bluuebunny/crossref_metadata_2025 huggingface dataset:
D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response
Authors: Jiang Jialong , Chen Sisi , Tsou Tiffany , McGinnis Christopher S. , Khazaei Tahmineh , Zhu Qin , Park Jong H. , Strazhnik Inna-Marie , Vielmetter Jost , Gong Yingying , Hanna John , Chow Eric D. , Sivak David A. , Gartner Zev J. , Thomson Matt
Published: April 2023

Gene regulatory networks within cells modulate the expression of the genome in response to signals and changing environmental conditions. Reconstructions of gene regulatory networks can reveal the information processing and control principles used by cells to maintain homeostasis and execute cell-state transitions. Here, we introduce a computational framework, D-SPIN, that generates quantitative models of gene regulatory networks from single-cell mRNA-seq datasets collected across thousands of distinct perturbation conditions. D-SPIN models the cell as a collection of interacting gene-expression programs, and constructs a probabilistic model to infer regulatory interactions between gene-expression programs and external perturbations. Using large Perturb-seq and drug-response datasets, we demonstrate that D-SPIN models reveal the organization of cellular pathways, sub-functions of macromolecular complexes, and the logic of cellular regulation of transcription, translation, metabolism, and protein degradation in response to gene knockdown perturbations. D-SPIN can also be applied to dissect drug response mechanisms in heterogeneous cell populations, elucidating how combinations of immunomodulatory drugs can induce novel cell states through additive recruitment of gene expression programs. D-SPIN provides a computational framework for constructing interpretable models of gene-regulatory networks to reveal principles of cellular information processing and physiological control.
Detecting directional epistasis and dominance from cross-line analyses in alpine populations ofArabidopsis thaliana
Authors: Le Rouzic Arnaud , Roumet Marie , Widmer Alex , Clo Josselin
Published: April 2023

The contribution of non-additive genetic effects to the genetic architecture of fitness, and to the evolutionary potential of populations, has been a topic of theoretical and empirical interest for a long time. Yet, the empirical study of these effects in natural populations remains scarce, perhaps because measuring dominance and epistasis relies heavily on experimental line crosses. In this study, we explored the contribution of dominance and epistasis in natural alpine populations ofArabidopsis thaliana, for two fitness traits, the dry biomass and the estimated number of siliques, measured in a greenhouse. We found that, on average, crosses between inbred lines ofA. thalianaled to mid-parent heterosis for dry biomass, but outbreeding depression for estimated number of siliques. While heterosis for dry biomass was due to dominance, we found that outbreeding depression for estimated number of siliques could be attributed to the breakdown of beneficial epistatic interactions. We simulated and discussed the implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect non-additive genetic effects.
Disease Tolerance Acquired Through RepeatedPlasmodiumInfection Involves Epigenetic Reprogramming of Innate Immune Cells
Authors: Nideffer Jason , Ty Maureen , Donato Michele , John Rek , Kajubi Richard , Ji Xuhuai , Maecker Holden , Nankya Felistas , Musinguzi Kenneth , Press Kathleen Dantzler , Greenhouse Bryan , Kamya Moses , Feeney Margaret E. , Dorsey Grant , Utz PJ , Pulendran Bali , Khatri Purvesh , Jagannathan Prasanna
Published: April 2023

The regulation of inflammation is a critical aspect of disease tolerance and naturally acquired immunity to malaria. Here, we demonstrate using RNA sequencing and epigenetic landscape profiling by cytometry by Time-Of-Flight (EpiTOF), that the regulation of inflammatory pathways during asymptomatic parasitemia occurs downstream of pathogen sensing—at the epigenetic level. The abundance of certain epigenetic markers (methylation of H3K27 and dimethylation of arginine residues) and decreased prevalence of histone variant H3.3 correlated with suppressed cytokine responses among monocytes of Ugandan children. Such an epigenetic signature was observed across diverse immune cell populations and not only characterized active asymptomatic parasitemia but also predicted long-term future disease tolerance when observed in uninfected children. This broad methylated signature likely develops gradually and was associated with age and recent parasite exposure. Our data support a model whereby exposure toPlasmodium falciparuminduces epigenetic changes that regulate excessive inflammation and contribute to naturally acquired immunity to malaria.
AI becomes a masterbrain scientist
Authors: Zijie Yang , Yukai Wang , Lijing Zhang
Published: April 2023

Abstract

Recent rapid and unexpected advancements in Artificial Intelligence (AI) have dramatically shocked the world. Large language models, such as ChatGPT and GPT-4, have demonstrated remarkable potential in aggregating and organizing knowledge while providing insights and solutions to specific questions. In this study, we further explore the possibility of GPT-4 taking on a central role in a complete closed-loop biological research, functioning as a masterbrain scientist responsible for generating hypotheses, designing experiments, analyzing results, and drawing conclusions. Our findings suggest that AI has the potential to evolve into a genuine scientist, and could lead an unprecedented revolution in the area of science.
Clinical guideline variability in the diagnosis and care of people at risk for hereditary hematopoietic malignancy syndromes
Authors: Hamidi Adam , Roloff Gregory W. , Shaw Reid , Acevedo Maria , Smith Shaili , Drazer Michael W.
Published: April 2023

