to the ever-expanding group of defined paraneoplastic neurological syndromes (PNS). In contrast to other phenotypes of PNS, OMS cannot be ascribed to a single pathogenic autoantibody. Here, we report the first detailed case of paraneoplastic, antibody-negative OMS occurring in association with a pancreatic neuroendocrine tumor (pNET).
Case presentation: A 33-year-old female presented with a two-week history of severe ataxia of stance and gait, dysarthria, head tremor, myoclonus of the extremities and opsoclonus. Her past medical history was notable for a metastatic pancreatic neuroendocrine tumor, and she was subsequently diagnosed with paraneoplastic opsoclonus-myoclonus syndrome. Further workup did not reveal a paraneoplastic autoantibody. She responded well to plasmapheresis, as she was refractory to the first-line therapy with corticosteroids.
Conclusions: This case expands current knowledge on tumors associated with paraneoplastic opsoclonus-myoclonus syndrome and the age group in which it can occur. It further adds evidence to the effectiveness of plasmapheresis in severe cases of opsoclonus-myoclonus syndrome with a lack of response to first-line therapy.
The ALICE Collaboration measures the production of low-mass dielectrons in pp, p-Pb and Pb-Pb collisions at the LHC. The main detectors used in the analyses are the Inner Tracking System, Time Projection Chamber and Time-Of-Flight detector, all located around mid-rapidity. The production of virtual photons relative to the inclusive yield in pp collisions is determined by analyzing the dielectron excess with respect to the expected hadronic sources. The direct photon cross section is then calculated and found to be in agreement with NLO pQCD calculations. Results from the invariant mass analysis in p-Pb collisions show an overall agreement between data and hadronic cocktail. In Pb-Pb collisions, uncorrected background-subtracted yields have been extracted in two centrality classes. A feasibility study for LHC run 3 after the ALICE upgrade indicates the possibility for a future measurement of the early effective temperature.
Structured management programs have been developed for single diseases but rarely for patients with multiple medications. We conducted a qualitative study to investigate the views of stakeholders on the development and implementation of a polypharmacy management program in Germany. Overall, we interviewed ten experts in the fields of health policy and clinical practice. Using content analysis, we identified inclusion criteria for the selection of suitable patients, the individual elements that should make up such a program, healthcare providers and stakeholders that should be involved, and factors that may support or hinder the program’s implementation. All stakeholders were well aware of polypharmacy-related risks and challenges, as well as the urgent need for change. Intervention strategies should address all levels of care and include all concerned patients, caregivers, healthcare providers and stakeholders, and involved parties should agree on a joint approach.
We investigate the thermodynamic geometry of the quark-meson model at finite temperature, T, and quark number chemical potential, μ. We extend previous works by the inclusion of fluctuations exploiting the functional renormalization group approach. We use recent developments to recast the flow equation into the form of an advection-diffusion equation. We adopt the local potential approximation for the effective average action. We focus on the thermodynamic curvature, R, in the (μ,T) plane, in proximity of the chiral crossover, up to the critical point of the phase diagram. We find that the inclusion of fluctuations results in a smoother behavior of R near the chiral crossover. Moreover, for small μ, R remains negative, signaling the fact that bosonic fluctuations reduce the capability of the system to completely overcome the fermionic statistical repulsion of the quarks. We investigate in more detail the small μ region by analyzing a system in which we artificially lower the pion mass, thus approaching the chiral limit in which the crossover is actually a second order phase transition. On the other hand, as μ is increased and the critical point is approached, we find that R is enhanced and a sign change occurs, in agreement with mean field studies. Hence, we completely support the picture that R is sensitive to a crossover and a phase transition, and provides information about the effective behavior of the system at the phase transition.
We investigate the thermodynamic geometry of the quark-meson model at finite temperature, T, and quark number chemical potential, μ. We extend previous works by the inclusion of fluctuations exploiting the functional renormalization group approach. We use recent developments to recast the flow equation into the form of an advection-diffusion equation. We adopt the local potential approximation for the effective average action. We focus on the thermodynamic curvature, R, in the (μ,T) plane, in proximity of the chiral crossover, up to the critical point of the phase diagram. We find that the inclusion of fluctuations results in a smoother behavior of R near the chiral crossover. Moreover, for small μ, R remains negative, signaling the fact that bosonic fluctuations reduce the capability of the system to completely overcome the fermionic statistical repulsion of the quarks. We investigate in more detail the small μ region by analyzing a system in which we artificially lower the pion mass, thus approaching the chiral limit in which the crossover is actually a second order phase transition. On the other hand, as μ is increased and the critical point is approached, we find that R is enhanced and a sign change occurs, in agreement with mean field studies. Hence, we completely support the picture that R is sensitive to a crossover and a phase transition, and provides information about the effective behavior of the system at the phase transition.
The photoelectric effect describes the ejection of an electron upon absorption of one or several photons. The kinetic energy of this electron is determined by the photon energy reduced by the binding energy of the electron and, if strong laser fields are involved, by the ponderomotive potential in addition. It has therefore been widely taken for granted that for atoms and molecules, the photoelectron energy does not depend on the electron’s emission direction, but theoretical studies have questioned this since 1990. Here, we provide experimental evidence that the energies of photoelectrons emitted against the light propagation direction are shifted toward higher values, while those electrons that are emitted along the light propagation direction are shifted to lower values. We attribute the energy shift to a nondipole contribution to the ponderomotive potential that is due to the interaction of the moving electrons with the incident photons.
