bluuebunny/crossref_metadata_2025 huggingface dataset:
Severe biventricular cardiomyopathy in both current and former long-term users of anabolic-androgenic steroids
Authors: Abdullah Rang , Bjørnebekk Astrid , Hauger Lisa E. , Hullstein Ingunn R. , Edvardsen Thor , Haugaa Kristina H. , Almaas Vibeke M.
Published: September 2023

Aims

Explore the cardiovascular effects of long-term anabolic-androgenic steroid (AAS)-use in both current and former weightlifting AAS-users, and estimate the occurrence of severe reduced myocardial function and the impact of duration and amount of AAS.

Methods

In this cross-sectional study 101 weightlifting AAS-users with at least one year cumulative AAS-use (mean 11±7 accumulated years of AAS-use) were compared to 71 non-using weightlifting controls (WLC) using clinical data and echocardiography.

Results

Sixty-nine were current, 30 former (> 1 year since quitted), and 2 AAS-users were not available for this classification. AAS-users had higher left ventricular mass index (LVMI) (106±26 versus 80±15 g/m2, P<0.001), worse LV ejection fraction (LVEF) (49±7 versus 59±5%, P<0.001) and right ventricular global longitudinal strain (RVGLS) (−17.3±3.5 versus −22.8±2.0%, P<0.001), and higher systolic blood pressure (SBP) (141±17 vs. 133±11 mmHg, p<0.001) compared with WLC. In current users accumulated duration of AAS-use was 12±7 years, and in former 9±6 years (quitted 6±6 years earlier). Compared to WLC, LVMI and LVEF were pathological in current and former users (p<0.05) with equal distribution of severely reduced myocardial function (LVEF ≤40%) (11% vs. 10%, NS). In current users estimated life time AAS-dose correlated with reduced LVEF and LVGLS, p<0.05, but not with LVMI, p=0.12. Regression analyses of the total population showed that the strongest determinant of reduced LVEF were not coexisting strength training or hypertension, but history of AAS-use (β −0.53, P<0.001).

Conclusions

Long-term AAS-users showed severely biventricular cardiomyopathy. The reduced systolic function was also found upon discountied use.
Sidedness in unilateral orofacial clefts: A systematic scoping review
Authors: Fell Matthew , Bradley Daniel , Chadha Ambika , Butterworth Sophie , Davies Amy , Russell Craig , Richard Bruce , Wren Yvonne , Lewis Sarah , Chong David
Published: September 2023

Objectives

An overview of the literature relating to the sidedness of unilateral cleft lip with or without cleft palate to map current knowledge on the cause and impact of directional asymmetry in the unilateral cleft lip phenotype.

Data Sources

Medline and Embase from inception to May 2023

Study selection

Studies including left and right unilateral cleft lip subgroups as a co-occurrence, an outcome or an exposure.

Data analysis

Narrative synthesis.

Results

Forty-one studies were eligible for inclusion; 12 studies reported cleft sidedness co-occurring with another phenotype, 12 studies report sidedness as an outcome and 17 studies as an exposure. Phenotypes which were reported to co-occur with either left or right sided clefts included congenital dental anomalies, handedness and additional congenital anomalies. Variables investigated as a potential cause of left or right sided clefts as an outcome included chromosomal anomalies, genetic variants and environmental factors. Outcomes investigated in relation to cleft sidedness as an exposure included facial anatomical features, facial growth, educational attainment, functional and psychological characteristics. More studies showed worse outcomes in right sided clefts versus left sided clefts than vice versa, although studies were inconsistent, and a quality assessment was not performed.

Conclusions

The field of cleft sidedness research is expanding and there are promising early findings to differentiate cause and outcome by sidedness of the cleft.
Emergence of disease-specific endothelial and stromal cell populations responsible for arterial remodeling during development of pulmonary arterial hypertension
Authors: Cober Nicholas D , McCourt Emma , Godoy Rafael Soares , Deng Yupu , Schlosser Ken , Situ Anu , Cook David P , Lemay Sarah-Eve , Klouda Timothy , Yuan Ke , Bonnet Sébastien , Stewart Duncan J
Published: September 2023

