bluuebunny/crossref_metadata_2025 huggingface dataset:
Looking for a needle in a haystack: de novo phenotypic target identification reveals Hippo pathway-mediated miR-202 regulation of egg production
Authors: Janati-Idrissi Sarah , de Abreu Mariana Roza , Guyomar Cervin , de Mello Fernanda , Nguyen Thaovi , Mechkouri Nazim , Gay Stéphanie , Montfort Jérôme , Gonzalez Anne Alicia , Abbasi Marzieh , Bugeon Jérôme , Thermes Violette , Seitz Hervé , Bobe Julien
Published: December 2023

Understanding microRNA (miRNA) functions has been hampered by major difficulties in identifying their biological target(s). Currently, the main limitation is the lack of a suitable strategy to identify biologically relevant targets among a high number of putative targets. Here we provide a proof of concept of successful de novo (i.e. without prior knowledge of its identity) miRNA phenotypic target (i.e. target whose de-repression contributes to the phenotypic outcomes) identification from RNA-seq data. Using the medaka mir-202 knock-out (KO) model in which inactivation leads to a major organism-level reproductive phenotype, including reduced egg production, we introduced novel criteria including limited fold-change in KO and low interindividual variability in gene expression to reduce the list of 2853 putative targets to a short list of 5. We selected tead3b, a member of the evolutionarily-conserved Hippo pathway, known to regulate ovarian functions, due to its remarkably strong and evolutionarily conserved binding affinity for miR-202-5p. Deleting the miR-202-5p binding site in the 3′ UTR of tead3b, but not of other Hippo pathway members sav1 and vgll4b, triggered a reduced egg production phenotype. This is one of the few successful examples of de novo functional assignment of a miRNA phenotypic target in vivo in vertebrates.
Gastrointestinal manifestations in systemic lupus erythematosus: data from an Indian multi-institutional inception (INSPIRE) cohort
Authors: Mehta Pankti , Aggarwal Amita , Rajasekhar Liza , Shobha Vineeta , Mathew Ashish J , Kavadichanda Chengappa , Ghosh Parasar , Das Bidyut , Rathi Manish , Srivastava Akansha , Gupta Ranjan , Jain Avinash
Published: December 2023

Objectives

To study the prevalence, correlates, and outcomes of GI manifestations in a prospectively enrolled nationwide cohort of SLE in India (INSPIRE).

Methods

It is an observational cohort study with analysis of the baseline database of the INSPIRE cohort with early outcomes assessed till 10 April 2023. Cases with GI manifestations as per the BILAG index were selected, pertinent clinical and laboratory data were retrieved for analysis. Patients with GI manifestations were compared with the rest of the cohort and factors associated with death were determined.

Results

Of the 2503 patients with SLE enrolled in the INSPIRE cohort, 243 (9.7%) had GI manifestations observed early in the disease course (1, 0–3 months). Ascites (162, 6.5%), followed by enteritis (41,1.6%), pancreatitis (35, 1.4%) and hepatitis (24, 0.9%) were the most prevalent manifestations. All patients received immunosuppressive therapy, and four patients required surgery. Twenty-nine patients died (11.9%), with uncontrolled disease activity (17, 58.6%) and infection (6, 20.7%) accounting for the majority of deaths. Low socioeconomic class [lower Hazard Ratio (95% confidence intervals, CI) 2.8 (1.1–7.9); upper lower 7.5 (2–27.7); reference as upper class] and SLEDAI 2K [1.06 (1.02–1.11)] were associated with death in the GI group. GI manifestations were significantly associated with age [odds ratio and 95% CI 0.97 (0.96–0.99)], pleural effusion [4.9 (3.6–6.7)], thrombocytopenia [1.7 (1.2–2.4)], myositis [1.7 (1.1–2.7)], albumin [0.7 (0.5–0.8)], alkaline phosphatase (ALP) [1.01 (1.0–1.002)], low C3 [1.9 (1.3–2.5)], total bilirubin [1.2 (1.03–1.3)], alopecia [0.62 (0.5–0.96], elevated anti-dsDNA [0.5 (0.4–0.8)], and anti-U1RNP antibody [0.8 (0.5–0.7)] in model one; and age [0.97 (0.96–0.99)], creatinine [1.2 (1.03–1.4)], total bilirubin [1.2 (1.03–1.3)], ALP [1.01 (1.0–1.002)], albumin [0.6 (0.5–0.7)], andanti-U1RNP antibody [0.6 (0.5–0.8)] in model two in multivariate analysis compared with patients without GI features. The mortality was higher in the GI group (11.9% and 6.6%, P = 0.01) as compared with controls.

Conclusion

GI manifestations were observed in 9.7% of the cohort and were always associated with systemic disease activity and had higher mortality.
IL-2 produced by HBV-specific T cells as a biomarker of viral control and predictor of response to PD-1 therapy across clinical phases of chronic hepatitis B
Authors: Chua Conan , Salimzadeh Loghman , Ma Ann T. , Adeyi Oyedele A. , Seo Hobin , Boukhaled Giselle M. , Mehrotra Aman , Patel Anjali , Ferrando-Martinez Sara , Robbins Scott H. , La Danie , Wong David , Janssen Harry L.A. , Brooks David G. , Feld Jordan J. , Gehring Adam J.
Published: December 2023

Background:

There are no immunological biomarkers that predict control of chronic hepatitis B (CHB). The lack of immune biomarkers raises concerns for therapies targeting PD-1/PD-L1 because they have the potential for immune-related adverse events. Defining specific immune functions associated with control of HBV replication could identify patients likely to respond to anti-PD-1/PD-L1 therapies and achieve a durable functional cure.

