bluuebunny/crossref_metadata_2025 huggingface dataset:
Homeostatic synaptic normalization optimizes learning in network models of neural population codes
Authors: Mayzel Jonathan , Schneidman Elad
Published: March 2023

Studying and understanding the code of large neural populations hinge on accurate statistical models of population activity. A novel class of models, based on learning to weigh sparse nonlinear Random Projections (RP) of the population, has demonstrated high accuracy, efficiency, and scalability. Importantly, these RP models have a clear and biologically-plausible implementation as shallow neural networks. We present a new class of RP models that are learned by optimizing the randomly selected sparse projections themselves. This ``reshaping" of projections is akin to changing synaptic connections in just one layer of the corresponding neural circuit model. We show that Reshaped RP models are more accurate and efficient than the standard RP models in recapitulating the code of tens of cortical neurons from behaving monkeys. Incorporating more biological features and utilizing synaptic normalization in the learning process, results in accurate models that are more efficient. Remarkably, these models exhibit homeostasis in firing rates and total synaptic weights of projection neurons. We further show that these sparse homeostatic reshaped RP models outperform fully connected neural network models. Thus, our new scalable, efficient, and highly accurate population code models are not only biologically-plausible but are actually optimized due to their biological features. These findings suggest a dual functional role of synaptic normalization in neural circuits: maintaining spiking and synaptic homeostasis while concurrently optimizing network performance and efficiency in encoding information and learning.
Closely relatedBacteroidesof the murine intestinal microbiota affect each other’s growth positively or negatively
Authors: Fokt Hanna , Sakalyte Gabija , Unni Rahul , Abukhalaf Mohammad , Cassidy Liam , Marinos Georgios , Godfroid Maxime , Kinfu Birhanu M , Schmitz Ruth A , Kaleta Christoph , Tholey Andreas , Baines John F , Dagan Tal , Unterweger Daniel
Published: March 2023

The mammalian intestine is a unique ecosystem for thousands of bacterial species and strains. How naturally coexisting bacteria of the microbiota interact with each other is not yet fully understood. Here, we isolated formerly coexisting, closely related strains of the genusBacteroidesfrom the intestines of healthy, wild-derived mice. The effect of one strain on another strain’s growth was tested in 169 pairsin vitro. We find a vast diversity of growth promoting and growth inhibiting activities. A strong positive effect was observed between two strains with differing metabolisms. Growth inhibition among a subset of strains was associated with the known bacterial toxin bacteroidetocin B. Across all strains, we observed growth promotion more often than growth inhibition. The effects were independent of two strains belonging to the same or different species. In some cases, one species differed in its effect on another according to host origin. These findings on obligate host-associated bacteria demonstrate that closely related and naturally coexisting strains have the potential to affect each other’s growth positively or negatively. These results have implications for our basic understanding of host-associated microbes and the design of synthetic microbial communities.
In vivoreprogramming of wound-resident cells generates skin with hair
Authors: Moriwaki Yuta , Qi Shen , Okada Hiroyuki , Zening Du , Suga Shogo , Kato Motoi , Numahata Takao , Li Kexin , Kanayama Koji , Okazaki Mutsumi , Hirabayashi Yusuke , Belmonte Juan Carlos Izpisua , Hojo Hironori , Kurita Masakazu
Published: March 2023

Summary Paragraph

Mammalian skin appendages, such as hair follicles and sweat glands, are complex mini-organs formed during skin development1, 2. As wounds heal, the resulting scar tissue lacks skin appendages. The clinical regeneration of skin appendages is an ongoing challenge3, 4. Skin epithelial tissues have been regeneratedin vivoby cellular reprogramming5, 6, but thede novogeneration of skin appendages has not previously been achieved. Here, we show that transplantation of a type of epithelial cell and two types of mesenchymal cells, reprogrammed from adult mouse subcutaneous mesenchymal cells to mimic developing skin cells, resulted in the generation of skin-appendage-like structures. Furthermore, with the development of a new AAV serotype,in vivoreprogramming of wound-resident cells with the same reprogramming factors generates skin withde novoappendages in adult mice. These findings may provide new therapeutic avenues for skin regeneration and frequent aging-associated skin appendage disorders, such as hair loss and dry skin, and may extend to other tissues and organs. This study also provides the potential forde novogeneration of complex organsin vivo.
Beyond the Genetic Code:A Tissue Code?
Authors: Boman Bruce M. , Dinh Thien-Nam , Decker Keith , Emerick Brooks , Modarai Shirin , Opdenaker Lynn , Fields Jeremy Z. , Raymond Christopher , Schleiniger Gilberto
Published: March 2023

