bluuebunny/crossref_metadata_2025 huggingface dataset:
Crosstalk in skin: Loss of desmoglein 1 in keratinocytes inhibits BRAFV600E-induced cellular senescence in human melanocytes
Authors: Tong Xin , Burks Hope E. , Ren Ziyou , Koetsier Jennifer L. , Roth-Carter Quinn R. , Green Kathleen J.
Published: February 2023

Melanoma arises from transformation of melanocytes in the basal layer of the epidermis where they are surrounded by keratinocytes, with which they interact through cell contact and paracrine communication. Considerable effort has been devoted to determining how the accumulation of oncogene and tumor suppressor gene mutations in melanocytes drive melanoma development. However, the extent to which alterations in keratinocytes that occur in the developing tumor niche serve as extrinsic drivers of melanoma initiation and progression is poorly understood. We recently identified the keratinocyte-specific cadherin, desmoglein 1 (Dsg1), as an important mediator of keratinocyte:melanoma cell crosstalk, demonstrating that its chronic loss, which can occur through melanoma cell-dependent paracrine signaling, promotes behaviors that mimic a malignant phenotype. Here we address the extent to which Dsg1 loss affects early steps in melanomagenesis. RNA-Seq analysis revealed that paracrine signals from Dsg1-deficient keratinocytes mediate a transcriptional switch from a differentiated to undifferentiated cell state in melanocytes expressing BRAFV600E, a driver mutation commonly present in both melanoma and benign nevi and reported to cause growth arrest and oncogene-induced senescence (OIS). Of ∼220 differentially expressed genes in BRAFV600Ecells treated with Dsg1-deficient conditioned media (CM), the laminin superfamily member NTN4/Netrin-4, which inhibits senescence in endothelial cells, stood out. Indeed, while BRAFV600Emelanocytes treated with Dsg1-deficient CM showed signs of senescence bypass as assessed by increased senescence-associated β-galactosidase activity and decreased p16, knockdown of NTN4 reversed these effects. These results suggest that Dsg1 loss in keratinocytes provides an extrinsic signal to push melanocytes towards oncogenic transformation once an initial mutation has been introduced.
Bacterial multispecies invasion of human epithelial bladder cells
Authors: Abell-King Charlotte , Pokhrel Alaska , Rice Scott A. , Duggin Iain G. , Söderström Bill
Published: February 2023

Urinary tract infections (UTI) are one of the most common bacterial infections worldwide. While the overall infection course is known on a macroscale, bacterial behavior is not fully understood at the cellular level and bacterial pathophysiology during multispecies infection is not well characterized. Here we establish co-infection models combined with high resolution imaging to compare single- and multi-species bladder cell invasion events in three common uropathogens: uropathogenicEscherichia coli(UPEC),Klebsiella pneumoniaeandEnterococcus faecalis. While all three species invaded the bladder cells, under flow conditions the Gram-positiveE. faecaliswas significantly less invasive compared to the Gram-negative UPEC andK. pneumoniae. When introduced simultaneously during an infection experiment, all three bacterial species sometimes invaded the same bladder cell, at differing frequencies suggesting complex interactions between bacterial species and bladder cells. Inside host cells, we observed encasement ofE. faecaliscolonies specifically by UPEC. During subsequent dispersal from the host cells, only the Gram-negative bacteria underwent infection-related filamentation (IRF). Taken together, our data suggest that bacterial multispecies invasions of single bladder cells are frequent and support earlier studies showing intraspecies cooperation on a biochemical level during UTI.
Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast
Authors: Yamamoto Tetsuya , Asanuma Takahiro , Murakami Yota
Published: February 2023

Heterochromatin has been thought to be assembled by phase separation of chromatin. However, a fission yeast has only three chromosomes and the heterochromatin of this organism is not likely to be assembled by phase separation, which is a collective phenomenon of many chains. Motivated by our recent experiments that demonstrate that the tandemly repeated genes become heterochromatin, we constructed a theory of heterochromatin assembly by taking into account the connectivity of these genes along the chromatin in the kinetic equations of small RNA production and histone methylation, which are the key biochemical reactions involved in the heterochromatin assembly. Our theory predicts that the polymeric nature of the tandemly repeated genes ensures the steady production of small RNAs because of the stable binding of nascent RNAs produced from the genes to RDRC/Dicers at the surface of nuclear membrane. This theory also predicts that the compaction of the tandemly repeated genes suppresses the production of small RNAs, consistent with our recent experiments. This theory can be extended to the small RNA-dependent gene silencing in higher organisms.
Proximity-dependent biotinylation and identification of flagellar proteins inTrypanosoma cruzi
Authors: Won Madalyn M. , Baublis Aaron , Burleigh Barbara A.
Published: February 2023

