bluuebunny/crossref_metadata_2025 huggingface dataset:
Niche construction through a Goldilocks principle maximizes fitness for a nest-sharing brood parasite
Authors: Antonson Nicholas D. , Schelsky Wendy M. , Tolman Deryk , Kilner Rebecca M. , Hauber Mark E.
Published: September 2022

Generalist brood parasites that share nests with host nestlings can optimize resource acquisition from host parents by balancing the benefits that host nest-mates provide, including attracting increased provisions to the nest, against the costs of competing with the same host young over foster parental resources. However, it is unclear how parasitic chicks cope when faced with more nest-mates than are optimal for their survival upon hatching. We suggest that, in the obligate brood parasitic brown-headed cowbird (
Molothrus ater
), chicks use a niche construction strategy and reduce larger, more competitive host broods to maximize the parasites' survival to fledging. We experimentally altered brood sizes to test for Goldilocks principle patterns (i.e. a ‘just right’ intermediate brood size) of cowbird survival in nests of prothonotary warbler (
Protonotaria citrea
) hosts. We found that intermediate brood sizes of two host nestlings maximized cowbird fledging success relative to 0 or 4 host nest-mates at hatching. Specifically, cowbird nestlings lowered host brood sizes towards this optimum when placed in broods with more host nestlings. The results suggest that cowbirds reduce, but do not eliminate, host broods as a niche construction mechanism to improve their own probability of survival.
Quantifying services and disservices provided by insects and vertebrates in cacao agroforestry landscapes
Authors: Vansynghel Justine , Ocampo-Ariza Carolina , Maas Bea , Martin Emily A. , Thomas Evert , Hanf-Dressler Tara , Schumacher Nils-Christian , Ulloque-Samatelo Carlos , Yovera Fredy F. , Tscharntke Teja , Steffan-Dewenter Ingolf
Published: September 2022

Animals provide services such as pollination and pest control in cacao agroforestry systems, but also disservices. Yet, their combined contributions to crop yield and fruit loss are mostly unclear. In a full-factorial field experiment in northwestern Peru, we excluded flying insects, ants, birds and bats from cacao trees and assessed several productivity indicators. We quantified the contribution of each group to fruit set, fruit loss and marketable yield and evaluated how forest distance and canopy closure affected productivity. Fruit set dropped (from 1.7% to 0.3%) when flying insects were excluded and tripled at intermediate (40%) compared to high (greater than 80%) canopy cover in the non-exclusion treatment. Fruit set also dropped with bird and bat exclusion, potentially due to increased abundances of arthropods preying on pollinators or flower herbivores. Overall, cacao yields more than doubled when birds and bats had access to trees. Ants were generally associated with fruit loss, but also with yield increases in agroforests close to forest. We also evidenced disservices generated by squirrels, leading to significant fruit losses. Our findings show that several functional groups contribute to high cacao yield, while trade-offs between services and disservices need to be integrated in local and landscape-scale sustainable cacao agroforestry management.
Mechanisms underlying interaction frequencies and robustness in a novel seed dispersal network: lessons for restoration
Authors: Vizentin-Bugoni Jeferson , Sperry Jinelle H. , Kelley J. Patrick , Foster Jeffrey T. , Drake Donald R. , Case Samuel B. , Gleditsch Jason M. , Hruska Amy M. , Wilcox Rebecca C. , Tarwater Corey E.
Published: September 2022

As human-caused extinctions and invasions accumulate across the planet, understanding the processes governing ecological functions mediated by species interactions, and anticipating the effect of species loss on such functions become increasingly urgent. In seed dispersal networks, the mechanisms that influence interaction frequencies may also influence the capacity of a species to switch to alternative partners (rewiring), influencing network robustness. Studying seed dispersal interactions in novel ecosystems on O‘ahu island, Hawai‘i, we test whether the same mechanisms defining interaction frequencies can regulate rewiring and increase network robustness to simulated species extinctions. We found that spatial and temporal overlaps were the primary mechanisms underlying interaction frequencies, and the loss of the more connected species affected networks to a greater extent. Further, rewiring increased network robustness, and morphological matching and spatial and temporal overlaps between partners were more influential on network robustness than species abundances. We argue that to achieve self-sustaining ecosystems, restoration initiatives can consider optimal morphological matching and spatial and temporal overlaps between consumers and resources to maximize chances of native plant dispersal. Specifically, restoration initiatives may benefit from replacing invasive species with native species possessing characteristics that promote frequent interactions and increase the probability of rewiring (such as long fruiting periods, small seeds and broad distributions).
Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle
Authors: Yuan Jianbo , Zhang Xiaojun , Li Shihao , Liu Chengzhang , Yu Yang , Zhang Xiaoxi , Xiang Jianhai , Li Fuhua
Published: September 2022

