bluuebunny/crossref_metadata_2025 huggingface dataset:
Charting the Cannabis plant chemical space with computational metabolomics
Authors: Myoli Akhona , Choene Mpho , Kappo Abidemi Paul , Madala Ntakadzeni Edwin , van der Hooft Justin J.J. , Tugizimana Fidele
Published: February 2024

Introduction

The chemical classification of Cannabis is typically confined to the cannabinoid content, whilst Cannabis encompasses diverse chemical classes that vary in abundance among all its varieties. Hence, neglecting other chemical classes within Cannabis strains results in a restricted and biased comprehension of elements that may contribute to chemical intricacy and the resultant medicinal qualities of the plant.

Objectives

Thus, herein, we report a computational metabolomics study to elucidate the Cannabis metabolic map beyond the cannabinoids.

Methods

Mass spectrometry-based computational tools were used to mine and evaluate the methanolic leaf and flower extracts of two Cannabis cultivars: Amnesia haze (AMNH) and Royal dutch cheese (RDC).

Results

The results revealed the presence of different chemical compound classes including cannabinoids, but extending it to flavonoids, polyketides, and phospholipids at varying distributions across the cultivar plant tissues. Therefore, the two cultivars were differentiated based on the overall chemical content of their plant tissues where AMNH was observed to be more dominant in the flavonoid content while RDC was more dominant in the lipid-like molecules. Additionally,in silicomolecular docking studies in combination with biological assay studies indicated the potentially differing anti-cancer properties of the two cultivars resulting from the elucidated chemical profiles.

Conclusion

These findings highlight distinctive chemical profiles beyond cannabinoids in Cannabis strains. This novel mapping of the metabolomic landscape of Cannabis provides actionable insights into plant biochemistry and justifies selecting certain varieties for medicinal use.
MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics
Authors: Hu Yunfei , Lin Zhenhan , Xie Manfei , Yuan Weiman , Li Yikang , Rao Mingxing , Liu Yichen Henry , Shen Wenjun , Zhang Lu , Zhou Xin Maizie
Published: February 2024

Recent advancements in spatial transcriptomics (ST) have underscored the importance of integrating data from multiple ST slices for joint analysis. A major challenge remains generating interpretable joint embeddings that preserve geometric information for downstream analyses. Here we introduce MaskGraphene, a graph neural network that combines self-supervised and self-contrastive training to integrate gene expression and spatial location into joint embeddings. By employing clusterwise alignment and a graph attention autoencoder with masked self-supervised and triplet loss optimizations, MaskGraphene effectively preserves geometric structures while achieving batch correction. In benchmarks against seven state-of-the-art methods, MaskGraphene consistently demonstrated superior alignment accuracy and geometric fidelity across diverse ST datasets. Its interpretable embeddings significantly enhanced downstream applications, including domain identification, spatial trajectory reconstruction, biomarker discovery, and the creation of topographical maps of brain slices. Notably, MaskGraphene successfully recovered layer-wise brain structures with near-perfect accuracy. MaskGraphene provides a powerful and versatile framework for advancing ST data integration and analysis, unlocking valuable biological insights.
Protein-structure-sensitive mid-infrared optoacoustic microscopy enables label-free assessment of drug therapy in myeloma cells
Authors: Gasparin Francesca , Tietje Marlene R. , Katab Eslam , Nurdinova Aizada , Yuan Tao , Chmyrov Andriy , Uluç Nasire , Jüstel Dominik , Bassermann Florian , Ntziachristos Vasilis , Pleitez Miguel A.
Published: February 2024

Conventional live-cell optical microscopy lacks sensitivity and specificity for label-free detection of intracellular protein-structure dynamics, such as conformational transition from α-helix to β-sheet. Detecting intermolecular β-sheet formation, for instance, is important because it is a hallmark of misfolded proteins and aggresome formation—which are intrinsic indicators of cell apoptosis in myeloma therapy. Going beyond conventional optical microscopy, we introduce a single-cell imaging technology with label-free sensitivity to intracellular intermolecular β-sheet formation in living cells. This unique ability was attained by exploiting the spectral specificity of the mid-infrared amide I region (1700 – 1600 cm-1) to protein structure and the positive-contrast nature of optoacoustic microscopy. By means of this technology, we were able to monitor the efficiency of proteasome inhibition in a myeloma cell line and—as a first demonstration towards clinical translation—in biopsied myeloma cells from patients. Achieving label-free monitoring of treatment at a single-cell level allows longitudinal assessment of response heterogeneity, which could provide crucial therapeutic information, such as patient-specific sensitivity to treatment, thus facilitating personalized medicine in myeloma therapy.
Blockade of Interleukin-6 (IL-6) Signaling in Dedifferentiated Liposarcoma (DDLPS) Decreases Mouse Double Minute 2 (MDM2) Oncogenicity via Alternative Splicing
Authors: Zewdu Abeba , Braggio Danielle , Lopez Gonzalo , Batte Kara , Khurshid Safiya , Costas de Faria Fernanda , Bid Hemant K. , Koller David , Casadei Lucia , Ladner Katherine J. , Wang David , Grignol Valerie , Iwenofu O. Hans , Chandler Dawn , Guttridge Denis C. , Pollock Raphael E.
Published: February 2024

