bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual-specific functional connectivity shows improved performance in detecting and predicting individualized symptoms of Alzheimer’s disease in elderly people with/without APOE ε4 allele
Authors: Hua Lin , Gao Fei , Xia Xiaoluan , Guo Qiwei , Zhao Yonghua , Yuan Zhen 
Published: November 2022

AbstractTo date, no reliable biomarkers are available that link individual-specific functional connectivity and patients’ individualized symptoms for early detection and prediction of Alzheimer’s disease (AD) in elderly people with specific genotypes. Meanwhile, functional magnetic resonance imaging (MRI) and machine learning are promising tools that can reveal the relationships between brain and behavior at individual level towards predicting the transition to AD. In this study, individual-specific functional connectivity was constructed in elderly participants with Apolipoprotein E (APOE) ε4 allele (N= 120) and without APOE ε4 allele (N= 115), respectively. In particular, machine learning based on a recursive feature selection technique was carried out to track multiple clinical symptoms among differing genotypes at individual level from normal aging (NA) and AD. It was found that the captured neuroimaging features in both APOE genotyping groups were able to distinguish the changes of clinical symptoms from NA to AD. Besides, our findings illustrated that the connections between individual-specific functional regions exhibited significantly higher correlation between estimated and observed scores in multiple clinical symptoms than those from atlas-based functional connectivity for both APOE genotyping groups, while no significant performance was detected when the data of two APOE genotyping groups were combined for the estimation models. Further, individual-specific between-network connectivity constitutes a major contributor for accessing cognitive symptoms in both APOE genotyping groups. Therefore, this study demonstrated the essential role of individual variation in cortical functional anatomy and the significance in combining brain and behavior for improving the accuracy in detection and prediction of AD in elderly people with specific genotypes.
The microbial composition and functional roles of different kombucha products in Singapore
Authors: Hooi Suet Li , Dwiyanto Jacky , Toh Kai Yee , Tan Gwendoline , Chong Chun Wie , Lee Jonathan Wei Jie , Lim Jeremy 
Published: November 2022

AbstractKombucha is a fermented tea traditionally known for its health-enhancing properties owing to the bioactive compounds generated by acetic acid bacteria (AAB) and lactic acid bacteria (LAB). We compared the distribution of AAB and LAB and their functional pathways across nine commercial kombucha products in Singapore using shotgun metagenomic sequencing. A high prevalence ofKomagataeibacterspecies includingKomagataeibacter saccharivorans(82.93% in B),Komagataeibacter xylinus(93.38% in D) andKomagataeibacter rhaeticus(92.20% and 30.62% in G and I) was detected in AAB-dominant kombucha. LAB-dominant kombucha was largely represented byBacillus coagulans(~99% in E and F) andLactobacillus nagelii(~60% in H). Despite differences in bacterial composition, both LAB-and AAB-dominant kombucha harbour pathways involved in the biosynthesis of short-chain fatty acids (SCFAs), amino and organic acids and vitamin B12. “Fatty acid and beta-oxidation II (peroxisome)” and “fatty acid and beta-oxidation I” were detected in the LAB but not the AAB-dominant kombucha.
Mechanistic divergence of piRNA biogenesis in Drosophila
Authors: Chary Shashank , Hayashi Rippei 
Published: November 2022

AbstractOrganisms require mechanisms to distinguish self and non-self RNA. This distinction is crucial to initiate the biogenesis of piRNAs. In Drosophila ovaries, PIWI-guided slicing and the recognition of piRNA precursor transcripts by the DEAD-box RNA helicase Yb are the two known mechanisms to licence an RNA for piRNA biogenesis in the germline and the soma, respectively. Both, the PIWI proteins and Yb are highly conserved across most Drosophila species and are thought to be essential to the piRNA pathway and for silencing transposons. However, we find that species closely related toD. melanogasterhave lost theybgene, as well as the PIWI geneAgo3. We show that the precursor RNA is still selected in the absence of Yb to abundantly generate transposon antisense piRNAs in the soma. We further demonstrate thatD. eugracilis, which lacksAgo3, is completely devoid of ping-pong piRNAs and exclusively produces phased piRNAs in the absence of slicing. Thus, there are more possible routes through which the piRNA pathway can achieve specificity than previously suggested.
Nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy (iU-ExM)
Authors: Louvel Vincent , Haase Romuald , Mercey Olivier , Laporte Marine. H. , Soldati-Favre Dominique , Hamel Virginie , Guichard Paul 
Published: November 2022

