Communications Biology
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Preprints posted in the last 90 days, ranked by how well they match Communications Biology's content profile, based on 993 papers previously published here. The average preprint has a 0.84% match score for this journal, so anything above that is already an above-average fit.
Kalkhoven, E.; Baak, R. E.; Hooiveld, G. J. E. J.; Schrauwen, P.; Hoeks, J.; Raymakers, R.; van der Stolpe, A.; Kersten, S.
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Cold acclimation holds therapeutic potential for improving metabolic health. We previously demonstrated that repeated cold-induced shivering enhances insulin sensitivity in humans. However, the molecular pathways that underlie the skeletal muscle shivering response, and how these relate to beneficial physiological effects, remain poorly understood. In this study, we combined complementary bioinformatics approaches to allow in-depth analysis of the transcriptomic response of human skeletal muscle to repeated shivering. We identified a robust transcriptional signature and show a sex-specific component in the shivering skeletal muscle response, which seemed to diminish following cold adaptation. Our findings provide mechanistic insights into cold-induced muscle adaptations, shed light on potential interesting molecular targets for further investigation, and emphasize the importance of including both sexes in future cold acclimation studies.
Dessert, J.; Marcotte, E. M.; Ochman, H.
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This study establishes a comprehensive genomic, transcriptomic, and proteomic foundation for the wild cochineal bug, Dactylopius opuntiae, a scale insect and agricultural pest of prickly pear cacti notable for its dense white waxy covering. Although fatty acyl reductases (FARs) are central to insect epicuticular wax biosynthesis, the genes underlying wax production in cochineal insects are largely unexplored due to a lack of genomic resources. We report a 359-Mb de novo genome assembly in which we identify 26 FAR genes. Through phylogenetic reconstruction of Coccoidea FAR enzymes we reveal lineage-specific expansions of tandemly arranged D. opuntiae FAR genes, and discuss these enzymes roles in the development of this insects epicuticular waxy coating.
Kaifu, Y.; Chang, C.-H.; Tarusawa, Y.; Sawafuji, R.; Yonemoto, S.; Shimamura, S.; Takai, M.; Kono, R. T.; Sun, C.-H.; Tsai, C.-H.; Yoneda, M.; Tsutaya, T.
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Denisovans are an extinct archaic Homo group whose lineage diverged from the Neanderthal lineage approximately 550,000 years ago and were widely distributed across eastern Asia until [~]45,000 years ago1-7. Their morphological features are known directly from the existing cranio- dental and phalangeal remains1,2,8-12. However, the body size and postcranial morphology of the Denisovans remain largely unknown. We here report that hominin femoral and tibial fossils recovered from the Penghu Channel, Taiwan, are Denisovans in their proteomic profiles. Morphologically, these specimens are among the largest leg bones known in Pleistocene Homo. They exhibit generally archaic features, but also show some modern human-like morphology, including a strong femoral pilaster. Our findings demonstrate that the Denisovan population at the northern circle had larger body size than earlier Homo erectus as well as Late Pleistocene Homo sapiens in eastern Asia. This challenges the generally held expectation that Pleistocene Homo followed Bergmanns rule that anticipates latitudinal decline of body size, and suggests that the large Denisovan brain resulted from their large body size at least partly. The strong pilaster developed in the Penghu femur suggests some behavioral similarities between the Denisovans and the Upper Palaeolithic modern humans and/or gene flow from the latter to the former.
Guyeux, C.
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A substantial fraction of the Mycobacterium tuberculosis proteome remains functionally uncharacterised. Rv1025, a 155-residue protein carrying the domain of unknown function DUF501 (Pfam PF04417), is essential by transposon mutagenesis and vulnerable by CRISPR interference, an attractive but neglected drug target, yet has never been functionally described. The family (4,370 proteins, no Gene Ontology term, no solved structure) is uncharacterised across all organisms and essential in three Actinobacterial genera. A Foldseek search of the AlphaFold model against complete structural databases finds no significant homolog, indicating a novel fold. The operon eno-divIC-Rv1025-ppx2 is conserved across the Actinobacteria phylum, yet AlphaFold-Multimer finds no direct complex between Rv1025 and its neighbour DivIC. Instead, conservation across 8,700 homologous sequences reveals a near-invariant Cys113-His115-Glu59 cluster forming a pocket. Holo AlphaFold3 predictions with Zn, Fe and Mn confidently place a divalent metal on this triad at 2.25-2.47 A; mutating the triad relocates the metal, and an independent backbone-geometry predictor recovers the same site, confirming specificity. The triad is universal across the family: present in all 1,472 near-complete bacterial sequences of the Pfam alignment, with no non-conservative substitution among the 2,228 sequences examined, a defining feature of bacterial DUF501 rather than a mycobacterial peculiarity. We propose that DUF501 is a metal-binding protein and candidate metalloenzyme, the first functional hypothesis for this family, whose conserved, essential metal pocket is a promising drug target. As the predictions build on a conservation-defined site within a fully computational study, they are supportive rather than proof of metal occupancy and warrant experimental validation.
