bluuebunny/crossref_metadata_2025 huggingface dataset:
Reading Epilepsy and Language Processing: A Proposed Role for Semantic Salience
Authors: Li Wentao , Seyal Masud
Published: October 2022

Reading epilepsy is a relatively rare reflex epilepsy syndrome that typically presents as orofacial reflex myoclonus triggered by reading. Seizures are thought to be because of activation of hyperexcitable language-related pathways in the dominant hemisphere that subsequently spreads to adjacent motor cortices. More difficult reading tasks are thought to be more provocative of seizures regardless of semantic understanding of the text. The authors sought to better characterize the role of text difficulty and comprehension in triggering seizures in a 27-year-old patient with reading epilepsy. As a part of his epilepsy monitoring unit admission, the patient underwent a series of reading trials with increasing semantic salience and/or difficulty, including pseudo-reading of colors and foreign-language texts, which demonstrated a positive correlation between spike count and clinical events and increasing semantic salience. This suggests that our novel reading task may be able to differentiate between different processes in the reading pathway and that increased semantic relevance of the text, rather than increased difficulty per se, can be associated with increased seizures in reading epilepsy. The authors theorize that this may be associated with his atypical (nondominant) right hemispheric seizure focus and propose that further study of patients with reading epilepsy syndrome may help elucidate the neurobiological networks involved in reading and language processing.
Tonic Seizures in a Patient With Lennox–Gastaut Syndrome Manifest as “Icicles” Rather Than “Flames” on Quantitative EEG Analysis
Authors: Catenaccio Eva , Bennett Mariko L. , Massey Shavonne L. , Abend Nicholas S. , Bergqvist Christina
Published: October 2022

Quantitative analysis of continuous electroencephalography (QEEG) is increasingly being used to augment seizure detection in critically ill patients. Typically, seizures manifest on QEEG as abrupt increases in power and frequency, a visual pattern often called “flames.” Here, we present a case of a 16-year-old patient with intractable Lennox–Gastaut syndrome secondary to a pathogenic variant in the SCN2A gene who had tonic seizures that manifest as abrupt decreases in power on QEEG, a visual pattern we term “icicles.” Recognition of QEEG patterns representative of different seizure types is important as QEEG use becomes more widespread including in pediatric populations.
Time of Sample Collection Critical for Microbiome Replicability
Authors: Allaband Celeste , Lingaraju Amulya , Ramos Stephany Flores , Kumar Tanya , Javaheri Haniyeh , Tiu Maria D. , Machado Ana Carolina Dantas , Richter Roland A. , Elijah Emmanuel , Haddad Gabriel G. , Leone Vanessa A. , Dorrestein Pieter C. , Knight Rob , Zarrinpar Amir
Published: October 2022

Although many aspects of microbiome studies have been standardized to improve experimental replicability, none account for how the daily diurnal fluctuations in the gut lumen cause dynamic changes in 16S amplicon sequencing. Here we show that sample collection time affects the conclusions drawn from microbiome studies and are larger than the effect size of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups are unique to each experiment. Sample collection times as short as only four hours apart lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. Without looking at other data, the impact on other fields is unknown but potentially significant.

One-Sentence Summary

If we are not controlling for host circadian rhythm time in microbiome studies when performing experiments, it is like trying to measure sea level rise while not knowing that tides or waves exist.
Gait speed and individual characteristics can be used to predict specific gait metric magnitudes in neurotypical adults
Authors: Bonilla Yanez Maryana , Kettlety Sarah A. , Finley James M. , Schweighofer Nicolas , Leech Kristan A.
Published: October 2022

Background

Gait biofeedback is commonly used to reduce gait dysfunction in a variety of clinical conditions. In these studies, participants alter their walking to reach the desired magnitude of a specific gait parameter (the biofeedback target) with each step. Biofeedback of parameters such as anterior ground reaction force and step length have been well-studied. Yet, there is no standardized methodology to set the target magnitude of these parameters. Here we present an approach to predict the anterior ground reaction force and step length of neurotypical adults walking at different speeds as a potential method for personalized gait biofeedback.

Research question

To determine if anterior ground reaction force and step lengths achieved during neurotypical walking could be predicted using gait speed and participants’ demographic and anthropomorphic characteristics.

Methods

We analyzed kinetic and kinematic data from 51 neurotypical adults who walked on a treadmill at up to eight speeds. We calculated the average peak anterior ground reaction force and step length of the right lower extremity at each speed. We used linear mixed-effects models to evaluate the effect of speed, leg length, mass, and age on anterior ground reaction force and step length. We fit the model to data from 37 participants and validated predictions from the final models on an independent dataset from 23 participants.

Results

Final prediction models for anterior ground reaction force and step length both included speed, speed squared, age, mass, and leg length. The models both showed strong agreement between predicted and actual values on an independent dataset.

