bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional annotation hypothetical proteins: a world to be explored in drug development in Trypanosomatids
Authors: de Lima Raissa Santos , Bulla Ana Carolina Silva , da Silva Manuela Leal
Published: December 2023

Hypothetical proteins can provide an alternative pathway for finding potential targets in the development of new drugs due to the fact that many Neglected tropical diseases are caused by Trypanosomatids (Chagas Disease, Leishmaniasis, and Human African Trypanosomiasis). In this work, we focus on applying functional prediction methods based on both sequence and structure to analyze the hypothetical proteins of the pathogenic agents that cause these diseases:T. cruzi(Tcr),T. brucei brucei(Tbr),T. brucei gambiense(Tbg),L. infantum(Lif),L. donovani(Ldo), andL. braziliensis(Lbz). By consulting databases and servers, we have predicted functional domains for twenty-six proteins in Tcr, thirteen in Tbr, fifteen in Tbg, ten in Lif, and one in both Ldo and Lbz. With the goal of developing multi-target therapies, we grouped the domains according to how they are shared among the organisms and investigated those that are shared among more species. By examining the existing literature using specific search strategies, we described what has already been reported for these domains and also analyzed protein structures and sequences, describing mutations among the species and potential drug sites. The published works have unveiled that some of these domains are non-essential for trypanosomatids, like the TRX domain, while others demand further investigation due to a lack of information about metabolic processes (UFC1, Ufm1, ACBP, AAA 18, and Fe-S). Although, we have identified three noteworthy domains that hold promise as targets: TPR, which plays a crucial role in the ciliogenesis process; Nuc deoxyrib tr, essential in purine recycling and recovery mechanisms; and MIX, important for protein targeting and the assembly of complexes such as COX. These three domains are promising targets for drug development due to their conservation, their potential to affect multiple species and their exclusivity.
The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastidclpP1intron2 splicing
Authors: Zhang Liqun , Zhu Yawen , Yang Keyi , Liao Fangsheng , Wang Jiaqi , Zhou Shuya , Huang Jirong , Cui Yong-Lan , Huang Weihua
Published: December 2023

Plastid intron splicing is an essential step for gene expression. Although many nucleus-encoded splicing factors have been identified for plastid intron splicing, how these proteins coordinately regulate intron splicing is unclear. Here we found that EMB1006, an Arabidopsis P-type PPR protein, is required for splicing several plastid introns includingclpP1intron 2 by analyzing the level of intron retention in its knockdown lines and RIP-qPCR (RNA immunoprecipitation and quantitative PCR) assay. In addition, RNA electrophoretic mobility shift assay (REMSA) showed that EMB1006 specifically binds to the sequence UUACCAAACGU close to the 3’ end ofclpP1exon 2in vitro. Furthermore, yeast two hybrid (Y2H), split luciferase complementation (Split-LUC) and semi-in vivopull-down assays showed that EMB1006 interacts with both EMB1270 and CFM2, which also interact each other. Taken together, our data indicate that EMB1006 forms a complex with EMB1270 and CFM2 to facilitateclpP1intron 2 splicing in chloroplasts.
Trying harder: how cognitive effort sculpts neural representations during working memory
Authors: Master Sarah L. , Li Shanshan , Curtis Clayton E.
Published: December 2023

The neural mechanisms by which motivational factors influence cognition remain unknown. Using fMRI, we tested how cognitive effort impacts working memory (WM). Participants were precued whether WM difficulty would be hard or easy. Hard trials demanded more effort as a later decision required finer mnemonic precision. Behaviorally, pupil size was larger and response times were slower on hard trials suggesting our manipulation of effort succeeded. Neurally, we observed robust persistent activity in prefrontal cortex, especially during hard trials. We found strong decoding of location in visual cortex, where accuracy was higher on hard trials. Connecting these across-region effects, we found that the amplitude of delay period activity in frontal cortex predicted decoded accuracy in visual cortex on a trial-wise basis. We conclude that the gain of persistent activity in frontal cortex may be the source of effort-related feedback signals that improve the quality of WM representations stored in visual cortex.
snPATHO-seq: unlocking the pathology archives
Authors: Wang Taopeng , Harvey Kate , Morlanes Javier Escudero , Kiedik Beata , Al-Eryani Ghamdan , Greenwald Alissa , Kalavros Nikolaos , Dezem Felipe Segato , Ma Yuling , Pita-Juarez Yered H. , Wise Kellie , Degletagne Cyril , Elz Anna , Hadadianpour Azi , Johanneson Jack , Pakiam Fiona , Ryu Heeju , Newell Evan W. , Tonon Laurie , Kohlway Andrew , Drennon Tingsheng , Abousoud Jawad , Stott Ryan , Lund Paul , Durruthy Jens , Vallejo Andres F , Kaczorowski Dominik , Warren Joanna , Butler Lisa M. , O’Toole Sandra , Plummer Jasmine , Vlachos Ioannis S , Lundeberg Joakim , Swarbrick Alexander , Martelotto Luciano
Published: December 2023

Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low DNA and RNA quality. In this study, leveraging recent single-cell genomic technology advances, we introduce a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples.
KatG inactivation generates vulnerabilities in isoniazid resistant strains ofMycobacterium tuberculosis
Authors: Wang XinYue , Jowsey William J , Cheung Chen-Yi , Seeto Noon E , Waller Natalie JE , Chrisp Michael T , Peterson Amanda L , Nijagal Brunda , Fineran Peter C , Cook Gregory M , Jackson Simon A , McNeil Matthew B
Published: December 2023

Drug-resistant strains ofMycobacterium tuberculosisare a major global health problem. Resistance to the front-line antibiotic isoniazid is often associated with mutations in thekatGencoded bifunctional catalase-peroxidase. We hypothesised that perturbed KatG activity would generate collateral vulnerabilities in INH-resistantkatGmutants, providing new pathways to combat isoniazid resistance. Here, we used whole genome CRISPRi screens, transcriptomics, and metabolomics to generate a genome-wide map of cellular vulnerabilities in aM. tuberculosis katGmutant. We discovered that metabolic and transcriptional remodelling compensates for the loss of KatG but in doing so generates vulnerabilities in ribosome biogenesis, and nucleotide and amino acid metabolism. These vulnerabilities were more sensitive to inhibition in an isoniazid-resistantkatGmutant underin vitroand host-relevant conditions and translated to clinical populations. These findings provide an experimental framework for developing novel strategies to combat antimicrobial resistance inM. tuberculosisand other bacterial pathogens.
High sugar diets can increase susceptibility to bacterial infection inDrosophila melanogaster
Authors: Darby Andrea M. , Okoro Destiny O. , Aredas Sophia , Frank Ashley M. , Pearson William H. , Dionne Marc S. , Lazzaro Brian P.
Published: December 2023

Overnutrition with dietary sugar can worsen infection outcomes in diverse organisms including insects and humans, generally through unknown mechanisms. In the present study, we show that adultDrosophila melanogasterfed high-sugar diets became more susceptible to infection by the Gram-negative bacteriaProvidencia rettgeriandSerratia marcescens,although diet had no significant effect on infection by Gram-positive bacteriaEnterococcus faecalisorLactococcus lactis.We found thatP. rettgeriandS. marcescensproliferate more rapidly inD. melanogasterfed a high-sugar diet, resulting in increased probability of host death.D. melanogasterbecome hyperglycemic on the high-sugar diet, and we find evidence that the extra carbon availability may promoteS. marcescensgrowth within the host. However, we found no evidence that increased carbon availability directly supports greaterP. rettgerigrowth.D. melanogasteron both diets fully induce transcription of antimicrobial peptide (AMP) genes in response to infection, butD. melanogasterprovided with high-sugar diets show reduced production of AMP protein. Thus, overnutrition with dietary sugar may impair host immunity at the level of AMP translation. Our results demonstrate that dietary sugar can shape infection dynamics by impacting both host and pathogen, depending on the nutritional requirements of the pathogen and by altering the physiological capacity of the host to sustain an immune response.

Author Summary

Diet has critical impact on the quality of immune defense, and high-sugar diets increase susceptibility to bacterial infection in many animals. Yet it is unknown which aspects of host and pathogen physiology are impacted by diet to influence infection dynamics. Here we show that high-sugar diets increase susceptibility to some, but not all, bacterial infections inDrosophila. We find that feeding on high sugar diet impairs the host immune response by reducing the level of antimicrobial peptides produced. The expression of genes encoding these peptides is not affected, so we infer that protein translation is impaired. We further show that flies on high-sugar diets are hyperglycemic, and that some pathogens may use the excess sugar in the host to promote growth during the infection. Thus, our study demonstrates that dietary impacts on infection outcome arise through physiological effects on both the host and pathogen.
Tracking transcription-translation coupling in real-time
Authors: Qureshi Nusrat Shahin , Duss Olivier
Published: December 2023