The calcareous shell and sessile lifestyle are the representative phenotypes of many molluscs, which happen to be present in barnacles, a group of unique crustaceans. The origin of these phenotypes is unclear, but it may be embodied in the convergent genetics of such distant groups (interphylum). Herein, we perform comprehensive comparative genomics analysis in barnacles and molluscs, and reveal a genome-wide strong convergent molecular evolution between them, including coexpansion of biomineralization and organic matrix genes for shell formation, and origination of lineage-specific orphan genes for settlement. Notably, the expanded biomineralization gene encoding alkaline phosphatase evolves a novel, highly conserved motif that may trigger the origin of barnacle shell formation. Unlike molluscs, barnacles adopt novel organic matrices and cement proteins for shell formation and settlement, respectively, and their calcareous shells have potentially originated from the cuticle system of crustaceans. Therefore, our study corroborates the idea that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs. In addition, notable non-convergence signatures are also present and may contribute to morphological and functional specificities.
Tonic and phasic effects of reward on the pupil: implications for locus coeruleus function
Authors: Cole Laura , Lightman Stafford , Clark Rosie , Gilchrist Iain D.
Published: September 2022

The locus coeruleus (LC), a nucleus in the pons of the brainstem, plays a significant role in attention and cognitive control. Here, we use an adapted auditory oddball paradigm and measured the pupil dilation response, to provide a marker of LC activity in humans. In Experiment 1, we show event-related pupil responses to rare auditory events which were further elevated by task relevant. In Experiment 2, by asking participants to silently count the number of oddballs, we demonstrated that the task-relevance elevation was not a result of the generation or execution of the manual response. In Experiment 3, we observed two separate effects of reward on the pupil response. First, we found an overall increase in pupil area in the high compared to the low-reward blocks: a sustained effect reminiscent of the tonic changes that occur in LC. Second, we found elevated event-related pupil responses to behaviourally relevant stimuli in the high-reward condition compared with the low-reward condition, consistent with phasic changes in LC in response to a stimulus. These results highlight the complexity of the relationship between the pupil response and reward, and the inferred role of LC in both top-down and bottom-up cognitive control.
Characterization of Shigella flexneri in Northern Vietnam in 2012–2016
Authors: Nguyen Dong Tu , Morita Masatomo , Ngo Tuan Cuong , Le Thanh Huong , Le Dang Hai , Nguyen Hoai Thu , Akeda Yukihiro , Ohnishi Makoto , Izumiya Hidemasa
Published: September 2022

Introduction: Shigellosis remains a considerable public health concern in developing countries. Shigella flexneri and Shigella sonnei are prevalent worldwide and S. sonnei has been replacing S. flexneri .
Gap Statement: S. flexneri still causes outbreaks in Northern Vietnam and limited information is available on its genetic characteristics.
Aim: This study aimed to characterize the genetic characteristics of S. flexneri strains from Northern Vietnam.
Methodology: This study used 17 isolates from eight incidents, collected in Northern Vietnam between 2012 and 2016. The samples were subjected to whole genome sequencing (WGS), molecular serotyping, cluster analysis, and identification of antimicrobial resistance genes. Additionally, phylogenetic analysis was performed including isolates from previous studies.
Results: Clusters were identified according to spatiotemporal backgrounds. The results suggested that two incidents in Yen Bai province in 2015 and 2016 were attributable to a single source. All isolates belonged to phylogroup (PG) 3, which was divided into two sub-lineages. Thirteen of 17 isolates, including those from the Yen Bai incidents, belonged to sub-lineage Sub-1 and were serotyped as 1a. The remaining four isolates belonged to sub-lineage Sub-2 and were the globally predominant serotype 2a. The Sub-1 S. flexneri isolates possessed the gtrI gene, which encodes the glycosyl transferase that determines serotype 1a, with bacteriophage elements in the vicinity.
Conclusion: This study revealed two PG3 sub-lineages of S. flexneri in Northern Vietnam, of which Sub-1 might be specific to the region.
Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation
Authors: Bray James E. , Correia Annapaula , Varga Margaret , Jolley Keith A. , Maiden Martin C. J. , Rodrigues Charlene M. C.
Published: September 2022

Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genomes stored in online databases increases rapidly and new species are frequently discovered. Existing database entries require regular re-evaluation to ensure that species annotations are consistent with the latest species definitions. We have developed an automated method for bacterial species identification that is an extension of ribosomal multilocus sequence typing (rMLST). The method calculates an ‘rMLST nucleotide identity’ (rMLST-NI) based on the nucleotides present in the protein-encoding ribosomal genes derived from bacterial genomes. rMLST-NI was used to validate the species annotations of 11839 publicly available