Methods:

We enrolled immunotolerant, HBeAg+ immune-active (IA+), HBeAg− immune-active (IA−), inactive carriers, and functionally cured patients to test ex vivo PD-1 blockade on HBV-specific T cell functionality. Peripheral blood mononuclear cells were stimulated with overlapping peptides covering HBV proteins +/−α-PD-1 blockade. Functional T cells were measured using a 2-color FluoroSpot assay for interferon-γ and IL-2. Ex vivo functional restoration was compared to the interferon response capacity assay, which predicts overall survival in cancer patients receiving checkpoint inhibitors.

Results:

Ex vivo interferon-γ+ responses did not differ across clinical phases. IL-2+ responses were significantly higher in patients with better viral control and preferentially restored with PD-1 blockade. Inactive carrier patients displayed the greatest increase in IL-2 production, which was dominated by CD4 T cell and response to the HBcAg. The interferon response capacity assay significantly correlated with the degree of HBV-specific T cell restoration.

Conclusions:

IL-2 production was associated with better HBV control and superior to interferon-γ as a marker of T cell restoration following ex vivo PD-1 blockade. Our study suggests that responsiveness to ex vivo PD-1 blockade, or the interferon response capacity assay, may support stratification for α-PD-1 therapies.
Mild Traumatic Brain Injury in the Maturing Brain: An Investigation of Symptoms and Cognitive Performance in Soldiers Returning From Afghanistan and Iraq
Authors: Ivins Brian , Risling Mårten , Wisén Niclas , Schwab Karen , Rostami Elham
Published: December 2023

Objective:

The majority of traumatic brain injuries (TBIs) are classified as mild and occur in young individuals. The course of recovery varies but can result in chronic or troubling outcomes. The impact of age on TBI outcomes in young adults before complete brain maturation is not well studied.

Methods:

In this study, we compared the effects of mild TBI on cognitive performance and self-reported TBI symptoms and posttraumatic stress disorder (PTSD) in 903 soldiers in 3 different age groups: 24 years or younger, 25 to 27 years, and 28 to 40 years. The soldiers had returned from war zones in Iraq and were screened for TBI within a few days of return. Cognitive performance was measured with the Automated Neuropsychological Assessment Metrics of Military TBI Version 4 (ANAM4). Symptoms associated with mild TBI were self-reported on the Neurobehavioral Symptom Inventory, and the PTSD Checklist—Civilian Version (PCL-C).

Results:

Soldiers with TBI in every age group had significantly higher prevalence of most symptoms than those with no TBI. Soldiers with TBI also reported more chronic pain sites, regardless of age. Soldiers aged 28 to 40 years with TBI had the lowest cognitive performance scores (ANAM) across several subtests, both unadjusted and adjusted. The Global Deficit Score was significantly higher for soldiers aged 28 to 40 years and 25 to 27 years with TBI than for soldiers younger than 24 years with no TBI. After adjusting for PTSD symptoms, education, and number of lifetime TBIs, the overall test battery mean for soldiers aged 28 to 40 years with TBI was significantly lower than for soldiers younger than 24 years with no TBI.

Conclusion:

Soldiers with mild TBI in the younger age group show more symptoms associated to frontal lobe function while soldiers in the older group suffer more cognitive impairment. This may warrant further study as it may indicate a propensity to later cognitive decline among soldiers who were older at the time of injury.
Development of adaptive anoikis resistance promotes metastasis that can be overcome by CDK8/19 Mediator kinase inhibition
Authors: Monavarian Mehri , Page Emily Faith , Rajkarnikar Resha , Kumari Asha , Macias Liz Quintero , Massicano Felipe , Lee Nam Y , Sahoo Sarthak , Hempel Nadine , Jolly Mohit Kumar , Ianov Lara , Worthey Elizabeth , Singh Abhyudai , Broude Eugenia V , Mythreye Karthikeyan
Published: December 2023

Anoikis resistance or evasion of cell death triggered by cell detachment into suspension is a hallmark of cancer that is concurrent with cell survival and metastasis. The effects of frequent matrix detachment encounters on the development of anoikis resistance in cancer remains poorly defined. Here we show using a panel of ovarian cancer models, that repeated exposure to suspension stress in vitro followed by attached recovery growth leads to the development of anoikis resistance paralleling in vivo development of anoikis resistance in ovarian cancer ascites. This resistance is concurrent with enhanced invasion, chemoresistance and the ability of anoikis adapted cells to metastasize to distant sites. Adapted anoikis resistant cells show a heightened dependency on oxidative phosphorylation and can also evade immune surveillance. We find that such acquired anoikis resistance is not genetic, as acquired resistance persists for a finite duration in the absence of suspension stress. Transcriptional reprogramming is however essential to this process, as acquisition of adaptive anoikis resistance in vitro and in vivo is exquisitely sensitive to inhibition of CDK8/19 Mediator kinase, a pleiotropic regulator of transcriptional reprogramming. Our data demonstrate that growth after recovery from repeated exposure to suspension stress is a direct contributor to metastasis and that inhibition of CDK8/19 Mediator kinase during such adaptation provides a therapeutic opportunity to prevent both local and distant metastasis in cancer.
Three-dimensional assessments are necessary to determine the true, spatially-resolved composition of tissues
Authors: Forjaz André , Vaz Eduarda , Romero Valentina Matos , Joshi Saurabh , Braxton Alicia M. , Jiang Ann C. , Fujikura Kohei , Cornish Toby , Hong Seung-Mo , Hruban Ralph H. , Wu Pei-Hsun , Wood Laura D. , Kiemen Ashley L. , Wirtz Denis
Published: December 2023