The ALICE experiment at the LHC investigates the properties of the hot and dense nuclear matter created in heavy-ion collisions. By comparing the particle production in pp and p-Pb collisions, possible nuclear initial state effects can be isolated. Measurements of the ω meson pT-spectra in pp and p-Pb collisions not only allow for a determination of the nuclear modification factor RpPb, but also provide insight into the fragmentation process and serve as vital input for decay background simulations for direct photons. In this contribution, measurements of the ω meson production in pp and p-Pb collisions at √sNN=5.02 TeV are presented. This includes the signal extraction and various corrections of the ω meson yields, leading to their production cross sections and the first measured nuclear modification factor RpPb of the ω meson at LHC energies.
The ALICE experiment at the LHC investigates the properties of the hot and dense nuclear matter created in heavy-ion collisions. By comparing the particle production in pp and p-Pb collisions, possible nuclear initial state effects can be isolated. Measurements of the ω meson pT-spectra in pp and p-Pb collisions not only allow for a determination of the nuclear modification factor RpPb, but also provide insight into the fragmentation process and serve as vital input for decay background simulations for direct photons. In this contribution, measurements of the ω meson production in pp and p-Pb collisions at √sNN=5.02 TeV are presented. This includes the signal extraction and various corrections of the ω meson yields, leading to their production cross sections and the first measured nuclear modification factor RpPb of the ω meson at LHC energies.
Objectives: To assess the impact of noise-optimised virtual monoenergetic imaging (VMI+) on image quality and diagnostic evaluation in abdominal dual-energy CT scans with impaired portal-venous contrast.
Methods: We screened 11,746 patients who underwent portal-venous abdominal dual-energy CT for cancer staging between 08/2014 and 11/2019 and identified those with poor portal-venous contrast.
Standard linearly-blended image series and VMI+ image series at 40, 50, and 60 keV were reconstructed. Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of abdominal organs and vascular structures were calculated. Image noise, image contrast and overall image quality were rated by three radiologists using 5-point Likert scale.
Results: 452 of 11,746 (4%) exams were poorly opacified. We excluded 190 cases due to incomplete datasets or multiple exams of the same patient with a final study group of 262. Highest CNR values in all abdominal organs (liver, 6.4 ± 3.0; kidney, 17.4 ± 7.5; spleen, 8.0 ± 3.5) and vascular structures (aorta, 16.0 ± 7.3; intrahepatic vein, 11.3 ± 4.7; portal vein, 15.5 ± 6.7) were measured at 40 keV VMI+ with significantly superior values compared to all other series. In subjective analysis, highest image contrast was seen at 40 keV VMI+ (4.8 ± 0.4), whereas overall image quality peaked at 50 keV VMI+ (4.2 ± 0.5) with significantly superior results compared to all other series (p < 0.001).
Conclusions: Image reconstruction using VMI+ algorithm at 50 keV significantly improves image contrast and image quality of originally poorly opacified abdominal CT scans and reduces the number of non-diagnostic scans.
Advances in knowledge: We validated the impact of VMI+ reconstructions in poorly attenuated DECT studies of the abdomen in a big data cohort.
In the deep-sea, the interaction between benthic fauna and substrate mainly occurs through bioturbational processes which can be preserved as traces (i.e., lebensspuren). Lebensspuren are common features of deep seafloor landscapes and usually more abundant than the organism that produce them (i.e., tracemakers), rendering them promising proxies to infer biodiversity. The density and diversity relationships between lebensspuren and benthic fauna are to the present day unclear and contradicting hypotheses have been proposed suggesting negative, positive, or even null correlations. To test these hypotheses, in this study lebensspuren, tracemakers (specific epibenthic fauna that produce these traces), degrading fauna (benthic fauna that can erase lebensspuren), and fauna in general were characterized taxonomically at eight deep-sea stations in the Kuril Kamchatka Trench area. No general correlation (over-all study area) could be observed between diversities of lebensspuren, tracemakers, degrading fauna and fauna. However, a diversity correlation was observed between specific stations, showing both negative and positive correlations depending on: 1) the number of unknown tracemakers (especially significant for dwelling lebensspuren); and 2) the lebensspuren with multiple origins; and 3) tracemakers that can produce different lebensspuren. Lebensspuren and faunal density were not correlated. However, lebensspuren density was either positively or negatively correlated with tracemaker densities, depending on the lebensspuren morphotypes. A positive correlation was observed for resting lebensspuren (e.g., ophiuroid impressions, Actinaria circular impressions), while negative correlations were observed for locomotion-feeding lebensspuren (e.g., echinoid trails). In conclusion, lebensspuren diversity may be a good proxy for tracemaker biodiversity when the lebensspuren-tracemaker tandem can be reliable characterized; and lebensspuren-density correlations vary depending the specific lebensspuren residence time, tracemaker density and associated behaviour (rate of movement), but on a global scale abiotic and other biotic 42 factors may also play an important role.
