bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of treatment-responsive genes in spatial transcriptomics data by leveraging injection site information
Authors: Masone Felicita Pia , Napolitano Francesco
Published: July 2023

Spatial Transcriptomics assays allow to study gene expression as a function of the spatial position of cells across a tissue sample. Although several methods have been proposed to identify spatially variable genes, they do not take into account the position of the injection site in the case of treated samples. In this study, we developed a method to identify treatment-responsive genes based on the assumption that the distance of the cells from the injection site across the tissue would affect the corresponding transcriptional response. In particular, we tested our approach using a publicly available ST dataset obtained after injection of heme into the striatum nucleus of a murine brain. We observed that several biologically relevant genes were detected by our method as showing a distance-dependent expression trend. We finally compared the results against a ground-truth gene set and a state-of art pattern-based method.
Larvicidal activity of the photosensitive insecticides, methylene blue and rose bengal, inAedes aegyptiandAnopheles gambiaemosquitoes
Authors: Meier Cole J. , Hillyer Julián F.
Published: July 2023

BACKGROUND

Insecticides are critical for controlling mosquito populations and mitigating the spread of vector–borne disease, but their overuse has selected for resistant populations. A promising alternative to classical chemical insecticides is photosensitive molecules—here called photosensitive insecticides or PSIs—that when ingested and activated by light, generate broadly toxic reactive oxygen species. This mechanism of indiscriminate oxidative damage decreases the likelihood that target site modification-based resistance evolves. Here, we tested whether the PSIs, methylene blue (MB) and rose bengal (RB), are viable insecticides across the mosquito lineage.

RESULTS

MB and RB are phototoxic to bothAe. aegyptiandAn. gambiaeat micromolar concentrations, with greatest toxicity when larvae are incubated in the dark with the PSIs for 2 hr prior to photoactivation. MB is ten times more toxic than RB, and microscopy-based imaging suggests that this is because ingested MB escapes the larval gut and disperses throughout the hemocoel whereas RB remains confined to the gut. Adding food to the PSI-containing water has a bidirectional, concentration-dependent effect on PSI toxicity; toxicity increases at high concentrations but decreases at low concentrations. Finally, adding sand to the water increases the phototoxicity of RB toAedes aegypti.

CONCLUSION

MB and RB are larvicidal via a light activated mechanism, and therefore, should be further investigated as an option for mosquito control.
Mitigating autocorrelation during spatially resolved transcriptomics data analysis
Authors: Maher Kamal , Wu Morgan , Zhou Yiming , Huang Jiahao , Zhang Qiangge , Wang Xiao
Published: July 2023

Several computational methods have recently been developed for characterizing molecular tissue regions in spatially resolved transcriptomics (SRT) data. However, each method fundamentally relies on spatially smoothing transcriptomic features across neighboring cells. Here, we demonstrate that smoothing increases autocorrelation between neighboring cells, causing latent space to encode physical adjacency rather than spatial transcriptomic patterns. We find that randomly sub-sampling neighbors before smoothing mitigates autocorrelation, improving the performance of existing methods and further enabling a simpler, more efficient approach that we callspatialintegration (SPIN). SPIN leverages the conventional single-cell toolkit, yielding spatial analogies to each tool: clustering identifies molecular tissue regions; differentially expressed gene analysis calculates region marker genes; trajectory inference reveals continuous, molecularly defined ana tomical axes; and integration allows joint analysis across multiple SRT datasets, regardless of tissue morphology, spatial resolution, or experimental technology. We apply SPIN to SRT datasets from mouse and marmoset brains to calculate shared and species-specific region marker genes as well as a molecularly defined neocortical depth axis along which several genes and cell types differ across species.
Statistical prediction of microbial metabolic traits from genomes
Authors: Li Zeqian , Selim Ahmed , Kuehn Seppe
Published: July 2023

The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source. Using these data as well as two existing datasets, we show that statistical approaches can accurately predict bacterial carbon utilization traits from genomes. First, we show that classifiers trained on gene content can accurately predict bacterial carbon utilization phenotypes by encoding phylogenetic information. These models substantially outperform predictions made by constraint-based metabolic models automatically constructed from genomes. However, phylogeny-based predictions fail to predict traits for taxa that are phyloge-netically distant from any strains in the training set. To overcome this we train improved models on gene presence/absence to predict carbon utilization traits from gene content. We show that models that predict carbon utilization traits from gene presence/absence can generalize to taxa that are phylogenetically distant from the training set either by exploiting biochemical information for feature selection or by having sufficiently large datasets. In the latter case, we provide evidence that a statistical approach can identify putatively mechanistic genes involved in metabolic traits. Our study demonstrates the potential power for predicting microbial phenotypes from genotypes using statistical approaches.
Seasonality effects and field-estimation of colony size in desert ants
Authors: Subach Aziz , Bega Darar , Saar Maya
Published: July 2023