Methods for spatially resolved cellular profiling using thinly cut sections have enabled in-depth quantitative tissue mapping to study inter-sample and intra-sample differences in normal human anatomy and disease onset and progression. These methods often profile extremely limited regions, which may impact the evaluation of heterogeneity due to tissue sub-sampling. Here, we applied CODA, a deep learning-based tissue mapping platform, to reconstruct the three-dimensional (3D) microanatomy of grossly normal and cancer-containing human pancreas biospecimens obtained from individuals who underwent pancreatic resection. To compare inter-and intra-sample heterogeneity, we assessed bulk and spatially resolved tissue composition in a cohort of two-dimensional (2D) whole slide images (WSIs) and a cohort of thick slabs of pancreas tissue that were digitally reconstructed in 3D from serial sections. To demonstrate the marked under sampling of 2D assessments, we simulated the number of WSIs and tissue microarrays (TMAs) necessary to represent the compositional heterogeneity of 3D data within 10% error to reveal that tens of WSIs and hundreds of TMA cores are sometimes needed. We show that spatial correlation of different pancreatic structures decay significantly within a span of microns, demonstrating that 2D histological sections may not be representative of their neighboring tissues. In sum, we demonstrate that 3D assessments are necessary to accurately assess tissue composition in normal and abnormal specimens and in order to accurately determine neoplastic content. These results emphasize the importance of intra-sample heterogeneity in tissue mapping efforts.
Normalization of RNA-Seq Data using Adaptive Trimmed Mean with Multi-reference
Authors: Singh Vikas , Kirtipal Nikhil , Song Byong-Sop , Lee Sunjae
Published: December 2023

The normalization of RNA sequencing data is a primary step for downstream analysis. The most popular method used for the normalization is the trimmed mean of M values (TMM) and DESeq. The TMM tries to trim away extreme log fold changes of the data to normalize the raw read counts based on the remaining non-deferentially expressed genes. However, the major problem with the TMM is that the values of trimming factor M are heuristic. This paper tries to estimate the adaptive value of M in TMM based on Jaeckel’s Estimator, and each sample acts as a reference to find the scale factor of each sample. The presented approach is validated on SEQC, MAQC2, MAQC3, PICKRELL, and two simulated datasets with two groups and three groups conditions by varying the percentage of differential expression and the number of replicates. The performance of the present approach is compared, and it shows better in terms of area under the receiver operating characteristic curve (AUC) and differential expression. The implementation of the present approach is available on the GitHub platform:https://github.com/vikkyak/Normalization-of-Bulk-RNA-seq.
“The impact of the Little Orange Book on how parents/carers manage symptoms of illness in children: A mixed methods study”
Authors: Johnson Amy , Carruthers Kathryn , Breckons Matthew , Shotton Lynette Harland
Published: December 2023

Background

Parental decision-making regarding children’s healthcare represents a complex and difficult process. While there is general agreement that information and education may play a key role in supporting self-care and the use of health services, there is potential for information to increase, as well as reduce anxiety.

Objectives

This article summarises the key recommendations of an applied evaluation of a paediatric health resource, The Little Orange Book.

Methods

A mixed-methods approach was used to collect data regarding parental perceptions on the health resource. Parents and carers in the North-East of England were invited to participate in an online survey and qualitative interviews. Qualitative data were analysed using thematic analysis and quantitative data analysed using descriptive statistical analytical methods.

Results

One-hundred-and-twenty-eight parents completed the online survey and 16 took part in interviews. Three themes were identified within the data:Increasing parental empowerment in managing their child’s health, Equality of Access to Health-based LiteratureandBarriers and Facilitators to using the Little Orange Book.

Conclusions

The Little Orange Book has the potential to be a useful form of information to support parents and carers in healthcare decisions. Further development should ensure inclusivity, widen access and view provision of the information as an opportunity for healthcare professionals to engage with parents.
State Adoption of Paid Sick Leave and Cardiovascular Disease Mortality Among Adults Aged 15-64 in the United States, 2008 to 2019
Authors: Swift Sam , O’Donnell Lexi , Horn Brady , Kezios Katrina , Elfassy Tali , Reagan Julie , Zeki Al Hazzouri Adina , Collins Tracie
Published: December 2023

Background

Cardiovascular Disease (CVD) is the leading cause of death in the United States and may be prevented through improved working conditions. The United States is one of the few high-income nations that does not guarantee paid sick leave (PSL) at the federal level. Our objective was to examine the relationship between state-level PSL policies and CVD mortality.

