bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-dimensional protein solubility optimization with an ultra-high-throughput microfluidic platform
Authors: Erkamp Nadia A. , Oeller Marc , Sneideris Tomas , Ausserwӧger Hannes , Levin Aviad , Welsh Timothy , Qi Runzhang , Qian Daoyuan , Zhu Hongjia , Sormanni Pietro , Vendruscolo Michele , Knowles Tuomas P.J.
Published: October 2022

Protein-based biologics are highly suitable for drug development, as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to very high concentrations, making insufficient solubility a critical bottleneck in drug development pipelines. Here, we report an ultra-high-throughput microfluidic platform for protein solubility screening. In comparison with previous methods, this microfluidic platform can make, incubate, and measure samples in a few minutes, uses just 20 micrograms of protein (> 10-fold improvement) and yields 10,000 data points (1000-fold improvement). This allows quantitative comparison of formulation additives, such as salt, polysorbate, histidine, arginine and sucrose. Additionally, we can measure how solubility is affected by different concentrations of multiple additives, find a suitable pH for the formulation, and measure the impact of single mutations on solubility, thus enabling the screening of large libraries. By reducing material and time costs, this approach makes detailed multi-dimensional solubility optimization experiments possible, streamlining drug development and increasing our understanding of biotherapeutic solubility and the effects of excipients.
Prediction of amyloid β accumulation from multiple biomarkers using a hierarchical Bayesian model
Authors: Yada Yuichiro , Naoki Honda
Published: October 2022

Accumulation of amyloid-beta (Aβ) in the brain is associated with neurodegeneration in Alzheimer’s disease and can be an indicator of early disease progression. Thus, the non-invasively and inexpensively observable features related to Aβ accumulation are promising biomarkers. However, in the experimental discovery of biomarkers in preclinical models, Aβ and biomarker candidates are usually not observed in identical sample populations. This study established a hierarchical Bayesian model that predicts Aβ accumulation level solely from biomarker candidates by integrating incomplete information. The model was applied to 5×FAD mouse behavioral experimental data. The predicted Aβ accumulation level obeyed the observed amount of Aβ when multiple features were used for learning and prediction. Based on the evaluation of predictability, the results suggest that the proposed model can contribute to discovering novel biomarkers, that is, multivariate biomarkers relevant to the accumulation state of abnormal proteins.
Biochemical analysis, photosynthetic gene (psbA) down–regulation, andin silicoreceptor prediction in weeds in response to exogenous application of phenolic acids and their analogs
Authors: Anwar Sobia , Naseem Saadia , Ali Zahid
Published: October 2022

Chemical herbicides are the primary weed management tool, although several incidences of herbicide resistance have been emerged, causing serious threat to agricultural sustainability. Plant derived phenolic acids with herbicidal potential may provide organic and eco-friendly substitute to such harmful chemicals. In present study, efficacy of two phenolic compounds, ferulic acid (FA) and gallic acid (GA), were evaluatedin vitroandin vivoagainst three prevalent herbicide-resistant weed species (Sinapis arvensis, Lolium multiflorumandParthenium hysterophorus). FA and GA not only suppressed the weed germination (80 to 60 % respectively), but also inhibited biochemical and photosynthetic pathway of weeds. In addition to significantly lowering the total protein and chlorophyll contents of the targeted weed species, the application of FA and GA treatments increased the levels of antioxidant enzymes and lipid peroxidation. Photosynthetic gene (psbA) expression was downregulated (10 to 30 folds) post 48 h of phenolic application.In silicoanalysis for receptor identification of FA and GA in psbA protein (D1) showed histidine (his-198) and threonine (thr-286) as novel receptors of FA and GA. These two receptors differ from the D1 amino acid receptors which have previously been identified (serine-264 and histidine-215) in response to PSII inhibitor herbicides. Based on its toxicity responses, structural analogs of FA were also designed. Four out of twelve analogs (0.25 mM) significantly inhibited weed germination (30 to 40%) while enhancing their oxidative stress. These results are unique which provide fundamental evidence of phytotoxicity of FA and GA and their analogs to develop cutting-edge plant based formulation to suppress weed growth in future.
Macrophage internalization creates a multidrug-tolerant fungal persister population, providing a permissive reservoir for the emergence of drug resistance
Authors: Arastehfar Amir , Daneshnia Farnaz , Cabrera Nathaly , Penalva-Lopez Suyapa , Sarathy Jansy , Zimmerman Matthew , Shor Erika , Perlin David S.
Published: October 2022