A growing understanding of the complexities of hematopoietic malignancies necessitates the existence of clinical recommendations that are sufficiently comprehensive. Although hereditary hematopoietic malignancies (HHMs) are increasingly recognized for conferring risk of myeloid malignancy, frequently utilized clinical recommendations have never been appraised for the ability to reliably guide HHM evaluation. We assessed established society-level clinical guidelines for inclusion of critical HHM genes and graded the strength of testing recommendations. We uncovered a substantial lack of consistency of recommendations guiding HHM evaluation. Such heterogeneity in guidelines likely contributes to refusal by payers to support HHM testing, leading to underdiagnoses and lost opportunities for clinical surveillance.
Role of the exercise professional in metabolic and bariatric surgery
Authors: Stults-Kolehmainen Matthew A. , Bond Dale S. , Richardson Laura A. , Herring Louisa Y. , Mulone Bethany , Garber Carol Ewing , Morton John , Ghiassi Saber , Duffy Andrew J. , Balk Ethan , Abolt Charles J. , Howard Matt C. , Ash Garrett I. , Williamson Susannah , Marcon Emilian Rejane , Los Santos Melissa De , Bond Samantha , Huehls Janet , Alowaish Osama , Heyman Nina Brojan , Gualano Bruno
Published: April 2023

Background

Physical activity (PA) is important for the long-term health and weight management of patients who undergo metabolic and bariatric surgery (MBS). However, the roles of exercise professionals in MBS settings have not been systematically determined.

Objectives

To investigate: (1) who are the professionals implementing PA programming in MBS clinical settings; and (2) what patient-centric tasks do they perform?

Setting

Clinical and academic exercise settings worldwide.

Methods

This multimethod study included a scoping review of PA programs in MBS described in the research literature. Data about job tasks were extracted and provided to 10 experts to sort into categories. Cluster analysis was utilized to find the hierarchical structure of tasks. A Delphi process was used to agree on a final model.

Results

The majority of PA professionals were exercise physiologists in the USA and physiotherapists or other types of exercise professionals elsewhere. Forty-three tasks were identified, the most reported being: supervision of exercise, fitness testing, and exercise prescription. Seven higher-order categories were determined: (1) Exercise-related health assessment, (2) Body composition and physical fitness assessment, (3) Lifestyle physical activity and sedentary behavior assessment, (4) Education, instruction, and prescription, (5) Exercise monitoring, (6) Behavioral counseling and psychosocial support, and (7) Dietary support. The following statements were rated an average of 9.0, classifying them as “imperative”: 1) “Pre- and post-operative PA/exercise guidelines for MBS patients are needed”, 2) “MBS programs need to include PA/exercise as part of multidisciplinary care”.

Conclusions

The expert group reached a consensus on 7 major classifications of job tasks for the exercise professional. It is important for governing medical associations across the world to formally recognize experienced exercise professionals as playing pivotal roles in continuing, multidisciplinary care for MBS patients. These findings also provide evidence-based information in the effort to solidify these positions within the greater context of healthcare.

Highlights

Results identified 43 patient-centered job tasks, which divided into 7 major categories.

The most common tasks were exercise prescription, supervision, and fitness testing.

Job tasks performed varied marginally by the type of exercise professional.

Including exercise in MBS patient care was deemed “imperative” by the Expert Group.
The unequal functional redundancy of ArabidopsisINCURVATA11andCUPULIFORMIS2is not dependent on genetic background
Authors: Nadi Riad , Juan-Vicente Lucía , Mateo-Bonmatí Eduardo , Micol José Luis
Published: April 2023

The paralogous genesINCURVATA11(ICU11) andCUPULIFORMIS2(CP2) encode components of the epigenetic machinery in Arabidopsis and belong to the 2-oxoglutarate and Fe (II)-dependent dioxygenase superfamily. We previously inferred unequal functional redundancy betweenICU11andCP2from a study of the synergistic phenotypes of the double mutant and sesquimutant combinations oficu11andcp2mutations, although they represented mixed genetic backgrounds. To avoid potential confounding effects arising from different genetic backgrounds, we generated theicu11-5andicu11-6mutants via CRISPR/Cas genome editing in the Col-0 background and crossed them tocp2mutants in Col-0. The resulting mutants exhibited a postembryonic-lethal phenotype reminiscent of strongembryonic flower(emf) mutants. Double mutants involvingicu11-5and mutations affecting epigenetic machinery components displayed synergistic phenotypes, whereascp2-3did not besidesicu11-5. Our results confirmed the unequal functional redundancy betweenICU11andCP2and demonstrated that it is not allele or genetic background specific. An increase in sucrose content in the culture medium partially rescued the post-germinative lethality oficu11 cp2double mutants and sesquimutants, facilitating the study of their morphological phenotypes throughout their life cycle, which include floral organ homeotic transformations. We thus established that theICU11-CP2module is required for proper flower organ identity.
Single cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging and disease
Authors: Kilfeather Peter , Khoo Jia Hui , Wagner Katherina , Liang Han , Caiazza Maria-Claudia , An Yanru , Zhang Xingju , Chen Xiaoyan , Connor-Robson Natalie , Shang Zhouchun , Wade-Martins Richard
Published: April 2023

