bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome
Authors: White Benjamen , Lux Thomas , Rusholme-Pilcher Rachel , Juhász Angéla , Kaithakottil Gemy , Duncan Susan , Simmonds James , Rees Hannah , Wright Jonathan , Colmer Josh , Ward Sabrina , Joynson Ryan , Coombes Benedict , Irish Naomi , Henderson Suzanne , Barker Tom , Chapman Helen , Catchpole Leah , Gharbi Karim , Bose Utpal , Okada Moeko , Handa Hirokazu , Nasuda Shuhei , Shimizu Kentaro K. , Gundlach Heidrun , Lang Daniel , Naamati Guy , Legg Erik J. , Bharti Arvind K. , Colgrave Michelle L. , Haerty Wilfried , Uauy Cristobal , Swarbreck David , Borrill Philippa , Poland Jesse A. , Krattinger Simon G. , Stein Nils , Mayer Klaus F.X. , Pozniak Curtis ,   10+ Wheat Genome Project, Spannagl Manuel , Hall Anthony 
Published: January 2024

AbstractWheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome withde novoannotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of thesede novoannotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.
Appropriate glycemic management protects the germline but not uterine environment in type 1 diabetes
Authors: Zhao Allan , Jiang Hong , Palomares Arturo Reyes , Larsson Alice , He Wenteng , Grünler Jacob , Zheng Xiaowei , Rodriguez Wallberg Kenny A. , Catrina Sergiu-Bogdan , Deng Qiaolin 
Published: January 2024

AbstractEmerging evidence indicates that parental diseases can impact the health of subsequent generations through epigenetic inheritance. Recently, it was shown that maternal diabetes alters the metaphase II oocyte transcriptome, causing metabolic dysfunction in offspring. However, the type 1 diabetes (T1D) mouse models frequently utilized in previous studies may be subject to several confounding factors as a result of severe hyperglycemia. This limits clinical translatability due to improvements in glycemic control for T1D subjects. Therefore, we optimized a T1D mouse model to investigate the effects of appropriately managed maternal glycemic levels on oocytes and intrauterine development. We show that diabetic mice with appropriate glycemic control exhibited better long-term health outcomes, which maintains the oocyte transcriptome and chromatin accessibility. Moreover, we find that human oocytes undergoing in vitro maturation challenged with mildly increased levels of glucose, reflecting appropriate glycemic management, also retained their transcriptome. However, the fetal growth and placental function were still affected despite appropriate glycemic control, underscoring the uterine environment rather than the germline as a pathological factor for developmental programming in appropriately managed diabetes.
Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria
Authors: Kropp Ashleigh , Gillett David L. , Venugopal Hari , Gonzálvez Miguel A. , Lingford James P. , Barlow Christopher K. , Zhang Jie , Greening Chris , Grinter Rhys 
Published: January 2024

AbstractDiverse bacteria and archaea use atmospheric carbon monoxide (CO) as an energy source during long-term survival. This process enhances the biodiversity of soil and marine ecosystems globally and removes 250 million tonnes of a toxic, climate-relevant pollutant from the atmosphere each year. Bacteria use [MoCu]-carbon monoxide dehydrogenases (Mo-CODH) to convert CO to carbon dioxide, then transfer the liberated high-energy electrons to the aerobic respiratory chain. However, given no high-affinity Mo-CODH has been purified, it is unknown how these enzymes oxidise CO at low concentrations and interact with the respiratory chain. Here we resolve these knowledge gaps by analysing Mo-CODH (CoxSML) and its hypothetical partner CoxG fromMycobacterium smegmatis. Kinetic and electrochemical analyses show purified Mo-CODH is a highly active high-affinity enzyme (Km= 139 nM,kcat= 54.2 s-1). Based on its 1.85 Å resolution cryoEM structure, Mo-CODH forms a CoxSML homodimer similar to characterised low-affinity homologs, but has distinct active site coordination and narrower gas channels that may modulate affinity. We provide structural, biochemical, and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chainviathe membrane-bound menaquinone-binding protein CoxG. Consistently, CoxG is required for CO-driven respiration, extracts menaquinone from mycobacterial membranes, and binds quinones in a hydrophobic pocket. Finally, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of a biogeochemically and ecologically important process, while demonstrating that the newly discovered process of long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
RNA regulates cohesiveness and porosity of a biological condensate
Authors: Chou Han-Yi , Aksimentiev Aleksei 
Published: January 2024

