bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and application of an algorithm for statin-induced myopathy based on electronic health record-derived structured elements
Authors: Oni-Orisan Akinyemi , Lu Meng , Peng Jonathan A. , Krauss Ronald M. , Iribarren Carlos , Medina Marisa W.
Published: April 2023

Objective

Considering the non-specific nature of muscle symptoms, studies of statin-induced myopathy (SIM) in electronic health records require accurate algortihms that can reliably identify true statinrelated cases. However, prior algorithms have been constructed in study populations that preclude broad applicability. Here we developed and validated an algorithm that accurately defines SIM from electronic health records using structured data elements and conducted a study of determinants of SIM after applying the algorithm.

Materials and Methods

We used electronic records from an integrated health care delivery system (including comprehensive pharmacy dispensing records) and defined SIM as elevated creatine kinase (CK) ≥4 x upper limit of normal. A diverse cohort of participants receiving a variety of statin regimens met the criteria for study inclusion.

Results

We identified multiple conditions strongly associated with elevated CK independent of statin use. A 2-step algorithm was developed using these all-cause conditions as secondary causes (step 1) along with evidence of a statin regimen change (step 2). We identified 1,262 algorithm-derived statininduced elevated CK cases. Gold standard SIM cases determined from manual chart reviews on a random subset of the all-cause elevated CK cases were used to validate the algorithm, which had a 76% sensitivity and 77% specificity for detecting the most certain cases. Pravastatin use was associated with a 2.18 odds (95% confidence interval 1.39-3.40, P=0.0007) for statin-induced CK elevation compared to lovastatin use after adjusting for dose and other factors.

Conclusions

We have produced an efficient, easy-to-apply methodological tool that can improve the quality of future research on statin-induced myopathy.
Stratigraphic distribution of ammonoids and other macrofossils from the upper Albian–lower Cenomanian interval in Putumayo, Colombia, northern South America: new data for mid-Cretaceous basin correlation
Authors: Luque Javier , Bustos Jonatan , Beltrán-Triviño Alejandro , Rodriguez Angie , Delgado Alexandra , Sanchez Johan M. , Caraballo Julián , Paez-Reyes Manuel , López-Horgue Mikel A.
Published: April 2023

Despite the rich paleontological heritage of Colombia, in the equatorial Neotropics, one of the least explored regions in terms of its fossil record is the Putumayo region near Ecuador, largely due to its considerable ground cover, thick vegetation, rock weathering, geographic remoteness, and overall inaccessibility to well-exposed outcrops. This precludes detailed comparisons with neighboring basins, and thus the generation of more comprehensive biostratigraphic correlations for western northern South America and other paleobiogeographic regions, e.g., Mediterranean Tethys, northern Africa, Western Interior Basin. Here, we report 67 occurrences of mid- Cretaceous ammonoids and other macrofossils (e.g., bivalves, decapod crustaceans, fish remains, plant remains), from the middle Albian of the uppermost Caballos Formation and the upper Albian–lower Cenomanian of the lower Villeta Formation, collected in-situ from a stratigraphic section cropping out on the Mocoa–San Francisco road in the Department of Putumayo, Colombia. Among the ammonoid taxa recovered are several morphotypes assignable to ?Schloenbachiasp., cf.Engonocerassp.,Oxytropidoceras(Venezoliceras) sp.,Oxytropidoceras(Laraiceras) sp., cf.Oxytropidocerassp.,Mortoniceras(Mortoniceras) cf.vespertinum,Mortoniceras(Mortoniceras) sp.,Algericerassp.,Hysterocerassp. 1,Hysterocerassp. 2, cf,Hysterocerassp., cf.Forbesicerassp.,Graysonitessp.,Hamitessp., and two isolated aptychi. The occurrence of the ammonoid generaOxytropidoceras,Mortoniceras, andSchloenbachia, suggest interconnection of the Putumayo Basin during the mid-Cretaceous with the Upper Magdalena Valley in Colombia and the Oriente Basin in Ecuador, which, together with the rest of the ammonoid assemblage, provide biostratigraphic data to define the upper Albian–lower Cenomanian in the basin and thus in northwestern South America.
Evaluating the efficiency and accuracy of a commercial test for estimating genetic risk of bovine congestive heart failure
Authors: Carlson Jaden M. , Heaton Michael P. , Allison Nathan , Hangman Alyssa , Petrik Dustin , Piscatelli Heather , Vander Ley Brian L.
Published: April 2023

Background

Bovine congestive heart failure (BCHF) is a significant cause of death in feedlot cattle in the Western Great Plains of North America. Single nucleotide polymorphisms (SNPs) in theARRDC3andNFIAgenes have been previously associated with BCHF and genetic tests can classify animals by their risk for disease. Here, our aims were to evaluate the efficiency (genotypes obtained / samples tested) of a rapid DNA extraction kit and the accuracy of a 2-SNP assay for BCHF risk.