A central question in biology is how macromolecular machines function cooperatively. In bacteria, transcription and translation occur in the same cellular compartment and can be physically and functionally coupled. While several recently published high-resolution structures of the ribosome-RNA polymerase (RNAP) complex provided first mechanistic insight into the coupling process, we do not know how these structural snapshots are placed along a dynamic reaction trajectory. Here, we reconstitute a complete active transcription-translation system and develop multi-color single-molecule fluorescence microscopy experiments to directly and simultaneously track transcription elongation, translation elongation and the physical and functional coupling between the ribosome and the RNAP in real-time. Our data show that the ribosome slows down while colliding with the RNAP and that coupling following a collision becomes less efficient. Unexpectedly, physical coupling can occur with hundreds of nucleotides of intervening mRNA between both machineries by mRNA looping, and increases in efficiency in presence of NusG. We detect active transcription elongation during mRNA looping and show that NusA-paused RNAPs can be activated by the ribosome by long-range physical coupling. We provide an alternative explanation on how the ribosome can rescue RNAP from frequent pausing without requiring collisions by a closely trailing ribosome. Our data mechanistically highlight an example of how macromolecular machines central to gene expression physically and functionally cooperate.
Heterogeneous collateral effects in daptomycin-resistantE. faecalis
Authors: Huynh Anh , Maltas Jeff , Wood Kevin B.
Published: December 2023

Daptomycin, a cyclic lipopeptide antibiotic that targets the cell membrane, is an important therapeutic option for treating multi-drug-resistant infections, including vancomycin-resistant enterococci (VRE). Recent work has uncovered an array of daptomycin resistance mechanisms in enterococci, but relatively little is known about how these molecular defenses contribute to collateral effects–that is, to increased resistance or sensitivity to other drugs. In this work, we investigate collateral effects that arise during daptomycin adaptation ofE. faecalisin four independent laboratory-evolved populations. Using a combination of growth assays and both single isolate and population sequencing, we identified DAP-resistant lineages with mutations in one or more genes previously associated with DAP resistance, and these isolates are characterized by divergent phenotypic properties–including different levels of DAP resistance and different growth rates (i.e. fitness costs) in drug-free media. Interestingly, we also observed strongly divergent collateral responses to different antibiotics, particularly CRO, with collateral resistance arising in mutants harboring DAP-resistance mutations in cardiolipin synthetase (cls) or in genes linked to the two-component signaling system YxdJK (bceRor a regulated transporterycvR). By contrast, mutations inliaX, a component of a LiaFSR two-component signaling system, arose in two of the four populations, with point mutations associated with CRO-sensitivity and a large structural integration of plasmid pTEF3 associated with extreme CRO-sensitivity and a dramatically reduced growth rate. Our results reveal considerable phenotypic differences in mutations targeting the LiaSFR system and highlight trade-offs between resistance to daptomycin, collateral profiles (most notably to CRO), and drug-free growth rates in evolving lineages. As a whole, these results underscore how rich–and remarkably diverse–evolutionary dynamics can emerge even in parallel populations adapting to simple daptomycin escalation protocols.
Reconstructing Spatial Transcriptomics at the Single-cell Resolution with BayesDeep
Authors: Jiang Xi , Dong Lei , Wang Shidan , Wen Zhuoyu , Chen Mingyi , Xu Lin , Xiao Guanghua , Li Qiwei
Published: December 2023

Spatially resolved transcriptomics (SRT) techniques have revolutionized the characterization of molecular profiles while preserving spatial and morphological context. However, most next-generation sequencing-based SRT techniques are limited to measuring gene expression in a confined array of spots, capturing only a fraction of the spatial domain. Typically, these spots encompass gene expression from a few to hundreds of cells, underscoring a critical need for more detailed, single-cell resolution SRT data to enhance our understanding of biological functions within the tissue context. Addressing this challenge, we introduce BayesDeep, a novel Bayesian hierarchical model that leverages cellular morphological data from histology images, commonly paired with SRT data, to reconstruct SRT data at the single-cell resolution. BayesDeep effectively model count data from SRT studiesviaa negative binomial regression model. This model incorporates explanatory variables such as cell types and nuclei-shape information for each cell extracted from the paired histology image. A feature selection scheme is integrated to examine the association between the morphological and molecular profiles, thereby improving the model robustness. We applied BayesDeep to two real SRT datasets, successfully demonstrating its capability to reconstruct SRT data at the single-cell resolution. This advancement not only yields new biological insights but also significantly enhances various downstream analyses, such as pseudotime and cell-cell communication.
Tree species richness and evenness affect forest biomass differently across biogeographic regions
Authors: Ondei Stefania , Buettel Jessie C. , Aandahl R. Zach , Brook Barry W. , Alroy John , Yates Luke A.
Published: December 2023