The flagellated kinetoplastid protozoan and causative agent of human Chagas disease,Trypanosoma cruzi, inhabits both invertebrate and mammalian hosts over the course of its complex life cycle. In these disparate environments,T. cruziuses its single flagellum to propel motile life stages and in some instances, to establish intimate contact with the host. Beyond its role in motility, the functional capabilities of theT. cruziflagellum have not been defined. Moreover, the lack of proteomic information for this organelle, in any parasite life stage, has limited functional investigation. In this study, we employed a proximity-dependent biotinylation approach based on the differential targeting of the biotin ligase, TurboID, to the flagellum or cytosol in replicative stages ofT. cruzi, to identify flagellar-enriched proteins by mass spectrometry. Proteomic analysis of the resulting biotinylated protein fractions yielded 218 candidate flagellar proteins inT. cruziepimastigotes (insect stage) and 99 proteins in intracellular amastigotes (mammalian stage). Forty of these flagellar-enriched proteins were common to both parasite life stages and included orthologs of known flagellar proteins in other trypanosomatid species, proteins specific to theT. cruzilineage and hypothetical proteins. With the validation of flagellar localization for several of the identified candidates, our results demonstrate that TurboID-based proximity proteomics is an effective tool for probing subcellular compartments inT. cruzi.The proteomic datasets generated in this work offer a valuable resource to facilitate functional investigation of the understudiedT. cruziflagellum.

Importance

Trypanosoma cruziis a protozoan parasite that causes Chagas disease, which contributes substantial morbidity and mortality in South and Central America. Throughout its life cycle,T. cruziinteracts with insect and mammalian hosts via its single flagellum, establishing intimate contact with host membranes. Currently, few flagellar proteins have been identified inT. cruzithat could provide insight into the mechanisms involved in mediating physical and biochemical interactions with the host. Here, we set out to identify flagellar proteins in the main replicative stages ofT. cruziusing a proximity-labeling approach coupled with mass spectrometry. The >200 candidate flagellar proteins identified represent the first large scale identification of candidate flagellar proteins inT. cruziwith preliminary validation. These data offer new avenues to investigate the biology ofT. cruzi- host interactions, a promising area for development of new strategies aimed at the control of this pathogen.
Broad sensitivity ofCandida aurisstrains to quinolones and mechanisms of resistance
Authors: Lohse Matthew B. , Laurie Matthew T. , Levan Sophia , Ziv Naomi , Ennis Craig L. , Nobile Clarissa J. , DeRisi Joseph , Johnson Alexander D.
Published: February 2023

The fungal pathogenCandida aurisrepresents a severe threat to hospitalized patients. Its resistance to multiple classes of antifungal drugs and ability to spread and resist decontamination in health-care settings make it especially dangerous. We screened 1,990 clinically approved and late-stage investigational compounds for the potential to be repurposed as antifungal drugs targetingC. aurisand narrowed our focus to five FDA-approved compounds with inhibitory concentrations under 10 µM forC. aurisand significantly lower toxicity to three human cell lines. These compounds, some of which had been previously identified in independent screens, include three dihalogenated 8-hydroxyquinolines: broxyquinoline, chloroxine, and clioquinol. A subsequent structure-activity study of 32 quinoline derivatives found that 8-hydroxyquinolines, especially those dihalogenated at the C5 and C7 positions, were the most effective inhibitors ofC. auris. To pursue these compounds further, we exposedC. auristo clioquinol in an extended experimental evolution study and found thatC. aurisdeveloped only 2- to 5-fold resistance to the compound. DNA sequencing of resistant strains and subsequent verification by directed mutation in naive strains revealed that resistance was due to mutations in the transcriptional regulatorCAP1(causing upregulation of the drug transporterMDR1) and in the drug transporterCDR1. These mutations had only modest effects on resistance to traditional antifungal agents, and theCDR1mutation renderedC. aurismore sensitive to posaconazole. This observation raises the possibility that a combination treatment involving an 8-hydroxyquinoline and posaconazole might preventC. aurisfrom developing resistance to this established antifungal agent.

Abstract Importance

The rapidly emerging fungal pathogenCandida aurisrepresents a growing threat to hospitalized patients, in part due to frequent resistance to multiple classes of antifungal drugs. We identify a class of compounds, the dihalogenated hydroxyquinolines, with broad fungistatic ability against a diverse collection of 13 strains ofC. auris. Although this compound has been identified in previous screens, we extended the analysis by showing thatC. aurisdeveloped only modest 2- to 5-fold increases in resistance to this class of compounds despite long-term exposure; a noticeable difference from the 30- to 500- fold increases in resistance reported for similar studies with commonly used antifungal drugs. We also identify the mutations underlying the resistance. These results suggest that the dihalogenated hydroxyquinolines are working inside the fungal cell and should be developed further to combatC. aurisand other fungal pathogens.