Candida glabratais a major fungal pathogen notable for causing recalcitrant infections, rapid emergence of drug-resistant strains, and its ability to survive and proliferate within macrophages. Resembling bacterial persisters, a subset of genetically drug-susceptibleC. glabratacells can survive lethal exposure to the fungicidal echinocandin drugs. Herein, we show that macrophage internalization induces cidal drug tolerance inC. glabrata, expanding the persister reservoir from which echinocandin-resistant mutants emerge. We show that this drug tolerance is associated with non-proliferation and is triggered by macrophage-induced oxidative stress, and that deletion of genes involved in reactive oxygen species detoxification significantly increases the emergence of echinocandin-resistant mutants. Finally, we show that the fungicidal drug amphotericin B can kill intracellularC. glabrataechinocandin persisters, reducing emergence of resistance. Our study supports the hypothesis that intra-macrophageC. glabratais a reservoir of recalcitrant/drug-resistant infections, and that drug alternating strategies can be developed to eliminate this reservoir.
A Computational Model for Storing Memories in the Synaptic Structures of the Brain
Authors: George Vivek , Morar Vikash , Silva Gabriel
Published: October 2022

Spike-timing dependent plasticity (STDP) is widely accepted as a mechanism through which the brain can learn information from different stimuli(1, 2). Basing synaptic changes on the timing between presynaptic and postsynaptic spikes enhances contributing edges within a network(3, 4). While STDP rules control the evolution of networks, most research focuses on spiking rates or specific activation paths when evaluating learned information(5–7). However, since STDP augments structural weights, synapses may also contain embedded information. While imaging studies demonstrate physical changes to synapses due to STDP, these changes have not been interrogated based on their embedding capacity of a stimulus(8–12). Here, we show that networks with biological features and STDP rules can embed information on their stimulus into their synaptic weights. We use a k-nearest neighbor algorithm on the synaptic weights of thousands of independent networks to identify their stimulus with high accuracy based on local neighborhoods, demonstrating that the network structure can store stimulus information. While spike rates and timings remain useful, structural embed-dings represent a new way to integrate information within a biological network. Our results demonstrate that there may be value in observing these changes directly. Beyond computational applications for monitoring these structural changes, this analysis may also inform investigation into neuroscience. Research is underway on the potential of astrocytes to integrate synapses in the brain and communicate that information elsewhere(13–15). In addition, observations of these synaptic embeddings may lead to novel therapies for memory disorders that are difficult to explain with current paradigms, such as transient epileptic amnesia.

Significance Statement

Learning in the brain is often achieved via spike-timing dependent plasticity changing the structure of synapses to augment the strength between neurons. Typically, these changes contribute to other behaviors in the network, such as spiking rates or spike timings. However, observing these changes themselves may be fruitful for interrogating the learning capability of networks in the brain. Using a computational model, we demonstrate that the synaptic weights contain an embedding of the stimulus after a certain amount of recurrent activity occurs. It is possible that networks in the brain embed information in a similar way and that external readers, such as astrocytes, can interrogate, integrate, and transport this synaptic weight information to process stimuli.
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut
Authors: Urtecho Guillaume , Moody Thomas , Huang Yiming , Sheth Ravi U. , Richardson Miles , Descamps Hélène C. , Kaufman Andrew , Lekan Opeyemi , Velez-Cortes Florencia , Qu Yiming , Cohen Lucas , Ricaurte Deirdre , Gibson Travis E. , Gerber Georg K. , Thaiss Christoph A. , Wang Harris H.
Published: October 2022

While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding for the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural ‘super-donor’ consortium that universally engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 hours followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally- dependent manner.
BEST: a web application for comprehensive biomarker exploration on large-scale data in solid tumors
Authors: Liu Zaoqu , Liu Long , Weng Siyuan , Xu Hui , Xing Zhe , Ren Yuqing , Ge Xiaoyong , Wang Libo , Guo Chunguang , Li Lifeng , Cheng Quan , Luo Peng , Zhang Jian , Han Xinwei
Published: October 2022

Data mining from RNA-seq or microarray data has become an essential part of cancer biomarker exploration. Certain existing web servers are valuable and broadly utilized, but the meta-analysis of multiple datasets is absent. Most web servers only contain tumor samples from the TCGA database with only one cohort for each cancer type, which also means that the analysis results mainly derived from a single cohort are thin and unstable. Indeed, consistent performance across multiple independent cohorts is the foundation for an excellent biomarker. Moreover, many analytical functions researchers require remain adequately unmet by these tools. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. BEST includes more than 50,000 samples of 27 cancer types. To ensure the comparability of genes between different sequencing technologies and the legibility of clinical traits, we re-annotated transcriptome data based on the GRCh38 patch 13 sequences and unified the nomenclature of clinical traits. BEST delivers fast and customizable functions, including clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration. Together, our web server provides multiple cleaned-up independent datasets and diverse analysis functionalities, helping unleash the value of current data resources. It is freely available athttps://rookieutopia.com/.