The genetic code determines how the precise amino acid sequence of proteins is specified by genomic information in cells. But what specifies the precise histologic organization of cells in plant and animal tissues is unclear. We now hypothesize that another code, thetissue code, exists at an even higher level of complexity which determines how tissue organization is dynamically maintained. Accordingly, we modeled spatial and temporal asymmetries of cell division and established that five simple mathematical laws (“the tissue code”) convey a set of biological rules that maintain the specific organization and continuous self-renewal dynamics of cells in tissues. These laws might even help us understand wound healing, and how tissue disorganization leads to birth defects and tissue pathology like cancer.
Phylogenetic analysis shows canine distemper virus outbreak in stray dogs possibly occurs through spillover from wild carnivore reservoirs
Authors: Manandhar Prajwol , Napit Rajindra , Pradhan Saman M , Rajbhandari Pragun G , Moravek Jessie A , Joshi Pranav R , Shrestha Rima D , Karmacharya Dibesh
Published: March 2023

Canine distemper is a highly contagious, often fatal disease caused by canine distemper virus (CDV) in domestic dogs and wild carnivores. The virus has caused mass epidemics in wild carnivores of high conservation value such as tigers, lions and leopards in both wild and captivity. Hence, understanding and managing CDV outbreaks is particularly important in Nepal, which is home to many species of threatened wild carnivores including tigers, leopards, snow leopards, dholes and wolves, as well as a large population of stray dogs. Previous studies have suggested that CDV may pose a threat to wild carnivores, but there has not been any studies characterizing the genetic strains of the virus circulating in Nepal’s carnivores. We collected invasive and non-invasive biological samples from stray dogs in Kathmandu Valley and genetically characterized the strains of CDV in the dogs to belong to Asia-5 lineage by using phylogenetic analysis. The same lineage also contained CDV strains isolated from dogs, civets, red panda and lions in India. Based on our phylogenetic analysis, we think it is likely that in Nepal CDV is maintained through sylvatic cycle among small carnivore guilds allowing the recurring spillovers and outbreaks among free-ranging stray dogs and possibly large carnivores. It is crucial to prevent the virus transmission from reservoir hosts to other species, especially threatened populations of large carnivores in Nepal. Hence, we recommend for regular surveillance of CDV targeting small wild carnivores as well as vaccination programmes to control the disease spillover in stray dogs.
IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events
Authors: Fujiwara Rina , Zhai Si-Nan , Liang Dongming , Tracey Matthew , Ma Xu-Kai , Shah Aayushi P. , Fields Christopher J. , Mendoza-Figueroa María Saraí , Meline Michele C. , Tatomer Deirdre C. , Yang Li , Wilusz Jeremy E.
Published: March 2023

The metazoan-specific Integrator complex catalyzes 3’ end processing of small nuclear RNAs (snRNAs) as well as premature transcription termination events that attenuate expression of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are always required for complex function. Here, we show that IntS6 (Integrator subunit 6) over-expression is sufficient to block Integrator function at a subset ofDrosophilaprotein-coding genes, while having no effect on snRNA processing or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits from the rest of the Integrator complex and thus the only loci affected are those where the phosphatase module is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not associate with Integrator, are also sufficient to inhibit Integrator function at select loci. Altogether, these results show that the phosphatase module is critical and limiting at only a subset of Integrator regulated genes and point to recruitment of PP2A via IntS6 as a tunable step that can be used to modulate transcription termination efficiency.
MAUDGAN: Motion Artifact Unsupervised Disentanglement Generative Adversarial Network of Multicenter MRI Data with Different Brain tumors
Authors: Safari Mojtaba , Fatemi Ali , Archambault Louis
Published: March 2023

Purpose

This study proposed a novel retrospective motion reduction method named motion artifact unsupervised disentanglement generative adversarial network (MAUDGAN) that reduces the motion artifacts from brain images with tumors and metastases. The MAUDGAN was trained using a mutlimodal multicenter 3D T1-Gd and T2-fluid attenuated inversion recovery MRI images.

Approach

The motion artifact with different artifact levels were simulated ink-space for the 3D T1-Gd MRI images. The MAUDGAN consisted of two generators, two discriminators and two feature extractor networks constructed using the residual blocks. The generators map the images from content space to artifact space and vice-versa. On the other hand, the discriminators attempted to discriminate the content codes to learn the motion-free and motion-corrupted content spaces.

Results

We compared the MAUDGAN with the CycleGAN and Pix2pix-GAN. Qualitatively, the MAUDGAN could remove the motion with the highest level of soft-tissue contrasts without adding spatial and frequency distortions. Quantitatively, we reported six metrics including normalized mean squared error (NMSE), structural similarity index (SSIM), multi-scale structural similarity index (MS-SSIM), peak signal-to-noise ratio (PSNR), visual information fidelity (VIF), and multi-scale gradient magnitude similarity deviation (MS-GMSD). The MAUDGAN got the lowest NMSE and MS-GMSD. On average, the proposed MAUDGAN reconstructed motion-free images with the highest SSIM, PSNR, and VIF values and comparable MS-SSIM values.

