bluuebunny/crossref_metadata_2025 huggingface dataset:
pH-responsive self-assembled compartments as tuneable model protocellular membrane systems
Authors: Sarkar Susovan , Dagar Shikha , Lahiri Kushan , Rajamani Sudha
Published: May 2022

Prebiotically plausible single-chain amphiphiles are enticing as model protocellular compartments to study the emergence of cellular life owing to their self-assembling properties. Here, we investigated the self-assembly behaviour of mono-N-dodecyl phosphate (DDP) and mixed systems of DDP with dodecyl 1-dodecanol (DOH) at varying pH conditions. Membranes composed of DDP showed pH-responsive vesicle formation in a wide range of pH with a low critical bilayer concentration (CBC). Further, the addition of DOH to DDP membrane system enhanced vesicle formation and stability in alkaline pH regimes. We also compared the high-temperature behaviour of DDP and DDP-DOH membranes with conventional fatty acid membranes. Both, DDP and DDP:DOH mixed membranes possess packing that is similar to decanoic acid membrane. However, the micropolarity of these systems are similar to phospholipid membranes. Finally, the pH-dependent modulation of different phospholipid membranes doped with DDP was also demonstrated to engineer tuneable membranes with potential translational implications.
Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems
Authors: Li Zexu , Li Zihan , Cheng Xiaolong , Wang Xiaofeng , Ma Shixin , Wang Shengnan , Lu Zhiyan , Zhang Han , Zhao Wenchang , Chen Zhisong , Yao Yingjia , Chao Lumen , Li Wei , Fei Teng
Published: May 2022

CRISPR-Cas13 systems have been adapted as versatile toolkits for RNA-related applications. Here we systematically evaluate the performance of several popular Cas13 family effectors (Cas13a, Cas13b and Cas13d) under lentiviral vectors and reveal surprisingly differential defects and characteristics of these systems. Using RNA immunoprecipitation sequencing, transcriptome profiling, biochemistry analysis, high-throughput CRISPR-Cas13 screening and machine learning approaches, we determine that each Cas13 system has its intrinsic RNA targets in mammalian cells. Viral process-related host genes can be targeted by Cas13 and affect production of fertile lentiviral particles, thereby restricting the utility of lentiviral Cas13 systems. Multiple RNase activities of Cas13 are involved in endogenous RNA targeting. Unlike target-induced nonspecific collateral effect, intrinsic RNA cleavage can be specific, target-independent and dynamically tuned by varied states of Cas13 nucleases. Our work provides guidance on appropriate use of lentiviral Cas13 systems and further raises cautions about intrinsic RNA targeting during Cas13-based basic and therapeutic applications.
Activity-based CRISPR Scanning Uncovers Allostery in DNA Methylation Maintenance Machinery
Authors: Ngan Kevin C. , Hoenig Samuel M. , Gosavi Pallavi M. , Tanner David A. , Lue Nicholas Z. , Garcia Emma M. , Lee Ceejay , Liau Brian B.
Published: May 2022

Allostery enables dynamic control of protein function. A paradigmatic example is the tightly orchestrated process of DNA methylation maintenance. Despite their fundamental importance, systematic identification of allosteric sites remains highly challenging. Here we perform CRISPR scanning on the essential maintenance methylation machinery—DNMT1 and its partner UHRF1—with the activity-based inhibitor decitabine to uncover allosteric mechanisms regulating DNMT1. Through computational analyses, we identify putative mutational hotspots in DNMT1 distal from the active site that encompass mutations spanning a multi-domain autoinhibitory interface and the uncharacterized BAH2 domain. We biochemically characterize these mutations as gain-of-function mutations that increase DNMT1 activity. Extrapolating our analysis to UHRF1, we discern putative gain-of-function mutations in multiple domains, including key residues across the autoinhibitory TTD–PBR interface. Collectively, our findings highlight the utility of activity-based CRISPR scanning for nominating candidate allosteric sites, even beyond the direct drug target.
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli
Authors: Cox Dezerae , Ormsby Angelique R. , Reid Gavin E. , Hatters Danny M.
Published: May 2022

Accurate spatio-temporal organization of the proteome is essential for cellular homeostasis. However, a detailed mechanistic understanding of this organization and how it is altered in response to external stimuli in the intact cellular environment is as-yet unrealized. To address this need, ‘protein painting’ methods have emerged as a way to gain insight into the conformational status of proteins within cells at the proteome-wide scale. For example, tetraphenylethene maleimide (TPE-MI) has previously been used to quantify the engagement of quality control machinery with client proteins in cell lysates. Here, we showcase the ability of TPE-MI to additionally reveal proteome network remodeling in whole cells in response to a cohort of commonly used pharmacological stimuli of varying specificity. We report specific, albeit heterogeneous, responses to individual stimuli that coalesce on a conserved set of core cellular machineries. This work expands our understanding of proteome conformational remodeling in response to cellular stimuli, and provides a blueprint for assessing how these conformational changes may contribute to disorders characterized by proteostasis imbalance.
Pathway and directional specificity of Hebbian plasticity induction in the cortical visual motion processing network
Authors: Bevilacqua Michele , Huxlin Krystel R. , Hummel Friedhelm C. , Raffin Estelle
Published: May 2022