Tweet

Lohse and colleagues characterize a class of compounds that inhibit the fungal pathogenC. auris. Unlike many other antifungal drugs,C. aurisdoes not readily develop resistance to this class of compounds.
Anti-inflammatory SARS-CoV-2 T cell immunity in asymptomatic seronegative Kenyan adults
Authors: Samandari Taraz , Ongalo Joshua , McCarthy Kim , Biegon Richard K. , Madiega Philister , Mithika Anne , Orinda Joseph , Mboya Grace M. , Mwaura Patrick , Anzala Omu , Onyango Clayton , Oluoch Fredrick O. , Osoro Eric , Dutertre Charles-Antoine , Tan Nicole , Hang Shou Kit , Hariharaputran Smrithi , Lye David C , Herman-Roloff Amy , Bert Nina Le , Bertoletti Antonio
Published: February 2023

Antibodies are used to estimate prevalence of past infection. However, T cell responses against SARS-CoV-2 may more accurately define prevalence because SARS-CoV-2-specific antibodies wane. In November-December 2021, we studied serological and cellular immune responses in residents of rural Kenya who had not experienced any respiratory symptom nor had contact with COVID-19 cases. Among participants we detected anti-spike antibodies in 41.0% and T cell responses against ≥2 SARS-CoV-2 proteins in 82.5%, which implies that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. Distinct from cellular immunity in European and Asian COVID-19 convalescents, strong T cell immunogenicity was observed against viral accessory proteins in these asymptomatic Africans, as well as a higher IL-10/IFN-γ ratio cytokine profile, suggesting that environmental or genetic factors modulate pro-inflammatory responses.

Funding

U.S. Centers for Disease Control and Prevention, Division of Global Health Protection. Singapore Ministry of Health’s National Medical Research Council under its COVID-19 Research Fund (COVID19RF3-0060, COVID19RF-001 and COVID19RF-008) and the Singapore Ministry of Health’s National Medical Research Council MOH-000019 (MOH-StaR17Nov-0001).
Prevalence of anti-SARS-CoV-2 antibodies in people attending the two main Goma markets in the eastern Democratic Republic of Congo
Authors: Prudence Mitangala Ndeba , Léonid Irenge Mwana Wa Bene , Edgar Musubao Tsongo , Bosco Kahindo Mbeva Jean , Patrick Ayonga Ndeba , Israël Safari Kyembwa , Janvier Kubuya Bonane , Edmon Ntabe Namegabe , Raphaël Kabangwa Kakongo Senga , Guy Mutombo Ndongala , Ambroise Jérôme , Gala Jean-Luc
Published: February 2023

According to official data, the Democratic Republic of the Congo (DRC) has a low prevalence of the coronavirus disease 19 (COVID-19) pandemic. The goal of this cross-sectional study was to determine the COVID-19 seroprevalence in people attending Goma’s two largest markets, Kituku and Virunga. This study was conducted between September and November 2021, overlapping by one month with another similar study carried out in a slum of Bukavu, and using the same methodology.

COVID-19 unvaccinated participants (n = 796 including 454 vendors and 342 customers, 60% of whom were women) were surveyed. The median age of vendors and customers was 34.2 and 30.1 years, respectively.

The crude and adjusted anti-SARS-CoV-2 antibody seroprevalence rates were 70.2% (95 % CI 66.9-73.4%) and 98.8% (95% CI 94.1-100%), respectively, with no difference between vendors and customers. COVID-19 symptoms were mild or absent in 58.9% and 41.1% of participants with anti-SARS-CoV-2 antibodies respectively. COVID-19 did not require hospitalisation for any of the seropositive participants.

These findings are consistent with those reported in Bukavu. They confirm that SARS-CoV-2 spread without causing severe symptoms in densely populated settlements and markets, and suggest that many COVID-19 cases went unreported. Based on these results, relevance of an untargeted hypothetical vaccination programme in these communities should be questioned.
Fixel-based analysis reveals macrostructural white matter changes associated with tau pathology in early stages of Alzheimer’s disease
Authors: Ahmadi Khazar , Pereira Joana B. , van Westen Danielle , Pasternak Ofer , Zhang Fan , Nilsson Markus , Stomrud Erik , Spotorno Nicola , Hansson Oskar
Published: February 2023

White matter (WM) alterations are commonly found across different stages of Alzheimer’s disease (AD). However, the association between these changes with underlying AD pathology such as amyloid-β (Aβ) and tau deposition is still poorly understood. Hitherto, most studies have assessed WM alterations in AD using diffusion tensor imaging (DTI). Nonetheless, DTI has methodological shortcomings that limit an accurate biological interpretation. To address this limitation, here we applied fixel-based analysis (FBA) to disentangle microscopic differences in fiber density (FD) from macroscopic morphological changes in fiber cross-section (FC) in early stages of AD. We further investigated the associations of FBA metrics with AD pathology and cognitive performance. Additionally, we compared FBA results with other commonly used WM metrics derived from DTI, free-water corrected (FW)-DTI and diffusion kurtosis imaging (DKI). To achieve these goals, we included 224 Aβ-negative and 91 Aβ-positive cognitively unimpaired individuals as well as 78 Aβ-positive patients with mild cognitive impairment (MCI) with diffusion-weighted MRI (dMRI), Aβ-PET and tau-PET scans from the Swedish BioFINDER-2 study. We found that tau-PET uptake in medial temporal regions was associated with macrostructural alterations reflected by reduced FC mainly in the parahippocampal part of the cingulum bundle in Aβ-positive individuals. This tau-related WM alteration was also associated with impaired memory. Interestingly, only FBA metrics were able to capture the association between tau-PET uptake and white matter degeneration. No association was found between global amyloid load and any dMRI metrics. Compared to both cognitively unimpaired groups, MCI patients showed a decrease in all FBA metrics in the entire cingulum bundle, uncinate fasciculus and anterior thalamic radiations. Metrics derived from DKI, and FW-DTI revealed a similar pattern of alterations whereas the spatial extent of WM abnormalities detected by DTI was more widespread. Altogether, our results indicate that early WM alterations in AD are mainly due to macrostructural changes identified by FBA metrics, being more closely associated with tau than Aβ pathology. These findings suggest that future studies assessing the effects of AD pathology in white matter tracts should consider using FBA metrics.
Comparison of synthesized and acquired highb-value diffusion-weighted MRI for detection of prostate cancer
Authors: Kallis Karoline , Conlin Christopher C. , Zhong Allison Y. , Hussain Troy S. , Chatterjee Aritrick , Karczmar Gregory S. , Rakow-Penner Rebecca , Dale Anders , Seibert Tyler
Published: February 2023