AbstractExpansion microscopy is an approach of super-resolution fluorescence microscopy that does not yet achieve the precision of nanoscopy techniques such as single-molecule light microscopy (SMLM). Here, we developed an iterative ultrastructure expansion microscopy approach (iU-ExM), which now matches the SMLM resolution as demonstrated using standard references such as the nuclear pores. Applicable to both cells and tissues, iU-ExM allows a broad research community to access high precision super-resolution microscopy.
Multifaceted contributions ofDicer2to arbovirus transmission byAedes aegypti
Authors: Merkling Sarah Hélène , Crist Anna Beth , Henrion-Lacritick Annabelle , Frangeul Lionel , Gausson Valérie , Blanc Hervé , Baidaliuk Artem , Saleh Maria-Carla , Lambrechts Louis 
Published: November 2022

AbstractArthropod-borne viruses (arboviruses) transmitted byAedes aegyptimosquitoes are an increasing threat to global health. The small interfering RNA (siRNA) pathway is considered the main antiviral immune pathway of insects, and thus represents a potential key target in the development of novel transmission-blocking strategies against arboviruses. Although the antiviral function of the siRNA pathway inAe. aegyptiis well established, its effective impact on arbovirus transmission is surprisingly poorly understood. Here, we used CRISPR/Cas9-mediated gene editing to create a line ofAe. aegyptiin which we mutatedDicer2, a gene encoding the RNA sensor and key component of the siRNA pathway. OurDicer2null mutant line is viable and fertile, and only displays minor fitness defects despite being unable to produce siRNAs. The loss ofDicer2affects early viral replication and systemic viral dissemination of four medically significant arboviruses (chikungunya, Mayaro, dengue, and Zika viruses) representing two viral families. However, measures of virus transmission potential indicate thatDicer2null mutants and wild-type mosquitoes display an overall similar level of vector competence. Additionally,Dicer2null mutants undergo significant virus-induced mortality during infection with chikungunya virus, but not dengue virus. Together, our results define a multifaceted role forDicer2in the transmission of arboviruses byAe. aegyptimosquitoes and pave the way for further mechanistic investigations.
Inducible co-stimulatory molecule (ICOS) alleviates Paclitaxel induced peripheral neuropathy via an IL-10-mediated mechanism in female mice
Authors: Sankaranarayanan Ishwarya , Tavares-Ferreira Diana , Mwrigi Juliet , Mejia Galo , Burton Michael D. , Price Theodore J. 
Published: November 2022

AbstractChemotherapy-induced peripheral neuropathy (CIPN) is a primary dose-limiting side effect caused by antineoplastic agents, such as paclitaxel. This causes damage to peripheral nerves and the dorsal root ganglia (DRG). Currently, there are no effective treatments for CIPN, which can lead to long-term morbidity in cancer patients and survivors. Neuro-immune interactions occur in CIPN and have been implicated both in the development and progression of the disease and disease resolution. We investigated the potential role of Inducible co-stimulatory molecule (ICOS) in the resolution of CIPN pain-like behaviors in mice. ICOS is an immune checkpoint molecule that is expressed on the surface of activated T cells and promotes proliferation and differentiation of T cells. We found that intrathecal administration of ICOS agonist antibody (ICOSaa) alleviates mechanical hypersensitivity caused by paclitaxel and facilitates the resolution of mechanical sensitivity in female mice. Administration of ICOSaa reduced astrocyte-gliosis in the spinal cord and satellite cell gliosis in the DRG of mice previously treated with paclitaxel. Mechanistically, ICOSaa intrathecal treatment promoted pain resolution by increasing interleukin 10 (IL-10) expression in the dorsal root ganglion. In line with these observations, blocking IL-10 receptor (IL-10R) activity occluded the effects of ICOSaa treatment on CIPN behavior in female mice. Suggesting a broader activity in neuropathic pain, ICOSaa also partially resolved mechanical hypersensitivity in the spared nerve injury (SNI) model. Our findings support a model wherein ICOSaa administration induces IL-10 expression to facilitate neuropathic pain relief in female mice. ICOSaa treatment is in clinical development for solid tumors and given our observation of T cells in the human DRG, ICOSaa therapy could be developed for combination chemotherapy - CIPN clinical trials.HighlightsICOS agonist antibody (ICOSaa) promotes pain resolution in female miceDRG T cells appear to enter an anti-inflammatory phenotype by ICOSaa treatmentICOSaa treatment increases DRG levels of IL-10 cytokineICOSaa effects in female mice are blocked by IL-10 sequestering treatment
Scene perception and visuospatial memory converge at the anterior edge of visually-responsive cortex
Authors: Steel Adam , Garcia Brenda D. , Goyal Kala , Mynick Anna , Robertson Caroline E. 
Published: November 2022