Kovach, C. K.; Gliske, S. V.; West, L. C.; Liu, J.; Summers, M. O.; Kumar, S.; Gonzales, J. A.; Cox, O.; Tsang, E. W.; Thompson, J. A.; Kushida, C. A.; Abosch, A.
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Sleep spindles, transient 11-16 Hz oscillatory bursts, are a defining electrographic feature of non-rem (NREM) sleep and a key biomarker of sleep physiology. A need for efficient and reliable identification of spindles motivates a large literature on automated detection algorithms. In this literature, annotation by trained sleep specialists remains the gold standard against which automated methods are trained, tuned and evaluated. However, inter-scorer agreement among experts is modest, which leaves a significant role for subjective judgment in the definition of a spindle. Finding objective, scorer-independent, criteria for identifying spindles remains an unresolved challenge. We report here a robust, highly specific, and previously unrecognized signature of spindle activity in the fourth-order spectrum (trispectrum), from which we identify the presence of spindles, characterize their waveforms, and obtain an optimal detection filter through a decomposition of the trispectrum (HOSD). Although it is a strictly blind, data-driven method, HOSD-based spindle identification and detection agrees well with expert annotation (median AUROC ~0.9), yet identifies many more events at the native threshold than both human scorers and comparison detectors. Many of these additional detections are confirmed as meeting AASM spindle criteria by four blinded specialists, demonstrating that spindle-like oscillatory bursting is prevalent below conventional human and automated detection thresholds. We observe that N2 sleep is distinguished principally by high-amplitude bursts, while low-amplitude bursting persists throughout NREM sleep, being globally suppressed only in REM sleep. We also describe robust identification of recording-specific spindle waveform properties such as frequency deceleration.
Benz, C.; Khan, R. T.; Hammond, M.; Gahura, O.; Koblar, U.; Cadena, L. R.; Skodova-Sverakova, I.; Butterill, P. T.; Vrbacky, M.; Hashimi, H.
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Proteins are frequently integrated into multicomponent complexes that execute the elaborate processes supporting life. Thus, a protein's function can only be defined by the company it keeps within a complex. Proteomes provide informative protein inventories but lack information about protein quaternary structures. Complexome profiling (CP) has been transformative in capturing the comprehensive population structure of complexes at a given moment within a cell. We have employed CP to chart the multiprotein complex landscape of two life cycle stages of Trypanosoma brucei. These data have allowed the observation of previously hidden interactions with and within the mitochondrial respiratory chain. We have found (1) an exceptional case of a SLC25 solute transporter that interacts with NADH dehydrogenase, (2) two ATP synthase subunit g paralogs that are intriguingly excluded from the enzyme's dimers, and (3) refined the known composition of ubiquinol:cytochrome c oxidoreductase by addition of missing subunits and removing an incorrectly assigned subunit, which more likely acts to insert the iron-sulfur co-factor into the complex. Further investigation into ubiquinol:cytochrome c oxidoreductase assembly revealed crosstalk between incorporation of its nuclear subunits with mitochondrial translation, possibly facilitating a hitherto unknown quality control mechanism. These discoveries demonstrate the power of our CP data for generation and testing of hypotheses about the mitochondrial and other organellar multiprotein complexes of T. brucei, a protist of medical and evolutionary importance.
Zahonova, K.; Gahura, O.; Benedikova, K.; Trusina, N.; Kalita, E.; Chmelova, L.; Skodova-Sverakova, I.; Zikova, A.; Yurchenko, V.