Background

Highb-value diffusion-weighted images (DWI) are used for detection of clinically significant prostate cancer (csPCa). To decrease scan time and improve signal-to-noise ratio, highb-value (>1000 s/mm2) images are often synthesized instead of acquired.

Purpose

Qualitatively and quantitatively compare synthesized DWI (sDWI) to acquired (aDWI) for detection of csPCa.

Study Type

Retrospective

Subjects

151 consecutive patients who underwent prostate MRI and biopsy.

Sequence

Axial DWI withb=0, 500, 1000, and 2000 s/mm2using a 3T clinical scanner using a 32-channel phased-array body coil

Assessment

We synthesized DWI forb=2000 s/mm2via extrapolation based on monoexponential decay, usingb=0 andb=500 s/mm2(sDWI500) andb=0,b=500, andb=1000 s/mm2(sDWI1000). Differences between sDWI and aDWI were evaluated within regions of interest (ROIs). The maximum DWI value within each ROI was evaluated for prediction of csPCa. Classification accuracy was also compared to Restriction Spectrum Imaging restriction score (RSIrs), a previously validated biomarker based on multi-exponential DWI.

Statistical Tests

Discrimination of csPCa was evaluated via area under the receiver operating characteristic curve (AUC). Statistical significance was assessed using bootstrap difference (two-sided α=0.05).

Results

Within the prostate, mean ± standard deviation of percent mean differences between sDWI and aDWI signal were -46±35% for sDWI1000and -67±24% for sDWI500. AUC for aDWI, sDWI500,sDWI1000, and RSIrs within the prostate 0.62[95% confidence interval: 0.53, 0.71], 0.63[0.54, 0.72], 0.65[0.56, 0.73] and 0.78[0.71, 0.86], respectively. When considering the whole field of view, classification accuracy and qualitative image quality decreased notably for sDWI compared to aDWI and RSIrs.

Data Conclusion

sDWI is qualitatively comparable to aDWI within the prostate. However, hyperintense artifacts are introduced with sDWI in the surrounding pelvic tissue that interfere with quantitative cancer detection and might mask metastases. In the prostate, RSIrs yields superior quantitative csPCa detection than sDWI or aDWI.
Discovery of novel microRNA mimic repressors of ribosome biogenesis
Authors: Bryant Carson J. , McCool Mason A. , Rosado-González Gabriela T. , Abriola Laura , Surovtseva Yulia V. , Baserga Susan J.
Published: February 2023

While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2,603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulatedCDKN1A(p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We discovered that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, directly and potently target the ribosomal protein mRNARPS28via tandem primate-specific 3’ UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.

Graphical Abstract
ArMo: An Articulated Mesh Approach for Mouse 3D Reconstruction
Authors: Bohnslav James P. , Osman Mohammed Abdal Monium , Jaggi Akshay , Soares Sofia , Weinreb Caleb , Datta Sandeep Robert , Harvey Christopher D.
Published: February 2023

Characterizing animal behavior requires methods to distill 3D movements from video data. Though keypoint tracking has emerged as a widely used solution to this problem, it only provides a limited view of pose, reducing the body of an animal to a sparse set of experimenter-defined points. To more completely capture 3D pose, recent studies have fit 3D mesh models to subjects in image and video data. However, despite the importance of mice as a model organism in neuroscience research, these methods have not been applied to the 3D reconstruction of mouse behavior. Here, we present ArMo, an articulated mesh model of the laboratory mouse, and demonstrate its application to multi-camera recordings of head-fixed mice running on a spherical treadmill. Using an end-to-end gradient based optimization procedure, we fit the shape and pose of a dense 3D mouse model to data-derived keypoint and point cloud observations. The resulting reconstructions capture the shape of the animal’s surface while compactly summarizing its movements as a time series of 3D skeletal joint angles. ArMo therefore provides a novel alternative to the sparse representations of pose more commonly used in neuroscience research.
The thalamic reticular nucleus-lateral habenula circuit regulates depressive-like behaviors in chronic stress and chronic pain
Authors: Xu Xiang , Chen Rui , Wang Xin-Yue , Jia Wen-Bin , Xu Peng-Fei , Liu Xiao-Qing , Zhang Ying , Liu Xin-Feng , Zhang Yan
Published: February 2023