Effective therapies for retroperitoneal (RP) dedifferentiated liposarcoma (DDLPS) remain unavailable. Loco-regional recurrence occurs in >80% of cases; 5-year disease-specific survival is only 20%. DDLPS is especially prevalent in the retroperitoneum and abdomen; evaluation of the DDLPS microenvironment in these high-fat compartments appears pertinent. Adipose is a main supplier of interleukin-6 (IL6); excessive activation of IL6 signal transducer glycoprotein 130 (GP130) underlies the development of some diseases. The role of GP130 pathway activation remains unstudied in DDLPS, so we examined the role of microenvironment fat cell activation of the IL6/GP130 signaling cascade in DDLPS. All DDLPS tumors and cell lines studied expressed elevated levels of the GP130-encoding geneIL6STand GP130 protein compared to normal tissue and cell line controls. IL6 increased DDLPS cell growth and migration, possibly through increased signal transducer and activator of transcription 1 (STAT1) and 3 (STAT3) activation, and upregulated mouse double minute 2 (MDM2). GP130 loss conveyed opposite effects; pharmacological blockade of GP130 by SC144 produced the MDM2 splice variant MDM2-ALT1, known to inhibit full length MDM2 (MDM2-FL). Although genomicMDM2amplification is pathognomonic for DDLPS, mechanisms driving MDM2 expression, regulation, and function beyond the MDM2:p53 negative feedback loop are poorly understood. Our findings suggest a novel preadipocyte DDLPS-promoting role due to IL6 release, via upregulation of DDLPS MDM2 expression. Pharmacological GP130 blockade reduced the IL6-induced increase in DDLPS MDM2 mRNA and protein levels, possibly through enhanced expression of MDM2-ALT1, a possibly targetable pathway with potential as future DDLPS patient therapy.
Feature selectivity of corticocortical feedback along the primate dorsal visual pathway
Authors: Korkian Yavar , Nakhla Nardin , Pack Christopher C.
Published: February 2024

Anatomical studies have revealed a prominent role for feedback projections in the primate visual cortex. Theoretical models suggest that these projections support important brain functions, like attention, prediction, and learning. However, these models make different predictions about the relationship between feedback connectivity and neuronal stimulus selectivity. We have therefore performed simultaneous recordings in different regions of the primate dorsal visual pathway. Specifically, we recorded neural activity from the medial superior temporal (MST) area, and one of its main feedback targets, the middle temporal (MT) area. We estimated functional connectivity from correlations in the single-neuron spike trains and performed electrical microstimulation in MST to determine its causal influence on MT. Both methods revealed that inhibitory feedback occurred more commonly when the source and target neurons had very different stimulus preferences. At the same time, the strength of feedback suppression was greater for neurons with similar preferences. Excitatory feedback projections, in contrast, showed no consistent relationship with stimulus preferences. These results suggest that corticocortical feedback could play a role in shaping sensory responses according to behavioral or environmental context.
The CryoEM structure of human serum albumin in complex with ligands
Authors: Catalano Claudio , Lucier Kyle W. , To Dennis , Senko Skerdi , Tran Nhi L. , Farwell Ashlyn C. , Silva Sabrina M. , Dip Phat V. , Poweleit Nicole , Scapin Giovanna
Published: February 2024

Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60% of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization.
RevealingIn SituMolecular Profiles of Glomerular Cell Types and Substructures with Integrated Imaging Mass Spectrometry and Multiplexed Immunofluorescence Microscopy
Authors: Esselman Allison B. , Moser Felipe A. , Tideman Léonore , Migas Lukasz G. , Djambazova Katerina V. , Colley Madeline E. , Pingry Ellie L. , Patterson Nathan Heath , Farrow Melissa A. , Yang Haichun , Fogo Agnes B. , de Caestecker Mark , Van de Plas Raf , Spraggins Jeffrey M.
Published: February 2024

Glomeruli filter blood through the coordination of podocytes, mesangial cells, fenestrated endothelial cells, and the glomerular basement membrane. Cellular changes, such as podocyte loss, are associated with pathologies like diabetic kidney disease (DKD). However, little is known regarding thein situmolecular profiles of specific cell types and how these profiles change with disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is well-suited for untargeted tissue mapping of a wide range of molecular classes. Additional imaging modalities can be integrated with MALDI IMS to associate these biomolecular distributions to specific cell types. Herein, we demonstrate an integrated workflow combining MALDI IMS and multiplexed immunofluorescence (MxIF) microscopy. High spatial resolution MALDI IMS (5 µm pixel size) was used to determine lipid distributions within human glomeruli, revealing intra-glomerular lipid heterogeneity. Mass spectrometric data were linked to specific glomerular cell types through new methods that enable MxIF microscopy to be performed on the same tissue section following MALDI IMS without sacrificing signal quality from either modality. A combination of machine-learning approaches was assembled, enabling cell-type segmentation and identification based on MxIF data followed by the mining of cell type or cluster-associated MALDI IMS signatures using classification models and interpretable machine learning. This allowed the automated discovery of spatially specific biomarker candidates for glomerular substructures and cell types. Overall, the work presented here establishes a toolbox for probing molecular signatures of glomerular cell types and substructures within tissue microenvironments and provides a framework that applies to other kidney tissue features and organ systems.
Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data
Authors: Iida Naoko , Okada Ai , Kobayashi Yoshihisa , Chiba Kenichi , Yatabe Yasushi , Shiraishi Yuichi
Published: February 2024

