bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature drives variation in flying insect biomass across a German malaise trap network
Authors: Welti Ellen A.R. , Zajicek Petr , Ayasse Manfred , Bornholdt Tim , Buse Jörn , Dziock Frank , Engelmann Rolf A. , Englmeier Jana , Fellendorf Martin , Förschler Marc I. , Frenzel Mark , Fricke Ute , Ganuza Cristina , Hippke Mathias , Hoenselaar Günter , Kaus-Thiel Andrea , Mandery Klaus , Marten Andreas , Monaghan Michael T. , Morkel Carsten , Müller Jörg , Puffpaff Stephanie , Redlich Sarah , Richter Ronny , Botero Sandra Rojas , Scharnweber Tobias , Scheiffarth Gregor , Yáñez Paul Schmidt , Schumann Rhena , Seibold Sebastian , Steffan-Dewenter Ingolf , Stoll Stefan , Tobisch Cynthia , Twietmeyer Sönke , Uhler Johannes , Vogt Juliane , Weis Dirk , Weisser Wolfgang W. , Wilmking Martin , Haase Peter
Published: February 2021

Among the many concerns for biodiversity in the Anthropocene, recent reports of flying insect loss are particularly alarming, given their importance as pollinators and as a food source for many predators. Few insect monitoring programs cover large spatial scales required to provide more generalizable estimates of insect responses to global change drivers.

We ask how climate and surrounding habitat affect flying insect biomass and day of peak biomass using data from the first year of a new standardized distributed monitoring network at 84 locations across Germany comprising spatial gradient of land-cover types from protected to urban areas.

Flying insect biomass increased linearly with monthly temperature across Germany. However, the effect of temperature on flying insect biomass flipped to negative in the hot months of June and July when local temperatures most exceeded long-term averages.

Land-cover explained little variation in insect biomass, but biomass was lowest in forested sites. Grasslands, pastures and orchards harbored the highest insect biomass. The date of peak biomass was primarily driven by surrounding land-cover type, with grasslands especially having earlier insect biomass phenologies.

Standardized, large-scale monitoring is pivotal to uncover underlying processes of insect decline and to develop climate-adapted strategies to promote insect diversity. In a temperate climate region, we find that the benefits of temperature on flying insect biomass diminish in a German summer at locations where temperatures most exceeded long-term averages. These results highlighting the importance of local adaptation in climate change-driven impacts on insect communities.
EGR4-dependent decrease of UTF1 is associated with failure to reserve spermatogonial stem cells in infertile men
Authors: Di Persio Sara , Tekath Tobias , Siebert-Kuss Lara Marie , Cremers Jann-Frederik , Wistuba Joachim , Li Xiaolin , Meyer zu Hörste Gerd , Drexler Hannes CA , Wyrwoll Margot Julia , Tüttelmann Frank , Dugas Martin , Kliesch Sabine , Schlatt Stefan , Laurentino Sandra , Neuhaus Nina
Published: February 2021

Despite the high incidence of male infertility, about 70% of infertile men do not receive a causative diagnosis. To gain insights into the regulatory mechanisms governing human germ cell function in normal and impaired spermatogenesis (cryptozoospermic patients, crypto), we combined single cell RNA sequencing (>30.000 cells), proteome, and histomorphometric analyses of testicular tissues. We found major alterations in the crypto spermatogonial compartment with increased numbers of the most undifferentiated spermatogonia (PIWIL4+State 0 cells). We also observed a transcriptional switch within the spermatogonial compartment driven by the increased and prolonged expression of the transcription factorEGR4.Intriguingly, EGR4-regulated genes included the chromatin-associated transcriptional repressorUTF1, which was downregulated. Histomorphometrical analyses showed that these transcriptional changes were mirrored at the protein level and accompanied by a change in the chromatin structure of spermatogonia. This resulted in a reduction of Adarkspermatogonia - characterized by tightly compacted chromatin and serving as reserve stem cells. These findings suggest that crypto patients are at a disadvantage especially in cases of gonadotoxic damage as they have less cells safeguarding the genetic integrity of the germline. We hypothesize that the more relaxed chromatin status of spermatogonia is dependent on decreased UTF1 expression caused by EGR4 activation. These identified regulators of the spermatogonial compartment will be highly interesting targets to uncover genetic causes of male infertility.