The bigger picture

Bioinformatics web servers enable researchers without computational programming skills to conduct various bioinformatics analyses. However, most web servers only contain tumor samples from the TCGA database with only one cohort for each cancer type, which also means that the analysis results mainly derived from a single cohort are thin and unstable. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. BEST includes more than 50,000 samples of 27 cancer types that have been uniformly re-annotated based on the GRCh38 patch 13 sequences, which ensures the comparability of genes between different sequencing technologies. BEST also offers prevalent functions including clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration. Together, BEST provides a curated database and innovative analytical pipelines to explore cancer biomarkers at high resolution.
Patient-specific deep offline artificial pancreas for blood glucose regulation in type 1 diabetes
Authors: Deng Yixiang , Arao Kevin , Mantzoros Christos S. , Karniadakis George Em
Published: October 2022

Due to insufficient insulin secretion, patients with type 1 diabetes mellitus (T1DM) are prone to blood glucose fluctuations ranging from hypoglycemia to hyperglycemia. While dangerous hypoglycemia may lead to coma immediately, chronic hyperglycemia increases patients’ risks for cardiorenal and vascular diseases in the long run. In principle, an artificial pancreas – a closed-loop insulin delivery system requiring patients manually input insulin dosage according to the upcoming meals – could supply exogenous insulin to control the glucose levels and hence reduce the risks from hyperglycemia. However, insulin overdosing in some type 1 diabetic patients, who are physically active, can lead to unexpected hypoglycemia beyond the control of common artificial pancreas. Therefore, it is important to take into account the glucose decrease due to physical exercise when designing the next-generation artificial pancreas. In this work, we develop a deep reinforcement learning algorithm using a T1DM dataset, containing data from wearable devices, to automate insulin dosing for patients with T1DM. In particular, we build patient-specific computational models using systems biology informed neural networks (SBINN), to mimic the glucose-insulin dynamics for a few patients from the dataset, by simultaneously considering patient-specific carbohydrate intake and physical exercise intensity.
A high-density 3-dimensional culture model of human glioblastoma for rapid screening of therapeutic resistance
Authors: Brown J , Zaben M , Ormonde C , Sharouf F , Spencer R , Bhatt H , Siebzehnrubl FA , Gray WP
Published: October 2022

Glioblastoma is among the most lethal cancers, with no known cure. A multitude of therapeutics are being developed or in clinical trials, but currently there are no ways to predict which patient may benefit the most from which drug. Assays that allow prediction of the tumor’s response to anti-cancer drugs may improve clinical decision-making. Here, we present a high-density 3D primary cell culture model for short-term testing from resected glioblastoma tissue that is set up on the day of surgery, established within 7 days and viable for at least 3 weeks. High-density 3D cultures contain tumor and host cells, including microglia, and retain key histopathological characteristics of their parent tumors, including proliferative activity, expression of the marker GFAP, and presence of giant cells. This provides a proof-of-concept that 3D primary cultures may be useful to model tumor heterogeneity. Importantly, we show that high-density 3D cultures can be used to test chemotherapy response within a 2– 3-week timeframe and are predictive of patient response to Temozolomide therapy. Thus, primary high-density 3D cultures could be a useful tool for brain cancer research and prediction of therapeutic resistance.
Brain signatures of chronic gut inflammation
Authors: Hall Caitlin V. , Radford-Smith Graham , Savage Emma , Robinson Conor , Cocchi Luca , Moran Rosalyn J.
Published: October 2022

Gut inflammation is thought to modify brain activity and behaviour via modulation of the gut-brain axis. However, how relapsing and remitting exposure to peripheral inflammation over the natural history of inflammatory bowel disease (IBD) contributes to altered brain dynamics is poorly understood. Here, we used electroencephalography (EEG) to characterise changes in spontaneous spatiotemporal brain states in Crohn’s Disease (CD) (n = 40) and Ulcerative Colitis (UC) (n = 30), compared to healthy individuals (n = 28). We first provide evidence of a significantly perturbed and heterogeneous microbial profile in CD, consistent with previous work showing enduring and long-standing dysbiosis in clinical remission. Results from our brain state assessment show that CD and UC exhibit alterations in the temporal properties of states implicating default-mode network, parietal, and visual regions, reflecting a shift in the predominance from externally to internally-oriented attentional modes. We investigated these dynamics at a finer sub-network resolution, showing a CD-specific and highly selective enhancement of connectivity between the insula and mPFC, regions implicated in cognitive-interoceptive appraisal mechanisms. Alongside overall higher anxiety scores in CD, we also provide preliminary support to suggest that the strength of chronic interoceptive hyper-signalling in the brain co-occurs with disease duration. Together, our results demonstrate that a long-standing diagnosis of CD is, in itself, a key factor in determining the risk of developing altered brain network signatures.
A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance
Authors: Smith Chase H. , Pinto Brendan J. , Kirkpatrick Mark , Hillis David M. , Pfeiffer John M. , Havird Justin C.
Published: October 2022

