bluuebunny/crossref_metadata_2025 huggingface dataset:
The West Coast Plastic Surgery Mentorship Program
Authors: Reghunathan Meera , Llaneras Jason , Segal Rachel , Gosman Amanda
Published: April 2023

Background

Students who are underrepresented in medicine experience limited access to mentorship throughout medical school and when applying to plastic surgery residency. This study describes the creation, growth, and results of the multi-institutional West Coast Plastic Surgery Mentorship Program (WCPSMP), specifically reflecting on barriers to implementation and room for future improvement.

Methods

Students were eligible to apply to the plastic surgery mentorship program if they were first-, second-, or third-year medical students in a US medical school interested in plastic surgery. Preference was given to students who are (1) underrepresented-in-medicine racial/ethnic minorities; (2) first generation, low income; (3) lesbian, gay, bisexual, transgender, queer; and/or (4) without a home integrated plastic surgery program. Preprogram and postprogram surveys were analyzed.

Results

The 2021–2022 cycle of the WCPSMP included 30 resident mentors and 30 resident mentees, with a 1:1 mentor-to-mentee relationship. The second annual Mentor-Mentee Day was hosted on June 25, 2022, in San Diego, California, with attendance from 18 mentees. There was a 63% response rate in the presurvey and postsurvey. Most students endorsed gaining didactic skills, technical skills, and networking, but only a few gained research opportunities.

Conclusion

The WCPSMP is a promising venue to offer underrepresented medical students valuable resident mentorship, as well as acquire surgical knowledge and skills. Further development of the program includes implementing a curriculum for residents on how to be an effective mentor and offering more research opportunities.
Multicenter, Prospective Cohort Study of Oesophageal Injuries and Related Clinical Outcomes (MUSOIC study)
Authors: Owen Richard P. , Chidambaram Swathikan , Griffiths Ewen A , Sultan Javed , Phillips Alexander W , Vohra Ravindra , Preston Shaun , Gossage James , Hanna George B. , Underwood Tim J. , Maynard Nick , Markar Sheraz R. ,   on behalf of the MUSOIC study group
Published: April 2023

Objective:

To identify prognostic factors associated with 90-day mortality in patients with oesophageal perforation (OP), and characterize the specific timeline from presentation to intervention, and its relation to mortality.

Background:

OP is a rare gastro-intestinal surgical emergency with a high mortality rate. However, there is no updated evidence on its outcomes in the context of centralized esophago-gastric services; updated consensus guidelines; and novel non-surgical treatment strategies.

Methods:

A multi-center, prospective cohort study involving eight high-volume esophago-gastric centers (January 2016 to December 2020) was undertaken. The primary outcome measure was 90-day mortality. Secondary measures included length of hospital and ICU stay, and complications requiring re-intervention or re-admission. Mortality model training was performed using random forest, support-vector machines, and logistic regression with and without elastic net regularisation. Chronological analysis was performed by examining each patient’s journey timepoint with reference to symptom onset.

Results:

The mortality rate for 369 patients included was 18.9%. Patients treated conservatively, endoscopically, surgically, or combined approaches had mortality rates of 24.1%, 23.7%, 8.7%, and 18.2%, respectively. The predictive variables for mortality were Charlson comorbidity index, haemoglobin count, leucocyte count, creatinine levels, cause of perforation, presence of cancer, hospital transfer, CT findings, whether a contrast swallow was performed, and intervention type. Stepwise interval model showed that time to diagnosis was the most significant contributor to mortality.

Conclusion

Non-surgical strategies have better outcomes and may be preferred in selected cohorts to manage perforations. Outcomes can be significantly improved through better risk-stratification based on afore-mentioned modifiable risk factors.
Enhancing CAR T cell therapy using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Matthew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Yuchen Bai , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: April 2023

Adoptive T cell therapy aims to achieve lasting tumour clearance, requiring enhanced engraftment and survival of the immune cells. Cytokines are paramount modulators of T cell survival and proliferation. Cytokine receptors signal via ligand-induced dimerization, and this principle has been hijacked utilising non-native dimerization domains. A major limitation of current technologies resides in the absence of a module that recapitulates the natural cytokine receptor heterodimeric pairing. To circumvent this, we created a new engineered cytokine receptor able to constitutively recreate receptor-heterodimer utilising the heterodimerization domain derived from the IgG1 antibody (dFab_CCR). We found that the signal delivered by the dFab_CCR-IL2 proficiently mimics the cytokine receptor heterodimerization, with transcriptomic signatures similar to that obtained by the activation of IL2 native receptor. Importantly, we found that this dimerization structure is agnostic, efficiently activating signaling through four cytokine receptor families.

Using a combination ofin vivoandin vitroscreening approaches, we characterized a library of 18 dFab_CCRs co-expressed with a clinically relevant solid tumor-specific GD2 CAR. Based on this characterization we suggest that the co-expression of either the common β-chain GMCSF or the IL18 dFab_CCRs is optimal to improve CAR T cell expansion, engraftment, and efficacy.

