bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome functional characterization of RE1 silencers using a modified massively parallel reporter assay
Authors: Mouri Kousuke , Dewey Hannah B , Castro Rodrigo , Berenzy Daniel , Kales Susan , Tewhey Ryan 
Published: February 2022

AbstractBoth upregulation and downregulation by cis-regulatory elements help establish precise gene expression. Our understanding of how elements repress transcriptional activity is far more limited than activating elements. To address this gap, we characterized RE1, a group of transcriptional silencers bound by REST, on a genome-wide scale using an modified massively parallel reporter assay (MPRAduo). MPRAduo empirically defined a minimal binding strength of REST required for silencing (REST m-value), above which multiple cofactors colocalize and act to directly silence transcription. We identified 1,500 human variants that alter RE1 silencing and found their effect sizes are predictable when they overlap with REST binding sites above the m-value. In addition, we demonstrate that non-canonical REST binding motifs exhibit silencer function only if they precisely align two half sites with specific spacer length. Our results show mechanistic insights into RE1 silencer which allows us to predict its activity and effect of variants on RE1, providing a paradigm for performing genome-wide functional characterization of transcription factors binding sites.
Antisense oligonucleotides targeting exon 11 are able to partially rescue the Neurofibromatosis Type 2 phenotype in vitro
Authors: Catasús N. , Rosas I. , Bonache S. , Negro A. , Torres-Martin M. , Plana A. , Salvador H. , Serra E. , Blanco I. , Castellanos E. 
Published: February 2022

AbstractNeurofibromatosis type 2 (NF2) is an autosomal dominant condition caused by loss of function variants in the NF2 gene, which codes for the protein Merlin, and characterized by the development of multiple tumours of the nervous system. The clinical presentation of the disease is variable and related to the type of the inherited germline variant. Here, we tested if PMOs could be used to correct the splice signalling caused by variants at +/-13 within the intron-exon boundary region. Here we show that the PMOs designed for these variants do not constitute a therapeutic approach. Furthermore, we evaluated the use of phosphorodiamidate morpholino oligomers (PMOs) to reduce the severity of the effects of NF2 truncating variants with the aim of generating milder hypomorphic isoforms in vitro through the induction of the in-frame deletion of the exon-carrying variant. We were able to specifically induce the skipping of exons 4, 8 and 11 maintaining the NF2 gene reading frame at cDNA level. Only the skipping of exon 11 produced a hypomorphic Merlin (Merlin-e11), able to partially rescue the observed phenotype in primary fibroblast cultures from NF2 patients, being encouraging for the treatment of patients harbouring truncating variants located in exon 11.
Delayed viral vector mediated delivery of neurotrophin-3 improves skilled hindlimb function and stability after thoracic contusion in rats
Authors: Sydney-Smith Jared D. , Koltchev Alice M. , Moon Lawrence D. F. , Warren Philippa M. 
Published: February 2022