Genomic variants causing abnormal splicing play an important role in genetic disorders and cancer development. Among them, variants that cause formations of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs, especially those found in deep intronic regions, are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs), offering therapeutic potential for rare disease patients. To leverage massive transcriptome sequence data such as those available from the Sequence Read Archive, we developed a novel framework to screen for SSCVs solely using transcriptome data. We have applied it to 322,072 publicly available transcriptomes and identified 30,130 SSCVs. Utilizing this extensive collection of SSCVs, we have revealed the characteristics of Alu exonization via SSCVs, especially the hotspots of SSCVs within Alu sequences and their evolutionary relationships. Many of the SSCVs affecting disease-causing variants were predicted to generate premature termination codons and are degraded by nonsense-mediated decay. On the other hand, several genes, such asCREBBPandTP53,showed characteristic SSCV profiles indicative of heterogeneous mutational functions beyond simple loss-of-function. Finally, we discovered novel gain-of-function SSCVs in the deep intronic region of theNOTCH1gene and demonstrated that their activation can be suppressed using splice-switching ASOs. Collectively, we provide a systematic approach for automatically acquiring a registry of SSCVs, which can be used for elucidating novel biological mechanisms for splicing and genetic variation, and become a valuable resource for pinpointing critical targets in drug discovery. Catalogs of SSCVs identified in this study are accessible on SSCV DB (https://sscvdb.io/).
A pan-tissue, pan-disease compendium of human orphan genes
Authors: Singh Urminder , Haltom Jeffrey A. , Guarnieri Joseph W. , Li Jing , Seetharam Arun , Beheshti Afshin , Aronow Bruce , Wurtele Eve Syrkin
Published: February 2024

Species-specific genes are ubiquitous in evolution, with functions ranging from prey paralysis to survival in subzero temperatures. Because they are typically expressed under limited conditions and lack canonical features, such genes may be vastly under-identified, even in humans. Here, we leverage terabytes of human RNA-Seq data to identify thousands of highly-expressed transcripts that do not correspond to any Gencode-annotated gene. Many may be novel ncRNAs although 80% of them contain ORFs that have the potential of encoding proteins unique toHomo sapiens(orphan genes). We validate our findings with independent strand-specific and single-cell RNA-seq datasets. Hundreds of these novel transcripts overlap with deleterious genomic variants; thousands show significant association with disease-specific patient survival. Most are dynamically regulated and accumulate selectively in particular tissues, cell-types, developmental stages, tumors, COVID-19, sex, and ancestries. As such, these transcripts hold potential as diagnostic biomarkers or therapeutic targets. To empower future discovery, we provide a compendium of these huge RNA-Seq expression data, and RiboSeq data, with associated metadata. Further, we supply the gene models for the novel genes as UCSC Genome Browser tracks.
Impact of Cervical Lymphatic Obstruction on Brain Pathophysiology in Cervical Lymphedema Animal Models
Authors: Cheon Hwayeong , Woo Dong Cheol , Cha Seungwoo , Chae Yeon Ji , Maeng Inhee , Oh Seung Jae , Jeon Jae Yong
Published: February 2024

Background

Injury to the cervical lymph nodes can lead to cervical lymphedema and subsequent fluid accumulation in the head and neck region, potentially causing pathophysiological alteration in the brain. This condition is thought to be linked with various neurological diseases, although the direct connection between cervical lymphatic obstruction and its effect on the brain has been difficult to establish.

Methods

We produced the disease animal models through lymph node dissection and radiation in fifteen male Sprague–Dawley rats aged 8 weeks and weighing 280–320 g. The models were specifically designed to induce lymphatic obstruction in the cervical region only, with no direct interventions applied to the brain. We evaluated swelling and lymphatic drainage in the head and neck for follow-up. The size of the lateral ventricles was verified through MRI, and changes in water content in brain tissue were directly measured. At 2 and 8 weeks, we observed immune cell infiltration, ventricular enlargement, and pathohistological changes in the harvested brain tissues.

Results

The experimental animals exhibited lymphatic obstruction in the cervical region, with swelling, abnormal lymphatic drainage, and immune cell infiltration into the brain’s white matter, reminiscent of extremities lymphedema. MRI revealed lateral ventricular enlargement in these animals, indicative of increased cerebrospinal fluid levels compared to the control group. This increase in cerebrospinal fluid was associated with an increase in brain tissue water content, leading to pathophysiological changes akin to those seen in hydrocephalus and cerebral edema.