Cortico-cortical paired associative stimulation (ccPAS), which repeatedly pairs single pulse TMS over two distant brain regions with a specific time interval, is thought to modulate synaptic plasticity. Applied to the motion cortical pathway, ccPAS has been shown to improve motion discrimination when specifically targeting backward projections, stimulating the medio-temporal area (MT) followed by the primary visual cortex (V1). However, there is no direct neuroimaging evidence of the spatial selectivity of the ccPAS effects (i.e., pathway or direction specificity) or detailing the exact nature of the ccPAS effects (i.e., the oscillatory signature, timing…). In this study, we applied ccPAS along the motion discrimination pathway, in the top-down direction (MT-to-V1: “Backward ccPAS”) and in the bottom-up direction (V1-to-MT: “Forward ccPAS”) in sixteen healthy volunteers and compared changes in visual network activity in response to single pulse TMS over V1 and MT using spectral granger causality (sGC). The sGC results showed common increases in direct V1-to-MT and V1-to-IPS bottom-up inputs in the high Beta/low Gamma band (25-40 Hz) for both ccPAS, probably reflecting task exposure. However, a clear distinction in information transfer occurred in the re-entrant MT-to-V1 signals, which were only modulated by Backward ccPAS. This difference was predictive of the behavioural improvements at the motion discrimination task. Our results support the view of the possibility to specifically enhance re-entrant Alpha oscillatory signals from MT-to-V1 to promote motion discrimination performance through Backward ccPAS. These findings contribute to better understanding visual processing in healthy subjects and how it can be modulated to pave the way to clinical translation in vision handicapped patients. The changes in re-entrant MT-to-V1 inputs could help to provide single-subject prediction scenarios in patients suffering from a visual system stroke, in whom visual recovery might partly rely on the top-down inputs to the spared V1 neurons.
DNA binding domain undergoes dynamic and selective protein–protein interactions to facilitate CTCF insulation
Authors: Rong Zhou , Kai Tian , Jie Huang , Wenjia Duan , Hongye Fu , Ying Feng , Hui Wang , Yongpeng Jiang , Yuanjun Li , Rui Wang , Jiazhi Hu , Hanhui Ma , Zhi Qi , Xiong Ji
Published: May 2022

CTCF is required for three-dimensional chromatin organization and a predominant insulator protein. However, its roles in insulating enhancers have not been fully explained in 3D nuclear organization. Here, we found that the CTCF DNA binding domain (DBD) forms dynamic self-interacting clusters. We next investigated the spatial relationships between these clusters and other transcription regulators with a light-induced imaging system. Strikingly, CTCF DBD clusters were found to incorporate other insulator proteins but are not coenriched with transcriptional activators in the nucleus. This property is not observed in other domains of CTCF or the DBDs of other transcription factors. Moreover, endogenous CTCF shows a phenotype consistent with the DBD by forming small protein clusters and interacts less transcriptional activators bound, CTCF motif arrays. Our results reveal an interesting phenomenon that CTCF DBD interacts with insulator proteins and selectively localizes to nuclear positions with lower concentrations of transcriptional activators, providing new insights into the insulation function of CTCF.
High-content cellular screen image analysis benchmark study
Authors: Bray Mark-Anthony , de Weck Antoine , Durand Eric , Fang Jian , Gabriel Daniela , Janssens Rens , Moutsatsos Ioannis , Spiegel Stephan , Zhang Xian
Published: May 2022

Recent development of novel methods based on deep neural networks has transformed how high-content microscopy cellular images are analyzed. Nonetheless, it is still a challenge to identify cellular phenotypic changes caused by chemical or genetic treatments and to elucidate the relationships among treatments in an unsupervised manner, due to the large data volume, high phenotypic complexity and the presence of a priori unknown phenotypes. Here we benchmarked five deep neural network methods and two feature engineering methods on a well-characterized public data set. In contrast to previous benchmarking efforts, the manual annotations were not provided to the methods, but rather used as evaluation criteria afterwards. The seven methods individually performed feature extraction or representation learning from cellular images, and were consistently evaluated for downstream phenotype prediction and clustering tasks. We identified the strengths of individual methods across evaluation metrics, and further examined the biological concepts of features automatically learned by deep neural networks.
The Individualized Neural Tuning Model: Precise and generalizable cartography of functional architecture in individual brains
Authors: Feilong Ma , Nastase Samuel A. , Jiahui Guo , Halchenko Yaroslav O. , Gobbini M. Ida , Haxby James V.
Published: May 2022