AbstractIt has been reported that intramuscular injection of an Adeno-associated viral vector serotype 1 (AAV1) encoding Neurotrophin-3 (NT3) into hindlimb muscles 24 hours after a severe T9 contusion in rats induced lumbar spinal neuroplasticity, partially restored locomotive function and reduced spasms during swimming. Here we investigated whether a targeted delivery of NT3 to lumbar and thoracic motor neurons 48 hours following a severe contusive injury aids locomotive recovery in rats. AAV1-NT3 was injected into the tibialis anterior, gastrocnemius and rectus abdominus muscles 48-hours following trauma, persistently elevating serum levels of the neurotrophin. NT3 improved trunk stability, accuracy of stepping during skilled locomotive tasks, and alternation of the hindlimbs during swimming, but it had no effect on gross locomotion function in the open field. The number of vGlut1+ (likely proprioceptive afferent) boutons on gastrocnemius α-motor neurons was increased after injury but normalised following NT3 treatment suggestive of a mechanism in which the functional effects may be mediated through proprioceptive feedback. Ex vivo MRI revealed substantial loss of grey and white matter at the lesion epicentre but no effect of delayed NT3 treatment to induce neuroprotection or prevent secondary damage. Spasms and hyperreflexia were not reliably induced in this severe injury model suggesting a more complex anatomical or physiological cause to their induction. We have shown that delayed intramuscular AAV-NT3 treatment can promote recovery in skilled stepping and coordinated swimming supporting a role for NT3 as a therapeutic strategy for spinal injuries potentially through modulation of somatosensory feedback.Key PointsTargeted delivery of NT3 to hindlimb and trunk muscles at a clinically relevant 48h following a severe thoracic contusion aids fine locomotor control and synchronised movement.NT3 mediated improvements in trunk stability, accuracy of stepping during skilled locomotive tasks, and alternation of the hindlimbs during swimming through the normalisation of vGlut1+ boutons on presumptive proprioceptive afferents innervating these muscles.250kDyn thoracic contusion does not reliably result in measurable signs of spasticity.
Exponential magnetophoretic gradient for the direct isolation of basophils from whole blood in a microfluidic system
Authors: Castaño Nicolas , Kim Sungu , Martin Adrian M. , Galli Stephen J. , Nadeau Kari C. , Tang Sindy K.Y. 
Published: February 2022

AbstractDespite their rarity in peripheral blood, basophils play important roles in allergic disorders and other diseases including sepsis and COVID-19. Existing basophil isolation methods require many manual steps and suffer from significant variability in purity and recovery. We report an integrated basophil isolation device (i-BID) in microfluidics for negative immunomagnetic selection of basophils directly from 100 μL of whole blood within 10 minutes. We use a simulation-driven pipeline to design a magnetic separation module to apply an exponentially increasing magnetic force to capture magnetically tagged non-basophils flowing through a microtubing sandwiched between magnetic flux concentrators sweeping across a Halbach array. The exponential profile captures non-basophils effectively while preventing their excessive initial buildup causing clogging. The i-BID isolates basophils with a mean purity of 93.9%±3.6% and recovery of 95.6%±3.4% without causing basophil degradation or unintentional activation. Our i-BID has the potential to enable basophil-based point-of-care diagnostics such as rapid allergy assessment.
Aspirin Synergizes with Regorafenib to Reduce Growth of Colorectal Cancer
Authors: Su Chang , Fennell Lochlan J , Bond Catherine E , Kane Alexandra M , Kerr Genevieve , Jardé Thierry , Micati Diana , Engel Rebekah M , Chan Wing Hei , Hlavca Sara , Archer Stuart , McMurrick Paul J , Hammerlindl Heinz , Lim Fayth , Salik Basit , McKeone Diane M , Hartel Gunter , Borowsky Jennifer , Ladwa Rahul , Leggett Barbara A , Schaider Helmut , Abud Helen E , Boyle Glen M , Burge Matthew E , Whitehall Vicki LJ 
Published: February 2022