One Sentence Summary

Reserve spermatogonial stem cell depletion in infertile men is regulated by an EGR4-dependent UTF1 decrease, which changes chromatin morphology.
The MAP She1 coordinates directional spindle positioning by spatially restricting dynein activity
Authors: Ecklund Kari H. , Bailey Megan E. , Dietvorst Carsten K. , Asbury Charles L. , Markus Steven M.
Published: February 2021

Dynein motors move the mitotic spindle to the cell division plane in many cell types, including in budding yeast, in which dynein is assisted by numerous factors including the microtubule-associated protein (MAP) She1. Evidence suggests that She1 plays a role in polarizing dynein-mediated spindle movements toward the daughter cell; however, how She1 performs this function is unknown. We find that She1 assists dynein in maintaining the spindle close to the bud neck, such that at anaphase onset the chromosomes are segregated to mother and daughter cells. She1 does so by attenuating the initiation of dynein-mediated spindle movements specifically within the mother cell, ensuring such movements are polarized toward the daughter cell. Our data indicate that this activity relies on She1 binding to the microtubule-bound conformation of the dynein microtubule-binding domain, and to astral microtubules within mother cells. Our findings reveal how an asymmetrically localized MAP directionally tunes dynein activity by attenuating motor activity in a spatially confined manner.
Spc1 regulates substrate selection for signal peptidase
Authors: Yim Chewon , Chung Yeonji , Kim Jeesoo , Nilsson IngMarie , Kim Jong-Seo , Kim Hyun
Published: February 2021

Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1 that is dispensable for the catalytic activity of SPase, and its role remains elusive. In the present study, we investigated the function of yeast Spc1. First, we set up anin vivoSPase cleavage assay using secretory protein CPY variants with SSs modified in thenandhregions. When comparing the SS cleavage efficiencies of these variants in cells with or without Spc1, we found that signal-anchored sequences become more susceptible to cleavage by SPase without Spc1. Further, SPase-mediated processing of transmembrane (TM) segments in model membrane proteins was reduced upon overexpression of Spc1. Spc1 was co-immunoprecipitated with membrane proteins carrying uncleaved signal-anchored or TM segments. These results suggest a role of Spc1 in shielding TM segments from SPase action, thereby contributing to accurate substrate selection for SPase.
Severe deficiency of voltage-gated sodium channel NaV1.2 elevates neuronal excitability in adult mice
Authors: Zhang Jingliang , Chen Xiaoling , Eaton Muriel , Lai Shirong , Park Anthony , Ahmad Talha S. , Wu Jiaxiang , Ma Zhixiong , Que Zhefu , Lee Ji Hea , Xiao Tiange , Li Yuansong , Wang Yujia , Olivero-Acosta Maria I. , Schaber James A. , Jayant Krishna , Huang Zhuo , Lanman Nadia A. , Skarnes William C. , Yang Yang
Published: February 2021

Scn2aencodes voltage-gated sodium channel NaV1.2, which mediates neuronal firing. The current paradigm suggests that NaV1.2 gain-of-function variants enhance neuronal excitability resulting in epilepsy, whereas NaV1.2 deficiency impairs neuronal excitability contributing to autism. In this paradigm, however, why about a third of patients with NaV1.2 deficiency still develop seizures remains a mystery. Here we challenge the conventional wisdom, reporting that neuronal excitability is increased with severe NaV1.2 deficiency. Using a unique gene-trap knockout mouse model ofScn2a, we found enhanced intrinsic excitabilities of principal neurons in the cortico-striatal circuit, known to be involved inScn2a-related seizures. This increased excitability is autonomous, and is reversible by genetic restoration ofScn2aexpression in adult mice. Mechanistic investigation reveals a compensatory downregulation of potassium channels including KV1.1, which could be targeted to alleviate neuronal hyperexcitability. Our unexpected findings may explain NaV1.2 deficiency-related epileptic seizures in humans and provide molecular targets for potential interventions.

TEASER

Severe NaV1.2 deficiency results in neuronal hyperexcitability via the compensatory downregulation of potassium channels.

HIGHLIGHTS

Severe NaV1.2 deficiency results in enhanced excitability of medium spiny neurons (MSNs) and pyramidal neurons in adult mice;

Increased neuronal excitability in MSNs is accompanied by elevated voltage threshold;

NaV1.2 deficiency-related hyperexcitability is reversible with the restoration ofScn2aexpression, and is autonomous;

The expression of the KV1.1 channel has a compensatory reduction in neurons with NaV1.2 deficiency, and KV channels openers normalize the neuronal excitability;

The enhanced excitability in brain slices translates to elevatedin vivofiring commonly associated with seizures.
Dnmt1a is essential for gene body methylation and the regulation of zygotic genome activation in the wasp
Authors: Arsala Deanna , Wu Xin , Yi Soojin V. , Lynch Jeremy A.
Published: February 2021