Significance

Anterior ground reaction force and step length for neurotypical adults can be predicted given an individual’s gait speed, age, leg length, and mass. This may provide a standardized method to personalize targets for individuals with gait dysfunction in future studies of gait biofeedback.
Discovery of prevalent, clinically actionable tumor neoepitopes via integrated biochemical and cell-based platforms
Authors: Gurung Hem , Heidersbach Amy , Darwish Martine , Chan Pamela , Li Jenny , Beresini Maureen , Zill Oliver , Wallace Andrew , Tong Ann-Jay , Hascall Dan , Torres Eric , Chang Andy , Lou Kenny “Hei-Wai” , Abdolazimi Yassan , Moore Amanda , Uche Uzodinma , Laur Melanie , Notturno Richard , Ebert Peter J.R. , Blanchette Craig , Haley Benjamin , Rose Christopher M.
Published: October 2022

Strategies for maximizing the potency and specificity of cancer immunotherapies have sparked efforts to identify recurrent epitopes presented in the context of defined tumor-associated neoantigens. Discovering these “neoepitopes” can be difficult owing to the limited number of peptides that arise from a single point mutation, a low number of copies presented on the cell surface, and variable binding specificity of the human leukocyte antigen (HLA) class I complex. Due to these limitations, many discovery efforts focus on identifying neoepitopes from a small number of cancer neoantigens in the context of few HLA alleles. Here we describe a systematic workflow to characterize binding and presentation of neoepitopes derived from 47 shared cancer neoantigens in the context of 15 HLA alleles. Through the development of a high-throughput neoepitope-HLA binding assay, we surveyed 24,149 candidate neoepitope-HLA combinations resulting in 587 stable complexes. These data were supplemented by computational prediction that identified an additional 257 neoepitope-HLA pairs, resulting in a total of 844 unique combinations. We used these results to build sensitive targeted mass spectrometry assays to validate neoepitope presentation on a panel of HLA-I monoallelic cell lines engineered to express neoantigens of interest as a single polypeptide. Altogether, our analyses detected 84 unique neoepitope-HLA pairs derived from 37 shared cancer neoantigens and presented across 12 HLA alleles. We subsequently identified multiple TCRs which specifically recognized two of these neoantigen-HLA combinations. Finally, these novel TCRs were utilized to elicit a T cell response suggesting that these neoepitopes are likely to be immunogenic. Together these data represent a validated, extensive resource of therapeutically relevant neoepitopes and the HLA context in which they can be targeted.
Quantitative analysis of cellular morphology duringin vitrodecidualization
Authors: Ant Luciana , Le Dily François , Beato Miguel , Saragüeta Patricia
Published: October 2022

Decidualization is a differentiation process involving shape reorganization from a fibroblast to an epithelioid-like appearance of endometrial stromal cells. Specificities of these cells impede the use of existing automated tools to follow morphological changes during differentiation; we therefore developed a simple but accurate methodology to quantify the phenotypical changes that occur in anin vitrodecidualization system.

The approach consists of the analysis of the circularity of the cells directly from light microscopy images. Here, we used this methodology to follow the effects of progesterone or progestin R5020 in combination with estradiol (E2) and cAMP on inducing the decidualization of human endometrial cells. We further implemented a statistical model to detect the differences in the kinetics of decidualization of the two hormonal stimuli before all the cell population acquired the decidual phenotype. We found that 2 days after stimulation are sufficient to detect statistical differences in morphology between decidualization induced and control cells. Here, we detail the model and scripts in order to provide a useful, practical and low cost tool to evaluate morphological aspects of endometrial stromal differentiation.

Availability and implementation

See supplementary methods

Supplementary information

Supplementary data is available online.
Loss of long-range co-expression is a common trait in cancer
Authors: García-Cortés Diana , Hernández-Lemus Enrique , Espinal Enríquez Jesús
Published: October 2022

Cancer cells display common traits and enabling-characteristics previously described as the Hallmarks of Cancer. These occur alongside alterations in the regulatory mechanisms controlling gene transcription. Gene co-expression networks (GCNs) identify correlated sets of genes that might share these mechanisms. We have previously reported loss of long-range co-expression for breast, lung, and kidney cancer GCNs. Here, we extend the study to fifteen tissues. Unlike in healthy phenotypes, the highest cancer gene-pair interactions are intra-chromosomal and their strength decays with base-pair distance. Communities in tumor GCNs are strongly associated with cancer related processes along with a wide presence of adaptive immune response. Riboproteins are highly co-expressed in cancer and normal GCNs, suggesting their relevance for cell viability. The loss of long-range co-expression is not observed in other chronic diseases such as Type-2 Diabetes or Alzheimer’s disease. These results suggest that the loss of long-range co-expression is a common trait in cancer.
Overcoming the Blood-Brain Barrier for Gene Therapy via Systemic Administration of GSH-Responsive Silica Nanocapsules
Authors: Wang Yuyuan , Wang Xiuxiu , Xie Ruosen , Burger Jacobus C. , Tong Yao , Gong Shaoqin
Published: October 2022

