bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions
Authors: Kodikara Sineth G. , Gyawali Prabesh , Gleeson James , Jakli Antal , Sprunt Samuel , Balci Hamza
Published: January 2023

Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked, as well as in plane ordered duplexes exhibit distinct signatures when studied via small angle x-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single molecule studies, which might reflect the elevated DNA concentrations in our studies.
Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning
Authors: Masuda Kairi , Abdullah Adib A. , Sahakyan Aleksandr B.
Published: January 2023

With the development of advanced predictive modelling techniques, we are witnessing a steep increase in model development initiatives in genomics that employ high-end machine learning methodologies. Of particular interest are models that predict certain genomic or biological characteristics based solely on DNA sequence information. These models, however, treat the DNA sequence as a mere collection of four, A, T, G and C, letters, thus dismissing the past physico-chemical advancements in science that can enable the use of more intricate information about nucleic acid sequences. Here, we provide a comprehensive database of quantum mechanical and geometric features for all the permutations of 7-meric DNA in their representative B, A and Z conformations. The database is generated by employing the applicable high-cost and time-consuming quantum mechanical methodologies. This can thus make it seamless to associate a wealth of novel molecular features to any DNA sequence, by scanning it with a matching k-meric window and pulling the pre-computed values from our database for further use in modelling. We demonstrate the usefulness of our deposited features through their exclusive use in developing a model for A to C mutation rate constants.
Item-specific memory reactivation during sleep supports memory consolidation in humans
Authors: Liu Jing , Xia Tao , Chen Danni , Yao Ziqing , Zhu Minrui , Antony James W. , Lee Tatia M.C. , Hu Xiaoqing
Published: January 2023

Memory consolidation stabilizes newly acquired information. Understanding how individual memories are reactivated during sleep is essential in theorizing memory consolidation. Via unobtrusively re-playing auditory memory cues to sleeping human participants, we identified the reactivation of individual memories during slow-wave sleep (SWS). Using representational similarity analysis (RSA) on cue-elicited electroencephalogram (EEG), we found functionally segregated item-specific representations: the early post-cue EEG activity (0-2 seconds) contained comparable representations for memory cues and for non-memory control cues, thus reflecting sensory processing. Critically, the later EEG activity (2.5-3 s) showed greater item-specific representations for post-sleep remembered items than for forgotten and control cues, demonstrating the reactivation and consolidation of individual memories. Moreover, spindles preferentially supported item-specific memory reactivation for items that were not tested before sleep. These findings delineated how cue-triggered item-specific memory reactivation, subserved by spindles during SWS, contributed to memory consolidation. These results will benefit future research aiming to perturb specific memory episodes during sleep.
Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny
Authors: Černý David , Simonoff Ashley L.
Published: January 2023

The interrelationships of the three major dinosaur clades (Theropoda, Sauropodomorpha, and Ornithischia) have come under increased scrutiny following the recovery of conflicting phylogenies by a large new character matrix and its extensively modified revision. Here, we use tools derived from recent phylogenomic studies to investigate the strength and causes of this conflict. Using both the original and rescored dataset, we examine the global support for alternative hypotheses as well as the distribution of phylogenetic signal among individual characters. We find the three possible ways of resolving the relationships among the main dinosaur lineages (Saurischia, Ornithischiformes, and Ornithoscelida) to be statistically indistinguishable and supported by nearly equal numbers of characters in both matrices. While the changes made to the revised matrix increased the mean phylogenetic signal of individual characters, this amplified rather than reduced their conflict, resulting in greater sensitivity to character removal or coding changes and little overall improvement in the ability to discriminate between alternative topologies. We conclude that early dinosaur relationships are unlikely to be resolved without fundamental changes to both the quality of available datasets and the techniques used to analyze them.
Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention
Authors: Avelar-Barragan Julio , Mendez Luque Laura F. , Nguyen Jenny , Nguyen Hellen , Odegaard Andrew O. , Fleischman Angela G. , Whiteson Katrine L.
Published: January 2023