In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to these assumptions is called doubly uniparental inheritance (DUI): a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluscan class Bivalvia. The phylogenetic distribution of male mitochondrial DNA in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female mitochondrial DNA. In this study, we use phylogenetic methods to test male mitochondrial DNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of male mitochondrial DNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of female and male mitochondrial DNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of theCOX2gene in male mitochondrial DNA. The loss of recombination may be neutral but could be connected to the role of M mtDNA in sex determination or sexual development. Our results support recombination events in DUI species may occur throughout their genomes. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of male mitochondrial DNA in protein coding genes.
Distinction between small RNA-bound and free ARGONAUTE via an N-terminal protein-protein interaction site
Authors: Bressendorff Simon , Zobbe Sjøgaard Ida Marie , Prestel Andreas , Kragelund Birthe B. , Poulsen Christian , Brodersen Peter
Published: October 2022

ARGONAUTE (AGO) proteins bind to small non-coding RNAs to form RNA Induced Silencing Complexes (RISCs). In the RNA-bound state, AGO proteins are stable while RNA-free AGOs turn over rapidly. Molecular determinants unique to RNA-free AGO that allow its specific recognition and degradation remain unknown. Here, we show that a confined, linear region in Arabidopsis AGO1, the N-coil, is accessible to antibodies preferentially in the RNA-free state of AGO1. Reanalysis of hydrogen-deuterium exchange data on human Ago2 indicates similar structural flexibility of the N-coil depending on small RNA binding. Unloaded Arabidopsis AGO1 interacts with the autophagy cargo receptor ATI1 via direct contact to specific amino acid residues in the N-coil, and mutation of residues required for ATI1 interaction reduces the degradation rate of unloaded AGO1in vivo. These results provide insight into the molecular basis for specific recognition and degradation of the RNA-free state of eukaryotic AGO proteins.
The ACE-2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion
Authors: Cervantes Marcos , Hess Tobin , Morbioli Giorgio G. , Sengar Anjali , Kasson Peter M.
Published: October 2022

The SARS-CoV-2 coronavirus infects human cells via the ACE-2 receptor. Circumstantial evidence suggests that ACE-2 may not just serve as an attachment factor but also help activate the SARS-CoV-2 spike protein for membrane fusion. Here, we test that hypothesis directly, using DNA-lipid tethering as a synthetic attachment factor in the place of ACE-2. We find that SARS-CoV-2 pseudovirus and viruslike particles are both capable of membrane fusion if attached in the absence of ACE-2 and activated with an appropriate protease. However, addition of soluble ACE-2 speeds the fusion reaction. This is observed for both the Wuhan strain and the B.1.1.529 Omicron variant. Kinetic analysis suggests that there are at least two rate-limiting steps for SARS-CoV-2 membrane fusion, one of which is ACE-2 dependent and one of which is not. These data establish that, in the presence of an alternative attachment factor, ACE-2 is not biochemically required for SARS-CoV-2 membrane fusion. Since ACE-2 serves as the high-affinity attachment factor on human cells, the possibility to replace it with other factors has implications for the evolvability of SARS-CoV-2 and the fitness landscape for future related coronaviruses.
Phenotypic alteration of low-density granulocytes in people with pulmonary post-acute sequalae of SARS-CoV-2 infection
Authors: Dean Logan S. , Devendra Gehan , Jiyarom Boonyanudh , Subia Natalie , Tallquist Michelle D. , Nerurukar Vivek R. , Chang Sandra P. , Chow Dominic C. , Shikuma Cecilia M. , Park Juwon
Published: October 2022

Low-density granulocytes (LDGs) are a distinct subset of neutrophils whose increased abundance is associated with the severity of COVID-19. However, the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on LDG levels and phenotypic alteration remain unexplored. Using participants naïve to SARS-CoV-2 (NP), infected with SARS-CoV-2 with no residual symptoms (NRS), and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC), we compared LDG levels and their phenotype by measuring the expression of markers for activation, maturation, and neutrophil extracellular trap (NET) formation using flow cytometry. The number of LDGs was significantly elevated in PPASC compared to NP. Individuals infected with SARS-CoV-2 (NRS and PPASC) demonstrated increased CD10+and CD16HI subset counts of LDGs compared to NP group. Further characterization of LDGs demonstrated that LDGs from PPASC displayed higher NET forming ability and aggregation with platelets compared to LDGs from NP and NRS. Our data demonstrates that mature neutrophils with a heightened activation phenotype remain in circulation long after initial SARS-CoV-2 infection. Persistent elevation of markers for neutrophil activation and NET formation on LDGs, as well as an enhanced proclivity for platelet-neutrophil aggregation (PNA) formation in individuals with PPASC may be associated with the development of long-term pulmonary sequelae.
Metformin use history and genome-wide DNA methylation profile: potential molecular mechanism for aging and longevity
Authors: Marra Pedro S. , Yamanashi Takehiko , Crutchley Kaitlyn J. , Wahba Nadia E. , Anderson Zoe-Ella M. , Modukuri Manisha , Chang Gloria , Tran Tammy , Iwata Masaaki , Cho Ryan , Shinozaki Gen
Published: October 2022

Background

While there are medications that treat and manage age-related diseases, a compound that prolongs lifespan is yet to be discovered. Nonetheless, metformin, a commonly prescribed anti-diabetic medication, has repeatedly been shown to hinder aging in pre-clinical models and to be associated with lower mortality for humans, even among cancer patients. It is, however, not well understood how metformin can potentially prolong lifespan from a biological standpoint. We hypothesized that metformin’s potential mechanism of action for longevity is through its epigenetic modifications.