Our results demonstrate how the Fab dimerization is efficient and versatile in recapitulating a cytokine receptor heterodimerization signal. This module could be applied for the enhancement of adoptive T cell therapies, and therapies based on other immune cell types. Furthermore, these results provide a choice of cytokine signal to incorporate with adoptive T cells therapies.
Chimeric protein EWS-FLI1 drives cell proliferation in Ewing Sarcomaviaoverexpression ofKCNN1
Authors: Dupuy Maryne , Gueguinou Maxime , Postec Anaïs , Brion Régis , Tesfaye Robel , Mullard Mathilde , Regnier Laura , Amiaud Jérôme , Potier-Cartereau Marie , Chantôme Aurélie , Royer Bénédicte Brounais-Le , Baud’huin Marc , Georges Steven , Lamoureux François , Ory Benjamin , Delattre Olivier , Rédini Françoise , Vandier Christophe , Verrecchia Franck
Published: April 2023

Ewing sarcoma (ES) is characterized by chimeric fusion proteins, which act as oncogenes. Over the last decade, patient survival has not increased, especially for high risk patients. Knowing that ion channels are studied for their implication in tumorigenesis, the aim of this work is to study the involvement of the SK1 potassium channels in ES. RNA-Seq analyses showed a high restricted expression ofKCNN1, the gene encoding SK1, only in ES patients, and its expression is inversely correlated with patient survival. EWS-FLI1 silencing demonstrated the regulation ofKCNN1by these fusion proteins, which bind at GGAA microsatellites nearKCNN1promoter. In addition,KCNN1has been shown to be involved in the regulation of ES cell proliferation, its silencing being associated with a slowing of the cell cycle. Finally,KCNN1expression modulates membrane potential and calcium flux suggesting the role of calcium inKCNN1driving cell proliferation. These results highlight thatKCNN1is a direct EWS-FLI1 and EWS-ERG target, and is involved in the regulation of ES cell proliferation, making it an interesting therapeutic target in ES.
Spatial transcriptomics reveal pitfalls and opportunities for the detection of rare high-plasticity breast cancer subtypes
Authors: Coutant Angèle , Cockenpot Vincent , Muller Lauriane , Degletagne Cyril , Pommier Roxane , Tonon Laurie , Ardin Maude , Michallet Marie-Cécile , Caux Christophe , Laurent Marie , Morel Anne-Pierre , Saintigny Pierre , Puisieux Alain , Ouzounova Maria , Martinez Pierre
Published: April 2023

Breast cancer is one of the most prominent types of cancers, in which therapeutic resistance is still a major clinical hurdle. Specific subtypes like Claudin-low (CL) and metaplastic breast cancers (MpBC) have been associated with high non-genetic plasticity, which can facilitate resistance. The overlaps and differences between these orthogonal subtypes, respectively identified by molecular and histopathological analyses, are however still insufficiently characterised. Adequate methods to identify high-plasticity tumours to better anticipate resistance are furthermore still lacking. Here we analysed 11 triple negative breast tumours, including 3 CL and 4 MpBC samples,viahigh-resolution spatial transcriptomics. We combined pathological annotations and deconvolution approaches to precisely identify tumour spots, on which we performed signature enrichment, differential expression and copy-number analyses. We used the TCGA and CCLE public databases for external validation of expression markers. By levying spatial transcriptomics to focus analyses only to tumour cells in MpBC samples, and therefore bypassing the negative impact of stromal contamination, we could identify specific markers that are not expressed in other subtypes nor stromal cells. Three markers (BMPER, POPDC3andSH3RF3) could furthermore be validated in external expression databases encompassing bulk tumour material and stroma-free cell lines. We find that existing bulk expression signatures of high-plasticity breast cancers are relevant in mesenchymal transdifferentiated compartments but can be hindered by stromal cell prevalence in tumour samples, negatively impacting their clinical applicability. Spatial transcriptomics analyses can however help identify more specific expression markers, and could thus enhance diagnosis and clinical care of rare high-plasticity breast cancers.
Analysis of Gene Expression Differences Between Eastern and Western Loblolly Pine Seed Sources
Authors: Festa Adam R , Whetten Ross
Published: April 2023

The selection of an appropriate seed source for a given geographic region is critical to ensuring prosperous southern pine plantations. The observed variation between eastern and western loblolly pine seed sources has shown differences in economically advantageous traits such as drought tolerance, growth rates, and disease resistance. Understanding what drives these local adaptations is of interest, given that current forecasted climate modeling suggests there will be increased temperatures and changes to precipitation by the year 2050. The objectives of this experiment were to 1) identify differentially expressed transcripts between eastern and western loblolly pine sources; 2) link these transcripts toArabidopsisorthologs; 3) compare GO categories of differentially-expressed transcripts. The findings highlighted include interesting pathways and genes that are related to the known differences among eastern and western seed provenances. Additionally, they represent fundamental differences in the beginning of seedling development without any treatment or disease pressure applied, showing that there are detectable differences between these two provenances at a young age. Overall, this experiment contributes to the body of literature on fundamental differences between loblolly pine seed sources.
Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk
Authors: Behera S. , Belyeu J. R. , Chen X. , Paulin L. F. , Nguyen N.Q.H. , Newman E. , Mahmoud M. , Menon V. K. , Qi Q. , Joshi P. , Marcovina S. , Rossi M. , Roller E. , Han J. , Onuchic V. , Avery C. L. , Ballantyne C.M. , Rodriguez C. J. , Kaplan R. C. , Muzny D. M. , Metcalf G. A. , Gibbs R. , Yu B. , Boerwinkle E. , Eberle M. A. , Sedlazeck F. J.
Published: April 2023