AbstractPurposeRegorafenib is a multi-kinase inhibitor approved for refractory metastatic colorectal cancer. Previous studies have suggested that combining kinase inhibitors with aspirin may improve patient outcomes. We aimed to determine the effects of aspirin and regorafenib combination treatment in preclinical models of colorectal cancer.Experimental DesignSW480, RKO and LIM1215 colorectal cancer cell lines were treated with aspirin and regorafenib to determine effects on proliferation and cytotoxicity. RNA sequencing and Western blotting were performed to explore underlying molecular effects. Aspirin and regorafenib combination treatment was also tested using organoids derived from three human colorectal cancer tissue specimens. For the in vivo study, SW480-derived tumors were established in athymic mice. Tumor volume was measured during treatment with aspirin and regorafenib, followed by immunohistochemical staining for markers of proliferation and apoptosis.ResultsAspirin and regorafenib synergistically inhibited proliferation of colorectal cancer cell lines and patient-derived organoids, irrespective of KRAS or BRAF mutation status. This was associated with inhibition of the PI3K-Akt-mTOR pathway and activation of the AMPK pathway. Aspirin and regorafenib effectively inhibited growth of microsatellite stable KRAS-mutant SW480-derived tumors in vivo. Immunohistochemical staining for Ki67 and cleaved caspase 3 showed that combination treatment elicited a synergistic anti-proliferative effect, in addition to a pro-apoptotic effect that was driven by regorafenib.ConclusionsAspirin and regorafenib demonstrate synergistic anti-proliferative effects in preclinical models of colorectal cancer. This suggests that combining regorafenib with aspirin may be an improved treatment strategy for patients with refractory metastatic colorectal cancer.
Functional assessment of the ionotropic receptors IR25a and IR93a in predator perception in the freshwater crustaceanDaphniausing RNA interference
Authors: Graeve A , Huster J , Mayweg J , Fiedler R , Plaßmann J , Wahle P , Weiss LC 
Published: February 2022

AbstractAcquiring environmental information is vital for organisms as it informs about the location of resources, mating partners, and predators. The freshwater crustaceanDaphniadetects predator specific chemical cues released by its predators and subsequently develops defensive morphological features that reduce the predation risk. The detection of such chemical information is generally processed via distinct chemoreceptors that are located on chemoreceptor cells. Lately an ancestral type of ionotropic receptors (IRs) has been identified in crustaceans. IRs and the putative co-receptors IR25a and IR93a are postulated to be involved in chemoreception However, functional roles have not been assessed. Here, using threeDaphniaspecies as model, we report that the two co-receptors are expressed within the chemosensory antennules and gene expression is increased with predator perception. Importantly, RNA interference mediated knock-down of the two IRs impedes species-specific defense expression in the threeDaphniaspecies. Our results suggest that (albeit not testing the enigmatic receptor protein directly), the reduction of two associated proteins has impaired the functional aggregation of the postulated chemoreceptor complex. This in turn has hampered the perception of environmentally relevant chemical cues resulting in a substantial reduction of defensive morphological features.
Structure of the vasopressin hormone-V2 receptor-β-arrestin1 ternary complex
Authors: Bous Julien , Fouillen Aurélien , Orcel Hélène , Trapani Stefano , Cong Xiaojing , Fontanel Simon , Saint-Paul Julie , Lai-Kee-Him Joséphine , Urbach Serge , Sibille Nathalie , Sounier Rémy , Granier Sébastien , Mouillac Bernard , Bron Patrick 
Published: February 2022

AbstractArrestins interact with G protein-coupled receptors (GPCRs) to stop G protein activation and to initiate key signaling pathways. Recent structural studies shed light on the molecular mechanisms involved in GPCR-arrestin coupling, but whether this process is conserved among GPCRs is poorly understood. Here, we report the cryo-electron microscopy active structure of the wild-type arginine-vasopressin V2 receptor (V2R) in complex with β-arrestin1. It reveals an atypical position of β-arrestin1 compared to previously described GPCR-arrestin assemblies, associated with an original V2R/β-arrestin1 interface involving all receptor intracellular loops. Phosphorylated sites of the V2R C-terminus are clearly identified and interact extensively with the β-arrestin1 N-lobe, in agreement with structural data obtained with chimeric or synthetic systems. Overall, these findings highlight a striking structural variability among GPCR-arrestin signaling complexes.
RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis
Authors: Mahmud A.K.M.F. , Navais R. , Nilsson K. , Choudhury R. , Avican K. , Fallman M. 
Published: February 2022