Quantifying how brain functional architecture differs from person to person is a key challenge in human neuroscience. Current individualized models of brain functional organization are based on brain regions and networks, limiting their use in studying fine-grained vertex-level differences. In this work, we present the Individualized Neural Tuning (INT) model, a fine-grained individualized model of brain functional organization. The INT model is designed to have vertex-level granularity, to capture both representational and topographic differences, and to model stimulus-general neural tuning. Through a series of analyses, we demonstrate that (a) our INT model provides a reliable individualized measure of fine-grained brain functional organization, (b) it accurately predicts individualized brain response patterns to new stimuli, and (c) it requires only 10–20 minutes of data for good performance. The high reliability, specificity, precision, and generalizability of our INT model affords new opportunities for building brain-based biomarkers based on naturalistic neuroimaging paradigms.
Adaptive diversification and niche packing on rugged fitness landscapes
Authors: Rubin Ilan N. , Ispolatov Yaroslav , Doebeli Michael
Published: May 2022

Explaining the emergence of diversity and the coexistence of competing types has long been one of the main goals of ecological theory. Rugged fitness landscapes have often been used to explain diversity through the presence of local peaks, or adaptive zones, in the fitness landscape acting as available niches for different species. Alternatively, niche-packing and theories based on limiting similarity describe frequency-dependent selection leading to the organic differentiation of a continuous phenotype space into multiple coexisting types. By combining rugged carrying capacity landscapes with frequency-dependent selection, here we investigate the effects of ruggedness on adaptive diversification and stably maintained diversity. We show that while increased ruggedness often leads to a decreased opportunity for adaptive diversification, it is the shape of the global carrying capacity function, not the local ruggedness, that determines the diversity of the ESS and the total diversity a system can stably maintain.
Effectiveness of integrated care for older adults with depression and hypertension in rural China: a cluster randomized controlled trial
Authors: Chen Shulin , Conwell Yeates , Xue Jiang , Li Lydia , Zhao Tingjie , Tang Wan , Bogner Hillary , Dong Hengjin
Published: May 2022

Background

Effectiveness of integrated care management for common, comorbid physical and mental disorders has been insufficiently examined in low- and middle-income countries. We tested hypotheses that older adults treated in rural Chinese primary care clinics with integrated care management of comorbid depression and HTN would show greater improvements in depression symptom severity and hypertension (HTN) control than those who received usual care.

Methods and findings

The study was a 12-month cluster randomized controlled trial conducted from 2014 through 2017, with analyses conducted in 2020-2021. Subjects were rural village clinics of randomly selected towns in Zhejiang Province, China. Ten towns with a total of 218 rural village primary care clinics were randomized, five towns each, to deliver the Chinese Older Adult Collaborations in Health (COACH) intervention or enhanced care-as-usual (eCAU). The COACH intervention consisted of algorithm-driven treatment of depression and HTN by village primary care doctors supported by village lay workers with consultation from centrally-located psychiatrists. Subjects included clinic patients aged ≥60 years with a diagnosis of HTN and clinically significant depressive symptoms (PHQ-9 score ≥10). Of 2899 eligible subjects, 2365 (82%) agreed to participate and were followed for 12 months. Observers were blinded to study hypotheses but not to group assignment. Primary outcomes specified a priori were change in depression symptom severity and proportion with controlled HTN.

Compared with 1133 subjects who received eCAU, 1232 COACH subjects showed greater reduction in depressive symptoms (Cohen’s d [±SD] = -0.21 [-0.25, -0.17]) and greater likelihood of achieving HTN control (OR [95% CI] = 18.24 [8.40, 39.63]). Exploratory post hoc analyses showed that COACH subjects who accepted an antidepressant had greater symptom reduction than either those who declined the medication or received eCAU. HTN control improved in COACH subjects regardless of antidepressant use.

Conclusions

The COACH model appears effective in managing comorbid depression and HTN in older adult residents of rural Chinese villages. Integrated care management of comorbid depression and common medical illness may be a useful approach in other low resourced settings in which specialty geriatric mental health care is lacking.
Multiple Burdens of Road Traffic Crashes in Pokhara, Nepal: A Patient Approach
Authors: Bishwokarma Sapana , Adhikari Chiranjivi , Khatri Dhurba , Gauchan Bikash , Sapkota Vishnu Prasad , Ranabhat Chhabi Lal
Published: May 2022

Background

The economic burden and cost-related evidence from primary data of road traffic crashes (RTCs) in Nepal are limited.

Aim

This study assessed the disability-adjusted life years (DALYs), the cost associated with RTCs, and socio-demographic and injury related factors.

Methods

We carried out a retrospective cross-sectional, institution-based survey of the RTC victims in the last one year to 45 days prior to the survey, in Pokhara and the surroundings in Kaski district, a mid-hilly district and the headquarter of Gandaki province of Nepal. A sample of 107 RTC victims, registered in different hospitals, police offices and health insurance offices, were retrospectively approached. A semi-structured interview schedule was used to collect data. Data were entered into EpiData before being imported, and analysed in the Statistical Package for Social Sciences (SPSS) and MS-Excel. Descriptive statistics were generated by calculating costs and DALYs, and inferential analysis was used to investigate the relationship between DALYs and independent variables.