Gene body methylation (GBM) is an ancestral aspect of DNA methylation (Sarda, Zeng, Hunt, & Yi, 2012; Yi, 2012; Zemach, McDaniel, Silva, & Zilberman, 2010) whose role in development has been obscured by the more prominent roles of promoter and CpG island methylation. The wasp Nasonia has little promoter and CpG island methylation, yet retains strong GBM (Park et al., 2011; Wang et al., 2013; Werren et al., 2010), making it an excellent model for elucidating the role of GBM. Here we show that Nasonia DNA methyl transferase 1a (Nv-Dnmt1a) knockdown leads to failures in cellularization and gastrulation of the embryo. Both of these disrupted events are hallmarks of the maternal-zygotic transition (MZT) in insects. Analysis of the embryonic transcriptome and methylome revealed strong reduction of GBM and widespread disruption of gene expression during embryogenesis after Nv-Dnmt1a knockdown. There was a strong correlation between loss of GBM and reduced gene expression in thousands of methylated loci, while affected unmethylated genes tended to be upregulated. We propose that reduced GBM and subsequent lower expression levels of methylated genes was the direct effect of Nv-Dnmt1 knockdown, and that this disruption led to widespread downstream dysregulation of MZT, and manifesting in developmental failure at gastrulation.

Significance Statement

The importance of gene-body methylation (GBM) in development is unclear, due to the difficulty in teasing apart the effects of cis-regulatory methylation from those of GBM in vertebrate model systems. Unlike vertebrate models, the methylation machinery in the jewel waspNasonia vitripennisappears to exclusively mediate GBM, thus simplifying interpretation of the role of GBM in development. Knockdown of DNMT1 (Nv-Dnmt1a) inNasonialeads to embryonic lethality, which we show is caused by a failure of cellularization and gastrulation. Nv-Dnmt1a knockdown resulted in a global loss of GBM in the embryo, which was strongly correlated with a down-regulation of gene expression. We propose that GBM facilitated by Nv-Dnmt1a is required for proper zygotic genome activation in the wasp.
Colonic epithelial adaptation to EGFR-independent growth induces chromosomal instability and is accelerated by prior injury
Authors: Chen Tiane , Zeineldin Maged , Johnson Blake , Dong Yi , Narkar Akshay , Li Taibo , Zhu Jin , Li Rong , Larman Tatianna C.
Published: February 2021

Although much is known about the gene mutations required to drive colorectal cancer (CRC) initiation, the tissue-specific selective microenvironments in which neoplasia arises remains less characterized. Here, we determined whether modulation of intestinal stem cell niche morphogens alone can exert a neoplasia-relevant selective pressure on normal colonic epithelium. Using adult stem cell-derived murine colonic epithelial organoids (colonoids), we employed a strategy of sustained withdrawal of EGF and EGFR inhibition to select for and expand survivors. EGFR-signaling-independent (iEGFR) colonoids emerged over rounds of selection and expansion. Colonoids derived from a mouse model of chronic mucosal injury showed an enhanced ability to adapt to EGFR inhibition. Whole-exome and transcriptomic analyses of iEGFR colonoids demonstrated acquisition of deleterious mutations and altered expression of genes implicated in EGF signaling, pyroptosis, and CRC. iEGFR colonoids acquired dysplasia-associated cytomorphologic changes, an increased proliferative rate, and the ability to survive independently of other required niche factors. These changes were accompanied by emergence of aneuploidy and chromosomal instability; further, the observed mitotic segregation errors were significantly associated with loss of interkinetic nuclear migration, a fundamental and dynamic process underlying intestinal epithelial homeostasis. This study provides key evidence that chromosomal instability and other phenotypes associated with neoplasia can be induced ex vivo via adaptation to EGF withdrawal in normal and stably euploid colonic epithelium, without introducing cancer-associated driver mutations. In addition, prior mucosal injury accelerates this evolutionary process.

Key definitions

Colonoids: adult stem cell-derived colonic epithelial organoids

iEGFR: in vitro selective conditions devoid of EGF (epidermal growth factor) and including an EGFR (EGF receptor) inhibitor 1

iEGFR colonoids: colonoids tolerant to iEGFR culture conditions with growth and survival similar to unselected passage-matched controls

INM: Interkinetic nuclear migration
Quantifying the severity of adverse drug reactions using social media
Authors: Lavertu Adam , Hamamsy Tymor , Altman Russ B
Published: February 2021