Klebsiella

and

Raoultella

genomes based on a comparison with a library of type strain genomes. rMLST-NI was compared with two whole-genome average nucleotide identity methods (OrthoANIu and FastANI) and the k-mer based Kleborate software. The results of the four methods agreed across a dataset of 11839 bacterial genomes and identified a small number of entries (n=89) with species annotations that required updating. The rMLST-NI method was 3.5 times faster than Kleborate, 4.5 times faster than FastANI and 1600 times faster than OrthoANIu. rMLST-NI represents a fast and generic method for species identification using type strains as a reference.
Antioxidant, antidiabetic and anti-inflammatory activities of bitter melon extracts obtained by ultrasonic-assisted extraction
Authors: Lee Jin-Ju , Yoon Kyung Young
Published: September 2022

We obtained polyphonol extracts from bitter melon containing various bioactive compounds to improve applicability as functional food materials. The total phenolic content (TPC), antioxidant, antidiabetic, and anti-inflammatory activities of bitter melon extracts obtained using various extraction methods were compared. The extracts obtained using ethanol as the solvent had a higher TPC than extracts obtained using water. The extracts obtained using ethanol also had high antioxidant, antidiabetic, and anti-inflammatory activities when performed using ultrasonic-assisted extraction (UE) with ethanol. The extract obtained using probe type-UE with ethanol (PUE-E) exhibited α-amylase and α-glucosidase inhibitory activity levels corresponding to 90% or more of acarbose (a diabetes treatment). An extract obtained using a bath type-UE with ethanol (BUE-E) exhibited high NO inhibitory activity at all concentrations. Therefore, UE with ethanol is a very effective method for recovering polyphenol extracts from bitter melon with antioxidant, antidiabetic, and anti-inflammatory activities. In addition, the polyphenol extracts obtained from bitter melon by UE with ethanol (especially PUE-E and BUE-E) have a high application potential as functional food materials.
Fermentation characteristics of yakju supplemented
with Jerusalem artichoke (Helianthus tuberosus L.) and
co-fermented by inulin-degrading yeast Wickerhamomyces
anomalus JS01 and Saccharomyces cerevisiae
KMBL7001
Authors: Choi Jun-Su , Choi Kyu-Taek , Kim Chan-Woo , Lee Sae-Byuk , Park Heui-Dong
Published: September 2022

Jerusalem artichoke (JA, Helianthus tuberosus L.) is a promising
functional food material. JA consists of inulin and fructo-oligosaccharide which
are indigestible carbohydrates in human. Previous research has develop various
food products supplemented with JA, however no studies have involved
yakju (Korean traditional rice wine) using JA because
Saccharomyces cerevisiae cannot utilize inulin. We isolated
several inulin-degrading non-Saccharomyces yeasts using
nuruk (a traditional Korean fermentation starter). The
isolate with the highest inulinase activity was Wickerhamomyces
anomalus JS01 with 538.14 Unit/mL after 72 hours of incubation. To
identify whether the inulin-degrading non-Saccharomyces yeast
could improve yakju quality, W. anomalus JS01
and S. cerevisiae KMBL7001 were co-fermented to produce
yakju supplemented with JA. We investigated the
fermentation characteristics. At the completion of the fermentation process, the
yakju co-fermented with W. anomalus JS01
and S. cerevisiae KMBL7001 (co-fermented
yakju) had similar fermentation characteristics including pH,
reducing sugar, alcohol, and organic acid contents compared to
yakju fermented with S. cerevisiae
KMBL7001 (control yakju). Moreover, co-fermented
yakju had higher total amino acid contents compared with
the control yakju. The W. anomalus JS01
digested some inulin into fructose which was fermented. Conversely, the control
wine did not ferment any inulin during fermentation. As a result of the sensory
evaluation, the co-fermented yakju obtained higher scores in
all the sensory categories, suggesting that supplementing with JA and utilizing
inulin-degrading yeast could improve yakju quality.
DrTransformer: Heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Authors: Badelt Stefan , Lorenz Ronny , Hofacker Ivo L.
Published: September 2022

Background

Folding during transcription can have an important influence on the structure and function of ℝNA molecules, as regions closer to the 5’ end can fold into metastable structures before potentially stronger interactions with the 3’ end become available. Thermodynamic ℝNA folding models are not suitable to analyze this problem, as they can only calculate properties of the equilibrium distribution. Other software packages that simulate the kinetic process of ℝNA folding during transcription exist, but they are mostly applicable for short sequences.

Results

We present a new algorithm that tracks changes to the ℝNA secondary structure ensemble during transcription. At every transcription step, new representative local minima are identified, a neighborhood relation is defined and transition rates are estimated for kinetic simulations. After every simulation, a part of the ensemble is removed and the remainder is used to search for new potentially relevant structures. The presented algorithm is deterministic (up to numeric instabilities of simulations), fast (in comparison with existing methods), and it is capable of folding ℝNAs much longer than 200 nucleotides.