Chronic stress and chronic pain are two major predisposing factors to trigger depression. Enhanced excitatory input to the lateral habenula (LHb) has been implicated in the pathophysiology of depression. However, the contribution of inhibitory transmission remains elusive. Here, we dissect an inhibitory projection from the sensory thalamic reticular nucleus (sTRN) to LHb, which is activated by acute aversive stimuli. However, chronic restraint stress (CRS) weakens sTRN-LHb synaptic strength, and this synaptic attenuation is indispensable for CRS-induced LHb neural hyperactivity and depression onset. Moreover, artificially inhibiting sTRN-LHb circuit induces depressive-like behaviors in healthy mice, while enhancing this circuit relieves depression induced by both chronic stress and chronic pain. Intriguingly, neither neuropathic pain nor comorbid pain in chronic stress is affected by this pathway. Together, our study demonstrates a novel sTRN-LHb circuit in establishing and modulating depression, thus shedding light on potential therapeutic targets for preventing or managing depression.
Hebbian priming of human spinal motor learning
Authors: Bjørndal Jonas Rud , Beck Mikkel Malling , Jespersen Lasse , Christiansen Lasse , Lundbye-Jensen Jesper
Published: February 2023

Learning or relearning of motor skills requires plasticity in relevant neural circuits. Motor recovery following lesions to the corticospinal system can be augmented through neuromodulation techniques targeting the affected or compensatory neural circuits. By repeatedly pairing transcranial magnetic stimulation of the primary motor cortex (M1) and motoneuronal electrical stimulation (i.e., paired corticomotoneuronal stimulation, PCMS) timed to arrive at the corticomotoneuronal (CM) synapses in close temporal proximity, spike-timing-dependent bidirectional changes in CM transmission can be induced in humans (Taylor & Martin, 2009). PCMS-induced increases in CM transmission have been demonstrated to transiently improve motor control in patients with spinal cord injury (Bunday & Perez 2012), whereas effects on the malleability of neural circuits are entirely unexplored. We hypothesized that PCMS can prime mechanisms of subsequent motor learning exclusively when directed to the neural circuitry underpinning the motor behavior. In three experiments, we provide the first evidence (‘Experiment I’) and a double-blinded, sham-controlled replication (‘Experiment II’) that PCMS targeting the spinal CM synapses can prime subsequent learning of rapid finger movements relying on spinal neuroplasticity. Finally, we demonstrate that the effects of PCMS are circuit-specific and bidirectional. When PCMS was timed to arrive at a facilitatory interval in M1 but an inhibitory interval at the CM synapses subsequent learning was transiently impeded (‘Experiment III’). Taken together, our results provide proof-of-principle that non-invasively induced plasticity governed by Hebbian learning rules interacts with experience-dependent plasticity in the spinal cord with positive implications for motor learning. Our results offer a mechanistic rationale for priming sensorimotor training with individualized PCMS to enhance the effects of motor practice in neurorehabilitation.

Highlights

Paired corticomotoneuronal stimulations (PCMS) promote ballistic motor learning and facilitate corticospinal excitability compared to rest and sham protocols.

A double-blinded sham experiment replicates priming effects of PCMS on ballistic motor learning and demonstrates long-term benefits of combined PCMS and motor practice.

The facilitating effect of PCMS on ballistic motor learning is circuit-specific with superior effects on ballistic motor learning after facilitating PCMS compared to control protocols.
Single-cell transcriptome analysis on the anatomic positional heterogeneity of pig skin
Authors: Zou Qin , Yuan Rong , Zhang Yu , Wang Yifei , Zheng Ting , Shi Rui , Zhang Mei , Li Yujing , Fei Kaixin , Feng Ran , Pan Binyun , Zhang Xinyue , Gong Zhengyin , Zhu Li , Tang Guoqing , Li Mingzhou , Li Xuewei , Jiang Yanzhi
Published: February 2023

Different anatomic locations of the body skin dermis come from different origins, and its positional hereditary information can be maintained in adults, while highly resolvable cellular specialization is less well characterized in different anatomical regions. Pig is regarded as excellent model for human research in view of its similar physiology to human. In this study, we performed single-cell RNA sequencing of six different anatomical skin regions from the Chenghua pig with superior skin thickness trait. We obtained 215,274 cells, representing seven cell types, among which we primarily characterized the heterogeneity of smooth muscle cells, endothelial cells and fibroblasts. We identified several phenotypes of smooth muscle cell and endothelial cell and presented genes expression of pathways such as the immune response in different skin regions. By comparing differentially expressed fibroblast genes among different skin regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main three cell types from different anatomic skin sites will contribute to a better understanding of hereditary information and places the potential focus on skin generation, transmission and transplantation, paving the foundation for human skin priming.
The differentiation and integration of the hippocampal dorsoventral axis are controlled by two nuclear receptor genes
Authors: Yang Xiong , Wan Rong , Liu Zhiwen , Feng Su , Yang Jiaxin , Jing Naihe , Tang Ke
Published: February 2023