Methods

Skin biopsies from 100 cattle were randomized and extracted with a proprietary rapid DNA extraction kit. A custom duplex, combined sequence amplification and nucleotide detection (C-SAND) assay was developed and run once on a commercial thermocycling machine to determine the genotypes. Both the rapidly extracted DNA and highly purified reference DNA from the same individuals were genotyped with the 2-SNP assay by operators blinded to the sample identity. The C-SAND genotypes were compared to known genotypes derived from a bead array assay.A prioristandards for missing and incorrect genotypes were set at less than 3% and 1%, respectively.

Results

When using reference DNA samples, there were no missing and no incorrect C-SAND-derived genotypes, meeting thea prioristandards. When DNA samples from the rapid extraction kit were used, genotypes were not determined for 5% of the samples. Of the 95 samples successfully extracted, there were 0% and 3% incorrect genotypes for the respectiveARRDC3andNFIASNPs.

Conclusions

This duplex C-SAND assay and thermocycling machine combination were efficient and accurate when reference DNA was used, meetinga prioristandards. Although the reduced efficiency of the rapid extraction kit can be overcome by repeated testing, increased genotype errors present an important issue. Despite these challenges, this rapid extraction kit and assay can be a reasonable tool for producers to select animals with reduced BCHF risk.
Females exhibit smaller volumes of brain activation and lower inter-subject variability during motor tasks
Authors: Andrushko Justin W. , Rinat Shie , Kirby Eric D. , Dahlby Julia , Ekstrand Chelsea , Boyd Lara A.
Published: April 2023

Past work has shown that brain structure and function differ between females and males. Males have larger cortical and sub-cortical volume and surface area (both total and subregional), while females have greater cortical thickness in most brain regions. Functional differences are also reported in the literature, yet to date little work has systematically considered whether patterns of brain activity indexed with functional magnetic resonance imaging (fMRI) differ between females and males. Recently, an attempt to modernize and improve our understanding of the homunculus, a somatotopic representation of the human body within the brain, was made. Still, in the decades since it was introduced, no research has considered sex differences in the somatotopic representation. The current study sought to remediate this issue by employing brain somatotopic motor mapping from a previously published and openly available dataset. We tested differences in patterns of functional brain activity associated with 12 voluntary movement patterns in females versus males. Results suggest that females exhibited smaller volumes of brain activation across all 12 movement tasks, and lower patterns of variability in 10 of the 12 movements. We also observed that females had greater cortical thickness, which is in alignment with previous analyses of structural differences. Overall, these findings provide a basis for considering biological sex in future fMRI research and provide a foundation of understanding differences in how neurological pathologies present in females vs males.
Capture-recapture for -omics data meta-analysis
Authors: Juodakis Julius
Published: April 2023

One of the major goals of modern -omics studies, in particular genome-wide association studies (GWASs), is to understand the polygenicity of various traits, i.e. the number of genetic factors causally determining them. Analogous measures could also be used to estimate the number of trait markers from non-genetic studies, such as proteomics or transcriptomics.

Here, we describe how capture-recapture (C-R) models, originating in animal ecology, can be applied to this task. Our approach works by comparing the lists of trait-associated genes (or other markers) from several studies. In contrast to existing methods, C-R is specifically designed to make use of heterogeneous input studies, differing in analysis methods, populations or other factors: it extrapolates from their variability to estimate how many causal genes still remain undetected.

We present a brief tutorial on C-R models, and demonstrate our proposed usage of it with code examples and simulations. We then apply it to GWASs and proteomic studies of preterm birth, a major clinical problem with largely unknown causes. The C-R estimates a relatively low number of causal genes for this trait, but many still undetected protein markers, suggesting that diverse environmentally-initiated pathways can lead to this clinical outcome.
Inhibitor-based modulation of huntingtin aggregation mechanisms mitigates fibril-induced cellular stress
Authors: Jain Greeshma , Trombetta-Lima Marina , Matlahov Irina , Taborda Ribas Hennrique , Chen Tingting , Parlato Raffaella , Portale Giuseppe , Dolga Amalia M. , van der Wel Patrick C.A.
Published: April 2023