Methods

To test our hypothesis, we conducted a post-hoc analysis of available genome-wide DNA methylation (DNAm) data obtained from whole blood collected from inpatients with and without a history of metformin use. We assessed the methylation profile of 171 patients (first run) and only among 63 diabetic patients (second run) and compared the DNAm rates between metformin users and nonusers.

Results

Enrichment analysis from the Kyoto Encyclopedia of Genes and Genome (KEGG) showed pathways relevant to metformin’s mechanism of action, such as longevity, AMPK, and inflammatory pathways. We also identified several pathways related to delirium whose risk factor is aging. Moreover, top hits from the Gene Ontology (GO) included HIF-1α pathways. However, no individual CpG site showed genome-wide statistical significance (p<5E-08).

Conclusion

This study may elucidate metformin’s potential role in longevity through epigenetic modifications and other possible mechanisms of action.
Anti-Inflammatory Tension-Activated Repair Patches Improve Repair After Intervertebral Disc Herniation
Authors: Peredo Ana P. , Gullbrand Sarah E. , Friday Chet S. , Orozco Briana S. , Bonnevie Edward D. , Hilliard Rachel L. , Zlotnick Hannah M. , Dodge George R. , Lee Daeyeon , Hast Michael W. , Schaer Thomas P. , Smith Harvey E. , Mauck Robert L.
Published: October 2022

Conventional treatment for intervertebral disc herniation alleviates pain but does not repair the annulus fibrosus (AF), resulting in a high incidence of recurrent herniation and persistent disfunction. The lack of repair and the acute inflammation that arise after injury further compromises the disc and can result in disc-wide degeneration in the long term. To address this clinical need, we developed tension-activated repair patches (TARPs) for annular repair and the local delivery of bioactive anti-inflammatory factors. TARPs transmit physiologic strains to mechanically-activated microcapsules (MAMCs) embedded within, which activate and release encapsulated biomolecules in response to physiologic loading. Here, we demonstrate that the TARP design modulates implant biomechanical properties and regulates MAMC mechano-activation. Next, the FDA-approved anti-inflammatory molecule, interleukin 1 receptor antagonist, Anakinra, was loaded in TARPs and the effects of TARP-mediated annular repair and Anakinra delivery was evaluated in a model of annular injury in the goat cervical spine. TARPs showed robust integration with the native tissue and provided structural reinforcement at the injury site that prevented disc-wide aberrant remodeling resulting from AF detensioning. The delivery of Anakinra via TARP implantation improved the retention of disc biochemical composition through increased matrix deposition and retention at the site of annular injury. Anakinra delivery additionally attenuated the inflammatory response associated by scaffold implantation, decreasing osteolysis in adjacent vertebrae and preserving disc cellularity and matrix organization throughout the AF. These results demonstrate the translational and therapeutic potential of this novel TARP system for the treatment of intervertebral disc herniations.

One Sentence Summary

Tension-activated repair patches delivering bioactive anti-inflammatory factors improve healing in an in vivo goat cervical disc injury model.
Transgene by Germplasm Interactions Can Impact Transgene Evaluation
Authors: Linares Julien F , Coles Nathan D , Mo Hua , Habben Jeff E , Humbert Sabrina , Messina Carlos , Tang Tom , Cooper Mark , Gho Carla , Carrasco Ricardo , Carter Javier , Flounders Jillian Wicher , Brummer E Charles
Published: October 2022

Transgenes have been successfully commercialized for qualitatively inherited insect and herbicide resistance traits that show similar effects across genetic backgrounds. However, for quantitative traits like yield, genetic background may affect the measured transgene value. In this paper, we evaluated whether different genetic backgrounds impact the estimated value of a transgene for grain yield, ear height, and anthesis-silking interval for maize by developing isogenic pairs of lines with and without a transgene and testing them in hybrid combination with non-transgenic lines from a complementary heterotic group across eleven environments in the USA. Over all hybrid combinations, the transgene increased yield by 0.2 Mg ha−1. Across multiple non-transgenic lines of the opposing heterotic group, the transgene effect within a line pair ranged from an increase of 0.8 Mg ha−1for the NSS4 and SS7 transgenic lines to a reduction of 0.3 Mg ha−1for the NSS5 transgenic line when compared to their non-transgenic isoline. Transgenic hybrids were often taller than non-transgenic hybrids (P<0.05). Anthesis to silking interval was reduced by 4□C growing degree units overall, but no transgene × genotype interaction was detected among line pairs. Our results show the importance of testing transgene efficacy across a large sample of elite hybrid pairs to assess the gene’s value. By only testing in a specific hybrid background, as may be done for qualitative traits like insect resistance, transgenes could be erroneously advanced or eliminated.
Targeting the pathological network: feasibility of network-based optimization of transcranial magnetic stimulation coil placement for treatment of psychiatric disorders
Authors: Cao Zhengcao , Xiao Xiang , Zhao Yang , Jiang Yihan , Xie Cong , Paillère-Martinot Marie-Laure , Artiges Eric , Li Zheng , Daskalakis Zafiris J. , Yang Yihong , Zhu Chaozhe
Published: October 2022