Results

More than one-third (37.4%) of the 107 victims were between the ages of 25 and 44, and more than half (60.7%) were men. The cost per million person-years of RTC was around US $ 82,800. Similarly, around 1021 DALYs per million person-years are attributed to RTC, and more than 99% of them are shared by YLL. We observed the highest number of frequencies of young (p<.01), having university degree (p<.01), unemployed (p<.05), motorcyclists (p<.01), highest economic quintile (p<.01), and seriously injured (p<.01). In addition, we also observed a low positive correlation (r=0.33, p<.01) between DALYs and the victim’s indirect cost.

Conclusion

The cost and DALYs associated by RTC of Kaski district were around US $ 82,800 and 1021 per million person-years in 2017, respectively. Young unemployed motorcyclists were the most frequent victims. Victim’s indirect cost is increased with DALYs, suggesting a policy implication.
Predictors of 90-Day Colectomy in Hospitalized Patients Receiving Infliximab for Acute Severe Ulcerative Colitis at a Tertiary Care Center
Authors: Berinstein Jeffrey A. , Atkuri Neelakanta Anurag , Berinstein Elliot M. , Sheehan Jessica L. , Johnson Laura A. , Cohen-Mekelburg Shirley A. , Jiang Hui , Wakim Nicole I. , Kidwell Kelley M. , Nahum-Shani Inbal Billie , Robert  , Waljee Akbar K. , Higgins Peter D.R.
Published: May 2022

BACKGROUND & AIMS

Acute severe ulcerative colitis (ASUC) is a life-threatening presentation of ulcerative colitis requiring prompt treatment. Infliximab (IFX) rescue therapy can prevent colectomy in patients with ASUC.

METHODS

We performed a cohort study of adult patients hospitalized with ASUC between 01/2014 – 02/2021 who received infliximab rescue therapy. Using multivariable logistic regression, baseline and longitudinal laboratory predictors of colectomy within 90 days of index hospitalization were identified and used to develop a risk prediction model and prognostic scoring system to identifying patients at risk for colectomy. Model performance was assessed using area under the receiver operator characteristic curve (AUC) analysis.

RESULTS

166 patients with ASUC who received infliximab rescue therapy were identified. Overall, 24.7% (n=41) underwent colectomy within 90 days. Multivariate analysis revealed that colectomy within 90 days could be predicted by having a calculated IFX clearance of >53L/d (OR 2.28, 95% CI 0.99, 5.22), a day 0 absolute C-reactive protein (CRP) > 91mg/L (OR 3.49, 95% CI 1.58 to 8.08), a decrease in CRP of < 43% from day 0 to day 3 (OR 4.13, 95% CI 1.84 to 9.94), and a decrease in CRP of < 9% from the day of IFX administration to one day post-IFX administration (OR 4.20, 95% CI 1.74 to 10.4). Using these predictors, two highly accurate prognostic scoring system were developed to identify patients at risk for requiring colectomy both prior to administering infliximab (AUC 0.76) and after administer infliximab rescue therapy (AUC 0.81).

CONCLUSION

We identified important baseline and longitudinal laboratory predictors of colectomy within 90-days among patients with ASUC receiving infliximab rescue therapy and developed accurate prognostic scores to determine risk of colectomy. These scores can be used risk-stratify patients and facilitate personalized management.
From recency to central tendency biases in working memory: a unifying network model
Authors: Boboeva Vezha , Pezzotta Alberto , Clopath Claudia , Akrami Athena
Published: May 2022

The central tendency bias, or contraction bias, is a phenomenon where the judgment of the magnitude of items held in working memory appears to be biased towards the average of past observations. It is assumed to be an optimal strategy by the brain, and commonly thought of as an expression of the brain’s ability to learn the statistical structure of sensory input. On the other hand, recency biases such as serial dependence are also commonly observed, and are thought to reflect the content of working memory. Recent results from an auditory delayed comparison task in rats, suggest that both biases may be more related than previously thought: when the posterior parietal cortex (PPC) was silenced, both short-term and contraction biases were reduced. By proposing a model of the circuit that may be involved in generating the behavior, we show that a volatile working memory content susceptible to shifting to the past sensory experience – producing short-term sensory history biases – naturally leads to contraction bias. The errors, occurring at the level of individual trials, are sampled from the full distribution of the stimuli, and are not due to a gradual shift of the memory towards the sensory distribution’s mean. Our results are consistent with a broad set of behavioral findings and provide predictions of performance across different stimulus distributions and timings, delay intervals, as well as neuronal dynamics in putative working memory areas. Finally, we validate our model by performing a set of human psychophysics experiments of an auditory parametric working memory task.
Reemergence of the Murine Bacterial Pathogen Chlamydia muridarum in Laboratory Mouse Colonies
Authors: Mishkin Noah , Ricart Arbona Rodolfo J , Carrasco Sebastian E , Lawton Samira , Henderson Kenneth S. , Momtsios Panagiota , Sigar Ira M , Ramsey Kyle H , Cheleuitte-Nieves Christopher , Monette Sebastien , Lipman Neil S
Published: May 2022