Huntington’s disease (HD) is a neurodegenerative disorder in which mutated fragments of the huntingtin protein (Htt) undergo misfolding and aggregation. Since misfolded and aggregated proteins can cause cellular stress and cytotoxicity, there is an interest in the development of small molecule aggregation inhibitors as potential modulators of HD pathogenesis. Here, we study how a polyphenol modulates the aggregation mechanism of huntingtin exon 1 (HttEx1) even at sub-stoichiometric ratios. Sub-stoichiometric amounts of curcumin impacted the primary and/or secondary nucleation events, extending the pre-aggregation lag phase. Remarkably, the disrupted aggregation process changed both the aggregate structure and its cell metabolic properties. When administered to neuronal cells, the ‘break-through’ protein aggregates induced a significantly reduced cellular stress compared to aggregates formed in absence of inhibitors. Structural analysis by electron microscopy, small angle X-ray scattering (SAXS), and solid-state NMR spectroscopy identified changes in the fibril structures, probing both the flanking domains that form the fuzzy coat, as well as the fibril core. The biggest changes affected the latter, which we propose to relate to the presence or absence of polyglutamine (polyQ) β-hairpin structures. Our findings highlight multifaceted consequences of small molecule inhibitors that modulate the protein misfolding landscape, with potential implications for treatment strategies in HD and other amyloid disorders.
Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum
Authors: Hu Yongfeng , He Chao , Shen Yuning , Zeng Gongjian , Bi Siteng , Huang Quanjun , Qin Xiner , Deng Zhuying , He Zhengquan , Shen Xiangling
Published: April 2023

Sorghum bicoloris a C4 plant with the characteristics of high stress tolerance, which may be conferred partly by the underlying epigenetic mechanism unique to sorghum. In this study, we revealed some epigenomic features in sorghum that have never been reported before. The long H3K27me3 regions clustered in four areas, which we defined as H3K27me3 islands, were identified in sorghum. H3K36me3 plays some role in inhibiting the deposition of both H3K27me3 and H2A.Z, which may serve as partial motivation for the removal of H3K27me3 and H2A.Z in leaf and root. All the 7 histone marks are involved in the regulation of tissue-specific genes, especially the specific expression of C4 genes in leaf and peroxidase (POD) encoding genes in root, which are involved in the photosynthesis in leaf and lignin synthesis in root, respectively. These marks except H3K36me3 and H3K27me3 also engage in the regulation of stress genes in response to PEG treatment. However, we found that differential enrichment of histone marks on many tissue-specific genes was observed only between leaf and root but hardly in response to PEG treatment, although expression of these genes changed after PEG treatment.
Integration of microbial and chemical synthesis for the efficient production of plitidepsin, a promising anticancer and antiviral agent
Authors: Zhang Haili , Hui Zhen , Cai Mingwei , Huang Shipeng , Shi Wenguang , Liang Mengdi , Lin Yang , Shen Jie , Sui Minghao , Li Xuyang , Lai Qiliang , Dou Jie , Ge Yun , Zheng Min , Shao Zongze , Luo Xiaozhou , Tang Xiaoyu
Published: April 2023

Plitidepsin, a marine-derived anticancer medicine, is being tested in phase III clinical trials for treating COVID-19. However, the current supply of plitidepsin relies on laborious chemical synthesis processes. Here, we present a new approach that combines microbial and chemical synthesis to produce plitidepsin. We screened a Tistrella strain library to identify a high-yield didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in the highest yield of didemnin B reported in the literature. Next, we developed two straightforward chemical strategies to convert didemnin B to plitidepsin, one of which involved a one-step synthetic route giving over 90% overall yield. We also synthesized two new didemnin analogues and assessed their anticancer and antiviral activities. Our findings offer a practical and sustainable solution for producing plitidepsin and its derivatives, potentially expediting didemnin drug development.
Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors
Authors: Lin Miin S. , Jo Se-Young , Luebeck Jens , Chang Howard Y. , Wu Sihan , Mischel Paul S. , Bafna Vineet
Published: April 2023

Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in which ecDNAs arise and progress, including chromosomally-driven transcription, is incompletely understood. We examined gene expression patterns of 870 tumors of varied histological types, to identify transcriptional correlates of ecDNA. Here we show that ecDNA containing tumors impact four major biological processes. Specifically, ecDNA containing tumors upregulate DNA damage and repair, cell cycle control, and mitotic processes, but downregulate global immune regulation pathways. Taken together, these results suggest profound alterations in gene regulation in ecDNA containing tumors, shedding light on molecular processes that give rise to their development and progression.
Interictal Spikes in Alzheimer’s Disease: Preclinical Evidence for Dominance of the Dentate Gyrus and Cholinergic Control by Medial Septum
Authors: Lisgaras Christos Panagiotis , Scharfman Helen E.
Published: April 2023

HIGHLIGHTS

Interictal spikes (IIS) occur in 3 mouse lines with Alzheimer’s disease features

IIS in all 3 mouse lines were most frequent during rapid eye movement (REM) sleep

The dentate gyrus showed larger IIS and earlier current sources vs. CA1 or cortex

Chemogenetic silencing of medial septum (MS) cholinergic neurons reduced IIS during REM

MS silencing did not change REM latency, duration, number of bouts or theta power

Interictal spikes (IIS) are a common type of abnormal electrical activity in Alzheimer’s disease (AD) and preclinical models. The brain regions where IIS are largest are not known but are important because such data would suggest sites that contribute to IIS generation. Because hippocampus and cortex exhibit altered excitability in AD models, we asked which areas dominate the activity during IIS along the cortical-CA1-dentate gyrus (DG) dorso-ventral axis. Because medial septal (MS) cholinergic neurons are overactive when IIS typically occur, we also tested the novel hypothesis that silencing the MS cholinergic neurons selectively would reduce IIS.