Conclusion

The outcomes in this study underscore a significant link between lymphatic circulatory dysfunction and the onset of neurophysiological diseases. Cervical lymphedema showed pathophysiological changes similar to those seen in extremities lymphedema. However, these changes in the brain could be more critical than in the extremities. Our finding highlights the importance of understanding lymphatic system health in preventing and managing neurological conditions.
Ubiquitin-mediated stabilization of SlPsbS regulates low night temperature tolerance in tomatoes
Authors: Lu Jiazhi , Yu Junchi , Liu Pengkun , Gu Jiamao , Chen Yu , Zhang Tianyi , Li Jialong , Wang Taotao , Yang Wenqiang , Lin Rongcheng , Wang Feng , Qi Mingfang , Li Tianlai , Liu Yufeng
Published: February 2024

Non-photochemical quenching (NPQ) plays a fundamental role in safely operating photosynthesis under low night temperatures (LNT). PsbS protein is essential for the rapid induction of NPQ, and its stability is often affected by adverse environmental conditions. However, the regulatory mechanism for the stability of PsbS or chloroplast proteins remains to be fully characterized. We showed that LNT decreased NPQ levels and SlPsbS protein abundance in tomato leaves. COP9 signalosome subunit 5A (SlCSN5A) facilitated SlPsbS ubiquitination and degradation in the cytosol. Further, tomato chloroplast vesiculation (SlCV) was activated by LNT. Under LNT, SlCV targeted the chloroplasts and induced the formation of CV-containing vesicles (CCVs) containing SlPsbS, which were exported from the chloroplasts. Subsequently, SlCV and SlPsbS contact SlCSN5A in the cytosol and are ubiquitinated and degraded. Genetic evidence demonstrated that overexpression of SlCV aggravated SlPsbS protein degradation, whereas silencing of SlCSN5 and SlCV delayed LNT-induced NPQ reduction and SlPsbS protein turnover. This study provides evidence that CSN5A is associated with chloroplast proteins, and reveals a ubiquitin-dependent degradation pathway of chloroplast proteins co-mediated by CV and CSN5A, thereby providing new insights into the regulation of chloroplast protein stability under stress conditions.
Loss of the APP regulator RHBDL4 preserves memory in an Alzheimer’s disease mouse model
Authors: Penalva Ylauna Christine Megane , Paschkowsky Sandra , Yang Jingyun , Recinto Sherilyn Junelle , Cinkorpumin Jessica , Hernandez Marina Ruelas , Xiao Bin , Nitu Albert , Wu Helen Yee-Li , Munter Hans Markus , Michalski Bernadeta , Fahnestock Margaret , Pastor William , Bennett David A. , Munter Lisa Marie
Published: February 2024

Characteristic cerebral pathological changes of Alzheimer’s disease (AD) such as glucose hypometabolism or the accumulation of cleavage products of the amyloid precursor protein (APP), known as Aβ peptides, lead to sustained endoplasmic reticulum (ER) stress and neurodegeneration. To preserve ER homeostasis, cells activate their unfolded protein response (UPR). The rhomboid-like-protease 4 (RHBDL4) is an enzyme that participates in the UPR by targeting proteins for proteasomal degradation. We demonstrated previously that RHBLD4 cleaves APP in HEK293T cells, leading to decreased total APP and Aβ. More recently, we showed that RHBDL4 processes APP in mouse primary mixed cortical cultures as well. Here, we aim to examine the physiological relevance of RHBDL4 in the brain. We first found that brain samples from AD patients and an AD mouse model (APPtg) showed increased RHBDL4 mRNA and protein expression. To determine the effects of RHBDL4’s absence on APP physiologyin vivo, we crossed APPtg mice to a RHBDL4 knockout (R4-/-) model. RHBDL4 deficiency in APPtg mice led to increased total cerebral APP and amyloidogenic processing when compared to APPtg controls. Contrary to expectations, as assessed by cognitive tests, RHBDL4 absence rescued cognition in 5-month-old female APPtg mice. Informed by unbiased RNAseq data, we demonstratedin vitroandin vivothat RHBDL4 absence leads to greater levels of active β-catenin due to decreased proteasomal clearance. Decreased β-catenin activity is known to underlie cognitive defects in APPtg mice and AD. Our work suggests that RHBDL4’s increased expression in AD, in addition to regulating APP levels, leads to aberrant degradation of β-catenin, contributing to cognitive impairment.
Mimivirus encodes an essential MC1-like non-histone architectural protein involved in DNA condensation
Authors: Sharma Deepti , Coulibaly Fasséli , Kondabagil Kiran
Published: February 2024

The first giant virus discovered,Acanthamoeba polyphagamimivirus (APMV), has a 1.2 Mb dsDNA genome organized as genomic fiber within the capsid. This fiber is comprised of a proteinaceous shell of ∼30 nm diameter that encloses the folded DNA. Surprisingly, for the assembly of the enormous genome of APMV, no DNA condensing protein has been reported to date. Our analysis of the uncharacterized packaged protein complement of Mimivirus led to the identification of a putative DNA-bending archaeal MC1 domain in a hypothetical protein (gp275) coded by the R252 gene. Gene knock-out analysis shows that gp275 is critical for viral multiplication. Biochemical and microscopic characterization further demonstrates the compaction of DNA upon binding to gp275. Together, this study suggests that gp275 is an MC1-like architectural protein involved in the organization of the genomic DNA within the capsid of Mimivirus.
High-throughput screening for Cushing’s disease: therapeutic potential of thiostrepton via cell cycle regulation
Authors: Hakata Takuro , Yamauchi Ichiro , Kosugi Daisuke , Sugawa Taku , Fujita Haruka , Okamoto Kentaro , Ueda Yohei , Fujii Toshihito , Taura Daisuke , Inagaki Nobuya
Published: February 2024