The relationship between tree species diversity, measures of forest structure, and forest biomass has long been debated, with local- or continental-scale studies often finding contrasting results. Given the importance of forests as global carbon sinks, understanding the characteristics that underpin biomass accumulation is thus a critical component of mitigating climate change. Here we present a global analysis of 11,400 forest plots, sourced from scientific publications and forest inventories, to investigate the association of forest basal area (used as a proxy for biomass) with stem density and measures of tree species diversity (richness and evenness). We used generalised additive models to account for the confounding effects of climate and spatial signal and we modelled the density, climate, and diversity effects both globally and for each biogeographic region. Stem density showed a strong positive association with basal area across all biogeographic regions, while the effect of species richness varied. In the Palearctic, Nearctic, and Neotropical biogeographic regions, basal area was positively associated with species richness, although this was only detectable for lower values of basal area. In the Ethiopian and Oriental biogeographic regions there was no relationship between richness and basal area, while in the Australian biogeographic regions it was negative. The weak-to-no association between species evenness and basal area in all bioregions other than Australia suggests that the overall correlation emerges from processes operating at more local scales. Our results highlight the importance of accounting for biogeographic processes when evaluating strategies to mitigate climate change and support nature conservation.
Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV)
Authors: Bristy Nishat Anjum , Fu Xuecong , Schwartz Russell
Published: December 2023

Clonal lineage inference (“tumor phylogenetics”) has become a crucial tool for making sense of somatic evolution processes that underlie cancer development and are increasingly recognized as part of normal tissue growth and aging. The inference of clonal lineage trees from single cell sequence data offers particular promise for revealing processes of somatic evolution in unprecedented detail. However, most such tools are based on fairly restrictive models of the types of mutation events observed in somatic evolution and of the processes by which they develop. The present work seeks to enhance the power and versatility of tools for single-cell lineage reconstruction by making more comprehensive use of the range of molecular variant types by which tumors evolve. We introduce Sc-TUSV-ext, an integer linear programming (ILP) based tumor phylogeny reconstruction method that, for the first time, integrates single nucleotide variants (SNV), copy number alterations (CNA) and structural variations (SV) into clonal lineage reconstruction from single-cell DNA sequencing data. We show on synthetic data that accounting for these variant types collectively leads to improved accuracy in clonal lineage reconstruction relative to prior methods that consider only subsets of the variant types. We further demonstrate the effectiveness on real data in resolving clonal evolution in the presence of multiple variant types, providing a path towards more comprehensive insight into how various forms of somatic mutability collectively shape tissue development.
Divergent Epigenetic and Transcriptomic Reprogramming of Monocyte Subpopulations in Systemic Lupus Erythematosus
Authors: Ferreté-Bonastre Anna Guiomar , Martínez-Gallo Mónica , Morante-Palacios Octavio , Calvillo Celia Lourdes , Calafell-Segura Josep , Rodríguez-Ubreva Javier , Esteller Manel , Cortés-Hernández Josefina , Ballestar Esteban
Published: December 2023

Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classical monocytes into intermediate monocytes and non-classical monocytes, assuming diverse roles. In this study, we investigated the epigenetic and transcriptomic profiles of these three monocyte subsets in an SLE cohort. In addition to common DNA methylation and transcriptomic alterations, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on the monocyte differentiation process. SLE classical monocytes exhibited a stronger proinflammatory profile, with an interferon signature and were primed for macrophage differentiation. SLE non-classical monocytes displayed a phenotype related to T cell differentiation regulation, and a Th17-promoting phenotype. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT1 pathway. Integrating bulk datasets with single-cell RNA-seq data of SLE patients further supported the interferon signature in classical monocytes, associating intermediate and non-classical populations with exacerbated complement activation pathways. Our results indicate a subversion of the epigenome and transcriptome in monocyte differentiation toward non-classical subsets in SLE, impacting function, in relation to disease activity and progression.
The genomes of theMacadamiagenus
Authors: Sharma Priyanka , Masouleh Ardashir Kharabian , Constantin Lena , Topp Bruce , Furtado Agnelo , Henry Robert J.
Published: December 2023

Macadamia, a genus native to Eastern Australia, comprises four species,Macadamia integrifolia, M. tetraphylla, M. ternifolia,andM. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 to 40534 genes. The ks distribution plot ofMacadamiaandTelopeasuggestsMacadamiahas undergone a whole genome duplication event prior to divergence of the four species and thatTelopeagenome was duplicated more recently. Synteny analysis revealed a high conservation and similarity of the genome structure in all four species. Differences in the content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the species. An antimicrobial gene with a conserved cysteine motif was found in all four species. The four genomes provide reference genomes for exploring genetic variation across the genus in wild and domesticated germplasm to support plant breeding.
Cortical signatures of sleep are altered following effective deep brain stimulation for depression
Authors: van Rheede Joram J. , Alagapan Sankaraleengam , Denison Timothy J. , Riva-Posse Patricio , Rozell Christopher J. , Mayberg Helen S. , Waters Allison C. , Sharott Andrew
Published: December 2023