CRISPR genome editing has demonstrated great potential to treat the root causes of many genetic diseases, including central nervous system (CNS) disorders. However, the promise of brain-targeted therapeutic genome editing relies on the efficient delivery of biologics bypassing the blood-brain barrier (BBB), which represents a substantial challenge in the development of CRISPR therapeutics. In this study, we created a library of GSH-responsive silica nanocapsules (SNCs) and screened them for brain targeting via systemic delivery of nucleic acids and CRISPR genome editors.In vivostudies demonstrated that systemically delivered SNCs conjugated with glucose and RVG peptide under glycemic control can efficiently bypass the intact BBB, enabling brain-wide delivery of various biologics (mRNA, Cas9 mRNA/sgRNA, and Cas9/sgRNA ribonucleoprotein) targeting both exogenous genes (i.e., Ai14 stop cassette) and disease-relevant endogenous genes (i.e.,AppandThgenes) in Ai14 reporter mice and wild-type mice, respectively. In particular, we observed up to 28% neuron editing via systemic delivery of Cre mRNA in Ai14 mice, up to 6.1% amyloid precursor protein (App) gene editing (resulting in 19.1% reduction in the expression level of intact APP), and up to 3.9% tyrosine hydroxylase (Th) gene editing (resulting in 30.3% reduction in the expression level of TH) in wild-type mice. This versatile SNC nanoplatform may offer a novel strategy for the treatment of CNS disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease.
Genome-wide mapping of fluoroquinolone-stabilized DNA gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence
Authors: Tang Juechun , Brynildsen Mark P.
Published: October 2022

Persisters are rare phenotypic variants that are suspected to be culprits of recurrent infections. Fluoroquinolones (FQs) are a class of antibiotic that facilitate DNA damage by stabilizing type II topoisomerases when they are in a complex with cleaved DNA. InEscherichia coli, DNA gyrase is the primary FQ target, and previous work has demonstrated that persisters are not spared from FQ-induced DNA damage. Since DNA gyrase cleavage sites (GCSs) largely govern the sites of DNA damage from FQ treatment, we hypothesized that GCS characteristics (e.g., number, strength, location) may influence persistence. To test this hypothesis, we measured genome-wide GCS distributions after treatment with a panel of FQs. We found drug-specific effects on the GCS distribution and discovered a strong negative correlation between the cumulative cleavage strength across the chromosome and FQ persister levels. Further experiments and analyses suggested that persistence was not governed by cleavage to individual sites, but rather survival was a function of the cumulative GCS distribution. Together, these findings demonstrate FQ-specific differences in GCS distribution that correlate with persister levels and suggest that FQs that better stabilize DNA gyrase in cleaved complexes with DNA will lead to lower levels of persistence.
The small non-coding RNA B11 regulates multiple facets ofMycobacterium abscessusvirulence
Authors: Bar-Oz Michal , Martini Maria Carla , Alonso Maria Natalia , Meir Michal , Lore Nicola Ivan , Miotto Paolo , Riva Camilla , Xiao Junpei , Masiello Catherine S. , Misiakou Maria-Anna , Sun Huaming , Moy Justin K. , Johansen Helle Krogh , Cirillo Daniela Maria , Shell Scarlet S. , Barkan Daniel
Published: October 2022

Mycobacterium abscessuscauses severe, virtually incurable disease in young patients with cystic fibrosis. Little is known inM. abscessusabout the roles of small regulatory RNAs (sRNA) in gene expression regulation. Here, we show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough colony morphology, increased pro-inflammatory signaling and virulence inin-vivoinfection models, and increased resistance to clinically relevant antibiotics. Examination of clinical isolate cohorts revealed some isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of two mutations found in clinical isolates. Approximate 230 genes were differentially expressed in the B11 deletion mutant. Strains with the clinical B11 mutations showed similar expression trends to the deletion mutant but of a lesser magnitude, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with a model of translational repression via base-pairing of B11 to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences in their RBS, consistent with B11 functioning as a negative regulator through direct binding of target mRNAs. Intriguingly, the genes upregulated in the absence of B11 included components of the ESX-4 secretion system, known to be critical forM. abscessusvirulence. One of these genes had a B11-complementary sequence at its RBS, and fusing the UTR of this gene to a reporter was sufficient to make the reporter suppressible by B11. Taken together, our data show that B11 may act as either a negative or positive regulator with pleiotropic effects on gene expression and clinically important phenotypes inM. abscessus. The presence of hypomorphic B11 mutations in clinical strains supports the idea that lower B11 activity may be advantageous forM. abscessusin some clinical contexts. To our knowledge, this is the first report of the role of an sRNA inM. abscessus.
Cortically-evoked movement in humans reflects history of prior executions, not plan for upcoming movement
Authors: Suleiman Abdelbaset , Solomonow-Avnon Deborah , Mawase Firas
Published: October 2022