Methods

We used quasi-experimental event study methods to examine the relationship between implementing a mandatory PSL policy for all employees at the state-level and county-level CVD mortality rates using National Center for Health Statistics data among working-age adults aged 15 to 64 over time from 2008 to 2019. During this time, 11 states implemented PSL policies. We examined the annual CVD mortality rates (2008-2019) in 1054 counties from all 50 states and Washington D.C., accounting for approximately 88% of the United States population in this analysis.

Results

We found that in the Northeastern region of the United States, there were drops in the CVD mortality rate for persons ages 15-64 for all years after PSL was implemented, ranging from 7.1 fewer deaths per 100,000 persons (β=-7.1, 95% CI = -9.7, -4.4) seven years post-treatment to 2.7 fewer deaths two years post-treatment (β=-2.7, 95% CI= -5.1, -0.3).

Conclusion

Our results support the use of state-level PSL policies to reduce county-level CVD mortality rates, especially in the Northeastern United States.
Towards explainable interaction prediction: Embedding biological hierarchies into hyperbolic interaction space
Authors: Pogány Domonkos , Antal Péter
Published: December 2023

Given the prolonged timelines and high costs associated with traditional approaches, accelerating drug development is crucial. Computational methods, particularly drug-target interaction prediction, have emerged as efficient tools, yet the explainability of machine learning models remains a challenge. Our work aims to provide more interpretable interaction prediction models using similarity-based prediction in a latent space aligned to biological hierarchies. We investigated integrating drug and protein hierarchies into a joint-embedding drug-target latent space via embedding regularization by conducting a comparative analysis between models employing traditional flat Euclidean vector spaces and those utilizing hyperbolic embeddings. Besides, we provided a latent space analysis as an example to show how we can gain visual insights into the trained model with the help of dimensionality reduction. Our results demonstrate that hierarchy regularization improves interpretability without compromising predictive performance. Furthermore, integrating hyperbolic embeddings, coupled with regularization, enhances the quality of the embedded hierarchy trees. Our approach enables a more informed and insightful application of interaction prediction models in drug discovery by constructing an interpretable hyperbolic latent space, simultaneously incorporating drug and target hierarchies and pairing them with available interaction information. Moreover, compatible with pairwise methods, the approach allows for additional transparency through existing explainable AI solutions.
Disease progression modelling reveals heterogeneity in trajectories of Lewy-type α-synuclein pathology
Authors: Mastenbroek Sophie E. , Vogel Jacob W. , Collij Lyduine E. , Serrano Geidy E. , Tremblay Cecilia , Young Alexandra L. , Arce Richard A. , Shill Holly A. , Driver-Dunckley Erika D. , Mehta Shyamal H. , Belden Christine M. , Atri Alireza , Choudhury Parichita , Barkhof Frederik , Adler Charles H. , Ossenkoppele Rik , Beach Thomas G. , Hansson Oskar
Published: December 2023

Lewy body (LB) disorders, characterized by the aggregation of misfolded α-synuclein proteins, exhibit notable clinical heterogeneity. This may be due to variations in accumulation patterns of LB neuropathology. By applying data-driven disease progression modelling to regional neuropathological LB density scores from 814 brain donors, we describe three inferred trajectories of LB pathology that were characterized by differing clinicopathological presentation and longitudinal antemortem clinical progression. Most donors (81.9%) showed earliest pathology in the olfactory bulb, followed by accumulation in either limbic (60.8%) or brainstem (21.1%) regions. The remaining donors (18.1%) exhibited the first abnormalities in brainstem regions. Early limbic pathology was associated with Alzheimer’s disease-associated characteristics. Meanwhile, brainstem-first pathology was associated with progressive motor impairment and substantial LB pathology outside of the brain. Our data provides evidence for heterogeneity in the temporal spread of LB pathology, possibly explaining some of the clinical disparities observed in LBDs.
Ancestral neural circuits potentiate the origin of a female sexual behavior
Authors: Li Minhao , Chen Dawn S. , Junker Ian P. , Szorenyi Fabianna , Chen Guan Hao , Berger Arnold J. , Comeault Aaron A. , Matute Daniel R. , Ding Yun
Published: December 2023

Courtship interactions are remarkably diverse in form and complexity among species. How neural circuits evolve to encode new behaviors that are functionally integrated into these dynamic social interactions is unknown. Here we report a recently originated female sexual behavior in the island endemicDrosophilaspeciesD. santomea, where females signal receptivity to male courtship songs by spreading their wings, which in turn promotes prolonged songs in courting males. Copulation success depends on this female signal and correlates with males’ ability to adjust his singing in such a social feedback loop. Functional comparison of sexual circuitry across species suggests that a pair of descending neurons, which integrates male song stimuli and female internal state to control a conserved female abdominal behavior, drives wing spreading inD. santomea. This co-option occurred through the refinement of a pre-existing, plastic circuit that can be optogenetically activated in an outgroup species. Combined, our results show that the ancestral potential of a socially-tuned key circuit node to engage the wing motor program facilitates the expression of a new female behavior in appropriate sensory and motivational contexts. More broadly, our work provides insights into the evolution of social behaviors, particularly female behaviors, and the underlying neural mechanisms.
Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation
Authors: Iwańska Olga , Latoch Przemysław , Kopik Natalia , Kovalenko Mariia , Lichocka Małgorzata , Serwa Remigiusz , Starosta Agata L
Published: December 2023

