bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep learning-based binary classification of beta-amyloid plaques using 18F florapronol PET
Authors: An Eui Jung , Kim Jin Beom , Son Junik , Jeong Shin Young , Lee Sang-Woo , Ahn Byeong-Cheol , Ko Pan-Woo , Hong Chae Moon
Published: October 2024

Purpose

This study aimed to investigate a deep learning model to classify amyloid plaque deposition in the brain PET images of patients suspected of Alzheimer’s disease.

Methods

A retrospective study was conducted on patients who were suspected of having a mild cognitive impairment or dementia, and brain amyloid 18F florapronol PET/computed tomography images were obtained from 2019 to 2022. Brain PET images were visually assessed by two nuclear medicine specialists, who classified them as either positive or negative. Image rotation was applied for data augmentation. The dataset was split into training and testing sets at a ratio of 8 : 2. For the convolutional neural network (CNN) analysis, stratified k-fold (k = 5) cross-validation was applied using training set. Trained model was evaluated using testing set.

Results

A total of 175 patients were included in this study. The average age at the time of PET imaging was 70.4 ± 9.3 years and included 77 men and 98 women (44.0% and 56.0%, respectively). The visual assessment revealed positivity in 62 patients (35.4%) and negativity in 113 patients (64.6%). After stratified k-fold cross-validation, the CNN model showed an average accuracy of 0.917 ± 0.027. The model exhibited an accuracy of 0.914 and an area under the curve of 0.958 in the testing set. These findings affirm the model’s high reliability in distinguishing between positive and negative cases.

Conclusion

The study verifies the potential of the CNN model to classify amyloid positive and negative cases using brain PET images. This model may serve as a supplementary tool to enhance the accuracy of clinical diagnoses.
Expression and Clinical Significance of Nuclear Phosphoglucomutase-1 in Hepatocellular Carcinoma
Authors: Xia Yechen , An Yan , Jin Riming , Huang Wentao , Jin Guang-Zhi , Xu Jing
Published: October 2024

This study aimed to evaluate the predictive values of phosphoglucomutase-1 (PGM1) expression for prognosis in patients with hepatocellular carcinoma (HCC). PGM1 expression was assessed by immunohistochemistry in tissue microarrays. The relationship of PGM1 expression level with pathologic parameters and prognosis values was respectively analyzed by χ2 test and Cox regression. The accuracy of independent risk factors in predicting prognosis was calculated by receiver operating characteristic curve. HCC patient-derived xenograft models were performed to evaluate the nuclear PGM1 antitumor effect. The results showed that PGM1 expression was low in HCC tissues. Nuclear PGM1 was an independent prognostic factor for overall survival and time to recurrence. Cox regression showed that nuclear PGM1, serum α-fetoprotein, liver cirrhosis, and TNM staging stage were independent risk predictors for HCC. Receiver operating characteristic curve demonstrated that combination of independent predictors had better prognostic value than TNM staging alone. Moreover, patient-derived xenograft models showed antitumor effect of nuclear PGM1. We found that low expression of nuclear PGM1 was detected in HCC tissues and associated with poor prognostic. Nuclear PGM1 was an independent prognostic factor in patients with HCC. Furthermore, nuclear PGM1 combining other independent risk factors showed a better prognostic value. Nuclear PGM1 was a useful prognostic biomarker for patients with HCC.
Evolution of plant metabolism: the state-of-the-art
Authors: Fernie Alisdair R. , de Vries Sophie , de Vries Jan
Published: September 2024

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO
2
and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes.

This article is part of the theme issue ‘The evolution of plant metabolism’.
Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism
Authors: Barkman Todd J.
Published: September 2024

Studies of enzymes in modern-day plants have documented the diversity of metabolic activities retained by species today but only provide limited insight into how those properties evolved. Ancestral sequence reconstruction (ASR) is an approach that provides statistical estimates of ancient plant enzyme sequences which can then be resurrected to test hypotheses about the evolution of catalytic activities and pathway assembly. Here, I review the insights that have been obtained using ASR to study plant metabolism and highlight important methodological aspects. Overall, studies of resurrected plant enzymes show that (i) exaptation is widespread such that even low or undetectable levels of ancestral activity with a substrate can later become the apparent primary activity of descendant enzymes, (ii) intramolecular epistasis may or may not limit evolutionary paths towards catalytic or substrate preference switches, and (iii) ancient pathway flux often differs from modern-day metabolic networks. These and other insights gained from ASR would not have been possible using only modern-day sequences. Future ASR studies characterizing entire ancestral metabolic networks as well as those that link ancient structures with enzymatic properties should continue to provide novel insights into how the chemical diversity of plants evolved.

This article is part of the theme issue ‘The evolution of plant metabolism’.
Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase
Authors: Conrado Ana Caroline , Lemes Jorge Gabriel , Rao R. S. P. , Xu Chunhui , Xu Dong , Li-Beisson Yonghua , Thelen Jay J.
Published: September 2024

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in
Arabidopsis
) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein–protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in
Arabidopsis thaliana
and
Chlamydomonas reinhardtii
unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in
Arabidopsis
, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory.

