bluuebunny/crossref_metadata_2025 huggingface dataset:
Prochlorococcuspredation by a globally abundant filter feeder
Authors: Sweeney Carey P. , Harman Avery , Kerkar Anvita U. , Aasjord Anne E. , Chouroutt Daniel M. , Hiebert Terra , Sutherland Kelly , Thompson Anne W.
Published: November 2024

Prochlorococcusis the most abundant photosynthetic cell on Earth and is critical to primary productivity and biogeochemical cycles of the open ocean. Appendicularians are ubiquitous gelatinous filter-feeding zooplankton that feed on marine microorganisms includingProchlorococcus. However, the details of this feeding interaction are extremely understudied relative to its potential importance in top-down controls onProchlorococcus. This is the first study to experimentally examine several dimensions of the feeding interaction between cultivated appendicularians andProchlorococcus. We found thatProchlorococcusretention rates by the appendicularianOikopleura dioicaincreased with prey concentration and predator age. We found that appendicularians grazed equally on the two most globally abundantProchlorococcusecotypes HLI and HLII and that the presence of larger diatom prey did not changeProchlorococcusretention rates. The quantitative insight and retention rates provided by this study will help fill gaps in models of the marine carbon cycle and marine microbial community dynamics and biogeography, and expand the knowledge ofProchlorococcusecology.

Importance

Appendicularians are a known predator of picocyanobacteria, but the details of their feeding on the globally abundant picocyanobacteriumProchlorococcushave not been investigated. We quantifiedProchlorococcusretention rates over a range of ecologically relevant conditions, which will inform microbial community predictions and carbon flux models and lead to improved understanding of carbon transfer in the ocean, microbial ecology, and microbial communities.
Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids
Authors: Wojciechowska Alicja W. , Wojciechowski Jakub W. , Zielinska Kinga , Soeding Johannes , Kosciolek Tomasz , Kotulska Malgorzata
Published: November 2024

Amyloids are insoluble protein aggregates with a cross-beta structure, which are traditionally associated with neurodegeneration. Similar structures, named functional amyloids, expressed mostly by microorganisms, play important physiological roles, e.g. bacterial biofilm stabilization. Using a bioinformatics approach, we identify gut microbiome functional amyloids and analyze their potential impact on human health via the gut-brain axis. The results point to taxonomically diverse sources of functional amyloids and their frequent presence in the extracellular space. The retrieved interactions between gut microbiome functional amyloids and human proteins indicate their potential to trigger inflammation, affect transport and signaling processes. We also find a greater relative abundance of bacterial functional amyloids in patients diagnosed with Parkinson’s disease and specifically a higher content of the curli amyloid protein, CsgA, in Alzheimer’s disease patients than in healthy controls. Our results provide a rationale for the tentative link between neurodegeneration and gut bacterial functional amyloids.
TCF3::HLF Orchestrates an Enhancer-Promoter Network with Activation of MEF2C to Promote Immature HSC gene Expression in Leukemia
Authors: Priebe Valdemar , Drakul Aneta , Galvan Bartimée , Aguadé-Gorgorió Júlia , Mikkola Hanna K. A. , Bornhauser Beat , Santoro Raffaella , Bourquin Jean-Pierre
Published: November 2024

Oncogenic fusion transcription factors (TFs) frequently drive hematopoietic malignancies by altering gene expression in key developmental programs. TCF3::HLF is a fusion TF that characterizes a rare, treatment-resistant subtype of B-cell acute lymphoblastic leukemia (t(17;19) TCF3::HLF-positive B-ALL). Despite its clinical significance, the mechanisms by which TCF3::HLF induces leukemia are unclear. We used HiChIP mapping and genetic interference to analyze TCF3::HLF at the 3D-genome level, revealing enhancer-promoter interactions that control gene activation or repression. Notably, TCF3::HLF directly regulatesMEF2Cexpression through its enhancer, as interference disruptedMEF2Ctranscription and inhibited leukemia propagation. This disruption also diminished embryonal hematopoietic stem cell (HSC) gene signatures and restored mature HSC and B-lymphoid markers. These findings highlightMEF2Cas a critical component of the transcriptional network reprogrammed by TCF3::HLF. Our study provides insight into how TCF3::HLF rewires the 3D genome to drive leukemia and serves as a resource for further exploration of the TCF3::HLF regulome.