Myeloproliferative neoplasms (MPN) are a class of hematological malignancies which result in the overproduction of myeloid lineage cells. These malignancies result in increased cytokine production and inflammation, which correlate with worsened symptom burden and prognosis. Other than bone marrow transplantation, there is no cure for myeloproliferative neoplasms. As such, treatments focus on reducing thrombotic risk, inflammation, and symptom burden. Because current pharmacological treatments carry significant side-effects, there is a need to explore low-risk therapies. One alternative is the Mediterranean diet, which is rich in anti-inflammatory foods, reduces inflammatory biomarkers, and beneficially alters the gut microbiome. Here, we performed a 15-week clinical trial of 28 individuals with MPN who were randomized to dietary counseling based on either a Mediterranean diet or standard U.S. Guidelines for Americans. Our primary objective was to determine if MPN patients were able to adopt a Mediterranean eating style when supported with dietician counseling. As exploratory endpoints, we investigated the impact of diet and inflammation on the gut microbiome. Using shotgun metagenomic sequencing, we found that microbiome diversity and composition were stable throughout the study duration in both cohorts. Furthermore, we discovered significant differences in the microbiomes between MPN subtypes, such as increased beta-dispersion in subjects with myelofibrosis. Lastly, we found several significant correlations between the abundances of multiple bacterial taxa and cytokine levels. Together, this study provides insight into the interaction between diet, inflammation, and the gut microbiome.

Importance

The gut microbiome serves as an interface between the host and diet. Diet and the gut microbiome both play important roles in managing inflammation, which is a key aspect of MPN. Studies have shown that a Mediterranean diet can reduce inflammation. Therefore, we longitudinally characterized the gut microbiomes of MPN patients in response to Mediterranean or US-style dietary counseling to determine whether there were microbiome-associated changes in inflammation. We did not find significant changes in the gut microbiome associated with diet, but we did find several associations with inflammation. This research paves the way for future studies by identifying potential mechanistic targets implicated in inflammation within the MPN gut microbiome.
Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization
Authors: Ojala Fanni , Abdul Sater Mohamad R. , Miller Loren G. , McKinnell James A. , Huang Susan S. , Grad Yonatan H. , Marttinen Pekka
Published: January 2023

Methicillin-resistantStaphylococcus aureus(MRSA) is a major cause of morbidity and mortality and one of the most serious infectious disease threats. Colonization by MRSA increases the risk of infection and transmission, underscoring the importance of decolonization efforts. However, success of these decolonization protocols varies, raising the possibility that some MRSA strains may be more persistent than others. Here, we studied how the persistence of MRSA colonization correlates with genomic presence of antibiotic resistance genes. Our analysis using a Bayesian mixed effects survival model found that high-level resistance to mupirocin was strongly associated with failure of the decolonization protocol. However, we did not see a similar effect with resistance to chlorhexidine or other antibiotics. Including strain-specific random effects improved the predictive performance, indicating that some strain characteristics other than resistance also contributed to persistence. Study subject-specific random effects did not improve the model. Our results highlight the need to consider the properties of the colonizing MRSA strain when deciding which treatments to include in the decolonization protocol.

Author summary

Methicillin-resistantStaphylococcus aureus(MRSA) is responsible for a high burden of morbidity and mortality. MRSA colonization incurs risk of MRSA infection and transmission, highlighting the need for highly effective decolonization protocols. However, decolonization protocols have had mixed success. The extent to which this mixed success is attributable to MRSA strain variations and their resistance to antibiotics, including those like mupirocin that are commonly used for decolonization, versus study subject factors, has been unclear. Here, we characterized the effect of antibiotic resistance genes on the efficiency of an MRSA decolonization protocol. We found that mupirocin resistance and strain-specific effects were associated with reduced effectiveness of an MRSA decolonization protocol, but that resistance to other antibiotics, including purported chlorhexidine resistance genes, and subject-specific effects had no discernible impact on protocol success. Our results highlight the need to consider the properties of the colonizing MRSA strain when deciding which treatments to include in the decolonization protocol.
Prevalence of BovineCysticercosis, Human Taeniasis and Asociated Risk Factors in Selected Towns of Silte Zone, Southern Ethiopia
Authors: mussa Solomon musema
Published: January 2023