Cushing’s disease is a life-threatening disorder caused by autonomous secretion of adrenocorticotropic hormone (ACTH) from pituitary neuroendocrine tumors (PitNETs). Few drugs are indicated for inoperative Cushing’s disease, in particular that due to aggressive PitNETs. To explore agents that regulate ACTH-secreting PitNETs, we conducted high-throughput screening (HTS) using AtT-20, a murine pituitary tumor cell line characterized by ACTH secretion. For the HTS, we constructed a live cell– based ACTH reporter assay for high-throughput evaluation of ACTH changes. This assay was based on HEK293T cells overexpressing components of the ACTH receptor and a fluorescent cAMP biosensor, with high-throughput acquisition of fluorescence images at the single-cell level. Of 2480 screened bioactive compounds, over 50% inhibition of ACTH secreted from AtT-20 cells was seen with 84 compounds at 10 μM, and 20 compounds at 1 μM. Among these hit compounds, we focused on thiostrepton (TS) and determined its antitumor effects in bothin vitroandin vivoxenograft models of Cushing’s disease. Transcriptome and flow cytometry analyses revealed that TS administration induced AtT-20 cell cycle arrest at the G2/M phase, which was mediated by FOXM1-independent mechanisms including downregulation of cyclins. Simultaneous TS administration with a CDK 4/6 inhibitor that affected the cell cycle at the G0/1 phase showed cooperative antitumor effects. Thus, TS is a promising therapeutic agent for Cushing’s disease. Our list of hit compounds and new mechanistic insights into TS effects serve as a valuable foundation for future research.
WITHDRAWN: Antibiotic Bacteria Interaction: Dataset and Benchmarking
Authors: Chatterjee Sayantika , Majumdar Angshul , Chouzenoux Emilie
Published: February 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to inability to reproduce the results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Improved Serodiagnosis ofTrypanosoma vivaxInfections in Cattle Reveals Higher Infection Rates in the Livestock Regions of Argentina
Authors: Bontempi Iván , Arias Diego G. , Castro Graciela V. , Peverengo Luz , Díaz Genaro , Allassia Martín , Greif Gonzalo , Marcipar Iván
Published: February 2024

Bovine trypanosomiasis, caused by Trypanosoma vivax, currently affects cattle, resulting in significant economic consequences in sub-Saharan Africa and South America. The development of new diagnostic antigens is crucial for improving and refining existing methods. Our study assessed the effectiveness of two recombinant antigens in detecting specific antibodies in cattle. These antigens are derivatives of an invariant surface glycoprotein (ISG) from T. vivax. We evaluated a fraction of an antigen previously described (TvY486_0045500), referred to as TvISGAf, from an African strain, and identified a new ISG antigen from an American isolate, TvISGAm. ELISA evaluation using these antigens was conducted on 212 samples from cattle. The diagnostic performance was enhanced when utilizing a combination of both antigens (denominated TvISG-based ELISA), achieving a sensitivity of 89.6% and specificity of 93.8%. Following validation of the TvISG-based ELISA, we determined the seroprevalence of T. vivax infection in 892 field samples from cattle in the central region of Argentina. The average seroprevalence of T. vivax was 53%, with variation across the six surveyed departments ranging from 21% to 69%. These results support the use of the TvISG ELISA as a valuable serological tool for detecting and monitoring T. vivax infection in cattle. They also reported for the first time T. vivax seroprevalence in Argentina, highlighting the widespread endemic nature of the disease in the region. To effectively manage the increasing spread of T. vivax in the vast livestock production areas of South America, we support the need for consistent surveillance programs and implementation of preventive strategies.
Differential cell type-specific function of the aryl hydrocarbon receptor and its repressor in diet-induced obesity and fibrosis
Authors: Graelmann Frederike J. , Gondorf Fabian , Majlesain Yasmin , Niemann Birte , Klepac Katarina , Gottschalk Marlene , Mayer Michelle , Iriady Irina , Hatzfeld Philip , Lindenberg Sophie K. , Wunderling Klaus , Thiele Christoph , Abdullah Zeinab , He Wei , Hiller Karsten , Händler Kristian , Beyer Marc D. , Ulas Thomas , Pfeifer Alexander , Esser Charlotte , Weighardt Heike , Förster Irmgard , Reverte-Salisa Laia
Published: February 2024