We used mice that simulate aspects of AD: Tg2576 mice, presenilin 2 (PS2) knockout mice and Ts65Dn mice. To selectively silence MS cholinergic neurons, Tg2576 mice were bred with choline-acetyltransferase (ChAT)-Cre mice and offspring were injected in the MS with AAV encoding inhibitory designer receptors exclusively activated by designer drugs (DREADDs). We recorded local field potentials along the cortical-CA1-DG axis using silicon probes during wakefulness, slow-wave sleep (SWS) and rapid eye movement (REM) sleep.

We detected IIS in all transgenic or knockout mice but not age-matched controls. IIS were detectable throughout the cortical-CA1-DG axis and occurred primarily during REM sleep. In all 3 mouse lines, IIS amplitudes were significantly greater in the DG granule cell layer vs. CA1 pyramidal layer or overlying cortex. Current source density analysis showed robust and early current sources in the DG, and additional sources in CA1 and the cortex also. Selective chemogenetic silencing of MS cholinergic neurons significantly reduced IIS rate during REM sleep without affecting the overall duration, number of REM bouts, latency to REM sleep, or theta power during REM. Notably, two control interventions showed no effects.

Consistent maximal amplitude and strong current sources of IIS in the DG suggest that the DG is remarkably active during IIS. In addition, selectively reducing MS cholinergic tone, at times when MS is hyperactive, could be a new strategy to reduce IIS in AD.
Supramolecular ‘catch-and-release’ strategy for bioorthogonal fluorogenic imaging across the visible spectrum
Authors: Sasmal Ranjan , Som Arka , Kumari Pratibha , Pahwa Meenakshi , Saha Nilanjana Das , Rao Sushma , Vasu Sheeba , Agasti Sarit S.
Published: April 2023

Fluorogenic probes that unmask fluorescence signals in response to a bioorthogonal reaction are a powerful new addition to biological imaging. They can provide significantly reduced background fluorescence and minimize non-specific signals, potentially allowing real-time high-contrast imaging without washing out excess fluorophores. While diverse classes of highly refined synthetic fluorophores are readily available now, their integration into a bioorthogonal fluorogenic scheme still necessitates another level of extensive design efforts and customized structural alterations to optimize quenching mechanisms for each given fluorophore scaffold. Herein, we present an easy-to-implement and highly generalizable supramolecular ‘catch-and-release’ strategy for generating an efficient bioorthogonal fluorogenic response from essentially any readily available fluorophores without further structural alterations. We designed this distinct strategy based on the macrocyclic cucurbit[7]uril (CB7) host, where a fluorogenic response is achieved by programming a guest displacement reaction from the macrocycle cavity. We used this strategy to rapidly generate fluorogenic probes across the visible spectrum from structurally diverse classes of fluorophore scaffolds, including coumarin, bodipy, rhodamine, and cyanine. These probes were applied to no-wash fluorogenic imaging of various target molecules in live cells and tissue with minimal background and no appreciable non-specific signal. Notably, the orthogonal reactivity profile of the system allowed us to pair this host-guest fluorogenic probe with the covalently clickable fluorogenic probe to achieve high-contrast super-resolution and multiplexed fluorogenic imaging in cells and tissue.
Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology
Authors: Castano Anna , Silvestre Margaux , Wells Carrow I. , Sanderson Jennifer L. , Ferrer Carla A. , Ong Han Wee , Liang Yi , Richardson William , Silvaroli Josie A. , Bashore Frances M. , Smith Jeffery L. , Genereux Isabelle M. , Dempster Kelvin , Drewry David H. , Pabla Navjot S. , Bullock Alex N. , Benke Tim A. , Ultanir Sila K. , Axtman Alison D.
Published: April 2023

Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD have indicated that CDKL5 kinase function is central to disease pathology.CDKL5encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further,Cdkl5knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces post-synaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated, key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity and human neuropathology.
Repurposing the atypical Type I-G CRISPR system for bacterial genome engineering
Authors: Shangguan Qilin , White Malcolm F
Published: April 2023