Human motor behavior involves planning and execution, but we often perform some actions more frequently. Experimentally manipulating the probability distribution of a movement through intensive repetition toward a certain direction causes physiological bias toward that direction, which can be cortically-evoked by transcranial magnetic stimulation (TMS). However, because movement execution and plan histories were indistinguishable to date, to what extent TMS-evoked biases are due to more frequently executed movement, or recent planning of movement, is unclear. Here, we use novel experimentation to separately manipulate recent history of movement plans and execution, and probe the effects of this on physiological biases using TMS, and on default plan for goal-directed actions using a behavioral timed-response task. At baseline, physiological biases shared similar low-level kinematic properties (direction) to default plan for upcoming movement. However, when recent movement execution history was manipulated via thumb movement repetitions toward a specific direction, we found a significant effect on physiological biases, but not plan-based goal-directed movement. To further determine if physiological biases reflect ongoing motor planning, we biased movement plan history by increasing the likelihood of a specific target location, and found a significant effect on the default plan for goal-directed movements. However, TMS-evoked movement during the preparation period did not become biased toward the most frequent plan. This suggests that physiological biases provide a readout of the default state of M1 population activity in the movement-related space, but not ongoing neural activation in the planning-related space, potentially ruling out relevance of cortically-evoked physiological biases to voluntary movements.

Highlights

Stimulating the human motor cortex selectively evoked thumb movements toward a specific direction (physiological bias)

At baseline, these physiological biases shared similar low-level kinematics with default plan for voluntary goal-directed movements

Modulating the probability distribution of prior movements had a significant effect on physiological biases

However, biasing history of plans for upcoming movement toward a specific direction had no effect on evoked movement direction

During ongoing planning of voluntary movement, evoked movements maintained the distinct and robust baseline bias, regardless of change in probability distribution of history of upcoming plans
Origin, exposure routes and xenobiotics impart nanoplastics with toxicity on freshwater bivalves
Authors: Arini Adeline , Muller Sandra , Coma Véronique , Grau Etienne , Sandre Olivier , Baudrimont Magalie
Published: October 2022

Various environmental aged plastic wastes were collected in the environment and crushed to the nanometric scale to get a mix of nanoplastics (NPs) of different natures – mostly polyolefins (PE, PP), polyesters (PET) and polyvinylics (PS and PVC) – and undefined shapes (noted NP-L, mean hydrodynamic diameter at 285 nm). We aimed to test the toxicity of NPs of environmentally relevance on freshwater bivalves and compare results to commonly used styrenic NP-PS (206 nm).Corbicula flumineawere exposed to four different conditions with NPs (0.008 to 10 μg/L), for 21 days and kept under depuration conditions for 21 additional days: 1) waterborne exposure to NP-L, 2) diet borne exposure to NP-L, 3) synergic waterborne exposure to NP-L and AlCl3salt (1 mg/L), 4) waterborne exposure to NP-PS. Enzyme activities, gene expressions and behavioural tests were assessed. Trophic and synergic exposures with Al triggered more gene modulations than direct exposure to NP-L (namely on12s, atg12, gal, segpx, p53andache). NP-PS were also more harmful than NP-L, but only at high concentrations (10 μg/L). The effects of each treatment lasted until 7 days of depuration and no more gene inductions were observed after 21 days in clean water. Very few effects were shown on phenol-oxidase (PO), and glutathione S-transferase (GST). However, the inhibition of acetylcholinesterase (AchE) was concomitant with an increase of the filtration activity of bivalves exposed to NP-L (trophic route) and NP-PS, suggesting neurotoxic effects. By disturbing the ventilatory activity, NPs could have direct effects on xenobiotic accumulation and excretion capacities. The results point out how the structure, aging, exposure routes and additional xenobiotics can interact with adverse outcomes of NPs in bivalves. These findings underline the importance to consider naturally aged environmental NPs in ecotoxicological studies rather than synthetic latexes,i.e. crosslinked nanospheres prepared from virgin polymers.