AbstractTo fluidly engage with the world, our brains must simultaneously represent both the scene in front of us and our memory of the immediate surrounding environment (i.e., local visuospatial context). How does the brain’s functional architecture enable sensory and mnemonic representations to closely interface, while also avoiding sensory-mnemonic interference? Here, we asked this question using first-person, head-mounted virtual reality (VR) and fMRI. Using VR, human participants of both sexes learned a set of immersive, real-world visuospatial environments in which we systematically manipulated the extent of visuospatial context associated with a scene image in memory across three learning conditions, spanning from a single field-of-view to a city street. We used individualized, within-subject fMRI to determine which brain areas support memory of the visuospatial context associated with a scene during recall (Exp. 1) and recognition (Exp. 2). Across the whole brain, activity in three patches of cortex was modulated by the amount of known visuospatial context, each located immediately anterior to one of the three scene perception areas of high-level visual cortex. Individual subject analyses revealed that these anterior patches corresponded to three functionally-defined place memory areas, which selectively respond when visually recalling personally familiar places. In addition to showing activity levels that were modulated by the amount of visuospatial context, multivariate analyses showed that these anterior areas represented the identity of the specific environment being recalled. Together, these results suggest a convergence zone for scene perception and memory of the local visuospatial context at the anterior edge of high-level visual cortex.Significance statementAs we move through the world, the visual scene around us is integrated with our memory of the wider visuospatial context. Here, we sought to understand how the functional architecture of the brain enables coexisting representations of the current visual scene and memory of the surrounding environment. Using a combination of immersive virtual reality and fMRI, we show that memory of visuospatial context outside the current field-of-view is represented in a distinct set of brain areas immediately anterior and adjacent to the perceptually-oriented scene-selective areas of high-level visual cortex. This functional architecture would allow efficient interaction between immediately adjacent mnemonic and perceptual areas, while also minimizing mnemonic-perceptual interference.
Detection of mitotic neuroblasts provides additional evidence of steady state neurogenesis in the adult small intestinal myenteric plexus
Authors: Gorecki Anastazja M. , Slosberg Jared , Hong Su Min , Seika Philippa , Puttapaka Srinivas , Migden Blake , Gulko Anton , Singh Alpana , Zhang Chengxiu , Gurumurthy Rohin , Kulkarni Subhash 
Published: November 2022

AbstractMaintenance of normal structure of the enteric nervous system (ENS), which regulates key gastrointestinal functions, requires robust homeostatic mechanisms, since by virtue of its location within the gut wall, the ENS is subject to constant mechanical, chemical, and biological stressors. Using transgenic and thymidine analogue-based experiments, we previously discovered that neuronal turnover – where continual neurogenesis offsets ongoing neuronal loss at steady state – represents one such mechanism. Although other studies confirmed that neuronal death continues into adulthood in the myenteric plexus of the enteric nervous system (ENS), the complicated nature of thymidine analogue presents challenges in substantiating the occurrence of adult neurogenesis. Therefore, it’s vital to employ alternative, well-recognized techniques to substantiate the existence of adult enteric neurogenesis in the healthy gut. Here, by using established methods of assessing nuclear DNA content and detecting known mitotic marker phosphor-histone H3 (pH3) in Hu+adult ENS cells, we show that ∼10% of adult murine small intestinal myenteric Hu+cells, and ∼20% of adult human small intestinal myenteric Hu+cells show evidence of mitosis and hence are cycling neuroblasts. We observe that proportions of Hu+cycling neuroblasts in the adult murine ENS neither vary with ganglia size, nor do they differ significantly between two intestinal regions – duodenum and ileum, or between sexes. Confocal microscopy provides further evidence of cytokinesis in Hu+cells. The presence of a significant population of cycling neuroblasts in adult ENS provide further evidence of steady state neurogenesis in the adult ENS.
Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography
Authors: Greisman Jack B. , Willmore Lindsay , Yeh Christine Y. , Giordanetto Fabrizio , Shahamadtar Sahar , Nisonoff Hunter , Maragakis Paul , Shaw David E. 
Published: November 2022