Adverse drug reactions (ADRs) impact the health of 100,000s of individuals annually in the United States with associated costs in the hundreds of billions. The monitoring and analysis of the severity of adverse drug reactions is limited by the current qualitative and categorical system of severity classifications. Previous efforts have generated quantitative estimates for a subset of ADRs, but were limited in scope due to the time and costs associated with the efforts. We present a semi-supervised approach that estimates ADR severity by using a lexical network of ADR word embeddings and label propagation. We use this method to estimate the severity of 28,113 ADRs, representing 12,198 unique ADR concepts from MedDRA. Our Severity of Adverse Events Derived from Reddit (Saedr) scores have good correlations with real-world outcomes. Saedrscores had Spearman correlations with ADR case outcomes in FAERS of 0.595, 0.633, and −0.748 for death, serious outcome, and no outcome, respectively. We investigate different methods for defining initial seed term sets and evaluate their impact on severity estimates. We analyzed severity distributions for ADRs based on their appearance in Boxed Warning drug label sections, as well as ADRs with sex-specific associations. We find that ADRs discovered postmarket have significantly greater severity compared to those discovered in the clinical trial. We create quantitative Drug RIsk Profile (Drip) scores for 968 drugs that have a Spearman correlation of 0.377 with drugs ranked by FAERS cases resulting in death, where the given drug was the primary suspect. We make the Saedrand Dripscores publicly available in order to enable more quantitative analysis of pharmacovigilance data.
Mechanoreceptor synapses in the brainstem shape the central representation of touch
Authors: Lehnert Brendan P. , Santiago Celine , Huey Erica L. , Emanuel Alan J. , Renauld Sophia , Africawala Nusrat , Alkislar Ilayda , Zheng Yang , Bai Ling , Koutsioumpa Charalampia , Hong Jennifer T. , Magee Alexandra R. , Harvey Christopher D. , Ginty David D.
Published: February 2021

Mammals use glabrous (hairless) skin of their hands and feet to navigate and manipulate their environment. Cortical maps of the body surface across species contain disproportionately large numbers of neurons dedicated to glabrous skin sensation, potentially reflecting a higher density of mechanoreceptors that innervate these skin regions. Here, we find that disproportionate representation of glabrous skin emerges over postnatal development at the first synapse between peripheral mechanoreceptors and their central targets in the brainstem. Mechanoreceptor synapses undergo developmental refinement that depends on proximity of their terminals to glabrous skin, such that those innervating glabrous skin make synaptic connections that expand their central representation. In mice that do not sense gentle touch, mechanoreceptors innervating glabrous skin still make more powerful synaptic connections in the brainstem. We propose that the skin region a mechanoreceptor innervates controls refinement of its central synapses over development to shape the representation of touch in the brain.
Advancing admixture graph estimation via maximum likelihood network orientation
Authors: Molloy Erin K. , Durvasula Arun , Sankararaman Sriram
Published: February 2021

Motivation

Admixture, the interbreeding between previously distinct populations, is a pervasive force in evolution. The evolutionary history of populations in the presence of admixture can be modeled by augmenting phylogenetic trees with additional nodes that represent admixture events. While enabling a more faithful representation of evolutionary history,admixture graphspresent formidable inferential challenges, and there is an increasing need for methods that are accurate, fully automated, and computationally efficient. One key challenge arises from the size of the space of admixture graphs. Given that exhaustively evaluating all admixture graphs can be prohibitively expensive, heuristics have been developed to enable efficient search over this space. One heuristic, implemented in the popular method TreeMix, consists of adding edges to a starting tree while optimizing a suitable objective function.

Results

Here, we present a demographic model (with one admixed population incident to a leaf) where TreeMix and any other starting-tree-based maximum likelihood heuristic using its likelihood function isguaranteedto get stuck in a local optimum and return an incorrect network topology. To address this issue, we propose a new search strategy that we term maximum likelihood network orientation (MLNO). We augment TreeMix with an exhaustive search for a MLNO, referring to this approach as OrientA-Graph. In evaluations including previously published admixture graphs, OrientAGraph outperformed TreeMix on 4/8 models (there are no differences in the other cases). Overall, OrientAGraph found graphs with higher likelihood scores and topological accuracy while remaining computationally efficient. Lastly, our study reveals several directions for improving maximum likelihood admixture graph estimation.

Availability

OrientAGraph is available under the GNU General Public License v3.0 on Github (https://github.com/sriramlab/OrientAGraph).
Marker-free imaging of α-Synuclein aggregates in a rat model of Parkinson’s disease using Raman microspectroscopy
Authors: Sevgi Fide , Brauchle Eva M , Carvajal Berrio Daniel A , Schenke-Layland Katja , Casadei Nicolas , Salker Madhuri S , Riess Olaf , Singh Yogesh
Published: February 2021

A hallmark of Parkinson’s disease (PD) is the formation of Lewy bodies in the brain. Lewy bodies are rich in the aggregated form of misfolded α-Synuclein (α-Syn). The brain from PD patients can only be analysed after post-mortem, limiting the diagnosis of PD to the manifestation of motor symptoms. In PD patients and animal models phosphorylated α-Syn was detected in the gut, thus, raising the hypothesizes that early-stage PD could be diagnosed based on colon tissues biopsies. Non-invasive marker-free technologies represent an ideal method to potentially detect aggregated α-Synin vivo.Raman microspectroscopy has been established for the detection of molecular changes such as alterations of protein structures. Here, the olfactory bulb in the brain and the muscularis mucosae of colon tissue sections of a human BAC-SNCA transgenic (TG) rat model was analysed using Raman imaging and microspectroscopy. Raman images from TG and WT rats were investigated using spectral, principal component and true component analysis. Spectral components indicated protein aggregates (spheroidal oligomers) in TG rat brain and colon tissues even at a young age but not in WT. In summary, we have demonstrated that Raman imaging is capable to detect α-Syn aggregates in colon tissues of a PD rat model and making it a promising tool for future use in PD pathology.
Factors affecting bacterial community dynamics and volatile metabolite profiles of Thai traditional salt fermented fish
Authors: Det-udom Rachatida , Settachaimongkon Sarn , Chancharoonpong Chuenjit , Suphamityotin Porrarath , Suriya Atchariya , Prakitchaiwattana Cheunjit
Published: February 2021