Conclusions

The MAUDGAN can disentangle motion artifacts from the 3D T1-Gd dataset under a multimodal framework. The motion reduction will improve automatic and manual post-processing algorithms including auto-segmentations, registrations, and contouring for guided therapies such as radiotherapy and surgery.
Relapse timing is associated with distinct evolutionary dynamics in DLBCL
Authors: Hilton Laura K. , Ngu Henry S. , Collinge Brett , Dreval Kostiantyn , Ben-Neriah Susana , Rushton Christopher K. , Wong Jasper C.H. , Cruz Manuela , Roth Andrew , Boyle Merrill , Meissner Barbara , Slack Graham W. , Farinha Pedro , Craig Jeffrey W. , Gerrie Alina S. , Freeman Ciara L. , Villa Diego , Crump Michael , Shepherd Lois , Hay Annette E. , Kuruvilla John , Savage Kerry J. , Kridel Robert , Karsan Aly , Marra Marco A. , Sehn Laurie H. , Steidl Christian , Morin Ryan D. , Scott David W.
Published: March 2023

Diffuse large B-cell lymphoma (DLBCL) is cured in over 60% of patients, but outcomes are poor for patients with relapsed or refractory disease (rrDLBCL). Here, we performed whole genome/exome sequencing (WGS/WES) on tumors from 73 serially-biopsied patients with rrDLBCL. Based on the observation that outcomes to salvage therapy/autologous stem cell transplantation are related to time-to-relapse, we stratified patients into groups according to relapse timing to explore the relationship to genetic divergence and sensitivity to salvage immunochemotherapy. The degree of mutational divergence increased with time between biopsies, yet tumor pairs were mostly concordant for cell-of-origin, oncogene rearrangement status and genetics-based subgroup. In patients with highly divergent tumors, several genes acquired exclusive mutations independently in each tumor, which, along with concordance of genetics-based subgroups, suggests that the earliest mutations in a shared precursor cell constrain tumor evolution. These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease.
Trends in voice characteristics in patients with heart failure (VENTURE) in Switzerland: Protocol for a longitudinal observational pilot study
Authors: Wu Fan , Nägele Matthias , Cleres David , Haider Thomas , Fleisch Elgar , Ruschitzka Frank , Flammer Andreas , Barata Filipe
Published: March 2023

Introduction

Heart Failure (HF) is a major health and economic issue worldwide. HF-related expenses are largely driven by hospital admissions and re-admissions, many of which are potentially preventable. Current self-management programs, however, have failed to reduce hospital admissions. This may be explained by their low predictive power for decompensation and high adherence requirements. Slight alterations in the voice profile may allow to detect decompensation in HF patients at an earlier stage and reduce hospitalizations. This pilot study investigates the potential of voice as a digital biomarker to predict health status deterioration in HF patients.

Methods and analysis

In a two-month longitudinal observational study, we collect voice samples and HF-related quality-of-life questionnaires from 35 stable HF patients. Patients use our developed study application installed on a tablet at home during the study period. From the collected data, we use signal processing to extract voice characteristics from the audio samples and associate them with the answers to the questionnaire data. The primary outcome will be the correlation between voice characteristics and HF-related quality-of-life health status.

Ethics and dissemination

The study was reviewed and approved by the Cantonal Ethics Committee Zurich (BASEC ID:2022-00912). Results will be published in medical and technical peer-reviewed journals.
White matter connectivity in resilience in a general population sample of 12,516 individuals
Authors: de Vries Baukje S. , van der Wee Nic J.A. , van der Werff Steven J.A.
Published: March 2023

Objective

Neurobiological correlates of resilience to stress or trauma have not been investigated extensively. Studies on white matter connectivity in resilience, in particular, have been few and far between. This explorative study included 12,516 participants from the UK Biobank to investigate white matter connectivity in resilience in 13 selected regions of interest (ROIs).

Methods

The data for this cross-sectional cohort study were retrieved from UK Biobank, a large-scale biomedical database and research resource. The study included 40-69-year-old participants divided into three groups: a trauma-exposed, healthy (resilient) group, a trauma-exposed, mentally ill (vulnerable) group and a nonexposed, healthy (control) group. The primary outcome measures consisted of mean fractional anisotropy values in the following ROIs: cingulate gyrus, cingulum hippocampus, superior fronto-occipital fasciculus, uncinate fasciculus, corpus callosum body, genu, splenium, and tapetum. Group differences in fractional anisotropy were assessed using a one-way ANOVA.

Results

This study did not find correlates of resilience in the investigated ROIs.