Availability

This software is open-source and available at https://github.com/ViennaRNA/drtransformer.
3-hour genome sequencing and targeted analysis to rapidly assess genetic risk
Authors: Galey Miranda , Reed Paxton , Wenger Tara , Beckman Erika , Chang Irene J. , Paschal Cate R. , Buchan Jillian G. , Lockwood Christina M. , Puia-Dumitrescu Mihai , Garalde Daniel R. , Guillory Joseph , Markham Androo J. , Stergachis Andrew B. , Bamshad Michael J. , Eichler Evan E. , Miller Danny E.
Published: September 2022

Rapid genetic testing in the critical care setting enables targeted evaluations, directs therapies, and helps families and care providers make informed decisions about goals of care. We tested whether we could perform ultra-rapid assessment of genetic risk for a Mendelian condition, based on information from an affected sibling, in a newborn via whole-genome sequencing using the Oxford Nanopore platform. By optimization of the DNA extraction and library preparation steps paired with targeted analysis, we were able to demonstrate within three hours of birth that the newborn was neither affected nor a carrier for variants underlying acrodermatitis enteropathica. This proof-of-concept experiment demonstrates how prior knowledge of familial variants can be used to rapidly evaluate an individual at-risk for a genetic disease.
In vivo Safety and Immunoactivity of Oncolytic Jurona Virus in Hepatocellular Carcinoma: A Comprehensive Proteogenomic Analysis
Authors: Zhang Yuguo , Tesfay Mulu , Ferdous Khandoker U. , Taylor Mika , Gabere Musa , Simoes Camila C. , Dumbauld Chelsae , Barro Oumar , Graham Alicia L. , Washam Charity L. , Alkam Duah , Gies Allen , Chamcheu Jean Christopher , Byrum Stephanie D. , Post Steven R. , Kelly Thomas , Borad Mitesh J. , Cannon Martin J. , Basnakian Alexei , Nagalo Bolni M.
Published: September 2022

Oncolytic viruses can effectively unwrap a multimodal anti-tumor activity, encompassing a selective tumor cell killing and promoting a systemic anti-tumor immunity, making them a formidable foe against cancer. Among these, several members of the Rhabdoviridae family are particularly attractive as oncolytic agents due to their natural tumor selectivity and non-pathogenicity in humans. In this study, we demonstrated that intratumorally (IT) administration of Jurona virus (JURV), a novel oncolytic Rhabdovirus, induces dynamic tumor regression in human HCC xenograft and syngeneic models. Our data shows that IT injections of JURV trigger the recruitment and activation of cytotoxic T (CTLs) and decrease the tumor-associated macrophages (TAM) infiltration leading to tumor growth delay in both local and distant murine HCC tumors in a syngeneic model. Moreover, when administered concomitantly, JURV and anti-PD-1 therapy profoundly modulate the tumor microenvironment (TME) via enhanced infiltration of CTLs, suggesting that immune checkpoint blockade therapy could potentiate the immunomodulatory effect of JURV and potentially provide durable anti-tumor immunity. Our analysis of the molecular and cellular mechanism of JURV-medicated anti-cancer activity unveiled that JURV and anti-PD-1 antibodies activate different effectors of the immune system but have complementary anti-tumor activities. Furthermore, our results indicate that the abscopal effect induced by JURV is likely mediated by the mechanism regulating the T helper cell responses. Our work supports the further development of JURV as a novel immunovirotherapy platform for hepatocellular carcinoma.
Does Vaping Increase the Likelihood of SARS-CoV-2 Infection? Paradoxically Yes and No
Authors: Phandthong Rattapol , Wong Man , Song Ann , Martinez Teresa , Talbot Prue
Published: September 2022

Data on the relationship between electronic cigarettes (ECs) and SARS-CoV-2 infection are limited and contradictory. Evidence indicates that EC aerosols or nicotine increase ACE2, SARS-CoV-2 virus receptors, which increase virus binding and susceptibility. Our objectives were to determine if EC aerosols increased SARS-CoV-2 infection of human bronchial epithelial cells and to identify the causative chemical(s). A 3D organotypic model (EpiAirway™) in conjunction with air liquid interface (ALI) exposure was used to test the effects of aerosols produced from JUUL™ “Virginia Tobacco” and BLU™ ECs, or individual chemicals (nicotine, propylene glycol, vegetable glycerin (PG/VG), and benzoic acid) on infection using SARS-CoV-2 pseudoparticles. Exposure of EpiAirway™ to JUUL™ aerosols increased ACE2, while BLU™ and lab-made EC aerosols containing nicotine increased ACE2 levels and TMPRSS2 activity, a spike protease that enables viral-cell fusion. Pseudoparticle infection of EpiAirway™ increased with aerosols produced from PG/VG, PG/VG plus nicotine, or BLU™ ECs. JUUL™ EC aerosols did not increase infection above controls. The baseline level of infection in JUUL™ treated aerosol groups was attributed to benzoic acid, which mitigated the enhanced infection caused by PG/VG or nicotine. The benzoic acid protection from enhanced infection continued at least 48 hours after exposure. TMPRSS2 activity was significantly correlated with e-liquid pH, which in turn was significantly correlated with infection, with lower pH blocking PG/VG and nicotine-induced-enhanced infection. While ACE2 levels increased in EpiAirway™ tissues exposed to EC aerosols, infection depended on the ingredients of the e-liquids. PG/VG and nicotine enhanced infection, an effect that was mitigated by benzoic acid.
Tropical high-altitude insects show limited capacity to handle high temperatures
Authors: Mayekar Harshad Vijay , Solanki Pooran Singh , Arya Homica , Aradhya Rajaguru , Suravajhala Prashanth , Loeschcke Volker , Rajpurohit Subhash
Published: September 2022