The colony level of eusocial insects is considered the reproductive unit on which natural selection operates. Therefore, seasonal demographic movements and estimations of colony size are crucial variables. Excavating colonies of ants to extract their size is daunting, unhealthy to the surrounding environment, and it may prevent long-term research, including testing seasonal effects on colony size. Previous capture-recapture methods that avoid excavating colonies have been proven inefficient when sampling mostly underground dwellers as ants. To address this issue, we offer a simple method to estimate the colony size of desert ants (Cataglyphis niger) in a field setting- based on a field experiment, a literature review, and four laboratory experiments. First, we find that between 10-15% of the colony size are outgoing foragers. Second, we find seasonal effects on colony size and foraging activity: colony size varies and is larger in winter than in summer, and in contrast - the proportion of foragers out of colony size is higher in summer than in winter. This suggests that the energetic requirements of the colonies are higher in summer than in winter. Based on uniquely large sample size, our proposed field method may be useful for other co-occurringCataglyphisspecies. Moreover, extracting ant colony sizes and evaluating ant biomass is advantageous for future studies to evaluate the carrying capacity of semi sand-dunes habitats.
MPK4 mediated phosphorylation of PIF4 controls thermosensing by regulation of H2A.Z deposition in Arabidopsis
Authors: Verma Neetu , Singh Dhanraj , Mittal Lavanya , Banerjee Gopal , Noryang Stanzin , Sinha Alok Krishna
Published: July 2023

Plants have the ability to perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis has been well established, although the regulatory pathway involved in thermosensing is not deciphered completely. In our study, we demonstrate that an increase in temperature from 22℃ to 28℃ induces the phosphorylation of PIF4 by MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) which shows high expression and activation at 28℃. Apparently, phosphorylated PIF4 represses the expression ofACTIN-RELATED PROTEIN 6(ARP6) that is required for mediating histone variant H2A.Z deposition at its target gene loci. We demonstrate that variation ofARP6expression in PIF4 phosphor -null and phosphor-mimetic seedlings affects hypocotyl growth and flowering at 22℃ and 28℃. Further, we show that change inARP6expression affects H2A.Z deposition at the loci of genes involved in hypocotyl elongation using PIF4 phosphor -null and phosphor-mimetic seedlings. Interestingly, the expression ofMPK4is also controlled by H2A.Z deposition in temperature dependent manner. Taken together, our findings highlight the cumulative molecular interplay between MPK4, PIF4, and chromatin modification by ARP6-mediated H2A.Z deposition as a regulatory mechanism of thermosensing.
Vascularized Brain Assembloids with Enhanced Cellular Complexity Provide Insights into The Cellular Deficits of Tauopathy
Authors: Kofman Simeon , Sun Xiaohuan , Ogbolu Victor C. , Ibric Larisa , Qiang Liang
Published: July 2023

Advanced technologies have enabled the engineering of self-organized 3-dimensional (3D) cellular structures from human induced pluripotent stem cells (hiPSCs), namely organoids, which recapitulate some key features of tissue development and functions of the human central nervous system (CNS). While hiPSC-derived 3D CNS organoids hold promise in providing a human-specific platform for studying CNS development and diseases, most of them do not incorporate the full range of implicated cell types, including vascular cell components and microglia, limiting their ability to accurately recreate the CNS environment and their utility in the study of certain aspects of the disease. Here we’ve developed a novel approach, called vascularized brain assembloids, for constructing hiPSC-derived 3D CNS structures with a higher level of cellular complexity. This is achieved by integrating forebrain organoids with common myeloid progenitors and phenotypically stabilized human umbilical vein endothelial cells (VeraVecs™), which can be cultured and expanded in serum-free conditions. Compared with organoids, these assembloids exhibited enhanced neuroepithelial proliferation, advanced astrocytic maturation, and increased synapse numbers. Strikingly, the assembloids derived from hiPSCs harboring the tauP301Smutation exhibited increased levels of total tau and phosphorylated tau, along with a higher proportion of rod-like microglia-like cells and enhanced astrocytic activation, when compared to the assembloids derived from isogenic hiPSCs. Additionally, they showed an altered profile of neuroinflammatory cytokines. This innovative assembloid technology serves as a compelling proof-of-concept model, opening new avenues for unraveling the intricate complexities of the human brain and accelerating progress in the development of effective treatments for neurological disorders.