Conclusions

The results indicate that there is no association between resilience and white matter connectivity in the selected ROIs in this large population sample, which is in contrast with previous studies on morphometric and functional correlates of resilience. To corroborate this finding, the authors recommend collection of longitudinal data and utilization of voxelwise analysis, if possible, to improve sensitivity. The authors also suggest a whole-brain analysis in a similar study population to investigate other white matter tracts that might be implicated in resilience.
Can the ChatGPT and other Large Language Models with internet-connected database solve the questions and concerns of patient with prostate cancer?
Authors: Zhu Lingxuan , Mou Weiming , Chen Rui
Published: March 2023

Large language models (LLMs), such as ChatGPT, have shown impressive natural language processing capabilities in various fields, including medicine. However, the answers provided by these models may sometimes be incorrect, and they may not have access to the latest data. In this study, we aimed to evaluate the performance of five state-of-the-art LLMs in providing correct and comprehensive information on common questions raised by prostate cancer patients. We also examined whether LLMs with internet-connected databases could provide more up-to-date information than ChatGPT. We designed a set of 22 questions covering various aspects of prostate cancer and evaluated the accuracy, comprehensiveness, patient readability, and inclusion of humanistic care in the answers provided by each model. Our findings suggest that although the performance of different LLMs varied, these LLMs could provide accurate basic knowledge and have the ability to analyze specific situations to a certain extent. We also found that the overall performance of the LLM model with internet-connected dataset was not superior to ChatGPT, and the paid version of ChatGPT did not show superiority over the free version. Our study highlights the potential of LLMs in bridging the gap between patients and healthcare providers. Current LLMs have the potential to be applied for patient education and consultation, providing patient-friendly information. Shared decision-making with the doctors and patients could be achieved easier. We believed that with the rapid development of AI technology, LLMs have unlimited potential.
Biobank-scale methods and projections for sparse polygenic prediction from machine learning
Authors: Raben Timothy G. , Lello Louis , Widen Erik , Hsu Stephen D.H.
Published: March 2023

In this paper we characterize the performance of linear models trained via widely-usedsparsemachine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and Correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of 0.63(0.02)and for height a correlation of 0.648(0.009)for a Taiwanese population. This is above the measured values of 0.61(0.01)and 0.631(0.008), respectively, for UK Biobank trained predictors applied to a European population.
Predictors of mortality among post-COVID-19 discharged patients in Northern India
Authors: Arjun  , Jatteppanavar Basavaraj , Panda Prasan Kumar , Dhanger Pathik
Published: March 2023

Background

The one-year post-discharge all-cause mortality rate of COVID-19 disease is 7.87 % with the majority of patients’ readmission and mortality occurring within the first 30 days post-discharge.

Objective

Understanding predictors of mortality will help in prioritising patient care and preventive approaches.

Methods

Ours a single-centre unmatched case control study at a tertiary care centre in northern India, conducted from April 2020 to September 2022. The data was extracted retrospectively from the electronic hospital medical records of patients and by trained physicians using standardised data extraction sheet.

Results

A total of 184 patients were enrolled with 92 cases and 92 controls. The mean age of patients was 49.3 ± 17.53 years. The mortality group had a higher mean age (53.24 ± 18.53 yrs) as compared to the control group (45.37 ± 15.58 yrs) [p – 0.002]. Bivariate analysis revealed a significant difference in the two groups with respect to O2 saturation at admission [Case - 91.12 ± 12.49 %, control - 95.46 ± 5.01 %, p – 0.003); Maximum O2 flow rate [L/min] (Case – 11.01 ± 22.2, Control – 6.41 ± 13.31, P – 0.04); ICU need (p – 0.005), Cancer (p – 0.001), O2 need at discharge (p – 0.001) and AKI (p – 0.007). On multiple regression analysis, Cancer (aOR-2.469; 95% CI-1.183-5.150, p-0.016), ICU admission (aOR- 2.446; 95% CI-1.212-4.938, p- 0.013), Oxygen at discharge (aOR- 2.340; 95% CI-0.971-5.640, p-0.0586) and Acute kidney injury (aOR- 5.6; 95% CI-2.351-13.370, p-0.00) only found to be significant.

Conclusion

Oxygen requirement at discharge (2.3 times), Malignancy (2.4 times), ICU admission (2.4 times), and Acute Kidney Injury (5.6 times) were risks of death among COVID-19-recovered patients, post discharge. The presence of these variables would warrant a close follow up for these patients in order to decrease post COVID mortality.
Gene Expression Profiling Unveils the Temporal Dynamics of CIGB-300-Regulated Transcriptome in AML Cells
Authors: Vázquez-Blomquist Dania , Ramón Ailyn C. , Rosales Mauro , Pérez George V. , Rosales Ailenis , Palenzuela Daniel , Perera Yasser , Perea Silvio E.
Published: March 2023