The brain is spatially organized and contains unique cell types, each performing diverse functions, and exhibiting differential susceptibility to neurodegeneration. This is exemplified in Parkinson’s disease with the preferential loss of dopaminergic neurons of the substantia nigra pars compacta. Using a Parkinson’s transgenic model, we conducted a single-cell spatial transcriptomic and dopaminergic neuron translatomic analysis of young and old mouse brains. Through the high resolving capacity of single-cell spatial transcriptomics, we provide a deep characterization of the expression features of dopaminergic neurons and 27 other cell types within their spatial context, identifying markers of healthy and aging cells, spanning Parkinson’s-relevant pathways. We integrate gene enrichment and GWAS data to prioritize putative causative genes for disease investigation, identifying CASR as a novel regulator of dopaminergic calcium handling. These datasets (see:spatialbrain.org) represent the largest public resource for the investigation of spatial gene expression in brain cells in health, aging and disease.
Characterization of Tryptophan Oxidation Affecting D1 Degradation by FtsH in the Photosystem II Quality Control of Chloroplasts
Authors: Kato Yusuke , Kuroda Hiroshi , Ozawa Shin-Ichiro , Saito Keisuke , Dogra Vivek , Scholz Martin , Zhang Guoxian , de Vitry Catherine , Ishikita Hiroshi , Kim Chanhong , Hippler Michael , Takahashi Yuichiro , Sakamoto Wataru
Published: April 2023

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed thatArabidopsismutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation inChlamydomonasindicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.

Competing Interest Statement

The authors have no conflict of interest, financial or otherwise, in relation to this study

Impact Statement

Oxidative modification of Tryptophan residues in the reaction center protein D1 may be a key to drive the Photosystem II repair, likely enhancing accessibility of FtsH protease to D1.
Phase-specific stimulation of the human brain with real-time measurement instead of prediction
Authors: Guggenberger Robert , Gebühr Julian-Samuel , Keute Marius , Gharabaghi Alireza
Published: April 2023

Background

The responsiveness of the human brain to external input fluctuates. Timing the external perturbation with regard to the oscillatory brain state may improve the intended stimulation effects. However, current brain state-dependent interventions targeting phases of the oscillatory cycle need to apply prediction algorithms to compensate for latencies between measurement and stimulation, and are therefore imprecise.

Objective

We investigated the phase-specific precision of a novel non-predictive approach on the basis of integrated real-time measurement and brain stimulation.

Methods

Applying a simulation, we estimated the circular standard deviation (SD) to hit 2, 4, 8, 16 or 32 equidistant phase bins of the oscillatory cycle with high precision. Furthermore, we used electroencephalography-triggered transcranial magnetic stimulation in healthy subjects to empirically determine the precision of hitting the targeted phase of the oscillatory cycle for 10 different frequencies from 4Hz to 40Hz using our approach.

Results

The simulation revealed that SDs of less than 17.6°, 9.7°, 5.1°, 2.5°, and 1.3° were necessary to precisely hit 2, 4, 8, 16, and 32 distinct phase bins of the oscillatory cycle. By completing measurement, signal-processing and stimulation with a round-time of 1ms, our empirical approach achieved SDs of 0.4° at 4Hz to 4.3° at 40Hz. This facilitates selective targeting of 32 phases (at 4Hz), 16 phases (at 8, 12, 16, 20, 24Hz) and 8 phases (at 28, 32, 36, 40Hz), respectively.

Conclusion

Integrated real-time measurement and stimulation circumvents the need for prediction and results in more precise phase-specific brain stimulation than with state-of-the-art procedures.
Diversity and abundance of pestiferous fruit flies (Diptera: Tephritidae) infesting cucurbit crops in Morogoro, eastern-central Tanzania
Authors: Tarimo Petronila , Kabota Sija , Mwatawala Maulid , Majubwa Ramadhan , Kudra Abdul , Virgilio Massimiliano , De Meyer Marc
Published: April 2023

Fruit flies represent a significant threat to cucurbit production. They inflict about 30% to 100% losses on cucurbit crops. The aim of this study was to characterize the community of fruit flies infesting cucurbit crops in Morogoro, Tanzania. We investigate the diversity and abundance of fruit fly species infesting cucumber, watermelon, and squash across the two agroecological zones of the Morogoro using three attractants (Cue Lure, Zingerone and Biolure). The attractants were deployed for 16 weeks from June to November 2020.