Significance Statement

Modeling neurodegeneration in humanin vitrosystems has proved challenging and requires innovative tissue engineering techniques to create systems that can accurately capture the physiological features of the CNS to enable the study of disease processes. The authors develop a novel assembloid model which integrates neuroectodermal cells with endothelial cells and microglia, two critical cell types that are commonly missing from traditional organoid models. They then apply this model to investigate early manifestations of pathology in the context of tauopathy and uncover early astrocyte and microglia reactivity as a result of the tauP301Smutation.
PAK3 downregulation induces cognitive impairment following cranial irradiation
Authors: Lee Haksoo , Kang Hyunkoo , Moon Changjong , Youn BuHyun
Published: July 2023

Cranial irradiation is used for prophylactic brain radiotherapy as well as treatment of primary brain tumors. Despite its high efficiency, it often induces unexpected side effects, including cognitive dysfunction. Herein, we observed that mice exposed to cranial irradiation exhibited cognitive dysfunction, including altered spontaneous behavior, decreased spatial memory, and reduced novel object recognition. Analysis of actin cytoskeleton revealed that ionizing radiation (IR) disrupted the filamentous/globular actin (F/G-actin) ratio and downregulated the actin turnover signaling pathway p21-activated kinase 3 (PAK3)-LIM kinase 1 (LIMK1)-cofilin. Furthermore, we found that IR could upregulate microRNA-206-3p (miR-206-3p) targeting PAK3. As the inhibition of miR-206-3p through antagonist (antagomiR), IR-induced disruption of PAK3 signaling is restored. In addition, intranasal administration of antagomiR-206-3p recovered IR-induced cognitive impairment in mice. Our results suggest that cranial irradiation-induced cognitive impairment could be ameliorated by regulating PAK3 through antagomiR-206-3p, thereby affording a promising strategy for protecting cognitive function during cranial irradiation, and promoting quality of life in patients with radiation therapy.
From the shallows to the depths: A new probe set to target ultraconserved elements for Malacostraca
Authors: Geburzi Jonas C. , Rodríguez-Flores Paula C. , Derkarabetian Shahan , Giribet Gonzalo
Published: July 2023

Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography and deep phylogenetics. UCE probe sets are available for an increasing range of major taxonomic groups, including cnidarians, vertebrates, terrestrial arthropods, and mollusks. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and other malacostracan lineages. Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,348 unique UCE loci. Preliminary analyses of UCE data obtained from an intertidal mangrove crab, and from deep-sea squat lobsters indicate high UCE recovery rates (about 1,000 loci per sample) in evolutionarily shallow datasets. To test the probe set at deeper phylogenetic levels, we compiled a dataset across Malacostraca (including representatives of Decapoda, Peracarida, Euphausiacea, Stomatopoda, and Phyllocarida), and were able to recover hundreds of UCEs for the non-decapod species, expanding the targeted use of this UCE probeset to all Malacostraca. Additionally, we recovered similar numbers of UCEs from historical museum specimens up to > 150 years old, that were included in all datasets, confirming that UCEs are a fruitful technique for leveraging museum specimens for genomic studies. Overall, our results highlight the versatility of this UCE probe set and its high potential for crustacean evolutionary studies.
Predictors of mortality among low birth weight neonates after hospital discharge in a low-resource setting: A case study in Uganda
Authors: Nsubuga Ronald , Rujumba Joseph , Nyende Saleh , Kisaka Stevens , Idro Richard , Nankunda Jolly
Published: July 2023

Background

Most neonatal deaths occur among low birth weight infants. However, in resource-limited settings, these infants are commonly discharged early which further exposes them to mortality. Previous studies on morbidity and mortality among low birth weight infants after early discharge mainly focused on very low birth weight infants, and none described post-discharge neonatal mortality. This study aimed to determine the proportion and predictors of mortality among low birth weight neonates discharged from the Special Care Baby Unit at Mulago National Referral Hospital in Uganda.

Methods

This was a prospective cohort study of 220 low birth weight neonates discharged from the Special Care Baby Unit at Mulago National Referral Hospital. These were followed up to 28 completed days of life, or death, whichever occurred first. Proportions were used to express mortality. To determine the predictors of mortality, Cox hazards regression was performed.

Results

Of the 220 enrolled participants, 216 (98.1%) completed the follow-up. The mean gestational age of study participants was 34 ±3 weeks. The median weight at discharge was 1,650g (IQR: 1,315g -1,922g) and 46.1% were small for gestational age. During follow-up, 14/216 (6.5%) of neonates died. Mortality was highest (7/34, 20.6%) among neonates with discharge weights less than 1,200g. The causes of death included presumed neonatal sepsis (10/14, 71.4%), suspected aspiration pneumonia (2/14, 14.3%), and suspected cot death (2/14, 14.3%). The median time to death after discharge was 11 days (range 3-16 days). The predictors of mortality were a discharge weight of less than 1,200g (adj HR: 23.47,p<0.001), a 5-minute Apgar score of less than 7 (adj HR: 4.25,p= 0.016), and a diagnosis of neonatal sepsis during admission (adj HR: 7.93,p =0.009).