Bovine cysticercosis is an infection of cattle caused by the larval stage of Cysticercus Bovis, the human intestinal cestodes and it has economic important and public health importance. Across-sectional study was conducted from March 2022 to August 2022 to determine the prevalence of Bovine Cysticercosis, Human Taeniasis and associated risk factors in selected towns of Silte zone. The study was conducted in Silte zone municipal abbatoir, Southern Ethiopia in cattle slaughtered randomly selected towns,namely, at Kilto,Kutery,Kirate and Werabe Tawon municipal abattoirs. Systematic random sampling technique was used to collect all the necessary data from abattoir survey of the study animals and questionnaire survey collected data stored by using in Epi data software and analyzed using (SPSS-22) software program. The sample size required for this study was determined to be based on the expected prevalence (50%) of C. bovis and the 5% desired absolute precision and 95% CI. Out of 422 carcasses examined during the study period in 4 municipality abattoirs, 36 % were infected with C.bovis. A prevalence of 35.7%, 35.92%, 37.96% and 34.11% were Kilto,Kutery,Kirate and Werabe Tawon were observed, respectively. Among considered risk factors, sex, body condition and breed showed statistically significant difference in prevalence of C. bovis in study area. Regarding the anatomical distribution of the cysts, shoulder muscle showed highest prevalence 28.44%, was followed by tongue 20.79% tricepsbrachi muscle 18.35%, masseter muscle 17.74%, heart 12.84%, and Liver 1.8%,. Out of 110 respondents, 64.5% had contracted T.saginata. Among considered risk factors, sex, age, occupation, education status, raw meat consumption and knowledge about the disease showed statistically significant difference in prevalence of T.saginata in study area. The findings of this study indicated that importance of Bovine Cysticercosis and Taeniasis in the study area. Therefore, attention should be given to the public awareness, detailed meat inspection to be safe to public health, consumption of well-cooked cattle meat should be implemented for breaking the cycle of the diseases and promote meat industry in the country.
Aspergillus fumigatustranscription factor ZfpA regulates hyphal development and alters susceptibility to antifungals and neutrophil killing during infection
Authors: Schoen Taylor J. , Calise Dante G. , Bok Jin Woo , Nwagwu Chibueze D. , Zarnowski Robert , Andes David , Huttenlocher Anna , Keller Nancy P.
Published: January 2023

Hyphal growth is essential for host colonization duringAspergillusinfection. The transcription factor ZfpA regulatesA. fumigatushyphal development including branching, septation, and cell wall composition. However, how ZfpA affects fungal growth and susceptibility to host immunity during infection has not been investigated. Here, we use the larval zebrafish-Aspergillusinfection model and primary human neutrophils to probe how ZfpA affectsA. fumigatuspathogenesis and response to antifungal drugsin vivo. ZfpA deletion promotes fungal clearance and attenuates virulence in wild-type hosts and this virulence defect is abrogated in neutrophil-deficient zebrafish. ZfpA deletion also increases susceptibility to human neutrophilsex vivowhile overexpression impairs fungal killing. Overexpression of ZfpA confers protection against the antifungal caspofungin by increasing chitin synthesis during hyphal development, while ZfpA deletion reduces cell wall chitin and increases caspofungin susceptibility in neutrophil-deficient zebrafish. These findings suggest a protective role for ZfpA activity in resistance to the innate immune response and antifungal treatment duringA. fumigatusinfection.

Author Summary

Aspergillus fumigatusis a common environmental fungus that can infect immunocompromised people and cause a life-threatening disease called invasive aspergillosis. An important step during infection is the development ofA. fumigatusfilaments known as hyphae.A. fumigatususes hyphae to acquire nutrients and invade host tissues, leading to tissue damage and disseminated infection. In this study we report that a regulator of gene transcription inA. fumigatuscalled ZfpA is important for hyphal growth during infection. We find that ZfpA activity protects the fungus from being killed by innate immune cells and decreases the efficacy of antifungal drugs during infection by regulating construction of the cell wall, an important protective layer for fungal pathogens. Our study introduces ZfpA as an important genetic regulator of stress tolerance during infection that protectsA. fumigatusfrom the host immune response and antifungal drugs.
The infectious salmon anaemia virus esterase prunes erythrocyte surfaces in infected Atlantic salmon and exposes terminal sialic acids to lectin recognition
Authors: Fosse Johanna Hol , Andresen Adriana Magalhaes Santos , Ploss Frieda Betty , Weli Simon Chioma , Heffernan Inger , Sapotka Subash , Lundgård Krister , Kuiper Raoul Valentin , Solhaug Anita , Falk Knut
Published: January 2023

Many sialic acid-binding viruses express a receptor-destroying enzyme (RDE) that removes the virus-targeted receptor and limits viral interactions with the host cell surface. Despite a growing appreciation of how the viral RDE promotes viral fitness, little is known about its direct effects on the host. Infectious salmon anaemia virus (ISAV) attaches to 4-O-acetylated sialic acids on the surface of Atlantic salmon epithelial, endothelial, and red blood cells. ISAV receptor binding and destruction are effectuated by the same surface molecule, the haemagglutinin esterase (HE). We recently discovered a global loss of vascular 4-O-acetylated sialic acids in ISAV-infected fish. The loss correlated with the expression of viral proteins, giving rise to the hypothesis that it was mediated by the HE.