In total, 12017 fruit fly specimens were collected. Of these, 77.23% were collected from the mountainous and the remaining 22.77% from the plateau zone. All specimens belonged to the generaDacus, ZeugodacusandBactrocera.Zeugodacus cucurbitaewas the most abundant species (77.6%) while the remaining species constituted 22.4%. The mountainous zone harboured a significantly higher number of fruit fly species than the plateau zone. The abundance of fruit flies was significantly influenced by altitudes and seasons. The study characterized the community of fruit flies in Morogoro and confirms the prevalence of Z.cucurbitae, D. bivittatus and D. punctatifronsas prominent species in this region. Therefore, management programs should focus on containing these species regardless of the agroecological zones and seasons.
Brn3a controls the soma localization and axonal extension patterns of developing spinal dorsal horn neurons
Authors: Nishida Kazuhiko , Matsumura Shinji , Uchida Hitoshi , Abe Manabu , Sakimura Kenji , Badea Tudor Constantin , Kobayashi Takuya
Published: April 2023

The spinal dorsal horn comprises heterogeneous neuronal populations, that interconnect with one another to form neural circuits modulating various types of sensory information. Decades of evidence has revealed that transcription factors expressed in each neuronal progenitor subclass play pivotal roles in the cell fate specification of spinal dorsal horn neurons. However, the development of subtypes of these neurons is not fully understood in more detail as yet and warrants the investigation of additional transcription factors. In the present study, we examined the involvement of the POU domain-containing transcription factor Brn3a in the development of spinal dorsal horn neurons. Analyses of Brn3a expression in the developing spinal dorsal horn neurons in mice demonstrated that Brn3a was downregulated in majority of the Brn3a-lineage neurons during embryonic stages (Brn3a-transient neurons), whereas a limited population continued to express Brn3a after E18.5 (Brn3a-persistent neurons). Brn3a knockout disrupted the localization pattern of Brn3a-persistent neurons, indicating a critical role of this transcription factor in the development of these neurons. In contrast, Brn3a overexpression in Brn3a-transient neurons directed their localization in a manner similar to that in Brn3a-persistent neurons. Moreover, Brn3a-overexpressing neurons exhibited increased axonal extension to the ventral and ventrolateral funiculi, where the axonal tracts of Brn3a-persistent neurons reside. These results suggest that Brn3a controls the soma localization and axonal extension patterns of Brn3a-persistent spinal dorsal horn neurons.
Persistently increased post-stress activity of paraventricular thalamic neurons is essential for the emergence of stress-induced maladaptive behavior
Authors: Jász Anna , Biró László , Buday Zsolt , Király Bálint , Szalárdy Orsolya , Horváth Krisztina , Komlósi Gergely , Bódizs Róbert , Kovács Krisztina J. , Diana Marco A. , Hangya Balázs , Acsády László
Published: April 2023

Traumatic events can immediately lead to debilitating symptoms collectively called Acute Stress Disorder (ASD), however the mechanisms of ASD are poorly understood. Using a rodent model of ASD here we identify a crucial communication bottleneck between the brainstem and the forebrain, the calretinin-positive neurons in the paraventricular thalamus (PVT/CR+), that controls ASD. We show that following a single acute stress event, the pre-sleep behavior of the mice is altered for several days in parallel with a persistent increase in the firing rate of PVT/CR+ cells. Optogenetic inhibition of PVT/CR+ neuronal activity after the stress event for one hour was sufficient to rescue both the ASD symptoms and the prolonged increase in PVT/CR+ firing rate. Inhibition applied 5 days later was still able to ameliorate some of the symptoms. These data suggest that post-stress activity of PVT/CR+ neurons play a critical role in mediating the acute forms of stress-related affective dysfunctions.

One-Sentence Summary

Post-stress inhibition of paraventricular thalamic neurons prevents the emergence of acute stressed phenotype.
Enhancer evolution as a driving force for lineage-specific paralog usage in the central nervous system
Authors: Fujimori Chika , Sugimoto Kohei , Ishida Mio , Yang Christopher , Kayo Daichi , Tomihara Soma , Sano Kaori , Akazome Yasuhisa , Oka Yoshitaka , Kanda Shinji
Published: April 2023