Conclusion

Post-discharge mortality among low birth weight neonates at Mulago National Referral Hospital is high. A discharge weight of less than 1,200g may be considered unsafe among neonates. Caregiver education about neonatal danger signs, and measures to prevent sepsis, aspiration, and cot death should be emphasized before discharge and during follow-up visits.
Small extracellular vesicles promote stiffness-mediated metastasis
Authors: Sneider Alexandra , Liu Ying , Starich Bartholomew , Du Wenxuan , Marar Carolyn , Faqih Najwa , Ciotti Gabrielle E. , Kim Joo Ho , Krishnan Sejal , Ibrahim Salma , Igboko Muna , Locke Alexus , Lewis Daniel M. , Hong Hanna , Karl Michelle , Vij Raghav , Russo Gabriella C. , Nair Praful , Gómez-de-Mariscal Estibaliz , Habibi Mehran , Muñoz-Barrutia Arrate , Gu Luo , Eisinger-Mathason T.S. Karin , Wirtz Denis
Published: July 2023

Tissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn drive their metastasis. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITGα2β1, ITGα6β4, ITGα6β1, CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) protein collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination through enhanced chemotaxis. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment.

Graphical Abstract
Configurational entropy is an intrinsic driver of tissue structural heterogeneity
Authors: Srivastava Vasudha , Hu Jennifer L. , Garbe James C. , Veytsman Boris , Shalabi Sundus F. , Yllanes David , Thomson Matt , LaBarge Mark A. , Huber Greg , Gartner Zev J.
Published: July 2023

Tissues comprise ordered arrangements of cells that can be surprisingly disordered in their details. How the properties of single cells and their microenvironment contribute to the balance between order and disorder at the tissue-scale remains poorly understood. Here, we address this question using the self-organization of human mammary organoids as a model. We find that organoids behave like a dynamic structural ensemble at the steady state. We apply a maximum entropy formalism to derive the ensemble distribution from three measurable parameters – the degeneracy of structural states, interfacial energy, and tissue activity (the energy associated with positional fluctuations). We link these parameters with the molecular and microenvironmental factors that control them to precisely engineer the ensemble across multiple conditions. Our analysis reveals that the entropy associated with structural degeneracy sets a theoretical limit to tissue order and provides new insight for tissue engineering, development, and our understanding of disease progression.
Optimal Transport Method-Based Gene Filter (GF) Denoising Algorithm for Enhancing Spatially Resolved Transcriptomics Data
Authors: Du Lin , Kang Jingmin , Sun Haixi , Zhang Bohan
Published: July 2023

The recent advancements in spatially resolved transcriptomics (SRT) technology have enabled the acquisition of gene expression data at near- or sub-single-cell resolution, along with simultaneous imaging of physical locations. Nevertheless, necessary experimental procedures such as tissue fixation, permeabilization, and tissue removal inevitably induce the diffusion of transcribed molecules. Consequently, this leads to the partial capture of ex-situ transcripts in SRT data, thereby introducing a considerable amount of noise into the dataset. To address this issue, in this study, we focused on evaluating the diffusion pattern of individual genes within tissue regions and quantitatively calculating their signal-to-noise ratio (SNR). Through this analysis, we successfully identified “invalid genes” exhibiting widespread expression across tissue regions. Then by filtering out these genes, we effectively reduced the high noise level present in SRT data. To achieve this, we developed the gene filter denoising (GF) algorithm, which utilizes the optimal transport method to compute the gene diffusion coefficient and generate denoised SRT data. One notable advantage of our GF algorithm is its ability to fully “respect” the raw sequencing data, thereby avoiding the introduction of false positives often associated with traditional interpolation and modification denoising methods. Furthermore, we conducted comprehensive validation of GF, and the GF-denoised SRT data demonstrated substantial improvements in clustering, identification of differentially expressed genes (DEGs), and cell type annotation. Taken together, we believe that the GF denoising technique will serve as an essential and crucial step in exploring SRT data and investigating the underlying biological processes.
A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
Authors: Parkash Vimal , Kulkarni Yashraj , Bylund Göran O. , Osterman Pia , Kamerlin Shina Caroline Lynn , Johansson Erik
Published: July 2023

The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2’-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.
A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits
Authors: Wietek Jonas , Nozownik Adrianna , Pulin Mauro , Saraf-Sinik Inbar , Matosevich Noa , Malan Daniela , Brown Bobbie J. , Dine Julien , Levy Rivka , Litvin Anna , Regev Noa , Subramaniam Suraj , Bitton Eyal , Benjamin Asaf , Copits Bryan A. , Sasse Philipp , Rost Benjamin R. , Schmitz Dietmar , Soba Peter , Nir Yuval , Wiegert J. Simon , Yizhar Ofer
Published: July 2023