This article is part of the theme issue ‘The evolution of plant metabolism’.
Characterization of a β-carotene isomerase from the cyanobacterium
Cyanobacteria aponinum
Authors: Alvarez Derry , Yang Yu , Saito Yoshimoto , Balakrishna Aparna , Goto Kosuke , Gojobori Takashi , Al-Babili Salim
Published: September 2024

Carotenoids are essential components of the photosynthetic apparatus and precursors of plant hormones, such as strigolactones (SLs). SLs are involved in various aspects of plant development and stress-response processes, including the establishment of root and shoot architecture. SL biosynthesis begins with the reversible isomerization of all-
trans
-carotene into 9-
cis
-β-carotene, catalysed by DWARF27 β-carotene isomerase (D27). Sequence comparisons have revealed the presence of D27-related proteins in photosynthetic eukaryotes and cyanobacteria lacking SLs. To gain insight into the evolution of SL biosynthesis, we characterized the activity of a cyanobacterial D27 protein (
Ca
D27) from
Cyanobacterim aponinum
, using carotenoid-accumulating
Escherichia coli
cells and
in vitro
enzymatic assays. Our results demonstrate that
Ca
D27 is an all-
trans
/
cis
and
cis
/
cis
-β-carotene isomerase, with a
cis
/
cis
conversion preference.
Ca
D27 catalysed 13-
cis
/15-
cis-
, all-
trans
/9-
cis
-β-carotene, and neurosporene isomerization. Compared with plant enzymes, it exhibited a lower 9-
cis
-/all-
trans
-β-carotene conversion ratio. A comprehensive genome survey revealed the presence of
D27
as a single-copy gene in the genomes of 20 out of 200 cyanobacteria species analysed. Phylogenetic and enzymatic analysis of
Ca
D27 indicated that cyanobacterial
D27
genes form a single orthologous group, which is considered an ancestral type of those found in photosynthetic eukaryotes.

This article is part of the theme issue ‘The evolution of plant meta‌bolism’.
Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering
Authors: Lee Yun Sun , Braun Edward L. , Grotewold Erich
Published: September 2024

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts.

This article is part of the theme issue ‘The evolution of plant metabolism’.
The evolution of plant responses underlying specialized metabolism in host–pathogen interactions
Authors: Agorio Astrid , Mena Eilyn , Rockenbach Mathias F. , Ponce De León Inés
Published: September 2024

In the course of plant evolution from aquatic to terrestrial environments, land plants (embryophytes) acquired a diverse array of specialized metabolites, including phenylpropanoids, flavonoids and cuticle components, enabling adaptation to various environmental stresses. While embryophytes and their closest algal relatives share candidate enzymes responsible for producing some of these compounds, the complete genetic network for their biosynthesis emerged in embryophytes. In this review, we analysed genomic data from chlorophytes, charophytes and embryophytes to identify genes related to phenylpropanoid, flavonoid and cuticle biosynthesis. By integrating published research, transcriptomic data and metabolite studies, we provide a comprehensive overview on how these specialized metabolic pathways have contributed to plant defence responses to pathogens in non-vascular bryophytes and vascular plants throughout evolution. The evidence suggests that these biosynthetic pathways have provided land plants with a repertoire of conserved and lineage-specific compounds, which have shaped immunity against invading pathogens. The discovery of additional enzymes and metabolites involved in bryophyte responses to pathogen infection will provide evolutionary insights into these versatile pathways and their impact on environmental terrestrial challenges.

This article is part of the theme issue ‘The evolution of plant metabolism’.
Identification and characterization ofugpErequired for the full virulence of Streptococcus suis
Authors: Yang Qiulei , Li Na , Tian Yanyan , Liang Qiao , Zhao Miaomiao , Chu Hong , Gong Yan , Wu Tong , Wei Shaopeng , Wang He , Yan Guangmou , Li Fengyang , Lei Liancheng
Published: September 2024

Streptococcus suis(S. suis) is an emerging zoonotic pathogen that threatens both animal and human health worldwide. UgpE is a protein subunit of the Ugp (uptake ofglycerolphosphate) transporter system that is involved in glycerophospholipid synthesis in bacterial membranes. In this study, anugpEdeletion mutant was constructed and the effects ofugpEdeletion on cell morphology, biofilm formation, and virulence were investigated. Deletion ofugpEdid not affect bacterial growth but impaired cell chain formation and capsular synthesis by downregulating the mRNA levels of the capsular regulon genescps-2B,cps-2C, andcps-2S. Deletion ofugpEalso led to decreased tolerance to heat, oxidative, and acid-base stress. Crystal violet staining and scanning electron microscopy demonstratedugpEnegatively regulated biofilm formation in liquid culture and the rdar biofilm morphotype on agar plates. Moreover,ugpEdeletion not only reduced hemolysin activity, survival in whole human blood, and anti-phagocytosis ability against porcine alveolar macrophages (PAM) but also enhanced bacterial adhesion and invasion of human cerebral microvascular endothelial cells (hCMEC/D3) by upregulating the expression of multiple genes associated with cell adhesion. In a mouse infection model,ugpEdeletion significantly attenuated virulence and lowered the number of viable bacteria in the blood and major organs, as well as distribution of macrophages. In conclusion, this study identified UgpE as a novel virulence factor that plays a pivotal role in the regulation of virulence and biofilm formation ofS. suis.
Advancing precision care in pregnancy through an actionable fetal findings list
Authors: Cohen Jennifer L. , Duyzend Michael , Adelson Sophia M. , Yeo Julie , Fleming Mark , Ganetzky Rebecca , Hale Rebecca , Mitchell Deborah M. , Morton Sarah U. , Reimers Rebecca , Roberts Amy , Strong Alanna , Tan Weizhen , Thiagarajah Jay R. , Walker Melissa A. , Green Robert C. , Gold Nina B.
Published: October 2024