The hippocampus executes crucial functions from declarative memory to adaptive behaviors associated with cognition and emotion. However, the mechanisms of how morphogenesis and functions along the hippocampal dorsoventral axis are differentiated and integrated are still largely unclear. Here, we show thatNr2f1andNr2f2genes are distinctively expressed in the dorsal and ventral hippocampus, respectively. The loss ofNr2f2results in ectopic CA1/CA3 domains in the ventral hippocampus. The deficiency ofNr2f1leads to the failed specification of dorsal CA1, among which there are place cells. The deletion of bothNr2fgenes causes almost agenesis of the hippocampus with abnormalities of trisynaptic circuit and adult neurogenesis. Moreover,Nr2f1/2may cooperate to guarantee appropriate morphogenesis and function of the hippocampus by regulating theLhx5-Lhx2axis. Our findings revealed a novel mechanism thatNr2f1andNr2f2converge to govern the differentiation and integration of distinct characteristics of the hippocampus in mice.
Wolbachia has subtle effects on thermal preference in highly inbred Drosophila melanogaster which vary with life stage and environmental conditions
Authors: Strunov Anton , Schoenherr Charlotte , Kapun Martin
Published: February 2023

Temperature fluctuations are challenging for ectotherms which are not able to regulate body temperature by physiological means and thus have to adjust their thermal environment via behavior. However, little is yet known about whether microbial symbionts influence thermal preference (Tp) in ectotherms by modulating their physiology. Several recent studies have demonstrated substantial effects ofWolbachiainfections on hostTpin differentDrosophilaspecies. These data indicate that the direction and strength of thermal preference variation is strongly dependent on host and symbiont genotypes and highly variable among studies. By employing highly controlled experiments, we investigated the impact of several environmental factors including humidity, food quality, light exposure, and experimental setup that may influenceTpmeasurements in adultDrosophila melanogasterflies. Additionally, we assessed the effects ofWolbachiainfection onTpofDrosophilaat different developmental stages, which has not been done before. We find only subtle effects ofWolbachiaon hostTpwhich are strongly affected by experimental variation in adult, but not during juvenile life stages. Our in-depth analyses show that environmental variation has a substantial influence onTpwhich demonstrates the necessity of careful experimental design and cautious interpretations ofTpmeasurements together with a thorough description of the methods and equipment used to conduct behavioral studies.
Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A
Authors: Harjes Stefan , Kurup Harikrishnan M. , Rieffer Amanda E. , Bayarjargal Maitsetseg , Filitcheva Jana , Su Yongdong , Hale Tracy K. , Filichev Vyacheslav V. , Harjes Elena , Harris Reuben S. , Jameson Geoffrey B.
Published: February 2023

The normally antiviral enzyme APOBEC3A1-4is an endogenous mutagen in many different human cancers5-7, where it becomes hijacked to fuel tumor evolvability. APOBEC3A’s single-stranded DNA C-to-U editing activity1, 8results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations5-7. Transgenic expression in mice demonstrates its tumorigenic potential9. APOBEC3A inhibitors may therefore comprise a novel class of anticancer agents that work by blocking mutagenesis, preventing tumor evolvability, and lessening detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2’-deoxy-5-fluorozebularine in place of the cytidine in the TC recognition motif that is part of a three-nucleotide loop. The nuclease-resistant phosphorothioated derivatives of these inhibitors maintain nanomolarin vitropotency against APOBEC3A, localize to the cell nucleus, and block APOBEC3A activity in human cells. These results combine to suggest roles for these inhibitors to study A3A activity in living cells, potentially as conjuvants, leading toward next-generation, combinatorial anti-mutator and anti-cancer therapies.
Prefronto-subcortical hypoconnectivity in schizophrenia: translation of critical pathways for symptom-related functions in nonhuman primates
Authors: Yahata Noriaki , Hirabayashi Toshiyuki , Minamimoto Takafumi
Published: February 2023