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ∼50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.
High throughput intracellular delivery by viscoelastic mechanoporation
Authors: Sevenler Derin , Toner Mehmet
Published: April 2023

Brief and intense electric fields (electroporation) and/or tensile stresses (mechanoporation) have been used to temporarily permeabilize the plasma membrane of mammalian cells for the purpose of delivering materials to the cytosol. However, electroporation can be harmful to cells, while efficient mechanoporation strategies have not been scalable due to the use of narrow constrictions or needles which are susceptible to clogging. Here we report a method of mechanoporation in which cells were stretched and permeabilized by viscoelastic flow forces without surface contact. Inertio-elastic cell focusing aligned cells to the center of the device, avoiding direct contact with walls and enabling efficient (95%) intracellular delivery to over 200 million cells per minute. Functional biomolecules such as proteins, RNA, and ribonucleoprotein complexes were successfully delivered to Jurkat cells. Efficient intracellular delivery to HEK293T cells and primary activated T cells was also demonstrated. Contact-free mechanoporation using viscoelastic fluid forces appears to be feasible method for efficient and high throughput intracellular delivery of biomolecules to mammalian cellsex vivo.
Interfacial residues in protein-protein complexes are in the eyes of the beholder
Authors: Parvathy Jayadevan , Yazhini Arangasamy , Srinivasan Narayanaswamy , Sowdhamini Ramanathan
Published: April 2023

Interactions between proteins are vital in almost all biological processes. The characterization of protein-protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein-protein complex are assumed to have the following two properties: a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein-protein complexes through these two methods. The study shows that a few residues are identified uniquely by each method, and the extent of conservation, propensities and their contribution to the stability of protein-protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics and function of protein-protein complexes are identified in a complementary manner.
A Common Cause for Nystagmus in Different Congenital Stationary Night Blindness Mouse Models
Authors: Hölzel Maj-Britt , Winkelman Beerend H. J. , Howlett Marcus H. C. , Kamermans Wouter , De Zeeuw Chris I. , Kamermans Maarten
Published: April 2023

InNyxnobmice, a model for congenital nystagmus associated with congenital stationary night blindness (CSNB), synchronous oscillating retinal ganglion cells (RGCs) lead to oscillatory eye movements, i.e., nystagmus. Given the distribution ofmGluR6andCav1.4in the retina as well as their clinical association with CSNB, we hypothesize thatmGluR6-/-andCav1.4-/-mutants show, like theNyxnobmouse, oscillations that originate in the AIIamacrine cells (AIIACs). Using eye movement and multi-electrode array (MEA) recordings of RGCs we show that the nystagmus as well as the underlying RGC oscillations are also present inmGluR6-/-andCav1.4-/-mice. Yet, we find that the oscillations in themGluR6-/-andCav1.4-/-mutants slightly differ from each other and also from those of theNyxnobmice. Moreover, each of the three mutations likely impacts the membrane potential of the AIIACs differently. Together our results indicate that nystagmus and oscillating RGCs are generalizable features associated with CSNB mutations localized at the photoreceptor-bipolar cell synapse.
Identifying the multiple drivers of Cactus diversification
Authors: Thompson Jamie B. , Hernández-Hernández Tania , Keeling Georgia , Priest Nicholas K.
Published: April 2023

Many drivers of diversification have been identified across the angiosperm Tree of Life, ranging from abiotic factors, such as climate change, to biotic factors such as key adaptations. While this provides invaluable evolutionary insight into the rise of major angiosperm lineages, our understanding of the complexity underlying this remains incomplete. In species-rich families such as Cactaceae, simple explanations of triggers of diversification are insufficient. Their sheer morphological and ecological diversity, and wide distribution across heterogeneous environments, render the identification of key forces difficult. Cactus diversification is likely shaped by multiple drivers, which themselves interact in complex ways. This complexity is extremely difficult to disentangle, but applying modern analytical methods to extensive datasets offers a solution. Here, we investigate the heterogeneous diversification of the iconic Cactus family. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance to tip-speciation rate variation using Machine Learning. State-dependent diversification models confirm that a rich range of eleven abiotic and biotic variables filtered as important by Machine Learning shape Cactus diversification. Of highest importance is an atypical latitudinal gradient in speciation rates, which is spatially decoupled from richness hotspots. Of medium importance is plant size, shaped by growth form. Of lesser, but significant, importance is soil composition, bioclimate, topography, geographic range size, and chromosome count. However, it is unlikely that any one of these eleven variables is of primary importance without the complex interactions formed with others. Our results contribute to our understanding of one of the most iconic angiosperm families, while revealing the need to account for the complexity underlying macroevolution.
Dietary zinc protects against methotrexate-induced neurotoxicity in rats via modulation of oxidative stress, inflammation and neuronal energy metabolism
Authors: Onaolapo Adejoke Y. , Okunola Olufemi B , Olofinnade Anthony T. , Onaolapo Olakunle J.
Published: April 2023