The use of genomic sequencing (GS) for prenatal diagnosis of fetuses with sonographic abnormalities has grown tremendously over the past decade. Fetal GS also offers an opportunity to identify incidental genomic variants that are unrelated to the fetal phenotype, but may be relevant to fetal and newborn health. There are currently no guidelines for reporting incidental findings from fetal GS.

In the United States, GS for adults and children is recommended to include a list of “secondary findings” genes (ACMG SF v3.2) that are associated with disorders for which surveillance or treatment can reduce morbidity and mortality. The genes on ACMG SF v3.2 predominantly cause adult-onset disorders. Importantly, many genetic disorders with fetal and infantile onset are actionable as well.

A proposed solution is to create a “fetal actionable findings list,” which can be offered to pregnant patients undergoing fetal GS or eventually, as a standalone cell-free fetal DNA screening test. In this integrative review, we propose criteria for an actionable fetal findings list, then identify genetic disorders with clinically available or emerging fetal therapies, and those for which clinical detection in the first week of life might lead to improved outcomes. Finally, we synthesize the potential benefits, limitations, and risks of an actionable fetal findings list.
Individual-specific strategies inform category learning
Authors: Collina Jared S. , Erdil Gozde , Xia Mingyi , Angeloni Christopher F. , Wood Katherine C. , Sheth Janaki , Kording Konrad P. , Cohen Yale E. , Geffen Maria N.
Published: October 2024

Categorization is an essential task for sensory perception. Individuals learn category labels using a variety of strategies to ensure that sensory signals, such as sounds or images, can be assigned to proper categories. Categories are often learned on the basis of extreme examples, and the boundary between categories can differ among individuals. The trajectories for learning also differ among individuals, as different individuals rely on different strategies, such as repeating or alternating choices. However, little is understood about the relationship between individual learning trajectories and learned categorization. To study this relationship, we trained mice to categorize auditory stimuli into two categories using a two-alternative forced choice task. Because the mice took several weeks to learn the task, we were able to quantify the time course of individual strategies and how they relate to how mice categorize stimuli around the categorization boundary. Different mice exhibited different trajectories while learning the task. Mice displayed preferences for a specific category, manifested by a choice bias in their responses, but this bias drifted with learning. We found that this drift in choice bias correlated with variability in the category boundary for sounds with ambiguous category membership. Next, we asked how stimulus-independent, individual-specific strategies informed learning. We found that the tendency to repeat choices, which is a form of perseveration, contributed to long-term learning. These results indicate that long-term trends in individual strategies during category learning affect learned category boundaries.
Increased bone inflammation in type 2 diabetes and obesity correlates with Wnt signaling downregulation and reduced bone strength
Authors: Leanza Giulia , Faraj Malak , Cannata Francesca , Viola Viola , Pellegrini Niccolò , Tramontana Flavia , Pedone Claudio , Vadalà Gianluca , Piccoli Alessandra , Strollo Rocky , Zalfa Francesca , Civitelli Roberto , Maccarrone Mauro , Papalia Rocco , Napoli Nicola
Published: September 2024