Here, we report that the capacity to bind new ISAV particles is also progressively lost from circulating erythrocytes in infected fish. Furthermore, salmon erythrocytes exposed to ISAVex vivolost their capacity to bind new ISAV particles. The loss of ISAV binding was not associated with receptor saturation. Moreover, upon loss of the ISAV receptor, erythrocyte surfaces became more available to the lectin wheat germ agglutinin, suggesting a potential to alter interactions with endogenous lectins of similar specificity. The pruning of erythrocyte surfaces was inhibited by an antibody that prevented ISAV attachment. Furthermore, recombinant HE, but not an esterase-silenced mutant, was sufficient to induce the observed surface modulation. Our results directly link the ISAV-induced erythrocyte modulation to the hydrolytic activity of the HE and show that the observed effects are not mediated by endogenous esterases.

Our findings are the first to directly link a viral esterase to extensive host cell surface modulation in infected individuals. This raises the question of how common the phenomenon is among sialic acid-binding viruses. It is also relevant to ask if the altered sialic acid landscape of the affected cells influences host biological functions with relevance to viral disease.
Summary tests of introgression are highly sensitive to rate variation across lineages
Authors: Frankel Lauren E. , Ané Cécile
Published: January 2023

Abstract

The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods are based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly broken in many groups. In this work, we quantify the effects of rate variation on theD-statistic (also known as ABBA-BABA test), theD3statistic, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and rate variation across gene-tree edges. We simulated species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies. For all three methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. TheD3statistic was the most sensitive, with around 80% type-1 error, such thatD3appears to more sensitive to a departure from the clock than to the presence of reticulation. For all three tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can “hide” one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics, and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.
Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma
Authors: Gier Rodrigo A. , Hueros Raúl A. Reyes , Rong Jiazhen , DeMarshall Maureen , Karakasheva Tatiana A. , Muir Amanda B. , Falk Gary W. , Zhang Nancy R. , Shaffer Sydney M.
Published: January 2023

Barrett’s esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett’s esophagus have not been resolved in humans. To address this, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis revealed discrete lineages in Barrett’s esophagus, normal esophagus, and gastric cardia. Transitional basal progenitor cells of the gastroesophageal junction were unexpectedly related to both esophagus and gastric cardia cells. Barrett’s esophagus was polyclonal, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic foci were initiated by the expansion of a single molecularly aberrant Barrett’s esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett’s esophagus, linking cell states along the full disease trajectory, from its origin to cancer.
The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense
Authors: Leibel Sandra L. , McVicar Rachael N. , Murad Rabi , Kwong Elizabeth M. , Clark Alex E. , Alvarado Asuka , Grimmig Bethany A. , Nuryyev Ruslan , Young Randee E. , Lee Jamie Casey , Peng Weiqi , Zhu Yanfang Peipei , Griffis Eric , Nowell Cameron J. , Liu Kang , James Brian , Alarcon Suzie , Malhotra Atul , Gearing Linden J. , Hertzog Paul J. , Galapate Cheska Marie , Galenkamp Koen M.O. , Commisso Cosimo , Smith Davey M. , Sun Xin , Carlin Aaron F. , Croker Ben A. , Snyder Evan Y.
Published: January 2023

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.
Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex
Authors: Wan Mandy S.M. , Muhammad Reyhan , Koliopoulos Marios G. , Roumeliotis Theodoros I. , Choudhary Jyoti S. , Alfieri Claudio
Published: January 2023

Histone deacetylase complexes remove histone lysine acetylation, a key post-translational modification that activates transcription at each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the first structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.
Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion
Authors: Xiang Limin , Yan Rui , Chen Kun , Li Wan , Xu Ke
Published: January 2023

Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficientsDin both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
Excitation energy transfer between higher excited states of photosynthetic pigments: 1. Carotenoids facilitate B → Q band conversion in chlorophylls
Authors: Götze Jan P. , Lokstein Heiko
Published: January 2023

Chlorophylls (Chls) are known for fast, sub-picosecond internal conversion (IC) from ultraviolet/blue absorbing (“B” or “Soret” states) to the energetically lower, red light-absorbing Q states. Consequently, excitation energy transfer (EET) in photosynthetic pigment-protein complexes involving the B states has so far not been considered. We present, for the first time, a theoretical framework for the existence of B-B EET in tightly coupled Chl aggregates, such as photosynthetic pigment-protein complexes. We show that according to a simple Förster resonance energy transport (FRET) scheme, unmodulated B-B EET likely poses an existential threat, in particular the photochemical reaction centers (RCs). This insight leads to so-far undescribed roles for carotenoids (Crts, this article) and Chlb(next article in this series) of possibly primary importance.