In the deep sea, interactions between benthic fauna and seafloor sediment primarily occur through bioturbation that can be preserved as traces (i.e. lebensspuren). Lebensspuren are common features of deep-sea landscapes and are more abundant than the organisms that produce them (i.e. tracemakers), rendering lebensspuren promising proxies for inferring biodiversity. The density and diversity relationships between lebensspuren and benthic fauna remain unclear, and contradicting correlations have been proposed (i.e. negative, positive, or even null correlations). To approach these variable correlations, lebensspuren and benthic fauna were characterized taxonomically at eight deep-sea stations in the Kuril-Kamchatka Trench area, together with two novel categories: tracemakers (specific epibenthic fauna that produce these traces) and degrading fauna (benthic fauna that can erase lebensspuren). No general correlation (overall study area) was observed between diversities of lebensspuren, tracemakers, degrading fauna, and fauna. However, a diversity correlation was observed at specific stations, showing both negative and positive correlations depending on: (1) the number of unknown tracemakers (especially significant for dwelling lebensspuren); (2) the lebensspuren with multiple origins; and (3) tracemakers that can produce different lebensspuren. Lebensspuren and faunal density were not correlated. However, lebensspuren density was either positively or negatively correlated with tracemaker densities, depending on the lebensspuren morphotypes. A positive correlation was observed for resting lebensspuren (e.g. ophiuroid impressions, Actiniaria circular impressions), while negative correlations were observed for locomotion-feeding lebensspuren (e.g. echinoid trails). In conclusion, lebensspuren diversity may be a good proxy for tracemaker biodiversity when the lebensspuren–tracemaker relationship can be reliable characterized. Lebensspuren–density correlations vary depending on the specific lebensspuren residence time, tracemaker density, and associated behaviour (rate of movement). Overall, we suggest that lebensspuren density and diversity correlations should be studied with tracemakers rather than with general benthic fauna. On a global scale, abiotic (e.g. hydrodynamics, substrate consistency) and other biotic factors (e.g. microbial degradation) may also play an important role.
By analyzing (27.12±0.14)×108 ψ(3686) events accumulated with the BESIII detector, the decay ηc(2S)→K+K−η is observed for the first time with a significance of 6.2σ after considering systematic uncertainties. The product of the branching fractions of ψ(3686)→γηc(2S) and ηc(2S)→K+K−η is measured to be B(ψ(3686)→γηc(2S))×B(ηc(2S)→K+K−η)=(2.39±0.32±0.34)×10−6, where the first uncertainty is statistical, and the second one is systematic. The branching fraction of ηc(2S)→K+K−η is determined to be B(ηc(2S)→K+K−η)=(3.42±0.46±0.48±2.44)×10−3, where the third uncertainty is due to the branching fraction of ψ(3686)→γηc(2S). Using a recent BESIII measurement of B(ηc(2S)→K+K−π0), we also determine the ratio between the branching fractions of ηc(2S)→K+K−η and ηc(2S)→K+K−π0 to be 1.49±0.22±0.25, which is consistent with the previous result of BaBar at a comparable precision level.
Search for X(3872)→π⁰π⁰χc₁,₂
(2024)
Using 10.1 fb−1 of e+e− collision data collected by the BESIII detector with center-of-mass energies between 4.15 GeV and 4.30 GeV, we search for the decays X(3872)→π0π0χc1,2, where the X(3872) is produced in e+e−→γX(3872). No evidence above 3σ is found for either decay. Upper limits at the 90% C.L. on the branching fractions of X(3872)→π0π0χc1,2 normalized to the branching fraction of X(3872)→π+π−J/ψ are set to be B(X(3872)→π0π0χc1)/B(X(3872)→π+π−J/ψ)<1.1 and B(X(3872)→π0π0χc2)/B(X(3872)→π+π−J/ψ)<0.5, taking into account both statistical and systematic uncertainties.
We perform the first investigation of the process e+e−→K+K−ψ(2S) and report its Born cross sections over a range of center-of-mass energies from 4.699 to 4.951~GeV. The measurements are carried out using several partial reconstruction techniques using data samples collected by the BESIII detector with a total integrated luminosity of 2.5~fb−1. We search for new tetraquark candidates Z±cs in the decays Z±cs→K±ψ(2S). No significant Z±cs signals are observed.
Using (2.712±0.014)×109 ψ(3686) events collected with the BESIII detector operating at the BEPCII, we find an evidence of the ηc(2S)→K+K−η′ decay with a statistical significance of 3.1σ. Its decay branching fraction is measured to be (12.24±4.60(stat.)±2.37(syst.)±4.68(extr.))×10−4, where the first uncertainty is statistical, the second is systematic, and the third uncertainty is from the branching fraction of the ψ(3686)→γηc(2S) decay. The upper limit on the product branching fraction B[ψ(3686)→γηc(2S)]× B[ηc(2S)→K+K−η′] is set to be 1.14×10−6 at 90% confidence level. In addition, the branching fractions of χc1→K+K−η′ and χc2→K+K−η′ are updated to be (8.47±0.09(stat.)±0.47(syst.))×10−4 and (1.53±0.04(stat.)±0.08(syst.))×10−4, respectively. The precision is improved by twofold.
Observation of χcJ → 3(K⁺K⁻)
(2024)
By analyzing (27.12±0.14)×108 𝜓(3686) events collected with the BESIII detector operating at the BEPCII collider, the decay processes 𝜒𝑐𝐽→3(𝐾+𝐾−) (𝐽=0, 1, 2) are observed for the first time with statistical significances of 8.2𝜎, 8.1𝜎, and 12.4𝜎, respectively. The product branching fractions of 𝜓(3686)→𝛾𝜒𝑐𝐽, 𝜒𝑐𝐽→3(𝐾+𝐾−) are presented and the branching fractions of 𝜒𝑐𝐽→3(𝐾+𝐾−) decays are determined to be ℬ𝜒𝑐0→3(𝐾+𝐾−)=(10.7±1.8±1.1)×10−6, ℬ𝜒𝑐1→3(𝐾+𝐾−)=(4.2±0.9±0.5)×10−6, and ℬ𝜒𝑐2→3(𝐾+𝐾−)=(7.2±1.1±0.8)×10−6, where the first uncertainties are statistical and the second are systematic.