Bacterial diversity of the Thai traditional salt fermented fish with roasted rice bran or Pla-ra, in Thai, was investigated using classical and molecular approaches. Pla-ra fermentation could be classified into two types, i.e., solid-state fermentation (SSF) and submerged fermentation (SMF). Bacterial population ranged from 102-106and 106-109CFU/g in SSF and SMF, respectively. TherRNAdetection revealed thatHalanaerobiumspp. andLentibacillusspp. were the main genera present in all types and most stages of fermentation.Tetragenococcus halophilluswere dominant during final stage of fermentation in the samples in which sea salt was used as one of the ingredients whileBacillusspp. were found in those that rock salt was used. In contrast, cultural plating demonstrated thatBacillusspp. were the dominant genera.B. amyloliquefacienswere the main species found in all types of Pla-ra whereasB. pumilus, B. autrophaeus,B.subtilis andB. velezensiswere specifically associated with the samples in which rock salt was used. The main volatile metabolites in all Pla-ra samples were butanoic acid and its derivatives. Dimethyl disulfide was observed during earlier stage of fermentation under high salt condition with a long fermentation period. Key factors affected bacterial profiles and volatile compounds of salt fermented fish are type of salt, addition of roasted rice bran, and fermenting conditions.

Importance

Protein hydrolysates with high salt fermentation from soy, fish as sauces and pastes are important food condiments commonly found in Asian food cultures. In Thailand, an indigenous semi-paste product derived from salted fish fermentation also called Pla-ra is well recognized and extensively in demands. In-depth information on Pla-ra fermentation ecosystems, in which roasted rice bran and different types of salt are incorporated, are still limited. In this study, we found thatHalanaerobiumspp. was the key autochthonous microbe initiating Pla-ra fermentation. Addition of roasted rice brand and rock salt were associated with the prevalence ofBacillusspp. while sea salt was associated with the presence ofTetragenococcus halophillus, The risk of pathogenicStaphylococcusspp. andClostridiumspp. needed to be also concerned. Geographical origin authentication of Pla-ra products could be discriminated based on their distinctive volatile profiles. This research provides novel insights for quality and safety control fermentation together with conservation of its authenticity.
In vivoantigen expression regulates CD4 T cell differentiation and vaccine efficacy againstMycobacterium tuberculosisinfection
Authors: Clemmensen Helena Strand , Dube Jean-Yves , McIntosh Fiona , Rosenkrands Ida , Jungersen Gregers , Aagaard Claus , Andersen Peter , Behr Marcel A. , Mortensen Rasmus
Published: February 2021

New vaccines are urgently needed againstMycobacterium tuberculosis(Mtb), which kills more than 1.4 million people each year. CD4 T cell differentiation is a key determinant of protective immunity against Mtb, but it is not fully understood how host-pathogen interactions shape individual antigen-specific T cell populations and their protective capacity. Here, we investigated the immunodominant Mtb antigen, MPT70, which is upregulated in response to IFN-γ or nutrient/oxygen deprivation ofin vitroinfected macrophages. Using a murine aerosol infection model, we compared thein vivoexpression kinetics of MPT70 to a constitutively expressed antigen, ESAT-6, and analysed their corresponding CD4 T cell phenotype and vaccine-protection. For wild-type Mtb, we found thatin vivoexpression of MPT70 was delayed compared to ESAT-6. This delayed expression was associated with induction of less differentiated MPT70-specific CD4 T cells but, compared to ESAT-6, also reduced protection after vaccination. In contrast, infection with an MPT70-overexpressing Mtb strain promoted highly differentiated KLRG1+CX3CR1+CD4 T cells with limited lung-homing capacity. Importantly, this differentiated phenotype could be prevented by vaccination and, against the overexpressing strain, vaccination with MPT70 conferred similar protection as ESAT-6. Together our data indicate that highin vivoantigen expression drives T cells towards terminal differentiation and that targeted vaccination with adjuvanted protein can counteract this phenomenon by maintaining T cells in a protective less-differentiated state. These observations shed new light on host-pathogen interactions and provide guidance on how future Mtb vaccines can be designed to tip the immune-balance in favor of the host.