Here we show that B → Q IC is assisted by the symmetry-allowed Crt state (S2) by using the plant antenna complex CP29 as a model: The sequence is B → S2(Crt, unrelaxed) →S2(Crt, relaxed) → Q. This sequence has the advantage of preventing ~ 39% of Chl-Chl B-B EET, since the Crt S2state is a highly efficient FRET acceptor. The likelihood of CP29 to forward potentially harmful B excitations towards the photosynthetic reaction center (RC) is thus reduced. In contrast to the B band of Chls, most Crt energy donation is energetically located near the Q band, which allows for 74/80% backdonation (from lutein/violaxanthin) to Chls. Neoxanthin, on the other hand, likely donates in the B band region of Chlb, with 76% efficiency. The latter is discussed in more detail in the next article in this series. Crts thus do not only act in their currently proposed photoprotective roles, but also as a crucial building block for any system that could otherwise deliver harmful “blue” excitations to the RCs.
Midi-metagenomics: A novel approach for cultivation independent microbial genome reconstruction from environmental samples
Authors: Vollmers John , Correa Cassal Maximiano , Kaster Anne-Kristin
Published: January 2023

Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions, that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions of sufficient size, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, co-assemblies become highly optimized for co- abundance variation based binning approaches. 'Midi-metagenomics' enables accurate metagenome assembled genome (MAG) reconstruction from individual sorted samples with higher quality than co-assembly of multiple distinct samples and has potential for the targeted enrichment and sequencing of microbial dark matter
Mapping a brain parasite: occurrence and spatial distribution in fish encephalon
Authors: Born-Torrijos Ana , Beest Gabrielle S. van , Merella Paolo , Garippa Giovanni , Raga Juan Antonio , Montero Francisco E.
Published: January 2023

Parasites, especially brain-encysting trematodes, can have an impact on host behaviour, facilitating the transmission to next host and completion of the life cycle, but insufficient research has been done on whether specific brain regions are targeted. Using the laboratory modelCardiocephaloides longicollis, the precise distribution of metacercariae in experimentally-infected, wild and farmed fish was mapped. The brain regions targeted by this parasite were explored, also from a histologic perspective, and potential pathologic effects were evaluated. Experimental infections allowed to reproduce the natural infection intensity ofC. longicollis, with four times higher infection intensity at the higher dose (150vs50 cercariae). The observed metacercarial distribution, similar among all fish groups, may reflect a species-specific pattern. Metacercariae occur with highest density in the optic lobe area (primarily infect the periventricular gray zone of optic tectum) and the medulla oblongata, whereas other areas such as the olfactory lobes and cerebellar lobes may be occupied when the more frequently invaded parts of the brain were crowded. Mono- and multicysts (i.e. formed either with a single metacercaria, or with 2 ̶ 25 metacercariae encapsulated together) may be formed depending on the aggregation and timing of metacercariae arrival, with minor host inflammatory response. Larvae ofC. longicolliscolonizing specific brain areas may have an effect on the functions associated with these areas, which are generally related to sensory and motor functions, but are also related to other host fitness traits such as school maintenance or recognition of predators. The detailed information on the extent and distribution ofC. longicollisin fish encephalon sets the ground to understand the effects of brain parasites on fish, but further investigation to establish ifC. longicollis, through purely mechanical damage (e.g., occupation, pressure and displacement), has an actual impact on host behaviour remains to be tested under controlled experimental conditions.
The respiratory syncytial virus surge in Austria, 2022, was caused by lineages present before the COVID-19 pandemic
Authors: Redlberger-Fritz Monika , Springer David N. , Aberle Stephan W. , Camp Jeremy V. , Aberle Judith H.
Published: January 2023