Observation of χcJ → 3(K⁺K⁻)
(2023)
By analyzing (27.12±0.14)×108 ψ(3686) events collected with the BESIII detector operating at the BEPCII collider, the decay processes χcJ→3(K+K−) (J=0,1,2) are observed for the first time with statistical significances of 8.2σ, 8.1σ, and 12.4σ, respectively. The product branching fractions of ψ(3686)→γχcJ, χcJ→3(K+K−) are presented and the branching fractions of χcJ→3(K+K−) decays are determined to be Bχc0→3(K+K−)=(10.7±1.8±1.1)×10−6, Bχc1→3(K+K−)=(4.2±0.9±0.5)×10−6, and Bχc2→3(K+K−)=(7.2±1.1±0.8)×10−6, where the first uncertainties are statistical and the second are systematic.
Using data samples with an integrated luminosity of 6.4~fb−1 collected by the BESIII detector operating at the BEPCII storage ring, the process of e+e−→γϕJ/ψ is studied. The processes of e+e−→ϕχc1,c2, χc1,c2→γJ/ψ are observed with a significance of more than 10σ. The s√-dependent cross section of e+e−→ϕχc1,c2 is measured between 4.600 and 4.951~GeV, and evidence of a resonance structure is found for the first time in the ϕχc2 process. We also search for the processes of e+e−→γX(4140), γX(4274) and γX(4500) via the γϕJ/ψ final state, but no obvious structures are found. The upper limits on the production cross section times the branching fraction for these processes at the 90% confidence level are reported.
The cross section of the process e+e−→K+K− is measured at a number of center-of-mass energies s√ from 2.00 to 3.08 GeV with the BESIII detector at the Beijing Electron Positron Collider (BEPCII). The results provide the best precision achieved so far. A resonant structure around 2.2 GeV is observed in the cross section line shape. A Breit-Wigner fit yields a mass of M=2239.2±7.1±11.3~and a width of Γ=139.8±12.3±20.6 MeV, where the first uncertainties are statistical and the second ones are systematic. In addition, the time-like electromagnetic form factor of the kaon is determined at the individual center-of-mass energy points.
Using a 3.19 fb−1 data sample collected at an 𝑒+𝑒− center-of-mass energy of 𝐸cm=4.178 GeV with the BESIII detector, we measure the branching fraction of the leptonic decay 𝐷+𝑠→𝜇+𝜈𝜇 to be ℬ𝐷+𝑠→𝜇+𝜈𝜇=(5.49±0.16stat±0.15syst)×10−3. Combining our branching fraction with the masses of the 𝐷+𝑠 and 𝜇+ and the lifetime of the 𝐷+𝑠, we determine 𝑓𝐷+𝑠|𝑉𝑐𝑠|=246.2±3.6stat±3.5syst MeV. Using the 𝑐→𝑠 quark mixing matrix element |𝑉𝑐𝑠| determined from a global standard model fit, we evaluate the 𝐷+𝑠 decay constant 𝑓𝐷+𝑠=252.9±3.7stat±3.6syst MeV. Alternatively, using the value of 𝑓𝐷+𝑠 calculated by lattice quantum chromodynamics, we find |𝑉𝑐𝑠|=0.985±0.014stat±0.014syst. These values of ℬ𝐷+𝑠→𝜇+𝜈𝜇, 𝑓𝐷+𝑠|𝑉𝑐𝑠|, 𝑓𝐷+𝑠 and |𝑉𝑐𝑠| are each the most precise results to date.
Using a data sample of 448.1×106 𝜓(3686) events collected at √𝑠=3.686 GeV with the BESIII detector at the Beijing Electron-Positron Collider II, we search for the rare decay 𝐽/𝜓→𝜙𝑒+𝑒− via 𝜓(3686)→𝜋+𝜋−𝐽/𝜓. No signal events are observed and the upper limit on the branching fraction is set to be ℬ(𝐽/𝜓→𝜙𝑒+𝑒−)<1.2×10−7 at the 90% confidence level, which is still about one order of magnitude higher than the Standard Model prediction.
Using a data sample of 448.1×106 ψ(3686) events collected at s√= 3.686 GeV with the BESIII detector at the BEPCII, we search for the rare decay J/ψ→ϕe+e− via ψ(3686)→π+π−J/ψ. No signal events are observed and the upper limit on the branching fraction is set to be B(J/ψ→ϕe+e−)<1.2×10−7 at the 90\% confidence level, which is still about one order of magnitude higher than the Standard Model prediction.
Dielectrons are an excellent probe for the QCD matter created in created in ultra-relativistic heavy-ion collisions, since they are emitted during the whole evolution of the collision and do not interact strongly with the medium. To isolate the QGP signals, measurement of the dielectron production in vacuum and its modifications due to the presence of cold nuclear matter is necessary. We present and discuss results from a low magnetic field detector setup in proton-proton collisions at √s = 13 TeV, as well as the measurement of dielectron production in pp, p-Pb, and Pb-Pb collisions at √sNN = 5 TeV.