The CRISPR-Cas system functions as a prokaryotic immune system and is highly diverse, with six major types and numerous sub-types. The most abundant are type I CRISPR systems, which utilise a multi-subunit effector, Cascade, and a CRISPR RNA (crRNA) to detect invading DNA species. Detection leads to DNA loading of the Cas3 helicase-nuclease, leading to long range deletions in the targeted DNA, thus providing immunity against mobile genetic elements (MGE). Here, we focus on the type I-G system, a streamlined, 4- subunit complex with an atypical Cas3 enzyme. We demonstrate that Cas3 helicase activity is not essential for immunity against MGEin vivoand explore applications of theThioalkalivibrio sulfidiphilusCascade effector for genome engineering inEscherichia coli. Long range, bidirectional deletions were observed when thelacZgene was targeted. Deactivation of the Cas3 helicase activity dramatically altered the types of deletions observed, with small deletions flanked by direct repeats that are suggestive of microhomology mediated end joining. When donor DNA templates were present, both the wild-type and helicase deficient systems promoted homology-directed repair (HDR), with the latter system providing improvements in editing efficiency, suggesting that a single nick in the target site may promote HDR inE. coliusing the type I-G system. These findings open the way for further application of the type I-G CRISPR systems in genome engineering.
On growth and form of the mammary gland: Mesenchyme instructs growth while epithelium directs branching
Authors: Lan Qiang , Trela Ewelina , Lindström Riitta , Satta Jyoti , Kaczyńska Beata , Christensen Mona M. , Holzenberger Martin , Jernvall Jukka , Mikkola Marja L.
Published: April 2023

Mammary gland is a unique organ that undergoes dynamic alterations throughout a female’s reproductive life, making it an ideal model for developmental, stem cell and cancer biology research. Mammary gland development beginsin uteroand proceeds via a quiescent bud stage before the initial outgrowth and subsequent branching morphogenesis. How mammary epithelial cells transit from quiescence to an actively proliferating and branching tissue during embryogenesis and, importantly, how the branch pattern is determined remain largely unknown. Here we provide evidence indicating that epithelial cell proliferation, segregation into basal and luminal lineages that characterize the postnatal mammary duct, and onset of branching are independent processes, yet partially coordinated by the Eda signaling pathway. By performing heterotypic and heterochronic epithelial-mesenchymal recombination experiments between mammary and salivary gland tissues andex vivolive imaging, we demonstrate that unlike previously concluded, the mode of branching is an intrinsic property of the mammary epithelium while the growth pace and density of the mammary ductal tree are governed by the mesenchyme. Transcriptomic profiling andex vivoandin vivofunctional studies disclose that mesenchymal Wnt/ß-catenin signaling, and in particular IGF-1 downstream of it critically regulate mammary gland growth. These results underscore the general need to carefully decompose the different developmental processes producing branched organs.
The evolution of multi-component weapons in the superfamily of leaf-footed bugs
Authors: Miller Christine W. , Kimball Rebecca T. , Forthman Michael
Published: April 2023

Sexually selected weapons, such as the antlers of deer, claws of crabs, and tusks of beaked whales, are strikingly diverse across taxa and even within groups of closely related species. Phylogenetic comparative studies have typically taken a simplified approach to investigating the evolution of weapon diversity, examining the gains and losses of entire weapons, major shifts in size or type, or changes in location. Less understood is how individual weapon components evolve and assemble into a complete weapon. We addressed this question by examining weapon evolution in the diverse, multi-component hind-leg and body weapons of leaf-footed bugs, Superfamily Coreoidea (Hemiptera: Heteroptera). Male leaf-footed bugs use their weapons to fight for access to mating territories. We used a large multilocus dataset comprised of ultraconserved element loci for 248 species and inferred evolutionary transitions among component states using ancestral state estimation. We found that weapons added components over time with some evidence of a cyclical evolutionary pattern — gains of components followed by losses and then gains again. Further, we found that certain trait combinations evolved repeatedly across the phylogeny. This work reveals the remarkable and dynamic evolution of weapon form in the leaf-footed bugs. It also highlights that multi-component weapons may be especially useful in providing insights into the evolutionary interplay of form and function.

TEASER TEXT

For centuries, humans have been fascinated by the morphological weapons animals use to engage in battle. The diversity of sexually selected weapons is surprising, with considerable variation across even closely related groups of animals. Studies are needed that take a detailed view of the components that comprise weapons and the evolutionary assembly of these components into a complete structure. Here, we reconstruct the evolution of a multi-component weapon in a superfamily of insects. Male leaf-footed bugs use spiky, enlarged hind legs to wrestle over mating territories. We measured 15 putative weapon components across 248 species, using phylogenetic comparative analyses. We found that the number of weapon components generally increased over time, with many gains and losses of components along the way. We found that certain components were more likely to evolve with others, suggesting that specific trait combinations might be especially functional in battle. This work highlights that evolutionary studies of complex, multi-component weapons may be useful for reconstructing the evolutionary assembly of weapons and the interplay of form and function.
Disrupting microglial TGF-β signaling triggers region-specific pathology in the spinal cord
Authors: Zhu Keying , Min Jin-Hong , Joshua Vijay , Liu Yun , Pieber Melanie , Suerth Valerie , Sarlus Heela , Harris Robert , Lund Harald
Published: April 2023