Protein kinase CK2 activity is implicated in the pathogenesis of various hematological malignancies like Acute Myeloid Leukemia (AML) that remains challenging concerning treatment. Consequently, here we used Illumina HT-12 microarray gene RNA expression profiling to study the molecular events that might support the anti-leukemic effect of CIGB-300 peptide which targets both CK2 substrates and the CK2α catalytic subunits on HL-60 and OCI-AML3 cell lines. As a result, 185 and 812 genes appeared significantly modulated in HL-60 cells at 30 min and 3 h of incubation with CIGB-300 for p< 0.01 and FC>│1.5│, respectively; while 222 and 332 genes appeared modulated in OCI-AML3 cells. Importantly, functional enrichment analysis evidenced that genes and transcription factors related to apoptosis, cell cycle, leukocyte differentiation, signaling by cytokines/interleukins, and NF-kB, TNF signaling pathways were significantly represented in AML cells transcriptomic profiles. The influence of CIGB-300 on these biological processes and pathways is dependent on the cellular background, in first place, and treatment duration. Of note, the impact of the peptide on NF-kB signaling was corroborated by the quantification of selected NF-kB target genes, as well as the measurement of p50 binding activity and soluble TNF-α induction. Quantification of CSF1/M-CSF and CDKN1A/P21 by PCR supports peptide effects on differentiation and cell cycle. Overall, here we explore for the first time the temporal dynamics of the gene expression profile regulated by CIGB-300 and provide fresh molecular clues concerning the antineoplastic effect of CIGB-300 in two relevant AML backgrounds.
AVibrioT6SS-mediated lethality in a marine animal model
Authors: Cohen Hadar , Gerlic Motti , Salomon Dor
Published: March 2023

Bacteria belonging to the genusVibrioinclude many known and emerging pathogens. Horizontal gene transfer of pathogenicity islands is a major contributor to the emergence of new pathogenicVibriostrains. In the current report, we use the brine shrimpArtemia salinaas a model to show that the marine bacteriumVibrio proteolyticususes a mobile type VI secretion system, T6SS3, to intoxicate eukaryotic hosts. Two T6SS3 effectors, which were previously shown to induce inflammasome-mediated pyroptotic cell death in mammalian phagocytic cells, contribute to this toxicity. Furthermore, we find a novel, widespread T6SS3 effector that also contributes to the lethality mediated by this system againstArtemia salina. Therefore, our results reveal a T6SS that is shared among diverse vibrios and mediates host lethality, indicating that it can lead to the emergence of new pathogenic strains.
Reprogramming an RNA-guided archaeal TnpB endonuclease for genome editing
Authors: Xu Ying , Liu Tao , Wang Jing , Xiong Binyang , Liu Ling , Peng Nan
Published: March 2023

RNA-guided endonucleases developed for genome editing have been identified exclusively from bacteria until now. Recently, the RNA-guided TnpB endonucleases encoded by bacterial IS200/IS605 and IS607 families have been reprogrammed for genome editing. In fact, these insertion sequence families are also widely distributed in archaea. However, whether archaea-derived TnpB could be used for genome editing remains unclear. Here, we found that TnpB derived fromSulfolobus islandicusREY15A (SisTnpB1) was an Mg2+/Mn2+-dependent RNA-guided endonuclease, and it could cleave DNA next to the 5’ TTTAA transposon-associated motif (TAM) to generate double-stranded DNA breaks at the 3’-end. We also found that SisTnpB1 was active at 37-85°C and tolerant to variations of TAM. Moreover, SisTnpB1 could be reprogrammed to edit bacterial cells with an editing efficiency of 100% at 37°C or 45°C. In summary, our finding expanded the resources of RNA-guided endonucleases for genome editing, especially those derived from archaea, the third domain of life.
The effect of pulse shape in theta-burst stimulation: monophasic vs biphasic TMS
Authors: Wendt Karen , Sorkhabi Majid Memarian , Stagg Charlotte J. , Fleming Melanie K. , Denison Timothy , O’Shea Jacinta
Published: March 2023

Background

Intermittent theta-burst stimulation (i)(TBS) is a transcranial magnetic stimulation (TMS) plasticity protocol. Conventionally, TBS is applied using biphasic pulses due to hardware limitations. However, monophasic pulses are hypothesised to recruit cortical neurons more selectively than biphasic pulses, thus yielding stronger plasticity effects. Monophasic and biphasic TBS can be generated using a custom-made pulse-width modulation-based TMS device (pTMS).

Objective

Using pTMS, we tested the hypothesis that monophasic iTBS would induce greater plasticity effects than biphasic, measured as induced changes in motor corticospinal excitability.

Methods

In a repeated-measures design, thirty healthy volunteers participated in three separate sessions, where monophasic and biphasic iTBS was applied to the primary motor cortex (M1 condition) or the vertex (control condition). Plasticity was quantified as changes in motor corticospinal excitability after versus before iTBS, by comparing peak-to-peak amplitudes of motor evoked potentials (MEP) measured at baseline and over 60 minutes after iTBS.

Results

Both monophasic and biphasic M1 iTBS led to significant increases in MEP amplitude. As predicted, monophasic iTBS induced a significantly larger effect than biphasic iTBS (linear mixed effect model analysis: (χ2(1) = 7.48, p = 0.006), which persisted even after subtracting each individual’s control (vertex) condition data from the M1 conditions (χ2(1) = 5.48, p = 0.019).