Abstract

Pulmonary arterial hypertension (PAH) is a severe and lethal pulmonary vascular disease characterized by arteriolar pruning and occlusive vascular remodeling leading to increased pulmonary vascular resistance and eventually right heart failure. While endothelial cell (EC) injury and apoptosis are known triggers for this disease, the mechanisms by which they lead to complex arterial remodeling remain obscure. We employed multiplexed single-cell RNA sequencing (scRNA-seq) at multiple timepoints during the onset and progression of disease in a model of severe PAH to identify mechanisms involved in the development of occlusive arterial lesions. There was significant loss of arterial volume as early as 1-week by microCT, preceding any evidence of occlusive arteriopathy, consistent with early arteriolar dropout. Maximal arterial pruning was seen by 5 to 8 weeks, with signs of progressive occlusive remodeling. Analysis of the scRNA-seq data resolved 44 lung cell populations, with widespread early transcriptomic changes at 1 week affecting endothelial, stromal and immune cell populations. Notably, this included emergence of a relatively dedifferentiated (dD) EC population that was enriched forCd74expression compared to general capillary (gCap) ECs which were primed to undergo endothelial-mesenchymal transition, as evidenced by RNA velocity analysis. However, at late timepoints (5 and 8 weeks), activated arterial ECs (aAECs) were the only cell population exhibiting persistent differential gene expression. This was characterized by a growth regulated state, including high expression ofTm4sf1, a gene implicated in cancer cell growth, which was also expressed by a smooth muscle (SM)-like pericyte cluster. Both these populations were localized to regions of arterial remodeling in the rat model and PAH patients, with aAECs contributing to intimal occlusive lesions and SM-like pericytes forming bands of medial muscularization. Together these findings implicate disease-specific vascular cells in PAH progression and suggest that TM4SF1 may be a novel therapeutic target for arterial remodeling.
Descending control and regulation of spontaneous flight turns inDrosophila
Authors: Ros Ivo G. , Omoto Jaison J. , Dickinson Michael H.
Published: September 2023

The clumped distribution of resources in the world has influenced the pattern of foraging behavior since the origins of life, selecting for a common locomotor search motif in which straight movements through resource-poor regions alternate with zig-zag exploration in resource-rich domains (Berg, 2000). For example, flies execute rapid changes in flight heading called body saccades during local search (Censi et al., 2013; Collett and Land, 1975; Schilstra and van Hateren, 1999; Wagner and Land, 1986), but suppress these turns during long-distance dispersal (Giraldo et al., 2018; Leitch et al., 2021) or when surging upwind after encountering an attractive odor plume (Budick and Dickinson, 2006; van Breugel and Dickinson, 2014). Here, we describe the key cellular components of a neural network in flies that generates spontaneous turns as well as a specialized neuron that inhibits the network to promote straight flight. Using 2-photon imaging, optogenetic activation, and genetic ablation, we show that only four descending neurons appear sufficient to generate the descending commands to execute flight saccades. The network is organized into two functional couplets—one for right turns and one for left—with each couplet consisting of an excitatory (DNae014) and inhibitory (DNb01) neuron that project to the flight motor neuropil within the ventral nerve cord. Using resources from recently published connectomes of the fly brain (Scheffer et al., 2020; Dorkenwald et al., 2023; Schlegel et al., 2023), we identified a large, unique interneuron (VES041) that forms inhibitory connections to all four saccade command neurons and created specific genetic driver lines for this cell. As predicted by its connectivity, activation of VES041 strongly suppresses saccades, suggesting that it regulates the transition between local search and long-distance dispersal. These results thus identify the critical elements of a network that not only structures the locomotor behavior of flies, but may also play a crucial role in their foraging ecology.
CTCF regulates hepatitis B virus cccDNA chromatin topology
Authors: Dobrica Mihaela Olivia , Varghese Christy Susan , Harris James M , Ferguson Jack , Magri Andrea , Arnold Roland , Várnai Csilla , Parish Joanna L , McKeating Jane A
Published: September 2023

Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcripts, however, the underlying mechanisms were not identified. We show that CTCF depletion in cells harbouring cccDNA-like HBV molecules and inde novoinfected cells resulted in an increase in spliced transcripts, which was most notable in the abundant SP1 spliced transcript. In contrast, depletion of CTCF in cell lines with integrated HBV DNA had no effect on the abundance of viral transcripts and in line with this observation there was limited evidence for CTCF binding to viral integrants, suggesting that CTCF-regulation of HBV transcription is specific to episomal cccDNA. Analysis of HBV chromatin topology by Assay for Transposase Accessibility/sequencing (ATAC-Seq) revealed an accessible region spanning Enhancers I and II and the basal core promoter (BCP). Mutating the CTCF binding sites within Enhancer I resulted in a dramatic rearrangement of chromatin accessibility where the open chromatin region was no longer detected, indicating loss of the phased nucleosome up- and down-stream of the HBV enhancer/BCP. These data demonstrate that CTCF functions to regulate HBV chromatin conformation and nucleosomal positioning in episomal maintained cccDNA, which has important consequences for HBV transcription regulation.
The characteristics of CTCF binding sequences contribute to enhancer blocking activity
Authors: Tsang Felice H. , Stolper Rosa J. , Hanifi Muhammad , Cornell Lucy J. , Francis Helena S. , Davies Benjamin , Higgs Douglas R. , Kassouf Mira T.
Published: September 2023