Background

Increasing incidence of cancers and cancer chemotherapy-induced neurotoxicities makes it imperative to research compounds with neuroprotective potential that can do not impede therapy.

Objective

To examine the effect of dietary zinc supplementation on methotrexate-induced changes in neurobehaviour and neurochemistry and hippocampal morphology in rats.

Methods

Adult male rats were assigned into five groups of twelve animals each. Group were normal control and methotrexate control fed standard rodent chow and three groups of rats fed zinc supplemented diet at 25, 50 and 100 mg/kg of feed respectively. Standard and zinc supplemented diet were administered daily for 21 days. Animals in the normal control were administered intraperitoneal injection (i.p) of normal saline at 2ml/kg, while those in the methotrexate and zinc groups were administered i.p methotrexate at 20 mg/kg/day on days 19-21. On day 22, animals were exposed to behavioural paradigm (open field, Y-maze, radial arm maze, elevated plus maze and behavioural despair test). After the last behavioural test, animals were sacrificed and blood taken for the assessment of Tumour necrosis factor-α, interleukin 1β and interleukin 10), malondialdehyde levels and total antioxidant capacity. The hippocampus was either homogenised for the assessment of dopamine, serotonin, acetylcholine and brain derived neurotropic factor levels or processed for histological study.

Results

Dietary zinc protected against methotrexate-induced changes in weight, food intake, cognition, hippocampal histomorphology and neuron specific enolase immunohistochemistry.

Conclusion

Dietary zinc supplementation protects against methotrexate induced neurotoxicities by modulating oxidative stress, inflammatory markers brain neurotransmitters and metabolism in rats.
Stent For Life Initiative in Portugal: progress through years and Covid-19 Impact
Authors: Pereira Ernesto , Calé Rita , Pereira Angela Maria , Pereira Hélder , Martins Luís Dias
Published: April 2023

Background

During Stent for Life Initiative in Portugal lifetime, positive changes in ST elevation myocardial infarction treatment were observed, by the increase of Primary Angioplasty numbers and improvements in patients’ behaviour towards myocardial infarction, with an increase in those who called 112 and the lower proportion attending non primary percutaneous coronary intervention centres. Despite public awareness campaigns and system educational programmes, patient and system delay did not change significantly over this period. The aim of this study was to address the public awareness campaign effectiveness on peoples’ behaviour facing STEMI, and how Covid-19 has affected STEMI treatment.

Methods

Data from 1381 STEMI patients were collected during a one-month period each year, from 2011 to 2016, and during one and a half month, matching first lockdown in Portugal 2020. Four groups were constituted: Group A (2011); Group B (2012&2013); Group C (2015&2016) and group D (2020).

Results

The proportion of patients who called 112, increased significantly (35.2% Group A; 38.7% Group B; 44.0% Group C and 49.6% Group D, p=0.005); significant reduction was observed in the proportion of patients who attended healthcare centres without PPCI (54.5% group A; 47.6% Group B; 43.2% Group C and 40.9% Group D, p=0.016), but there were no differences on groups comparison. Total ischemic time, measured from symptoms onset to reperfusion increased progressively from group A [250.0 (178.0-430.0)] to D [296.0 (201.0 – 457.5.8)] p=0.012, with statistically significant difference between group C and D (p=0.034).

Conclusions

During the term of SFL initiative in Portugal, patients resorted less to primary health centres and called more to 112. These results can be attributed the public awareness campaign. Nevertheless, patient and system delays did not significantly change over this period, mainly in late years of SFL, probably for low efficacy of campaigns and in 2020 due to Covid-19 pandemic.
Gut microbiota and maternal immune transfer at birth influence pre-allergic clinical outcome
Authors: Villette Remy , Traore Djelika , Dhilly Elise , Foucault Pierre , Parisel Eleonore , Sauce Delphine , Gorochov Guy , Kayem Gilles , Schuhmacher Marta , Annesi-Maesano Isabella , Larsen Martin ,   EarlyFOOD study group
Published: April 2023

