bluuebunny/crossref_metadata_2025 huggingface dataset:
HDAC inhibitors rescue MeCP2T158Mspeckles in a high content screen
Authors: Lata Rodrigo , Steegmans Liesbeth , Kellens Ranie , Nijs Marnik , Klaassen Hugo , Versele Matthias , Christ Frauke , Debyser Zeger
Published: November 2023

Rett syndrome (OMIM 312750) is a rare neurodevelopmental disorder caused byde novomutations in the Methyl-CpG Binding Protein 2 (MeCP2) gene located on the X-Chromosome, typically affecting girls. Currently, available therapy for Rett Syndrome is only symptomatic. Rett syndrome symptoms first appear between 6 to 18 months of age, characterized by microcephaly and lack of motor coordination being the most prevalent. The disease continues to progress until adulthood when it reaches a stationary phase. More than 800 different mutations causing Rett syndrome have been described, yet the most common is T158M (9% prevalence), located in the Methyl-Binding domain (MBD) of MeCP2. Due to its importance for DNA binding through recognition of methylated CpG, mutations in the MBD have a significant impact on the stability and function of MeCP2. MeCP2 is a nuclear protein and accumulates in liquid-liquid phase condensates visualized as speckles in NIH3T3 by microscopy. We developed a high content phenotypic assay, detecting fluorescent MeCP2 speckles in NIH3T3 cells. The assay allows to identify small molecules that stabilize MeCP2-T158M and phenotypically rescue speckle formation. To validate the assay, a collection of 3572 drugs was screened, including FDA-approved drugs, compounds in clinical trials and biologically annotated tool compounds. 18 hits were identified showing at least 25% of rescue of speckles in the mutant cell line while not affecting wild-type MeCP2 speckles. Primary hits were confirmed in a dose response assay and in a thermal shift assay with recombinant MeCP2. One class of identified hits represents histone deacetylase inhibitors (HDACis) showing 25% speckle rescue of mutant MeCP2 without toxicity. This screening strategycan be expanded to additional compound libraries and support novel drug discovery.
H3K9me regulates heterochromatin silencing through incoherent feedforward loops
Authors: Yabe Kannosuke , Kamio Asuka , Oya Satoyo , Kakutani Tetsuji , Hirayama Mami , Tanaka Yuriko , Inagaki Soichi
Published: November 2023

Histone H3 lysine-9 methylation (H3K9me) is associated with condensed and transcriptionally inactive heterochromatin1. Although it has long been known that H3K9me silences transcription to control a wide variety of biological phenomena in many eukaryotic species2,3, how the silencing is regulated under the control of H3K9me is still largely unclear. Moreover, how cells delimit regions with H3K9me to avoid silencing essential genes remains unexplored. Here, using Arabidopsis genetic systems that induce H3K9me2 and its associated non-CG DNA methylation (mCH) in the transcribed region of genesde novo, we show that the accumulation of H3K9me2/mCH paradoxically also leads to the deposition of the euchromatic mark H3K36me3. This induction of H3K36me3 depends on a SET domain methyltransferase, ASHH3, and brings about anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2/mCH4. H3K9me2/mCH-driven antagonistic actions of ASHH3-H3K36me3 and LDL2-H3K4me1-loss also regulate thede novosilencing of reactivated transposable elements (TEs). These results demonstrate that H3K9me2 both facilitates and impedes silencing, and the incoherent feedforward loops fine-tune the fate of genes and TEs. Our results illuminate a novel elaborate mechanism for partitioning chromatin domains and provide insights into the molecular basis underlying natural epigenetic variation.
Exploring thienothiadiazine dioxides as isosteric analogues of benzo- and pyridothiadiazine dioxides in the search of new AMPA and kainate receptor positive allosteric modulators
Authors: Francotte Pierre , Bay Yasmin , Goffin Eric , Colson Thomas , Lesenfants Cindy , Dorosz Jerzy , Laulumaa Saara , Fraikin Pierre , de Tullio Pascal , Beaufour Caroline , Botez Iuliana , Pickering Darryl S. , Frydenvang Karla , Danober Laurence , Kristensen Anders Skov , Kastrup Jette Sandholm , Pirotte Bernard
Published: November 2023

The synthesis and biological evaluation on AMPA and kainate receptors of new examples of 3,4-dihydro-2H-1,2,4-thieno[3,2-e]-1,2,4-thiadiazine 1,1-dioxides is described.

The introduction of a cyclopropyl chain instead of an ethyl chain at the 4-position of the thiadiazine ring was found to dramatically improve the potentiator activity on AMPA receptors, with compound32(BPAM395) expressingin vitroactivity on AMPARs (EC2x = 0.24 µM) close to that of the reference 4-cyclopropyl-substituted benzothiadiazine dioxide10(BPAM344).

Interestingly, the 4-allyl-substituted thienothiadiazine dioxide27(BPAM307) emerged as the most promising compound on kainate receptors being a more effective potentiator than the 4-cyclopropyl-substituted thienothiadiazine dioxide32and supporting the view that the 4-allyl substitution of the thiadiazine ring could be more favorable than the 4-cyclopropyl substitution to induce marked activity on kainate receptors versus AMPA receptors.