Information is transmitted between brain regions through the release of neurotransmitters from long-range projecting axons. Understanding how the activity of such long-range connections contributes to behavior requires efficient methods for reversibly manipulating their function. Chemogenetic and optogenetic tools, acting through endogenous G-protein coupled receptor (GPCRs) pathways, can be used to modulate synaptic transmission, but existing tools are limited in sensitivity, spatiotemporal precision, or spectral multiplexing capabilities. Here we systematically evaluated multiple bistable opsins for optogenetic applications and found that thePlatynereis dumeriliiciliary opsin (PdCO) is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precisionin-vivo.PdCO has superior biophysical properties that enable spectral multiplexing with other optogenetic actuators and reporters. We demonstrate thatPdCO can be used to conduct reversible loss-of-function experiments in long-range projections of behaving animals, thereby enabling detailed synapse-specific functional circuit mapping.
Dopamine neurons drive spatiotemporally heterogeneous striatal dopamine signals during learning
Authors: Engel Liv , Wolff Amy R , Blake Madelyn , Collins Val L. , Sinha Sonal , Saunders Benjamin T
Published: July 2023

Environmental cues, through Pavlovian learning, become conditioned stimuli that invigorate and guide animals toward acquisition of rewards. Dopamine neurons in the ventral tegmental area (VTA) and substantia nigra (SNC) are crucial for this process. Dopamine neurons are embedded in a reciprocally connected network with their striatal targets, the functional organization of which remains poorly understood. Here, we investigated how learning during optogenetic Pavlovian cue conditioning of VTA or SNC dopamine neurons directs cue-evoked behavior and shapes subregion-specific striatal dopamine dynamics. We used a fluorescent dopamine biosensor to monitor dopamine in the nucleus accumbens (NAc) core and shell, dorsomedial striatum (DMS), and dorsolateral striatum (DLS). We demonstrate spatially heterogeneous, learning-dependent dopamine changes across striatal regions. While VTA stimulation evoked robust dopamine release in NAc core, shell, and DMS, cues predictive of this activation preferentially recruited dopamine release in NAc core, starting early in training, and DMS, late in training. Corresponding negative prediction error signals, reflecting a violation in the expectation of dopamine neuron activation, only emerged in the NAc core and DMS, and not the shell. Despite development of vigorous movement late in training, conditioned dopamine signals did not similarly emerge in the DLS, even during Pavlovian conditioning with SNC dopamine neuron activation, which elicited robust DLS dopamine release. Together, our studies show broad dissociation in the fundamental prediction and reward-related information generated by different dopamine neuron populations and signaled by dopamine across the striatum. Further, they offer new insight into how larger-scale plasticity across the striatal network emerges during Pavlovian learning to coordinate behavior.
Single Cell Multi-Omics of an iPSC Model of Human Sinoatrial Node Development Reveals Genetic Determinants of Heart Rate and Arrhythmia Susceptibility
Authors: Engel James L. , Zhang Xianglong , Lu Daniel R. , Vila Olaia F. , Arias Vanessa , Lee Jasper , Hale Christopher , Hsu Yi-Hsiang , Li Chi-Ming , Wu Roland S. , Vedantham Vasanth , Ang Yen-Sin
Published: July 2023

Cellular heterogeneity within the sinoatrial node (SAN) is functionally important but has been difficult to modelin vitro, presenting a major obstacle to studies of heart rate regulation and arrhythmias. Here we describe a scalable method to derive sinoatrial node pacemaker cardiomyocytes (PCs) from human induced pluripotent stem cells that recapitulates differentiation into distinct PC subtypes, including SAN Head, SAN Tail, transitional zone cells, and sinus venosus myocardium. Single cell (sc) RNA-sequencing, sc-ATAC-sequencing, and trajectory analyses were used to define epigenetic and transcriptomic signatures of each cell type, and to identify novel transcriptional pathways important for PC subtype differentiation. Integration of our multi-omics datasets with genome wide association studies uncovered cell type-specific regulatory elements that associated with heart rate regulation and susceptibility to atrial fibrillation. Taken together, these datasets validate a novel, robust, and realisticin vitroplatform that will enable deeper mechanistic exploration of human cardiac automaticity and arrhythmia.
Sequence-dependent orientational coupling and electrostatic attraction in cation-mediated DNA-DNA interactions
Authors: He Weiwei , Qiu Xiangyun , Kirmizialtin Serdal
Published: July 2023