The gut microbiota of 2-3 month-old infants is associated with later pre-allergic signs, while the microbiota at the time of allergic manifestation is not. We hypothesized that the infant gut microbiota and immune system are primed shortly after birth, and that this is influenced by maternal transfer of humoral immunity. We investigated the association between allergic outcomes and composition and humoral immunity to gut microbiota at birth, 2 months, and 2 years-of-age. Meconium microbiota clustered into three groups dominated byEscherichia,Enterococcus, and mixed genera, respectively. TheEscherichiacluster was associated with protection against later allergic manifestations. We moreover studied the proportion and specificity of humoral immunity to gut microbiota. Humoral immunity to gut microbiota at birth was associated with future allergies. Future studies should evaluate whether interventions to alter gut microbiota and humoral immunity in early-life protects against allergy.
Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)
Authors: Liu Shuiyin , Yang Yingying , Tian Qin , Yang Zhiyun , Li Shufeng , Valdes Paul J. , Farnsworth Alex , Kates Heather R. , Siniscalchi Carolina M. , Guralnick Robert P. , Soltis Douglas E. , Soltis Pamela S. , Stull Gregory W. , Folk Ryan A. , Yi Tingshuang
Published: April 2023

Abstract

Oaks (Quercus), one of the most species-rich and ecologically dominant woody plant clades in the Northern Hemisphere, are well known for their propensity to hybridize and form syngameons, complexes where alleles are readily exchanged among closely related species. While hybridization has been extensively studied towards the tips of the oak phylogeny, the extent, timeline, and evolutionary scenarios of hybridization during the early radiation of oaks and related genera (Quercoideae) remain poorly known. Using an expansive new dataset of nuclear and chloroplast sequences (including up to 431 spp.), we conducted a multifaceted phylogenomic investigation ofQuercusaimed at characterizing gene-tree and cytonuclear (chloroplast-nuclear) discordance and identifying ancient reticulation in the early evolution of the group. We document extensive nuclear gene-tree and cytonuclear discordance at deep nodes inQuercusand Quercoideae, withQuercusrecovered as non-monophyletic in the chloroplast phylogeny. Analyses recovered clear signatures of gene flow against a backdrop of incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand Quercoideae during their initial radiation, dated to the early-middle Eocene. Ancestral reconstructions including fossil data suggest that the ancestors ofCastanea+Castanopsis,Lithocarpus, and the Old World oak clade co-occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus,and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Following this initial phase of radiation and reticulation, we detected multiple niche shifts inQuercusand other Quercoideae genera that likely facilitated their expansion into new habitats arising from post-Eocene climatic changes. Our study shows that hybridization—perhaps in the form of ancient syngameons similar to those seen today—has been a common and important process throughout the evolutionary history of oaks and their close relatives.
DEGAP: Dynamic Elongation of a Genome Assembly Path
Authors: Huang Yicheng , Wang Ziyuan , Schmidt Monica A. , Zhang Jianwei
Published: April 2023

Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembler software programs and algorithms, it is still a great challenge to assemble a complete genome with no gaps. With the latest DNA Circular Consensus Sequencing (CCS) technology, several assembler programs now can build a genome from raw sequencing data to contigs, however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software DEGAP that can resolve gap regions in genomes by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP optimizes HiFi reads by identifying the differences between reads and provides ‘GapFiller’ or ‘CtgLinker’ modes to eliminate or shorten gaps in genomes. DEGAP adopts a cyclic elongation strategy that automatically and dynamically adjusts parameters according to the complexity of the sequences and selects the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.
SnRK2-mediated phosphorylation of SIZ1 enhances global SUMOylation under osmotic stress in Arabidopsis
Authors: Sang Tian , Jia Bei , Wang Pengcheng
Published: April 2023

SUMOylation is a highly dynamic posttranslational modification that plays a critical role in regulating plant stress responses. The global SUMOylation is quickly induced by dehydration and hyperosmotic stresses in plants, while the detailed mechanism underlying such SUMOylation dynamics is largely unknown. Here, we report that the SNF1-related protein kinase 2 (SnRK2) and SUMO E3 ligase SIZ1 module is crucial for the stress-induced increment of SUMOylation in Arabidopsis. Under osmotic stress, or application of phytohormone Abscisic Acid (ABA), the rapidly activated SnRK2s physically interact with and phosphorylate SIZ1, enhancing its stability. The Ser820 residue in C-terminal region of SIZ1 proteins is a functional SnRK2 phosphosite, whose phosphorylation is abolished in the high-order mutant ofSnRK2s. The non-phosphorylatable SIZ1S820Ais unstable bothin vivoandin vitro. We also noticed the degradation of SIZ1 is largely darkness-dependent, interestingly, independent of COP1, a key ubiquitin E3 ligase regulating photomorphogenesis. Multiple SUMOylation, Ubiquitination, and phosphorylation sites in SIZ1 proteins, which may coordinate the dynamics of SIZ1 proteins and global SUMOylation upon environmental changes. Our findings highlight the critical role of the SnRK2-SIZ1 module in regulating SUMOylation dynamics during plant stress responses and provide new insights into the regulatory mechanisms underlying this essential posttranslational modification.
The potential of Senicapoc, a KCNN4 inhibitor, for the prevention and treatment of breast cancer
Authors: Xiao Christos , Miranda Mariska , Shi Wei , Beesley Jonathan , Saunus Jodi M. , Civitarese Andrew , Black Debra M. , Ruppert Meagan , Pereira Melrine , Jackson Susan , Teale Zachary , Carter-Cusack Dylan , Kalinowski Lauren , Kutasovic Jamie R. , McCart Reed Amy E. , Handoko Herlina Y. , Chen XiaoQing , Bessette Darrell , MacDonald Kelli , Lakhani Sunil R. , Chenevix-Trench Georgia , Britt Kara , Al-Ejeh Fares
Published: April 2023