This manuscript presents the first data of toxicity on freshwater organisms exposed to nanoplastics coming from natural sources. Whereas the majority of papers are dealing with non-environmentally representative plastics (mainly commercially-available polystyrene latexes) to evaluate nanoplastic effects on organisms, this study develops methods to prepare model nanoplastics from plastic wastes collected in rivers, and to assess their real adverse effects on aquatic organisms. Our results show significant differences between the inflammatory effects triggered by nanoplastics coming from natural sources and polystyrene nanobeads. This work suggests that the data published so far in the literature may underestimate the toxicity of nanoplastics spread into the environment on the aquatic organisms at the bottom of the food chain, which might consequently impart halieutic resources on the long term.
Transcriptomic analyses of differentially expressed genes, micro RNAs and long-non-coding RNAs in severe, symptomatic and asymptomatic malaria infection
Authors: Oboh Mary A. , Morenikeji Olanrewaju B. , Ojurongbe Olusola , Thomas Bolaji N.
Published: October 2022

Background

Malaria transmission and endemicity in Africa remains hugely disproportionate compared to the rest of the world. The complex life cycle ofP. falciparum(Pf) between the vertebrate human host and the anopheline vector results in differential expression of genes within and between hosts. An in-depth understanding ofPfinteraction with various human genes through regulatory elements will pave way for identification of additional tool in the arsenal for malaria control. Therefore, the regulatory elements (REs) involved in the over- or under-expression of various host immune genes hold a key to alternative control measures that can be applied for prompt diagnosis and treatment.

Methods

We carried out an RNAseq analysis to identify differentially expressed genes and network analysis of non-coding RNAs and target genes associated with immune response in individuals with different clinical outcomes. Raw RNAseq datasets, retrieved for analyses include individuals with severe (Gambia - 20), symptomatic (Burkina Faso - 15), asymptomatic (Mali - 16) malaria as well as uninfected controls (Tanzania - 20; Mali - 36).

Results

Of the total 107 datasets retrieved, we identified 5534 differentially expressed genes (DEGs) among disease and control groups. A peculiar pattern of DEGs was observed, with individuals presenting with severe/symptomatic malaria having the highest and most diverse upregulated genes, while a reverse phenomenon was recorded among the asymptomatic and uninfected individuals. In addition, we identified 141 differentially expressed (DE) miRNA, of which 78 and 63 were upregulated and downregulated respectively. Interactome analysis revealed a moderate interaction between DEGs and miRNAs. Of all identified miRNA, five were unique (hsa-mir-32, hsa-mir-25, hsa-mir-221, hsa-mir-29 and hsa-mir-148) because of their connectivity to several genes, including hsa-mir-221 connected to 16 genes. Six-hundred and eight DE lncRNA were identified, including SLC7A11, LINC01524 among the upregulated ones.

Conclusion

Our study provides important insights into host immune genes undergoing differential expression under different malaria conditions. It also identified unique miRNAs and lncRNAs that modify and/or regulate the expression of various immune genes. These regulatory elements, we surmise have the potential to serve a diagnostic purpose in discriminating between individuals with severe/symptomatic malaria and those with asymptomatic infection or uninfected.
Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing
Authors: Hsu Justine , Jarroux Julien , Joglekar Anoushka , Romero Juan P. , Nemec Corey , Reyes Daniel , Royall Ariel , He Yi , Belchikov Natan , Leo Kirby , Taylor Sarah E.B. , Tilgner Hagen U
Published: October 2022

Barcoding strategies are fundamental to droplet-based single-cell sequencing, and understanding the biases and caveats between approaches is essential. Here, we comprehensively evaluated both short and long reads of the cDNA obtained through the two marketed approaches from 10x Genomics, the “3’ assay” and the “5’ assay”, which attach barcodes at different ends of the mRNA molecule. Although the barcode detection, cell-type identification, and gene expression profile are similar in both assays, the 5’ assay captured more exonic molecules and fewer intronic molecules compared to the 3’ assay. We found that 13.7% of genes sequenced have longer average read lengths and are more complete (spanning both polyA-site and TSS) in the long reads from the 5’ assay compared to the 3’ assay. These genes are characterized by long average transcript length, high intron number, and low expression overall. Despite these differences, cell-type-specific isoform profiles observed from the two assays remain highly correlated. This study provides a benchmark for choosing the single-cell assay for the intended research question, and insights regarding platform-specific biases to be mindful of when analyzing data, particularly across samples and technologies.
Wnt signaling regulates passive cell competition in the retina by inducing differential cell adhesion
Authors: Min Xuanyu , Mao Yingyu , Wu Hao , Bock Josh , Tao Chenqi , Zhang Xin
Published: October 2022

Self-assortation of progenitor cells during development is essential for establishment of distinct tissue identity. This is exemplified in the eye, where the early optic cup is divided into the neural retina (NR) in the center and the ciliary margin (CM) in the periphery. Previous studies have demonstrated that Wnt signaling is required for specification of the CM, but here we show that genetic ablation of Wnt signaling mediator β-catenin in the peripheral optic cup failed to prevent the formation of the CM-derived ciliary body and iris in adult animals. Mosaic analysis revealed that this was only partially due to loss of adherens junctions among β-catenin deficient cells, which were preferentially excluded from the CM. Even in β-catenin mutant cells that can maintain adherens junctions, their inability to mediate Wnt signaling resulted in a change from P-cadherin to N-cadherin expression. We showed that this cadherin switch was sufficient to segregate otherwise identical cells into separate clusters. As a result, the ciliary body and iris were still formed after inactivation of Wnt signaling in the peripheral retina. These results showed that the dual functions of β-catenin in adherens junction and Wnt signaling are required for the passive cell competition to constitute retinal compartments.
Long-Range Hopping Conductivity in Proteins
Authors: Krishnan Siddharth , Aksimentiev Aleksei , Lindsay Stuart , Matyushov Dmitry
Published: October 2022