Type 2 diabetes (T2D) and obesity (OB) are associated with chronic low-grade inflammation and increased fracture risk.In vitrostudies showed that inflammation induces bone erosion and inhibits bone formation by increasing Wnt canonical pathway inhibitors. However, the impact of inflammation on Wnt pathway regulation and bone quality in T2D and OB remains unclear. To this end, we studied 63 postmenopausal women (age >65 years) undergoing hip replacement for osteoarthritis. Among these women, 19 had T2D and OB (HbA1c 6.8±0.79%; BMI 29.9±5.2 kg/m2), 17 had OB but they were normoglycemic (BMI 32.5±5.4 kg/m2), and 27 served as controls (BMI 23.1±5.5 kg/m2). Serum inflammatory cytokines by automated immunoassay (ELLA), revealed higher TNF-α (p=0.0084) and lower adiponectin (p=0.0402) in T2D, and higher IL-6 (p=0.0003) levels in OB vs controls. Gene expression analysis of trabecular bone showed increased TNF-α (p=0.0019) and SFRP5 (p=0.0084) in T2D vs controls. IL-10 was lower in both T2D (p=0.0285), and OB (p=0.0324), while adiponectin (ADIPOQ) was only lower in T2D (p=0.0041) vs controls. Interestingly, the Wnt inhibitor SOST was higher in T2D (p<0.0001) and OB (p<0.0001) vs controls. Conversely, WNT10B mRNA levels were lower in T2D (p=0.0071) and in OB (p=0.0196) vs controls, while LEF-1 were only lower in T2D (p=0.0009). WNT5A (p=0.0025) and GSK3β (p=0.0003) mRNA levels were higher only T2D vs controls. Importantly, TNF-α mRNA levels positively correlated with SOST (r=0.5121, p=0.0002), WNT5A (r=0.3227, p=0.0396) and GSK3β (r=0.3789, p=0.0146) mRNA levels, but negatively correlated with WNT10B (r=0.3844, p=0.0188) and LEF-1(r=-0.3310, p=0.0322) mRNA levels. Conversely, IL-10 was negatively correlated with SOST mRNA levels (r=0.3100, p=0.0457). ADIPOQ was negatively correlated with SOST (r=-0.3864, p=0.0105) and WNT5A (r=-0.3025, p=0.0515) mRNA levels. Moreover, SFRP5 was negatively correlated with LEF-1 mRNA levels (r=0.3991, p=0.0131). Finally, serum levels of TNF-α (r=-0.3473, p=0.0352) and IL-6 (r=-0.3777, p=0.0302) negatively correlated with Young’s Modulus, an index of bone strength. These findings suggest that increased inflammation in bone of subjects with T2D and obesity is negatively associated with Wnt pathway and bone strength, shedding light on pathophysiology of bone impairment in T2D and obesity.
Somatic mutant selection is altered by priorNOTCH1mutation in aging esophageal epithelium
Authors: King Charlotte , Abby Emilie , Fowler Joanna C. , Abnizova Irina , Sood Roshan K. , Ong Swee Hoe , Hall Michael W. J. , Lynch-Williams Faye , Hall Benjamin A. , Jones Philip H.
Published: September 2024

In cancer evolution, genome alterations often occur in a specific order, implying selection depends on the prior clonal genotype1-3. It is unknown if similar constraints operate in normal epithelia. Here, we mapped mutations in normal mid-esophagus of aged UK subjects. MutantNOTCH1clones colonized most of the epithelium by age 60 and the tissue became saturated with mutants under strong competitive selection by age 70. Compared to samples that were mostlyNOTCH1wildtype, samples predominantly mutant forNOTCH1showed weaker selection of mutantTP53and increased selection ofNOTCH2mutants. In mouse esophagus lackingNotch1we observed strong selection of mutantNotch2, not seen in wild type epithelium. In aging esophagus, the first driver mutation may change the trajectory of subsequent somatic evolution by altering mutational selection and by restricting space available for the expansion of other mutant clones.
Effects of alcohol on the transcriptome, methylome, and metabolome ofin vitrogastrulating human embryonic cells
Authors: Wallén E , Rämö K , Vehviläinen J , Sokka J , Lehtonen M , Otonkoski T , Trokovic R , Auvinen P , Kärkkäinen O , Kaminen-Ahola N
Published: September 2024

Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neurodevelopmental disorders and birth defects. To explore the effects of PAE on gastrulation, we used anin vitromodel with subchronic moderate (20 mM) and severe (70 mM) ethanol exposures during the differentiation of human embryonic stem cells into germ layer cells. We analysed genome-wide gene expression (mRNA sequencing), DNA methylation (EPIC Illumina microarrays), and metabolome (non-targeted LC-MS method) of the endodermal, mesodermal, and ectodermal cells. The largest number of ethanol-induced alterations were observed in the endodermal cells, whereas the most prominent changes were seen in the ectodermal cells. Genes of the major morphogen signaling pathways involved in gastrulation and body patterning were affected by ethanol. Many of the altered genes, such asBMP4,FGF8,SIX3,andLHX2, have been previously associated with PAE and phenotypes of FASD, like defects in heart and corpus callosum development as well as holoprosencephaly. Furthermore, methionine metabolism was altered in all germ layer cells. Our findings support the early origin of alcohol-induced developmental disorders and strengthen the role of methionine cycle in the etiology of FASD.
Alternative splicing of transposable elements in human breast cancer
Authors: Nesta Alex , Veiga Diogo F. T. , Banchereau Jacques , Anczukow Olga , Beck Christine R.
Published: September 2024