Translational control during the intricate process of sporulation inBacillus subtilisas a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape ofB. subtilisduring sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. Using a triple knock-out strain (3KO) of zinc-independents paralogs of three zinc-dependent ribosomal proteins L31, L33 and S14, we investigated the potential regulatory role of ribosome during sporulation. The 3KO strain exhibited delayed sporulation, reduced germination efficiency, and dysregulated translation including expression of key metabolic and sporulation-related genes as well as disruptions in translation silencing, particularly in late sporulation.
Structure and dynamics of the RF-amide QRFP receptor GPR103
Authors: Iwama Aika , Akasaka Hiroaki , Sano Fumiya K. , Oshima Hidetaka S. , Shihoya Wataru , Nureki Osamu
Published: December 2023

Pyroglutamylated RF amide peptide (QRFP) is a type of peptide hormone with a C-terminal RF-amide motif. QRFP selectively activates class-A categorized GPCR, GPR103 to exert various physiological functions such as energy metabolism and appetite regulation. Here, we report the cryo-electron microscopy structure of the QRFP-GPR103-Gqcomplex at 3.3 Å resolution. Unlike class-A GPCR, QRFP adopts an extended structure baring no secondary structure, with its N-terminal and C-terminal sides recognized by extracellular and transmembrane domains, respectively, of GPR103. The C-terminal heptapeptide of QRFP penetrates into the orthosteric pocket to act in receptor activation. Particularly, the residues that recognize the RF-amide are highly conserved in the RF-amide receptors. Notably, the unique N-terminal helix-loop-helix of the receptor traps the N-terminal side of QRFP with the pendulum-like motion to guide QRFP into the ligand-binding pocket. This movement, reminiscent of class B1 GPCRs except for orientation and structure of the ligand, is critical for the high affinity binding and receptor specificity of QRFP. Structural comparisons with closely related receptors, including RY-amide peptide-recognizing GPCRs, revealed conserved and diversified peptide recognition mechanisms, providing profound insights into the biological significance of RF-amide peptides. This study not only advances our understanding of GPCR-ligand interactions, but also paves the way for the development of novel therapeutics targeting metabolic and appetite disorders and emergency medical care.
Sequence-based GWAS in 180 000 German Holstein cattle reveals new candidate genes for milk production traits
Authors: Križanac Ana-Marija , Reimer Christian , Heise Johannes , Liu Zengting , Pryce Jennie , Bennewitz Jörn , Thaller Georg , Falker-Gieske Clemens , Tetens Jens
Published: December 2023

Background

The use of genome-wide association studies (GWAS) has led to the identification of numerous quantitative trait loci and candidate genes in dairy cattle. To obtain sufficient power of GWAS and to identify quantitative trait nucleotides, whole-genome sequence data is required. Sequence data facilitates the identification of potential causal variants; however, sequencing of whole genomes is still expensive for a large number of animals. Imputation is a quick and efficient way of obtaining sequence data from large datasets. Milk production traits are complex and influenced by many genetic and environmental factors. Although extensive research has been performed for these traits, with many associations unveiled thus far, due to their crucial economic importance, complex genetic architecture, and the fact that causative variants in cattle are still scarce, there is a need for a better understanding of their genetic background. In this study, we aimed to identify new candidate loci associated with milk production traits in German Holstein cattle, the most important dairy breed in Germany and worldwide. For that purpose, 252,285 cattle were imputed to the sequence level and large-scale GWAS was carried out to identify new association signals.

Results

We confirmed many known and identified 30 previously unreported candidate genes for milk, fat, and protein yield. While all of the genes were functionally associated with the traits, some showed pleiotropic effects as well. Specifically, association with mammary gland development, fatty acid synthesis, metabolism of lipids, or milk production QTLs in other farm animals has been reported. Variants associated with these genes explained a large percentage of genetic variance, compared to random ones.

Conclusions

Our findings proved the power of large samples and sequence-based GWAS in detecting new association signals. In order to fully exploit the power of GWAS, one should aim at very large samples combined with whole-genome sequence data. Although milk production traits in cattle are comprehensively researched, the genetic background of these traits is still not fully understood, with the potential for many new associations to be revealed, as shown in our study. With constantly growing sample sizes, we expect more insights into the genetic architecture of production traits in the future.
Rapid Vacuolar Sorting of the Borate Transporter BOR1 Requires the Adaptor Protein Complex AP-4 in Arabidopsis
Authors: Yoshinari Akira , Shimizu Yutaro , Hosokawa Takuya , Nakano Akihiko , Uemura Tomohiro , Takano Junpei
Published: December 2023

Plants maintain nutrient homeostasis by controlling the activities and abundance of nutrient transporters. InArabidopsis thaliana, the borate (B) transporter BOR1 plays a role in the efficient translocation of B under low-B conditions. BOR1 undergoes polyubiquitination in the presence of sufficient B and is then transported to the vacuole via multivesicular bodies (MVBs) to prevent B accumulation in tissues at a toxic level. A previous study indicated that BOR1 physically interacts with μ subunits of adaptor protein complexes AP-3 and AP-4, both involved in vacuolar sorting pathways. In this study, we investigated the roles of AP-3 and AP-4 subunits in BOR1 trafficking in Arabidopsis. The lack of AP-3 subunits did not affect either vacuolar sorting or polar localization of BOR1-GFP, whereas the absence of AP-4 subunits resulted in a delay in high-B-induced vacuolar sorting without affecting polar localization. Super-resolution microscopy revealed a rapid sorting of BOR1-GFP into AP-4-positive spots in thetrans-Golgi network (TGN) upon high-B supply. These results indicate that AP-4 is involved in sequestration of ubiquitinated BOR1 into a TGN-specific subdomain “vacuolar-trafficking zone,” and is required for efficient sorting to MVB and vacuole. Our findings elucidate the rapid vacuolar sorting process facilitated by AP-4 in plant nutrient transporters.