Deep brain stimulation (DBS) of the subcallosal cingulate cortex (SCC) is an experimental therapy for treatment-resistant depression (TRD). Chronic SCC DBS leads to long-term changes in the electrophysiological dynamics measured from local field potential (LFP) during wakefulness, but it is unclear how it impacts sleep-related brain activity. This is a crucial gap in knowledge, given the link between depression and sleep disturbances, and an emerging interest in the interaction between DBS, sleep, and circadian rhythms. We therefore sought to characterise changes in electrophysiological markers of sleep associated with DBS treatment for depression. We analysed key electrophysiological signatures of sleep – slow-wave activity (SWA, 0.5-4.5Hz) and sleep spindles – in LFPs recorded from the SCC of 9 patients who responded to DBS for TRD. This allowed us to compare the electrophysiological changes before and after 24 weeks of therapeutically effective SCC DBS.

SWA power was highly correlated between hemispheres, consistent with a global sleep state. Furthermore, SWA occurred earlier in the night after chronic DBS and had a more prominent peak. While we found no evidence for changes to slow wave power or stability, we found an increase in the density of sleep spindles. Our results represent a first-of-its-kind report on long-term electrophysiological markers of sleep recorded from the SCC in patients with TRD, and provides evidence of earlier NREM sleep and increased sleep spindle activity following clinically effective DBS treatment. Future work is needed to establish the causal relationship between long-term DBS and the neural mechanisms underlying sleep.

Conflict of interest statement

JJvR has received honoraria from Medtronic. TD is a founder and director of Amber who own Bioinduction Ltd, has received honoraria from Medtronic, and is an advisor for Cortec Neuro and Synchron. PR-P receives consulting fees from Abbott Labs, LivaNova, and Janssen Pharmaceuticals. HM receives consulting and Intellectual Property licensing fees from Abbott Labs. SA, CR, ACW and AS have nothing to declare.
Reengineering of an artificial protein cage for efficient packaging of active enzymes
Authors: Azuma Yusuke , Gaweł Szymon , Pasternak Monika , Woźnicka Olga , Pyza Elżbieta , Heddle Jonathan G.
Published: December 2023

Protein cages that readily encapsulate active enzymes of interest present useful nanotools for delivery and catalysis, wherein those with programmable disassembly characteristics serve as particularly attractive platforms. Here we establish a general guest packaging system based on an artificial protein cage, TRAP-cage, the disassembly of which can be induced by the addition of reducing agents. In this system, TRAP-cage with SpyCatcher moieties in the lumen was prepared using genetic modification of the protein building block and assembled into a cage structure with either monovalent gold ions or molecular crosslinkers. The resulting protein cage can efficiently capture guest proteins equipped with a SpyTag by simply mixing them in aqueous solution. This post-assembly loading system which circumvents the exposure of guests to thiol-reactive crosslinkers, enables packaging of enzymes possessing a catalytic cysteine or a metal cofactor while retaining their catalytic activity.
Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes
Authors: Paukner Dawn , Wildenberg Gregg A. , Badalamente Griffin S. , Littlewood Peter B. , Kronforst Marcus R. , Palmer Stephanie E. , Kasthuri Narayanan
Published: December 2023

1. Comparative anatomy is an important tool for investigating evolutionary relationships amongst species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations.

2. We describe a method using synchrotron source micro-x-ray computed tomography (syn-µXCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e.,butterfly and moth) eyes. Our pipeline allows for imaging at rates of ∼ 15 min/mm3at 600 nm3resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species independent manner thus removing any barrier to imaging any species of interest.

3. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species.

4. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.
Rhythmic sampling of multiple decision alternatives in the human brain
Authors: Siems Marcus , Cao Yinan , Tohidi-Moghaddam Maryam , Donner Tobias H , Tsetsos Konstantinos
Published: December 2023