The thieno-analogue36(BPAM279) of the clinically tested S18986 (11) was selected forin vivoevaluation in mice as a cognitive enhancer due to a safer profile than32after massiveper osdrug administration. Compound36was found to increase the cognition performance in mice at low doses (1 mg/kg)per ossuggesting that the compound was well absorbed after oral administration and able to reach the central nervous system.

Finally, compound32was selected for co-crystallization with the GluA2-LBD (L504Y,N775S) and glutamate to examine the binding mode of thienothiadiazine dioxides within the allosteric binding site of the AMPA receptor. At the allosteric site, this compound established similar interactions as the previously reported BTD-type AMPA receptor modulators.

Highlights

The study explored AMPA/kainate receptor PAMs belonging to thienothiadiazine dioxides

The 4-cyclopropyl-substituted compound32was the most potent AMPA receptor modulator

4-Allyl substitution improved activity and selectivity for kainate receptors

The tricyclic compound36expressed cognitive improvementin vivoin mice

Compound32was co-crystallized with GluA2-LBD to examine receptor binding mode

Graphical abstract
Predictive Uncertainty in State-Estimation Drives Active Sensing
Authors: Karagoz Osman Kaan , Kilic Aysegul , Aydin Emin Yusuf , Ankarali Mustafa Mert , Uyanik Ismail
Published: November 2023

Animals use active sensing movements to shape the spatiotemporal characteristics of sensory signals to better perceive their environment under varying conditions. However, the underlying mechanisms governing the generation of active sensing movements are not known. To address this, we investigated the role of active sensing movements in the refuge tracking behavior ofEigenmannia virescens, a species of weakly electric fish. These fish track the longitudinal movements of a refuge in which they hide by swimming back and forth in a single linear dimension. During refuge tracking,Eigenmanniaexhibits stereotyped whole-body oscillations when the quality of the sensory signals degrades. We developed a feedback control model to examine the role of these ancillary movements on the task performance. Here, we show that the proposed model generates fish trajectories that are statistically indistinguishable from the actual fish, implying that active sensing movements are regulated to minimize the predictive uncertainty in state estimation.
Lac-Phe mediates the anti-obesity effect of metformin
Authors: Xiao Shuke , Li Veronica L. , Lyu Xuchao , Chen Xudong , Wei Wei , Abbasi Fahim , Knowles Joshua W. , Deng Shuliang , Tiwari Gaurav , Shi Xu , Zheng Shuning , Farrell Laurie , Chen Zsu-Zsu , Taylor Kent D. , Guo Xiuqing , Goodarzi Mark O. , Wood Alexis C. , Chen Yii-Der Ida , Lange Leslie A. , Rich Stephen S. , Rotter Jerome I. , Clish Clary B. , Tahir Usman A. , Gerszten Robert E. , Benson Mark D. , Long Jonathan Z.
Published: November 2023

Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformin’s effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levelsin vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformin’s anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformin’s effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.
Female cichlids attack and avoid—but will still mate with—androgen receptor mutant males that lack male-typical body coloration
Authors: Howard Megan R. , Ramsaroop Maxximus G. , Hoadley Andrew P. , Jackson Lillian R. , Lopez Mariana S. , Saenz Lauren A. , Alward Beau
Published: November 2023

A key challenge in animal behavior is disentangling the social stimuli that drive conspecific behaviors. For behaviors like birdsong, insights can be made through the experimental isolation of relevant cues that affect behavior. However, for some species like teleost fish, putative sexual signaling cues are inextricably linked to others, making it difficult to parse the precise roles distinct signals play in driving conspecific behaviors. In the African cichlidAstatotilapia burtoni, males are dominant or subordinate, wherein bright coloration and territorial and courtship behavior inextricably correlate positively with rank. Here, we leveraged androgen receptor (AR) mutant maleA. burtonithat lack dominance-typical coloration but not behavior to isolate the role of male coloration in driving female mating behaviors in this species. We found in independent behavioral assays that females behave aggressively towards AR mutant but not WT males but still mated with both types of males. Females showed enhanced activation ofesr2b+cells in the hypothalamus when housed with either mutant or WT males and this activation scaled with spawning activities. Therefore, there is not a simple relationship between male coloration and female mating behaviors inA. burtoni, suggesting independent sensory mechanisms converge on hypothalamicesr2b+cells to coordinate behavioral output.
Genome-scale annotation of protein binding sites via language model and geometric deep learning
Authors: Yuan Qianmu , Tian Chong , Yang Yuedong
Published: November 2023

Revealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accurately and efficiently identify these binding sites from sequences becomes essential. However, current methods mostly rely on expensive multiple sequence alignments or experimental protein structures, limiting their genome-scale applications. Besides, these methods haven’t fully explored the geometry of the protein structures. Here, we propose GPSite, a multi-task network for simultaneously predicting binding residues of DNA, RNA, peptide, protein, ATP, HEM, and metal ions on proteins. GPSite was trained on informative sequence embeddings and predicted structures from protein language models, while comprehensively extracting residual and relational geometric contexts in an end-to-end manner. Experiments demonstrate that GPSite substantially surpasses state-of-the-art sequence-based and structure-based approaches on various benchmark datasets, even when the structures are not well-predicted. The low computational cost of GPSite enables rapid genome-scale binding residue annotations for over 568,000 sequences, providing opportunities to unveil unexplored associations of binding sites with molecular functions, biological processes, and genetic variants. The GPSite webserver and annotation database can be freely accessed athttps://bio-web1.nscc-gz.cn/app/GPSite.
Feeding Behavior Modifies the Circadian Variation in RR and QT intervals by Distinct Mechanisms in Mice
Authors: Ono Makoto , Burgess Don E. , Johnson Sidney R. , Elayi Claude S. , Esser Karyn A. , Seward Tanya S. , Boychuk Carie R. , Carreño Andrés P. , Stalcup Rebecca A. , Prabhat Abhilash , Schroder Elizabeth A. , Delisle Brian P.
Published: November 2023

Rhythmic feeding behavior is critical for regulating the phase and amplitude in the ≍24-hour variation of the heart rate (RR intervals), ventricular repolarization (QT intervals), and core body temperature in mice. We hypothesized the changes in cardiac electrophysiology associated with feeding behavior were secondary to changes in core body temperature. Telemetry was used to record electrocardiograms and core body temperature in mice during ad libitum-fed conditions and after inverting normal feeding behavior by restricting food access to the light cycle. Light cycle-restricted feeding quickly modified the phase and amplitude of the 24-hour rhythms in RR intervals, QT intervals, and core body temperature to realign with the new feeding time. Heart rate variability analysis and inhibiting β-adrenergic and muscarinic receptors suggested that the changes in the phase and amplitude of the 24-hour rhythms in RR intervals were secondary to changes in autonomic signaling. In contrast, the changes in the QT intervals closely mirrored changes in core body temperature. Studies at thermoneutrality confirmed the daily variation in the QT interval, but not the RR interval, and reflected daily changes in core body temperature (even in ad libitum-fed conditions). Correcting the QT interval for differences in core body temperature helped to unmask QT interval prolongation after starting light cycle-restricted feeding and in a mouse model of long QT syndrome. We conclude feeding behavior alters autonomic signaling and core body temperature to regulate the phase and amplitude in RR and QT intervals, respectively.
The Effects of Flow Speeds on Smooth Pursuit Tracking and Active Sensing Movements of Weakly Electric Fish
Authors: Aydin Emin Yusuf , Unlutabak Burcu , Uyanik Ismail
Published: November 2023

Weakly electric fish employ refuge-tracking behavior to survive, seeking and utilizing hiding places to shield themselves from predators and unfavorable environmental conditions. This adaptive mechanism enables them to minimize the risk of predation, maintain optimal electrocommunication, and adapt to changing surroundings. While studies have explored smooth pursuit tracking and active sensing movements of these fish in stationary environments, limited emphasis has been given to how varying flow speeds in their natural habitats may impact these behaviors. This study addresses this gap by investigating the effects of different flow speeds on smooth pursuit tracking and active sensing movements in weakly electric fish. Active sensing provides sensory data and multisensory integration processes and combines this data to create a holistic perception of the environment. The synergy between these processes is fundamental for enhancing an organism’s sensory capabilities and enabling it to adapt and interact effectively with its surroundings. For this study, a specialized experimental setup was designed and built to facilitate refuge-tracking behavior under controlled flow conditions. The experiments involvedApteronotus albifronsfish exposed to visual and complex electrosensory stimuli, which consisted of a sum of sine signals. Data was recorded for different sensory conditions, including variations in flow speeds, illumination levels, and refuge structures. The analysis revealed that increased flow speeds correlated with reduced tracking gain and phase lag in the fish. Additionally, it was observed that active sensing movements were more pronounced in dark conditions. These findings highlight the significant impact of flow speeds on smooth pursuit tracking and active sensing movements and emphasize the importance of studying these behaviors within the context of water flow. Understanding the biological motivations underlying these effects is vital for their potential application in engineering fields.
‘Optical Von-Frey’ method to determine nociceptive thresholds: a novel paradigm for preclinical pain assessment and analgesic screening
Authors: Iredale Jacqueline A , Pearl Amy J , Callister Robert J , Dayas Christopher V , Manning Elizabeth E , Graham Brett A
Published: November 2023