Subject areas

(7) Membrane and transport
Oligodendrocyte-specific expression ofPSG8-AS1suggests a role in myelination with prognostic value in oligodendroglioma
Authors: de los Angeles Becerra Rodriguez Maria , Gonzalez Muñoz Elena , Moore Tom
Published: December 2023

The segmentally duplicated Pregnancy-specific glycoprotein (PSG) locus on chromosome 19q13 may be one of the most rapidly evolving in the human genome. It comprises ten coding genes (PSG1-9, 11) and one predominantly non-coding gene (PSG10) that are expressed in the placenta and gut, in addition to several poorly characterized long non-coding RNAs. We report that long non-coding RNAPSG8-AS1has an oligodendrocyte-specific expression pattern and is co-expressed with genes encoding key myelin constituents.PSG8-AS1exhibits two peaks of expression during human brain development coinciding with the most active periods of oligodendrogenesis and myelination.PSG8-AS1orthologs were found in the genomes of several primates but significant expression was found only in the human, suggesting a recent evolutionary origin of its proposed role in myelination. Additionally, because co-deletion of chromosomes 1p/19q is a genomic marker of oligodendroglioma, expression ofPSG8-AS1was examined in these tumors.PSG8-AS1may be a promising diagnostic biomarker for glioma, with prognostic value in oligodendroglioma.
Circuit dynamics of superficial and deep CA1 pyramidal cells and inhibitory cells in freely-moving macaques
Authors: Abbaspoor S. , Hoffman K.L.
Published: December 2023

Diverse neuron classes in hippocampal CA1 have been identified through the heterogeneity of their cellular/molecular composition. How these classes relate to hippocampal function and the network dynamics that support cognition in primates remains unclear. Here we report inhibitory functional cell groups in CA1 of freely-moving macaques whose diverse response profiles to network states and each other suggest distinct and specific roles in the functional microcircuit of CA1. In addition, pyramidal cells that were segregated into superficial and deep layers differed in firing rate, burstiness, and sharp-wave ripple-associated firing. They also showed strata-specific spike-timing interactions with inhibitory cell groups, suggestive of segregated neural populations. Furthermore, ensemble recordings revealed that cell assemblies were preferentially organized according to these strata. These results suggest sublayer-specific circuit organization in hippocampal CA1 of the freely-moving macaques that may underlie its role in cognition.
Single cell transcriptional changes across the blood stages of artemisinin resistant K13580YPlasmodium falciparumupon dihydroartemisinin exposure
Authors: Oduor Cliff I. , Connelly Sean V. , Cunningham Clark , Rustamzade Nazrin , Zuromski Jenna , Chin Deborah M. , Nixon Chris , Kurtis Jonathan , Juliano Jonathan J. , Bailey Jeffrey A
Published: December 2023

Artemisinins have been a cornerstone of malaria control, but resistance inPlasmodium falciparum, due to mutations in the Kelch13 (K13) protein, threaten these advances. Artemisinin exposure results in a dynamic transcriptional response across multiple pathways, but most work has focused on ring stages andex vivotranscriptional analysis. We applied single cell RNAseq to two unsynchronized coisogenic parasite lines (K13C580and K13580Y) over 6 hrs after a pulse exposure to dihydroartemisinin (DHA). Transcription was altered across all stages, with the greatest occurring at the trophozoite and ring stage in both lines. This response involved the arrest of metabolic processes, support for a dormancy phenomenon upon treatment, and the enhancement of protein trafficking and the unfolded protein response. While similar, the response was consistent across stages in K13580Y, with enhanced parasite survival to drug induced stress. Increased surface protein expression was seen in K13580Yparasites at baseline and upon drug exposure, highlighted by the increased expression ofPfEMP1andGARP,a potential therapeutic target. Antibody targeting GARP maintained anti-parasitic efficacy in K13580Yparasites. This work provides single cell insight of gene transcription across all life cycle stages revealing transcriptional changes that could initiate a dormancy state and mediate survival upon treatment.