Humans and other animals navigate real-world decisions by sequentially attending to (sampling) subsets of the available information. The neural mechanisms underlying the selective sampling of decision-relevant information remain unknown. Here we used magnetoencephalography (MEG) recordings and neural decoding to track the spontaneous dynamics of the locus and strength of covert attention as human participants performed a three-alternative perceptual choice task. The strength of covert attention fluctuated rhythmically around 11 Hz. At the peak of this oscillation, attention re-focused on the location of the previously sampled alternative, presumably promoting the in-depth evaluation of a single alternative. By contrast, at the trough, attention was oriented to a different alternative, that way facilitating the comparison between alternatives. Further, switching attention to a different alternative intrinsically reset the attentional rhythmicity. We propose rhythmic attentional sampling as a cognitive mechanism underpinning the flexible information processing necessary for key decision computations.
A conserved trypanosomatid differentiation regulator controls substrate attachment and morphological development inTrypanosoma congolense
Authors: Silvester Eleanor , Szoor Balazs , Ivens Alasdair , Awuah-Mensah Georgina , Gadelha Caterina , Wickstead Bill , Matthews Keith R.
Published: December 2023

Trypanosomatid parasites undergo developmental regulation to adapt to the different environments encountered during their life cycle. InTrypanosoma brucei, a genome wide selectional screen previously identified a regulator of the protein family ESAG9, which is highly expressed in stumpy forms, a morphologically distinct bloodstream stage adapted for tsetse transmission. This regulator, TbREG9.1, has an orthologue inTrypanosoma congolense, despite the absence of a stumpy morphotype in that parasite species, which is an important cause of livestock trypanosomosis. RNAi mediated gene silencing of TcREG9.1 inTrypanosoma congolensecaused a loss of attachment of the parasites to a surface substrate in vitro, a key feature of the biology of these parasites that is distinct fromT. brucei. This detachment was phenocopied by treatment of the parasites with a phosphodiesterase inhibitor, which also promotes detachment in the insect trypanosomatidCrithidia fasciculata. RNAseq analysis revealed that TcREG9.1 silencing caused the upregulation of mRNAs for several classes of surface molecules, including transferrin receptor-like molecules, immunodominant proteins, and molecules related to those associated with stumpy development inT. brucei. Depletion of TcREG9.1 in vivo also generated an enhanced level of parasites in the blood circulation consistent with reduced parasite attachment to the microvasculature. The morphological progression to insect forms of the parasite was also perturbed. We propose a model whereby TcREG9.1 acts as a regulator of attachment and development, with detached parasites being adapted for transmission.

Author summary

Trypanosoma congolenseis a major cause of livestock trypanosomosis in sub-Saharan Africa where it contributes to lost economic productivity and poverty. These parasites differ in two key respects from the better-studied African trypanosomes,Trypanosoma brucei. Firstly,T. congolenseadheres to surfaces in vitro and in the vaculature in vivo. Secondly, they lack a morphologically distinct transmission stage equivalent to the stumpy form ofT. brucei. In the current work we identify aT congolenseorthologue of a key developmental regulator inT. brucei, REG9.1, previously identified by a genome-wide RNAi screen. By RNA interference in transgenicT. congolensewe demonstrate that TcREG9.1 functions both in parasite adherence in vitro and in vivo, and also in parasite development. The work provides a first insight into the unusual adherence and developmental biology ofT. congolenseand also suggests a possible model for how these characteristics interact to promote disease spread.
Characterisation of protective vaccine antigens from the thiol-containing components of excretory/secretory material ofOstertagia ostertagi
Authors: Price Daniel R. G. , Steele Philip , Frew David , McLean Kevin , Androscuk Dorota , Geldhof Peter , Borloo Jimmy , Albaladejo Javier Palarea , Nisbet Alasdair J. , McNeilly Tom N.
Published: December 2023

Previous vaccination trials have demonstrated that thiol proteins affinity purified fromOstertagia ostertagiexcretory-secretory products (O. ostertagiES-thiol) are protective against homologous challenge. Here we have shown that protection induced by this vaccine was consistent across four independent vaccine-challenge experiments. Protection is associated with reduced cumulative faecal egg counts across the duration of the trials, relative to control animals. To better understand the diversity of antigens inO. ostertagiES-thiol we used high-resolution shotgun proteomics to identify 490 unique proteins in the vaccine preparation. The most numerous ES-thiol proteins, with 91 proteins identified, belong to the sperm-coating protein/Tpx/antigen 5/pathogenesis-related protein 1 (SCP/TAPS) family. This family includes previously identifiedO. ostertagivaccine antigensO. ostertagiASP-1 and ASP-2. The ES-thiol fraction also has numerous proteinases, representing three distinct classes, including: metallo-; aspartyl– and cysteine proteinases. In terms of number of family members, the M12 astacin-like metalloproteinases, with 33 proteins, are the most abundant family inO. ostertagiES-thiol. TheO. ostertagiES-thiol proteome provides a comprehensive database of proteins present in this vaccine preparation and will guide future vaccine antigen discovery projects.
Tuft cell-derived acetylcholine is an effector of type 2 immunity and directly targets helminth parasites in the gut lumen
Authors: Ndjim Marième , Herbert Fabien , Gasmi Imène , Joséphine Charlène , Henri Sylvain , Turtoi Evgenia , Thirard Steeve , Giordano Alicia , Ciancia Claire , Britton Collette , Devaney Eileen , McNeilly Tom N. , Berrard Sylvie , Turtoi Andrei , Maizels Rick M. , Gerbe François , Jay Philippe
Published: December 2023