AbstractBiological condensates have emerged as key elements of a biological cell function, concentrating disparate biomolecules to accomplish specific biological tasks. RNA was identified as a key ingredient of such condensates, however, its effect on the physical properties of the condensate was found to depend on the condensate’s composition while its effect on the microstructure has remained elusive. Here, we characterize the physical properties and the microstructure of a protein–RNA condensate by means of large-scale coarse-grained (CG) molecular dynamics simulations. By developing a custom CG model of RNA compatible with a popular CG model of proteins, we systematically investigate the structural, thermodynamic, and kinetic properties of condensate droplets containing thousands of individual protein and RNA molecules over a range of temperatures. While we find RNA to increase the condensate’s cohesiveness, its effect on the condensate’s fluidity is more nuanced with longer molecules compacting the condensate and making it less fluid. We show that a biological condensate has a sponge-like morphology of interconnected channels of size that increases with temperature and decreases in the presence of RNA. Our results suggest that longer RNA form a dynamic scaffold within a condensate, regulating not only its fluidity but also permeability to intruder molecules.
Hydrophobic bulk conservation and genetic code determine the pattern of prokaryotic genome organization
Authors: Teng Wenkai , Zhou Yangkai , Zheng Lingling , Xu Yongqian , Rao Yangzhi , Chen Siruo , Xia Tian , Shu Wensheng , Chen Mengyun 
Published: January 2024

AbstractProkaryotic genomes in general exhibit marked organizational asymmetry, and differ substantially in GC-skew, AT-skew, and GS-bias (gene strand bias). Despite enigmatic origins, these organizational features and genomic GC-content have been described to be widely associated with each other recently, providing an opportunity to probe the evolutionary mechanisms. By analyzing sequence data of 4,012 leading strands from all available representative genomes, we found that the unusual nucleotide usage of coding genes under low GC-content contributed to a shift between two organizational patterns in the context of mutational biases. Analysis of artificially established neutral and natural models further suggests that in genes both GC-skew and AT-skew increase with decreasing GC-content, mostly contributed by synonymous substitutions because of genetic code, and by nonsynonymous substitutions because of hydrophobic bulk conservation in amino acid usage, respectively. This novel mechanistic framework in our study highlights the importance of evolutionary processes “operating at lower levels of organization” in the microbial world.
Stimulus-induced gamma sources reduce in power but not in spatial extent with healthy aging in human EEG
Authors: Biswas Ankan , Kumar Wupadrasta Santosh , Sharma Kanishka , Ray Supratim 
Published: January 2024

AbstractAging alters brain structure and function, and studying such changes may help understand the neural basis underlying aging and devise interventions to detect deviations from healthy progression. Electroencephalogram (EEG) offers an effective way to study healthy aging owing to its high temporal resolution and affordability. Recent studies have shown that narrow- band stimulus-induced gamma oscillations (20-70 Hz) in EEG, induced with cartesian gratings in a fixation task paradigm, weaken with healthy aging and onset of Alzheimer’s Disease (AD) while remaining highly reproducible for a given subject, and thus hold promise as potential biomarkers. However, functional connectivity (FC) sometimes changes in a different way compared to sensor power with aging. This difference could be potentially addressed by studying how underlying gamma sources change with aging, since either a reduction in source power or a shrinkage of the sources (or both) could reduce the power in the sensors but may have different effects on other measures such as FC. We therefore reconstructed EEG gamma sources through a linear inverse method called exact Low-resolution Tomography Analysis (eLORETA) on a large (N=217) cohort of healthy elderly subjects (>50 years). We further characterized gamma distribution in cortical space as an exponential fall-off from a seed voxel with maximal gamma source power to delineate a reduction in magnitude versus shrinkage. We found significant reduction in magnitude but not shrinkage with healthy aging. Overall, our results shed light on changes in EEG gamma source distribution with healthy aging, which could provide clues about underlying neural mechanisms.
Measuring concentration of nanoparticles in polydisperse mixtures using interferometric nanoparticle tracking analysis (iNTA)
Authors: Kashkanova Anna D. , Albrecht David , Küppers Michelle , Blessing Martin , Sandoghdar Vahid 
Published: January 2024

AbstractQuantitative measurements of nanoparticle concentration in liquid suspensions are in high demand, for example, in the medical and food industries. Conventional methods remain unsatisfactory, especially for polydisperse samples with overlapping size ranges. Recently, we introduced interferometric nanoparticle tracking analysis (iNTA) as a new method for high-precision measurement of nanoparticle size and refractive index. Here, we show that by counting the number of trajectories that cross the focal plane, iNTA can measure concentrations of subpopulations in a polydisperse mixture in a quantitative manner and without the need for a calibration sample. We evaluate our method on both monodisperse samples and mixtures of known concentrations. Furthermore, we assess the concentration of SARS-CoV-2 in supernatant samples obtained from infected cells.
A network optimisation condition uncovers the role of functional groups in the feasibility and dynamical stability of microbial model ecosystems
Authors: Buchenel Léo , Bonhoeffer Sebastian , Pascual-García Alberto 
Published: January 2024