Expression patterns of paralogous genes in the functionally homologous cells sometimes show differences across species. However, no reasonable explanation for the mechanism underlying such phenomena has been discovered. To understand this mechanism, the present study focused on the hypophysiotropic GnRH neurons in vertebrates as a model. These neurons express eithergnrh1orgnrh3paralogs depending on species, and apparent switching of the expressed paralogs in them occurred at least four times in vertebrate evolution. First, we found redundant expressions ofgnrh1andgnrh3in a single neuron in piranha and hypothesized that this situation may indicate an ancestral condition. We tested this hypothesis by examining the activity of piranhagnrh1/gnrh3enhancers in zebrafish and medaka, in which the twognrhparalogs are not co-expressed. Here, thegnrh1/gnrh3enhancer of piranha induced reporter RFP/GFP co-expressions in a single hypophysiotropic GnRH neuron in both zebrafish and medaka. From these results, we propose that long-lasting (∼550 My) redundancy aftergnrh1/3duplication in 1R/2R WGD may be the key to apparent switching of the paralog usage among the present-day species. Moreover, interspecies analyses of enhancers indicated that the loss of enhancers rather than changes in trans-regulatory elements drove the role-division of these paralogs.
Dysregulation of GABAergic System in the Hippocampus and Inferior Colliculi of Rats during the Development of Audiogenic Epilepsy
Authors: Ivlev Andrey P. , Chernigovskaya Elena V. , Nikolaeva Svetlana D. , Kulikov Alexey A. , Glazova Margarita V. , Naumova Alexandra A.
Published: April 2023

Epilepsy is tightly associated with dysfunction of inhibitory γ-aminobutyric acid (GABA) neurotransmission. In this study, Krushinsky-Molodkina (KM) rats genetically prone to audiogenic seizures (AGS) were used. KM rats are characterized by the development of audiogenic epilepsy during postnatal ontogenesis, with AGS onset at the age of 1.5-2 months and fully developed AGS expression by 3rdmonth. We analyzed GABAergic system of the inferior colliculi (IC) and the hippocampus of KM rats at different stages of postnatal development. Wistar rats were used as a control. In the IC of young KM rats, Na+/K+/Cl−cotransporter 1 (NKCC1) expression was increased, while in adults K+/Cl−cotransporter 2 (KCC2) was downregulated indicating impairment of postsynaptic GABA action both at early and later stages of postnatal development. In the hippocampus of young KM rats, we observed a decrease in activity of GABAergic neurons and downregulation of KCC2 and NKCC1. Adult rats, in opposite, demonstrated elevated activity of the hippocampal GABAergic cells and unchanged expression of chlorine transporters indicating upregulation of GABA transmission. Thus, GABA dysregulation in the IC can mediate the seizure susceptibility in adult KM rats, while in the hippocampus, upregulation of GABAergic system can restrict the spreading of epileptiform activity from the brainstem.
MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport inMethanosarcina acetivorans
Authors: Gupta Dinesh , Chen Keying , Elliott Sean J. , Nayak Dipti D.
Published: April 2023

Methanogens are a diverse group of Archaea that couple energy conservation to the production of methane gas. While most methanogens have no alternate mode of energy conservation, strains likeMethanosarcina acetivoransare known to also conserve energy by dissimilatory metal reduction (DSMR) in the presence of soluble ferric iron or iron-containing minerals. The ecological ramifications of energy conservation decoupled from methane production in methanogens are substantial, yet the molecular details are poorly understood. In this work, we conductedin vitroandin vivostudies with a multihemec-type cytochrome (MHC), called MmcA, to establish its role during methanogenesis and DSMR inM. acetivorans. MmcA purified fromM. acetivoranscan donate electrons to methanophenazine, a membrane-bound electron carrier, to facilitate methanogenesis. In addition, MmcA can also reduce Fe(III) and the humic acid analog anthraquinone-2,6-disulfonate (AQDS) during DSMR. Furthermore, mutants lackingmmcAhave slower Fe(III) reduction rates. The redox reactivities of MmcA are consistent with the electrochemical data where MmcA displays reversible redox features ranging from -100 to -450 mV versus SHE. MmcA is prevalent in members of the OrderMethanosarcinalesbut does not belong to a known family of MHCs linked to extracellular electron transfer, bioinformatically, and instead forms a distinct clade that is closely related to octaheme tetrathionate reductases. Taken together, this study shows that MmcA is widespread in methanogens with cytochromes where it acts as an electron conduit to support a variety of energy conservation strategies that extend beyond methanogenesis.
Comparative genomics of pesticide-degradingEnterococcussymbionts ofSpodoptera frugiperda(Lepidoptera: Noctuidae) leads to the identification of two new species and the reappraisal of insect-associatedEnterococcusspecies
Authors: Gomes Ana Flávia Freitas , de Almeida Luís Gustavo , Cônsoli Fernando Luis
Published: April 2023