IMPORTANCE

Single cell RNA sequencing allows deconvolution of the cellular stages of malaria and investigation of their response to treatment conditions. Utilizing two different genetic backgrounds of a key resistance marker to artemisinin treatment, we compared the response to dihydroartemisinin between these genetic backgrounds. We found a distinct transcriptional profile post treatment in both genetic backgrounds, with downregulation of metabolic process genes and upregulation of stress response genes. Comparing these two genetic backgrounds post treatment using traditional differential expression, and a novel computational method called MELD, we found consistent increased expression of GARP and pathogenesis related genes, likePfEMP1. This study identifies possible gene dependencies of parasite survival post artemisinin treatment, providing targets for inhibiting the dormancy state.
A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts
Authors: Johnson Ben , Iuliano Maria , Lam TuKiet , Biederer Thomas , De Camilli Pietro
Published: December 2023

Junctions between the ER and the plasma membrane (ER/PM junctions) are implicated in calcium homeostasis, non-vesicular lipid transfer and other cellular functions. Two ER proteins that function both as membrane tethers to the PM via a polybasic motif in their C-terminus and as phospholipid transporters are brain-enriched TMEM24 (C2CD2L) and its paralog C2CD2. Based on an unbiased proximity ligation analysis, we found that both proteins can also form a complex with band 4.1 family members, which in turn can bind a variety of plasma membrane proteins including cell adhesion molecules such as SynCAM 1. This complex results in the enrichment of TMEM24 and C2CD2 containing ER/PM junctions at sites of cell contacts. Dynamic properties of TMEM24-dependent ER/PM contacts are impacted when in complex as TMEM24 present at cell adjacent junctions is not shed by calcium rise, unlike TMEM24 at non-cell adjacent junctions. These findings suggest that cell-contact interactions control ER/PM junctions via TMEM24 complexes involving band 4.1 proteins.

The ER-anchored lipid transfer proteins TMEM24/C2CD2L and its paralog C2CD2 mediate formation of ER-plasma membrane junctions at sites of cell-cell contacts by interacting with band 4.1 family members and indirectly with cell adhesion proteins.
Neuropilin-1 is a co-receptor for Nerve Growth Factor-evoked pain
Authors: Peach Chloe J. , Tonello Raquel , Damo Elisa , Gomez Kimberly , Calderon-Rivera Aida , Bruni Renato , Bansia Harsh , Maile Laura , Manu Ana-Maria , Hahn Hyunggu , Thomsen Alex R.B. , Schmidt Brian L. , Davidson Steve , des Georges Amedee , Khanna Rajesh , Bunnett Nigel W.
Published: December 2023

Nerve growth factor (NGF) monoclonal antibodies inhibit chronic pain yet, failed to gain approval due to worsened joint damage in osteoarthritis patients. We report that neuropilin-1 (NRP1) is a co-receptor for NGF and tropomyosin-related kinase A (TrkA) pain signaling. NRP1 is coexpressed with TrkA in human and mouse nociceptors. NRP1 inhibitors suppress NGF-stimulated excitation of human and mouse nociceptors and NGF-evoked nociception in mice. NRP1 knockdown inhibits NGF/TrkA signaling, whereas NRP1 overexpression enhances signaling. NGF binds NRP1 with high affinity and interacts with and chaperones TrkA from the biosynthetic pathway to the plasma membrane and endosomes, enhancing TrkA signaling. Molecular modeling suggests that C-terminal R/KXXR/K NGF motif interacts with extracellular “b” NRP1 domain within a plasma membrane NGF/TrkA/NRP1 of 2:2:2 stoichiometry. G Alpha Interacting Protein C-terminus 1 (GIPC1) scaffolds NRP1 and TrkA to myosin VI and colocalizes in nociceptors with NRP1/TrkA. GIPC1 knockdown abrogates NGF-evoked excitation of nociceptors and pain-like behavior. NRP1 is a nociceptor-enriched co-receptor that facilitates NGF/TrkA pain signaling. NRP binds NGF and chaperones TrkA to the plasma membrane and signaling endosomes via the GIPC1 adaptor. NRP1 and GIPC1 antagonism in nociceptors offers a long-awaited non-opioid alternative to systemic antibody NGF sequestration for the treatment of chronic pain.

Neuropilin-1 and G Alpha Interacting Protein C-terminus 1 are necessary for nerve growth factor-evoked pain and are non-opioid therapeutic targets for chronic pain.
Fluorescent tagging of endogenous IRS2 with an auxin-dependent degron to assess dynamic intracellular localization and function
Authors: Jo Minjeong , Lee Ji-Sun , Lero Michael W. , Morgan Jennifer S. , Shaw Leslie M.
Published: December 2023

Insulin Receptor Substrate 2 (IRS2) is a signaling adaptor protein for the insulin (IR) and Insulin-like Growth Factor-1 (IGF-1R) receptors. In breast cancer, IRS2 contributes to both initiation of primary tumor growth and establishment of secondary metastases through regulation of cancer stem cell (CSC) function and invasion. However, how IRS2 mediates its diverse functions is not well understood. We used CRISPR/Cas9-mediated gene editing to modify endogenous IRS2 to study the expression, localization, and function of this adaptor protein. A cassette containing an auxin inducible degradation (AID) sequence, 3X-FLAG tag and mNeon-green was introduced at the N-terminus of the IRS2 gene to provide rapid and reversible control of IRS2 protein degradation and analysis of endogenous IRS2 expression and localization. Live fluorescence imaging of these cells revealed that IRS2 shuttles between the cytoplasm and nucleus in response to growth regulatory signals, and deletion of a putative nuclear export sequence in the C-terminal tail promotes nuclear retention of IRS2. Moreover, acute induction of IRS2 degradation reduces CSC function, similar to the constitutive knockout of IRS2. Our data highlight the value of our model of endogenously tagged IRS2 as a tool to elucidate IRS2 localization and function.
Diverse 3D cellular patterns underlie the development ofCardamine hirsutaandArabidopsis thalianaovules
Authors: Mody Tejasvinee Atul , Rolle Alexander , Stucki Nico , Roll Fabian , Bauer Ulrich , Schneitz Kay
Published: December 2023