Chlamydia muridarum (Cm) was detected in mice from 2 colonies with lymphoplasmacytic pulmonary infiltrates using PCR and immunohistochemistry. This discovery was unexpected as Cm infection had not been reported in laboratory mice since the 1940’s. A Cm specific PCR assay was developed and testing implemented for resident colonies from 8 vivaria from 3 academic institutions, 58 incoming mouse shipments from 39 academic institutions, and mice received from 55 commercial breeding colonies (4 vendors). To estimate Cm’s global prevalence in laboratory colonies, a database containing 11,387 metagenomic fecal microbiota samples from 120 institutions and a cohort of 900 diagnostic samples from 96 institutions were examined. Results indicate significant prevalence amongst academic institutions with Cm detected in 62.9% of soiled bedding sentinels from 3 institutions; 32.7% of incoming mouse shipments from 39 academic institutions; 14.2% of 120 institutions submitting microbiota samples; and 16.2% of the diagnostic sample cohort. All samples from commercial breeding colonies were negative. Additionally, naïve NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice exposed to Cm shedding mice and their soiled bedding developed clinical disease 21 to 28 days following exposure. These mice had a moderate-to-severe histiocytic and neutrophilic bronchointerstitial pneumonia with respiratory epithelium demonstrating inclusions, chlamydial major outer membrane protein immunostaining, and hybridization with a Cm reference sequence (GenBank accession no. U68436). Cm was isolated on HeLa 229 cells from lungs, cecum, and feces of a Cm infected NSG mouse. The considerable prevalence of Cm is likely attributed to widespread global interinstitutional distribution of unique mouse strains and failure to recognize that some of these mice were from enzootically infected colonies. Given that experimental Cm colonization of mice results in a robust immune response and, on occasion, pathology, natural infection may confound experimental results. Therefore, Cm should be excluded and eradicated from endemically infected laboratory mouse colonies.
Integration of sound and locomotion information by auditory cortical neuronal ensembles
Authors: Vivaldo Carlos Arturo , Lee Joonyeup , Shorkey MaryClaire , Keerthy Ajay , Rothschild Gideon
Published: May 2022

The ability to process and act upon incoming sounds during locomotion is critical for survival. Intriguingly, sound responses of auditory cortical neurons are on average weaker during locomotion as compared to immobility and these results have been suggested to reflect a computational resource allocation shift from auditory to visual processing. However, the evolutionary benefit of this hypothesis remains unclear. In particular, whether weaker sound-evoked responses during locomotion indeed reflect a reduced involvement of the auditory cortex, or whether they result from an alternative neural computation in this state remains unresolved. To address this question, we first used neural inactivation in behaving mice and found that the auditory cortex plays a critical role in sound-guided behavior during locomotion. To investigate the nature of this processing, we used two-photon calcium imaging of local excitatory auditory cortical neural populations in awake mice. We found that underlying a net inhibitory effect of locomotion on sound-evoked response magnitude, spatially intermingled neuronal subpopulations were differentially influenced by locomotion. Further, the net inhibitory effect of locomotion on sound-evoked responses was strongly shaped by elevated ongoing activity. Importantly, rather than reflecting enhanced “noise”, this ongoing activity reliably encoded the animal’s locomotion speed. Prediction analyses revealed that sound, locomotive state and their integration are strongly encoded by auditory cortical ensemble activity. Finally, we found consistent patterns of locomotion-sound integration in electrophysiologically recorded activity in freely moving rats. Together, our data suggest that auditory cortical ensembles are not simply suppressed by locomotion but rather encode it alongside sound information to support sound perception during locomotion.
A kinetic basis for curvature sensing by septins
Authors: Shi Wenzheng , Cannon Kevin S. , Curtis Brandy N. , Edelmaier Christopher , Gladfelter Amy S. , Nazockdast Ehssan
Published: May 2022

The ability of cells to sense and communicate their shape is central to many of their functions. Much is known about how cells generate complex shapes, yet how they sense and respond to geometric cues remains poorly understood. Septins are GTP-binding proteins that localize to sites of micron-scale membrane curvature. Assembly of septins is a multi-step and multi-scale process but it is unknown how these discrete steps lead to curvature sensing. Here we experimentally examine the time-dependent binding of septins at different curvatures and septin bulk concentrations. These experiments unexpectedly indicated that the curvature preference of septins is not absolute but rather is sensitive to the combinations of membrane curvatures present in a reaction, suggesting there is competition between different curvatures for septin binding. To understand the basis of this result, we developed a kinetic model that connects septins’ self-assembly and curvature sensing properties. Our experimental and modeling results are consistent with curvature-sensitive assembly being driven by cooperative associations of septin oligomers in solution with the bound septins. When combined, the work indicates septin curvature sensing is kinetically determined, sensitive to bulk concentration, and the available membrane curvatures. While much geometry-sensitive assembly in biology is thought to be guided by intrinsic material properties of molecules, this is an important example of how kinetics can drive mesoscale curvature-sensitive assembly of polymers.