While the elements encoding enhancers and promoters have been relatively well studied, the full spectrum of insulator elements which bind the CCCTC binding factor (CTCF), is relatively poorly characterised. This is partly due to the genomic context of CTCF sites greatly influencing their roles and activity. Here we have developed an experimental system to determine the ability of consistently sized, individual CTCF elements to interpose between enhancers and promoters and thereby reduce gene expression during differentiation. Importantly, each element is tested in the identical location thereby minimising the effect of genomic context. We found no correlation between the ability of CTCF elements to block enhancer-promoter activity with the amount of CTCF or cohesin bound at the natural genomic sites of these elements; the degree of evolutionary conservation; or their resemblance to the consensus core sequences. Nevertheless, we have shown that the strongest enhancer-promoter blockers include a previously described bound element lying upstream of the CTCF core motif. In addition, we found other uncharacterised DNaseI footprints located close to the core motif that may affect function. We have developed an assay of CTCF sequences which will enable researchers to sub-classify CTCF elements in a uniform and unbiased way.
ATAD1 and the integrated stress response prevent clogging of TOM and damage caused by un-imported mitochondrial proteins
Authors: Kim John , Goldstein Madeleine , Zecchel Lauren , Weidberg Hilla
Published: September 2023

Mitochondria require the constant import of nuclear-encoded proteins for proper functioning. Impaired protein import not only depletes mitochondria of essential factors but also leads to toxic accumulation of un-imported proteins outside the organelle. Defects in mitochondrial protein import are associated with neurodegenerative and bioenergetic diseases. Here, we investigated the consequences of mitochondrial protein import stress in human cells. We demonstrated that un-imported proteins can clog the mitochondria by stalling inside the translocase of the outer membrane (TOM). We found that the integrated stress response (ISR) acted as the first line of defense to mitochondrial clogging by attenuating global protein translation and preventing excessive accumulation of un-imported proteins. A second mechanism, mediated by a mitochondrial ATPase, ATAD1, acted specifically to remove proteins from TOM and clear the entry gate into the mitochondria. ATAD1 interacted with both TOM and stalled proteins, and its knockout resulted in extensive accumulation of mitochondrial precursors as well as decreased protein import. Increased ATAD1 expression improved tolerance of cells to defective mitochondrial protein import, demonstrating the importance of this quality control pathway in surveilling protein import and its contribution to cellular health.
The brain’s topographical organization shapes dynamic interaction patterns to support flexible behavior
Authors: Wang Xiuyi , Krieger-Redwood Katya , Lyu Baihan , Lowndes Rebecca , Wu Guowei , Souter Nicholas E. , Wang Xiaokang , Kong Ru , Shafiei Golia , Bernhardt Boris C. , Cui Zaixu , Smallwood Jonathan , Du Yi , Jefferies Elizabeth
Published: September 2023

Understanding how human cognition flexibly supports distinct forms of behavior is a key goal of neuroscience. Adaptive behavior relies on context-specific rules that vary across situations, as well as on stable knowledge gained from experience. However, the mechanisms that allow these influences to be appropriately balanced remain elusive. Here, we show that this cognitive flexibility is partly supported by the topographical organization of the cortex. The frontoparietal control network (FPCN) is located between regions implicated in top-down attention and memory-guided cognition. We hypothesized that the FPCN is topographically divided into discrete systems that support these distinct forms of behavior. These FPCN subsystems exhibit multiple anatomical and functional similarities to their neighboring systems (the dorsal attention network and default mode network respectively). This topographic architecture is also mirrored in the functional patterns that emerge in different situations: the FPCN subnetworks act as a unified system when long-term memory can support behavior, but they segregate into discrete units when working memory, rather than long term memory, is necessary for behavioral control. In this way, the topographic organization of brain function provides crucial insights into how the human cortex supports flexible behavior.
Oral immunization of goats and foxes with a recombinant NDV vectored rabies vaccine
Authors: Murr Magdalena , Freuling Conrad , Pérez-Bravo David , Grund Christian , Mettenleiter Thomas C. , Römer-Oberdörfer Angela , Müller Thomas , Finke Stefan
Published: September 2023

Vaccination of the reservoir species is a key component in the global fight against rabies. For wildlife reservoir species and hard to reach spillover species (e. g. ruminant farm animals), oral vaccination is the only solution. In search for a novel potent and safe oral rabies vaccine, we generated a recombinant vector virus based on lentogenic Newcastle disease virus (NDV) strain Clone 30 that expresses the glycoprotein G of rabies virus (RABV) vaccine strain SAD L16 (rNDV_GRABV). Transgene expression and virus replication was verified in avian and mammalian cells.

To test immunogenicity and viral shedding, in a proof-of-concept study six goats and foxes, representing herbivore and carnivore species susceptible to rabies, each received a single dose of rNDV_GRABV(108.5TCID50/animal) by direct oral application. For comparison, three animals received the similar dose of the empty viral vector (rNDV). All animals remained clinically inconspicuous during the trial. Viral RNA could be isolated from oral and nasal swabs until four (goats) or seven days (foxes) post vaccination, while infectious NDV could not be re-isolated. After four weeks, three out of six rNDV_GRABVvaccinated foxes developed RABV binding and virus neutralizing antibodies. Five out of six rNDV_GRABVvaccinated goats displayed RABV G specific antibodies either detected by ELISA or RFFIT. Additionally, NDV and RABV specific T cell activity was demonstrated in some of the vaccinated animals by detecting antigen specific interferon γ secretion in lymphocytes isolated from pharyngeal lymph nodes. In conclusion, the NDV vectored rabies vaccine rNDV_GRABVwas safe and immunogenic after a single oral application in goats and foxes, and highlight the potential of NDV as vector for oral vaccines in mammals.