Importance

Tuberculosis, caused by Mtb, constitutes a global health crisis of massive proportions and the impact of the current COVID-19 pandemic is expected to cause a rise in tuberculosis-related deaths. Improved vaccines are therefore needed more than ever, but a lack of knowledge on protective immunity hampers their development. The present study shows that constitutively expressed antigens with high availability drive highly differentiated CD4 T cells with diminished protective capacity, which could be a survival strategy by Mtb to evade T cell immunity against key antigens. We demonstrate that immunisation with such antigens can counteract this phenomenon by maintaining antigen-specific T cells in a state of low differentiation. Future vaccine strategies should therefore explore combinations of multiple highly expressed antigens and we suggest that T cell differentiation could be used as a readily measurable parameter to identify these in both preclinical and clinical studies.
Proximity-labeling reveals novel host and parasite proteins at theToxoplasmaparasitophorous vacuole membrane
Authors: Cygan Alicja M. , Jean Beltran Pierre M. , Branon Tess C. , Ting Alice Y. , Carr Steven A. , Boothroyd John C.
Published: February 2021

Toxoplasma gondiiis a ubiquitous, intracellular parasite that envelopes its parasitophorous vacuole with a protein-laden membrane (PVM). The PVM is critical for interactions with the infected host cell such as nutrient transport and immune defense. Only a few parasite and host proteins have so far been identified on the host-cytosolic side of the PVM. We report here the use of human foreskin fibroblasts expressing the proximity-labeling enzyme miniTurbo, fused to a domain that targets it to this face of the PVM, in combination with quantitative proteomics to specifically identify proteins present at this crucial interface. Out of numerous human and parasite proteins with candidate PVM localization, we validate three novel parasite proteins (TGGT1_269950, TGGT1_215360, and TGGT1_217530) and four new host proteins (PDCD6IP/ALIX, PDCD6, CC2D1A, and MOSPD2) as localized to the PVM in infected human cells through immunofluorescence microscopy. These results significantly expand our knowledge of proteins present at the PVM and, given that three of the validated host proteins are components of the ESCRT machinery, they further suggest that novel biology is operating at this crucial host-pathogen interface.

Importance

Toxoplasmais an intracellular pathogen which resides and replicates inside a membrane-bound vacuole in infected cells. This vacuole is modified by both parasite and host proteins which participate in a variety of host-parasite interactions at this interface, including nutrient exchange, effector transport, and immune modulation. Only a small number of parasite and host proteins present at the vacuolar membrane and exposed to the host cytosol have thus far been identified. Here we report the identification of several novel parasite and host proteins present at the vacuolar membrane using enzyme-catalyzed proximity-labeling, significantly increasing our knowledge of the molecular players present and novel biology occurring at this crucial interface.
Identification of novel inner membrane complex and apical annuli proteins of the malaria parasitePlasmodium falciparum
Authors: Wichers Jan Stephan , Wunderlich Juliane , Heincke Dorothee , Pazicky Samuel , Strauss Jan , Schmitt Marius , Kimmel Jessica , Wilcke Louisa , Scharf Sarah , von Thien Heidrun , Burda Paul-Christian , Spielmann Tobias , Löw Christian , Filarsky Michael , Bachmann Anna , Gilberger Tim W.
Published: February 2021

The inner membrane complex (IMC) is a defining feature of apicomplexan parasites, which confers stability and shape to the cell, functions as a scaffolding compartment during the formation of daughter cells and plays an important role in motility and invasion during different life cycle stages of these single celled organisms. To explore the IMC proteome of the malaria parasitePlasmodium falciparumwe applied a proximity-dependent biotin identification (BioID)-based proteomics approach, using the established IMC marker protein Photosensitized INA-Labelled protein 1 (PhIL1) as bait in asexual blood-stage parasites. Subsequent mass spectrometry-based peptide identification revealed enrichment of twelve known IMC proteins and several uncharacterized candidate proteins. We validated nine of these previously uncharacterized proteins by endogenous GFP-tagging. Six of these represent new IMC proteins, while three proteins have a distinct apical localization that most likely represent structures described as apical annuli inToxoplasma gondii. Additionally, various Kelch13 interacting candidates were identified, suggesting an association of the Kelch13 compartment and the IMC in schizont and merozoite stages. This work extends the number of validated IMC proteins in the malaria parasite and reveals for the first time the existence of apical annuli proteins inP. falciparum.Additionally, it provides evidence for a spatial association between the Kelch13 compartment and the IMC in late blood-stage parasites.
CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
Authors: Wittig Alice , Miranda Fábio , Hölzer Martin , Altenburg Tom , Bartoszewicz Jakub M. , Beyvers Sebastian , Dieckmann Marius A. , Genske Ulrich , Giese Sven H. , Nowicka Melania , Richard Hugues , Schiebenhoefer Henning , Schmachtenberg Anna-Juliane , Sieben Paul , Tang Ming , Tembrockhaus Julius , Renard Bernhard Y. , Fuchs Stephan
Published: February 2021