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Background. Alternative oxidase (AOX) is a mitochondrial terminal oxidase that provides an alternative route for electron transfer, contributing to respiratory flexibility and redox homeostasis under stress conditions. In trypanosomatids, AOX displays a highly uneven distribution associated with extensive diversification of mitochondrial electron transport chains (ETCs). In addition to canonical AOX, many trypanosomatids encode an enigmatic AOX-like protein (AOX-L), whose evolutionary origin and functional significance remain unresolved. Results. Here, we investigated the evolutionary distribution, phylogenetic relationships, structural conservation, and functional divergence of AOX and AOX-L across euglenozoans. Comparative genomic analyses revealed a patchy distribution of both proteins among kinetoplastids, with multiple independent losses during evolution. Phylogenetic analyses demonstrated that AOX and AOX-L represent distinct evolutionary lineages, indicating independent origins rather than duplication-derived divergence. While AOX showed a conserved eukaryotic origin, AOX-L occupied a separate phylogenetic position and lacked key residues required for ubiquinol oxidation. Structural modelling revealed that AOX-L retained the characteristic AOX fold, predicted membrane association, and dimeric organization, but lacked the catalytic architecture necessary for enzymatic activity. Transcriptomic and biochemical analyses of four AOX-containing trypanosomatid species showed that AOX expression and activity correlated with mitochondrial ETC organization. Species lacking cytochrome-dependent complexes III and IV displayed substantially higher AOX expression and enzymatic activity, consistent with AOX functioning as the primary terminal oxidase in these lineages. Conversely, species retaining a canonical ETC exhibited lower AOX activity, suggesting a role in metabolic flexibility and redox regulation. Conclusions. Our study provides a comprehensive evolutionary and functional framework for alternative oxidases in trypanosomatids. We demonstrate that AOX and AOX-L are evolutionarily distinct proteins with different predicted functions: AOX maintains respiratory electron flow according to lineage-specific mitochondrial requirements, whereas AOX-L represents a structurally conserved but catalytically inactive protein family that may have acquired an alternative regulatory role. These findings highlight how mitochondrial respiratory components diversify during eukaryotic evolution and provide a basis for future investigations into the biological function of AOX-L.
Fujiwara, J.; Tobler, P. N.; Tsutsui, K.-I.; Ugawa, Y.; Eifuku, S.; Taira, M.
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We conform not only to the opinions and behaviors of others but also to those of ourselves, suggesting that the motivation to appear consistent leads us to treat ourselves like others. However, the neural mechanisms of self-conformity remain unclear. We used a sequential facial attractiveness-rating task with ostensible reminders of participants own previous ratings to investigate self-conformity and compare it against group conformity. Rating data showed that participants on average conformed to both themselves and the group. While some individuals conformed excessively (over-conformity), others went against their previous behavior (anti-conformity), similarly in self and group conditions. Neurally, dorsomedial and ventrolateral prefrontal cortex activity correlated with both self- and group conformity. Moreover, self-versus group conformity engaged more medial versus lateral prefrontal regions, and over-versus anti-conformity more ventral versus dorsal regions. These results suggest that self- and group conformity rely on both common and dedicated neural mechanisms.
Mikutta, C. A.; Planta, M.; Koenig, T.; Feher, K.; Henckaerts, P.; Angelillo, M.; Hertenstein, E.; Schneider, C. L.; De Lucia, M.; Riemann, D.; Feige, B.; Vyazovskiy, V. V.; Nissen, C.
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Communication between the brain and cardiovascular system is increasingly recognized as a fundamental determinant of health, yet the mechanisms coordinating neural and cardiac rhythms remain poorly understood. Sleep provides a unique physiological state for investigating neurovisceral integration because cortical slow oscillations (SOs), thalamocortical sleep spindles, and autonomic activity undergo profound reorganization during non-rapid eye movement (NREM) sleep. We analyzed overnight high-density electroencephalography and electrocardiography recordings from 30 healthy adults and quantified interactions among SOs, sleep spindles, cardiac R-peaks, heart rate variability (HRV), spectral slope, and Lempel-Ziv complexity. To assess integrated brain-heart coordination, we developed a Joint Phase-Amplitude Coupling (JPAC) metric that quantifies the corelation between SO phase-dependent modulation of spindle amplitude and cardiac timing. SO-spindle coupling showed the expected fronto-central distribution but was not significantly related to autonomic or cortical state markers. In contrast, SO-R-peak coupling and JPAC systematically tracked physiological state. Stronger JPAC was associated with higher high-frequency HRV, steeper spectral slopes, and lower neural complexity, indicating enhanced coupling during synchronized, parasympathetically dominated NREM sleep. These findings demonstrate coordinated organization of cortical, thalamocortical, and cardiac rhythms within a common oscillatory framework and identify NREM sleep as a state and potential treatment target of large-scale neurovisceral integration.