It has been recognized that the efficacy of TMS-based modulation may depend on the network profile of the stimulated regions throughout the brain. However, what profile of this stimulation network optimally benefits treatment outcomes is yet to be addressed. The answer to the question is crucial for informing network-based optimization of stimulation parameters, such as coil placement, in TMS treatments. In this study, we aimed to investigate the feasibility of taking a disease-specific network as the target of stimulation network for guiding individualized coil placement in TMS treatments. We present here a novel network-based model for TMS targeting of the pathological network. First, combining E-field modeling and resting-state functional connectivity, stimulation networks were modeled from locations and orientations of the TMS coil. Second, the spatial anti-correlation between the stimulation network and the pathological network of a given disease was hypothesized to predict the treatment outcome. The proposed model was validated to predict treatment efficacy from the position and orientation of TMS coils in two depression cohorts and one auditory verbal hallucinations cohort. We further demonstrate the utility of the proposed model in guiding individualized TMS treatment for psychiatric disorders. In this proof-of-concept study, we demonstrated the feasibility of the novel network-based targeting strategy that uses the whole-brain, system-level abnormity of a specific psychiatric disease as a target. Results based on empirical data suggest that the strategy may potentially be utilized to identify individualized coil parameters for maximal therapeutic effects.

Highlights

Proposed a model of targeting pathological brain networks for pre-treatment TMS coil placement planning in the treatment of psychiatric disorders;

Validated the network targeting model in three cohorts of patients with depression or auditory verbal hallucinations, via prediction of individual TMS treatment efficacy from the parameters of coil placement;

Demonstrated the utility of the network targeting model in guiding individualized TMS coil placement.
miR-148a-3pinhibits osteogenesis by targetingItga11via PI3K/Akt/GSK3/β-catenin pathway
Authors: Chen Xiaojun , Rong Kewei , Li Xin , Han Wenqing , Pang Yichuan , Chai Gang
Published: October 2022

In previous research, miR-148a-3p deficiency was observed in bone malformation in hemifacial microsomia. Nevertheless, the mechanism of miR-148a regulating osteogenesis remains unclear. Herein, in this article, we probed into the role of miR-148a-3p in bone physiology by utilizing miR-148a knock-out (KO) mice. Compared with wild-type (WT) or heterozygotic (HE) littermates, miR-148a knock-out mice manifested lower body weight, bone dysplasia with increased bone mass. Throughin-vitroexperiments, in terms of miR-148a-3p overexpression (miRNA mimic transfection) and knockout (primary cells from WT and KO littermates), we found that miR-148a-3p can suppress osteogenesis, either in the ALP activity or bone nodules formation. Afterward, by means of proteomics, combined with RNA-sequencing and prediction databases of microRNA targets (miRDB and TargetScan), nine candidate genes targeted by miR-148a-3p were identified. Among them, onlyItga11was regulated by mRNA degradation, while the others were modulated via post-transcriptional inhibition. Based on several online databases (GenePaint, BioGPS, STRING),Integrin Subunit Alpha 11(Itga11) was suggested to play an essential role in osteogenesis and it was confirmed as one direct target of miR-148a-3p by dual-luciferase reporter assay. Meanwhile, gene set enrichment analysis (GSEA) indicated activation of PI3K-Akt signaling pathway and WNT signaling pathway in miR-148a KO mice. The thereafter western blot confirmed that PI3K/Akt/GSK3/β-catenin signaling pathway was involved. Finally, with the help of esterase-response bone-affiliative liposome with theItga11siRNA delivery system, the enhanced osteogenesis in miR-148a KO mice was partly rescued. Taken together, we demonstrated that miR-148a-3p can inhibit osteogenesis by targeting Itga11 via PI3K/Akt/GSK3/β-catenin pathway.
From Initial Formation to Developmental Refinement: GABAergic Inputs Shape Neuronal Subnetworks in the Primary Somatosensory Cortex
Authors: Huang Jui-Yen , Hess Michael , Bajpai Abhinav , Li Xuan , Hobson Liam N , Xu Ashley J , Barton Scott J , Lu Hui-Chen
Published: October 2022