Significance Statement

Cells use their membrane curvature to coordinate the activation and spatiotemporal compartmentalization of molecules during key cellular processes. Recent works have identified different proteins that can sense or induce membrane curvature from nano- to micron-scale. Septins are nanoscopic cytoskeletal proteins that preferentially bind to membranes with a narrow range of micron-scale curvatures. Yet the sensing mechanism remains ambiguous. Using a combination of microscopy and kinetic modeling, we show that, unlike most proteins that sense curvature in a single protein scale, curvature sensing in septins is determined kinetically through their multi-step hierarchical assembly on the membrane. This introduces a novel kinetic basis of fidelity, where the same protein can be deployed for differential binding sensitivities in different cellular contexts.
Cachd1 is a novel Frizzled- and LRP6-interacting protein required for neurons to acquire left-right asymmetric character
Authors: Powell Gareth T. , Faro Ana , Zhao Yuguang , Stickney Heather , Novellasdemunt Laura , Henriques Pedro , Gestri Gaia , White Esther Redhouse , Ren Jingshan , Lu Weixian , Young Rodrigo M. , Hawkins Thomas A. , Cavodeassi Florencia , Schwarz Quenten , Dreosti Elena , Raible David W. , Li Vivian S. W. , Wright Gavin J. , Jones E. Yvonne , Wilson Stephen W.
Published: May 2022

Neurons on left and right sides of the nervous system frequently show asymmetric properties but how these differences arise is poorly understood. Through a forward genetic screen in zebrafish, we find that loss of function of the transmembrane protein Cachd1 results in right-sided habenula neurons adopting left-sided character. Cachd1 is expressed in habenula neuron progenitors, functions symmetrically downstream of asymmetric environmental signals that determine laterality and influences timing of the normally left-right asymmetric patterns of neurogenesis. Unbiased screening for Cachd1 partners identified the Wnt co-receptor Frizzled7 and further biochemical and structural analysis revealed Cachd1 can bind simultaneously to Fzd proteins and Lrp6, bridging between these two Wnt co-receptors. Consistent with these structural studies, lrp6 mutant zebrafish show symmetric habenulae with left-sided character and epistasis experiments with other Wnt pathway genes support an in vivo role for Cachd1 in modulating Wnt pathway activity in the brain. Together, these studies identify Cachd1 as a conserved novel Wnt-receptor interacting protein with roles in regulating neurogenesis and neuronal identity.
Quantitative analysis of three-dimensional cell organisation and concentration profiles within curved epithelial tissues
Authors: Prabhakara Chaitra , Iyer Krishnan Swaminathan , Rao Madan , Saunders Timothy E , Mayor Satyajit
Published: May 2022

Organogenesis involves folding of flat epithelial tissues into three-dimensional (3D) shapes. Quantitative analysis in 3D of the concentration gradients of biochemical and mechano-chemical cues that shape the tissue has remained a challenge, due to the complex tissue geometries. Towards addressing this, we present a methodology that transforms the cartesian images acquired by high-resolution confocal microscopy of curved tissues into a laminar organisation from the outer-most tissue surface. We further detail a data-based intensity correction method to account for the intensity variations that arise as a consequence of the global geometry. Applying our approach to the dome-shaped Drosophila wing disc, we quantitatively estimate the concentration profiles of different biochemical signals, including the Wingless morphogen gradient. The laminar data-organisation method also enabled visualisation of apical and basal layers facilitating an accurate 3D reconstruction of cell shapes within the pseudostratified epithelium. We find that the columnar disc proper cells have irregular 3D shapes and undergo frequent apico-basal cell intercalations, concomitantly leading to cell neighbour exchanges along the apico-basal axis. The workflow of image processing described here may be employed to quantify 3D concentration gradients and 3D cellular organisation in any layered curved tissue, provided a marker describing the reference surface manifold is available.
A curated human cellular microRNAome based on 196 primary cell types
Authors: Patil Arun H. , Baran Andrea , Brehm Zachary P. , McCall Matthew N. , Halushka Marc K.
Published: May 2022

Background

An incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA sequencing datasets, there is an opportunity to more fully understand the general distribution of miRNAs at the cell level.

Results

From the NCBI Sequence Read Archive, we obtained 6,054 human primary cell datasets and processed 4,184 of them through the miRge3.0 small RNA-seq alignment software. This dataset was curated down, through shared miRNA expression patterns, to 2,077 samples from 196 unique cell types derived from 175 separate studies. Of 2,731 putative miRNAs listed in miRBase (v22.1), 2,452 (89.8%) were detected. Among reasonably expressed miRNAs, 108 were designated as cell specific/near specific, 59 as infrequent, 52 as frequent, 54 as near ubiquitous and 50 as ubiquitous. The complexity of cellular microRNA expression estimates recapitulates tissue expression patterns and informs on the miRNA composition of plasma.