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor regulating xenobiotic responses as well as physiological metabolism. Dietary AhR ligands activate the AhR signaling axis in the intestine and throughout the organism, whereas AhR activation is negatively regulated by the AhR repressor (AhRR). While AhR-deficient mice are known to be resistant to diet-induced obesity (DIO), we here demonstrate that AhRR deficiency also leads to a robust, but not as profound protection from DIO and hepatosteatosis. Under conditions of DIO, AhRR-/-mice did not accumulate TCA cycle intermediates in the circulation in contrast to wild-type (WT) mice, indicating protection from metabolic dysfunction. This effect could be mimicked by dietary supplementation of AhR ligands in WT mice. Because of the predominant expression of the AhRR in myeloid cells, AhRR-deficient macrophages were analyzed for changes in metabolism and showed major metabolic alterations regarding oxidative phosphorylation and mitochondrial activity as well as increased expression of genes involved inde novolipogenesis and mitochondrial biogenesis. Mice with a genetic deficiency of the AhRR in myeloid cells did not show alterations in weight gain after high fat diet (HFD) but demonstrated ameliorated liver damage compared to control mice. Further, deficiency of the AhR in myeloid cells also did not affect weight gain but led to enhanced liver damage and adipose tissue fibrosis compared to controls. Although conditional ablation of either the AhR or AhRR in myeloid cells did not recapitulate the phenotype of the global knockout, our findings suggest that enhanced AhR signaling in myeloid cells deficient for AhRR protects from diet-induced liver damage and fibrosis, whereas myeloid cell-specific AhR deficiency is detrimental.
Evolution and inhibition of the FIKK effector kinase family inP. falciparum
Authors: Belda Hugo , Bradley David , Christodoulou Evangelos , Nofal Stephanie D. , Broncel Malgorzata , Jones David , Davies Heledd , Bertran M. Teresa , Purkiss Andrew G. , Ogrodowicz Roksana W. , Joshi Dhira , O’Reilly Nicola , Walport Louise , Claessens Antoine , Powell Andrew , House David , Kjaer Svend , Landry Christian R. , Treeck Moritz
Published: February 2024

Among the ∼200Plasmodiumspecies that infect vertebrates, six infect humans. Of these,P. falciparumcauses >95% of all ∼500,000 annual fatalities. Phylogenetically,P. falciparumbelongs to theLaveraniasubgenus, a group ofPlasmodiumspecies that infect great apes. Common toLaveraniaspecies is the family of FIKK kinases. One million years ago, a single FIKK kinase conserved in allPlasmodiumspecies gained an export element in theLaveraniasubgenus and expanded into the family of ∼20 atypical FIKK kinases, most of which are exported into the host cell. Thefikkgenes are conserved in syntenic loci across theLaverania, arguing for a rapid expansion controlling important functions in host cell remodelling and pathogenesis. We provide evidence that the FIKK paralogues evolved specific and mutually exclusive phosphorylation motif preferences, conserved across theirLaveraniaorthologues, in a short evolutionary timeframe. Surprisingly, we find that FIKK13 has evolved exclusive tyrosine-phosphorylation preference, which was thought to be absent inPlasmodiumspecies. Combining a crystal structure with AlphaFold2 predictions, we identify residues that determine kinase-specificity within the FIKK family in a fast-evolving flexible loop. Finally, we show that all expressed members of the FIKK kinase family can be chemically inhibitedin vitrousing a single compound. Such a pan-specific inhibitor of this kinase family important for virulence could reduce the ability of the parasite to gain escape-mutations and resistance.
Silicon-rhodamine functionalized evocalcet probes (EvoSiR) potently and selectively label calcium sensing receptors (CaSR) in vitro, in vivo and ex vivo
Authors: Batora Daniel , Fischer Jerome P , Kaderli Reto M , Varga Mate , Lochner Martin , Gertsch Jurg
Published: February 2024

The calcium sensing receptor (CaSR) is a ubiquitously expressed G-protein coupled receptor (GPCR) that regulates extracellular calcium signals via the parathyroid glands. CaSR has recently also been implicated in non-calcitropic pathophysiologies like asthma, gut inflammation and cancer. To date, molecular tools that enable the bioimaging of CaSR in tissues are lacking. Based on in silico analyses of available structure-activity relationship data on CaSR ligands, we designed and prepared silicon-rhodamine (SiR) conjugates of the clinically approved drug evocalcet. The new probes EvoSiR4 and EvoSiR6, with differing linker lengths at the evocalcet carboxyl end, both showed a 6-fold and 3-fold increase in potency towards CaSR (EC50<45 nM) compared to evocalcet and the evocalcet-linker conjugate, respectively, in a FLIPR®-based cellular functional assay. The specificity of the EvoSiR probes towards CaSR binding and the impact of albumin was evaluated in live cell experiments. Both probes showed strong albumin binding, which facilitated the clearance of nonspecific binding interactions. Accordingly, in zebrafish embryos, EvoSiR4 specifically labelled the high CaSR expressing neuromasts of the lateral line in vivo. EvoSiR4 was also assessed in human parathyroid tissues ex vivo, showing a specific absolute CaSR associated fluorescence compared to parathyroid autofluorescence. In summary, functionalization of evocalcet by SiR led to the preparation of potent and specific fluorescent CaSR probes. EvoSiR4 is a versatile small molecular probe that can be employed in CaSR-related biomedical analyses where antibodies are not applicable.
Molecular, Cellular, and Developmental Organization of the Mouse Vomeronasal organ at Single Cell Resolution
Authors: Hills Max , Ma Limei , Fang Ai , Chiremba Thelma , Malloy Seth , Scott Allison , Perera Anoja , Yu C. Ron
Published: February 2024