Growing summer season and increased anthropogenic activities pose a continual challenge to resident species. Ectotherms like insects are especially vulnerable to rapid climatic changes. High-altitude tropical insect populations have been rarely examined for their responses to high-temperature. We exposed a tropical out-bred highland population ofDrosophila melanogasterfrom the Himalayas to growing summer conditions in outdoor mesocosm units. Population response to thermal changes was tracked over ninety days at both phenotypic and genotypic level. Whole genomic resequencing data suggested a clear seasonal shift in allele frequencies. Interestingly, the general heat responsive genes were missing in the summer due to monsoon allele shift; an atypical response noted for high-altitude tropical populations. Instead, candidates involved in kinases and phosphorylation emerged as key players. Heat-knockdown time decreased over time indicating a limited ability to handle increasing temperature. Merging data from both allelic shifts and heat-knockdown time indicated a limited capacity for high-altitude insects in coping with climate warming.
Modeling effects of inter-group contact on links between population size and cultural complexity
Authors: Ben-Oren Yotam , Strassberg Sarah Saxton , Hovers Erella , Kolodny Oren , Creanza Nicole
Published: September 2022

Human populations rely on cultural artifacts and complex cumulative culture for their survival. Populations vary dramatically in the size of their tool repertoires, and the determinants of these cultural repertoire sizes have been the focus of extensive study in recent years. A prominent hypothesis, supported by computational models of cultural evolution, asserts that tool repertoire size increases with population size. However, not all empirical studies seeking to test this hypothesis have found such a correlation; this has led to a contentious and ongoing debate. As a possible resolution to this longstanding controversy, we suggest that accounting for even rare cultural migration events that allow sharing of knowledge between different-sized populations may help explain why a population’s size might not always predict its cultural repertoire size. Using an agent-based model to explore different assumptions about the effects of population size and migration on tool repertoires, we find that connectivity of one population to others, particularly to large populations, may significantly boost its tool repertoire size when population interactions lead to cultural exchange. Thus, two populations of identical size may have drastically different tool repertoire sizes, hinging upon their access to other groups’ knowledge. Intermittent contact between populations boosts cultural repertoire size and still allows for the development of unique tool repertoires that have limited overlap between populations.
Percolate: an exponential family JIVE model to design DNA-based predictors of drug response
Authors: Mourragui Soufiane M.C. , Loog Marco , van Nee Mirrelijn , van de Wiel Mark A , Reinders Marcel J.T. , Wessels Lodewyk F.A.
Published: September 2022

Motivation

Anti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard to interpret and show poor robustness.

Results

To capture the best of both worlds, i.e. the accuracy of gene expression and the robustness of other genomic levels, such as mutations, copy-number or methylation, we developed Percolate, a computational approach which extracts the joint signal between gene expression and the other omic data types. We developed an out-of-sample extension of Percolate which allows predictions on unseen samples without the necessity to recompute the joint signal on all data. We employed Percolate to extract the joint signal between gene expression and either mutations, copy-number or methylation, and used the out-of sample extension to perform response prediction on unseen samples. We showed that the joint signal recapitulates, and sometimes exceeds, the predictive performance achieved with each data type individually. Importantly, molecular signatures created by Percolate do not require gene expression to be evaluated, rendering them suitable to clinical applications where only one data type is available.