Condensation of DNA is vital for its biological functions and controlled nucleic acid assemblies. However, the mechanisms of DNA condensation are not fully understood due to the inability of experiments to access cation distributions and the complex interplay of energetic and entropic forces during assembly. By constructing free energy surfaces using exhaustive sampling, and detailed analysis of cation distributions, we elucidate the mechanism of DNA condensation in different salt conditions and with different DNA sequences. We found that DNA condensation is facilitated by the correlated dynamics of localized cations at the grooves of DNA helices. These dynamics are strongly dependent on salt conditions and DNA sequences. In the presence of magnesium ions, major groove binding facilitates attraction. In contrast, in the presence of poly-valent cations, minor groove binding serves to create charge patterns leading to condensation. Our findings present a novel advancement to the field and have broad implications for understanding and controlling nucleic acid complexesin vivoandin vitro.
Orchestration of differential mesodermal fate choice from ESCs by Wnt-USP3 link and H2A/H2B contextual deubiquitination
Authors: Haran Varun , Lenka Nibedita
Published: July 2023

Wnt, an evolutionarily conserved morphogen, is vital for various cell fates specification during early development. However, a concrete mechanistic understanding of the precise and fine-tuned regulation of Wnt underlying these processes is yet to be uncovered. Using the murine embryonic stem cells (ESCs) model, we have identified USP3, a histone deubiquitinase (DUB), displaying bimodal action, serving both as a downstream Wnt target and a regulator of canonical Wnt signalling. Using both loss- and gain-of-function approaches, we could identify USP3 as essential for mesoderm specification, exerting a differential influence during further differentiation. While cardiogenic mesoderm was negatively regulated and so also cardiomyogenesis, USP3 positively regulated hemangioblasts differentiation. Interestingly, however, these induced hemangioblasts promoted the haematopoietic program at the expense of endothelial differentiation. The mechanistic underpinning revealed USP3 localizing to chromatin and differentially modulating these fate choices by precise and contextual deposition of H2AUb/H2BUb in the promoters of mesoderm genes. Collectively our study underscored the Wnt-USP3 link underlying differential mesodermal fate modulation.
The subacromial bursa is a key regulator of the rotator cuff and a new therapeutic target for improving repair
Authors: Marshall Brittany P. , Ferrer Xavier E. , Kunes Jennifer A. , Innis Astia C. , Luzzi Andrew J. , Forrester Lynn Ann , Burt Kevin G. , Lee Andy J. , Song Lee , Hung Clark T. , Levine William N. , Kovacevic David , Thomopoulos Stavros
Published: July 2023

Rotator cuff injuries result in over 500,000 surgeries performed annually, an alarmingly high number of which fail. These procedures typically involve repair of the injured tendon and removal of the subacromial bursa. However, recent identification of a resident population of mesenchymal stem cells and inflammatory responsiveness of the bursa to tendinopathy indicate an unexplored biological role of the bursa in the context of rotator cuff disease. Therefore, we aimed to understand the clinical relevance of bursa-tendon crosstalk, characterize the biologic role of the bursa within the shoulder, and test the therapeutic potential for targeting the bursa. Proteomic profiling of patient bursa and tendon samples demonstrated that the bursa is activated by tendon injury. Using a rat to model rotator cuff injury and repair, tenotomy-activated bursa protected the intact tendon adjacent to the injured tendon and maintained the morphology of the underlying bone. The bursa also promoted an early inflammatory response in the injured tendon, initiating key players in wound healing.In vivoresults were supported by targeted organ culture studies of the bursa. To examine the potential to therapeutically target the bursa, dexamethasone was delivered to the bursa, prompting a shift in cellular signaling towards resolution of inflammation in the healing tendon. In conclusion, contrary to current clinical practice, the bursa should be retained to the greatest extent possible and provides a new therapeutically target for improving tendon healing outcomes.

One Sentence Summary

The subacromial bursa is activated by rotator cuff injury and regulates the paracrine environment of the shoulder to maintain the properties of the underlying tendon and bone.
Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study
Authors: Kebiri Hamza , Gholipour Ali , Vasung Lana , Krsnik Željka , Karimi Davood , Bach Cuadra Meritxell
Published: July 2023

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. Fiber orientation distribution functions (FODs) are a common way of representing the orientation and density of white matter fibers. However, with standard FOD computation methods, accurate estimation of FODs requires a large number of measurements that usually cannot be acquired for newborns and fetuses. We propose to overcome this limitation by using a deep learning method to map as few as six diffusion-weighted measurements to the target FOD. To train the model, we use the FODs computed using multi-shell high angular resolution measurements as target. Extensive quantitative evaluations show that the new deep learning method, using significantly fewer measurements, achieves comparable or superior results to standard methods such as Constrained Spherical Deconvolution. We demonstrate the generalizability of the new deep learning method across scanners, acquisition protocols, and anatomy on two clinical datasets of newborns and fetuses. Additionally, we compute agreement metrics within the HARDI newborn dataset, and validate fetal FODs with post-mortem histological data. The results of this study show the advantage of deep learning in inferring the microstructure of the developing brain from in-vivo dMRI measurements that are often very limited due to subject motion and limited acquisition times, but also highlight the intrinsic limitations of dMRI in the analysis of the developing brain microstructure. These findings, therefore, advocate for the need for improved methods that are tailored to studying the early development of human brain.
Insight into perfluorooctanoic acid-induced impaired mouse embryo implantation via single cell RNA-seq
Authors: Sheng Xiaoqiang
Published: July 2023