Background

Genome-wide association studies have identified a breast cancer risk locus at 19q13.31. The candidate causal variants at this locus are located in the first exon ofKCNN4.KCNN4, which regulates membrane potential and Ca2+signaling, is a good candidate for drug repositioning because its inhibitor, Senicapoc, has been shown to be well tolerated in Phase-II and -III clinical trials for asthma and sickle cell anemia.

Methods

We evaluated public mRNA expression data to determine whether the allele at 19q13.31 associated with increased breast cancer risk was associated withKCNN4expression. We also used immunohistochemistry to evaluate the relationship between KCNN4 protein expression and breast cancer survival. We then used Senicapoc in two murine mammary tumor models to determine if it would delay tumor development. We also treated mice bearing 4T1 mammary tumors with Senicapoc, by subcutaneous injection and by oral gavage. Finally we used gene editing to make deletions withinKcnn4in 4T1 to determine whether Senicapoc had off-target effects on tumor growth.

Results

Analysis of the Genotype-Tissue Expression Project showed that the allele at 19q13.31 associated with increased breast cancer risk is associated with increasedKCNN4expression, suggesting that inhibiting KCNN4 might reduce breast cancer risk. Using immunohistochemistry in a large breast cancer cohort, we found that membrane and cytoplasmic expression is a marker of poor prognosis in triple negative breast cancer. We then tested the efficacy of Senicapoc to prevent and treat breast cancer. This showed that it delays the development of mammary tumors in two murine models, and slows growth of a syngeneic (4T1) model of triple negative breast cancer. Senicapoc monotherapy showed similar efficacy to anthracycline/taxane-based chemotherapy in these studies, with a stronger effect when they were combined.

Conclusions

These results provide a rationale for clinical testing of Senicapoc for treating, and even preventing, breast cancer.
The mitochondrial Ca2+channel MCU is critical for tumor growth by supporting cell cycle progression and proliferation
Authors: García Emily Fernández , Paudel Usha , Noji Michael C. , Bowman Caitlyn E. , Pitarresi Jason R. , Rustgi Anil K. , Wellen Kathryn E. , Arany Zolt , Weissenrieder Jillian S. , Foskett J. Kevin
Published: April 2023

The mitochondrial uniporter (MCU) Ca2+ion channel represents the primary means for Ca2+uptake into mitochondria. Here we employedin vitroandin vivomodels with MCU genetically eliminated to understand how MCU contributes to tumor formation and progression. Transformation of primary fibroblastsin vitrowas associated with increased MCU expression, enhanced mitochondrial Ca2+uptake, suppression of inactivating-phosphorylation of pyruvate dehydrogenase, a modest increase of basal mitochondrial respiration and a significant increase of acute Ca2+-dependent stimulation of mitochondrial respiration. Inhibition of mitochondrial Ca2+uptake by genetic deletion of MCU markedly inhibited growth of HEK293T cells and of transformed fibroblasts in mouse xenograft models. Reduced tumor growth was primarily a result of substantially reduced proliferation and fewer mitotic cellsin vivo, and slower cell proliferationin vitroassociated with delayed progression through S-phase of the cell cycle. MCU deletion inhibited cancer stem cell-like spheroid formation and cell invasionin vitro, both predictors of metastatic potential. Surprisingly, mitochondrial matrix Ca2+concentration, membrane potential, global dehydrogenase activity, respiration and ROS production were unchanged by genetic deletion of MCU in transformed cells. In contrast, MCU deletion elevated glycolysis and glutaminolysis, strongly sensitized cell proliferation to glucose and glutamine limitation, and altered agonist-induced cytoplasmic Ca2+signals. Our results reveal a dependence of tumorigenesis on MCU, mediated by a reliance on mitochondrial Ca2+uptake for cell metabolism and Ca2+dynamics necessary for cell-cycle progression and cell proliferation.
MitoSort: robust demultiplexing of pooled single-cell genomics data using endogenous germline mitochondrial variants
Authors: Tang Zhongjie , Zhang Weixing , Shi Peiyu , Li Sijun , Li Xinhui , Xu Yicong , Shu Yaqing , Xu Jin
Published: April 2023