Simony, E.; Yahav, N.; Malach, R.
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Neural systems adapt to prolonged sensory input through mechanisms such as gain control or homeostatic plasticity to maintain stable operating ranges. However, this phenomenon has so far been documented under extreme, non-ecological stimuli targeting specific sensory systems. Here, we reveal a widespread adaptation process across diverse human cortical regions following naturalistic movie watching conditions. The effect was evident in 218 out of 251 cortical regions (87%) that exhibit significant stimulus-driven activations. Analyzing the HCP fMRI data set in which 170 participants watched 14 movie clips, followed by rest periods - we found robust evidence for a movie-induced adaptation process, revealed in the post-movies rest periods. Within a region, voxels highly activated at the end of movies subsequently reduced their activity below baseline during rest, with the magnitude of this drop proportional to initial activation levels, manifested as a consistent voxel-population inversion effect. Conversely, persistently movie-inactivated voxels exhibited increased activation above baseline. Importantly, this Movie After-Effect (MvAE) enabled successful decoding of the specific rest periods following individual movie clips. Our findings suggest that under naturalistic conditions, cortical neurons dynamically change their gain to achieve homeostatic balance in a process akin to batch instance normalization in artificial neural networks. Whether this ubiquitous MvAE has additional cognitive and memory-related implications remains to be explored.
Tupe, C.; Goyal, B.; De, T. D.; Bhatt, D.; Dixit, B.; pandey, K. C.; Na, B. K.; Emami, S. N.; Chakraborti, S.
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Iron homeostasis is essential for both the Plasmodium parasite and its hosts, the mosquito and human; however, the molecular mechanisms governing intracellular iron trafficking remain poorly understood. In mammals, poly(rC)-binding proteins (PCBPs) function as major iron chaperones by delivering Fe2+ to ferritin and other iron-dependent proteins, yet their role in insects has not been investigated. Here, we provide the first structural and functional characterization of the PCBP from a major malaria vector, Anopheles stephensi. Comparative structural and evolutionary analyses showed that insect PCBPs are most closely related to human PCBP3. Coordinated expression and co-localization of AsPCBP with ferritin following blood feeding suggested a conserved role in mosquito iron homeostasis. Functional analyses demonstrated that KH2-KH3 linker and KH3 domain of PCBP, plays an important role in the AsPCBP-ferritin interaction and that deletion of these regions, unexpectedly increased ferritin binding affinity but impaired iron delivery, indicating that these regions are dispensable for complex formation but essential for efficient iron transfer. Collectively, our results identify PCBP as a key component of mosquito iron homeostasis that could be exploited for the development of novel antimalarial strategies.
Olaciregui-Dague, K. R.; Acero-Pousa, I.; Berjaga-Buisan, T.; Kaller, M. S.; Sitt, J.; Deco, G.; Kringelbach, M. L.