Conclusions

In this study, monophasic iTBS induced a stronger motor corticospinal excitability increase than biphasic within participants. This greater physiological effect suggests that monophasic iTBS may also have potential for greater functional impact, of interest for future fundamental and clinical applications of TBS.
Reactive blue 2 labels protamine in late-haploid spermatids and spermatozoa and can be used for toxicity evaluation
Authors: Yokota Satoshi , Wakayama Tomohiko , Miyaso Hidenobu , Suga Kousuke , Fujinoki Masakatsu , Kaneko Satoru , Kitajima Satoshi
Published: March 2023

Background

Reactive blue 2 (RB2) dye specifically binds to the nuclei of human spermatozoa under weakly alkaline conditions, thus providing a new method to assess sperm quality. However, this technique has not yet been applied to other mammalian species, such as well-established rodent models, which could enable evaluation of the male reproductive toxicity of drug candidates in non-clinical studies.

Objectives

We aimed to evaluate the usefulness of RB2 staining in assessing testicular and epididymal sperm toxicity in mice using a busulfan-induced infertility model.

Methods

Male C57BL/6J mice were intraperitoneally administered 40 mg/kg of busulfan. After 28 days, the testes and epididymis were collected and stained with RB2 at pH 10. In vitro evaluations were conducted on uncoated glass slides with RB2 mixed with either protamines extracted from the spermatozoa or intracellular protein components from somatic cells without protamines.

Results

Following peanut agglutinin (PNA) lectin histochemistry, RB2-positive cells were observed in elongating and elongated spermatids at all stages except for stages IX–XI of the seminiferous epithelium. After busulfan administration, the proportion of RB2-positive germ cells in the seminiferous tubules decreased significantly, and no RB2-positive spermatozoa were found in the caput epididymis of treated mice. Aggregates were observed in the mixture of RB2 dye (pH 10) with protamines but not in the mixture of intracellular protein components without protamines, and this specificity was lost at neutral pH.

Discussion and Conclusion

Our study demonstrates that RB2 specifically stains steps 12–16 spermatids, indicating specific binding to protamine expressed in these spermatids. The RB2 staining technique has potential as a biomarker for male reproductive toxicity, allowing for the rapid visualization of protamination.
Loss of kinase Atg1 increases yeast maintenance energy requirement
Authors: Chen Xin , van Aalst Aafke C. A. , Petranovic Dina , Bisschops Markus M.M.
Published: March 2023

Maintenance of cellular homeostasis underlies healthy aging. The processes involved in homeostasis rely on the so-called maintenance energy requirement and changes in this maintenance energy requirement impact aging and survival. Among maintenance processes, autophagy plays a crucial role as it is involved in the turn-over and recycling of damaged cellular material, such as organelles or proteins. The contribution of autophagy to the maintenance energy requirement is however unknown. Taking advantage of the high degree of conservation of autophagy between humans andSaccharomyces cerevisiae, we have used this yeast as a model organism to study the impact of macroautophagy on the maintenance energy requirement. The combination of the GFP-Atg8 cleavage assay with yeast retentostat cultures showed that autophagy is highly active in chronologically aging yeast cells, in non-dividing, but non-starving conditions. Deletion of the autophagy-activating kinaseATG1, homolog of humanULK1, resulted in a 60% increase in the maintenance energy requirement and doubled the specific death rate. Both these increases cannot be solely attributed to an observed increase in loss of respiratory capacity. Intriguingly, loss of Atg1 only reduced GFP-Atg8 cleavage by 20% under these conditions, indicating that Atg1-indendent modes of autophagy might be active. Overall, we illustrate the importance of autophagy on the energetics of aging cells and propose an alternative system for the widely applied yeast stationary phase cultures in chronological aging studies.
Maternal diet and gut microbiome composition modulate early life immune development
Authors: Grant Erica T , Boudaud Marie , Muller Arnaud , Macpherson Andrew J , Desai Mahesh S
Published: March 2023

In early life, the intestinal mucosa and immune system undergo a critical developmental process to contain the expanding gut microbiome while promoting tolerance towards commensals, yet the influence of maternal diet and gut microbial composition on offspring immune maturation remains poorly understood. We colonized gnotobiotic mice with a defined consortium of 14 strains, fed them a standard fiber-rich chow or a fiber-free diet, and then longitudinally assessed offspring development during the weaning period. Unlike pups born to dams fed the fiber-rich diet, pups of fiber-deprived dams demonstrated delayed colonization withAkkermansia muciniphila, a mucin-foraging bacterium that can also utilize milk oligosaccharides. The pups of fiber-deprived dams exhibited an enrichment of colonic tissue transcripts corresponding to defense response pathways and a peak inIl22expression at weaning. Removal ofA.muciniphilafrom the community, but maintenance on the fiber-rich diet, was associated with reduced proportions of RORγt-positive innate and adaptive immune cell subsets. Our results highlight the potent influence of maternal dietary fiber intake and discrete changes in microbial composition on the postnatal microbiome assemblage and early immune development.
Active self-touch restores bodily self-awareness following disruption by “rubber hand illusion”
Authors: Crivelli Damiano , Cataldo Antonio , Bottini Gabriella , Gomi Hiroaki , Haggard Patrick
Published: March 2023