The attention on the protein PURA has increased recently following the discovery of the rare PURA Syndrome. This neurodevelopmental disorder is caused by de novo mutations in the PURA gene. Notably, our collaborators could show that the protein PURA can bind DNA and RNA in vitro. As a result, I was motivated to explore PURA's cellular RNAbinding activity. Furthermore, I inquired on the connection of PURA-RNA binding to the cellular effect of a reduction of functional PURA as present in PURA Syndrome patients.
To investigate the binding of PURA and the impact of PURA de ciency on cellular RNA and protein expression, I performed an integrative computational analysis of multimodal data from complementary high-throughput experiments. An essential component was the examination of UV Crosslinking and immunoprecipitation (CLIP) experiments, which can query the global RNA-binding behaviour of a given protein in a cellular context. As the processing and analysis of CLIP data are rather complex, I introduce an automated command line tool for the processing of CLIP data named racoon_clip as part of this dissertation. Therefore, this dissertation comprises two major segments. Firstly, I describe the implementation and usage of racoon clip for CLIP data analysis. Secondly, I discuss my research on the protein PURA, demonstrating its global RNA-binding properties, the effects of PURA depletion and its association with neuronal functions and P-bodies, among others.
racoon_clip is a command line application that I have developed for processing of individualnucleotide resolution CLIP (iCLIP) and enhanced CLIP (eCLIP) experiments - two of the most commonly used types of CLIP experiments - in a comparable and user-friendly way.
For this, I built racoon_clip as an automated work how that encompasses all CLIP processing steps from raw data to single-nucleotide resolution crosslink events. racoon_clip is available as a command line tool that users can run with a single command. The work how is implemented with Snakemake work how management providing computational advantage tages including parallelisation, scalability and portability of the work how. The main task of racoon_clip is to extract single-nucleotide crosslink events from iCLIP, iCLIP2, eCLIP and similar data types. To strike a balance between being highly customisable and easy to use, racoon_clip supplies pre-set options for the most common types of experiments.
Additionally, it is possible for users to create a custom setup of barcode and adapter architectures, which allows them to use the software for other types of CLIP data. While accounting for the different architectures in the reads, the performed central processing steps remain the same. This leads to a high degree of comparability between the different experiment types, which I demonstrate in the exemplary processing of U2AF2 iCLIP and eCLIP data. Taken together, I am confident that racoon_clip will be beneficial to numerous researchers interested in RNA-Protein interactions as it offers easily accessible processing for CLIP data and enhances the comparability of multiple CLIP datasets across di erent experiment types.
In the second part of this dissertation, I focus on the cellular function of the RNAbinding protein PURA. Through in-depth computational analysis of one iCLIP data set of endogenous PURA and two iCLIP data sets of overexpressed PURA in HeLa cells, I establish that PURA is a global RNA-binding protein. It preferentially binds RNAs in either the coding sequence (CDS) or the 3' untranslated region (3'UTR) of mature protein-coding transcripts by recognising a Purine-rich degenerated sequence motif. Even though overexpression of PURA results in less specific binding behaviour, the same overall binding patterns as from endogenous PURA persist. Overall characteristics of PURA binding remain similar in three distinct PURA iCLIP data sets with and without PURA overexpression.
To learn about the molecular consequences of a depletion of functional PURA in a cellular context, I used a 50% reduction of PURA in HeLa cells as a model for the heterozygous loss of PURA in PURA Syndrome and evaluated its impact on global RNA and protein expression. The results demonstrate that PURA depletion globally a ects RNA and protein expression. Additionally, I integrate PURA RNA binding with the changes in expression of RNAs and proteins in the context of PURA depletion. This reveals 234 targets of PURA that are bound by PURA and are impacted at both RNA and protein levels by the PURA protein. RNAs that are bound by PURA or change in abundance upon PURA depletion are enriched in neuronal development factors, RNA lifecycle regulators, and mitochondrial factors, among others. Consistent with a possible role of PURA in neuronal transport, there is considerable overlap between PURA bound transcripts and transcripts, that are transported to the dendritic end of neurons.
Notably, there is a link between PURA and P-bodies, as documented by the enrichment of PURA-bound RNAs in both the P-body and stress granule transcriptome. Further, PURA was found by our collaborators to be localised within P-bodies and P-body numbers were strongly reduced in cells that are depleted of PURA. This absence might be attributed to the downregulation of the proteins encoded by the PURA targets LSM14A and DDX6 as both of them were previously identified as essential for P-body formation.
Overall, the reduction of P-body numbers in PURA depletion, the neuronal function of PURA, and its association with mitochondria and RNA lifecycle regulation may indicate the cellular foundation of both PURA Syndrome and related neuronal diseases.
In summary, I present a versatile and user-friendly computational tool for the analysis of CLIP data. Subsequently, I conduct a thorough computational analysis of CLIP and other high-throughput data in the context of the RNA-binding protein PURA, which offers valuable insights into the cellular functions of PURA. These insights advance our understanding of the impact of PURA loss in PURA Syndrome and other disease contexts.