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BackgroundConsciousness is increasingly understood as an emergent property of large-scale brain dynamics that depend upon flexible interactions among distributed cortical and subcortical systems. Although disorders of consciousness (DOC) have traditionally been associated with impaired integration and reduced network complexity, the role of hierarchical brain organization in supporting conscious awareness remains poorly understood. Here, we investigated how hierarchical organization relates to behavioral responsiveness in DOC by combining trophic-level analysis, trophic coherence, and whole-brain dynamical metrics. MethodsResting-state functional MRI data were analyzed from healthy controls (CNT), minimally conscious state (MCS) patients, and unresponsive wakefulness syndrome (UWS) patients drawn from a previously published DOC cohort. Static global and regional measures of functional hierarchy were computed from directed effective-connectivity networks. Dynamic trophic states were identified using time-resolved phase-coupling analyses and clustering of recurrent coordination patterns. State occupancy, dwell time, metastability, synchrony, and behavioral associations with Coma Recovery Scale-Revised (CRS-R) scores were evaluated. ResultsRegional trophic levels were positively associated with behavioral responsiveness, with higher frontal and thalamic trophic levels and lower insular trophic levels predicting higher Coma Recovery Scale-Revised (CRS-R) scores. Dynamic trophic-state analysis identified a pathological hyper-hierarchical state, defined by elevated frontal, thalamic, and insular trophic levels, that exhibited progressively greater occupancy and longer dwell times from healthy controls to minimally conscious state and unresponsive wakefulness syndrome patients. In contrast, occupancy and dwell time of this state distinguished diagnostic groups but were not significantly associated with behavioral responsiveness. Independent analyses demonstrated significant reductions in metastability and global synchrony across disorders of consciousness. Anatomical mapping localized elevated trophic levels within the pathological state predominantly to fronto-thalamo-limbic systems. ConclusionsDisorders of consciousness are characterized not simply by loss of hierarchical organization but by prolonged stabilization within recurrent hyper-hierarchical brain states. Conscious awareness appears to depend not only on hierarchical organization itself but also on the capacity to flexibly transition between distinct brain states. Severe disorders of consciousness are associated with persistent occupation of pathological hyper-hierarchical states, potentially restricting the dynamical repertoire available for conscious processing.
Ahmad, A.; bakar, A.; Laeeque, S. M.; Khan, W. A.; Kaul, H.; Manan, A.; mustafa, h.
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Genomic signatures of selection can reveal loci underlying adaptation and disease resistance in livestock populations, but such analyses in water buffalo (Bubalus bubalis) have historically been constrained by the absence of a chromosome-level, species-native reference genome for SNP array data. We re-analyzed genotype data from 85 Nili-Ravi buffalo (Axiom Buffalo Genotyping 90K array, originally positioned using bovine (Bos taurus, UMD3.1) proxy coordinates, by performing a full coordinate liftover to the buffalo-native UOA_WB_1 assembly using an independently published SNP remapping resource. Following quality control (51,209 markers retained), haplotype phasing, and genome-wide integrated haplotype score (iHS) and Wrights Fst (case/control) selection scans, we evaluated 14 classical bovine-tuberculosis (bTB) candidate genes and identified six additional genes with putative immune function through an unbiased genome-wide screen. None of the 14 classical candidates (including SLC11A1, the Toll-like receptors, and IFNG) reached genome-wide significance in either scan. In contrast, six novel loci TNFSF18, IL2RB, TNFRSF19, IRF2, IL15, and CD28 showed significant iHS or Fst signals, four of which (TNFSF18, IL2RB, IL15, CD28) converge functionally on T-cell costimulation and cytokine receptor signaling (KEGG pathways map04660 and map04060, Bos taurus proxy annotation). Using extended haplotype homozygosity (EHH) decay, haplotype furcation structure, and per-marker haplotype counts as three independent lines of corroborating evidence, we classified these six genes into confidence tiers: TNFSF18 and IL2RB showed the strongest, most balanced support, while CD28 and IL15 signals were driven by very few haplotypes (3 and 5 of 30, respectively) and should be interpreted cautiously pending replication. These findings suggest that adaptive, cell-mediated immune signaling rather than the innate/macrophage-centred mechanisms emphasized by existing bTB candidate gene panels may be a more productive avenue for future selection studies in Nili-Ravi buffalo, while underscoring the value of buffalo-native coordinate systems for accurate genomic inference in this species.
Breit, A. M.; Takeshita, R. S. C.; Ehmke, E.; Walls, C.; Billington, C.; Larsen, P.; McLain, A.; Faulk, C.