Bodily self-awareness relies on a constant integration of visual, tactile, proprioceptive, and motor signals. In the “Rubber Hand Illusion” (RHI), conflicting visuo-tactile stimuli lead to changes in self- awareness. It remains unclear whether other, somatic signals could compensate for the alterations in self-awareness caused by visual information about the body. Here, we used the RHI in combination with robot-mediated self-touch to systematically investigate the role of tactile, proprioceptive, and motor signals in protecting and restoring bodily self-awareness. Participants moved the handle of a leader robot with their right hand and simultaneously received corresponding tactile feedback on their left hand from a follower robot. This self-touch stimulation was performed either before or after the induction of a classical RHI. Across three experiments, active self-touch delivered after – but not before – the RHI, significantly reduced the proprioceptive drift caused by RHI, supporting a restorative role of active self-touch on bodily self-awareness. The effect was not present during involuntary self-touch, where the participants’ hand was passively moved, suggesting that the restorative effect depends on the presence of a voluntary motor command, and that synchrony of bilateral sensory events is insufficient. Unimodal control conditions confirmed that the coordination of both tactile and motor components of self-touch was necessary to restore bodily self-awareness. These results suggest that voluntary self-touch can restore an intrinsic representation of the body following visual capture during RHI.
The cell type composition of the adult mouse brain revealed by single cell and spatial genomics
Authors: Langlieb Jonah , Sachdev Nina , Balderrama Karol , Nadaf Naeem , Raj Mukund , Murray Evan , Webber James , Vanderburg Charles , Gazestani Vahid , Tward Daniel , Mezias Chris , Li Xu , Cable Dylan , Norton Tabitha , Mitra Partha Pratim , Chen Fei , Macosko Evan
Published: March 2023

The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types, and their positions within individual anatomical structures, remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA-seq with Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution, across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain, and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signaling, elucidated region-specific specializations in activity-regulated gene expression, and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource (BrainCellData.org) should find diverse applications across neuroscience, including the construction of new genetic tools, and the prioritization of specific cell types and circuits in the study of brain diseases.
Engineering and implementation of synthetic molecular tools in the basidiomycete fungusUstilago maydis
Authors: Heucken Nicole , Tang Kun , Hüsemann Lisa , Heßler Natascha , Müntjes Kira , Feldbrügge Michael , Göhre Vera , Zurbriggen Matias D.
Published: March 2023

The basidiomyceteUstilago maydisis a well-characterized model organism for studying pathogen-host interactions and of great interest for a broad spectrum of biotechnological applications. To facilitate research and enable applications, in this study, three luminescence-based and one enzymatic quantitative reporter were implemented and characterized. We generated dual-reporter constructs for ratiometric normalization that can be used as a fast-screening platform for reporter gene expression, applicable toin vitroandin vivodetection. Furthermore, we constructed and implemented synthetic bi-directional promoters, that enable bicisitronic expression for gene expression studies and engineering strategies. These non-invasive, quantitative reporters and expression tools will widen significantly the application range of biotechnology inU. maydisand enable in planta detection of fungal infection.
Immunoproximity biotinylation reveals the axon initial segment proteome
Authors: Zhang Wei , Fu Yu , Peng Luxin , Ogawa Yuki , Ding Xiaoyun , Rasband Anne , Zhou Xinyue , Shelly Maya , Rasband Matthew N. , Zou Peng
Published: March 2023

The axon initial segment (AIS) is a specialized neuronal compartment required for action potential generation and neuronal polarity. However, understanding the mechanisms regulating AIS structure and function has been hindered by an incomplete knowledge of its molecular composition. Here, using immuno-proximity biotinylation we further define the AIS proteome and its dynamic changes during neuronal maturation. Among the many AIS proteins identified, we show that SCRIB is highly enriched in the AIS bothin vitroandin vivo,and exhibits a periodic architecture like the axonal spectrin-based cytoskeleton. We found that ankyrinG interacts with and recruits SCRIB to the AIS. However, loss of SCRIB has no effect on ankyrinG. This powerful and flexible approach further defines the AIS proteome and provides a rich resource to elucidate the mechanisms regulating AIS structure and function.
A novel role of macrophage PIST protein in regulatingLeishmania majorinfection
Authors: Banerjee Sourav , Gadpayle Mandip Pratham , Das Swagata , Samanta Suman , Datta Rupak , Maiti Sankar
Published: March 2023

PDZ protein interacting specifically with Tc10 or PIST is a mammaliantrans-Golgi resident protein that regulates subcellular sorting of plasma membrane receptors. PIST has recently been found to play an important role in regulating viral pathogenesis. Alteration in PIST expression is linked to the reprogramming of cell surface receptors which is crucial in determining herpes simplex virus1 infection. In this context, PIST is crucial in triggering autophagy via Beclin 1 -PI3KC3 pathway. However, there is complete lack in our knowledge on the role of this protein in any parasitic infection.Leishmaniaparasites infect their host macrophage cells via phagocytosis and their survival within the parasitophorous compartment has recently been found to be dependent on host autophagy by a yet to be identified mechanism. UsingLeishmania major(L. major)-macrophage infection model system we, for the first-time report here that in infected macrophages Golgi resident PIST protein migrates towards the parasite containing compartment. We have also found that PIST associates with Beclin 1, however, not with LC3 withinL. majorparasite containing compartment of infected macrophages. Further, we performed genetic ablation of PIST by siRNA and observed that knockdown of macrophage PIST in turn helps in parasite replication. Contrary to this, overexpression of PIST in macrophages restricted the multiplication ofL. major. Collectively, our study for the first time reveals that PIST is essential in regulating intracellular parasite,L. majorinfection within macrophage cells.