Availability

Percolate is available as a Python 3.7 package and the scripts to reproduce the results are available here.
A new route for integron cassette dissemination among bacterial genomes
Authors: Loot Céline , Millot Gael A. , Richard Egill , Littner Eloi , Vit Claire , Lemoine Frédéric , Cury Jean , Darracq Baptiste , Niault Théophile , Lapaillerie Delphine , Parissi Vincent , Rocha Eduardo PC , Mazel Didier
Published: September 2022

Integrons are genetic elements involved in bacterial adaptation. They can capture, shuffle and express adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination betweenattCandattIintegron sites. Here, we demonstrated that the integrase can efficiently catalyze insertion of cassettes in bacterial genomes, outside theattsites. We showed that, once inserted in genomes, cassettes can be expressed, if located near bacterial promoters, and can be excised at the insertion point and even outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105independent insertion events revealed a very large genomic insertion landscape with recombination sites greatly different, in terms of sequence and structure, from classicalattsites. We named these new sitesattG. These results unveil a new efficient route for dissemination of adaptive functions and expand the role of integrons in bacterial evolution.
Quantifying coexistence concentrations in multi-component phase-separating systems using analytical HPLC
Authors: Bremer Anne , Posey Ammon E. , Borgia Madeleine B. , Borcherds Wade M. , Farag Mina , Pappu Rohit V. , Mittag Tanja
Published: September 2022

Over the last decade, evidence has accumulated to suggest that numerous instances of cellular compartmentalization can be explained by the phenomenon of phase separation. This is a process by which a macromolecular solution separates spontaneously into dense and dilute coexisting phases. Semi-quantitative,in vitroapproaches for measuring phase boundaries have proven very useful in determining some key features of biomolecular condensates, but these methods often lack the precision necessary for generating quantitative models. Therefore, there is a clear need for techniques that allow quantitation of coexisting dilute and dense phase concentrations of phase-separating biomolecules, especially in systems with more than one type of macromolecule. Here we report the design and deployment of analytical High-Performance Liquid Chromatography (HPLC) forin vitroseparation and quantification of distinct biomolecules that allows us to measure dilute and dense phase concentrations needed to reconstruct coexistence curves in multicomponent mixtures. This approach is label-free, detects lower amounts of material than is accessible with classic UV-spectrophotometers, is applicable to a broad range of macromolecules of interest, is a semi-high-throughput technique, and if needed, the macromolecules can be recovered for further use. The approach promises to provide quantitative insights into the balance of homotypic and heterotypic interactions in multicomponent phase-separating systems.
Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths
Authors: Gijsbers JC , Englebert N , Prata KE , Pichon M , Dinesen Z , Brunner R , Eyal G , González-Zapata FL , Kahng SE , Latijnhouwers KRW , Muir P , Radice VZ , Sánchez JA , Vermeij MJA , Hoegh-Guldberg O , Jacobs SJ , Bongaerts P
Published: September 2022

Mesophotic coral communities are increasingly gaining attention for the unique biological species they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies rarely include mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within genera and current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, which were consistently detected across different methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.
MAPK11 (p38β) is a major determinant of cellular radiosensitivity by enhancing IR-associated senescence
Authors: Fernández-Aroca DM , García-Flores N , Frost S , Jiménez-Suarez J , Rodríguez-González A , Fernández-Aroca P , Sabater S , Andrés I , Garnés-García C , Belandia B , Cimas FJ , Villar D , Ruiz-Hidalgo MJ , Sánchez-Prieto R
Published: September 2022

Background and purpose

MAPKs are among the most relevant signalling pathways involved in coordinating cell responses to different stimuli. This group includes p38MAPKs, constituted by 4 different proteins with a high sequence homology: MAPK14 (p38α), MAPK11 (p38β), MAPK12 (p38γ) and MAPK13 (p38δ). Despite their high similarity, each member shows unique expression patterns and even exclusive functions. Thus, analysing protein-specific functions of MAPK members is necessary to unequivocally uncover the roles of this signalling pathway. Here, we investigate the possible role of MAPK11 in the cell response to ionizing radiation (IR).

Materials and methods

We developed MAPK11/14 knockdown through shRNA and CRISPR interference gene perturbation approaches, and analysed the downstream effects on cell responses to ionizing radiation in A549, HCT-116 and MCF-7 cancer cell lines. Specifically, we assessed IR toxicity by clonogenic assays; DNA damage response activity by immunocytochemistry; apoptosis and cell cycle by flow cytometry (Annexin V and propidium iodide, respectively); DNA repair by comet assay; and senescence induction by both X-Gal staining and gene expression of senescence-associated genes by RT-qPCR.

Results

Our findings demonstrate a critical role of MAPK11 in the cellular response to IR by controlling the associated senescent phenotype, and without observable effects on DDR, apoptosis, cell cycle or DNA damage repair.

Conclusion

Our results highlight MAPK11 as a novel mediator of the cellular response to ionising radiation through the control exerted onto IR-associated senescence.

Highlights

Genetic perturbation of MAPK11, but not MAPK14, promotes radiosensitivity in a panel of tumor cell lines.