Transposable elements (TEs) drive genome evolution and can affect gene expression through diverse mechanisms. In breast cancer, disrupted regulation of TE sequences may facilitate tumor-specific transcriptomic alterations. We examine 142,514 full-length isoforms derived from long-read RNA sequencing (LR-seq) of 30 breast samples to investigate the effects of TEs on the breast cancer transcriptome. Approximately half of these isoforms contain TE sequences, and these contribute to half of the novel annotated splice junctions. We quantify splicing of these LR-seq derived isoforms in 1,135 breast tumors from The Cancer Genome Atlas (TCGA) and 1,329 healthy tissue samples from the Genotype-Tissue Expression (GTEx), and find 300 TE-overlapping tumor-specific splicing events. Some splicing events are enriched in specific breast cancer subtypes – for example, a TE-driven transcription start site upstream ofERBB2in HER2+ tumors, and several TE-mediated splicing events are associated with patient survival and poor prognosis. The full-length sequences we capture with LR-seq reveal thousands of isoforms with signatures of RNA editing, including a novel isoform belonging toRHOA; a gene previously implicated in tumor progression. We utilize our full-length isoforms to discover polymorphic TE insertions that alter splicing and validate one of these events in breast cancer cell lines. Together, our results demonstrate the widespread effects of dysregulated TEs on breast cancer transcriptomes and highlight the advantages of long-read isoform sequencing for understanding TE biology. TE-derived isoforms may alter the expression of genes important in cancer and can potentially be used as novel, disease-specific therapeutic targets or biomarkers.

One Sentence Summary

Transposable elements generate alternative isoforms and alter post-transcriptional regulation in human breast cancer.
Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics
Authors: Smeal Steven W. , Mokashi Chaitanya S. , Kim A. Hyun , Chiknas P. Murdo , Lee Robin E. C.
Published: September 2024

Temporal properties of molecules within signaling networks, such as sub-cellular changes in protein abundance, encode information that mediate cellular responses to stimuli. How dynamic signals relay and process information is a critical gap in understanding cellular behaviors. In this work, we investigate transmission of information about changing extracellular cytokine concentrations from receptor-level supramolecular assemblies of IκB kinases (IKK) downstream to the nuclear factor κB (NF-κB) transcription factor (TF). In a custom robot-controlled microfluidic cell culture, we simultaneously measure input-output (I/O) encoding of IKK-NF-κB in dual fluorescent-reporter cells. When compared with single cytokine pulses, dose-conserving pulse trains prolong IKK assemblies and lead to disproportionately enhanced retention of nuclear NF-κB. Using particle swarm optimization, we demonstrate that a mechanistic model does not recapitulate this emergent property. By contrast, invoking mechanisms for NF-κB-dependent chromatin remodeling to the model recapitulates experiments, showing how temporal dosing that prolongs IKK assemblies facilitates switching to permissive chromatin that sequesters nuclear NF-κB. Remarkably, using simulations to resolve single-cell receptor data accurately predicts same-cell NF-κB time courses for more than 80% of our single cell trajectories. Our data and simulations therefore suggest that cell-to-cell heterogeneity in cytokine responses are predominantly due to mechanisms at the level receptor-associated protein complexes.
Comparative Analysis of AAV Serotypes for Transduction of Olfactory Sensory Neurons
Authors: Belfort Benjamin D.W. , Jia Johnathan D. , Garza Alexandra , Insalaco Anthony M. , McGinnis JP , Pekarek Brandon T. , Ortiz-Guzman Joshua , Tepe Burak , Chen Hu ,   aSCENT-PD Investigators, Liu Zhandong , Arenkiel Benjamin R.
Published: September 2024

Olfactory sensory neurons within the nasal epithelium detect volatile odorants and relay odor information to the central nervous system. Unlike other sensory inputs, olfactory sensory neurons interface with the external environment and project their axons directly into the central nervous system. The use of adeno-associated viruses to target these neurons has garnered interest for applications in gene therapy, probing olfactory sensory neuron biology, and modeling disease. To date, there is no consensus on the optimal AAV serotype for efficient and selective transduction of olfactory sensory neuronsin vivo. Here we utilized serial confocal imaging and single-nucleus RNA sequencing to evaluate the efficacy of 11 different AAV serotypes in transducing murine olfactory sensory neurons via non-invasive nasal inoculation. Our results reveal that AAV1, while highly effective, exhibited broad tropism, whereas AAV-DJ/8 showed the greatest specificity for olfactory sensory neurons.
EmbedSimScore: Advancing Protein Similarity Analysis with Structural and Contextual Embeddings
Authors: Saha Gourab , Tahmid Md Toki , Bayzid Md. Shamsuzzoha
Published: September 2024

Accurately computing protein similarity is challenging due to the intricate interplay between local substructures and the global structure within protein molecules. Traditional metrics like TM-score often focus on aligning the global structures of the proteins in a rather geometry-based algorithmic way, potentially overlooking critical local-global relations and contextual comparisons. We introduce Embed-SimScore, a novel self-supervised method that generates structural and contextual embeddings by jointly considering both local substructures and global proteins’ structures. Utilizing contrastive language-structure pre-training (CLSP) and structural contrastive learning, EmbedSimScore captures comprehensive features across different scales of protein structure. These embeddings provide a more precise and holistic means of computing protein similarities, resulting in the identification of intrinsic relations among proteins that traditional approaches overlook.
ABA-regulated JAZ1 Proteins Bind NAC42 Transcription Factors to Suppress the Activation of Phytoalexin Biosynthesis in Plants
Authors: Lin Jie , Monsalvo Ivan , Jahan Md Asraful , Ly Melissa , Wi Dasol , Martirosyan Izabella , Jahan Israt , Kovinich Nik
Published: September 2024