Enterococcusspecies have been described as core members of the microbial community ofSpodoptera frugiperda(Lepidoptera:Noctuidae) and have been reported in previous studies as insecticide degrading agents. Phenotypic assays and comparative genomics analyses of several pesticide-degradingEnterococcusisolated from the larval gut ofS. frugiperdaled to the identification ofEnterococcus entomosociumn. sp. andEnterococcus spodopteracolusn. sp. Their identities as new species were confirmed by whole genome alignment using the cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA:DNA hybridization (dDDH) values. The systematic positioning of these new species within the genusEnterococcuswas resolved using genome-based analysis, placingEnterococcus casseliflavusas the sister group ofE. entomosociumn. sp., andEnterococcus mundtiiofE. spodopteracolusn. sp. Comparative genomic analyses of several isolates ofE. entomosociumn. sp. andE. spodopteracolusn. sp. led to a better assessment of the interactions established in the symbiotic association withS. frugiperda, and the discovery of misidentified new species ofEnterococcusassociated with insects. Our analyses also indicated the potential ofE. entomosociumn. sp. AndE. spodopteracolusn. sp. to metabolize different pesticides arises from molecular mechanisms that result in the rapid evolution of new phenotypes in response to environmental stressors; in this case, the pesticides their host insect is exposed to.
A Computational Growth and Remodeling Framework for Adaptive and Maladaptive Pulmonary Arterial Hemodynamics
Authors: Szafron Jason M. , Yang Weiguang , Feinstein Jeffrey A. , Rabinovitch Marlene , Marsden Alison L.
Published: April 2023

Hemodynamic loading is known to contribute to the development and progression of pulmonary arterial hypertension (PAH). This loading drives changes in mechanobiological stimuli that affect cellular phenotypes and lead to pulmonary vascular remodeling. Computational models have been used to simulate mechanobiological metrics of interest, such as wall shear stress, at single time points for PAH patients. However, there is a need for new approaches that simulate disease evolution to allow for prediction of long-term outcomes. In this work, we develop a framework that models the pulmonary arterial tree through adaptive and maladaptive responses to mechanical and biological perturbations. We coupled a constrained mixture theory-based growth and remodeling framework for the vessel wall with a morphometric tree representation of the pulmonary arterial vasculature. We show that non-uniform mechanical behavior is important to establish the homeostatic state of the pulmonary arterial tree, and that hemodynamic feedback is essential for simulating disease time courses. We also employed a series of maladaptive constitutive models, such as smooth muscle hyperproliferation and stiffening, to identify critical contributors to development of PAH phenotypes. Together, these simulations demonstrate an important step towards predicting changes in metrics of clinical interest for PAH patients and simulating potential treatment approaches.
Anin vitroexperimental pipeline to characterize the binding specificity of SARS-CoV-2 neutralizing antibodies
Authors: Atanasoff Kristina E. , Brambilla Luca , Adelsberg Daniel C. , Kowdle Shreyas , Stevens Christian S. , Hung Chuan-Tien , Fu Yanwen , Lim Reyna , Tran Linh , Allen Robert , Andrew Duty J. , Bajic Goran , Lee Benhur , Tortorella Domenico
Published: April 2023

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has led to over 760 million cases and >6.8 million deaths worldwide. We developed a panel of human neutralizing monoclonal antibodies (mAbs) targeting the SARS-CoV-2 Spike protein using Harbour H2L2 transgenic mice immunized with Spike receptor binding domain (RBD) (1). Representative antibodies from genetically-distinct families were evaluated for inhibition of replication-competent VSV expressing SARS-CoV-2 Spike (rcVSV-S) in place of VSV-G. One mAb (denoted FG-10A3) inhibited infection of all rcVSV-S variants; its therapeutically-modified version, STI-9167, inhibited infection of all tested SARS-CoV-2 variants, including Omicron BA.1 and BA.2, and limited virus proliferationin vivo(1). To characterize the binding specificity and epitope of FG-10A3, we generated mAb-resistant rcVSV-S virions and performed structural analysis of the antibody/antigen complex using cryo-EM. FG-10A3/STI-9167 is a Class 1 antibody that prevents Spike-ACE2 binding by engaging a region within the Spike receptor binding motif (RBM). Sequencing of mAb-resistant rcVSV-S virions identified F486 as a critical residue for mAb neutralization, with structural analysis revealing that both the variable heavy and light chains of STI-9167 bound the disulfide-stabilized 470-490 loop at the Spike RBD tip. Interestingly, substitutions at position 486 were later observed in emerging variants of concern BA.2.75.2 and XBB. This work provides a predictive modeling strategy to define the neutralizing capacity and limitations of mAb therapeutics against emerging SARS-CoV-2 variants.