Recent advances in genetic neuromodulation technology have enabled circuit-specific interventions in nonhuman primates (NHPs), thereby revealing the causal functions of specific neural circuits. Going forward, an important step is to use these findings to better understand neuropsychiatric and neurological disorders in humans, in which alterations in functional connectivity between brain regions are demonstrated. We recently identified the causal roles of the pathways from the dorsolateral prefrontal cortex (DLPFC) to the lateral part of the mediodorsal thalamic nucleus (MDl) and dorsal caudate nucleus (dCD) in working memory and decision-making, respectively. In the present study, we examined the resting-state functional connectivity of these two prefronto-subcortical circuits in healthy controls (HCs) and patients with various neuropsychiatric disorders including schizophrenia (SCZ), major depressive disorder (MDD), and autism spectrum disorders (ASD) in humans. We found that the functional connectivity of two pathways, DLPFC-MDl and DLPFC-dCD, was significantly reduced in the SCZ groups compared to HCs; however, this hypoconnectivity was not observed in the ASD or MDD groups, suggesting a disease-specific profile of altered prefronto-subcortical connectivity at rest. These results suggest that causal findings of pathway-specific functions revealed in NHPs can be effectively translated to identify the altered connectivity in neuropsychiatric disorders with related symptoms in humans.
Whole mouse body histology using standard IgG antibodies
Authors: Mai Hongcheng , Luo Jie , Hoeher Luciano , Al-Maskari Rami , Horvath Izabela , Paetzold Johannes C. , Todorov Mihail , Hellal Farida , Ertürk Ali
Published: February 2023

Most diseases involve multiple interconnected physiological systems, but histological evaluation of their pathology is currently limited to small tissue samples. Here, we present wildDISCO, a technology that uses cholesterol extraction to enable deep tissue penetration of standard 150 kDa IgG antibodies in chemically fixed whole mice. Combining wildDISCO with whole mouse clearing, we generate whole-body maps of the nervous, immune, and lymphatic systems and show their close interactions throughout the mouse body.

Graphical Abstract

Highlights

WildDISCO uses new tissue chemistry based on β-cyclodextrin to enable histology in whole mouse bodies using full-size antibodies

WildDISCO generates the first whole mouse body atlases for neurons, immune cells, blood and lymph vessels

The whole mouse atlases are available online to study the biological systems in health and disease

Virtual Reality (VR) exploration of these atlases disentangles complex anatomical structures between organs and biological systems

Supplementary Videos can be seen at

http://discotechnologies.org/wildDISCO/
Classification of Multiple Emotional States from Facial Expressions in Mice using a Deep Learning-Based Image Analysis
Authors: Takana Yudai , Nakata Takuto , Hibino Hiroshi , Nishiyama Masaaki , Ino Daisuke
Published: February 2023

Facial expressions are widely recognized as universal indicators of underlying internal states in most species of animals, thereby presenting as a non-invasive measure for predicting physical and mental conditions. Despite the advancement of artificial intelligence-assisted tools for automated analysis of voluminous facial expression data in human subjects, the corresponding tools for mice still remain limited so far. Considering that mice are the most prevalent model animals for studying human health and diseases, a comprehensive characterization of emotion-dependent patterns of facial expressions in mice could extend our knowledge on the basis of emotions and the related disorders. Here, we present a framework for the development of a deep learning-powered tool for classifying mouse facial expressions. We demonstrate that our machine vision was capable of accurately classifying three different emotional states from mouse facial images. Moreover, we objectively determined how our classifier characterized the differences among the facial images through the use of an interpretation technique called Gradient-weighted Class Activation Mapping. Our approach is likely to facilitate the non-invasive decoding of a variety of emotions from facial images in mice.
Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability
Authors: Duveau Fabien , Cordier Céline , Chiron Lionel , LeBec Matthias , Pouzet Sylvain , Séguin Julie , Llamosi Artémis , Sorre B. , Meglio Jean-Marc Di , Hersen Pascal
Published: February 2023

Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
Structural Conservation of Insulin/IGF Signalling Axis at the Insulin Receptors Level inDrosophilaand humans
Authors: Viola Cristina M. , Frittmann Orsolya , Jenkins Huw T. , Shafi Talha , Meyts Pierre De , Brzozowski Andrzej M.
Published: February 2023

The insulin-related hormones regulate key life processes in Metazoa, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin signalling axis (IIS). In humans the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. InDrosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR). This report describes the cryoEM structure of the dmIR ectodomain:DILP5 complex, revealing high structural homology between dmIR and hIR. The excess of DILP5 yields dmIR complex in an asymmetric ‘T’ conformation, similar to that observed in some complexes of human IRs. However, dmIR binds three DILP5 molecules in a hitherto-unseen arrangement, showing also dmIR-specific features. This work adds structural support to evolutionary conservation of the IIS axis at the IR level, underpinning also a better understanding of an important model organism.
Assessing preferences for adult vs juvenile features in young animals: newly-hatched chicks spontaneously approach red and large stimuli
Authors: Freeland Laura , Vasas Vera , Gomes Josephine , Versace Elisabetta
Published: February 2023