The goal of this study was to characterize a model that specifically activates peripheral nociceptors, allowing pure nociceptive thresholds to be monitored over a range of conditions including pathology or in screening analgesic compounds. Transgenic mice expressing channelrhodopsin-2 (ChR2) in cell populations positive for the transient receptor potential cation channel subfamily V member 1 (TRPV1) gene were bred to enable peripheral nociceptor photostimulation. Preliminary experiments confirmed the expected localisation pattern of ChR2 positive profiles in the dorsal root ganglion and superficial dorsal horn, mirroring TPRV1 expression. Brief hindpaw photostimulation with 470nm light caused hindpaw withdrawal and nocifensive behaviours in ChR2 positive animals but not control ChR2 negative animals. Using a simplified up/down approach, ‘optical’ nociceptive thresholds were assessed with a 5-intensity hindpaw photostimulation paradigm, establishing the minimum intensity required to produce a withdrawal response (optical threshold). All testing was also video recorded and analysed post-hoc to assess additional photostimulation evoked behaviours. Repeated testing over several days showed optical nociceptive thresholds and response duration were similar, supporting the stability of these variables across a timeframe relevant to onset of pathology or drug administration. Optical nociceptive thresholds were also assessed following morphine administration (30 mg/kg), which significantly raised thresholds, highlighting analgesic screening utility of this model. Together, these findings demonstrate the peripheral photostimulation with optical thresholding is a useful addition to the preclinical nociception assessment toolkit, with the key advantage of inducing a purely nociceptive response to a non-invasive, non-tissue damaging stimulus.
The use of bacterial consortia improves seed tuber production in potato varieties for frying
Authors: Mauricio Ramírez Rodrigo , Rodriguez-Grados Pedro , Quiliche Jean Piere , Contreras-Liza Sergio , Montemayor Mantilla José , Palomares Anselmo Edison
Published: November 2023

Objective

To determine the effect of a consortium of growth-promoting rhizobacteria on potato varieties for frying under controlled conditions.

Methodology

The research was conducted at the Universidad Nacional José Faustino Sánchez Carrión, Huacho, Peru. The experiment was carried out in pots in a greenhouse using a completely randomized design with 6 replications, under a factorial arrangement. Four potato genotypes for frying (cv. Bicentenaria, advanced clones UH-9, CIP 396311.1, CIP 399101.1) and four inoculant treatments were used,Azotobactersp. (T1),Azotobactersp.+Bacillus simplex(T2),Azotobactersp.+B. subtilis(T3),Azotobactersp.+B. subtilis+B. simplex(T4) and an uninoculated control (T0). The variables studied were vegetative vigor, plant height, number of stems per plant, number of leaves per plant, fresh and dry weight per plant, tuber diameter, and number and weight of tubers per plant. Data were statistically processed and analysed by performing Scott-Knott’s comparison of treatments and using principal component analysis.

Results

The inoculation alone withAzotobactersp. (T1) or with the consortiumAzotobactersp.+B. simplex+B. subtilis(T4) significantly promoted potato growth with respect to the number of stems and number of leaves per plant, as well as weight and number of tubers per plant; for vegetative vigor, the control treatment (T0) obtained differences in comparison with the inoculated treatments. Plant height, number of shoots, fresh and dry weight of foliage and tuber diameter did not show significant differences due to the effect of the inoculation. Interactions between varieties and treatments were found for vegetative vigor, the number of leaves and tubers per plant, being positive for the inoculation with some bacterial consortia.

Conclusion

Bacterial consortia withAzotobactersp. promote the growth and productivity of potato varieties for processing under greenhouse conditions.
Aryl amino acetamides prevent the development ofPlasmodium falciparumrings via inhibition of the lipid transfer protein PfSTART1
Authors: Dans Madeline G. , Boulet Coralie , Watson Gabrielle M. , Nguyen William , Dziekan Jerzy M. , Evelyn Cindy , Reaksudsan Kitsanapong , Mehra Somya , Razook Zahra , Geoghegan Niall D. , Mlodzianoski Michael J. , Goodman Christopher Dean , Ling Dawson B. , Jonsdottir Thorey K. , Tong Joshua , Famodimu Mufuliat Toyin , Kouskousis Betty , Delves Michael J. , McFadden Geoffrey I. , Barry Alyssa E. , Crabb Brendan S. , de Koning-Ward Tania F. , Rogers Kelly L. , Cowman Alan F. , Tham Wai-Hong , Sleebs Brad E. , Gilson Paul R.
Published: November 2023

With resistance to most antimalarials increasing, it is imperative that new antimalarial drugs are developed to replace or complement front-line artemisinin therapies. We previously identified an aryl acetamide compound, MMV006833 (M-833), that inhibited ring development of newly invaded merozoites. Here, we selected parasites resistant to M-833 and identified independent mutations arising in the START lipid transfer protein (PF3D7_0104200, PfSTART1). Introduction of the identified PfSTART1 mutations into wildtype parasites reproduced resistance to both M-833 and highly potent analogues, confirming PfSTART1 mutations were sufficient to confer resistance. The analogues bound to recombinant PfSTART1 with nanomolar affinity. We also demonstrated selective PfSTART1 engagement by the analogues using organic solvent-based Proteome Integral Solubility Alteration (Solvent PISA) assay for the first time inPlasmodium.Imaging of newly invaded merozoites showed the inhibitors prevented the conversion into larger amoeboid ring-stage parasites potentially through the inhibition of phospholipid transfer from the parasite to the encasing parasitophorous vacuole membrane (PVM) and/or within the parasite. We show that these PfSTART1 inhibitors also block transmission. With multiple stages of the parasite’s lifecycle being targeted by PfSTART1 inhibitors, this protein therefore represents a novel drug target with a new mechanism of action.
Comparative Analysis of GPT-4Vision, GPT-4 and Open Source LLMs in Clinical Diagnostic Accuracy: A Benchmark Against Human Expertise
Authors: Han Tianyu , Adams Lisa C , Bressem Keno , Busch Felix , Huck Luisa , Nebelung Sven , Truhn Daniel
Published: November 2023

Importance

Medicine is poised for transformation with artificial general intelligence becoming integral to almost all clinical environments. Currently, the performance of multimodal AI, specifically one powered by GPT-4, in real clinical cases remains uncharted.