Author Summary

Oral vaccination of rabies reservoir and spill-over species is the key to control the disease and prevent human rabies. In the past, baits containing live-attenuated rabies vaccines decreased significantly carnivore-mediated rabies in Central and Western Europe as well as North America. However, certain susceptible species are refractory to the oral immunization using so far licensed vaccines. Our vector vaccine based on avian Newcastle disease virus (NDV) has the potential to contribute to the targeted rabies eradication as it was safe and immunogenic after oral administration in goats and foxes. A single vaccine application elicited a rabies virus (RABV) specific systemic humoral immune response in the majority of the vaccinated animals as well as RABV specific T cells in some of the vaccinated animals. NDV can be manufactured at low-cost using already existing infrastructure of influenza vaccines, opening new possibilities especially for middle- and low-income countries that suffer under the economically burden of rabies.
The glucocorticoid receptor as a master regulator of Müller cell gliosis in the diabetic retina
Authors: Pfaller Anna M. , Kaplan Lew , Carido Madalena , Grassmann Felix , Díaz-Lezama Nundehui , Ghaseminejad Farhad , Wunderlich Kirsten A. , Glänzer Sarah , Pannicke Thomas , Weber Bernhard H.F. , Koch Susanne F. , Bonev Boyan , Hauck Stefanie M. , Grosche Antje
Published: September 2023

Diabetic retinopathy (DR) is considered a primarily microvascular complication of diabetes. Müller glia cells are at the center of the retinal neurovascular unit and play a critical role in DR. We therefore investigated Müller cell-specific signaling pathways that are altered in DR to identify novel targets for gene therapy. Using a multi-omics approach on purified Müller cells from diabetic db/db mice, we found the mRNA and protein expression of the glucocorticoid receptor (GR) to be significantly decreased, while its target gene cluster was down-regulated. Further, oPOSSUM TF analysis and ATAC-sequencing identified the GR as a master regulator of Müller cell gliosis in DR. Cortisol not only increased GR phosphorylation. It also induced changes in the expression of known GR target genes in retinal explants. Finally, retinal functionality was improved by AAV-mediated overexpression of GR in Müller cells. Our study demonstrates an important role of the glial GR in DR and implies that therapeutic approaches targeting this signalling pathway should be aimed at increasing GR expression rather than the addition of more ligand.

Graphical abstract
Morphological and microbial diversity of hydromagnesite microbialites in Lake Salda, A Ma8rs Analog Alkaline Lake
Authors: Gunes Yagmur , Sekerci Fatih , Avcı Burak , Ettema Thijs J. G. , Balci Nurgul
Published: September 2023

Abstract

Lake Salda, recognized as a terrestrial analog for the paleolake in Jezero Crater on Mars, hosts modern, sub/fossil and fossil hydromagnesite microbialites. A comprehensive study was conducted to reveal the distribution, and morphological-mineralogical, microbial diversity of the microbialites that are currently growing in the shallow (<1 m) and deeper waters (up to 15 m) of the lake. Six major microbialite forming zones were identified (Zone I-VI) comprising previously unknown morphotypes of the microbialites. These newly identified morphologies include; linked columns and microbial pavements, exhibiting distinct surface textures such as bulbous, mini columnar, knobby, cerebroidal and smooth. The shallow microbialites showed well-preserved radially growing stromatolitic layers in cm-scale, producing cauliflower structures while the deeper samples exhibit mm scale layering within the mini columnar structures. 16S rRNA amplicon data reveal that abundance of major bacterial taxa of the thrombolitic microbialites from deeper regions are distinct than those of the shallow-growing microbialites with stromatolitic structures. Cyanobacteria were found to be generally less abundant (0.01% to 2%) in the thrombolitic microbialites compared to the stromatolitic microbialites with smooth surface. The Anaerolineae class of the phylum Chloroflexi was prominently present in the stromatolitic microbialites with smooth surface. Notably, the lake exhibited a high abundance of the genusExiguobacterium, particularly in the deep thrombolitic microbialites (e.g., 93%). Microscopy analysis of the deep microbial mats showed the presence of abundant nano and microcrystalline platy/flakey hydrated Mg carbonate crystals that co- existed with mineralized filaments and spherulitic aggregates within abundant exopolymeric substances (EPSs). Moreover, palygorskite mineral was exclusively identified within the deep microbialites. Co-existence of aragonite and hydromagnesite minerals in particular within the deep microbialites that grow under non-evaporative conditions and the abundant presence of entombed biomass (e.g., filamentous) collectively suggest the potential preservation of biosignatures within the hydrated Mg carbonate build-ups in Lake Salda.
Growth deficiency and enhanced basal Immunity inArabidopsis thalianamutants ofEDM2,EDM3andIBM2are genetically interlinked
Authors: Wang Jianqiang , Eulgem Thomas
Published: September 2023

