bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apicosome: newly identified cell-type-specific organelle in mouse cochlear and vestibular hair cells
Authors: Li Xiaofen , Zhao Qirui , Yu Xiaojie , Cao Wenhan , Zhang Yingyi , Feng Wanying , Jiang Liwen , He David Z. , Qi Robert Z. , Huang Pingbo 
Published: July 2022

ABSTRACTCochlear and vestibular hair cells in the inner ear are highly specialized sensory receptors for sound waves and acceleration of body movements; these cells can perform their specialized functions because of their distinctive morphology and some unique organelles that they harbor. Here, we report a serendipitous identification in the mouse of a hair-cell-specific organelle, which we name “apicosome.” The apicosome was recognized by anti-FLRT1 antibodies but contains no FLRT1, and the organelle presents several distinctive characteristics: (1) the apicosome typically appears as a single entity (∼500 nm in diameter), but occasionally as two entities, in hair cells; (2) it first appears in the subapical region at the neural side at embryonic day (E) 17–18 in cochlear hair cells, subsequently descends to the perinuclear region during the first postnatal week, and completely disappears around postnatal day (P) 10; (3) in vestibular hair cells, it can be detected in the subapical region of neonatal (P3) cells and persists in adult hair cells although it becomes smaller and more distant from the subapical region; (4) the timing of apicosome translocation and disappearance during development is correlated in kinocilium maintenance; (5) the organelle is potentially associated with microtubules; and (6) the appearance of the apicosome is irregular in supernumerary hair cells and this is likely linked to anomalous lateral inhibition. Thus, our study identifies a previously undescribed organelle in sensory hair cells and lays the foundation for further characterization of this specialized structure potentially linked to hair-cell development and morphogenesis.
Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
Authors: Aghakhani Sahar , Soliman Sylvain , Niarakis Anna 
Published: July 2022

AbstractRheumatoid Arthritis (RA) is an autoimmune disease characterized by a highly invasive pannus formation consisting mainly of synovial fibroblasts (RASFs). This pannus leads to cartilage, bone and soft tissue destruction in the affected joint. RASFs’ activation is associated with metabolic alterations resulting from dysregulation of extracellular signals transduction and gene regulation machinery. Deciphering the intricate mechanisms at the origin of this metabolic reprogramming may provide significant insight into RASFs’ involvement in RA’s pathogenesis and offer new therapeutic strategies. Qualitative and quantitative dynamic modeling can address some of these features, but hybrid models represent a real asset in their ability to span multiple layers of biological machinery. This work presents the first hybrid RASF model: the combination of a cell-specific qualitative regulatory network with a global metabolic network. The automated framework for hybrid modeling exploits the regulatory network’s trap-spaces as additional constraints on the metabolic networks. Subsequent flux balance analysis allows assessment of RASFs’ regulatory outcomes’ impact on their metabolic flux distribution. The hybrid RASF model simulates the experimentally observed metabolic reprogramming induced by signaling and gene regulation in RASFs. Simulations also enable further hypotheses on the potential reverse Warburg effect in RA. RASFs may undergo metabolic reprogramming to turn into “metabolic factories”, producing high levels of energy-rich fuels and nutrients for neighboring demanding cells through the crucial role of HIF1.Author SummaryWe successfully built the first large-scale hybrid dynamical model for human Rheumatoid Arthritis Synovial Fibroblasts (RASFs) including signaling, gene regulation and metabolism. We used a state-of-the-art molecular map for upstream signaling and gene regulation, the tool CaSQ to infer a large-scale Boolean model, and a genome-scale metabolic model. Trap-spaces of the Boolean asynchronous model were used to infer additional metabolic constraints on the metabolic network for subsequent flux balance analysis. This method allowed us to study the impact of various regulatory initial conditions on RASFs’ metabolic fluxes distribution. Our model successfully reproduces the metabolic reprogramming of RASFs which shift their ATP production from oxidative pathways to glycolysis, highlighting the key role of HIF1 in this process. Our findings allow us to hypothesize a reverse Warburg relationship occurring between RASFs and other RA joint cells. Similarly to tumor microenvironment’s fibroblasts, RASFs would undergo a metabolic switch and reprogram their metabolism to adapt to their hypoxic environment and provide crucial metabolic intermediates to neighboring cells to sustain their inflammatory activity.
Identification of Antigenic Regions Responsible for inducing Type 1 diabetes mellitus
Authors: Kumar Nishant , Patiyal Sumeet , Choudhury Shubham , Tomer Ritu , Dhall Anjali , Raghava Gajendra P. S. 
Published: July 2022