Single molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1V. In the conventional fast transport scenario where the free energy barrier is zero, the hopping rate is determined by the reorganization energy of approximately 0.8 eV, which sets the time scale of a single hopping event to at least 1μs. Furthermore, the Fermi energies of metal electrodes used in experiments are far-removed from the equilibrium redox states of the aromatic residues of the protein, which should additionally slow down the electron transfer. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transfer. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the nonergodic sampling of molecular configurations by the protein results in reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ~ 0.2 eV, which is small enough to enable long-range hopping. Using the MD values of the reorganization energies we calculate a current decay with distance that is in agreement with experiment.

Significance

Electron transfer is fundamental to biology, facilitating a range of metabolic processes and efficient energy conversion. Conventionally, electron transfer through proteins is thought to occur via a chain of metal or organic co-factors connecting one side of the protein to another. Recent experiments, however, show that proteins lacking any co-factors can nonetheless transport electrons with high efficiency if properly connected to metal electrodes. This study provides a theoretical model of such cofactor-less transfer, showing that transient occupation of non-equilibrium states of the protein’s aromatic residues reduces the barrier to electron hopping, facilitating long range and rapid transport. Our results widen the pool of proteins potentially involved in biological electron transport and provide theoretical underpinning to design of protein molecular electronics.
Iterative remodeling of the mouse uterus requires Hedgehog signaling
Authors: Roberson Elle C. , Tran Ngan Kim , Godambe Anushka N. , Rust Trinity , Nguimtsop Michelle , Mark Harrison , Fitch Rebecca D. , Wallingford John B.
Published: October 2022

The adult uterus regenerates in the human during the menstrual cycle, and remodels in the mouse during the estrous cycle. Decades of work has demonstrated that this process is controlled by cycling steroid hormones, estrogen and progesterone. However, downstream signaling pathways that link hormonal action to this regeneration and remodeling are yet to be identified in the cycling uterus. We set out to identify these pathways, with the overarching hypothesis that developmental signaling pathways are redeployed in the adult uterus to control remodeling in the mouse. We were surprised to find that the majority of Hedgehog signaling components were transcriptionally co-regulated throughout the estrous cycle. To test the role of Hh signaling in cyclical uterine remodeling, we conditionally knocked out the major activator of the pathway,smoothened(Smo) using theprogesterone receptor cre(PR-Cre). In the absence of Hh signaling, the uterus no longer remodels throughout the estrous cycle. We also show that the smooth muscle fibers of the uterus are significantly larger in the conditional knockouts compared to the controls suggesting hypertrophy of the smooth muscle. Our findings support the possibility that this smooth muscle homeostasis may underlie important aspects of uterine function such as contractility during late-stage pregnancy or the development of uterine smooth muscle tumors.
Convection-enhanced diffusion and directed withdrawal of methylene blue in agarose hydrogel using finite element analyses
Authors: Shaw C. , Hossain K. , Riviere-Cazaux Cecile , Burns Terry , Khan M. Rashed
Published: October 2022

Precision drug delivery for optimized therapeutic targeting requires knowledge of momentum transport and molecular diffusion of molecules within the patient’s interstitial tissue, especially for tumor treatment within the brain. Dispersion in the interstitial space is impacted by delivery method, tissue material properties, individual-specific fluid flow, and particle size of the input solute. Knowledge of a drug’s dispersion allows for optimizing solute delivery, concentration, and flow rates to maximize drug distribution and biomarker recovery. For delivering drugs, increased knowledge of drug location after delivery can improve therapeutic treatment by optimizing the dosing of healthy and unhealthy tissue. Finite element methods (FEM) tools, such as COMSOL Multiphysics, can simulate molecular distribution inside-individual specific shapes and porous material properties. Furthermore, an additional unmet need is delivery methods that can be adjusted to manipulate diffusion regions through tissue via techniques such as directed flow. This would be especially valuable in targeted drug delivery within tumors to increase the cancerous surface area covered while limiting damage to surrounding tissues. In this project, the directed flow was induced by perfusing the injected solution at an input probe while withdrawing fluid at an output probe, enabling targeted flow through the desired region. FEM computation faithfully replicated these conditions and could be used to determine the effective concentrations perfused over the region of interest. We leveraged COMSOL Multiphysics to perform a computational study simulating convection-enhanced delivery (CED) with an output probe pulling the concentration profile over the region of interest. This simulation system can be applied to therapeutics targeting, vaccine subcutaneous injection, and waste and media diffusion in tissue engineering.
Stereochemistry Determines Immune Cellular Responses to Polylactide Implants
Authors: Maduka Chima V. , Alhaj Mohammed , Ural Evran , Kuhnert Maxwell M. , Habeeb Oluwatosin M. , Schilmiller Anthony L. , Hankenson Kurt D. , Goodman Stuart B. , Narayan Ramani , Contag Christopher H.
Published: October 2022