PFOA (perfluorooctanoic acid) is a difficult-to-degrade chemical that poses significant risks to human health and the environment. Studies have shown that PFOA affect female reproduction, but effect and mechanism of low doses PFOA expose on endometrial receptivity are unclear. In this study, we found that exposure to low doses of PFOA damaged endometrial receptivity in mice, resulting in decreased embryo implantation rates in mice. Furthermore, using single-cell sequencing technology, we systematically analyzed the specific mechanisms by which PFOA damages endometrial epithelial cell function and the ANGTL signaling pathway between endometrial stromal cells and epithelial cells, leading to embryo implantation failure. The elucidation of this mechanism provides new targets for the treatment of infertility about exposed to PFOA.
ROM1 is redundant to PRPH2 as a molecular building block of photoreceptor disc rims
Authors: Lewis Tylor R. , Makia Mustafa S. , Castillo Carson M. , Hao Ying , Al-Ubaidi Muayyad R. , Skiba Nikolai P. , Conley Shannon M. , Arshavsky Vadim Y. , Naash Muna I.
Published: July 2023

Visual signal transduction takes place within a stack of flattened membranous “discs” enclosed within the light-sensitive photoreceptor outer segment. The highly curved rims of these discs, formed in the process of disc enclosure, are fortified by large hetero-oligomeric complexes of two homologous tetraspanin proteins, PRPH2 (a.k.a. peripherin-2 or rds) and ROM1. While mutations in PRPH2 affect the formation of disc rims, the role of ROM1 remains poorly understood. In this study, we found that the knockout of ROM1 causes a compensatory increase in the disc content of PRPH2. Despite this increase, discs of ROM1 knockout mice displayed a delay in disc enclosure associated with a large diameter and lack of incisures in mature discs. Strikingly, further increasing the level of PRPH2 rescued these morphological defects. We next showed that disc rims are still formed in a knockin mouse in which the tetraspanin body of PRPH2 was replaced with that of ROM1. Together, these results demonstrate that, despite its contribution to the formation of disc rims, ROM1 can be replaced by an excess of PRPH2 for timely enclosure of newly forming discs and establishing normal outer segment structure.
3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogenE. intestinalis
Authors: Antao Noelle V. , Lam Cherry , Davydov Ari , Riggi Margot , Sall Joseph , Petzold Christopher , Liang Feng-Xia , Iwasa Janet , Ekiert Damian C. , Bhabha Gira
Published: July 2023

Microsporidia are an early-diverging group of fungal pathogens that infect a wide range of hosts. Several microsporidian species infect humans, and infections can lead to fatal disease in immunocompromised individuals. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on metabolites from their hosts for successful replication and development. Our knowledge of how microsporidian parasites develop inside the host remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has thus far relied largely on 2D TEM images and light microscopy. Here, we use serial block face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting microsporidian,Encephalitozoon intestinalis, within host cells. We track the development ofE. intestinalisthrough its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembledde novoin each developing spore. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled duringE. intestinalisinfection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Together, our data provide insights into parasite development, polar tube assembly, and microsporidia-induced mitochondrial remodeling in the host cell.
Homologous mutations in β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generation
Authors: Liu Chao , Karabina Anastasia , Meller Artur , Bhattacharjee Ayan , Agostino Colby J , Bowman Greg R , Ruppel Kathleen M , Spudich James A , Leinwand Leslie A
Published: July 2023