Upon parasitic helminth infection, activated intestinal tuft cells secrete IL-25, which initiates a type 2 immune response during whichlamina propriaILC2s produce IL-13. This causes epithelial remodelling, including tuft cell hyperplasia with an unknown function. We describe a novel cholinergic effector function of tuft cells, which we show are the only epithelial cells expressing Choline Acetyltransferase (ChAT). During parasite infections, mice with epithelial-specific deletion of ChAT have increased worm burden and faecal egg counts although they are able to mount a comparable type 2 immune response. Mechanistically, IL-13-amplified tuft cells release acetylcholine (ACh) into the gut lumen. We demonstrate a direct effect of ACh on worms, reducing their viability and fecundity via helminth muscarinic ACh receptors, with effects promoted by inhibition of acetylcholinesterase, an helminth-secreted enzyme. Thus, tuft cells are sentinels in naive mice, and their amplification upon helminth infections serves an additional type 2 immune response effector function.
Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms
Authors: Greenshields-Watson Alexander , Abanades Brennan , Deane Charlotte M
Published: December 2023

Deep learning models have been shown to accurately predict protein structure from sequence, allowing researchers to explore protein space from the structural viewpoint. In this paper we explore whether “novel” features, such as distinct loop conformations can arise from these predictions despite not being present in the training data.

Here we have used ABodyBuilder2, a deep learning antibody structure predictor, to predict the structures of ∼1.5M paired antibody sequences. We examined the predicted structures of the canonical CDR loops and found that most of these predictions fall into the already described CDR canonical form structural space. We also found a small number of “new” canonical clusters composed of heterogeneous sequences united by a common sequence motif and loop conformation. Analysis of these novel clusters showed their origins to be either shapes seen in the training data at very low frequency or shapes seen at high frequency but at a shorter sequence length.

To evaluate explicitly the ability of ABodyBuilder2 to extrapolate, we retrained several models whilst with-holding all antibody structures of a specific CDR loop length or canonical form. These “starved” models showed evidence of generalisation across CDRs of different lengths, but they did not extrapolate to loop conformations which were highly distinct from those present in the training data. However, the models were able to accurately predict a canonical form even if only a very small number of examples of that shape were in the training data.

Our results suggest that deep learning protein structure prediction methods are unable to make completely out-of-domain predictions for CDR loops. However, in our analysis we also found that even minimal amounts of data of a structural shape allow the method to recover its original predictive abilities. We have made the ∼1.5 M predicted structures used in this study available to download athttps://doi.org/10.5281/zenodo.10280181.
Escape problem of magnetotactic bacteria - physiological magnetic field strengths help magnetotactic bacteria navigate in simulated sediments
Authors: Codutti Agnese , Charsooghi Mohammad A. , Marx Konrad , Cerdá-Doñate Elisa , Munoz Omar , Zaslansky Paul , Telezki Vitali , Robinson Tom , Faivre Damien , Klumpp Stefan
Published: December 2023

Bacterial motility is typically studied in bulk solution, while their natural habitats often are complex environments. Here, we produced microfluidic channels that contained sediment-mimicking obstacles to study swimming of magnetotactic bacteria in a near-realistic environment. Magnetotactic bacteria are microor-ganisms that form chains of nanomagnets and that orient in Earth’s magnetic field. The obstacles were produced based on micro-computer tomography reconstructions of bacteria-rich sediment samples. We characterized the swimming of the cells through these channels and found that swimming throughput was highest for physiological magnetic fields. This observation was confirmed by extensive computer simulations using an active Brownian particle model, which were parameterized based on experimental trajectories, in particular with the trajectories near the sediment-mimicking obstacles, from which the interactions of the swimming bacteria with the obstacles were determined. The simulations were used to quantify the swimming throughput in detail. They showed the behavior seen in experiments, but also exhibited considerable variability between different channel geometries. The simulations indicate that swimming at strong fields is impeded by the trapping of bacteria in “corners” that require transient swimming against the magnetic field for escape. At weak fields, the direction of swimming is almost random, making the process inefficient as well. We confirmed the trapping effect in our experiments and showed that lowering the field strength allows the bacteria to escape. We hypothesize that over the course of evolution, magnetotactic bacteria have thus evolved to produce magnetic properties that are adapted to the geomagnetic field in order to balance movement and orientation in such crowded environments.
Diverse Genetic Contexts of HicA Toxin Domains Propose a Role in Anti-Phage Defense
Authors: Gerdes Kenn
Published: December 2023

Toxin – antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, theMycobacterium tuberculosisgenome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands have unveiled a wide array of systems, including TAs that serve in anti-phage defence. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involvehicAadjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles.