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Madagascars dwarf lemurs (genus Cheirogaleus) are the only obligate-hibernating primates and closest relative to humans capable of hibernation. Endemic to the increasingly fragmented dry forests of Madagascar, the fat tailed dwarf lemur (Cheirogaleus medius) represents a unique model for understanding primate physiology and tropical hibernation. Here we present FatTail1, a highly contiguous diploid genome assembly generated from a male C. medius at the Duke Lemur Center using Oxford Nanopore Technologies PromethION sequencing. The assembly spans 2.3 Gb, with an N50 of 103Mb, L50 of 10, and a BUSCO completeness score of over 99%. In addition to a complete mitogenome, we generated allele-specific DNA methylation profiles and annotated 23,925 genes using NCBIs EGAPX. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes, representing the first telomere-to-telomere genome of a Strepsirrhine primate, and providing a foundation for future studies of primate hibernation, epigenetic regulation, and conservation genomics. ARTICLE SUMMARYDwarf lemurs are the only primates and closest relative to humans capable of months-long hibernation, making them an important model for understanding metabolic adaptations with relevance to human physiology. Here we present FatTail1, the first telomere-to-telomere genome assembly of a strepsirrhine primate, generated from a fat-tailed dwarf lemur (Cheirogaleus medius) using Oxford Nanopore Technologies PromethION sequencing. In addition to a highly complete nuclear genome, we assembled the mitogenome, identified allele-specific DNA methylation profiles and annotated 23,925 genes. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes and provides an improved genomic resource for studies of hibernation, comparative genomics, epigenetic regulation, evolutionary biology, and conservation of this threatened primate.
Nakhostin, S.; Weiss, I. M.
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In molluscs, chitin synthases are essential for biologically controlled biomineralization, with some variants possessing a myosin motor domain that may link polymer synthesis to the cytoskeleton. Experimentally, we established a reliable workflow for expressing ArCS1_E22TM in Dictyostelium discoideum and developed effective purification methods to reconstitute ArCS1_E22TM in nanodiscs using MSPs and specific lipid composition. MSP1D1deltaH5 proved optimal for nanodisc formation, yielding homogeneous, monodisperse discs (~8.2 nm). Lipids were refined to POPC:POPE:POPG (3:1:1) with 20% cholesterol, improving nanodisc quality and uniformity as observed by negative-stain EM. The full-length ArCS1 and its subdomains were modeled using AlphaFold3; the myosin motor, glycosyltransferase, and transmembrane regions are well-defined internally but loosely constrained relative to one another, suggesting flexible linking and conformational coupling. Modelling with Mg2+ and oleic acid as ligands and comparative analyses with bacterial cellulose synthase and yeast chitin synthase 1 provided insights into substrate binding and a potential mechanism for chitin polymerization and translocation. This research establishes a standard procedure for comprehensive structural analyses of recombinant molluscan chitin synthase in near-native or biomimetic membranes. This sets the stage for high-resolution cryo-electron microscopy to determine the first experimentally resolved structure of a molluscan chitin synthase and to provide insight into the enzyme's architecture and the regulatory mechanisms of biomineralization.
Guillen Samander, A.; Ahmed, Y.; Ribeiro-Holbein, A.; Cubillan-Marin, J.; Hoehn, K.; Rocha-Roa, C.; Droege, J.; Panitzsch, L. S.; Burda, P.-C.; Gilberger, T.; Vanni, S.; Spielmann, T.
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Malaria parasites endocytose large quantities of hemoglobin from the host erythrocyte, a process critical for parasite survival, leading to extensive membrane internalization. While hemoglobin degradation in the digestive vacuole (DV) is well studied, how the parasite deals with the membranes arriving within the DV is unknown. Here we identified PfTUPA, a previously uncharacterized lipid transfer protein in the DV membrane that is needed for this function. PfTUPA contains a soluble TULIP-like lipid transport domain exposed to the DV lumen and a transmembrane lipid transfer domain of bacterial origin (PqiA) in the DV membrane. Structural comparisons revealed proteins with various PqiA and TULIP-like domain combinations across distant eukaryotic clades, indicating this is a frequent functional partnership. Hence, PfTUPA belongs to a new class of eukaryotic lipid transfer proteins that in malaria parasites is needed for a key function of its biology.
Wei, Y.; Ma, K.; Hao, K.; Bai, Q.; Zhao, J.; Xie, X.; Li, R.; Chen, Q.; Li, Y.; Zhang, H.; Cao, Z.; Hu, T.; Zhao, Y.