Objective

To ascertain whether GPT-4V can consistently comprehend complex diagnostic scenarios through both imagery and textual data.

Design

A selection of 140 clinical cases from the JAMA Clinical Challenge and 348 from the NEJM Image Challenge were used. Each case, comprising a clinical image and corresponding question, was processed by GPT-4V, and responses were documented. The significance of imaging information was assessed by comparing GPT-4V’s performance with that of four other leading-edge large language models (LLMs).

Main Outcomes and Measures

The accuracy of responses was gauged by juxtaposing the model’s answers with the established ground truths of the challenges. The confidence interval for the model’s performance was calculated using bootstrapping methods. Additionally, human performance on the NEJM Image Challenge was chronicled, reflected by the choice percentage selected by challenge participants.

Results

GPT-4V demonstrated superior accuracy in analyses of both sources, achieving 73.3% for JAMA and 88.7% for NEJM, notably outperforming text- only LLMs such as GPT-4, GPT-3.5, Llama2, and Med-42. Remarkably, both GPT-4V and GPT-4 exceeded average human participants’ performance at all complexity levels within the NEJM Image Challenge.

Conclusions and Relevance

GPT-4V has exhibited considerable promise in clinical diagnostic tasks, surpassing the capabilities of its predecessors as well as those of human experts. However, while its proficiency in identification tasks is commendable, it requires further refinement in decision-making and strategic planning. Despite these encouraging results, such models should be adopted with prudence in clinical settings, serving to augment rather than replace human discretion. Continual research is imperative to fully evaluate the potential impact on patient care.
An integrated single-cell reference atlas of the human endometrium
Authors: Marečková Magda , Garcia-Alonso Luz , Moullet Marie , Lorenzi Valentina , Petryszak Robert , Sancho-Serra Carmen , Oszlanczi Agnes , Mazzeo Cecilia Icoresi , Hoffman Sophie , Krassowski Michał , Garbutt Kurtis , Kelava Iva , Gaitskell Kezia , Yancheva Slaveya , Woon Ee Von , Male Victoria , Granne Ingrid , Hellner Karin , Mahbubani Krishnaa T , Saeb-Parsy Kourosh , Lotfollahi Mohammad , Prigmore Elena , Southcombe Jennifer , Dragovic Rebecca A , Becker Christian M , Zondervan Krina T , Vento-Tormo Roser
Published: November 2023

The human endometrium, the inner lining of the uterus, exhibits complex, dynamic changes throughout the menstrual cycle in response to ovarian hormones. Aberrant response of endometrial cells to hormones is associated with multiple disorders, including endometriosis. Previous single-cell studies of the endometrium profiled a limited number of donors and lacked consensus in defining cell types and states. Here, we introduce the Human Endometrial Cell Atlas (HECA), a high-resolution single-cell reference atlas, combining published and newly generated single-cell transcriptomics datasets of endometrial biopsies of women with and without endometriosis. The HECA assigned consensus cell types and states, and uncovered novel ones, which we mapped in situ using spatial transcriptomics. We quantified how coordinated interactions between cell states in space and time contribute to endometrial regeneration and differentiation. In the continuously changingfunctionalislayer, we identified an intricate coordination of TGFβ signalling between stromal and epithelial cells, likely crucial for cell differentiation. In thebasalislayer, we defined signalling between fibroblasts and a new epithelial cell population expressing epithelial stem/progenitor markers, suggesting their role in endometrial regeneration. Additionally, integrating the HECA single-cell data with genome-wide association study data and comparing endometrial samples from women with and without endometriosis, we pinpointed subsets of decidualised stromal cells and macrophages as the most dysregulated cell states in endometriosis. Overall, the HECA is an invaluable resource for studying endometrial physiology, investigating endometrial disorders, and guiding the creation of endometrial microphysiologicalin vitrosystems.
Target-agnostic identification of human antibodies toPlasmodium falciparumsexual forms reveals cross stage recognition of glutamate-rich repeats
Authors: Amen Axelle , Yoo Randy , Fabra-García Amanda , Bolscher Judith , Stone William J.R. , Bally Isabelle , Dergan-Dylon Sebastián , Kucharska Iga , de Jong Roos M. , de Bruijni Marloes , Bousema Teun , Richter King C. , MacGill Randall S. , Sauerwein Robert W. , Julien Jean-Philippe , Poignard Pascal , Jore Matthijs M.
Published: November 2023