Importance

Prokaryotic organisms harbor a multitude of Toxin – Antitoxin (TA) systems, which have long puzzled scientists as “genes in search for a function”. Recent scientific advancement have shed light on a primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This manuscript describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world.
The energy metabolic footprint of predictive processing in the human brain
Authors: Hechler André , de Lange Floris P. , Riedl Valentin
Published: December 2023

Neural activity is a highly energy-intensive process. In the human brain, signaling consumes up to 75% of the available energy resources with postsynaptic potentials as the largest factor. Visual processing is especially costly, with increases in energy consumption of up to 20% in the visual cortex. In recent years, vision has been cast as a constructive process, harnessing prior knowledge in a constant feedback loop of top-down prediction and bottom-up sensory input. Interestingly, sensory input that is in line with our predictions might be processed at lower energy metabolic cost. However, there is no evidence for this claim yet, possibly due to the scarcity of measures that quantify energy consumption in the human brain.

Here, we used a novel MR method measuring the cerebral metabolic rate of oxygen during sensory stimulation of visual sequences that varied in their predictability. Since predictive processing is driven by estimates of uncertainty, we assessed how confident subjects were in their knowledge of the underlying patterns. We found that processing predictable sequences steeply decreased in energetic cost with increasing confidence. Strikingly, these energetic effects were not limited to visual areas, summing up to a cortical difference of 13% between high and low levels of confidence. Furthermore, sequences deviating from expectations were energetically cheaper than predictable ones for low confidence levels, but costlier for high levels. These results speak for a major role of predictive processing in balancing the brain’s energy budget and emphasize the impact of interindividual differences when learning predictive patterns.
Ffp1, an ancestralPorphyromonasspp. fimbrillin
Authors: Acuña-Amador Luis , Barloy-Hubler Frédérique
Published: December 2023

Background

Little is known about fimbriae in thePorphyromonasgenus. Besidesfimandmfa, a thirdPorphyromonas gingivalisadhesin called Ffp1 has been described, and seems to be capital for outer membrane vesicle (OMV) production.

Objective

We aimed to investigate the distribution and diversity of type V fibrillin, particularly Ffp1, in thePorphyromonasgenus.

Methods

A bioinformatic phylogenomic analysis was conducted using all accessiblePorphyromonasgenomes in order to generate a domain search for fimbriae, using HMM profiles.

Results

Ffp1 was found as the sole fimbrillin in all the analyzed genomes. After manual biocuration and 3D modeling, this protein was determined to be a type V fimbrillin, with a closer structural resemblance to aBacteroides ovatusfimbrillin than to FimA or Mfa1 fromP. gingivalis.

Conclusion

It appears that Ffp1 represents ancestral fimbriae present in allPorphyromonasspecies. Additional investigations are necessary to elucidate the biogenesis of Ffp1 fimbriae and his potential role in OMV production and niche adaptation.
APE1 associates with 60S ribosomes and tRNAs and regulates the expression of IGF2BP1
Authors: Li Wai Ming , Tafech Belal , Lee Chow H.
Published: December 2023

Apurinic/apyrimidinic endonuclease 1 (APE1), a multifunctional protein known for its DNA repair function and redox regulation, is often found overexpressed in cancers. APE1 can be found in the nucleus, cytoplasm and secreted extracellularly. APE1 subcellular distribution in the cytoplasm is frequently reported in various types of cancer but the biological significance remains unknown. In this study, APE1 in the cytoplasm of HepG2 cells was investigated using various techniques including microscopy, differential centrifugation, sucrose gradient fractionation and CL-IP. APE1 was found to associate with 60S ribosomes and tRNAs under native conditions, suggesting it may have a specific function in the translational machinery. Knockdown of APE1 in HepG2 cells led to increased protein expression of IGF2BP1 as well as enhanced HepG2 cell migration, suggesting that APE1 can act as a tumor suppressor in this cell line model of hepatocellular carcinoma. When APE1 was depleted, the translation of a reporter construct containing the 3’UTR of IGF2BP1 was enhanced. This study provides evidence in support of the role of cytoplasmic APE1 in the control of IGF2BP1 protein translation and sheds light on the potential novel function of cytoplasmic APE1.