AbstractThere are a number of antigens that induce autoimmune response against β-cells, leading to Type 1 diabetes mellitus (T1DM). Recently several antigen-specific immunotherapies have been developed to treat T1DM. Thus identification of T1DM associated peptides with antigenic regions or epitopes is important for peptide based-therapeutics (e.g., immunotherapeutic). In this study, for the first time an attempt has been made to develop a method for predicting, designing and scanning of T1DM associated peptides with high precision. We analyzed 815 T1DM associated peptides and observed that these peptides are not associated with a specific class of HLA alleles. Thus, HLA binder prediction methods are not suitable for predicting T1DM associated peptides. Firstly, we developed a similarity/alignment based method using BLAST and achieved a high probability of correct hits with poor coverage. Secondly, we developed an alignment free method using machine learning techniques and got maximum AUROC 0.89 using dipeptide composition. Finally, we developed a hybrid method that combines the strength of both alignment free and alignment based methods and achieve maximum AUROC 0.95 with MCC 0.81 on independent dataset. We developed a webserver “DMPPred” and standalone server, for predicting, designing and scanning of T1DM associated peptides (https://webs.iiitd.edu.in/raghava/dmppred/).Key PointsPrediction of peptides responsible for inducing immune system against β-cellsCompilation and analysis of Type 1 diabetes associated HLA bindersBLAST based similarity search against Type 1diabetes associated peptidesAlignment free method using machine learning techniques and compositionA hybrid method using alignment free and alignment based approachAuthor’s BiographyNishant Kumar is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaSumeet Patiyal is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaShubham Choudhury is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaRitu Tomer is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, IndiaAnjali Dhall is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.Gajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
Cannabinoids Activate the Insulin Pathway to Modulate Mobilization of Cholesterol in C. elegans
Authors: Hernandez-Cravero Bruno , Gallino Sofia , Florman Jeremy , Vranych Cecilia , Diaz Philippe , Belén Elgoyhen Ana , Alkema Mark J. , de Mendoza Diego 
Published: July 2022

AbstractThe nematode Caenorhabditis elegans requires exogenous cholesterol to survive and its depletion leads to early development arrest. Thus, tight regulation of cholesterol storage and distribution within the organism is critical. Previously, we demonstrated that the endocannabinoid (eCB) 2-arachidonoylglycerol (2-AG) plays a key role in C. elegans modulating sterol mobilization, but the mechanism is unknown. Here we show that mutations in the ocr-2 and osm-9 genes coding for transient receptors potential V (TRPV) ion channels, dramatically reduces the effect of 2-AG in cholesterol mobilization. Through genetic analysis combined with the rescuing of larval arrest induced by sterol starvation we found that the insulin/IGF-1signaling (IIS) pathway and UNC-31/CAPS, a calcium-activated regulator of neural dense-core vesicles release, are essential for 2-AG-mediated stimulation of cholesterol mobilization. These findings indicate that 2-AG-dependent cholesterol trafficking requires the release of insulin peptides and signaling through the DAF-2 insulin receptor. These results suggest that 2-AG acts as an endogenous modulator of TRPV signal transduction to control intracellular sterol traffic through modulation of the IGF-1 signaling pathway.Author summaryAlthough cannabis extracts have been used in folklore medicine for centuries, the past few years have seen an increased interest in the medicinal uses of cannabinoids, the bioactive components of the cannabis plant, for treatment of many diseases of the nervous system. However, the human body naturally produces endocannabinoids that are similar to the cannabinoids present in Cannabis sativa. Our goal is to understand how endocannabinoids maintain cholesterol homeostasis in animals, underscoring the importance of cholesterol balance for healthy life. Both cholesterol excess and cholesterol deficiency can have detrimental effects on health, and a myriad of regulatory processes have thus evolved to control the metabolic pathways of sterol metabolism. The nematode C. elegans is auxotroph for sterols, that is; contrary to mammals they cannot synthesize sterols, therefore, dietary supply is essential for survival. The aim of our study was to elucidate the mechanism by which endocannabinoids abolish larval arrest of C. elegans induced by cholesterol depletion. We discovered that endocannabinoids stimulate the insulin pathway, which affects development, reproduction and life span, to modulate mobilization of cholesterol in C. elegans. Our studies have important implications for a better understanding of human pathological conditions associated with impaired cholesterol homeostasis.
Synthesis and characterization of poly(propylene imine) dendrimers, as nanocarriers of Benznidazole: an in vitro controlled release assay
Authors: Ordoñez-Benavides Jenny , Andrade-Caicedo Henry 
Published: July 2022