Multiplexing across donors has emerged as a popular strategy to increase throughput, reduce costs, overcome technical batch effects, and improve doublet detection in single-cell genomic studies. Using endogenous genetic barcodes eliminates the need for additional experimental processing steps. Among the available choices for endogenous barcodes, the unique features of mtDNA variants render them a more computationally efficient and robust option compared to genome variants. Here we present MitoSort, a method that uses mtDNA germline variants to assign cells to their donor of origin and identify cross-genotype doublets. We evaluated the performance of MitoSort byin silicopooled mtscATAC-seq libraries and experimentally multiplexed data using cell hashing method. MitoSort achieve both high accuracy and efficiency on genotype clustering and doublet detection for mtscATAC-seq data, which fills a void left by the inadequacies of current computational techniques tailored for scRNA-seq data. Moreover, MitoSort exhibits versatility and can be applied to various single-cell sequencing approaches beyond mtscATAC-seq, as long as the mtDNA variants can be reliably detected. Furthermore, through a case study, we demonstrated that demultiplexing 8 individuals assayed at the same time with MitoSort, enables the comparison of cell composition without batch effects.
A SREBF2-dependent gene program drives an immunotolerant dendritic cell population during cancer progression
Authors: Plebanek Michael P. , Xue Yue , Nguyen Y-Van , DeVito Nicholas C. , Wang Xueying , Holtzhausen Alisha , Beasley Georgia M. , Yarla Nagendra , Thievanthiran Bala , Hanks Brent A.
Published: April 2023

Dendritic cells (cDCs) are essential mediators of anti-tumor immunity. Cancers have developed mechanisms to render DCs dysfunctional within the tumor microenvironment. Utilizing CD63 as a unique surface marker, we demonstrate that mature regulatory DCs (mregDCs) suppress DC antigen cross-presentation while driving TH2 and regulatory T cell differentiation within tumor-draining lymph node tissues. Transcriptional and metabolic studies show that mregDC functionality is dependent upon the mevalonate biosynthetic pathway and the master transcription factor, SREBP2. Melanoma-derived lactate activates DC SREBP2 in the tumor microenvironment (TME) and drives mregDC development from conventional DCs. DC-specific genetic silencing and pharmacologic inhibition of SREBP2 promotes anti-tumor CD8+T cell activation and suppresses melanoma progression. CD63+mregDCs reside within the sentinel lymph nodes of melanoma patients. Collectively, this work describes a tumor-driven SREBP2-dependent program that promotes CD63+mregDC development and function while serving as a promising therapeutic target for overcoming immune tolerance in the TME.

One Sentence Summary

The metabolic transcription factor, SREBF2, regulates the development and tolerogenic function of the mregDC population within the tumor microenvironment.
Deconstructing the brain bases of emotion regulation: A systems-identification approach using Bayes factors
Authors: Bo Ke , Kraynak Thomas E. , Kwon Mijin , Sun Michael , Gianaros Peter J. , Wager Tor D.
Published: April 2023

Cognitive reappraisal is fundamental to cognitive therapies and everyday emotion regulation. Analyses using Bayes factors and an axiomatic systems-identification approach identified four reappraisal-related components encompassing distributed neural activity patterns across two independent fMRI studies (n=182 and n=176): (1) An anterior prefrontal system selectively involved in cognitive reappraisal; (2) A fronto-parietal-insular system engaged by both reappraisal and emotion generation, demonstrating a general role in appraisal; (3) A largely subcortical system activated during negative emotion generation but unaffected by reappraisal, including amygdala, hypothalamus, and periaqueductal gray; and (4) a posterior cortical system of negative emotion-related regions down-regulated by reappraisal. These systems covaried with individual differences in reappraisal success and were differentially related to neurotransmitter binding maps, implicating cannabinoid and serotonin systems in reappraisal. These findings challenge ‘limbic’-centric models of reappraisal and provide new systems-level targets for assessing and enhancing emotion regulation.
Dedifferentiating germ cells regain stem-cell specific polarity checkpoint prior to niche reentry
Authors: Bener Muhammed Burak , Twillie Autumn , Chadha Rakshan , Patel Naiya , Inaba Mayu
Published: April 2023

In the Drosophila germline stem cell system, maintenance of the stem cell pool requires “dedifferentiation”, in which differentiating cells reattach to the niche and reacquire stem cell properties. However, the mechanism of dedifferentiation remains poorly understood. Here, using long-term live imaging, we show that dedifferentiated cells immediately re-enter mitosis with correct spindle orientation after reattachment to the niche. Analysis of cell cycle markers revealed that these dedifferentiating cells are all in G2 phase. In addition, we found that the observed G2 block during dedifferentiation likely corresponds to a centrosome orientation checkpoint (COC), a previously reported polarity checkpoint. We show that re-activation of a COC is likely required for the dedifferentiation thus ensuring asymmetric division even in dedifferentiated stem cells. Taken together, our study demonstrates the remarkable ability of dedifferentiating cells to reacquire the ability to divide asymmetrically.
The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genusCorylus
Authors: Brainard Scott H. , Sanders Dean M. , Bruna Tomas , Shu Shengqiang , Dawson Julie C.
Published: April 2023