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Inhibitory neurotransmission, essential for neural circuit homeostasis and proper neurological function, depends on the efficient sequestration of {gamma}-aminobutyric acid (GABA) and glycine into synaptic vesicles. This critical process is mediated exclusively by the vesicular inhibitory amino acid transporter (VIAAT). Despite extensive biochemical and physiological investigation, the molecular mechanism governing VIAAT-mediated transport has remained incompletely understood. Here, we determined structures of human VIAAT in multiple functional states, including apo, GABA-bound, and glycine-bound states, as well as apo state in chloride-free condition. VIAAT adopts a classical LeuT-fold and we elucidated how its large, electronegative binding pocket accommodates both GABA and glycine. Moreover, we resolved two previously unidentified chloride-binding sites. Through integrative molecular dynamics simulations and functional mutagenesis, our results support roles for chloride and the conserved residue E213 in substrate binding and proton-coupled transport. Together, our findings establish a structural framework for VIAAT-mediated inhibitory neurotransmitter transport that illuminates the molecular basis of inhibitory synaptic transmission and provides a foundation for understanding VIAAT dysfunction in epilepsy and related neurodevelopmental disorders.
Millena, R. J. A.; Frandsen, P. B.; James, M.; Tolman, E. R.; Uy, F. M.-K.; Ware, J. L.
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The twisted-wing parasites (order Strepsiptera) are well-known for their unusual life histories as obligate endoparasites of a wide variety of other insect orders. Here, we present the first high-quality genome assembly of a leafhopper-parasitizing strepsipteran species. We sequenced the genome of Elenchus koebelei using PacBio HiFi technology, yielding a primary assembly of 63.7Mb in 96 contigs, with an N50 of 1.60Mb and a BUSCO completeness score of 82.3%. In total, we recovered 8,167 protein-coding gene annotations, and 34.2% of the genome annotated as repeats. For the first time, we compare the genome content of three strepsipteran species and find that they are remarkably consistent in broad structure, with approximately 600 insect universal single-copy orthologs that appear to be completely missing from the order. These similarities imply a conserved genomic blueprint for strepsipteran parasitic strategy and/or differences that must be investigated at the post-translational level.
Wang, R.; Keerativittayayut, R.; Morioka, S.; Takeda, M.; Jimura, K.; Hasegawa, I.; Nakahara, K.
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The standard model of memory consolidation posits a temporary role for the hippocampus. We challenge this view by combining a novel face-name associative memory task with cross-modal decoding of fMRI data. We demonstrate that the hippocampus remains persistently engaged in representing both recent and remote memories, with distinct subregional contributions: recent memories were represented in the right posterior hippocampus, whereas remote memories additionally recruited the left anterior hippocampus. This sustained hippocampal involvement occurred alongside a large-scale network reorganization. Remote memory retrieval was accompanied by increased global connectivity among semantic regions, yet the hippocampus itself did not emerge as a major hub. Instead, network hubs shifted from the medial prefrontal cortex (mPFC) for recent memories to the mPFC and bilateral inferior parietal lobule for remote memories. These findings reveal a dynamic process in which the hippocampus preserves long-lasting representational functions while the broader memory network undergoes extensive reorganization.
Margaretha, F.; Sakamoto, M.; Seike, H.; Nagata, S.; Nakamura, Y.; Mochizuki, T.
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Neuropeptides and their G protein-coupled receptors (GPCRs) control much of insect physiology and behaviour, but in Gryllus bimaculatus, an emerging model and edible insect, receptor sequence similarity hinders the mapping of which peptide each GPCR activates. We re-annotated a chromosome-scale genome (BUSCO 95.3%, from 86.7% on insecta_odb12) with comprehensive curation of 48 neuropeptide precursor families (51 loci, including seven not previously identified) and 134 candidate GPCRs (66 rhodopsin-class, 68 secretin-class), providing a near complete neuropeptide-receptor interactome catalogue. We modelled all 15,946 peptide-receptor pairs with AlphaFold3 and Boltz-2 and scored each interface with pLDDT and ipSAE. Ranking these scores, and cross-checking the top candidate for each family against a receptor phylogeny of known ligand specificity, gave a confident, phylogenetically related receptor for 27 of 35 curated receptor groups. These matches confirm the structural scorings with existing deorphanization data and propose receptors for peptides with no prior functional evidence. The annotation, curated peptide and receptor sets, and ranked complexes are available through CricketBase (https://cricket.annotation.jp), a genome browser with a structure viewer of peptide-receptor complexes, providing a resource for G. bimaculatus endocrinology and a workflow to deorphanize GPCRs in other non-model insects.