Abrogation of MAPK11 did not modify DNA damage response, proliferation, apoptosis or cell cycle in response to ionizing radiation

MAPK11 controls ionizing radiation-induced senescence

MAPK11 expression could be a novel target and biomarker for radiosensitivity
Virucidal Activity of Potassium Hydroxide Modeling on Tospovirus
Authors: Zumrutdal Emin , Kamberoglu Muharrem Arap , Saglam Havva Nur
Published: September 2022

Viral agents that cause disease in the respiratory system have led to widespread health problems in the world. The continuation of mutations in these viruses and the lack of an effective treatment agent bring possible public health risks. In this study, the virucidal activity of potassium hydroxide (KOH) was evaluated. The intermolecular interactions of KOH and envelope-structured molecules in enveloped viruses and the virucidal activity of these interactions on Tospovirus, which has the ability to infect, were evaluated.

For this study model, the intermolecular interactions of KOH in the lipid bilayer of the virus envelope were evaluated in silico by Doking method. Then, the plant virulence ability of Tospovirus was observed by the direct interaction of KOH with Tospovirus.

It was observed that KOH interacted exergonically with the glycerophosphate structure in the envelope structure. It was determined by clinical and laboratory observations that Tospovirus in plants lost its virucidal activity after interaction with KOH.

In the light of this information, it was thought that KOH had a virucidal effect in enveloped viruses. It is thought that KOH creates this virucidal activity by KOH-glycerophosphate intermolecular interactions and viral envelope lipid layer hydrolysis.

The mucolytic, alkalinizing and possible low-weight immunoglobulin-forming potential of KOH has been demonstrated in previous studies and no pathology was detected in toxicity studies in mice.

In the light of this information, optimized KOH inhalation has a very serious potential as a virucidal agent in diseases caused by enveloped viruses in the respiratory system such as Coronavirus, H. influenza.
Modeling bee movement shows how a perceptual masking effect can influence flower discovery, foraging efficiency and pollination
Authors: Morán Ana , Lihoreau Mathieu , Pérez Escudero Alfonso , Gautrais Jacques
Published: September 2022

Understanding how pollinators move across space is key to understanding plant mating patterns. Bees are typically assumed to search for flowers randomly or using simple movement rules, so that the probability of discovering a flower should primarily depend on its distance to the nest. However, experimental work shows this is not always the case. Here, we explored the influence of flower size and density on their probability of being discovered by bees by developing a movement model of central place foraging bees, based on experimental data collected on bumblebees. Our model produces realistic bee trajectories by taking into account the autocorrelation of the bee’s angular speed, the attraction to the nest, and a gaussian noise. Simulations revealed a « masking effect » that reduces the detection of flowers close to another, which may have critical consequences for pollination and foraging success. At the plant level, flowers distant to the nest were more often visited in low density environments, suggesting lower probabilities of pollination at high densities. At the bee colony level, foragers found more flowers when they were small and at medium densities, suggesting that there is an optimal flower size and density at which collective foraging efficiency is optimized. Our results indicate that the processes of search and discovery of resources are potentially more complex than usually assumed, and question the importance of resource distribution and abundance on plant-pollinator interactions.

Author’s summary

Understanding how pollinators move in space is key to understanding plant reproduction, which in turn shapes entire ecosystems. Most current models assume simple movement rules that predict that flowers are more likely to be visited—and hence pollinated—the closer they are to the pollinators’ nest. Here we developed an explicit movement model that incorporates realistic features of bumblebees, including their flight characteristics and their tendency to return regularly to the nest, and calibrated it with experimental data collected in naturalistic conditions. This model revealed that the probability to visit a flower does not only depend on its position, but also on the position of other flowers that may mask it from the forager. This masking effect means that pollination efficiency depends on the density and spatial arrangement of flowers around the pollinator’s nest, often in counter-intuitive ways. Taking these effects into account will be key for improving precision pollination and pollinator conservation.
A high-throughput exonuclease assay based on the fluorescent base analog 2-aminopurine
Authors: Botto Margherita M. , Murthy Sudarshan , Lamers Meindert H.
Published: September 2022

Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far have been little exploited. Here we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3’ and 5’ DNA ends, over a wide range of protein activities and suitable for a high throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.
Methamphetamine Self-Administration Differential Effects on Mesolimbic Glutathione Levels, Mitochondrial Respiration and Dopamine Neuron Firing Activity
Authors: Dominguez-Lopez Sergio , Ahn Bumsoo , Sataranatarajan Kavithalakshmi , Ranjit Rojina , Premkumar Pavithra , Van Remmen Holly , Beckstead Michael J.
Published: September 2022