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern U.S. for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses ofC. americanarequires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation withinC. americana, as well as patterns of syntenic relationships across theCorylusgenus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1,343C. americana, C. avellana, andC. americanaxC. avellanahybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently publishedCorylusgenomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility inCorylus.
Dispersal in Kentish plovers (Charadrius alexandrinus): Adult females perform furthest movements
Authors: Cimiotti Dominic V. , Eberhart-Hertel Luke , Audevard Aurélien , Garcias Salas Pere Joan , Gelinaud Guillaume , Günther Klaus , Rocha Afonso , Schulz Rainer , van der Winden Jan , Schmaljohann Heiko , Küpper Clemens
Published: April 2023

Dispersal is an important behavioural process that plays a significant role in, among others, speciation, population viability, and individual fitness. Despite progress in avian dispersal research, there are still many knowledge gaps. For example, it is of interest to study how movement propensity (i.e., nomadic vs. philopatric) relates to age- and/or sex-specific patterns of dispersal. Here, we investigated the role of sex and life-stage on natal (i.e., displacement between birth site and first breeding site) and breeding dispersal (i.e., displacement between sequential breeding sites) in the Kentish plover (Charadrius alexandrinus). This small and inconspicuous wader is characterised by flexible mating behaviour that includes monogamy, and serial polygyandry. Using a continent-wide dataset of ringing and re-encounter data throughout the species’ range in Europe, we found that adult females generally dispersed further than adult males between seasons, but we detected no sex-difference in natal dispersal distances and no general difference between natal and breeding dispersal distances. Furthermore, females were the main group exhibiting ‘long-distance’ breeding dispersal, which we defined as breeding movements greater than ≥108 km (i.e., upper 10% percentile of our dataset). Our work detected two females breeding in the Mediterranean before dispersing and breeding at the North Sea in the subsequent year, distances of 1,290 and 1,704 km, respectively – this represents the longest known breeding dispersal within the genusCharadrius. The long-distance dispersal records we identified are consistent with low genetic differentiation between mainland populations shown in previous work. The dispersive nature of the Kentish plover is likely attributed to its breeding behaviour: polyandrous females exhibit extensive mate searching and habitat prospecting. We recommend that the dispersal traits of Kentish plover be incorporated into the species’ conservation and management planning to more accurately inform models of population connectivity and metapopulation dynamics.
ANDA: An open-source tool for automated image analysis of neuronal differentiation
Authors: Wæhler Hallvard Austin , Labba Nils-Anders , Paulsen Ragnhild Elisabeth , Sandve Geir Kjetil , Eskeland Ragnhild
Published: April 2023

Background

Imaging ofin vitroneuronal differentiation and measurements of cell morphologies has led to novel insights into neuronal development. Live-cell imaging techniques and large datasets of images has increased the demand for automated pipelines for quantitative analysis of neuronal morphological metrics.

Results

We present ANDA, an analysis workflow for quantification of various aspects of neuronal morphology from high-throughput live-cell imaging screens. This tool automates the analysis of neuronal cell numbers, neurite lengths and neurite attachment points. We used rat, chicken and humanin vitromodels for neuronal differentiation and have demonstrated the accuracy, versatility, and efficiency of the tool.

Conclusions

ANDA is an open-source tool that is easy to use and capable of automated processing from time-course measurements of neuronal cells. The strength of this pipeline is the capability to analyse high-throughput imaging screens.
Pigment-Dispersing Factor is present in circadian clock neurons of pea aphids and may mediate photoperiodic signalling to insulin-producing cells
Authors: Colizzi Francesca Sara , Veenstra Jan A. , Rezende Gustavo L. , Helfrich-Förster Charlotte , Martínez-Torres David
Published: April 2023

The neuropeptide Pigment-Dispersing Factor (PDF) plays a pivotal role in the circadian clock of most Ecdysozoa and is additionally involved in the timing of seasonal responses of several photoperiodic species. The pea aphid,Acyrthosiphon pisum,is a paradigmatic photoperiodic species with an annual life cycle tightly coupled to the seasonal changes in day length. Nevertheless, PDF could not be identified inA. pisumso far. In the present study, we identified a PDF-coding gene that has undergone significant changes in the otherwise highly conserved insect C-terminal amino acid sequence. A newly generated aphid-specific PDF antibody stained four neurons in each hemisphere of the aphid brain that co-express the clock protein Period and have projections to thepars lateralisthat are highly plastic and change their appearance in a daily and seasonal manner, resembling those of the fruit fly PDF neurons. Most intriguingly, the PDF terminals overlap with dendrites of the insulin-like peptide (ILP) positive neurosecretory cells in thepars intercerebralisand with putative terminals of Cryptochrome (CRY) positive clock neurons. Since ILP has been previously shown to be crucial for seasonal adaptations and CRY might serve as a circadian photoreceptor vital for measuring day length, our results suggest that PDF plays a critical role in aphid seasonal timing.