AbstractBackgroundAmerican trypanosomiasis, or Chagas disease, is the result of an infection caused by the Trypanosoma cruzi parasite. The disease is endemic in Latin America, where the main clinical manifestation and cause of death of Chagas patients is cardiomyopathy. The current approved treatment for this disease is based on the use of the nitroheterocyclic compound, Benznidazole. The drug is administered in high doses and for prolonged periods, which causes serious adverse effects, eventually leading to treatment discontinuation. In addition, it has only shown efficacy in the acute phase of the disease. Benznidazole has low solubility, low permeability, low bioavailability and high toxicity in the body. These physicochemical characteristics can be improved by using dendritic structures that serve as nanocarriers.MethodsIn this research, poly(propylene imine) PPI dendrimers in generations 4.0 G and 5.0 G were synthesized and characterized. We performed the synthesis by divergent approach. We encapsulated Benznidazole using the equilibrium dialysis method, and we evaluated the loading efficiency and the concentration of the released drug by high-performance liquid chromatography (HPLC).ResultsPreliminary results showed a drug loading efficiency on the dendrimer of 78% and an entrapment percentage of 99.6%. The release kinetics showed a controlled and sustained release over time compared to dendrimer-free Benznidazole.ConclusionsThe PPI 5.0 G - Benznidazole dendrimer system could be considered as an alternative to be evaluated in vitro and in vivo, as an alternative to conventional treatment of Chagas disease. The next stage of the experimental work consists of standardizing an infection model of H9C2 cardiomyocytes with Colombian strains of Trypanosoma cruzi, in order to evaluate the effect of the encapsulated drug on nanocarriers.
Visuomotor phase-locked loop reproduces elliptic hand trajectories across different rhythms
Authors: Matić Adam 
Published: July 2022

AbstractA well-known phenomenon in human hand movement is the correlation between speed and curvature, also known as the speed-curvature power law (V≈kCβ). In drawing elliptic shapes, the exponent is often found to be β ≈ −1/3, however it is not clear why the power law appears and why the exponent is near −1/3. More fundamentally, it is not clear how do people track elliptic targets. In answering these questions, I’ve analyzed trajectories of participants’ cursors while they tracked visual targets moving along elliptical paths, across different target speed profiles and cycle frequencies. The speed-curvature power law emerged when drawing ellipses at about 1 Hz or faster, regardless of the target speed profile, and it did not emerge for lower frequency movements. Analysis of the position frequency spectrum shows that the target-cursor trajectory transformation may be seen as a low-pass filter. Comparison of different hypothetical salient features of the visual field shows that phase difference (angular difference between the cursor and the target) and size difference (difference in the sizes of the elliptic paths) are the features most likely used in the task. The next experiment confirmed that phase and size difference could be controlled variables because participants kept them stable even under direct pseudorandom disturbances. A numerical model simulating the sensorimotor processes of the participant, similar to a phase-locked loop, using the visual features of phase and size difference as controlled variables, performed the same target tracking tasks as the participants. When fitted, the model closely replicated position and speed profiles of the participants across all trials, as well as the emergence of the power law at high frequencies. The model also reproduced the trajectories of participants in the experiment with direct pseudorandom disturbances. In conclusion (1) the speed-curvature power law emerges as a side effect of movement system properties, namely low-pass filtering in the sensorimotor loop; (2) people could be tracking elliptical targets by varying the frequency and amplitude of an internal pattern generator until the produced phase and shape size match the target’s phase and shape size. The model generates new hypotheses about the neural mechanisms of rhythmic movement control.
Behaviour of pyrethroid resistant Anopheles gambiae at the interface of two dual active-ingredient bed nets, assessed by room-scale infrared video tracking
Authors: Gleave K. , Guy A. , Mechan F. , Emery M. , Murphy A. , Voloshin V. , Towers C. E. , Towers D. , Ranson H. , Foster G. M. , McCall P. J. 
Published: July 2022