Mutants of theArabidopsis thalianagenes,EDM2,EDM3andIBM2are known to show defects in a diverse set of defense and developmental processes. For example, they jointly exhibit enhanced levels of basal defense and stunted growth. Here we show that these two phenotypes are functionally connected by their dependency on the salicylic acid biosynthesis geneSID2and the basal defense regulatory genePAD4. Stunted growth ofedm2,edm3andibm2plants is a consequence of up-regulated basal defense. Constitutively enhanced activity of reactive oxygen species-generating peroxidases, we observed in these mutants, appears also to contribute to both, their enhanced basal defense and their growth retardation phenotypes. Furthermore, we found the histone H3 demethylase geneIBM1, a direct regulatory target of EDM2, EDM3 and IBM2, to be at least partially required for the basal defense and growth-related effects observed in these mutants. We recently reported thatEDM2,EDM3andIBM2coordinate the extent of basal immunity with the timing of the floral transition. Together with these observations, data presented here show that at least some of the diverse phenotypic effects inedm2,edm3andibm2mutants are genetically interlinked and functionally connected.
Structural characterization of two nanobodies targeting the ligand-binding pocket of human Arc
Authors: Muñoz José M. Godoy , Neset Lasse , Markússon Sigurbjörn , Weber Sarah , Krokengen Oda C. , Sutinen Aleksi , Christakou Eleni , Moreno Andrea J. Lopez , Bramham Clive R. , Kursula Petri
Published: September 2023

The activity-regulated cytoskeleton-associated protein (Arc) is a complex regulator of synaptic plasticity in glutamatergic neurons. Understanding its molecular function is key to elucidate the neurobiology of memory and learning, stress regulation, and multiple neurological and psychiatric diseases. The recent development of anti-Arc nanobodies has promoted the characterization of the molecular structure and function of Arc. This study aimed to validate two anti-Arc nanobodies, E5 and H11, as selective modulators of the human Arc N-lobe (Arc-NL), a domain that mediates several molecular functions of Arc through its peptide ligand binding site. The structural characteristics of recombinant Arc-NL-nanobody complexes were solved at atomic resolution using X-ray crystallography. The structures revealed that both anti-Arc nanobodies specifically bind to the multi-peptide binding site of Arc-NL. Isothermal titration calorimetry showed that the Arc-NL-nanobody interactions occur at nanomolar affinity, and that the nanobodies can displace a TARPγ2-derived peptide from the Arc-NL binding site. Thus, both anti-Arc-NL nanobodies can be usedin vitroas competitive inhibitors of endogenous Arc ligands. Differences in the CDR3 loops between the two nanobodies indicate that the spectrum of short linear motifs recognized by the Arc-NL should be expanded. We provide a robust biochemical background to support the use of anti-Arc nanobodies in attempts to target Arc-dependent synaptic plasticity. Function-blocking anti-Arc nanobodies could eventually help unravel the complex neurobiology of synaptic plasticity and help diagnose and treat Arc-associated synaptic disorders.
Retrotransposon-driven environmental regulation ofFLCleads to adaptive response to herbicide
Authors: Raingeval Mathieu , Leduque Basile , Baduel Pierre , Edera Alejandro , Roux Fabrice , Colot Vincent , Quadrana Leandro
Published: September 2023

The mobilization of retrotransposons yields major-effect mutations. Here, we report an adaptive retrotransposon insertion within the first intron of the Arabidopsis floral-repressor locusFLOWERING LOCUS C (FLC). The insertion-mutation augments the environmental sensitivity ofFLCby affecting the balance between coding and non-coding transcript isoforms in response to environmental threads. We show that this balance is modulated epigenetically by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatin. The stress-sensitive allele ofFLChas recently spread across populations subjected to recurrent chemical weeding, and we demonstrate that retrotransposon-driven acceleration of life cycle represents a rapid response to herbicide. Our findings illustrate how retrotransposition can create environmentally-sensitive alleles that facilitate adaptation to anthropogenic disturbances of the environment.
Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via beta-Klotho and Perilipin 2
Authors: Tzur Yonat , Winek Katarzyna , Madrer Nimrod , Dubnov Serafima , Bennett Estelle R , Greenberg David S , Hanin Geula , Gammal Asaad , Tam Joseph , Arkin Isaiah T , Paldor Iddo , Soreq Hermona
Published: September 2023

Non-alcoholic fatty liver disease (NAFLD) involves hepatic accumulation of intracellular lipid droplets via incompletely understood processes. Here, we report distinct and cooperative NAFLD roles of LysTTT-5'tRF transfer RNA fragments and microRNA miR-194-5p. Unlike lean animals, dietary-induced NAFLD mice showed hepatic co-declined LysTTT-5'tRF and miR-194-5p levels, restored following hepatic steatosis-suppressing miR-132 antisense oligonucleotide treatment. Moreover, exposing human-derived Hep G2 cells to oleic acid for 7 days co-suppressed miR-194-5p and LysTTT-5'tRF levels while increasing lipid accumulation. Importantly, transfecting fattened cells with a synthetic LysTTT-5'tRF mimic elevated the metabolic regulator beta-Klotho mRNA levels while declining triglyceride amounts by 30% within 24 hours. In contradistinction, antisense suppression of miR-194-5p induced accumulation of its novel target, the NAFLD-implicated lipid droplet-coating PLIN2 protein. Further, two out of 15 steatosis-alleviating screened drug repurposing compounds, Danazol and Latanoprost elevated miR-194-5p or LysTTT-5'tRF levels. The different yet complementary roles of miR-194-5p and LysTTT-5'tRF offer new insights into the complex roles of small non-coding RNAs and the multiple pathways involved in NAFLD pathogenesis.
Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering
Authors: Nguyen Ha-Ngoc-Anh , Sharp Liam , Lyman Edward , Saenz James P
Published: September 2023