Phytoalexins are plant defense metabolites whose biosynthesis remains suppressed until elicited by a pathogen or stress, yet the mechanism of their suppression has remained elusive. The transcription factor GmNAC42-1 is an important and direct activator of the biosynthesis of glyceollin phytoalexins in soybean. Yet, without elicitation, overexpressing GmNAC42-1 is insufficient to activate the expression of glyceollin biosynthetic genes, suggesting that the activity of GmNAC42-1 may be suppressed by a negative regulator. JAZ1 proteins are negative regulators of the canonical jasmonic acid (JA) signaling pathway. JAZ protein degradation and JAZ gene transcription comprise antagonistic mechanisms that activate and suppress JA signaling, respectively. In search for negative regulators of glyceollin biosynthesis, we identified by RNA-seq analysis abscisic acid (ABA) signaling and GmJAZ1 genes that are oppositely regulated compared to glyceollin biosynthesis. Long-term ABA treatment upregulated GmJAZ1 transcripts, whereas its biosynthesis inhibitor fully suppressed their upregulation by dehydration stress. Opposite patterns were observed for glyceollin biosynthesis. RNAi silencing of GmJAZ1s prevented the suppression of glyceollin biosynthesis by dehydration and derepressed glyceollin synthesis in non-elicited tissues. Overexpressing GmJAZ1-9 in hairy roots elicited with Phytophthora sojae wall glucan elicitor partially suppressed glyceollin biosynthesis. The GmJAZ1-9 protein physically interacted with GmNAC42-1 and inhibited its transactivation and DNA binding activities in promoter-luciferase and yeast-three hybrid systems. Silencing JAZ1s in Arabidopsis and grapevine has been reported to derepress camalexin and stilbene phytoalexin biosynthesis. Here, we found that JAZ1 and NAC42 proteins from all three plant species physically interact, suggesting a conserved mechanism negatively regulates phytoalexin biosynthesis in plants.

Abstract Figure
Overestimation of sex differences in psychostimulant activity via comparisons of males and females from different behavioral groups
Authors: Tigano Anthony M. , Job Martin O
Published: September 2024

Background

There are inconsistencies in the observation of sex differences in baseline activity and psychostimulant activity. To address this, we have developed the MISSING (Mapping Intrinsic Sex Similarities as an Integral quality of Normalized Groups) model. MISSING model proposes that sex similarities are observed when we compare similar behavioral groups of males and females, with sex differences occurring when we compare distinct groups of sexes, but this model has not been tested.

Methods

To test this model, we identified within-sex groups of Sprague Dawley rats (male n = 22, female n = 23) by conducted normal mixtures clustering of baseline activity, cocaine activity (as distance traveled in cm over 90 min) and cocaine activity normalized-to-baseline activity (NBA) of all subjects. We employed 2-way ANOVA to determine the impact of within-sex heterogeneity on sex differences. We compared our cluster-based method to current median-split approaches.

Results

Our new cluster-based method revealed three distinct clusters, each consisting of both males and females. We determined there were no sex differences in any of the variables when males and females from the same clusters were compared. The within-sex clusters for females were not defined by estrous phase. Median split analysis was ineffective in accurately identifying within-sex groups.

Conclusions

Our results validate the MISSING model: there are no sex differences in psychostimulant activity except when we compare males and females from different behavioral groups. This has significant implications for how we proceed with research towards understanding the mechanism governing sex differences in psychostimulant activity.
Anatomically and Physiologically Accurate Engineered Neurovascular Unit and Blood-Brain Barrier Model Using Microvessels Isolated from Postmortem Human Brain Tissue
Authors: O’Grady Brian J. , McCall A. Scott , Cullison Samuel , Chavarria Daniel , Kjar Andrew , Schrag Matthew S. , Lippmann Ethan S.
Published: September 2024

Brain vasculature is a complex and heterogeneous physiological structure that serves specialized roles in maintaining brain health and homeostasis. There is substantial interest in developing representative human models of the brain vasculature for drug screening and disease modeling applications. Many contemporary strategies have focused on culturing neurovascular cell types in hydrogels and microdevices, but it remains challenging to achieve anatomically relevant vascular structures that have physiologically similar function to theirin vivocounterparts. Here, we present a strategy for isolating microvessels from cryopreserved human cortical tissue and culturing these vessels in a biomimetic gelatin-based hydrogel contained in a microfluidic device. We provide histological evidence of arteriole and capillary architectures within hydrogels, as well as anastomosis to the hydrogel edges allowing lumen perfusion. In capillaries, we demonstrate restricted diffusion of a 10 kDa dextran, indicating intact passive blood-brain barrier function. We anticipate this bona fide human brain vasculature-on-a-chip will be useful for various biotechnology applications.
Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets
Authors: Song Minfang , Ma Shuai , Wang Gong , Wang Yukun , Yang Zhenzhen , Xie Bin , Guo Tongkun , Huang Xingxu , Zhang Liye
Published: September 2024