AbstractBackgroundThe success of Insecticide Treated Bednets (ITNs) for malaria vector control in Africa relies on the behaviour of the major malaria vectors, Anopheles species. Research into mosquito behavioural traits influencing the performance of ITNs has focused largely on time or location of biting. Here we investigated less tractable behaviours including timings of net contact, willingness to refeed and longevity post exposure to two next-generation nets, PermaNet® 3.0 (P3) and Interceptor® G2 (IG2) in comparison with a standard pyrethroid only net (Olyset (OL)) and an untreated net.MethodsSusceptible and resistant Anopheles gambiae mosquitoes were exposed to the nets with a human volunteer host in a room scale assay. Mosquito movements were tracked for two hours using an infrared video system, collecting flight trajectory, spatial position and net contact data. Post-assay, mosquitoes were monitored for a range of sublethal insecticide effects.ResultsOL, P3 and IG2 all killed over 90% of susceptible mosquitoes 24 hours after exposure, but this effect was not seen with resistant mosquitoes where mortality ranged from 16% to 72%. Total mosquito activity was higher around untreated nets than ITNs. There was no difference in total activity, the number, or duration, of net contact, between any mosquito strain, with similar behaviours recorded in susceptible and resistant strains at all ITNs. Net contact was focussed predominantly on the roof for all bednets. We observed a steep decay in activity for both susceptible strains when P3 and OL were present and with IG2 for one of the two susceptible strains. All treated nets reduced the willingness of resistant strains to re-feed when offered blood one-hour post-exposure, with a more pronounced effect seen with P3 and OL than IG2.ConclusionResults indicate that the effects of ITNs on mosquito behaviour are consistent, with no major differences in responses between strains of different pyrethroid susceptibility.
Structural characterization of functionally important chloride binding sites in the marine Vibrio alkaline phosphatase
Authors: Markússon Sigurbjörn , Hjörleifsson Jens G. , Kursula Petri , Ásgeirsson Bjarni 
Published: July 2022

ABSTRACTEnzyme stability and function can be affected by various environmental factors, such as temperature, pH and ionic strength. Enzymes that are located outside the relatively unchanging environment of the cytosol, such as those residing in the periplasmic space of bacteria or extracellularly secreted, are challenged by more fluctuations in the aqueous medium. Bacterial alkaline phosphatases (APs) are generally affected by ionic strength of the medium, but this varies substantially between species. An AP from the marine bacterium Vibrio splendidus (VAP) shows complex pH-dependent activation and stabilization in the 0 – 1.0 M range of halogen salts and has been hypothesized to specifically bind chloride anions. Here, using X-ray crystallography and anomalous scattering, we have located two chloride binding sites in the structure of VAP, one in the active site and another one at a peripheral site. Further characterization of the binding sites using site-directed mutagenesis and small angle X-ray scattering (SAXS) showed that upon binding of chloride to the peripheral site, structural dynamics decreased locally, resulting in thermal stabilization of the VAP active conformation. Binding of the chloride ion in the active site did not displace the bound inorganic phosphate product, but it may promote product release by facilitating rotational stabilization of the substrate-binding Arg129. Overall, these results reveal the complex nature and dynamics of chloride binding to enzymes through long-range modulation of electronic potential in the vicinity of the active site, resulting in increased catalytic efficiency and stability.
Infrared Spectroscopy for Structure Analysis of Protein Inclusion Bodies
Authors: Schwaighofer Andreas , Lendl Bernhard 
Published: July 2022

AbstractInfrared (IR) spectroscopy is a widely used technique for evaluation of protein secondary structure. In this chapter, we focus on the application of this analytical technique for analysis of inclusion bodies. After a general introduction to protein analysis by IR spectroscopy different approaches for spectra acquisition, data processing and secondary structure evaluation are presented.
Structural basis for differential targeting properties of small RNAs in plants and animals
Authors: Xiao Yao , MacRae Ian J. 
Published: July 2022

AbstractmicroRNAs (miRNAs) regulate gene expression in plants and animals. Animals use miRNAs to sculpt the transcriptome, with each miRNA modestly repressing hundreds of otherwise unrelated targets. By contrast, each plant miRNA potently silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal Argonaute (AGO) proteins. A 7-amino-acid loop in the PIWI domain of Arabidopsis Argonaute10 (AtAGO10) reduces the affinity of the miRNA seed region for target RNAs. Swapping the PIWI-loop from human Argonaute2 (HsAGO2) into AtAGO10 increases seed strength and target-binding promiscuity, resembling animal miRNA targeting. Conversely, swapping the plant PIWI-loop into HsAGO2 increases targeting stringency and elevates target cleavage rates. The loop-swapped HsAGO2-siRNA complex silences targets more potently, with reduced off-targeting, than wild-type HsAGO2 and small interfering RNA (siRNA) duplexes in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles and HsAGO2 can be engineered for potential applications in siRNA therapeutics.
Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing
Authors: Torelli Emanuela , Shirt-Ediss Benjamin , Navarro Silvia A. , Manzano Marisa , Vizzini Priya , Krasnogor Natalio 
Published: July 2022

ABSTRACTBinary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence.First, an RNA three-way junction harbouring the split system was assembled in an E. coli based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a ‘bio-orthogonal’ hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect femtomoles of a Campylobacter spp. DNA target sequence.Potential applications of our system include real-time monitoring of the self-assembly of nucleic acid-based devices in vivo and of intracellular delivery of therapeutic nanostructures, as well as in vitro and in vivo detection of different DNA/RNA target.