Stimulated emission depletion (STED) microscopy is a super-resolution technique that surpasses the diffraction limit and has contributed to the study of dynamic processes in living cells. However, high laser intensities induce fluorophore photobleaching and sample phototoxicity, limiting the number of fluorescence images obtainable from a living cell. Here, we address these challenges by using ultra-low irradiation intensities and a neural network for image restoration, enabling extensive imaging of single living cells. The endoplasmic reticulum (ER) was chosen as the target structure due to its dynamic nature over short and long timescales. The reduced irradiation intensity combined with denoising permitted continuous ER dynamics observation in living cells for up to 7 hours with a temporal resolution of seconds. This allowed for quantitative analysis of ER structural features over short (seconds) and long (hours) timescales within the same cell, and enabled fast 3D live-cell STED microscopy. Overall, the combination of ultra-low irradiation with image restoration enables comprehensive analysis of organelle dynamics over extended periods in living cells.
Five new species of the spider genus Heteropoda Latreille, 1804 (Araneae: Sparassidae) from China
(2024)
Five new species of Heteropoda (Araneae, Sparassidae, Heteropodinae) are described from China: H. bawanglingensis sp. nov. (female; Hainan), H. dulongensis sp. nov. (male, female; Yunnan), H. hainanensis sp. nov. (male, female; Hainan), H. longa sp. nov. (female; Guizhou), and H. vaginalis sp. nov. (female; Yunnan). We provide descriptions and illustrations for each species as well as a distribution map in the current paper.
Scalibregmatidae Malmgren, 1867 is a family of annelids, with only few taxa reported from Brazil. In this work, we describe two new species of Asclerocheilus Ashworth, 1901. The new species A. geiseae sp. nov. and A. blakei sp. nov. were collected during scientific expeditions to the Espírito Santo and Campos sedementary basins. These expeditions were coordinated by PETROBRAS/CENPES. The species A. geiseae sp. nov. is unique among its congeners by the presence of acicular spines with rounded and curved tips in two rows. The second species, A. blakei sp. nov., differs from its congeners by the combination of the presence of a trapezoidal prostomium, acicular spines on chaetigers 1–3, lyrate chaetae from chaetiger 3 on notopodia and 2 on neuropodia. Moreover, we report the species A. tropicus Blake, 1981 from the localities sampled on this study. We also provide an identification key to all species of Asclerocheilus of the world.
Sipunculans are a poorly studied group in the Tropical Eastern Pacific. For the Southern Mexican Pacific (SMP) there is only one record of a sipunculan species. The main objective of this work was to determine the species composition of the phylum Sipuncula present in the SMP. The study area covered three Mexican states: Guerrero, Oaxaca and Chiapas; specimens from 28 localities were examined from both intertidal and subtidal zones. A total of 551 specimens were reviewed, from which 11 species were identified. Five of them have previously been recorded in the Tropical Eastern Pacific (TEP): Apionsoma (A.) hespera comb. nov., A. (Edmondsius) pectinatum, Aspidosiphon (A.) elegans, Phascolosoma (P.) puntarenae and Themiste (T.) hennahi; four species are similar to nominal species: Sipunculus (S.) cf. polymyotus, Siphonosoma cf. vastum, Siphonosoma cf. cumanense and Phascolosoma (P.) cf. perlucens; and two new species are described: Aspidosiphon (Paraspidosiphon) cutleri sp. nov. and Aspidosiphon (Paraspidosiphon) pastori sp. nov. A checklist and an identification key for all sipunculan species from the TEP are presented. The checklist includes 53 taxa, 25 of which are questionable records. This work generated 11 new records of sipunculans in the SMP and five new records in the TEP.
A taxonomic study on the Afrotropical genera Afrepipona Giordani Soika, 1965 and Afrepsilon gen. nov. is presented. Twenty new species are described, of which 15 are in Afrepipona (Afrepipona anomala sp. nov., Afrepipona cellularis sp. nov., Afrepipona clonata sp. nov., Afrepipona cuprea sp. nov., Afrepipona lamellata sp. nov., Afrepipona lamptula sp. nov., Afrepipona lobulata sp. nov., Afrepipona meridionalis sp. nov., Afrepipona occidentalis sp. nov., Afrepipona orientalis sp. nov., Afrepipona punctatissima sp. nov., Afrepipona scabra sp. nov., Afrepipona segregata sp. nov., Afrepipona ulterior sp. nov., Afrepipona vulcanica sp. nov.) and five are in Afrepsilon (Afrepsilon aterrimum gen. et sp. nov., Afrepsilon ferrugineoaureum gen. et sp. nov., Afrepsilon hybridum gen. et sp. nov., Afrepsilon minor gen. et sp. nov., and Afrepsilon pictum gen. et sp. nov.). Afrepipona lamptoensis Giordani Soika, 1965 is withdrawn from synonymy with A. angusta (de Saussure, 1863) and subsequently revalidated. Afrepipona unifasciata Gusenleitner, 2012 is transferred to the genus Antodynerus de Saussure, 1855 (Antodynerus unifasciatus comb. nov.). Keys to all known species are provided.
Description of four new species of the Neotropical genus Scione Walker, 1850 (Diptera: Tabanidae)
(2024)
After 94 years after the last revision of the genus and after 22 years since the last species was named, we describe four new species of Scione from Ecuador and Peru: S. cooperi sp. nov., S. gertrudeae sp. nov., S. kroeberi sp. nov. and S. merianae sp. nov. We provide diagnoses, descriptions, photographs and discussions for each of the species.