AbstractInvestigating mechanisms favouring stable coexistence of complex microbial communities is central to understand their formation and maintenance in the natural environment and, eventually, controlling and designing synthetic communities. In this work, we studied microbial model ecosystems in which consumption and secretion of resources was explicit, determining ecological interactions (e.g. competition for resources, facilitation, mutualism). We found a sufficient condition for the dynamical stability of microbial model ecosystems. This condition allowed us to derive an objective function whose optimization selected specific configurations of consumption and secretion of resources. Optimized configurations stood out as a compromise between having a large parameter space in which species coexistence was feasible (dominated by systems in which microbes do not secrete any resources), and having a high rate of return to equilibrium after a perturbation (dominated by systems in which every microbe secrete all resources). We explained the behaviour observed for optimized configurations by noting that they host sets of species with differentiated niches -as defined by their consumption and secretion strategies-, termed functional groups. We speculated that, since increasing the number of functional groups increased the number of niches, competition between species should be reduced, favouring coexistence. Therefore, our results suggest that the formation of functional groups have an important role in microbial coexistence, which has ramifications for the design of complex microbial communities.
Photo-crosslinking hERG channels causes a U.V.-driven, state-dependent disruption of kinetics and voltage dependence of activation
Authors: Codding Sara J. , Trudeau Matthew C. 
Published: January 2024

AbstractHuman ether-à-go-go related gene (hERG) voltage-activated potassium channels are critical for cardiac excitability. Characteristic slow closing (deactivation) in hERG is regulated by direct interaction between the N-terminal Per-Arnt-Sim (PAS) domain and the C-terminal cyclic nucleotide binding homology domain (CNBHD). We aim to understand how the PAS domain that is distal to the pore rearranges during gating to allosterically regulate the channel pore (and ion flux). To achieve this, we utilized the non-canonical amino acid 4-Benzoyl-L-phenylalanine (BZF) which is a photo-activatable cross-linkable probe, that when irradiated with ultraviolet (U.V.) light forms a double radical capable of forming covalent cross-links with C-H bond-containing groups, enabling selective and potent U.V.-driven photoinactivation of ion channel dynamics. Here we incorporate BZF directly into the hERG potassium channel PAS domain at three locations (G47, F48, and E50) using TAG codon suppression technology. hERG channels with BZF incorporated into the PAS domain (hERG-BZF) showed a significant change in the biophysical properties of the channel. hERG-G47BZF activated slowly when irradiated in the closed state (-100mV) but deactivated quickly when irradiated in both the open (0mV) and closed state. hERG-F48BZF channels showed a state independent and U.V. dose-dependent change in channel activation (slowing down) and channel deactivation (speeding up), as well as a marked change (right-shift) in the voltage-dependence of conductance. When irradiated at -100 mV hERG-E50BZF showed a state dependent and U.V. dose-dependent change in a channel activation (slowing down) and deactivation (speeding up) of channel deactivation, as well as a marked change (right-shift) in the voltage-dependence of conductance that occurred only when the channel was irradiated in the closed state (-100mV). This approach demonstrated that direct photo-crosslinking of the PAS domain in hERG channels causes a measurable change in biophysical parameters and more broadly stabilized the closed state of the channel. We propose that altered channel gating is as a direct result of reduced dynamic motions in the PAS domain of hERG due to photo-chemical crosslinking.
Traveling waves shape neural population dynamics enabling predictions and internal model updating
Authors: Mohanta S , Cleveland DM , Afrasiabi M , Rhone AE , Górska U , Cooper Borkenhagen M , Sanders RD , Boly M , Nourski KV , Saalmann YB 
Published: January 2024

AbstractThe brain generates predictions based on statistical regularities in our environment. However, it is unclear how predictions are optimized through iterative interactions with the environment. Because traveling waves (TWs) propagate across the cortex shaping neural excitability, they can carry information to serve predictive processing. Using human intracranial recordings, we show that anterior-to-posterior alpha TWs correlated with prediction strength. Learning about priors altered neural state space trajectories, and how much it altered correlated with trial-by-trial prediction strength. Learning involved mismatches between predictions and sensory evidence triggering alpha-phase resets in lateral temporal cortex, accompanied by stronger alpha phase-high gamma amplitude coupling and high-gamma power. The mismatch initiated posterior-to-anterior alpha TWs and change in the subsequent trial’s state space trajectory, facilitating model updating. Our findings suggest a vital role of alpha TWs carrying both predictions to sensory cortex and mismatch signals to frontal cortex for trial-by-trial fine-tuning of predictive models.
Broadly conserved FlgV controls flagellar assembly andBorrelia burgdorferidissemination in mice
Authors: Zamba-Campero Maxime , Soliman Daniel , Yu Huaxin , Lasseter Amanda G. , Chang Yuen-Yan , Liu Jun , Aravind L. , Jewett Mollie W. , Storz Gisela , Adams Philip P. 
Published: January 2024