A fundamental question in biology is how organ morphogenesis comes about. The ovules ofArabidopsis thalianahave been established as a successful model to study numerous aspects of tissue morphogenesis; however, little is known regarding the relative contributions and dynamics of differential tissue and cellular growth and architecture in establishing ovule morphogenesis in different species. To address this issue, we generated a 3D digital atlas ofCardamine hirsutaovule development with full cellular resolution. We combined quantitative comparative morphometrics and topological analysis to explore similarities and differences in the 3D cellular architectures underlying ovule development of the two species. We discovered that they show diversity in the way the three radial cell layers of the primordium contribute to its growth, in the formation of a new cell layer in the inner integument and, in certain cases, in the topological properties of the 3D cell architectures of homologous tissues despite their similar shape. Our work demonstrates the power of comparative 3D cellular morphometry and the importance of internal tissues and their cellular architecture in organ morphogenesis.

Summary Statement

Quantitative morphometric comparison of 3D digital ovules at full cellular resolution reveals diversity in internal 3D cellular architectures between similarly shaped ovules ofCardamine hirsutaandArabidopsis thaliana.
The vestibulospinal nucleus is a locus of balance development
Authors: Hamling Kyla R. , Harmon Katherine , Kimura Yukiko , Higashijima Shin-ichi , Schoppik David
Published: December 2023

Mature vertebrates maintain posture using vestibulospinal neurons that transform sensed instability into reflexive commands to spinal motor circuits. Postural stability improves across development. However, due to the complexity of terrestrial locomotion, vestibulospinal contributions to postural refinement in early life remain unexplored. Here we leveraged the relative simplicity of underwater locomotion to quantify the postural consequences of losing vestibulospinal neurons during development in larval zebrafish of undifferentiated sex. By comparing posture at two timepoints, we discovered that later lesions of vestibulospinal neurons led to greater instability. Analysis of thousands of individual swim bouts revealed that lesions disrupted movement timing and corrective reflexes without impacting swim kinematics, and that this effect was particularly strong in older larvae. Using a generative model of swimming, we showed how these disruptions could account for the increased postural variability at both timepoints. Finally, late lesions disrupted the fin/trunk coordination observed in older larvae, linking vestibulospinal neurons to postural control schemes used to navigate in depth. Since later lesions were considerably more disruptive to postural stability, we conclude that vestibulospinal contributions to balance increase as larvae mature. Vestibulospinal neurons are highly conserved across vertebrates; we therefore propose that they are a substrate for developmental improvements to postural control.

SIGNIFICANCE STATEMENT

Many animals experience balance improvements during early life. Mature vertebrates use vestibulospinal neurons to transform sensed instability into postural corrections. To understand if/how these neurons shape postural development, we ablated them at two developmentally important timepoints in larval zebrafish. Loss of vestibulospinal neurons disrupted specific stabilizing behaviors (swim timing, tilt correction, and fin/body coordination) more profoundly in older fish. We conclude that postural development happens in part by changes to vestibulospinal neurons — a significant step towards understanding how developing brains gain the ability to balance.
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
Authors: Harvey William T. , Ebert Peter , Ebler Jana , Audano Peter A. , Munson Katherine M. , Hoekzema Kendra , Porubsky David , Beck Christine R. , Marschall Tobias , Garimella Kiran , Eichler Evan E.
Published: December 2023

Advances in long-read sequencing (LRS) technologies continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo genome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant-calling precision and recall of Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) HiFi platforms over a range of sequence coverages. For read-based applications, LRS sensitivity begins to plateau around 12-fold coverage with a majority of variants called with reasonable accuracy (F1score above 0.5), and both platforms perform well for SV detection. Genome assembly increases variant-calling precision and recall of SVs and indels in HiFi data sets with HiFi outperforming ONT in quality as measured by the F1score of assembly-based variant call sets. While both technologies continue to evolve, our work offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.
Learning experience network analysis for design-based research
Authors: Donaldson Jonan Phillip , Han Ahreum , Yan Shulong , Lee Seiyon , Kao Sean
Published: December 2023

Purpose

Design-based research (DBR) involves multiple iterations, and innovations are needed in analytical methods for understanding how learners experience a learning experience in ways that both embrace the complexity of learning and allow for data-driven changes to the design of the learning experience between iterations. The purpose of this paper is to propose a method of crafting design moves in DBR using network analysis.

Design/methodology/approach

This paper introduces learning experience network analysis (LENA) to allow researchers to investigate the multiple interdependencies between aspects of learner experiences, and to craft design moves that leverage the relationships between struggles, what worked and experiences aligned with principles from theory.

Findings

The use of network analysis is a promising method of crafting data-driven design changes between iterations in DBR. The LENA process developed by the authors may serve as inspiration for other researchers to develop even more powerful methodological innovations.

Research limitations/implications

LENA may provide design-based researchers with a new approach to analyzing learner experiences and crafting data-driven design moves in a way that honors the complexity of learning.

Practical implications

LENA may provide novice design-based researchers with a structured and easy-to-use method of crafting design moves informed by patterns emergent in the data.

Originality/value

To the best of the authors’ knowledge, this paper is the first to propose a method for using network analysis of qualitative learning experience data for DBR.