Transforming growth factor-β (TGF-β) signaling is critical for microglial maturation during development and the maintenance of microglial homeostasis in adulthood. It remains unclear whether regional susceptibilities to the loss of TGF-β signaling in microglia also exist, and the contributing factors have yet to be identified. We find that deletion ofTgfbr2on microglia leads to microglial activation and demyelination in mouse spinal cords, primarily in the dorsal column (DC).Tgfbr2-deficient microglia exhibit distinct transcriptomic changes, and those sorted from the DC display a more proinflammatory profile compared to those from the ventral column (VC) and grey matter (GM). Single nucleus RNA sequencing (snRNA-seq) of the spinal cord uncovers a microglial subtype that emerges exclusively followingTgfbr2deletion (termed TGFβ signaling-suppressed microglia, TSM), exhibiting high expression ofMmp12, Gpnmb, Lgals3, Mgll, and Alcam,predominantly located in the DC. Phenotypically, disruption of microglial TGF-β signaling results in behavioral deficits that are more severe in female and older mice, whereas young male mice are less affected. Mechanistically, we reveal a significantly higher level of TGF-β1/TGFBR2 in the spinal cords of normal older mice compared to the young mice, with the DC region richer in genes of the TGF-β signaling pathway than the VC and GM regions. This indicates that older mice and the DC region require more TGFβ1 to maintain tissue homeostasis and, reciprocally, are more responsive and sensitive to the disruption of TGF-β signaling in microglia. Herein, we report a demyelinating disease with region-specificity and its susceptibility to the loss of microglial TGF-β signaling with gender and age differences. Our findings contribute valuable information to our understanding of the importance of microglia in regulating myelin health, especially during the aging process.
RavA-ViaA linksVibrio choleraeCpx- and Zra2- envelope stress to antibiotic response
Authors: Krin Evelyne , Carvalho André , Lang Manon , Babosan Anamaria , Mazel Didier , Baharoglu Zeynep
Published: April 2023

RavA-ViaA were reported to play a role in aminoglycoside sensitivity but the mechanisms remain elusive. Here, we performed competition and survival experiments to confirm that deletion ofravA-viaAincreases tolerance of the Gram-negative pathogenVibrio choleraeto low and high aminoglycoside concentrations, during aerobic growth. Using high throughput strategies in this species, we identify Cpx and Zra2 two-component systems as new partners of RavA-ViaA. We show that the aminoglycoside tolerance ofΔravviarequires the presence of these membrane stress sensing two-component systems. We propose that deletion of the RavA-ViaA function facilitates the response aminoglycosides because of a pre-activated state of Cpx and Zra2 membrane stress response systems. We also find an impact of these genes on polymyxin B sensitivity and vancomycin resistance, and we show that simultaneous inactivation ofravviafunction together with envelope stress response systems leads to outer membrane permeabilization. Vancomycin is mostly used for Gram-positive because of its low efficiency for crossing the Gram-negative outer membrane. Targeting of theravA-viaAoperon for inactivation could be a future strategy to allow uptake of vancomycin into multidrug resistant Gram-negative bacteria.
Leptin activation of dorsal raphe neurons inhibits feeding behavior
Authors: Maxwell N.D. , Smiley C.E. , Sadek A.T. , Loyo-Rosado F.Z. , Giles D.C. , Macht V.A. , Woodruff J.L. , Taylor D.L. , Wilson S.P. , Fadel J.R. , Reagan L.P. , Grillo C.A.
Published: April 2023

Leptin is a homeostatic regulatory element that signals the presence of energy stores -in the form of adipocytes-which ultimately reduces food intake and increases energy expenditure. Similarly, serotonin (5-HT), a signaling molecule found in both the central and peripheral nervous systems, also regulates food intake. Here we use a combination of pharmacological manipulations, optogenetics, retrograde tracing, andin situhybridization, combined with behavioral endpoints to physiologically and anatomically identify a novel leptin-mediated pathway between 5-HT neurons in the dorsal raphe nucleus (DRN) and hypothalamic arcuate nucleus (ARC) that controls food intake. In this study, we show that microinjecting leptin directly into the DRN reduces food intake in male Sprague-Dawley rats. This effect is mediated by leptin-receptor expressing neurons in the DRN as selective optogenetic activation of these neurons at either their ARC terminals or DRN cell bodies also reduces food intake. Anatomically, we identified a unique population of serotonergic raphe neurons expressing leptin receptors that send projections to the ARC. Finally, by utilizingin vivomicrodialysis and high-performance liquid chromatography, we show that leptin administration to the DRN increases 5-HT efflux into the ARC. Overall, this study identifies a novel circuit for leptin-mediated control of food intake through a DRN-ARC pathway, utilizing 5-HT as a mechanism to control feeding behavior. Characterization of this new pathway creates opportunities for understanding how the brain controls eating behavior, as well as opens alternative routes for the treatment of eating disorders.