Circulating sexual stages ofPlasmodium falciparum (Pf)can be transmitted from humans to mosquitoes, thereby furthering the spread of malaria in the population. It is well established that antibodies (Abs) can efficiently block parasite transmission. In search for naturally acquired Ab targets on sexual stages, we established an efficient method for target-agnostic single B cell activation followed by high-throughput selection of human monoclonal antibodies (mAbs) reactive to sexual stages ofPfin the form of gamete and gametocyte extract. We isolated mAbs reactive against a range ofPfproteins including well-established targets Pfs48/45 and Pfs230. One mAb, B1E11K, was cross-reactive to various proteins containing glutamate-rich repetitive elements expressed at different stages of the parasite life cycle. A crystal structure of two B1E11K Fab domains in complex with its main antigen, RESA, expressed on asexual blood stages, showed binding of B1E11K to a repeating epitope motif in a head-to-head conformation engaging in affinity-matured homotypic interactions. Thus, this mode of recognition ofPfproteins, previously described only for PfCSP, extends to other repeats expressed across various stages. The findings augment our understanding of immune-pathogen interactions to repeating elements of thePlasmodiumparasite proteome and underscore the potential of the novel mAb identification method used to provide new insights into the natural humoral immune response againstPf.

Impact Statement

A naturally acquired human monoclonal antibody recognizes proteins expressed at different stages of thePlasmodium falciparumlifecycle through affinity-matured homotypic interactions with glutamate-rich repeats
Pan-sphingolipid profiling reveals differential functions of sphingolipid biosynthesis isozymes ofC. elegans
Authors: Luo Hui , Zhao Xue , Wang Zi-Dan , Wu Gang , Xia Yu , Dong Meng-Qiu , Ma Yan
Published: November 2023

Multiple isozymes are encoded in theC. elegansgenome for the various sphingolipid biosynthesis reactions, but the contributions of individual isozymes are characterized only in part. We developed a simple but effective reversed-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method that enables simultaneous identification and quantification of ceramides (Cer), glucosylceramides (GlcCer), and sphingomyelins (SM), three important classes of sphingolipids from the same MS run. Validating this pan-sphingolipid profiling method, we show that nearly all 47 quantifiable sphingolipid species found in young adult worms were reduced upon RNA interference (RNAi) ofsptl-1orelo-5, which are required for synthesis of the id17:1 sphingoid base. We also confirm that HYL-1 and HYL-2, but not LAGR-1, constitute the major ceramide synthase activity with different preference for fatty acid substrates, and that CGT-3 plays a greater role than CGT-1 does in producing glucosylceramides. Intriguingly,lagr-1RNAi lowers the abundance of all sphingomyelin species and that of several glucosylceramide species, which suggests that LAGR-1 may have functions beyond what is predicted. Additionally, RNAi ofsms-1, −2,and-3all lower the abundance of sphingomyelins with an odd number of carbon atoms (mostly C21 and C23, with or without hydroxylation) in the N-acyl chain, and onlysms-1RNAi does not elevate sphingomyelins containing even-numbered N-acyl chains. This suggests that sphingolipids containing even-numbered N-acyl chains could be regulated separately, sometimes in opposite directions, with those containing odd-numbered N-acyls, presumably monomethyl branched chain fatty acyls. We also find that ceramide levels are kept in balance with those of glucosylceramides and sphingomyelins.
Geographic patterns of living tetrapod diversity reveal the signature of global diversification dynamics
Authors: Tejero-Cicuéndez Héctor , Menéndez Iris , Steell Elizabeth M. , Navalón Guillermo , Blanco Fernando , Šmíd Jiří
Published: November 2023

Biodiversity is distributed unevenly among lineages and regions, and understanding the processes generating these global patterns is a central goal in evolutionary research, particularly in light of the current biodiversity crisis. Here, we integrate phylogenetic relatedness with species diversity patterns in four major clades of living tetrapods (amphibians, squamates, birds and mammals) to approach this challenge. We studied geographic patterns of richness-corrected phylogenetic diversity (residual PD), identifying regions where species are phylogenetically more closely or distantly related than expected by richness. We explored the effect of different factors in residual PD: recent speciation rates, temporal trends of lineage accumulation, and environmental variables. Specifically, we searched for evolutionary and ecological differences between regions of high and low residual PD. Our results reveal a nuanced relationship between recent speciation rates and residual PD, underscoring the role of recent speciation events in structuring current biogeographic patterns. Furthermore, we found differences between endothermic and ectothermic tetrapods in response to temperature and precipitation, highlighting the pivotal role of thermal physiology in shaping diversity dynamics. By illuminating the multifaceted factors underpinning global diversity patterns, our study represents a significant advancement towards more effective and holistic conservation approaches that are crucial to facing ongoing environmental challenges.
The evolutionary conserved choroid plexus sustains the homeostasis of brain ventricles in zebrafish
Authors: Jeong Inyoung , Andreassen Søren N. , Hoang Linh , Poulain Morgane , Seo Yongbo , Park Hae-Chul , Fürthauer Maximilian , MacAulay Nanna , Jurisch-Yaksi Nathalie
Published: November 2023