ABSTRACTFlagella propel pathogens through their environments yet are expensive to synthesize and are immunogenic. Thus, complex hierarchical regulatory networks control flagellar gene expression. Spirochetes are highly motile bacteria, but peculiarly in the Lyme spirocheteBorrelia burgdorferi, the archetypal flagellar regulator σ28is absent. We rediscovered genebb0268inB. burgdorferiasflgV,a broadly-conserved gene in the flagellar superoperon alongside σ28in many Spirochaetes, Firmicutes and other phyla, with distant homologs in Epsilonproteobacteria. We found thatB. burgdorferiFlgV is localized within flagellar motors.B. burgdorferilackingflgVconstruct fewer and shorter flagellar filaments and are defective in cell division and motility. During the enzootic cycle,B. burgdorferilackingflgVsurvive and replicate inIxodesticks but are attenuated for dissemination and infection in mice. Our work defines infection timepoints when spirochete motility is most crucial and implicates FlgV as a broadly distributed structural flagellar component that modulates flagellar assembly.
Transposon fusion gave birth toFem,Bombyx morifemale determining gene
Authors: Lee Jung , Fujimoto Toshiaki , Yamaguchi Katsushi , Shigenobu Shuji , Sahara Ken , Toyoda Atsushi , Shimada Toru 
Published: January 2024

AbstractFemis a W-linked piRNA precursor, andFempiRNA is a master gene of female determination inBombyx mori. SinceFemhas significantly low similarity to any known sequences and the origin ofFemremains unclear, two hypotheses have been proposed for the origin ofFem. The first one is thatFemis an allele ofMasc,while the second one is thatFemarose by transposition ofMasc. To draw a solid conclusion, we determined the W chromosome sequences ofB. moriand a closely relative bombycid species ofTrilocha varianswith aFem-independent sex determination system. Comprehensive genome comparison led us to the “third” hypothesis:Femis a chimeric sequence of transposons. Although we still cannot completely exclude the first hypothesis, at least a large portion of the parts other than the 44-bpMascsimilarity region is derived from transposons, and even the 44-bp region could correspond to the boundary of the two transposons, gypsy and satellite DNA.
Regulators H-NS and LeuO inversely control swarming motility and biofilm formation inVibrio parahaemolyticus
Authors: Bhide S.M. , Tague J.G. , Andrews J. A. , Lichty K.E. Boas , Boyd E.F. 
Published: January 2024

Vibrio parahaemolyticusis a halophile present in marine environments worldwide and is a leading cause of bacterial seafood-borne gastroenteritis. Free livingVibrio parahaemolyticusplanktonic cells can either attach to surfaces to form swarming cells or develop into a sessile three-dimensional biofilm structure. Swarming motility requires lateral flagella (lafoperon) and the expression of the surface sensing operonscrABCto produce a spreading cauliflower colony morphology. Biofilms are formed from capsule polysaccharide (CPS) encoded by thecpsA-Koperon that is positively regulated by CpsR and CpsQ. In enteric bacteria, H-NS is a global gene silencer and LeuO is an antagonist of H-NS. In this work, we examined the role of these regulators in the decision between swarming and biofilm behaviors using deletion mutants ofleuO, hns,and a double deletionleuO/hns. The wild type and ΔleuOstrains produced swarming colonies whereas Δhnsproduced a hyper swarming whereas in ΔleuO/Δhns,the phenotype reverted to wild type. Transcriptional reporter assays of PlafB-gfpand PscrA-gfpshowed significantly increased fluorescence in Δhnscompared to wild type. In the ΔleuO/Δhnsmutant, PlafB-gfpfluorescence reverted to wild type levels and PscrA-gfpshowed increased fluorescence compared to wild type. In CPS assays, ΔleuOhad a less dense rugose morphology compared to wild type and Δhnsproduced a smooth colony, which also produced significantly less biofilm. ΔleuO/Δhnshad an opaque morphology and produced significantly more biofilm. Reporter expression assays of PcpsA-gfpand PcpsR-gfpconfirmed the roles of both H-NS and LeuO in CPS and biofilm formation.ImportanceThis study determined the role of LeuO and H-NS in controlling the decision between two surface based behaviors, swarming motility and sessile biofilm formation inV. parahaemolyticus. The effects of deletions ofleuO,hns,and a double ΔleuO/Δhnsmutant showed that H-NS was a negative regulator of swarming, but a positive regulator of biofilm formation. The mechanism of this control was in part due to H-NS inhibition of LeuO at loci required for swarming and biofilm formation.