AbstractFragment-based drug discovery has led to six approved drugs, but the small size of the chemical fragments used in such methods typically results in only weak interactions between the fragment and its target molecule, which makes it challenging to experimentally determine the three-dimensional poses fragments assume in the bound state. One computational approach that could help address this difficulty is long-timescale molecular dynamics (MD) simulation, which has been used in retrospective studies to recover experimentally known binding poses of fragments. Here, we present the results of long-timescale MD simulations that we used to prospectively discover binding poses for two series of fragments in allosteric pockets on a difficult and important pharmaceutical target, protein-tyrosine phosphatase 1b (PTP1b). Our simulations reversibly sampled the fragment association and dissociation process. One of the binding pockets found in the simulations has not to our knowledge been previously observed with a bound fragment, and the other pocket adopted a very rare conformation. We subsequently obtained high-resolution crystal structures of members of each fragment series bound to PTP1b, and the experimentally observed poses confirmed the simulation results. To the best of our knowledge, our findings provide the first demonstration that MD simulations can be used prospectively to determine fragment binding poses to previously unidentified pockets.
Regulatory imbalance between LRRK2 kinase, PPM1H phosphatase, and ARF6 GTPase disrupts the axonal transport of autophagosomes
Authors: Dou Dan , Smith Erin M. , Evans Chantell S. , Boecker C. Alexander , Holzbaur Erika L.F. 
Published: November 2022

SUMMARYGain-of-function mutations in theLRRK2gene cause Parkinson’s disease (PD), increasing phosphorylation of RAB GTPases through hyperactive kinase activity. We found that LRRK2-hyperphosphorylated RABs disrupt the axonal transport of autophagosomes by perturbing the coordinated regulation of cytoplasmic dynein and kinesin motors. In iPSC-derived human neurons, knock-in of the strongly-hyperactiveLRRK2-p.R1441H mutation caused striking impairments in autophagosome transport, inducing frequent directional reversals and pauses. Knock-out of the opposing Protein Phosphatase 1H (PPM1H) phenocopied the effect of hyperactive LRRK2. Overexpression of ADP-ribosylation factor 6 (ARF6), a GTPase that acts as a switch for selective activation of dynein or kinesin, attenuated transport defects in both p.R1441H knock-in and PPM1H knock-out neurons. Together, these findings support a model where a regulatory imbalance between LRRK2-hyperphosphorylated RABs and ARF6 induces an unproductive “tug-of-war” between dynein and kinesin, disrupting processive autophagosome transport. This disruption may contribute to PD pathogenesis by impairing the essential homeostatic functions of axonal autophagy.
One-carbon Pathways and Methylation Potential in Glutamatergic Neurons Regulate Behavioral Alcohol Responses
Authors: Lathen Daniel , Merrill Collin , Ducker Gregory S. , Rodan Aylin R. , Rothenfluh Adrian 
Published: November 2022