The choroid plexus produces cerebrospinal fluid (CSF) by transport of electrolytes and water from the vasculature to the brain ventricles. The choroid plexus plays additional roles in brain development and homeostasis by secreting neurotrophic molecules, and by serving as a CSF-blood barrier and immune interface. Prior studies have identified transporters on the epithelial cells that transport water and ions into the ventricles and tight junctions involved in the CSF-blood barrier. Yet, how the choroid plexus epithelial cells maintain the brain ventricle system and control brain physiology remain unresolved. To provide novel insights into the physiological roles of the choroid plexus, we use juvenile and adult zebrafish as model systems. Upon histological and transcriptomic analyses, we first identified that the zebrafish choroid plexus is highly conserved with the mammalian choroid plexus and that it expresses all transporters necessary for CSF secretion. Using novel genetic lines, we also identified that the choroid plexus secretes proteins into the CSF. Next, we generated a transgenic line allowing us to ablate specifically the epithelial cells in the choroid plexus. Using the ablation system, we identified a reduction of the ventricular sizes, but no alterations of the CSF-blood barrier. Altogether, our findings identified that the zebrafish choroid plexus is evolutionarily conserved and critical for maintaining the size and homeostasis of the brain ventricles.

Graphical abstract

Highlights

The zebrafish choroid plexus has similar anatomical features with the mammalian choroid plexus.

The expression of choroid plexus transporters involved in CSF secretion is evolutionarily conserved across vertebrates.

Generation of a novel choroid plexus specific driver line shows that the choroid plexus epithelial cells secrete proteins into CSF.

Ablation of the choroid plexus decreases the size of the brain ventricles.
DNA Origami Vesicle Sensors with Triggered Cargo Transfer
Authors: Büber Ece , Yaadav Renukka , Schröder Tim , Franquelim Henri G. , Tinnefeld Philip
Published: November 2023

Interacting with living systems typically involves the ability to address lipid membranes of cellular systems. The first step of interaction of a nanorobot with a cell will thus be the detection of binding to a lipid membrane. Leveraging the programmable nature of DNA origami, we engineered a biosensor harnessing single-molecule Fluorescence Resonance Energy Transfer (smFRET) as transduction mechanism for precise lipid vesicle detection. The system hinges on a hydrophobic ATTO647N modified single-stranded DNA (ssDNA) leash, protruding from a rectangular DNA origami. In a vesicle-free environment, the ssDNA adopts a coiled stance, ensuring high FRET efficiency. However, upon lipid vesicle binding to cholesterol anchors on the DNA origami, the hydrophobic ATTO647N induces the ssDNA to stretch towards the lipid bilayer, leading to reduced FRET efficiency. The strategic placement of cholesterol anchors further modulates this interaction, affecting the observed FRET populations. Beyond its role as a vesicle sensor, we show targeted cargo transport of the acceptor dye unit to the vesicle. The cargo transport is initiated by vesicle bound DNA and a strand displacement reaction. Our interaction platform opens pathways for innovative interaction such as biosensing and molecular transport with complex biosystems.
Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus
Authors: Rasetto Natalí B. , Giacomini Damiana , Berardino Ariel A. , Waichman Tomás Vega , Beckel Maximiliano S. , Di Bella Daniela J. , Brown Juliana , Davies-Sala M. Georgina , Gerhardinger Chiara , Lie Dieter Chichung , Arlotta Paola , Chernomoretz Ariel , Schinder Alejandro F.
Published: November 2023

The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressingSox4orSox11remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.
Lactate accumulation induced genioglossus myoblast injury under hypoxia
Authors: Zhang Menghan
Published: November 2023

Obstructive sleep apnea (OSA) is an increasingly common disorder of repeated upper airway collapse during sleep, leading to chronic intermittent hypoxia and metabolic alteration such as lactate accumulation. Genioglossus (GG), the largest upper airway dilator, is of great significance in maintaining the patency of the upper airway collapse. However, the lactate mechanism in OSA/CIH models is incomplete understood. Here, extracellular and intracellular contents of lactate were detected, and found hypoxia induced lactate accumulation in GG myoblasts. The we treat GG with lactate, and found lactate inhibited myoblasts proliferation and myotubes formation under hypoxia. When the lactate efflux was blocked by monocarboxylic acid transporter 1 (MCT1, a lactate transport) inhibitor AZD3965 (AZD), the expression levels of myogenic markers MyoD, Myogenin and MyHC were reduced. In summary, lactate efflux obstruction and lactate accumulation induced GG myoblast injury under hypoxia. These findings provide a theoretical basis for regulation lactate metabolism to alleviate muscle fatigue in the treatment of OSA.
SWISH-X, an expanded approach to detect cryptic pockets in proteins and at protein-protein interfaces
Authors: Borsatto Alberto , Gianquinto Eleonora , Rizzi Valerio , Gervasio Francesco Luigi
Published: November 2023