The SARS-CoV-2 pandemic underlined the importance of molecular surveillance to track the evolution of the virus and inform public health interventions. Fast analysis, easy visualization and convenient filtering of the latest virus sequences are essential for this purpose. However, access to computational resources, the lack of bioinformatics expertise, and the sheer volume of sequences in public databases complicate surveillance efforts. CovRadar combines an analytical pipeline and a web application designed for the molecular surveillance of the spike gene of SARS-CoV-2, an important vaccine target. The intuitive web front-end focuses on mutations rather than viral lineages and provides easy access to frequencies and spatio-temporal distributions from global sample collections. The data is regularly updated based on a scalable and reproducible analytical back-end. With this platform, we aim to give users, those with or without bioinformatics skills or sufficient computational resources, the possibility to track and explore mutational changes in the SARS-CoV-2 spike gene and to filter, download, and further analyze data that meet their questions and needs. Advanced computational users have the ability to apply the analytical pipeline and data visualization methods locally on their own data. CovRadar is freely accessible athttps://covradar.net, source code is available athttps://gitlab.com/dacs-hpi/covradar.

GRAPHICAL ABSTRACT
Full Brain and Lung Prophylaxis against SARS-CoV-2 by Intranasal Lentiviral Vaccination in a New hACE2 Transgenic Mouse Model or Golden Hamsters
Authors: Ku Min-Wen , Authié Pierre , Bourgine Maryline , Anna François , Noirat Amandine , Moncoq Fanny , Vesin Benjamin , Nevo Fabien , Lopez Jodie , Souque Philippe , Blanc Catherine , Chardenoux Sébastien , Lafosse llta , Hardy David , Nemirov Kirill , Guinet Françoise , Vives Francina Langa , Majlessi Laleh , Charneau Pierre
Published: February 2021

Non-integrative, non-cytopathic and non-inflammatory lentiviral vectors are particularly suitable for mucosal vaccination and recently emerge as a promising strategy to elicit sterilizing prophylaxis against SARS-CoV-2 in preclinical animal models. Here, we demonstrate that a single intranasal administration of a lentiviral vector encoding a prefusion form of SARS-CoV-2 spike glycoprotein induces full protection of respiratory tracts and totally avoids pulmonary inflammation in the susceptible hamster model. More importantly, we generated a new transgenic mouse strain, expressing the human Angiotensin Converting Enzyme 2, with unprecedent brain permissibility to SARS-CoV-2 replication and developing a lethal disease in <4 days post infection. Even though the neurotropism of SARS-CoV-2 is now well established, so far other vaccine strategies under development have not taken into the account the protection of central nervous system. Using our highly stringent transgenic model, we demonstrated that an intranasal booster immunization with the developed lentiviral vaccine candidate achieves full protection of both respiratory tracts and brain against SARS-CoV-2.
APICURON: a database to credit and acknowledge the work of biocurators
Authors: Hatos András , Quaglia Federica , Piovesan Damiano , Tosatto Silvio C.E.
Published: February 2021

APICURON is an open and freely accessible resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data - mainly from literature - requires a huge effort which is difficult to quantify and acknowledge. APICURON collects biocuration events from third party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources and for biocurators themselves. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities. Biocurators are identified through their ORCID. The definition of curation events, scoring systems and rules for assigning badges and medals are resource-specific and easily customizable. Registered resources can transfer curation activities on the fly through a secure and robust Application Programming Interface (API). Here we show how simple and effective it is to connect a resource to APICURON describing the DisProt database of intrinsically disordered proteins as a use case. We believe APICURON will provide biological knowledgebases with a service to recognize and credit the effort of their biocurators, monitor their activity and promote curators engagement.

Database URL:https://apicuron.org
Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography
Authors: Walsh C. , Tafforeau P. , Wagner Willi L. , Jafree D. J. , Bellier A. , Werlein C. , Kühnel M. P. , Boller E. , Walker-Samuel S. , Robertus J. L. , Long D. A. , Jacob J. , Marussi S. , Brown E. , Holroyd N. , Jonigk D. D. , Ackermann M. , Lee P. D.
Published: February 2021

Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facility’s Extremely Brilliant Source: the world’s first high-energy 4thgeneration X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organ’s structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organ’s individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.
Energy-harnessing problem solving of primordial life: modeling the emergence of catalytic host-parasite life cycles
Authors: Conrad Bernard , Pirovino Magnus
Published: February 2021

All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer – the genome – conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using the Lotka-Volterra equations that three host-parasite pairs – individually a unit of a host and a parasite that is itself parasitized – are sufficient for robust and stable homeostasis, forming a life cycle. This catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for an original quasispecies evolving through a host-parasite life cycle.
Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N2-fixingBradyrhizobium
Authors: Tao Jinjin , Wang Sishuo , Liao Tianhua , Luo Haiwei
Published: February 2021