Copy number aberrations (CNAs) are an important type of genomic variation which play a crucial role in the initiation and progression of cancer. With the explosion of single-cell RNA sequencing (scRNA-seq), several computational methods have been developed to infer CNAs from scRNA-seq studies. However, to date, no independent studies have comprehensively benchmarked their performance. Herein, we evaluated five state-of-the-art methods based on their performance in tumor vs normal cell classification, CNAs profile accuracy, tumor subclone inference and aneuploidy identification in non-malignant cells. Our results showed that Numbat outperformed others across most evaluation criteria, while CopyKAT excelled in scenarios when expression matrix alone was used as input. In specific tasks, SCEVAN showed the best performance in clonal breakpoint detection and Numbat showed high sensitivity in copy number neutral LOH (cnLOH) detection. Additionally, we investigated how referencing settings, inclusion of tumor microenvironment cells, tumor type, and tumor purity impact the performance of these tools. This study provides a valuable guideline for researchers in selecting the appropriate methods for their datasets.
AMPK agonism optimizes thein vivopersistence and anti-leukemia efficacy of chimeric antigen receptor T cells
Authors: Braverman Erica L , Qin Mengtao , Schuler Herbert , Brown Harrison , Wittmann Christopher , Ramgopal Archana , Kemp Felicia , Mullet Steven J , Yang Aaron , Poholek Amanda C , Gelhaus Stacy L , Byersdorfer Craig A.
Published: September 2024

BACKGROUND

Chimeric antigen receptor T cell (CART) therapy has seen great clinical success. However, up to 50% of leukemia patients relapse and long-term survivor data indicate that CART cell persistence is key to enforcing relapse-free survival. Unfortunately, ex vivo expansion protocols often drive metabolic and functional exhaustion, reducing in vivo efficacy. Preclinical models have demonstrated that redirecting metabolism ex vivo can improve in vivo T cell function and we hypothesized that exposure to an agonist targeting the metabolic regulator AMP-activated protein kinase (AMPK), would create CARTs capable of both efficient leukemia clearance and increased in vivo persistence.

METHODS

CART cells were generated from healthy human via lentiviral transduction. Following activation, cells were exposed to either Compound 991 or DMSO for 96 hours, followed by a 48-hour washout. During and after agonist treatment, T cells were harvested for metabolic and functional assessments. To test in vivo efficacy, immunodeficient mice were injected with luciferase+ NALM6 leukemia cells, followed one week later by either 991- or DMSO-expanded CARTs. Leukemia burden and anti-leukemia efficacy was assessed via radiance imaging and overall survival.

RESULTS

Human T cells expanded in Compound 991 activated AMPK without limiting cellular expansion and gained both mitochondrial density and improved handling of reactive oxygen species (ROS). Importantly, receipt of 991-exposed CARTs significantly improved in vivo leukemia clearance, prolonged recipient survival, and increased CD4+ T cell yields at early times post-injection. Ex vivo, 991 agonist treatment mimicked nutrient starvation, increased autophagic flux, and promoted generation of mitochondrially-protective metabolites.

DISCUSSION

Ex vivo expansion processes are necessary to generate sufficient cell numbers, but often promote sustained activation and differentiation, negatively impacting in vivo persistence and function. Here, we demonstrate that promoting AMPK activity during CART expansion metabolically reprograms cells without limiting T cell yield, enhances in vivo anti-leukemia efficacy, and improves CD4+ in vivo persistence. Importantly, AMPK agonism achieves these results without further modifying the expansion media, changing the CART construct, or genetically altering the cells. Altogether, these data highlight AMPK agonism as a potent and readily translatable approach to improve the metabolic profile and overall efficacy of cancer-targeting T cells.
Genome-wide association study of delay discounting in 134,935 individuals identifies novel loci and transdiagnostic associations across mental and physical health
Authors: Thorpe Hayley HA , Cupertino Renata B , Pakala Shreya Reddy , Fontanillas Pierre , Jennings Mariela V , Yang Jane , Meredith John J , Greenwood Tiffany , Bianchi Sevim B , Vilar-Ribo Laura , Niarchou Maria ,   23andMe Research Team, Elson Sarah L , Ideker Trey , Davis Lea K , MacKillop James , deWit Harriet , Gustavson Daniel , Mallard Travis T , Palmer Abraham A , Sanchez-Roige Sandra
Published: October 2024