Importance

The COVID-19 pandemic remains a significant public health concern for the global population; development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as SARS-CoV-2 variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread with the caveat that they interact with the circulating variants. The epitope and binding specificity of a broadly neutralizing anti-SARS-CoV-2 Spike RBD antibody clone against many SARS-CoV-2 VOC was characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines.
Nano-silver and forskolin regulate rice seed germination mediated byOsPIP2-1
Authors: Chen Bingxian , Peng Yuanxuan , Zhang Qi , Chen Zhongjian , Li Hongmei , Liu Jun
Published: April 2023

As timely germination of seeds is crucial to crop yield and quality, the low germination percentage for direct seeding in rice and pre-harvest sprouting during late stage of maturity have extremely adverse effects on rice production. Herein, we found that nano-silver inhibited rice seed germination while forskolin promoted this process. Germination assay showed that 20 μM AgNPs and 0.5 μM forskolin could be the optimal concentrations regulating rice seed germination. At the molecular level, an aquaporin gene,OsPIP2-1, was most highly expressed among those homologous genes during rice seed germination, and was decreased by AgNPs and increased by forskolin. Meanwhile, the activity of α-amylase and its genes expression were also inhibited by AgNPs and promoted by forskolin. Next, the germination percentage ofOsPIP2-1overexpressing seeds was significantly higher than that of wild-type, and that ofOsPIP2-1knockout seeds was dramatically reduced. Furthermore, compared with the wild type, α-amylase activity and the transcription ofOsAmy3CandOsAmy3Ewere increased inOsPIP2-1overexpressing seeds and decreased inOsPIP2-1knockout seeds, indicating thatOsPIP2-1positively regulates α-amylase. Interestingly, seed germination, α-amylase activity and its genes expression inOsPIP2-1overexpressed and knockdout lines could also be inhibited by nano-silver and promoted by forskolin. In conclusion, we propose that nano-silver and forskolin regulated seed germination by modulating the expression ofOsPIP2-1and thus α-amylase. Our results may bring new application of nano-silver and forskolin in rice cultivation.
Comparative genome microsynteny illuminates the fast evolution of nuclear mitochondrial segments (NUMTs) in mammals
Authors: Uvizl Marek , Puechmaille Sebastien J. , Power Sarahjane , Pippel Martin , Carthy Samuel , Haerty Wilfried , Myers Eugene W. , Teeling Emma C. , Huang Zixia
Published: April 2023

The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past ∼200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes, and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from non-random regions in mtDNA, tend to locate in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This strongly indicates that NUMT gain-and-loss over evolutionary time provides great insights into mammal evolution. However, we also demonstrated that one should be cautious when using ancestral NUMT trees to infer phylogenetic relationships. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
Trial participants are frequently excluded based on their symptoms rather than their condition: A systematic review of Cochrane reviews and their component trials
Authors: Stocking Katie , Watson Andrew , Kirkham Jamie J , Wilkinson Jack , Vail Andy
Published: April 2023

Objectives

Identify strategies used in the design of recent randomised controlled trials (RCTs) and their associated Cochrane reviews where patients with the same gynaecological condition present with different symptoms.

Study Design and Setting

We searched the Cochrane library (February 2022) for reviews in polycystic ovarian syndrome (PCOS) and endometriosis. Reviews were included if the intervention was intended to treat all condition-specific symptoms. We restricted to trials published since 2012 to consider ‘current’ approaches. For each trial we recorded the number of potentially eligible participants excluded as a direct result of the chosen strategy. For each review we recorded the numbers of RCTs and participants excluded unnecessarily.

Results

There were 89 distinct PCOS trials in 13 reviews, and 13 Endometriosis trials in 11 reviews. Most trials restricted their eligibility to participants with specific symptoms (55% PCOS, 46% endometriosis). The second most common strategy was to measure and analyse clinical outcomes that were not relevant to all participants (38% PCOS, 31% endometriosis). Reviews excluded 27% of trials based just on outcome data.

Conclusions

Current gynaecological research is inefficient. Most trials either exclude patients who could benefit from treatment or measure outcomes not relevant to all participants.

Registration

PROSPERO (CRD42022334776)

What is new?

Key findings

Over a quarter of Cochrane reviews included in this review excluded trials based on the outcomes reported.

Typically, recent randomised controlled trials in Polycystic Ovarian Syndrome and Endometriosis trials either exclude patients who could potentially benefit from the treatment given, or measure outcomes of no relevance to some participants.

What this adds to what is known?

Strategies developed that are employed in the design and measurement of outcomes in gynaecological trials.

There are multiple sources of waste in the current gynaecological research landscape. The population of patients available is under-utilised by excluding patients based on the outcomes measured, or alternatively, researchers are measuring outcomes in patients who do not experience the associated symptom(s).

What is the implication and what should change now?

Gynaecological patients experience heterogeneity in their symptoms and therefore it is crucial to employ appropriate outcome measures in order to reduce research waste. Cochrane Reviews should include all trials which report outcomes that are relevant to the population of interest if the intervention under investigation is deemed to plausibly treat the associated symptom(s).
Ornithine is the central intermediate in the arginine degradative pathway and its regulation inBacillus subtilis
Authors: Warneke Robert , Garbers Tim Benedict , Herzberg Christina , Aschenbrandt Georg , Ficner Ralf , Stülke Jörg
Published: April 2023