The alphaproteobacterial genusBradyrhizobiumhas been best known as N2-fixing members that nodulate legumes, supported by thenifandnodgene clusters. Recent environmental surveys show thatBradyrhizobiumrepresents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding ofBradyrhizobiumcomes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88Bradyrhizobiumstrains derived from diverse soil samples, including bothnif-carrying and non-nif-carrying free-living (nodfree) members. Phylogenomic analyses of these and 252 publicly availableBradyrhizobiumgenomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, thenifphylogeny shows that allnif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotesnifexpansion among the free-livingBradyrhizobiumand that the free-livingnifcluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that thenifin free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-livingBradyrhizobium nifand the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance ofBradyrhizobiumin world’s soils, our findings have implications for global nitrogen cycles and agricultural research.
Enzyme kinetics of CRISPR molecular diagnostics
Authors: Ramachandran Ashwin , Santiago Juan G.
Published: February 2021

CRISPR diagnostic assays have gained significant interest in the last few years. This interest has grown rapidly during the current COVID-19 pandemic where CRISPR diagnostics have been frontline contenders for rapid testing solutions. This surge in CRISPR diagnostics research prompts the following question: What exactly are the achievable limits of detection and associated assay times enabled by the kinetics of Cas12 and Cas13 enzymes? To address this question, we here present a model based on Michaelis-Menten enzyme kinetics theory applied to Cas enzymes. We use the model to develop analytical solutions for reaction kinetics and develop back-of-the­ envelope criteria to validate and check for consistency in reported enzyme kinetics parameters. We applied our analyses to all studies known to us which report Michaelis-Menten-type kinetics data for CRISPR associated enzymes. These studies include all subtypes of Cas12 and Cas13 and orthologs. We found all studies but one clearly violate at least two of our three rules of consistency. We further use our model to explore ranges of reaction time scales and degree of reaction completion for practically relevant target concentrations applicable to CRISPR-diagnostic assays.
Chimpanzees use numerous flexible vocal sequences with more than two vocal units: A step towards language?
Authors: Girard-Buttoz Cédric , Zaccarella Emiliano , Bortolato Tatiana , Friederici Angela D. , Wittig Roman M. , Crockford Catherine
Published: February 2021

A major question in evolutionary science is how did language evolve? Syntax, as the core of language, combines meaning-bearing units (words) into hierarchical structures, thereby creating new meanings. Some other mammals and birds combine meaning-bearing vocalisations, but no documented examples exist of non-human animals combining more than two meaning-bearing vocalisations. Was the two-unit threshold only surpassed in the hominid lineage? Here, we examine the positional patterning of vocal sequences of chimpanzees. We analysed 4826 vocal utterances of 46 wild adult female and male chimpanzees. We found a flexible system with 390 multi-unit vocal sequences, some showing positional or transitional regularities. Two-unit pairs embedded in three-unit sequences predictably occurred either in head or tail positions, and co-occurred with specific other elements. The capacity to organise vocal output beyond the two-unit level may thus exist in species other than humans and could be viewed as an important evolutionary step towards language.
Mutational effects of ubiquitously present gamma radiation onArabidopsis thaliana: insight into radiosensitivity in the reproductive stage
Authors: Hirao Akira S. , Watanabe Yoshito , Hasegawa Yoichi , Takagi Toshihito , Ueno Saneyoshi , Kaneko Shingo
Published: February 2021

Earth has always been exposed to ionizing radiation from natural sources, and man-made sources have added to this radiation. In order to assess mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life-cycle ofArabidopsis thalianaunder controlled conditions. Resequencing data from 12 M1lines and 36 M2progeny derived under gamma-irradiation conditions ranging from 0.0 to 2.0 Gy/d were obtained to identifyde novomutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship betweende novomutation frequency and a low-to-middling dose of radiation was assessed by statistical modeling. The increasing ofde novomutations in response to doses of irradiation fit the negative binomial model, accounting for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, with deletions being more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation are more intensive during the reproductive stage. These outcomes could provide valuable insights into practical strategies for environmental radioprotection of plants on Earth and in space.
Structural variability and concerted motions of the T cell receptor – CD3 complex
Authors: Pandey Prithvi R. , Różycki Bartosz , Lipowsky Reinhard , Weikl Thomas R.
Published: February 2021

We investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) – CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined byDong et al.(2019). We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15° to 55°. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR – CD3 complex, in particular in the EC interactions of the Cβ FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR – CD3 complex revealed in our simulations provide atomistic insights for force-based models of TCR activation, which involve such structural changes in response to tilt-inducing forces on antigen-bound TCRs.