Correlative dynamic imaging of cellular landmarks, such as nuclei and nucleoli, cell membranes, nuclear envelope and lipid droplets is critical for systems cell biology and drug discovery, but challenging to achieve with molecular labels. Virtual staining of label-free images with deep neural networks is an emerging solution for correlative dynamic imaging. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining leaves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Current approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. We report training protocols for virtual staining of nuclei and membranes robust to variations in imaging parameters, cell states, and cell types. We describe a flexible and scalable convolutional architecture, UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including human cell lines, neuromasts of zebrafish and stem cell (iPSC)-derived neurons, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and cell membranes. The models rescue missing labels, non-uniform expression of labels, and photobleaching. We share three pre-trained models (VSCyto3D, VSNeuromast, and VSCyto2D) and a PyTorch-based pipeline (VisCy) for training, inference, and deployment that leverages current community standards for image data and metadata.
Snapshots of acetyl-CoA synthesis, the final step of CO₂ fixation in the Wood-Ljungdahl pathway
(2024)
In the ancient microbial Wood-Ljungdahl pathway, CO2 is fixed in a multi-step process with acetyl-CoA synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). Here, we present catalytic snapshots of the CODH/ACS from the gas-converting acetogen Clostridium autoethanogenum, characterizing the molecular choreography of the overall reaction including electron transfer to the CODH for CO2 reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme crucial for CO2 fixation in anaerobic organisms.
Members of the arginine–serine-rich protein family (SR proteins) are multifunctional RNA-binding proteins that have emerged as key determinants for mRNP formation, identity and fate. They bind to pre-mRNAs early during transcription in the nucleus and accompany bound transcripts until they are translated or degraded in the cytoplasm. SR proteins are mostly known for their essential roles in constitutive splicing and as regulators of alternative splicing. However, many additional activities of individual SR proteins, beyond splicing, have been reported in recent years. We will summarize the different functions of SR proteins and discuss how multifunctionality can be achieved. We will also highlight the difficulties of studying highly versatile SR proteins and propose approaches to disentangle their activities, which is transferrable to other multifunctional RBPs.
Cell-free (CF) synthesis with highly productive E. coli lysates is a convenient method to produce labeled proteins for NMR studies. Despite reduced metabolic activity in CF lysates, a certain scrambling of supplied isotope labels is still notable. Most problematic are conversions of 15N labels of the amino acids L-Asp, L-Asn, L-Gln, L-Glu and L-Ala, resulting in ambiguous NMR signals as well as in label dilution. Specific inhibitor cocktails suppress most undesired conversion reactions, while limited availability and potential side effects on CF system productivity need to be considered. As alternative route to address NMR label conversion in CF systems, we describe the generation of optimized E. coli lysates with reduced amino acid scrambling activity. Our strategy is based on the proteome blueprint of standardized CF S30 lysates of the E. coli strain A19. Identified lysate enzymes with suspected amino acid scrambling activity were eliminated by engineering corresponding single and cumulative chromosomal mutations in A19. CF lysates prepared from the mutants were analyzed for their CF protein synthesis efficiency and for residual scrambling activity. The A19 derivative “Stablelabel” containing the cumulative mutations asnA, ansA/B, glnA, aspC and ilvE yielded the most useful CF S30 lysates. We demonstrate the optimized NMR spectral complexity of selectively labeled proteins CF synthesized in “Stablelabel” lysates. By taking advantage of ilvE deletion in "Stablelabel", we further exemplify a new strategy for methyl group specific labeling of membrane proteins with the proton pump proteorhodopsin.
Measurements of vertical velocity from vertically pointing Doppler lidars are used to derive the profiles of vertical velocity variance. Observations were taken during the FESSTVaL (Field Experiment on Submesoscale Spatio-Temporal Variability in Lindenberg) campaign during the warm seasons of 2020 and 2021. Normalized by the square of convective velocity scale, the average vertical velocity variance profile follows the universal profile of Lenschow et al. (1980), however, daily profiles still show a high day-to-day variability. We found that moisture transport and the content of moisture in the boundary layer could explain the remaining variability of the normalized vertical velocity variance. The magnitude of the normalized vertical velocity variance is highest on clear-sky days, and decreases as the relative humidity increase and surface latent heat flux decrease in cloud-topped and rainy days. This suggests that moisture content and moisture transport are limiting factors for the intensity of turbulence in the convective boundary layer. We also found that the intensity of turbulence decreases with an increase in boundary layer cloud fraction during FESSTVaL, while the latent heating in the cloud layer was not a relevant source of turbulence in this case. We conclude that a new vertical velocity scale has to be defined that would take into account the moist processes in the convective boundary layer.
Measurements of vertical velocity from vertically pointing Doppler lidars are used to derive the profiles of normalized vertical velocity variance. Observations were taken during the FESSTVaL (Field Experiment on Submesoscale Spatio-Temporal Variability in Lindenberg) campaign during the warm seasons of 2020 and 2021. Normalized by the square of the convective velocity scale, the average vertical velocity variance profile follows the universal profile of Lenschow et al. (1980). However, daily profiles still show a high day-to-day variability. We found that moisture transport and the content of moisture in the boundary layer could explain the remaining variability of the normalized vertical velocity variance. The magnitude of the normalized vertical velocity variance is highest on clear-sky days and decreases as the absolute humidity increases and surface latent heat flux decreases on cloud-topped days. This suggests that moisture content and moisture transport are limiting factors for the intensity of turbulence in the convective boundary layer. We also found that the intensity of turbulence decreases with an increase in the boundary layer cloud fraction during FESSTVaL, while the latent heating in the cloud layer was not a relevant source of turbulence in this case. We conclude that a new vertical velocity scale has to be defined that would take into account the moist processes in the convective boundary layer.