In 2022, Austria experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Nationwide multiyear genomic surveillance revealed that the surge was driven by RSV-B, however genotypes consisted of multiple lineages that were circulating prior to the pandemic.
First virological and pathological study of Göttingen Minipigs with Dippity Pig Syndrome (DPS)
Authors: Jhelum Hina , Grand Nanna , Jacobsen Kirsten Rosenmay , Halecker Sabrina , Salerno Michelle , Prate Robert , Krüger Luise , Kristiansen Yannik , Krabben Ludwig , Möller Lars , Laue Michael , Kaufer Benedikt , Kaaber Kari , Denner Joachim
Published: January 2023

Dippity Pig Syndrome (DPS) is a well-known but rare complex of clinical signs affecting minipigs, which has not been thoroughly investigated yet. Clinically affected animals show acute appearance of red, exudating lesions across the spine. The lesions are painful, evidenced by arching of the back (dipping), and the onset of clinical symptoms is generally sudden. In order to understand the pathogenesis, histological and virological investigations were performed in affected and unaffected Göttingen Minipigs (GöMPs). The following DNA viruses were screened for using PCR-based methods: Porcine cytomegalovirus (PCMV), which is a porcine roseolovirus (PCMV/PRV), porcine lymphotropic herpesviruses (PLHV-1, PLHV-2, PLHV-3), porcine circoviruses (PCV1, PCV2, PCV3, PCV4), porcine parvovirus 1 (PPV1), and Torque Teno sus virus (TTSuV1, TTSuV2). Screening was also performed for integrated porcine endogenous retroviruses (PERV-A, PERV-B, PERV-C) and recombinant PERV-A/C and their expression as well as for the RNA viruses hepatitis E virus (HEV) and SARS-CoV-2. Eight clinically affected and one unaffected GöMPs were analyzed. Additional unaffected minipigs had been analyzed in the past. The analyzed GöMPs contained PERV-A and PERV-B integrated in the genome, which are present in all pigs and PERV-C, which is present in most, but not all pigs. In one affected GöMPs recombinant PERV-A/C was detected in blood. In this animal a very high expression of PERV mRNA was observed. PCMV/PRV was found in three affected animals, PCV1 was found in three animals with DPS and in the healthy minipig, and PCV3 was detected in two animals with DPS and in the unaffected minipig. Most importantly, in one animal only PLHV-3 was detected. It was found in the affected and unaffected skin, and in other organs. Unfortunately, PLHV-3 could not be studied in all other affected minipigs. None of the other viruses were detected and using electron microscopy, no virus particles were found in the affected skin. This data identified some virus infections in GöMPs with DPS and assign a special role to PLHV-3. Since PCMV/PRV, PCV1, PCV3 and PLHV-3 were also found in unaffected animals, a multifactorial cause of DPS is suggested. However, elimination of the viruses from GöMPs may prevent DPS.
Contribution of circulating host and microbial tryptophan metabolites towards Ah receptor activation
Authors: Morgan Ethan W. , Dong Fangcong , Annalora Andrew , Murray Iain A. , Wolfe Trenton , Erickson Reece , Gowda Krishne , Amin Shantu G. , Petersen Kristina S. , Kris-Etherton Penny M. , Marcus Craig , Walk Seth T. , Patterson Andrew D. , Perdew Gary H.
Published: January 2023

The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that plays an integral role in homeostatic maintenance by regulating cellular functions such as cellular differentiation, metabolism, barrier function, and immune response. An important but poorly understood class of AHR activators are compounds derived from host and bacterial metabolism of tryptophan. The commensal bacteria of the gut microbiome are major producers of tryptophan metabolites known to activate the AHR, while the host also produces AHR activators through tryptophan metabolism. We used targeted mass spectrometry-based metabolite profiling to determine the presence and metabolic source of these metabolites in the sera of conventional mice, germ-free mice, and humans. Surprisingly, sera concentrations of many tryptophan metabolites are comparable between germ-free and conventional mice. Therefore, many major AHR-activating tryptophan metabolites in mouse sera are produced by the host, despite their presence in feces and mouse cecal contents. AHR activation is rarely studied in the context of a mixture at relevant concentrations, as we present here. The AHR activation potentials of individual and pooled metabolites were explored using cell-based assays, while ligand binding competition assays and ligand docking simulations were used to assess the detected metabolites as AHR agonists. The physiological and biomedical relevance of the identified metabolites was investigated in the context of cell-based models for cancer and rheumatoid arthritis. We present data here that reframe AHR biology to include the presence of ubiquitous tryptophan metabolites, improving our understanding of homeostatic AHR activity and models of AHR-linked diseases.
Evolution of affinity between p53 and MDM2 across the animal kingdom demonstrates high plasticity of motif-mediated interactions
Authors: Mihalic Filip , Åberg Emma , Farkhondehkish Pouria , Theys Niels , Andersson Eva , Jemth Per
Published: January 2023