ABSTRACTDespite the enormous harms of alcohol use disorders (AUDs), many mechanisms, as well as effective prevention or treatment strategies remain elusive. Genetic factors dictate a majority of AUD risk. These risk factors can manifest as reduced naïve sensitivity to alcohol’s intoxicating effects and increased functional tolerance, i.e., brain-mediated decreases in sensitivity upon repeat exposure. The underlying neurobiology of how AUD-associated genes alter these endophenotypes remains poorly understood. Genes implicated in AUDs include epigenetic modifiers, such as histone demethylases, includingKdm3. We previously showed that whole-body and neuronalKdm3strongly affect ethanol sensitivity and tolerance inDrosophila. Here, we investigate the mechanisms of these effects, and, by extension, mechanisms of sensitivity and tolerance. RNA-seq and pathway analysis onKdm3KOflies revealed disproportionate upregulation of genes involved in amino acid metabolism, including 1-carbon pathways. We show that acute amino acid feeding modulates sensitivity and tolerance in aKdm3-dependent manner. Global manipulation of 1-carbon genes, especially glycineN-methyltransferase (Gnmt), glycine decarboxylase (Gldc), and sarcosine dehydrogenase (Sardh), alters alcohol sensitivity and tolerance. These changes in alcohol responses are likely mediated by global glycine levels (a substrate of these enzymes) rather than by 1-carbon input. Conversely, neuronal manipulations of 1-carbon pathways change alcohol sensitivity and tolerance in a pattern that suggests a mechanism throughS-adenosyl methionine (SAM), a 1-carbon metabolite that is the universal methyl donor required for epigenetic methylation. Increasing SAM production specifically in glutamatergic neurons increases sensitivity and tolerance. Together, these findings reveal distinct mechanisms affecting alcohol sensitivity and tolerance globally (via glycine) and neuronally (via SAM), thus revealing an important and complex role of 1-carbon metabolism in mediating AUD phenotypes.
ESYT1 tethers the endoplasmic reticulum to mitochondria and is required for mitochondrial lipid and calcium homeostasis
Authors: Janer Alexandre , Morris Jordan L. , Krols Michiel , Antonicka Hana , Aaltonen Mari J. , Lin Zhen-Yuan , Gingras Anne-Claude , Prudent Julien , Shoubridge Eric A. 
Published: November 2022

SUMMARYMitochondria interact with the endoplasmic reticulum (ER) at structurally and functionally specialized membrane contact sites known as mitochondria-ER contact sites (MERCs). MERCs are crucial for a myriad of physiological functions including lipid synthesis and transport, and calcium signaling. Alterations in the structure, composition or regulation of MERCs contribute to the aetiology of many pathologies including neurodegenerative and metabolic diseases. The proteins mediating the formation of MERCs have been extensively studied in yeast, where the ER-mitochondria encounter structure (ERMES) complex mediates the transport of lipids between the ER and mitochondria via three lipid binding SMP-domain proteins. However, none of the SMP proteins of the ERMES complex have orthologues in mammals suggesting that alternate pathways have evolved in metazoans. Combining proximity labelling (BioID), confocal microscopy and subcellular fractionation, we found that the ER resident SMP-domain containing protein ESYT1 was enriched at MERCs, where it forms a complex with the outer mitochondrial membrane protein SYNJ2BP. The deletion of ESYT1 or SYNJ2BP reduced the number and length of MERCs, indicating that the ESYT1-SYN2JBP complex plays a role in tethering ER and mitochondria. Loss of this complex impaired ER to mitochondria calcium flux and provoked a significant alteration of the mitochondrial lipidome, most prominently a reduction of cardiolipins and phosphatidylethanolamines. Both phenotypes were rescued by re-expression of wild-type ESYT1 as well as an artificial mitochondria-ER tether. Together, these results reveal a novel function of ESYT1 in mitochondrial and cellular homeostasis through its role in the regulation of MERCs.
An RNA interference (RNAi) toolkit and its utility for functional genetic analysis ofLeishmania (Viannia)
Authors: Lye Lon-Fye , Owens Katherine L. , Jang Soojin , Marcus Joseph E. , Brettmann Erin A. , Beverley Stephen M. 
Published: November 2022

ABSTRACTRNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including mostLeishmaniasp. RNAi was retained in species of theLeishmaniasubgenusViannia, and here we describe the development, optimization, and application of RNAi tools to the study ofL. (Viannia) braziliensis. We developed vectors facilitating generation of long-hairpin or “stem-loop” (StL) RNAi knockdown constructs, using Gateway™site-specific recombinase technology. A survey of applications of RNAi inL. braziliensisincluded genes interspersed within multigene tandem arrays such asQDPR, a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting theL. braziliensishypoxanthine-guanine phosphoribosyltransferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful ‘hypomorphic’ approach not possible with other gene ablation strategies, with shorterIFT140stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase(APRT1)using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a useful tool that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studyingLeishmaniagene function with some unique advantages.