Mutations at a highly conserved homologous residue in three closely related muscle myosins cause three distinct diseases involving muscle defects: R671C in β-cardiac myosin causes hypertrophic cardiomyopathy, R672C and R672H in embryonic skeletal myosin cause Freeman Sheldon syndrome, and R674Q in perinatal skeletal myosin causes trismus- pseudocamptodactyly syndrome. It is not known if their effects at the molecular level are similar to one another or correlate with disease phenotype and severity. To this end, we investigated the effects of the homologous mutations on key factors of molecular power production using recombinantly expressed human β, embryonic, and perinatal myosin subfragment-1. We found large effects in the developmental myosins, with the most dramatic in perinatal, but minimal effects in β myosin, and magnitude of changes correlated partially with clinical severity. The mutations in the developmental myosins dramatically decreased the step size and load-sensitive actin-detachment rate of single molecules measured by optical tweezers, in addition to decreasing ATPase cycle rate. In contrast, the only measured effect of R671C in β myosin was a larger step size. Our measurements of step size and bound times predicted velocities consistent with those measured in an in vitro motility assay. Finally, molecular dynamics simulations predicted that the arginine to cysteine mutation in embryonic, but not β, myosin may reduce pre-powerstroke lever arm priming and ADP pocket opening, providing a possible structural mechanism consistent with the experimental observations. This paper presents the first direct comparisons of homologous mutations in several different myosin isoforms, whose divergent functional effects are yet another testament to myosin’s highly allosteric nature.
Karyological diversity among six medicinally important species of Acanthaceae in Bangladesh
Authors: Anjum Nowshin , Dash Chandan Kumar , Sultana Syeda Sharmeen
Published: July 2023

Six medicinally important species of Acanthaceae family namely,Asystasia gangetica(L.) T. Anderson,Barleria cristataL.,Braleria prionitisL.,Ruellia simplexC. Wright,Thunbergia erecta(Benth.) T. Anderson andThunbergia mysorensis(Wright) T. Anderson were cytogenetically investigated to evaluate the karyotype diversity and chromosomal relationship. The somatic chromosome numbers and the centromeric formulas of these species were 2n = 2x = 24 (22m + 2sm) forA. gangetica, 2n = 4x = 40 (38m + 2sm) forB. cristata, 2n = 4x = 40 (36m + 4sm) forB. prionitis, 2n = 2x = 36 (34m + 2sm) forR. simplex, 2n = 4x+6 = 62 (56m + 6sm) forT. erectaand 2n = 2x = 34 (34m) forT. mysorensis. Considering the karyotype assessment parameters,T. erecta, R. simplex, B. cristataandB. prionitiswere shown to be cytogenetially more advanced thanA. gangeticaandT. mysorensis. Three categories of karyotypes were observed such as 1B type inB. cristata, B. prionitis, R. simplexandT. mysorensis, whereas the most primitive one 1A inA. gangeticaand the most advanced karyotype 2B inT. erecta. Three new reports of somatic chromosome count yielded in case ofA. gangetica, R. simplexandT. mysorensiswhich might have been resulted from aneuploidy or allopolyploidy. The cytological data presented for six species of the Acanthaceae family demonstrated significant variation and distinctiveness from one another, assisting in the evaluation of the karyological diversity that aided in the understanding of evolutionary changes.
Auxin signaling in the cambium promotes tissue attachment and vascular development duringArabidopsis thalianagraft formation
Authors: Serivichyaswat Phanu T. , Kareem Abdul , Feng Ming , Melnyk Charles W.
Published: July 2023

The remarkable ability of plants to regenerate wounds is exemplified during the process of plant grafting when two plants are cut and joined together to grow as one. During graft healing, damaged tissues attach, cells proliferate and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role and mutants perturbed in auxin response fail to successfully graft. Here, we investigated the role of individual cell types and their response to auxin duringArabidopsis thalianagraft formation. By employing an inducible misexpression system, we blocked auxin response in individual cell types using thebodenlosmutation. We found that auxin signaling in procambial tissues was critical for both successful tissue attachment and also for vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambium and procambium are key tissues that allow both tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of regeneration biology and the function of cambium.
Sub-surface deformation of individual fingerprint ridges during tactile interactions
Authors: Corniani Giulia , Lee Zing S , Carré Matt J , Lewis Roger , Delhaye Benoit P , Saal Hannes P
Published: July 2023

The human fingertip can detect small tactile features with a spatial acuity roughly the width of a fingerprint ridge. However, how individual ridges deform under contact to support accurate and high-precision tactile feedback is currently unknown. The complex mechanical structure of the glabrous skin, composed of multiple layers and intricate morphology within which mechanoreceptors are embedded, makes this question challenging. Here, we used optical coherence tomography to image and track sub-surface deformations of hundreds of individual fingerprint ridges during contact events at high spatial resolution in vivo. We calculated strain patterns in both the stratum corneum and viable epidermis in response to a variety of tactile stimuli, including static indentation, stick-to-slip events, sliding of a flat surface in different directions, and interaction with small tactile features, such as edges and grooves. We found that ridges could stretch, compress, and undergo considerable shearing orthogonal to the skin surface, but there was limited horizontal shear. Therefore, it appears that the primary components of ridge deformation and, potentially, neural responses are deformations of the ridge flanks and their relative movement, rather than overall bending of the ridges themselves. We conclude that the local distribution of mechanoreceptors across the ridges might be ideally suited to extract the resulting strain gradients and that the fingertip skin may possess a higher mechanical spatial resolution than that of a single ridge.