Young precocial birds benefit from staying close to both their mother and siblings, while prioritising adults, which provide better care. Which features of the stimuli are used by young birds to prioritise attachment to adults over siblings is unknown. We started to address this question in newly hatched domestic chicks (Gallus gallus), focusing on their spontaneous preferences for visual stimuli that systematically vary between adult and juvenile chickens: size (larger in adults than in juveniles) and colour (darker and redder in adults than in juveniles). Overall, chicks at their first visual experience, that had never seen a conspecific beforehand, were most attracted to the red and large stimuli (two adult features) and interacted with red stimuli more than with yellow stimuli. When tested with red large vs. small objects (Exp. 1), chicks preferred the large shape. When tested with yellow large and small objects (Exp. 2), chicks did not show a preference. These results suggest that the combination of size and colour form the predisposition that helps chicks to spontaneously discriminate between adult and juvenile features from the first stages of life, in the absence of previous experience.
Hsp70/Hsp90 organizing protein (HOP) maintains CRAF kinase activity and regulates MAPK signaling by enhancing Hsp90-CRAF association
Authors: Gayen Nilanjan , Mitra Sahana , Roy Somesh , Mandal Atin K.
Published: February 2023

The stability and activity of CRAF kinase are stringently regulated by heat shock protein 90 (Hsp90). Hsp90-mediated client folding and maturation is governed by its co-chaperones, but their functionality in chaperoning CRAF/Raf1 kinase to accomplish signaling under physiological conditions remains poorly understood. Here, we show that Hsp70/Hsp90 organizing protein (HOP) associates with CRAF kinase for maintaining its kinase activity and facilitates the activation of the MAPK pathway. Such activation is mediated by TPR2A-2B-DP2 domain of HOP and requires efficient binding to Hsp90. Being a recruiter of Hsp90, Cdc37 is unable to supplement the function of HOP/Sti1. Downregulation of HOP/Sti1 in yeast andin vitrocell culture significantly reduces the CRAF signaling. Our data suggest that Hsp90 is recruited to CRAF in two steps, separately initiated by co-chaperones HOP and Cdc37 respectively during CRAF folding/maturation, and again upon CRAF activation mediated by HOP during MAPK signaling. Therefore, HOP is a regulator of CRAF kinase during activation of MAPK pathway and serves as a sensor of growth signaling beyond its client folding and maturation function.
Sequence assignment validation in protein crystal structure models with checkMySequence
Authors: Chojnowski Grzegorz
Published: February 2023

Sequence register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication I have shown that register shifts in cryo-EM models of proteins can be detected using a systematic re-assignment of short model fragments to the target sequence. Here, I show that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias corrected electron-density maps. I describe in detail five register shift errors detected using the method in models deposited in the PDB.

Synopsis

I show thatcheckMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used for validating crystal structure models.
Diversity in the internal functional feeding elements of sympatric morphs of Arctic charr (Salvelinus alpinus)
Authors: Jónsdóttir Guðbjörg Ósk , von Elm Laura-Marie , Ingimarsson Finnur , Tersigni Samuel , Snorrason Sigurður Sveinn , Pálsson Arnar , Steele Sarah Elizabeth
Published: February 2023

The diversity of functional feeding anatomy is particularly impressive in fishes and correlates with various interspecific ecological specializations. Intraspecific polymorphism can manifest in divergent feeding morphology and ecology, often along a benthic–pelagic axis. Arctic charr (Salvelinus alpinus) is a freshwater salmonid known for morphological variation and sympatric polymorphism and in Lake Þingvallavatn, Iceland, four morphs of charr coexist that differ in preferred prey, behaviour, habitat use, and external feeding morphology. We studied variation in six upper and lower jaw bones in adults of these four morphs using geometric morphometrics and univariate statistics. We tested for allometric differences in bone size and shape among morphs, morph effects on bone size and shape, and divergence along the benthic-pelagic axis. We also examined the degree of integration between bone pairs. We found differences in bone size between pelagic and benthic morphs for two bones (dentary and premaxilla). There was clear bone shape divergence along a benthic–pelagic axis in four bones (dentary, articular-angular, premaxilla and maxilla), as well as allometric shape differences between morphs in the dentary. Notably for the dentary, morph explained more shape variation than bone size. Comparatively, benthic morphs possess a compact and taller dentary, with shorter dentary palate, consistent with visible (but less prominent) differences in external morphology. As these morphs emerged in the last 10,000 years, these results indicate rapid functional evolution of specific feeding structures in arctic charr. This sets the stage for studies of the genetics and development of rapid and parallel craniofacial evolution.
doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models
Authors: Chojnowski Grzegorz
Published: February 2023

Sequence assignment is a key step of the model building process in both cryogenic electron microscopy (cryo-EM) and macromolecular crystallography (MX). If the assignment fails, it can result in difficult to identify errors affecting the interpretation of a model. There are many model validation strategies that help experimentalists in this step of protein model building, but they are virtually non-existent for nucleic acids. Here I present doubleHelix – a comprehensive method for assignment, identification, and validation of nucleic acid sequences in structures determined using cryo-EM and MX. The method combines a neural network classifier of nucleobase identities and a sequence-independent secondary structure assignment approach. I show that the presented method can successfully assist model building at lower resolutions, where visual map interpretation is very difficult. Moreover, I present examples of sequence assignment errors detected using doubleHelix in cryo-EM and MX structures of ribosomes deposited in the Protein Data Bank, which escaped the scrutiny of available model-validation approaches.

The doubleHelix program source code is available under BSD-3 license athttps://gitlab.com/gchojnowski/doublehelix.