The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the thermodynamic ordering of lipids. Most Eukaryotes employ sterols, which are uniquely capable of modulating lipid order to decouple membrane stability from fluidity. Ancient sterol analogues known as hopanoids are found in many bacteria and are proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. We reveal that both hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid’s acyl chain. We find that cholesterol and diplopterol’s methyl group distributions lead to distinct effects on unsaturated lipids. InMesoplasma florum, diplopterol’s constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest cholesterol’s broader lipid ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.
Brain-wide human oscillatory LFP activity during visual working memory
Authors: Singh Balbir , Wang Zhengyang , Madiah Leen M. , Gatti S. Elizabeth , Fulton Jenna N. , Johnson Graham W. , Li Rui , Dawant Benoit M. , Englot Dario J. , Bick Sarah K. , Roberson Shawniqua Williams , Constantinidis Christos
Published: September 2023

Oscillatory activity is thought to be a marker of cognitive processes, although its role and distribution across the brain during working memory has been a matter of debate. To understand how oscillatory activity differentiates tasks and brain areas in humans, we recorded local field potentials (LFPs) in 12 adults as they performed visual-spatial and shape-matching memory tasks. Tasks were designed to engage working memory processes at a range of delay intervals between stimulus delivery and response initiation. LFPs were recorded using intracranial depth electrodes implanted to localize seizures for management of intractable epilepsy. Task-related LFP power analyses revealed an extensive network of cortical regions that were activated during the presentation of visual stimuli and during their maintenance in working memory, including occipital, parietal, temporal, insular, and prefrontal cortical areas, and subcortical structures including the amygdala and hippocampus. Across most brain areas, the appearance of a stimulus produced broadband power increase, while gamma power was evident during the delay interval of the working memory task. Notable differences between areas included that occipital cortex was characterized by elevated power in the high gamma (100-150 Hz) range during the 500 ms of visual stimulus presentation, which was less pronounced or absent in other areas. A decrease in power centered in beta frequency (16-40 Hz) was also observed after the stimulus presentation, whose magnitude differed across areas. These results reveal the interplay of oscillatory activity across a broad network, and region-specific signatures of oscillatory processes associated with visual working memory.
A Multi-Layered Computational Structural Genomics Approach Enhances Domain-Specific Interpretation of Kleefstra Syndrome Variants in EHMT1
Authors: Chi Young-In , Jorge Salomão D. , Jensen Davin R. , Smith Brian C. , Volkman Brian F. , Mathison Angela J. , Lomberk Gwen , Zimmermann Michael T. , Urrutia Raul
Published: September 2023

This study investigates the functional significance of assorted variants of uncertain significance (VUS) in euchromatic histone lysine methyltransferase 1 (EHMT1), which is critical for early development and normal physiology. EHMT1 mutations cause Kleefstra syndrome and are linked to various human cancers. However, accurate functional interpretation of these variants are yet to be made, limiting diagnoses and future research. To overcome this, we integrate conventional tools for variant calling with computational biophysics and biochemistry to conduct multi-layered mechanistic analyses of the SET catalytic domain of EHMT1, which is critical for this protein function. We use molecular mechanics and molecular dynamics (MD)-based metrics to analyze the SET domain structure and functional motions resulting from 97 Kleefstra syndrome missense variants within this domain. Our approach allows us to classify the variants in a mechanistic manner into SV (Structural Variant), DV (Dynamic Variant), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). Our findings reveal that the damaging variants are mostly mapped around the active site, substrate binding site, and pre-SET regions. Overall, we report an improvement for this method over conventional tools for variant interpretation and simultaneously provide a molecular mechanism of variant dysfunction.
Spatial landscape of malignant pleural and peritoneal mesothelioma tumor immune microenvironment
Authors: Ma Xiaojun , Lembersky David , Kim Elena S , Bruno Tullia C , Testa Joseph R. , Osmanbeyoglu Hatice U
Published: September 2023

Immunotherapies have shown modest clinical benefit thus far for malignant mesothelioma (MM). A deeper understanding of immune cell spatial distribution within the tumor immune microenvironment (TIME) is needed to identify interactions between tumor and different immune cell types that might impact the effectiveness of potential immunotherapies. We performed multiplex immunofluorescence (mIF) using tissue microarrays (TMAs, n=3) of samples from patients with malignant peritoneal (n=25) and pleural (n=88) mesothelioma (MPeM and MPM, respectively) to elucidate the spatial distributions of major immune cell populations and their association with LAG3, BAP1, NF2, and MTAP expression, the latter as a proxy for CDKN2A/B. We also analyzed the relationship between the spatial distribution of major immune cell types with MM patient prognosis and clinical features. The distribution of immune cells within the TIME is similar between MPM and MPeM. However, there is a higher level of interaction between immune cells and tumor cells in MPM than MPeM. Within MPM tumors, there is increased amount of interaction between tumor cells and CD8+T cells in BAP1-low than in BAP1-high expressing tumors. The cell-cell interactions identified in this investigation have potential implications for the immune response against MM tumors and could be a factor in the different behaviors of MPM and MPeM. Our findings provide a valuable resource for the MM cancer research community and exemplifies the utility of spatial resolution within single-cell analyses.