Acute and neurotoxic regimens of METH are known to increase reactive oxygen species (ROS), affect redox homeostasis, and lead to cellular damage in dopamine neurons. However, functional changes induced by long-term METH self-administration on mitochondrial respiratory metabolism and redox homeostasis are less known. To fill this gap in our knowledge, we implanted adult mice with a jugular catheter and trained them to nose poke for METH infusions in operant chambers. After completing several weeks of METH self-administration exposure, we collected samples of the ventral striatum (vSTR) and the ventral midbrain (vMB), containing the nucleus accumbens (NAc) and the ventral tegmental area (VTA), respectively. We used HPLC to determine the levels of the ROS scavenger glutathione in its reduced (GSH) and oxidized (GSSG) forms. Then, we used high-resolution respirometry to determine the oxygen consumption rate (OCR) of mitochondrial complexes under several substrates and inhibitors. Finally, we used in vivo single-unit extracellular recordings to assess changes in dopamine neuron firing activity in the VTA. METH self-administration produces a progressive decrease of the GSH pool in vST, which correlates with METH lifetime intake. We observed increased mitochondrial respiration across the two mesolimbic regions, but only vMB OCR correlates with METH lifetime intake. We recorded an increased number of spontaneously active dopamine neurons with decreased firing rate and burst activity in the VTA. METH lifetime intake inversely correlates with firing rate, the percentage of spikes in a burst, and directly correlates with the number of neurons per track. We conclude that METH self-administration progressively decreased the antioxidant pool in sites of higher dopamine release and produced an increased mitochondrial metabolism in the mesolimbic areas, probably derived from the increased number of dopamine neurons actively firing. However, dopamine neuron firing activity is decreased by METH self-administration, reflecting a new basal level of dopamine neurotransmission in response to the prolonged effects of METH on dopamine release and circuitry feedback.
Roles of the 5-HT2C receptor on zebrafish sociality
Authors: de Moura Layana Aquino , Pyterson Maryana Pereira , Pimentel Ana Flávia Nogueira , Araújo Fernanda , de Souza Loanne Valéria Xavier Bruce , Mendes Caio Henrique Moura , Costa Bruna Patrícia Dutra , de Siqueira-Silva Diógenes Henrique , Lima-Maximino Monica , Maximino Caio
Published: September 2022

Serotonin (5-HT) receptors have been implicated in social behavior in vertebrates. Zebrafish (Danio rerio) have been increasingly being used behavioral neuroscience to study the neurobiological correlates of behavior, including sociality. Nonetheless, the role of 5-HT2C receptors in different social functions were not yet studied in this species. Zebrafish were treated with the agonist MK-212 (2 mg/kg) or the antagonist RS-102221 (2 mg/kg) and tested in the social interaction and social novelty tests, conditional approach test, or mirror-induced aggressive displays. MK-212 increased preference for an unknown conspecific in the social investigation test, but also increased preference for the known conspecific in the social novelty test; RS-102221, on the other hand, decreased preference in the social investigation test but increased preference for the novel conspecific in the social novelty test. MK-212 also decreased predator inspection in the conditional approach test. While RS-102221 decreased time in the display zone in the mirror-induced aggressive display test, it increased display duration. Overall, these results demonstrate the complex role of 5-HT2C receptors in different social contexts in zebrafish, revealing a participation in social plasticity in vertebrates.
Mining for ions: diagnostic feature detection in MS/MS spectra of post-translationally modified peptides
Authors: Geiszler Daniel J. , Polasky Daniel A. , Yu Fengchao , Nesvizhskii Alexey I.
Published: September 2022

Post-translational modifications (PTMs) are an area of great interest in proteomics, with a surge in methods to detect them in recent years. However, PTMs can introduce complexity into proteomics searches by fragmenting in unexpected ways. Detecting post-translational modifications in mass spectrometry-based proteomics traditionally relies on identifying ions shifted by the masses of the modifications. This presents challenges for many PTMs. Labile PTMs lose part of their modification mass during fragmentation, rendering shifted fragment ions unidentifiable, and isobaric PTMs are indistinguishable by mass, requiring other diagnostic ions for disambiguation. Furthermore, even modifications that have undergone extensive characterization often produce different fragmentation patterns across instruments and conditions. To address these deficiencies and facilitate the next generation of PTM identification, we have developed a method to automatically find diagnostic spectral features for any PTM, allowing subsequent searches to take advantage of additional metrics and increase PTM identification and localization rates. The method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
Kinetic and Structural Analysis of Ribonucleotide Extension by DNA Polymerase η
Authors: Chang Caleb , Luo Christie Lee , Eleraky Sarah , Lin Aaron , Zhou Grace , Gao Yang
Published: September 2022

DNA polymerases catalyze DNA synthesis with high fidelity, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rN) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes rNTP binding, mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does not reduce the catalytic efficiency of Pol η. However, rN ended primers alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η fidelity drops significantly across different sequence context. Systematic structural studies suggest that the rN at the primer end improved primer alignment and reduced barriers in C2’-endo to C3’-endo sugar conformation change. Our work provides important insights for rN extension and implicates a possible mechanism for rN removal.