Conclusions

This study represents the most complete reference, to date, of miRNA expression patterns by primary cell type. The data is available through the human cellular microRNAome track at the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgHubConnect) and an R/Bioconductor package (https://bioconductor.org/packages/microRNAome/).
Membrane stretching activates calcium-permeability of a putative channel Pkd2 during fission yeast cytokinesis
Authors: Poddar Abhishek , Hsu Yen-Yu , Zhang Faith , Shamma Abeda , Kreais Zachary , Muller Clare , Malla Mamata , Ray Aniruddha , Liu Allen , Chen Qian
Published: May 2022

Pkd2 is the fission yeast homolog of polycystins. This putative ion channel localizes to the plasma membrane. It is required for the expansion of cell volume during interphase growth and cytokinesis, the last step of cell division. However, the channel activity of Pkd2 remains untested. Here, we examined the calcium permeability and mechanosensitivity of Pkd2 through in vitro reconstitution and calcium imaging of the pkd2 mutant cells. Pkd2 was translated and inserted into the lipid bilayer of giant unilamellar vesicles using a cell-free expression system. The reconstituted Pkd2 permeated calcium when the membrane was stretched via hypo-osmotic shock. In vivo, inactivation of Pkd2 through a temperature-sensitive mutation pkd2-B42 reduced the average intracellular calcium level by 34%. Compared to the wild type, the hypomorphic mutation pkd2-81KD reduced the amplitude of hypo-osmotic shock-triggered calcium spikes by 59%. During cytokinesis, mutations of pkd2 reduced by 60% the calcium spikes that accompany the cell separation and the ensuing membrane stretching. We concluded that fission yeast polycystin Pkd2 allows calcium influx when activated by membrane stretching, representing a likely mechanosensitive channel that contributes to the cytokinetic calcium spikes.
Toxic effects of elevated bile acid levels on fetal myocardium in intrahepatic cholestasis of pregnancy, a retrospective study from a neonatal perspective
Authors: Wang Junnai , Shi Wei , Lun Weiwei
Published: May 2022

Introduction

Intrahepatic cholestasis of pregnancy (ICP) is a liver disease which may lead to a sudden fetal death. Previous studies have suggested that the fetal accident may be related to their cardiac dysfunction. However, the relationship between fetal cardiac dysfunction and their maternal bile acid levels is not clear. The objective was to clarify the relationship from a neonatal perspective and to furtherly make clear the after-effect by analysing the cardiac parameters of the older neonates.

Materials and methods

In this case-control study, patients and their neonates, managed between 10 September 2018 and 30 June 2021 at a Chinese university hospital center, were divided into severe ICP group, mild ICP group and control gestational group. The maternal bile acid levels and the cardiac paramerers of one-day-old neonates and five-day-old neonates were analysed, respectively.

Results

The specific-myocardial enzyme(CK-MB) and left ventricular fraction shortening(FS) of neonates showed significant differences between ICP group and control group, and were meaningfully correlated with maternal bile acid levels. However, There was no significant difference in cardiac injury parameters of older neonates between the ICP and control groups.

Conclusions

The elevated maternal bile acid levels can lead to fetal myocardial injury and the injury can be recovered after removel from high concentrations of bile acid.
Identification of CD133+Intercellsomes in Intercellular Communication to Offset Intracellular Signal Deficit
Authors: Kaneko Kota , Liang Yan , Liu Qing , Zhang Shuo , Scheiter Alexander , Song Dan , Feng Gen-Sheng
Published: May 2022

CD133 (prominin 1) is widely viewed as a cancer stem cell marker in association with drug resistance and cancer recurrence. Herein we report that with impaired RTK-Shp2 Ras-Erk signaling, heterogenous hepatocytes form clusters that manage to divide during liver regeneration. These hepatocytes are characterized by upregulated CD133 while negative for other progenitor cell markers. Pharmaceutical inhibition of proliferative signaling also induced CD133 expression in various cancer cell types, suggesting an inherent and common mechanism of stress response. Super-resolution and electron microscopy localize CD133 on intracellular vesicles that apparently migrate between cells, which we name “intercellsome”. Isolated CD133+intercellsomes are enriched with mRNAs rather than miRNAs. Single-cell RNA sequencing reveals lower intracellular diversity (entropy) of mitogenic mRNAs in Shp2-deficient cells, which may be remedied by intercellular mRNA exchanges between CD133+cells. CD133-deficient cells are more sensitive to proliferative signal inhibition in livers and intestinal organoids. These data suggest a mechanism of intercellular communication to compensate intracellular signal deficit in various cell types.
Characterization of protein isoform diversity in human umbilical vein endothelial cells (HUVECs) via long-read proteogenomics
Authors: Mehlferber Madison M. , Jordan Ben T. , Jeffery Erin D. , Sheynkman Leon , Saquing Jamie , Acharya Bipul R. , Hirschi Karen K. , Sheynkman Gloria M.
Published: May 2022

Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by protein isoforms. To characterize the isoform landscape within ECs, we applied a long read proteogenomics approach to analyze human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream MS analysis to infer protein isoform expression. We detected 53,836 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related geneCDH5, suggesting potential changes in its associated signaling pathways. Finally, we identified novel protein isoforms arising from a diversity of splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.