Significance:

Leptin and serotonin both play a vital role in the regulation of food intake, yet there is still uncertainty in how these two molecules interact to control appetite. The purpose of this study is to further understand the anatomical and functional connections between leptin receptor expressing neurons in the dorsal raphe nucleus, the main source of serotonin, and the arcuate nucleus of the hypothalamus, and how serotonin plays a role in this pathway to reduce food intake. Insight gained from this study will contribute to a more thorough understanding of the networks that regulate food intake, and open alternative avenues for the development of treatments for obesity and eating disorders.
Target Detection Modulates EEG Spectral Correlates of Memory Encoding
Authors: Broitman Adam W. , Swallow Khena M.
Published: April 2023

The current study investigates whether changes in scalp electroencephalographic (EEG) activity over time reflect the effects of target detection and divided attention on memory encoding. We recorded EEG activity in 61 young adults as they memorized lists of words either under full attention (single-task) or while performing a secondary task (dual-task). In both cases, colored squares appeared with each word. However, in the dual-task condition participants also pressed a button when the colored squares were in a predefined color (target) but made no response when the squares were in a different color (distractor). Subsequent memory effects in the alpha (8-12 Hz) and high gamma (50-100 Hz) frequency bands changed throughout the trial, and these effects differed across conditions. Prior to word presentation, high gamma activity was associated with encoding success in the target and single-task conditions, but not in the distractor conditions. In contrast, alpha band activity decreased following word presentation, and these decreases were greater for successfully encoded words in the target condition than in the distractor or single-task conditions. The results are consistent with the view that alpha and gamma activity reflect distinct neural processes which both contribute to memory formation, but are differentially sensitive to task demands and momentary shifts in attention.
Selective Vulnerability of Layer 5a Corticostriatal Neurons in Huntington’s Disease
Authors: Pressl Christina , Mätlik Kert , Kus Laura , Darnell Paul , Luo Ji-Dung , Paul Matthew R. , Weiss Alison R. , Liguore William , Carroll Thomas S. , Davis David A. , McBride Jodi , Heintz Nathaniel
Published: April 2023

The properties of the cell types that are selectively vulnerable in Huntington’s disease (HD) cortex, the nature of somatic CAG expansions ofmHTTin these cells, and their importance in CNS circuitry have not been delineated. Here we employed serial fluorescence activated nuclear sorting (sFANS), deep molecular profiling, and single nucleus RNA sequencing (snRNAseq) to demonstrate that layer 5a pyramidal neurons are vulnerable in primary motor cortex and other cortical areas of HD donors. ExtensivemHTT-CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layer 6a, layer 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify the vulnerable layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somaticmHTT-CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in the HD cerebral cortex.
A generalizable computational mechanism underlying the interaction between momentary craving and decision-making
Authors: Kulkarni Kaustubh R. , Berner Laura A. , Rhoads Shawn A. , Fiore Vincenzo G. , Schiller Daniela , Gu Xiaosi
Published: April 2023

Substance craving and maladaptive choices are intertwined across addictive disorders. However, the computational mechanisms connecting craving and decision-making remain elusive. Here, we tested a hypothesis that momentary craving and value-based decision-making influence each other during substance-related reinforcement learning. We measured momentary craving as two groups of human participants (alcohol drinkers and cannabis users; totaln=132) performed a reinforcement learning task in which they received group-specific addictive cue or monetary rewards. Using computational modeling, we found that, across both groups, momentary craving biased learning rate related to substance-associated prediction errors (RPEs), but not monetary RPEs. Additionally, expected values and RPEs jointly influenced elicited craving across reward types and participant groups. Alcohol and cannabis users also differed in the extent to which their craving and decision-making influenced each other, suggesting important computational divergence between the two groups. Finally, regressions incorporating model-derived parameters best predicted substance use severity in the alcohol, but not cannabis group, supporting the utility of using these model-based parameters in making clinical predictions for selective substance groups. Together, these findings provide a computational mechanism for the interaction between substance craving and maladaptive choices that is generalizable across addictive domains.
Understanding natural selection in Holocene Europe using multi-locus genotype identity scans
Authors: Pandey Devansh , Harris Mariana , Garud Nandita R. , Narasimhan Vagheesh M.
Published: April 2023

Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan,G12ancient,on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.
Permethylation as a Strategy for High Molecular Weight Polysaccharide Structure Analysis by NMR – Case Study ofXylella fastidiosaEPS
Authors: Ndukwe Ikenna E. , Black Ian , Castro Claudia A. , Vlach Jiri , Heiss Christian , Roper Caroline , Azadi Parastoo
Published: April 2023