Protein-protein interactions mediate most molecular processes in the cell, offering a significant opportunity to expand the set of known druggable targets. Unfortunately, targeting these interactions can be challenging due to their typically flat and featureless interaction surfaces, which often change as the complex forms. Such surface changes may reveal hidden (cryptic) druggable pockets. Here, we analyse a set of well-characterised protein-protein interactions harbouring cryptic pockets and investigate the predictive power of current computational methods. Based on our observations, we develop a new computational strategy, SWISH-X (SWISH Expanded), which combines the established cryptic pocket identification capabilities of SWISH with the rapid temperature range exploration of OPES MultiThermal. SWISH-X is able to reliably identify cryptic pockets at protein-protein interfaces while retaining its predictive power for revealing cryptic pockets in isolated proteins, such as TEM-1β-lactamase.
Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian ‘ilima (Sida fallax)
Authors: Triplett Genevieve , Buckley Thomas N. , Muir Christopher D.
Published: November 2023

Premise of the study

The adaptive significance of stomata on both upper and lower leaf surfaces, called amphistomy, is unresolved. A widespread association between amphistomy and open, sunny habitats suggests the adaptive benefit of amphistomy may be greatest in these contexts, but this hypothesis has not been tested experimentally. Understanding why amphistomy evolves can inform its potential as a target for crop improvement and paleoenvironment reconstruction.

Methods

We developed a new method to quantify “amphistomy advantage”, AA, as the log-ratio of photosynthesis in an amphistomatous leaf to that of the same leaf but with gas exchange blocked through the upper (adaxial) surface, which we term “pseudohypostomy”. We used humidity to modulate stomatal conductance and thus compare photosynthetic rates at the same total stomatal conductance. We estimated AA and related physiological and anatomical traits in 12 populations, six coastal (open, sunny) and six montane (closed, shaded), of the indigenous Hawaiian species ‘ilima (Sida fallax).

Key results

Coastal ‘ilima leaves benefit 4.04 times more from amphistomy compared to their montane counterparts. Our evidence was equivocal with respect to two hypotheses – that coastal leaves benefit more because 1) they are thicker and therefore have lower CO2conductance through the internal airspace, and 2) that they benefit more because they have similar conductance on each surface, as opposed to most of the conductance being on the lower (abaxial) surface.

Conclusions

This is the first direct experimental evidence that amphistomyper seincreases photosynthesis, consistent with the hypothesis that parallel pathways through upper and lower mesophyll increase the supply of CO2to chloroplasts. The prevalence of amphistomatous leaves in open, sunny habitats can partially be explained the increased benefit of amphistomy in ‘sun’ leaves, but the mechanistic basis of this observation is an area for future research.
reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting
Authors: Mishra Sarthak , Smith Megan L. , Hahn Matthew W.
Published: November 2023

Reconciliation algorithms provide an accounting of the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizontal transfer), ignoring effects of the coalescent process, including incomplete lineage sorting (ILS). Here, we present a new heuristic algorithm for carrying out reconciliation that accurately accounts for ILS by treating it as a series of nearest neighbor interchange (NNI) events. For discordant branches of the gene tree identified by last common ancestor (LCA) mapping, our algorithm recursively chooses the optimal history by comparing the cost of duplication and loss to the cost of NNI and loss. We demonstrate the accuracy of our new method, which we callreconcILS, using a new simulation engine (dupcoal) that can accurately generate gene trees produced by the interaction of duplication, loss, and ILS. Despite being a heuristic method, we show thatreconcILSis much more accurate than models that ignore ILS, and at least as accurate or better than leading methods that can model ILS, while also being able to handle much larger datasets. We demonstrate the use ofreconcILSby applying it to a dataset of 23 primate genomes, highlighting its accuracy compared to standard methods in the presence of large amounts of ILS.
Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy
Authors: Katti Sachin S. , Igumenova Tatyana I.
Published: November 2023

One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca2+and Zn2+. The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application ofin-celland lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intactE. colicells and their lysates, revealed that Cd2+can profoundly affect the quinary interactions of its protein partners, and can replace Zn2+in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd2+can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α3DIV to sequester intracellular cadmium. Our data suggests thatin-cellNMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
SuPreMo: a computational tool for streamliningin silicoperturbation using sequence-based predictive models
Authors: Gjoni Ketrin , Pollard Katherine S.
Published: November 2023

Computationally editing genome sequences is a common bioinformatics task, but current approaches have limitations, such as incompatibility with structural variants, challenges in identifying responsible sequence perturbations, and the need for vcf file inputs and phased data. To address these bottlenecks, we presentSequence Mutator forPredictiveModels (SuPreMo), a scalable and comprehensive tool for performingin silicomutagenesis. We then demonstrate how pairs of reference and perturbed sequences can be used with machine learning models to prioritize pathogenic variants or discover new functional sequences.

Availability and Implementation

SuPreMo was written in Python, and can be run using only one line of code to generate both sequences and 3D genome disruption scores. The codebase, instructions for installation and use, and tutorials are on the Github page:https://github.com/ketringjoni/SuPreMo/tree/main.

Contact

katherine.pollard@gladstone.ucsf.edu

Supplementary information

Supplementary data are available at Bioinformatics online.