We have generated single cell transcriptomic atlases of vomeronasal organs (VNO) from juvenile and adult mice. Combined with spatial molecular imaging, we uncover a distinct, previously unidentified class of cells that express the vomeronasal receptors and a population of canonical olfactory sensory neurons in the VNO. High resolution trajectory and cluster analyses reveal the lineage relationship, spatial distribution of cell types, and a putative cascade of molecular events that specify the V1r, V2r, and OR lineages from a common stem cell population. The expression of vomeronasal and olfactory receptors follow power law distributions, but there is high variability in average expression levels between individual receptor and cell types. Substantial co-expression is found between receptors across clades, from different classes, and between olfactory and vomeronasal receptors, with nearly half from pairs located on the same chromosome. Interestingly, the expression of V2r, but not V1r, genes is associated with various transcription factors, suggesting distinct mechanisms of receptor choice associated with the two cell types. We identify association between transcription factors, surface axon guidance molecules, and individual VRs, thereby uncovering a molecular code that guides the specification of the vomeronasal circuitry. Our study provides a wealth of data on the development and organization of the accessory olfactory system at both cellular and molecular levels to enable a deeper understanding of vomeronasal system function.
The Origins of ATP Dependence in Biological Nitrogen Fixation
Authors: Harris Derek F. , Rucker Holly R. , Garcia Amanda K. , Yang Zhi-Yong , Chang Scott D. , Feinsilber Hannah , Kaçar Betül , Seefeldt Lance C.
Published: February 2024

Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the key N2-reducing enzyme nitrogenase. We show that the ancestor has a strict requirement for ATP and its hydrolysis is coupled to electron transfer for N2reduction. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme, and underscore how biomolecular constraints can entirely decouple cofactor selection from environmental availability.
Genome-wide analysis of TFIIB’s role in termination of transcription
Authors: O’Brien Michael J. , Schrader Jared , Ansari Athar
Published: February 2024

Apart from its well-established role in initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remains largely unexplored. To determine the prevalence of TFIIB’s role in termination, we performed GRO-seq analyses insua7-1mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains of yeast. Almost a three-fold increase in readthrough of the poly(A)-termination signal was observed in TFIIBsua7-1mutant compared to the TFIIBWTcells. Of all genes analyzed in this study, nearly 74% genes exhibited a statistically significant increase in terminator readthrough in the mutant. To gain an understanding of the mechanistic basis of TFIIB involvement in termination, we performed mass spectrometry of TFIIB, affinity purified from chromatin and soluble cellular fractions, from TFIIBsua7-1and TFIIBWTcells. TFIIB purified from the chromatin fraction of TFIIBWTcells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with both CF1A and Rat1 termination complexes in TFIIBsua7-1mutant. ChIP assay revealed that the recruitment of Pta1 subunit of CPF complex, Rna15 subunit of CF1 complex and Rat1 subunit of Rat1 complex registered nearly 90% decline in the mutant over wild type cells. The overall conclusion of these results is that TFIIB affects termination of transcription on a genome-wide scale, and TFIIB-termination factor interaction may play a crucial role in the process.
Modularity in the evolution of visual signals associated with aggressive displays
Authors: Fialko Kristina , Price Trevor D.
Published: February 2024

Interactions between conspecifics commonly involve the use of stereotyped display movements, which can vary markedly between species. Theoretically, sexual selection by female choice can lead to large differences between species, but sexual selection by male competition may result in more limited diversification. Here, we evaluate display evolution in the aggressive signals of 10 leaf warbler species. Using high-speed videography of territorial behavior, we quantify differences in wing motion intensity and form. We find that both the rate of wing motion and the form of the display remain similar across species, which we attribute to an effective signal maintained through multiple speciation events. Differences among species arise though discrete additions to the behavioral repertoire (three species), loss of display (one species) and the presence of a pale patch on the wing. While some habitats differ discretely and dramatically in light intensity, this cannot account for all the differences in display behavior. We conclude that display evolution proceeds largely in a modular fashion. The basic conventional signal is maintained across species, enabling modifications to appear without loss of efficacy.
Stability of the Wheat Seed Mycobiome Across North Carolina’s Longitudinal Gradient
Authors: Becker Lindsey E. , Hawkes Christine V. , Heiniger Ryan , Cubeta Marc A.
Published: February 2024

Improving wheat yield and performance involves selecting varieties that are well adapted for a regional area. Although host genotype and environment are major factors that impact crop performance and resilience, less is known about the relative contribution and occurrence of wheat seed endophytic fungal communities across spatial and temporal scales. An increased understanding of composition and assembly of beneficial endophytic fungal communities across regional scales provides valuable insight into the stability of the endophytic seed mycobiome. Our aim in this study was to examine the relative contribution and impact of latitude and longitude gradients within North Carolina (NC) on wheat seed fungal community structure of two regionally adapted soft red winter wheat cultivars, Hilliard and USG 3640. We examined the endophytic wheat seed microbiome of the two winter wheat cultivars planted in official variety trials at five geographic locations across NC in 2021 and two geographic locations in 2022. ITS1 sequence-based analysis of surface disinfested wheat seeds was conducted to determine alpha and beta diversity. Species richness is influenced by geographical location, however wheat seed mycobiome community structure is stable across cultivars and years. Latitude and longitude contributed to the observed variation in wheat seed mycobiome structure, in addition to yield, seed moisture, and leaf nutrients. When surveying taxa present within all cultivars, geographical sites and years,AlternariaandEpicoccumspp. exhibited high relative abundance in the wheat seed mycobiome. Our results provide a comprehensive catalog of core fungal taxa well-adapted to diverse environments and conserved across wheat cultivars.
MetaWorm: An Integrative Data-Driven Model SimulatingC. elegansBrain, Body and Environment Interactions
Authors: Zhao Mengdi , Wang Ning , Jiang Xinrui , Ma Xiaoyang , Ma Haixin , He Gan , Du Kai , Ma Lei , Huang Tiejun
Published: February 2024