The interaction between the transcription factor p53 and the ubiquitin ligase MDM2 results in degradation of p53 and is well studied in cancer biology and drug development. Available sequence data suggest that both p53 and MDM2-family proteins are present across the animal kingdom. However, the interacting regions are missing in some animal groups, and it is not clear whether MDM2 interacts with, and regulates p53 in all species. We used phylogenetic analyses and biophysical measurements to examine the evolution of affinity between the interacting protein regions: a conserved 12-residue intrinsically disordered binding motif in the p53 transactivation domain (TAD) and the folded SWIB domain of MDM2. The affinity varied significantly across the animal kingdom. The p53TAD/MDM2 interaction among jawed vertebrates displayed high affinity, in particular for chicken and human proteins (KDaround 0.1 μM). The affinity of the bay mussel p53TAD/MDM2 complex was lower (KD= 15 μM) and those from a placozoan, an arthropod and a jawless vertebrate were very low or non-detectable (KD> 100 μM). Binding experiments with reconstructed ancestral p53TAD/MDM2 variants suggested that a micromolar affinity interaction was present in the ancestral bilaterian animal and was later enhanced in tetrapods while lost in other linages. The different evolutionary trajectories of p53TAD/MDM2 affinity during speciation demonstrate high plasticity of motif-mediated interactions and the potential for rapid adaptation of p53 regulation during times of change. Neutral drift in unconstrained disordered regions may underlie the plasticity and explain the observed low sequence conservation in transactivation domains such as p53TAD.

Statement for broader audience

The protein p53 regulates central cellular processes including cell division and programmed cell death. p53 is regulated by another protein, MDM2, which binds to p53 and marks it for destruction. We measured the interaction between present-day and reconstructed ancient p53 and MDM2 proteins and found a range of binding strengths. Our findings suggest that rapid evolution of the p53/MDM2 interaction facilitates adaptation of p53 regulation during speciation.
Contrasting drivers of abundant phage and prokaryotic communities in tropical, coastal ecosystems across the Isthmus of Panama
Authors: Weinheimer Alaina R. , Aylward Frank O. , Leray Matthieu , Scott Jarrod J.
Published: January 2023

Phages, or viruses that infect bacteria and archaea, are ubiquitous and abundant members of Earth’s ecosystems that impact the flow of nutrients, evolution of microbes, and food web dynamics by selectively infecting and killing their prokaryotic hosts. Because phages can only replicate through their hosts, they are inherently linked to processes impacting their hosts’ distribution and susceptibility to infection. Despite these links, phages can also be affected by environmental parameters independent of their hosts, such as pH or salinity which impact cell adsorption or virion degradation. To understand these complex links, in this study, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (TEP) and Tropical Western Atlantic (TWA) provinces and compare factors that shape active marine phage and prokaryotic communities. Metagenomic sequencing of seawater from mangroves and reefs of both the TEP and TWA coasts of Panama suggest that pronounced environmental gradients, such as along the TEP mangrove rivers, result in common dispersal and physicochemical parameters shaping both prokaryotic and phage community composition and diversity. Conversely, we find that when environmental conditions are relatively similar across adjacent habitats, such as between the mangroves and reefs in the TWA, prokaryotic communities are more influenced by local abiotic conditions while phage communities are shaped more by dispersal. Collectively, this work provides a framework for addressing the co-variability between viruses and their hosts in marine systems and for identifying the different factors that drive consistent versus disparate trends in community shifts, which is essential to inform models of these interactions in biogeochemical cycling.
Intonation Units in spontaneous speech evoke a neural response
Authors: Inbar Maya , Genzer Shir , Perry Anat , Grossman Eitan , Landau Ayelet N.
Published: January 2023