Delay discounting (DD), a person's preference for smaller immediate rewards over larger delayed rewards, is a heritable trait that is associated with psychiatric and physical outcomes, yet the biological mechanisms underlying these links are not known. We performed a GWAS of DD using 134,935 adults and identified 14 genome-wide significant loci. We observed genetic correlations between DD and 73 behavioral, physical and neuroimaging traits, many of which persisted even after accounting for educational attainment, intelligence, and executive function. Network analysis revealed that the associations between DD and certain traits were explained by both overlapping and trait-specific biological processes. In a hospital-based cohort (N = 66,917), DD polygenic scores were associated with 212 medical conditions. These results demonstrate that DD has a pleiotropic and polygenic common variant architecture, and is genetically associated with numerous outcomes, making it a promising endophenotype for psychiatric and physical health.
A Southern African Map of Blood Regulatory Variation Enables GWAS Interpretation
Authors: Castel Stephane E , Tluway Furahini , Emde Anne-Katrin , Smyth Nicole , Karim Mohd , Sengupta Dhriti , Gray Olivia O , Hendershott Melissa , LeBaron von Baeyer Sarah , Burke Erin , Kaewert Sarah , Nguyen KD , Choma Solomon , Mashaba Given , Micklesfield Lisa , Kabudula Chodziwadziwa , Kahn Kathleen , Gomez-Olive F , Tollman Stephen , Choudhury Ananyo , Mpangase Phelelani , Hazelhurst Scott , Wasik Kaja A , Yerges-Armstrong Laura , Ramsay Michele
Published: September 2024

Functional genomics resources are critical for interpreting human genetic studies, however they are predominantly from European-ancestry individuals. Here we present the Southern African Blood Regulatory (SABR) resource, a map of blood regulatory variation that includes three South Eastern Bantu-speaking groups. Using paired whole genome and blood transcriptome data from over 600 individuals, we map the genetic architecture of 40 blood cell traits derived from deconvolution analysis, as well as expression, splice, and cell type interaction quantitative trait loci. We comprehensively compare SABR to the Genotype Expression (GTEx) Project and characterize the thousands of African-enriched and African-specific regulatory variants mapped. Finally, we demonstrate the increased utility of SABR for interpreting African association studies by identifying putatively causal genes and molecular mechanisms through colocalization analysis of 83 blood-relevant traits from the PAN-UK Biobank. Importantly, we make full SABR summary statistics publicly available to support the African genomics community.
Less is more: Slow-codon windows enhance eGFP mRNA resilience against RNA interference
Authors: Mueller Judith Anna , Schwake Gerlinde , Reiser Anita , Woschee Daniel , Alirezaeizanjani Zahra , Raedler Joachim Oskar , Rudorf Sophia
Published: September 2024

Extensive efforts have been devoted to enhance the translation efficiency of mRNA delivered to mammalian cells via codon optimization. However, the impact of codon choice on mRNA stability remains underexplored. In this study, we investigated the influence of codon usage on mRNA degradation kinetics in cultured human cell lines using live-cell imaging on single-cell arrays (LISCA). By measuring mRNA lifetimes at the single-cell level for synthetic mRNA constructs, we confirmed that mRNAs containing slowly translated codon windows have shorter lifetimes. Unexpectedly, these mRNAs did not exhibit decreased stability in the presence of siRNA compared to the unmutated sequence, suggesting an interference of different concurrent degradation mechanisms. We employed stochastic simulations to predict ribosome density along the open reading frame, revealing that the ribosome densities correlated with mRNA stability in a cell-type- and codon-position-specific manner. In summary, our results suggest that the effect of codon choice and its influence on mRNA lifetime is context dependent with respect to cell type, codon position, and RNA interference.
MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families, and updated covariance models
Authors: Clarke Alexander W. , Høye Eirik , Hembrom Anju Angelina , Paynter Vanessa Molin , Vinther Jakob , Wyrożemski Łukasz , Biryukova Inna , Formaggioni Alessandro , Ovchinnikov Vladimir , Herlyn Holger , Pierce Alexandra , Wu Charles , Aslanzadeh Morteza , Cheneby Jeanne , Martinez Pedro , Friedländer Marc R. , Hovig Eivind , Hackenberg Michael , Umu Sinan Uğur , Johansen Morten , Peterson Kevin J. , Fromm Bastian
Published: September 2024

We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21, 822 microRNA genes (5, 160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway, and is publicly and freely available atmaster.cloud.mirgenedb.org.

Key Points

Major update to the manually curated and uniformly named microRNA gene database MirGeneDB

114 animal species, >1700 microRNA families and ∼20 000 genes searchable, browsable and downloadable

New features to download all smallRNA read data and updated covariance models for each family
Biologically informed cortical models predict optogenetic perturbations
Authors: Sourmpis Christos , Petersen Carl CH , Gerstner Wulfram , Bellec Guillaume
Published: September 2024

A recurrent neural network fitted to large electrophysiological datasets should reveal the chain of cortical information transmission. In particular, successful network reconstruction methods should enable a model to predict the response to optogenetic perturbations. We test recurrent neural network (RNN) fitted to electrophysiological datasets on unseen optogenetic interventions, and we propose an RNN extraction method that better predicts the response of the biological circuit to these perturbations. Our method uses gradient descent optimization to reproduce various aspects of neuronal activity patterns, and introduces biologically informed inductive biases like spiking neuron dynamics and structured connectivity reflecting excitatory and inhibitory cell types. We show that including these biological inductive biases can drastically improve the robustness of optogenetic perturbations compared to sigmoidal RNN models used predominantly in the field. Furthermore, we show that gradients of the fitted RNN can predict the effect of micro-perturbations in the recorded circuits, and discuss potentials for measuring brain gradients and designing experimental setups with gradient-targeted stimulation to bias an animal behavior.