Our mesothelioma spatial atlas mIF dataset is available athttps://mesotheliomaspatialatlas.streamlit.app/.
CRISPR-COPIES: Anin silicoplatform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration
Authors: Boob Aashutosh Girish , Zhu Zhixin , Intasian Pattarawan , Jain Manan , Petrov Vassily Andrew , Tan Shih-I , Xun Guanhua , Zhao Huimin
Published: September 2023

The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, aCOmputationalPipeline for theIdentification of CRISPR/Cas-facilitated intEgrationSites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and a human cell line. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals and support human gene and cell therapy applications.

Graphical abstract

Overview and application of CRISPR-COPIES in the field of biotechnology.
Flexible Methods for Standard Error Calculation in digital PCR Experiments
Authors: Chen Yao , De Spiegelaere Ward , Trypsteen Wim , Gleerup David , Vandesompele Jo , Thas Olivier
Published: September 2023

Digital PCR (dPCR) is a highly accurate and precise technique for the quantification of target nucleic acid(s) in a biological sample. This digital quantification relies on the binomial or Poisson distribution to estimate the amount of target molecules based on positive and negative partitions. However, the implementation of these distributions require adherence to underlying assumptions that are often neglected, leading to a suboptimal (too optimistic) variance estimation of the target concentration, especially when considering the multiple sources of variation in experimental dPCR setups. Moreover, these parametric methods cannot be easily used for downstream statistical inference when more advanced analysis are required, such as for copy number variation.

We evaluated the performance of three new statistical methods (BootsVar, NonPVar, BinomVar) in both simulations and real-life datasets for target and variance estimation in dPCR setups while taking into account a combination of commonly observed sources of experimental variability that can interfere with the underlying assumptions of the current parametric methods.

The results demonstrate the capability of the new methods for variance estimation and present a more accurate reflection of the true variability over the classical binomial approach. In addition, these statistical methods are flexible and generic in the way that they work well for the variance estimation of non-linear statistics that work with ratios (e.g. CNV) and for multiplex dPCR setups.

In this study, we provide guidelines when to use the binomial-assumption based methods and when the non-parametric one is better to achieve more accurate variance estimates.
Distilling Mechanistic Models From Multi-Omics Data
Authors: Erwin Samantha , Fletcher Joshua R. , Sweeney Daniel C. , Theriot Casey M. , Lanzas Cristina
Published: September 2023

High-dimensional multi-omics data sets are increasingly accessible and now routinely being generated as part of medical and biological experiments. However, the ability to infer mechanisms of these data remains low due to the abundance of confounding data. The gap between data generation and interpretation highlights the need for strategies to harmonize and distill complex multi-omics data sets into concise, mechanistic descriptions. To this end, a four-step analysis approach for multiomics data is herein demonstrated, comprising: filling missing data and harmonizing data sources, inducing sparsity, developing mechanistic models, and interpretation. This strategy is employed to generate a parsimonious mechanistic model from high-dimensional transcriptomics and metabolomics data collected from a murine model ofClostridioides difficileinfection. This approach highlighted the role of the Stickland reactor in the production of toxins during infection, in agreement with recent literature. The methodology present here is demonstrated to be feasible for interpreting multi-omics data sets and it, to the authors knowledge, one of the first reports of a successful implementation of such a strategy.
Bibliometric and visualized mapping: two decades of lipidomics, with special focus on pregancy and women
Authors: Zhang Lin , Zhou Ying , Zhou Jiashun
Published: September 2023

To perform a bibliometric visualization in lipidomics-related research with two decades. The primary data was retrieved from the Web of Science, three sotwares (VOSviewer, CiteSpace, and R) provided an overview of this field. The countries, institutions, authors, key terms, and keywords were tracked and corresponding mapping was generated. From January 1st in 2001 to March 21th in 2022, 45,325 authors from 234 organizations in 101 countries published 7,338 publications in 382 journals were found.Journal of Lipid Researchwas the most productive (284 publications) and highly cited journal (18,293 citations). We clustered four keywords themes. The niche theme were shotgun lipidomics, tandem mass-spectrometry, and electrospray-ionization. The motor theme were expression, diseases, and inflammation. The emerging or decling theme were identification, mass-spectrometry, and fatty acids.The basic theme were metabolism, cell, and plasma. Though eight categories the lipid were classified, the keywords showed two of which were got more attention for research, fatty acyls and glycerophospholipids. The top 3 lipidomics-favoured diseases were insulin resistance, obesity, and Alzheimer’s disease. The top 3 lipidomics-favoured tissue was plasma, brain, and adipose tissue. Burst citations show “women” and “pregnancy” with the strength of 8.91 and 7.1, both topics may be a potential hotspot in the future.
Involvement of the splicing factor SART1 in the BRCA1-dependent homologous recombination repair of DNA double-strand breaks
Authors: Yamauchi Motohiro , Kato Reona , Yasuhara Takaaki , Uchihara Yuki , Hirakawa Miyako , Ozaki Kie , Abe Yu , Shibata Hiroki , Kawabata-Iwakawa Reika , Shakayeva Aizhan , Kot Palina , Miyagawa Kiyoshi , Suzuki Keiji , Shibata Atsushi , Matsuda Naoki
Published: September 2023