AbstractPathogenic bacteria use a broad range of virulence factors to thrive within their host. Yersinia pseudotuberculosis, a gram-negative enteropathogen in humans, utilises a Type III secretion system to overcome the host’s innate immune response. A global regulator previously shown to be essential for virulence in Y. pseudotuberculosis is RpoN. We show here that a strain lacking RpoN has a severely reduced capacity to secrete Yop effectors. This strain has a substantially reduced expression of genes encoding structural components of the secretion apparatus, the ysc operons, while expression of genes encoding effectors and translocators is less affected. We show that RpoN regulates a complex network, where one part is suggested to contribute to inducing Type III secretion via the enhancer-binding protein GlrR/RpoN regulon. By analogy, during inducement of Type III secretion, RpoN has a positive effect on expression of the sigma factor RpoE, which also is known to act downstream of GlrR. Interestingly, we found putative RpoE binding sites upstream of the ysc operons, and also a partial rescue of Yop secretion in the rpoN mutant strain by overexpression of RpoE. Our findings suggest that the RpoN-mediated effect on expression of type III genes involves a sigma factor hierarchy, where RpoN via RpoE contributes to inducing Type III secretion.
Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory
Authors: Sump Bethany , Brickner Donna Garvey , D’Urso Agustina , Kim Seo Hyun , Brickner Jason H. 
Published: February 2022

ABSTRACTFor some inducible genes, the rate and molecular mechanism of transcriptional activation depends on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation and requires both changes in chromatin structure and recruitment of poised RNA Polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.
Vagal involvement in non-dipping phenotype of Hsd11b2 knockout rats
Authors: Mullins Linda J , Koutraki Yolanda G S , Bailey Matthew A , Mullins John J 
Published: February 2022

AbstractThe Syndrome of Apparent Mineralocorticoid Excess (SAME) is a hypertensive disorder caused by deficiency of 11b-hydroxysteroid dehydrogenase type 2. Blood pressure is directly influenced by dietary salt intake, but the causes of salt-sensitivity are not fully resolved. We modelled SAME in Fischer 344 rats, using zinc finger nuclease targeting of the Hsd11b2 gene. The F344 genetic background showed modest salt sensitivity: blood pressure increased by ∼6mmHg when diet was switched from control (0.3% Na) to high salt (3% Na) diet. Homozygous knockout (Hsd2-/-) rats exhibited severe hypertension on control diet (mean arterial blood pressure of ∼180 mmHg compared to ∼115 mmHg in wild-types) and displayed no dipping in blood pressure in the inactive/sleep phase. They also displayed reduced heart rate (339 bpm versus 384 bpm in F344 controls). Low salt diet (0.03% Na) caused a dramatic fall in Hsd2-/- blood pressure (to ∼141mmHg), restoration of robust circadian variation in blood pressure, and an increase in heart rate (to 364bpm). This was mirrored by a restoration of circadian variation in the Poincare plot descriptor, SD1, suggesting involvement of parasympathetic dysfunction in the non-dipping phenotype. Alpha adrenoceptor blockade with prazosin treatment resulted in a further decrease in blood pressure (to ∼124mmHg), which blunted circadian rhythm, together with an increase in heart rate (to ∼394bpm). This rat model of human hypertension reveals clear links between dietary salt, autonomic nervous system dysfunction, and the non-dipping blood pressure phenotype.
Rearing environment persistently modulates the phenotype of mice
Authors: Jaric Ivana , Voelkl Bernhard , Clerc Melanie , Schmid Marc W. , Novak Janja , Rosso Marianna , Rufener Reto , von Kortzfleisch Vanessa Tabea , Richter S. Helene , Buettner Manuela , Bleich André , Amrein Irmgard , Wolfer David P. , Touma Chadi , Sunagawa Shinichi , Würbel Hanno 
Published: February 2022