The behavior of an organism is profoundly influenced by the complex interplay between its brain, body, and environment. Existing data-driven models focusing on either the brain or the body-environment separately. A model that integrates these two components is yet to be developed. Here, we present MetaWorm, an integrative data-driven model of a widely studied organism,C. elegans. This model consists of two sub-models: the brain model and the body & environment model. The brain model was built by multi-compartment models with realistic morphology, connectome, and neural population dynamics based on experimental data. Simultaneously, the body & environment model employed a lifelike body and a 3D physical environment, facilitating easy behavior quantification. Through the closed-loop interaction between two sub-models, MetaWorm faithfully reproduced the realistic zigzag movement towards attractors observed inC. elegans. Notably, MetaWorm is the first model to achieve seamless integration of detailed brain, body, and environment simulations, enabling unprecedented insights into the intricate relationships between neural structures, neural activities, and behaviors. Leveraging this model, we investigated the impact of neural system structure on both neural activities and behaviors. Consequently, MetaWorm can enhance our understanding of how the brain controls the body to interact with its surrounding environment.
Melting curve analysis reveals false-positive norovirus detection in a molecular syndromic panel
Authors: Matic Nancy , Lawson Tanya , Young Matthew , Jang Willson , Bilawka Jennifer , Gowland Leah , Ritchie Gordon , Leung Victor , Payne Michael , Stefanovic Aleksandra , Romney Marc G. , Lowe Christopher F.
Published: February 2024

Background

Molecular syndromic panels can improve rapidity of results and ease clinical laboratory workflow, although caution has been raised for potential false-positive results. Upon implementation of a new panel for infectious diarrhea (BioFire® FilmArray® Gastrointestinal [GI] Panel, bioMérieux) in our clinical laboratory, a high number of stool samples with norovirus were detected.

Objectives

To investigate positive percent agreement and the false-positive rate of norovirus detected by the multiplex Biofire GI panel compared to a singleplex commercial assay.

Study design

From October 2023 to January 2024, all prospective stool samples with a positive norovirus result by BioFire had melting curves reviewed manually using the BioFire FilmArray Torch System. Stool samples further underwent testing by a supplementary real-time RT-PCR assay (Xpert® Norovirus, Cepheid) for comparative analysis.

Results

Of the 50 stool samples with norovirus detected by BioFire, 18 (36%) tested negative by Xpert (deemed “false-positives”). Melting curve analysis revealed nearly all of these samples had atypical melting curve morphologies for the “Noro-1” target on BioFire (16/18, 89%), which was statistically significant (Odds Ratio 173.2, 95% CI [22.2, 5326.9],p<0.0001). Stool samples with multiple pathogens including norovirus detected by BioFire were not more likely to produce false-positive norovirus results (Odds Ratio 1, 95% CI [0.3, 3.3],p=1).

Conclusions

Although not described in the manufacturer’sInstructions for Use, we propose routine manual review of melting curves for the BioFire GI panel prior to reporting, to avoid potential false-positive norovirus results.
Dissecting the genetic overlap between three complex phenotypes with trivariate MiXeR
Authors: Shadrin Alexey A , Hindley Guy , Hagen Espen , Parker Nadine , Tesfaye Markos , Jaholkowski Piotr , Rahman Zillur , Kutrolli Gleda , Fominykh Vera , Djurovic Srdjan , Smeland Olav B , O'Connell Kevin S , van der Meer Dennis , Frei Oleksandr , Andreassen Ole A , Dale Anders M
Published: February 2024

Comorbidities are an increasing global health challenge. Accumulating evidence suggests overlapping genetic architectures underlying comorbid complex human traits and disorders. The bivariate causal mixture model (MiXeR) can quantify the polygenic overlap between complex phenotypes beyond global genetic correlation. Still, the pattern of genetic overlap between three distinct phenotypes, which is important to better characterize multimorbidities, has previously not been possible to quantify. Here, we present and validate the trivariate MiXeR tool, which disentangles the pattern of genetic overlap between three phenotypes using summary statistics from genome-wide association studies (GWAS). Our simulations show that the trivariate MiXeR can reliably reconstruct different patterns of genetic overlap. We further demonstrate how the tool can be used to estimate the proportions of genetic overlap between three phenotypes using real GWAS data, providing examples of complex patterns of genetic overlap between diverse human traits and diseases that could not be deduced from bivariate analyses. This contributes to a better understanding of the etiology of complex phenotypes and the nature of their relationship, which may aid in dissecting comorbidity patterns and their biological underpinnings.