Repeating L- and D-chiral configurations determine polylactide (PLA) stereochemistry which affects its thermal and physicochemical properties, including degradation profiles. Clinically, degradation of implanted PLA biomaterials promotes prolonged inflammation and excessive fibrosis, but the role of PLA stereochemistry is unclear. Additionally, although PLA of varied stereochemistries cause differential immune responses in-vivo, this observation has yet to be effectively modeled in-vitro. A bioenergetic model was applied to study immune cellular responses to PLA containing > 99% L-lactide (PLLA), > 99% D-lactide (PDLA) and a 50/50 melt-blend of PLLA and PDLA (stereocomplex PLA). Stereocomplex PLA breakdown products increased IL-1β, TNF-α and IL-6 protein levels but not MCP-1. Expression of these proinflammatory cytokines is mechanistically driven by increases in glycolysis in primary macrophages. In contrast, PLLA and PDLA degradation products selectively increase MCP-1 protein expression. Whereas both oxidative phosphorylation and glycolysis are increased with PDLA, only oxidative phosphorylation is increased with PLLA. For each biomaterial, glycolytic inhibition reduces proinflammatory cytokines and markedly increases anti-inflammatory (IL-10) protein levels; differential metabolic changes in fibroblasts were observed. These findings provide mechanistic explanations for the diverse immune responses to PLA of different stereochemistries, and underscore the pivotal role of immunometabolism on the biocompatibility of biomaterials applied in medicine.
Identifying Neuropsychiatric Disorder Subtypes and Subtype-dependent Variation in Diagnostic Deep Learning Classifier Performance
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D.
Published: October 2022

Clinicians and developers of deep learning-based neuroimaging clinical decision support systems (CDSS) need to know whether those systems will perform well for specific individuals. However, relatively few methods provide this capability. Identifying neuropsychiatric disorder subtypes for which CDSS may have varying performance could offer a solution. Dynamic functional network connectivity (dFNC) is often used to study disorders and develop neuroimaging classifiers. Unfortunately, few studies have identified neurological disorder subtypes using dFNC. In this study, we present a novel approach with which we identify 4 states of dFNC activity and 4 schizophrenia subtypes based on their time spent in each state. We also show how the performance of an explainable diagnostic deep learning classifier is subtype-dependent. We lastly examine how the dFNC features used by the classifier vary across subtypes. Our study provides a novel approach for subtyping disorders that (1) has implications for future scientific studies and (2) could lead to more reliable CDSS.
Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome ofCannabis sativa
Authors: Suwanchaikasem Pipob , Nie Shuai , Idnurm Alexander , Selby-Pham Jamie , Walker Robert , Boughton Berin A.
Published: October 2022

Fungal pathogens pose a major threat toCannabis sativaproduction, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects onC. sativawill advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in thein vitroRoot-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. No significant effects on plant defense were observed upon chitin treatment. These results indicate that colloidal chitosan significantly promoted production and secretion of plant defense proteins inC. sativaroot system and could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.

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Chitosan induces defense protein productions and secretions in the root tissues and exudates ofC. sativa, offering a potential pathway to enhance plant resistance against fungal attack.
Salt-inducible kinase inhibition promotes the adipocyte thermogenic program and adipose tissue browning
Authors: Shi Fubiao , de Fatima Silva Flaviane , Liu Dianxin , Patel Hari U , Xu Jonathan , Zhang Wei , Turk Clara , Kruger Marcus , Collins Sheila
Published: October 2022