Summary Statement

Mammalian PIST protein plays a crucial role in regulating cellular trafficking events. Here, we showed that PIST status is altered withinLeishmania majorparasite infected macrophages. Further, we confirmed that PIST is essential in restricting parasite growth. Additionally, a potential interacting axis between PIST and Beclin 1 is identified during infection.
OneOPES, a combined enhanced sampling method to rule them all
Authors: Rizzi Valerio , Aureli Simone , Ansari Narjes , Gervasio Francesco Luigi
Published: March 2023

Enhanced sampling techniques have revolutionised molecular dynamics (MD) simulations, enabling the study of rare events and the calculation of free energy differences in complex systems. One of the main families of enhanced sampling techniques uses physical degrees of freedom called collective variables (CVs) to accelerate a system’s dynamics and recover the original system’s statistics. However, encoding all the relevant degrees of freedom in a limited number of CVs is challenging, particularly in large biophysical systems. Another category of techniques, such as parallel tempering, simulates multiple replicas of the system in parallel, with-out requiring CVs. However, these methods may explore less relevant high-energy portions of the phase space and become computationally expensive for large systems. To overcome the limitations of both approaches, we propose a replica exchange method called OneOPES that combines the power of multi-replica simulations and CV-based enhanced sampling. This method efficiently accelerates the phase space sampling without the need for ideal CVs, extensive parameters fine tuning nor the use of a large number of replicas, as demonstrated by its successful applications to protein-ligand binding and protein folding benchmark systems. Our approach shows promise as a new direction in the development of enhanced sampling techniques for molecular dynamics simulations, providing an efficient and robust framework for the study of complex and unexplored problems.

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An expanded GCaMP reporter toolkit for functional imaging inC. elegans
Authors: Ding Jimmy , Peng Lucinda , Moon Sihoon , Lee Hyun Jee , Patel Dhaval S. , Lu Hang
Published: March 2023

In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levelsin vivo. In particular, GCaMP, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to theCaenorhabditis elegansresearch community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized forC. elegansstudies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters are also well-suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
Calorie Restriction activates a gastric Notch-FOXO1 pathway to expand Ghrelin cells
Authors: McKimpson Wendy M. , Spiegel Sophia , Mukhanova Maria , Kraakman Michael , Du Wen , Kitamoto Takumi , Yu Junjie , Pajvani Utpal , Accili Domenico
Published: March 2023

Calorie restriction increases lifespan. While some tissue-specific protective effects of calorie restriction have been described, the impact of calorie restriction on the gastrointestinal tract remains unclear. We found increased abundance of chromogranin A+, including orexigenic ghrelin+, endocrine cells in the stomach of calorie-restricted mice. This effect coincided with increased Notch target Hes1 and Notch ligand Jag1 and was reversed when Notch signaling was blocked using the γ-secretase inhibitor DAPT. Using primary cultures and genetically-modified reporter mice, we determined that increased endocrine cell abundance was due to altered stem and progenitor proliferation. Different from the intestine, calorie restriction decreased gastric Lgr5+ stem cells, while increasing a FOXO1/Neurog3+ subpopulation of endocrine progenitors in a Notch-dependent manner. Further, calorie restriction triggered nuclear localization of FOXO1, which was sufficient to promote endocrine cell differentiation. Taken together, the data indicate that calorie restriction promotes gastric endocrine cell differentiation triggered by active Notch signaling and regulated by FOXO1.
DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity
Authors: Ryder Bryan D. , Ustyantseva Elizaveta , Boyer David R. , Mendoza-Oliva Ayde , Kuska Mikołaj I. , Wydorski Paweł M. , Macierzynska Paulina , Morgan Nabil , Sawaya Michael R. , Diamond Marc I. , Kampinga Harm H. , Joachimiak Lukasz A.
Published: March 2023

J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8, that drives self-assembly through ν-ν stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerizationin vitroand in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregationin vitroand in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.

HIGHLIGHTS

DNAJB8 oligomerization is mediated by a short phenylalanine-based motif in the S/T domain

Mutation of a single phenylalanine yields a monomeric form of DNAJB8

Monomeric DNABJ8 binds to an aggregation-prone substrate

Monomeric DNAJB8 retains substrate aggregation prevention activity