AbstractThe phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions1–4. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment5. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between rearing facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multi-center study, where inbred mice from the same breeding stock were reared in five different facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that common variation among rearing facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organization. We detected changes in chromatin organization in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity and regulation of behavior. Our findings demonstrate that common environmental differences between rearing facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. We expect our findings to stimulate further research into the mechanisms and drivers of these epigenetic changes mediated by the laboratory environment. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and a need to account for the animals’ environmental background in study design to produce robust and replicable findings.
Tumor elimination by clustered microRNAs miR-306 and miR-79 via non-canonical activation of JNK signaling
Authors: Wang Zhaowei , Xia Xiaoling , Igaki Tatsushi 
Published: February 2022

AbstractJNK signaling plays a critical role in both tumor promotion and tumor suppression. Here, we identified clustered microRNAs (miRNAs) miR-306 and miR-79 as novel tumor-suppressor miRNAs that specifically eliminate JNK-activated tumors in Drosophila. While showing no significant effect on normal tissue growth, miR-306 and miR-79 strongly suppressed growth of multiple tumor models including malignant tumors caused by Ras activation and cell polarity defects. Mechanistically, these miRNAs commonly target the mRNA of an E3 ubiquitin ligase Drosophila ring finger protein 146 (dRNF146). We found that DRNF146 promotes degradation of tankyrase (Tnks), an ADP-ribose polymerase that promotes JNK activation in a non-canonical manner. Thus, downregulation of dRNF146 by miR-306 and miR-79 leads to hyper-enhancement of JNK activation. Our data show that, while JNK activity is essential for tumor growth, elevation of miR-306 or miR-79 overactivate JNK signaling to the lethal level via non-canonical JNK pathway and thus eliminate tumors, providing a new miRNA-based strategy against cancer.
Interaction of Fungal lipase with potential phytotherapeutics
Authors: Naz Farheen , Khan Imran , Islam Asimul , Khan Luqman A 
Published: February 2022

AbstractInteraction of thymol, carvacrol and linalool with fungal lipase and Human Serum Albumin (HSA) have been investigated employing UV-Vis, Fluorescence and Circular dichroism spectroscopy along with docking studies. Thymol, carvacrol and linalool displayed approximately 50% inhibition at 1.5 mmol/litre concentrations using para-nitrophenyl palmitate. UV-Vis spectroscopy give evidence of the formation of lipase-linalool, lipasecarvacrol and lipase-thymol complex at the ground state. Three molecules also showed complex formation with HSA at the ground state. Fluorescence spectroscopy shows strong binding of lipase to thymol (Ka of 2.6 x 109 M-1) as compared to carvacrol (4.66 x 107 M-1) and linalool (5.3 x 103 M-1). Number of binding sites showing stoichiometry of association process on lipase is found to be 2.52 (thymol) compared to 2.04 (carvacrol) and 1.12 (linalool). Secondary structure analysis by CD spectra results, following 24 hours incubation at 25°C, with thymol, carvacrol and linalool revealed decrease in negative ellipticity for lipase indicating loss in helical structure as compared with the native protein. The lowering in negative ellipticity was in the order of thymol > carvacrol > linalool.Results of Fluorescence and CD spectroscopy taken together suggests that thymol and carvacrol are profound disrupter of lipase structure.Fluorescence spectra following binding of all three molecules with HSA caused blue shift which suggests the compaction of the HSA structure. Association constant of thymol and HSA is 9.6 x 108 M-1 which along with ‘n’ value of 2.41 suggests strong association and stable complex formation, association constant for carvacrol and linalool was in range of 107 and 103 respectively.Docking results give further insight into strong binding of thymol, carvacrol and linalool with lipase having free energy of binding as -7.1 kcal/mol, -5.0 kcal/mol and -5.2 kcal/mol respectively.To conclude, fungal lipases can be attractive target for controlling their growth and pathogenicity. Employing UV-Vis, Fluorescence and Circular dichroism spectroscopy we have shown that thymol, carvacrol and linalool strongly bind and disrupt structure of fungal lipase, these three phytochemicals also bind well with HSA. Best anti-lipase molecules based on disruption of lipase structure and HSA structure conservation is thymol.