Current practices for structure analysis of extremely large molecular weight polysaccharides via solution-state NMR spectroscopy incorporate partial depolymerization protocols that enable polysaccharide solubilization in suitable solvents. Non-specific depolymerization techniques utilized for glycosidic bond cleavage, such as chemical degradation or ultrasonication, potentially generate structure fragments that can complicate the complete characterization of polysaccharide structures. Utilization of appropriate enzymes for polysaccharide degradation, on the other hand, requires prior structure information and optimal enzyme activity conditions that are not available to the analyst working with novel or unknown compounds. Herein, we describe the application of a permethylation strategy that allows the complete dissolution of the intact polysaccharides for NMR structure characterization. This approach is utilized for NMR analysis ofXylella fastidiosaEPS, which is essential for the virulence the plant pathogen that affects multiple commercial crops and is responsible for multibillion dollar losses each year.
Development of a Xylose-Inducible Promoter and Riboswitch Combination System for Manipulating Gene Expression inFusobacterium nucleatum
Authors: Bibek GC , Zhou Peng , Naha Arindam , Gu Jianhua , Wu Chenggang
Published: April 2023

Inducible gene expression systems are important for studying bacterial gene function, yet most exhibit leakage. In this study, we engineered a leakage-free hybrid system for precise gene expression controls inFusobacterium nucleatumby integrating the xylose-inducible expression system with the theophylline-responsive riboswitch. This innovative method enables concurrent control of target gene expression at both transcription and translation initiation levels. Using luciferase and the indole-producing enzyme tryptophanase (TnaA) as reporters, we demonstrated that the hybrid system displays virtually no observable signal in the absence of inducers. We employed this system to express FtsX, a protein related to fusobacterial cytokinesis, in anftsXmutant strain, unveiling a dose-dependent manner in FtsX production. Without inducers, cells form long filaments, while increasing FtsX levels by increasing inducers concentrations led to a gradual reduction in cell length until normal morphology was restored. Crucially, this system facilitated essential gene investigation, identifying the signal peptidaselepBgene as vital forF. nucleatum. LepB’s essentiality stems from depletion, affecting outer membrane biogenesis and cell division. This novel hybrid system holds the potential for advancing research on essential genes and accurate gene regulation inF. nucleatum.
Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile
Authors: Azat Claudio , Alvarado-Rybak Mario , Aguilera José Fernando , Benavides Julio A.
Published: April 2023

Highly pathogenic avian influenza A H5N1 clade 2.3.4.4b (hereafter H5N1) is causing vast impacts on biodiversity and poultry around the globe. In Chile it was first reported on December 7th, 2022, in a pelican (Pelecanus thagus) found dead in the northern city of Arica. In the following months, lethal H5N1 cases were reported in a wide range of wild bird species, marine mammals, backyard and industrial poultry, and in a human. Despite its high impact and spread, it is not well-known what environmental factors are associated with outbreaks. This study describes the spatio-temporal patterns of the current epizootic of H5N1 in Chile and test ecological and anthropogenic drivers that could be associated with outbreak occurrence. We used H5N1 cases reported by the Chilean national animal health authority to the World Animal Health Information System (WAHIS) from December 9th, 2022, to March 3rd, 2023. These included bird cases confirmed through avian influenza specific real-time PCR assay (qPCR), obtained from passive and active surveillance. Data was analyzed to detect the presence of H5N1 clusters under space-time permutation probability modelling, H5N1 association between distance and days since first outbreak through linear regression, and correlation between H5N1 presence with a range of ecological and anthropogenic variables by general linear modelling. From the 197 H5N1 identified outbreaks, involving 478 individual cases among wild and domestic birds, a wave-like steady spread of H5N1 from north to south was identified, that can help predict hotspots of outbreak risk and establish targeted preventive measures. For instance, 14 statistically significant clusters were identified, with the largest located in central Chile (18-29 km in radius) where poultry production is concentrated. Also, one of the clusters was identified in Tocopilla, location where the H5N1 human case occurred time later. In addition, the presence of H5N1 outbreaks was positively correlated with bird richness, human footprint, precipitation of the wettest month, minimum temperature of the coldest month, and mean diurnal temperature. In contrast, presence of H5N1 was negatively correlated to distance to the closest urban center, precipitation seasonality and isothermality. Preventive actions based on our modeling approach include developing wildlife surveillance diagnostic capabilities in Chilean regions concentrating outbreaks. It is urgent that scientists, the poultry sector, local communities and national health authorities co-design and implement science-based measures from a One Health perspective to avoid further H5N1 spillover from wildlife to domestic animals and humans, including rapid removal and proper disposal of wild dead animals, and the closure of public areas (i.e., beaches) reporting high wildlife mortalities.