Spontaneous speech is produced in chunks called Intonation Units (IUs). IUs are defined by a set of prosodic cues and occur in all human languages. Linguistic theory suggests that IUs pace the flow of information and serve as a window onto the dynamic focus of attention in speech processing. IUs provide a promising and hitherto unexplored theoretical framework for studying the neural mechanisms of communication, thanks to their universality and their consistent temporal structure across different grammatical and socio-cultural conditions. In this article, we identify a neural response unique to the boundary defined by the IU. We measured the EEG of participants who listened to different speakers recounting an emotional life event. We analyzed the speech stimuli linguistically, and modeled the EEG response at word offset using a GLM approach. We find that the EEG response to IU-final words differs from the response to IU-nonfinal words when acoustic boundary strength is held constant. To the best of our knowledge, this is the first time this is demonstrated in spontaneous speech under naturalistic listening conditions, and under a theoretical framework that connects the prosodic chunking of speech, on the one hand, with the flow of information during communication, on the other. Finally, we relate our findings to the body of research on rhythmic brain mechanism in speech processing by comparing the topographical distributions of neural speech tracking in model-predicted and empirical EEG. This qualitative comparison suggests that IU-related neural activity contributes to the previously characterized delta-band neural speech tracking.
Helminth-derived metabolites induce tolerogenic functional, metabolic, and transcriptional signatures in dendritic cells that attenuate experimental colitis
Authors: Malacco Nathalia L. , Michi Aubrey N. , Siciliani Elizabeth , Madrigal Ana G. , Sternlieb Tamara , Fontes Ghislaine , King Irah L. , Cestari Igor , Jardim Armando , Stevenson Mary M. , Lopes Fernando
Published: January 2023

Inflammatory bowel diseases (IBD) are chronic inflammatory diseases in which abdominal pain, bloody diarrhea, weight loss, and fatigue collectively result in diminished quality of patient life. The disappearance of intestinal helminth infections in Western societies is associated with an increased prevalence of IBD and other immune-mediated inflammatory diseases. Evidence indicates that helminths induce tolerogenic dendritic cells (tolDCs), which promote intestinal tolerance and attenuate intestinal inflammation characteristic of IBD, but the exact mechanism is unclear. Helminth-derived excretory-secretory (HES) products including macromolecules, proteins, and polysaccharides have been shown to modulate the antigen presenting function of DCs with down-stream effects on effector CD4+T cells. Previous studies indicate that DCs in helminth-infected animals induce tolerance to unrelated antigens and DCs exposed to HES display phenotypic and functional features of tolDCs. Here, we identify that nonpolar metabolites (HnpM) produced by a helminth, the murine gastrointestinal nematodeHeligmosomoides polygyrus bakeri(Hpb), induce tolDCs as evidenced by decreased LPS-induced TNF and increased IL-10 secretion and reduced expression of MHC-II, CD86, and CD40. Furthermore, these DCs inhibited OVA-specific CD4+T cell proliferation and induced CD4+Foxp3+regulatory T cells. Adoptive transfer of HnpM-induced tolDCs attenuated DSS-induced intestinal inflammation characteristic of IBD. Mechanistically, HnpM induced metabolic and transcriptional signatures in BMDCs consistent with tolDCs. Collectively, our findings provide groundwork for further investigation into novel mechanisms regulating DC tolerance and the role of helminth secreted metabolites in attenuating intestinal inflammation associated with IBD.

Summary Sentence:Metabolites produced byHeligmosomoides polygyrusinduce metabolic and transcriptional changes in DCs consistent with tolDCs, and adoptive transfer of these DCs attenuated DSS-induced intestinal inflammation.
miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner
Authors: Jara Cledi A. Cerda , Kim Seung Joon , Thomas Gwendolin , Farsi Zohreh , Zolotarov Grygoriy , Georgii Elisabeth , Woehler Andrew , Piwecka Monika , Rajewsky Nikolaus
Published: January 2023

The circular RNA (circRNA) Cdr1as is conserved across mammals and highly expressed in neurons, where it directly interacts with microRNA miR-7. However, the biological function of this interaction is unknown. Here, using primary forebrain murine neurons, we demonstrate that stimulating neurons by sustained depolarization rapidly induced two-fold transcriptional up-regulation of Cdr1as and strong post-transcriptional stabilization of miR-7. Cdr1as loss caused doubling of glutamate release from stimulated synapses and increased frequency and duration of local neuronal bursts. Moreover, periodicity of neuronal networks was increased and synchronicity was impaired. Strikingly, these effects were reverted by sustained expression of miR-7 which also cleared Cdr1as molecules from neuronal projections. Consistently, without Cdr1as, transcriptomic changes caused by miR-7 overexpression were stronger (including miR-7-targets down-regulation) and enriched in secretion/synaptic plasticity pathways. Altogether, our results suggest that in forebrain neurons Cdr1as buffers miR-7 activity to control glutamatergic excitatory transmission and neuronal connectivity important for long-lasting synaptic adaptations.