Objective: Norepinephrine stimulates the adipose tissue thermogenic program through a β-adrenergic receptor (βAR) - cyclic adenosine monophosphate (cAMP) - protein kinase A (PKA) signaling cascade. We discovered that a noncanonical activation of the mechanistic target of rapamycin complex 1 (mTORC1) by PKA is required for the βAR-stimulation of adipose tissue browning. However, the downstream events triggered by PKA–phosphorylated mTORC1 activation that drive this thermogenic response are not well understood. Methods: We used a proteomic approach of Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) to characterize the global protein phosphorylation profile in brown adipocytes treated with the βAR agonist. We identified salt-inducible kinase 3 (SIK3) as a candidate mTORC1 substrate and further tested the effect of SIK3 deficiency or SIK inhibition on the thermogenic gene expression program in brown adipocytes and in mouse adipose tissue. Results: SIK3 interacts with RAPTOR, the defining component of the mTORC1 complex, and is phosphorylated at Ser884 in a rapamycin-sensitive manner. Pharmacological SIK inhibition by a pan-SIK inhibitor (HG-9-91-01) in brown adipocytes increases basalUcp1gene expression and restores its expression upon blockade of either mTORC1 or PKA. Short-hairpin RNA (shRNA) knockdown ofUcp1augments, while overexpression of SIK3 suppresses,Ucp1gene expression in brown adipocytes. The regulatory PKA phosphorylation domain of SIK3 is essential for its inhibition. CRISPR-mediatedUcp1deletion in brown adipocytes increases type IIa histone deacetylase (HDAC) activity and enhances the expression of genes involved in thermogenesis such asUcp1,Pgc1α, and mitochondrial OXPHOS complex protein. We further show that HDAC4 interacts with PGC1α after βAR stimulation and reduces lysine acetylation in PGC1α. Finally, a SIK inhibitor well-tolerated in vivo (YKL-05-099) can stimulate the expression of thermogenesis-related genes and browning of mouse subcutaneous adipose tissue. Conclusions: Taken together, our data reveal that SIK3, with the possible contribution of other SIKs, functions as a phosphorylation switch for β-adrenergic activation to drive the adipose tissue thermogenic program and indicates that more work to understand the role of the SIKs is warranted. Our findings also suggest that maneuvers targeting SIKs could be beneficial for obesity and related cardiometabolic disease.
An Inducible T7 Polymerase System for High-Level Protein Expression in Diverse Gram-Negative Bacteria
Authors: Greenwich Jennifer L. , Alakavuklar Melene A. , Fuqua Clay
Published: October 2022

A broad host range (BHR) inducible T7 RNA Polymerase system was developed, enabling induction with IPTG, similar to theEscherichia colistrain BL21(DE3), but now applicable in a wide range of bacteria. This allows for high protein yields and purification from diverse gram-negative bacteria including the native host.
Acellular Cartilage-Bone Allografts Restore Structure, Mechanics, and Surface Properties In Vivo, but Limit Recellularization and Integrative Repair
Authors: Barthold Jeanne E. , Cai Luyao , McCreery Kaitlin P. , Fischenich Kristine , Eckstein Kevin , Ferguson Virginia , Emery Nancy , Breur Gert , Neu Corey P.
Published: October 2022

The repair of articular cartilage after damage is challenging, and clinical interventions to promote regeneration remain elusive. The most effective treatment for cartilage defects utilizes viable osteochondral allografts from young donors, but unfortunately suffers from severe source limitations and short storage time. Decellularized tissue offers the potential to utilize native tissue structure and composition while also overcoming source limitations, but the long-term efficacy of acellular allografts is unknown. Here, we show that acellular osteochondral allografts improve functional and integrative cartilage repair in defect regions after 6 months in a preclinical (sheep) animal model. Functional measures of intratissue strain and structure assessed by MRI demonstrate similar biomechanical performance between implants and native cartilage. Compared to native tissue, the structure, composition, and tribology of acellular allografts conserve surface roughness and lubrication, native cartilage material properties under compression and relaxation, and compositional ratios of collagen:glycosaminoglycan and collagen:phosphate. However, while high cellularity was observed in the integration zones between native cartilage and acellular allografts, recellularization throughout the chondral implant was largely lacking, potentially limiting long-term cellular maintenance in the graft and repair success. Our results advance a suite of joint-to-cellular functional assays, demonstrate the biomechanical efficacy of acellular allografts for at least six monthsin vivo, and suggest that long-term implant success may suffer from a lack of cell migration into the dense decellularized chondral tissue.
Phase separation as higher-order catalyst
Authors: Huang Kai , Quan Xuebo , Qin Shiyi
Published: October 2022

The long-distance communication between multiple cis-regulatory elements (CREs), the self-limiting size and lifetime of regulatory condensates, are two puzzling phenomena in biology. To reconcile these puzzles, we introduce the concept of higher-order catalysis into chromatin-mediated reactions. Essentially, multi-way contact between the CREs defines a transition state that is required for the downstream cascade of chemical reactions. The entropic penalty of chromatin reorganization sets a high activation barrier to enter this transition state. Phase separation of trans-acting agents induced by the CREs reduces this barrier and stabilizes the transition state via forming a regulatory condensate. The downstream reaction then pays back energy to dissolve the condensate and resets the agents to a metastable single-phase state. Accelerating the reactions without consuming agents or changing their state, the cycled phase transitions construct a higher-order catalyst or super-enzyme that is beyond the form of a single molecule. We discuss how chromatin employs such super-enzymes to catalyze higher-order reactions mediated by itself.