The Gram-positive model bacteriumBacillus subtilisis able to utilize a variety of proteinogenic and non proteinogenic amino acids as sources of carbon, energy and nitrogen. The utilization of the amino acids arginine, citrulline and ornithine is catalyzed by enzymes that are encoded in therocABCandrocDEFoperons and by therocGgene. Expression of these genes is under control of the alternative sigma factor SigL. RNA polymerase associated to this sigma factor depends on an ATP-hydrolyzing transcription activator to initiate transcription. The RocR protein acts as transcription activator for therocgenes. In this work, we have studied the contributions of all enzymes of the Roc pathway to the degradation of arginine, citrulline and ornithine. This identified the previously uncharacterized RocB protein as responsible for the conversion of citrulline to ornithine.In vitroassays with the purified enzyme suggest that it acts as a manganese-dependent N-carbamoyl-L-ornithine hydrolase that cleaves citrulline to ornithine and carbamate. So far, the molecular effector that triggers transcription activation by RocR has not been unequivocally identified. Using a combination of transcription reporter assays and biochemical experiments we demonstrate that ornithine is the molecular inducer for RocR activity. Our work suggests that binding of ATP to RocR triggers its hexamerization, and binding of ornithine then allows ATP hydrolysis and activation ofrocgene transcription. Thus, ornithine is the central molecule of therocdegradative pathway as it is the common intermediate of arginine and citrulline degradation and the molecular effector for the transcription regulator RocR.

IMPORTANCE

Amino acids serve as building blocks for protein biosynthesis in each living cell but can also be used as sources of carbon, energy and nitrogen. In this work we have identified ornithine as the central player in the utilization of arginine, citrulline and ornithine in the Gram-positive bacteriumB. subtilis. Ornithine is the common intermediate after the first steps of arginine and citrulline degradation. We have identified the so far uncharacterized protein RocB as the enzyme responsible for the cleavage of citrulline to ornithine and carbamate. Moreover, we demonstrate that ornithine is the molecular effector that triggers ATPase activity of the transcription factor RocR. Binding of ornithine to RocR and the subsequent hydrolysis of ATP allow a functional interaction with the alternative sigma factor SigL and subsequent transcription activation of all genes of the degradative pathway.
Nucleus accumbens neurons dynamically encode positive and aversive associative learning
Authors: Deseyve Catarina , Domingues Ana Verónica , Carvalho Tawan T. A. , Vieitas-Gaspar Natacha , Pinto Luísa , Sousa Nuno , Coimbra Bárbara , Rodrigues Ana João , Soares-Cunha Carina
Published: April 2023

To survive, individuals must learn to associate cues in the environment with emotionally relevant outcomes. This association is partially mediated by the nucleus accumbens (NAc), a key brain region of the reward circuit that is mainly composed by GABAergic medium spiny neurons (MSNs), that express either dopamine receptor D1 or D2. Recent studies showed that both populations can drive reward and aversion, however, the activity of these neurons during appetitive and aversive Pavlovian conditioning remains to be determined.

Here, we investigated the relevance of D1- and D2-neurons in Pavlovian associations, by measuring calcium transients with fiber photometry during appetitive and aversive Pavlovian tasks. Sucrose was used as a positive unconditioned stimulus (US) and foot shock was used as a negative US. We show that during appetitive Pavlovian conditioning, D1- and D2-neurons exhibit a general decrease in activity in response to CS and to US across learning, with dynamic, and partially overlapping, activity responses to CS and US. During the aversive Pavlovian conditioning, D1- and D2-neurons showed an increase in the activity in response to the CS and to the US (shock).

Our data supports a synchronous role for D1- and D2-neurons in appetitive and aversion processing.
Mutualism at the leading edge: Insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion
Authors: Martignoni Maria M , Tyson Rebecca C , Kolodny Oren , Garnier Jimmy
Published: April 2023

The evolution of mutualism between host and symbiont communities plays an essential role in maintaining ecosystem function and should therefore have a pro-found effect on their range expansion dynamics. In particular, the presence of mutualistic symbionts at the leading edge of a host-symbiont community should enhance its propagation in space. We develop a theoretical framework that captures the eco-evolutionary dynamics of host-symbiont communities, to investigate how the evolution of resource exchange may shape community structure during range expansion. We consider a community with symbionts that are mutualistic or parasitic to various degrees, where parasitic symbionts receive the same amount of resource from the host as mutualistic symbionts, but at lower cost. The selective advantage of parasitic symbionts over mutualistic ones is strengthened with resource availability (i.e. with host density), promoting mutualism at the range edges, where host density is low, and parasitism in the population core, where host density is higher. This spatial selection also influences the speed of spread. We find that the host growth rate (which depends on the average benefit provided by the symbionts) is maximal at the range edges, where symbionts are more mutualistic, and that host-symbiont communities with high symbiont density at their core (e.g. resulting from more mutualistic hosts) spread faster into new territories. These results indicate that the expansion of host-symbiont communities is pulled by the hosts but pushed by the symbionts, in a unique push-pull dynamic where both the host and symbionts are active and tightly-linked players.