Although previous studies have reported that pre-mRNA splicing factors (SFs) are involved in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR), their exact role in promoting HR remains poorly understood. Here, we showed that SART1, an SF upregulated in several types of cancer, promotes DSB end resection, which is an essential step in HR, without affecting the expression of HR factors. In the promotion of resection, SART1 is epistatic with BRCA1, an HR factor known to promote resection. Mechanistically, SART1 cooperates with BRCA1 to counteract the resection blockade posed by 53BP1 and RIF1. Moreover, SART1 is required for recruitment of the HR-promoting portion of BRCA1 to DSBs. Laser microirradiation experiments revealed that SART1 is recruited to DSBs in a BRCA1-dependent manner, and that the arginine/serine (RS)-rich domain is required for SART1 recruitment to DSBs. We also obtained evidence that SART1 is involved in transcription-associated HR together with BRCA1. Furthermore, chromosome analysis demonstrated that SART1 and BRCA1 epistatically suppressed genomic alterations caused by DSB misrepair in the G2 phase. Collectively, these results indicate that SART1 and BRCA1 cooperatively facilitate resection of DSBs arising in transcriptionally active genomic regions, thereby promoting faithful HR repair of such DSBs and suppressing genome instability.
SpatialPrompt: spatially aware scalable and accurate tool for spot deconvolution and clustering in spatial transcriptomics
Authors: Swain Asish Kumar , Pandit Vrushali , Sharma Jyoti , Yadav Pankaj
Published: September 2023

Spatial transcriptomics has advanced our understanding of tissue biology by enabling sequencing while preserving spatial coordinates. In sequencing-based spatial technologies, each measured spot typically consists of multiple cells. Deconvolution algorithms are required to decipher the cell-type distribution at each spot. Existing spot deconvolution algorithms for spatial transcriptomics often neglect spatial coordinates and lack scalability as datasets get larger. We introduce SpatialPrompt, a spatially aware and scalable method for spot deconvolution as well as domain identification for spatial transcriptomics. Our method integrates gene expression, spatial location, and single-cell RNA sequencing (scRNA-seq) reference data to infer cell-type proportions of spatial spots accurately. At the core, SpatialPrompt uses non-negative ridge regression and an iterative approach inspired by graph neural network (GNN) to capture the local microenvironment information in the spatial data. Quantitative assessments on the human prefrontal cortex dataset demonstrated the superior performance of our tool for spot deconvolution and domain identification. Additionally, SpatialPrompt accurately decipher the spatial niches of the mouse cortex and the hippocampus regions that are generated from different protocols. Furthermore, consistent spot deconvolution prediction from multiple references on the mouse kidney spatial dataset showed the impressive robustness of the tool. In response to this, SpatialPromptDB database is developed to provide compatible scRNA-seq references with cell-type annotations for seamless integration. In terms of scalability, SpatialPrompt is the only method performing spot deconvolution and clustering in less than 2 minutes for large spatial datasets with 50,000 spots. SpatialPrompt tool along with the SpatialPromptDB database are publicly available as open sourcesoftwarefor large-scale spatial transcriptomics analysis.
The hydrogen-bond network in sodium chloride tridecahydrate: analogy with ice VI
Authors: Yamashita Keishiro , Nakayama Kazuya , Komatsu Kazuki , Ohhara Takashi , Munakata Koji , Hattori Takanori , Sano-Furukawa Asami , Kagi Hiroyuki
Published: September 2023

The structure of a recently found hyperhydrated form of sodium chloride (NaCl·13H2O and NaCl·13D2O) has been determined by in
situ single-crystal neutron diffraction at 1.7 GPa and 298 K. It has large hydrogen-bond networks and some water molecules have distorted bonding features such as bifurcated hydrogen bonds and five-coordinated water molecules. The hydrogen-bond network has similarities to ice VI in terms of network topology and disordered hydrogen bonds. Assuming the equivalence of network components connected by pseudo-symmetries, the overall network structure of this hydrate can be expressed by breaking it down into smaller structural units which correspond to the ice VI network structure. This hydrogen-bond network contains orientational disorder of water molecules in contrast to the known salt hydrates. An example is presented here for further insights into a hydrogen-bond network containing ionic species.