Neuronal subnetworks, also known as ensembles, are functional units formed by interconnected neurons for information processing and encoding in the adult brain. Our study investigates the establishment of neuronal subnetworks in the mouse primary somatosensory (S1) cortex from postnatal days (P)11 to P21 usingin vivotwo-photon calcium imaging. We found that at P11, neuronal activity was highly synchronized but became sparser by P21. Clustering analyses revealed that while the number of subnetworks remained constant, their activity patterns became more distinct, with increased coherence, independent of cortical layer or sex. Furthermore, the coherence of neuronal activity within individual subnetworks significantly increased when synchrony frequencies were reduced by augmenting GABAergic activity at P15/16, a period when the neuronal subnetworks were still maturing. Together, these findings indicate the early formation of subnetworks and underscore the pivotal roles of GABAergic inputs in modulating S1 neuronal subnetworks.
C-4-Modified Isotetrones Prevent Biofilm Growth and Persister Cell Resuscitation inMycobacterium smegmatis
Authors: Bag Kingshuk , Pal Aditya Kumar , Basu Subhadip , Singla Mamta , Chatterji Dipankar , Maiti Prabal Kumar , Ghosh Anirban , Jayaraman Narayanaswamy
Published: October 2022

Hyperphosphorylated guanosine nucleotide (p)ppGpp, synthesized by Rel proteins, regulates the stringent response pathway responsible for biofilm growth and persister cell formation in the stationary phase of mycobacteria. The discovery of vitamin C as a potent inhibitor of Rel protein activities raises the prospect of such a tetrone lactone to prevent biofilm growth and persister cell formation. The closely related isotetrone lactone derivatives are identified in the present study as potent inhibitors of the above processes in a mycobacterium. Isotetrone lactone derivatives are synthesized from appropriate α-ketocarboxylic acids, derived from the a-amino acids. Aldol condensation with formaldehyde, followed by the lactone formation, completes synthesis of isotetrone derivatives, possessing varied substituents atC-4 carbon, in good yields. A series of biochemical evaluations of biofilm growth and persister cell formation inM. smegmatisis conducted. Among the derivatives, isotetrone possessing phenyl substituent atC-4 carbon completely inhibit the biofilm formation at 400 μg mL-1concentration, 84 h of post-exposure, followed by a moderate inhibition by the isotetrone possessingp-hydroxyphenyl substituent. Whereas, the latter isotetrone inhibits the growth of cells at 400 μg mL-1f.c. when monitored for 2 weeks, under PBS starvation condition. Isotetrones also potentiate the inhibition of antibiotic tolerant regrowth of cells by ciprofloxacin antibiotic (0.75 μg mL-1) and thus act as bio-enhancers. The combination is shown to significantly arrest the emergence of ciprofloxacin-resistant genetic mutants. The observations suggest that isotetrones in combination with ciprofloxacin are therapeutically superior when administered together. Systematic molecular dynamics studies show that isotetrone derivative binds to Rel protein more efficiently than vitamin C and the binding is aided by hydrogen bonding, van der Waals and electrostatic interactions at a binding site possessing serine, threonine, lysine and arginine residues. The present study establishes that the identified isotetrone derivatives (i) act as inhibitors ofM. smegmatisbiofilm growth and (ii) arrest the re-emergence of recalcitrant persister cells when administered together with ciprofloxacin antibiotic. Results of this study establish that isotetrones as new chemical entities that interfere with stringent response pathways in a mycobacterium under stress and permit overcoming the multidrug-resistant persister cell emergence in the bacterium.
STIM1 signals through NFAT independently of Orai1 and SOCE to regulate breast cancer cell migration
Authors: Hammad Ayat S. , Yu Fang , Horgen F. David , Machaca Khaled
Published: October 2022

Store-operated calcium entry (SOCE) contributes to several physiological and pathological conditions including transcription, secretion, immunodeficiencies, and cancer. SOCE has been shown to be important for breast cancer cell migration where knockdown of SOCE components (STIM1 or Orai1) decreases cancer metastasis. Here we show unexpectedly that STIM1 knockout (KO) metastatic MDA-MB-231 breast cancer cells migrate faster and have enhance invasion capacity compared to parental cells. In contrast, Orai1-KO cells, which have similar levels of SOCE inhibition as STIM1-KO, migrate slower than the parental cell line. This shows that the enhanced migration phenotype of STIM1-KO cells is not due to the loss of a Ca2+entry through SOCE, rather it involves transcriptional remodeling. Interestingly, NFATC2 is significantly downregulated in STIM1-KO cells and overexpression of NFATC2 reversed the enhanced migration of STIM1-KO cells. This demonstrates that STIM1 modulates NFATC2 expression independently of its role in SOCE.