Graphical Abstract
Domestication of different varieties in the cheese-making fungusGeotrichum candidum
Authors: Bennetot Bastien , Vernadet Jean-Philippe , Perkins Vincent , Hautefeuille Sophie , Rodríguez de la Vega Ricardo C. , O’Donnell Samuel , Snirc Alodie , Grondin Cécile , Lessard Marie-Hélène , Peron Anne-Claire , Labrie Steve , Landaud Sophie , Giraud Tatiana , Ropars Jeanne
Published: May 2022

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions.Geotrichum candidumis a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication inG. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation.
YAP promotes cell-autonomous immune responses to tackle intracellularStaphylococcus aureus in vitro
Authors: Robin Caire , Estelle Audoux , Mireille Thomas , Elisa Dalix , Aurélien Peyron , Killian Rodriguez , Yann Dickerscheit , Hubert Marotte , François Vandenesch , Frédéric Laurent , Jérôme Josse , Verhoeven Paul. O
Published: May 2022

Transcriptional cofactors YAP/TAZ have recently been found to support autophagy and inflammation, which are part of cell autonomous immunity and are critical in antibacterial defense. Here, we studied the role of YAP againstStaphylococcus aureususing CRISPR/Cas9-mutated HEK293 cells and a primary cell-based organoid model. We found thatS. aureusinfection increases YAP transcriptional activity, which is required to reduce intracellularS. aureusreplication. A 770-gene targeted transcriptomic analysis revealed that YAP upregulates genes involved in autophagy/lysosome and inflammation pathways in both infected and uninfected conditions. The YAP/TEAD transcriptional activity promotes autophagic flux and lysosomal acidification, which are important for defense against intracellularS. aureus. Furthermore, the staphylococcal toxin C3 exoenzyme EDIN-B was found effective in preventing YAP-mediated cell-autonomous immune response. This study provides new insights on the anti-S. aureusactivity of YAP, which could be conserved for defense against other intracellular bacteria.

GRAPHICAL ABSTRACT
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting
Authors: Fulcher James M. , Markillie Lye Meng , Mitchell Hugh D. , Williams Sarah M. , Engbrecht Kristin M. , Degnan David J. , Bramer Lisa M. , Moore Ronald J. , Chrisler William B. , Cantlon-Bruce Joshua , Bagnoli Johannes W. , Qian Wei-Jun , Seth Anjali , Paša-Tolić Ljiljana , Zhu Ying
Published: May 2022

Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells using RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrated excellent measurement precision, with deep proteomic and transcriptomic profiling of single-cells. We applied nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing new insights into cell cycle regulation. We also extended nanoSPLITS to single-cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types, and detecting their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Herein, we establish nanoSPLITS as a new multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of single-cell systems.
Enterococcus faecalisandStaphylococcus aureusmixed species infection attenuates pathogen-specific neutrophil responses and impairs bacterial clearance
Authors: Kao Patrick Hien-Neng , Ch’ng Jun-Hong , Chong Kelvin K.L. , Wong Siu Ling , Kline Kimberly A.
Published: May 2022

Enterococcus faecalisis an opportunistic pathogen that is frequently co-isolated with other microbes in catheterized urinary tract infections and chronically infected wounds. WhileE. faecaliscan subvert the host immune response and promote the survival of other microbes via interbacterial synergy, little is known about the impact of immune suppression mediated byE. faecalisand howE. faecalisimpacts the survival of co-infecting microbes. We hypothesized thatE. faecaliscan attenuate neutrophil-mediated responses in mixed-species infection to promote survival of the co-infecting species. Here, we show thatE. faecalisandStaphylococcus aureusmono-species infection activates intracellular ROS production and NET formation, respectively, enabling effective neutrophil-mediated control of the microbial infection. Growth of both bacterial species was enhanced during co-infection in neutrophilsin vitroand in woundsin vivo. E. faecalisreducedS. aureus-induced NET formation andS. aureussuppressedE. faecalis-induced intracellular ROS production. When the species ratios were skewed, the neutrophil reaction profile resembled that elicited by the more abundant species, favoring enhanced survival of the less abundant species. These findings highlight the complexity of the immune response to polymicrobial infections and show that attenuated pathogen-specific immune responses contribute to microbial survival in the mammalian host.
MAGScoT - a fast, lightweight, and accurate bin-refinement software
Authors: Rühlemann Malte Christoph , Wacker Eike Matthias , Ellinghaus David , Franke Andre
Published: May 2022

We introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality metagenome-assembled genomes (MAGs) from the output of multiple genome-binning softwares. MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption. MAGScoT is available via GitHub (https://github.com/ikmb/MAGScoT) and as an easy-to-use Docker container (https://hub.docker.com/repository/docker/ikmb/magscot).