Highlights
• Linking ecological and ecotoxicological data from 30 river sites.
• Bioassays indicate complex mixture of chemicals with different modes of action.
• Macroinvertebrate community deteriorates along a toxicity gradient.
• Macroinvertebrate response has low potential for toxicity-specific bioindicators.
• Effect-based methods could isolate toxicity effects from multiple stressors.
Abstract
Chemical pollution is one of the most important threats to freshwater ecosystems. The plethora of potentially occurring chemicals and their effects in complex mixtures challenge standard monitoring methods. Effect-based methods (EBMs) are proposed as complementary tools for the assessment of chemical pollution and toxic effects. To investigate the effects of chemical pollution, the ecological relevance of EBMs and the potential of macroinvertebrates as toxicity-specific bioindicators, ecological and ecotoxicological data were linked. Baseline toxicity, mutagenicity, dioxin-like and estrogenic activity of water and sediment samples from 30 river sites in central Germany were quantified with four in vitro bioassays. The responses of macroinvertebrate communities at these sites were assessed by calculating 16 taxonomic and functional metrics and by investigating changes in the taxonomic and trait composition. Principal component analysis revealed an increase in toxicity along a joint gradient of chemicals with different modes of action. This toxicity gradient was associated with a decrease in biodiversity and ecological quality, as well as significant changes in taxonomic and functional composition. The strength of the effects suggested a strong impact of chemical pollution and underlined the suitability of EBMs in detecting ecological relevant effects. However, the metrics, taxa, and traits associated with vulnerability or tolerance to toxicity were found to also respond to other stressors in previous studies and thus may have only a low potential as toxicity-specific bioindicators. Because macroinvertebrates respond integratively to all present stressors, linking both ecological and environmental monitoring is necessary to investigate the overall effects but also isolate individual stressors. EBMs have a high potential to separate the toxicity of chemical mixtures from other stressors in a multiple stressor scenario, as well as identifying the presence of chemical groups with specific modes of action.
We investigate the early time dynamics of heavy ion collisions studying the time evolution of the energy-momentum tensor as well as energy-momentum correlations within a uniformly thermalizing holographic QGP. From these quantities, we suggest a far-from equilibrium definition of shear viscosity, which is a crucial property of QCD matter as it significantly determines the generation of elliptic flow already at early times. During an exemplary initial heating phase of the holographic QGP the shear viscosity of entropy density ratio decreases down to 60%, followed by an overshoot to 110% of the near-equilibrium value, η/s=1/(4π). Implications for the QCD QGP are discussed. Subsequently, we consider a holographic QGP which is Bjorken-expanding. Its energy-momentum tensor components have a known hydrodynamic attractor to which all time evolutions collapse independent of the initial conditions. Based on this, we propose a definition for a far from equilibrium speed of sound, and analytically compute its hydrodynamic attractor. Subjecting this Bjorken-expanding plasma to an external magnetic field and an axial chemical potential, we study the chiral magnetic effect far from equilibrium.
We investigate the early time dynamics of heavy ion collisions studying the time evolution of the energy-momentum tensor as well as energy-momentum correlations within a uniformly thermalizing holographic QGP. From these quantities, we suggest a far-from equilibrium definition of shear viscosity, which is a crucial property of QCD matter as it significantly determines the generation of elliptic flow already at early times. During an exemplary initial heating phase of the holographic QGP the shear viscosity of entropy density ratio decreases down to 60%, followed by an overshoot to 110% of the near-equilibrium value, η/s=1/(4π). Implications for the QCD QGP are discussed. Subsequently, we consider a holographic QGP which is Bjorken-expanding. Its energy-momentum tensor components have a known hydrodynamic attractor to which all time evolutions collapse independent of the initial conditions. Based on this, we propose a definition for a far from equilibrium speed of sound, and analytically compute its hydrodynamic attractor. Subjecting this Bjorken-expanding plasma to an external magnetic field and an axial chemical potential, we study the chiral magnetic effect far from equilibrium.
Heavy quarks are useful probes to investigate the properties of the Quark-Gluon Plasma (QGP) produced in heavy-ion collisions at the LHC, since they are produced in initial hard scattering processes. To single out the signals that are characteristic of the QGP, it is nevertheless crucial to understand the primordial heavy-quark production in vacuum, and to disentangle hot from cold nuclear matter effects. Moreover, observations of collective effects in high-multiplicity pp and p-Pb collisions show surprising similarities with those in heavy-ion collisions. Heavy-flavour production in such collisions could give further insight into the underlying processes. The heavy-flavour production can be studied with e+e− pairs from correlated semileptonic decays of heavy-flavour hadrons. Compared to single heavy-flavour measurements, the dielectron yield contains information about the initial kinematical correlations between the charm and anti-charm quarks, which is otherwise not accessible, and is sensitive to soft heavy-flavour production. We report results on correlated e+e− pairs in pp collisions recorded by the ALICE detector at different collision energies. The production of heavy quarks is discussed by comparing the yield of dielectrons from heavy-flavour hadron decays as a function of invariant mass, pair transverse momentum and distance of closest approach to the primary vertex with different Monte Carlo event generators. The heavy-flavour production cross sections are also presented. Results from high-multiplicity pp collisions at √s=13 TeV and the status of the p-Pb analysis at √sNN=5.02 TeV are reported as well.