SUMMARY STATEMENT

Breast cancer cells migrate faster when the ER Ca2+sensor STIM1 in knocked out due to downregulation of NFAT1 expression independent of Ca2+influx.
A genome-wide association study identified new variants associated with mathematical abilities in Chinese children
Authors: Zhang Liming , Wang Zhengjun , Zhu Zijian , Yang Qing , Cheng Chen , Zhao Shunan , Liu Chunyu , Zhao Jingjing
Published: October 2022

Mathematical ability is moderately heritable, and it is a complex trait which can be evaluated in several different categories. A few genetic studies have been published on general mathematical ability. However, no genetic study focused on specific mathematical ability categories. In this study, we separately performed genome-wide association studies (GWASs) on 11 mathematical ability categories in 1 146 students from Chinese elementary schools. We identified 7 genome-wide significant single nucleotide polymorphisms (SNPs) with strong linkage disequilibrium (LD) among each other (all r2>0.8) associated with mathematical reasoning ability (top SNP: rs34034296,p=2.01×10−8, nearest gene: CUB and Sushi multiple domains 3, CSMD3). We replicated one SNP (rs133885) from 585 SNPs previously reported to be associated with general mathematical ability associated with division ability in our data (p=1.053×10−5). In the gene- and gene-set enrichment analysis by MAGMA, we found three significant enrichments of associations with three mathematical ability categories for three genes. We also observed four significant enrichments of associations with four mathematical ability categories for three gene sets. Our results suggest new candidate genetic loci for the genetics of mathematical ability.
Universal chimeric Fcγ receptor T cells with appropriate affinity for IgG1 antibody exhibit optimal antitumor efficacy
Authors: Zhu Wen , Wang Yang , Lv Liangyin , Wang Hui , Shi Wenqiang , Liu Zexin , Zhou Mingzhe , Zhu Jianwei , Lu Huili
Published: October 2022

Developing universal CARs with improved flexible targeting and controllable activities is urgently needed. While several studies have suggested the potential of CD16a in tandem with monoclonal antibodies to construct universal CAR T cells, the weak affinity between them is one of the limiting factors for efficacy. Herein, we systematically investigated the impact of Fcγ receptor (FcγR) affinity on CAR T cells properties by constructing universal CARs using Fcγ receptors with different affinities for IgG1 antibodies, namely CD16a, CD32a, and CD64. We demonstrated that the activities of these universal CAR T cells on tumor cells could be redirected and regulated by IgG1 antibodies. In xenografted mice, 64CAR chimeric Jurkat cells with the highest affinity showed significant antitumor effects in combination with herceptin in the Her2 low expression U251 MG model. However, in the CD20 high expression Raji model, 64CAR caused excessive activation of CAR-T cells, which resulted in cytokine release syndrome (CRS) and the decline of antitumor activity, and 32CAR with a moderate affinity brought the best efficacy. Our work extended the knowledge about FcγR-based universal CAR T cells and suggested that only the FcγRCAR with an appropriate affinity can offer the optimal antitumor advantages of CAR T cells.

Graphical abstract

Universal CAR T cells based on Fcγ receptors exhibit a specific tumor-killing effect. However, the affinities of Fcγ receptors greatly influence the efficacy and adverse effectsin vivo.
Synaptopodin regulates denervation-induced plasticity at hippocampal mossy fiber synapses
Authors: Kruse Pia , Brandes Gudrun , Hemeling Hanna , Huang Zhong , Wrede Christoph , Hegermann Jan , Vlachos Andreas , Lenz Maximilian
Published: October 2022

Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. Nevertheless, the molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in spatial learning. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, in CA3-PCs, and their direct synaptic connections as revealed by paired recordings (GC-to-CA3). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-related protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and its integral protein synaptopodin are associated with ribosomes in close proximity to synaptic sites and unravel a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle, failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.
Time or distance: predictive coding of Hippocampal cells
Authors: Abramson Shai , Kraus Benjamin J. , White John A. , Hasselmo Michael E. , Morris Genela , Derdikman Dori
Published: October 2022

The discovery of place cells within the hippocampus has pointed to the importance of the hippocampus for navigation. The more recent discovery of hippocampal time cells has broadened the perspective of encoding in the hippocampus. An alternative hypothesis to the existence of time cells is based on the notion that hippocampal cells deduce location by integrating travelled distance (“path integration”). According to this alternate hypothesis, time cells, which fire at particular times when animals are running on a treadmill without changing location, actually encode accumulated distance on the treadmill. To examine this hypothesis, Kraus et al.1performed treadmill experiments in which animals either ran for a fixed time or a fixed distance with varying velocities. Two distinct coding modes of hippocampal principal cells were found. Some cells encoded travelled distance and others elapsed time, thus refuting the notion that all hippocampal cells were performing path integration. Using the data from these experiments, we asked whether the two populations depended on the type of task the rats were engaged in. We show that the type of experiment determined the cells’ encoding, such that in fixed-distance experiments distance-encoding cells dominated, while on fixed-time experiments time-encoding cells dominated. These results suggest that the cells’ encoding contains a predictive element, dependent on the important variables of the experiment.