Teaser

Unraveling the 3D genomic interactions mediated by TCF3::HLF fusion protein in t(17;19) positive acute lymphoblastic leukemia.
Compositional Flexibility of the ER-Mitochondria Encounter Structure
Authors: Covill-Cooke Christian , Hirashima Takashi , Kawano Shin , Ganellin Joe , Moody Andrew , van Schie Sabine N.S. , John Peter Arun T. , Saito Chika , Endo Toshiya , Kornmann Benoît
Published: November 2024

Yeast mitochondria receive the majority of their lipids from the endoplasmic reticulum (ER) via the heterotetrameric ERMES lipid transport complex. This complex is thought to establish a lipid transporting tube of fixed composition spanning the space between both organelles. Intriguingly, however, some of the lipid-transporting components of the complex can be replaced by an artificial ER-mitochondria tether without lipid transport activity, indicating that ERMES subunits are not all of equal importance for lipid transport. Here, we propose a model whereby lipid transfer by the ERMES complex can occur with various sub-ensembles of ERMES, and minimally with only one of the four members, namely Mmm1. Our results imply flexibility in the composition of the ERMES complex, which might help it accommodate various interorganelle distances.
Limited impact of the siRNA pathway on transposable element expression inAedes aegypti
Authors: Bergman Alexander , Crist Anna B. , Lopez-Maestre Hélène , Blanc Hervé , Castelló-Sanjuán Mauro , Frangeul Lionel , Varet Hugo , Daron Josquin , Merkling Sarah H. , Saleh Maria-Carla , Lambrechts Louis
Published: November 2024

Transposable elements (TEs) are DNA sequences that can change their position within a genome. In the germline of arthropods, post-transcriptional regulation of TE expression is mainly mediated by the Piwi-interacting RNA (piRNA) pathway. piRNAs are small RNAs of 24-30 nucleotides (nt) in length produced from genomic precursor transcripts as well as through a ‘ping-pong’ amplification cycle. In somatic tissues, certain insects, such asDrosophila, instead rely on the small interfering RNA (siRNA) pathway as a key regulator of TE expression. siRNAs are 21nt small RNAs produced from double-stranded RNA by the endonuclease Dicer2, which guides an RNA-induced silencing complex to degrade a complementary RNA. However, whether the siRNA pathway also regulates TE expression in the mosquitoAedes aegypti, a medically significant vector species with abundant somatic piRNAs, is unknown. To address this question, we investigated the expression of TEs and small RNAs in both somatic and gonadal tissues of aDicer2mutant line ofAe. aegyptiand its wild-type counterpart. Our results show a modified pattern of TE expression and a decrease in TE-derived 21nt small RNAs in theDicer2mutant, but no major shift of TE transcript abundance. The lack of a functional siRNA pathway also causes perturbations in piRNA ping-pong signatures and the expression of certain piRNA-associated genes, but without clear evidence for compensation by increased piRNA pathway activity. We conclude that the mosquitoAe. aegyptiproduces siRNAs targeting TEs but these lack a critical role in the regulation of TE expression both in somatic and in gonadal tissues.
Enhancedin vivogene knockout with undetectable off-targets using multiplexed Cas12a sgRNAs
Authors: Port Fillip , Buhmann Martha A. , Zhou Jun , Stricker Mona , Vaughan-Brown Alexander , Michalsen Ann-Christin , Roßmanith Eva , Pöltl Amélie , Großkurth Lena , Huber Julia , Menendez Kury Laura B. , Weberbauer Bea , Hübl Maria , Heigwer Florian , Boutros Michael
Published: November 2024

CRISPR nuclease-mediated gene knock-out is limited by suboptimal sgRNAs, inaccessible target sites, and silent mutations. Here, we present a Cas12a-based system that targets each gene with four sgRNAs to overcome these limitations, usingDrosophilaas a tractablein vivomodel. We show that multiplexed sgRNAs act synergistically to create deletions between target sites, substantially increasing the fraction of loss-of-function mutations. To systematically assess off-target effects, we developed a novel screening assay that visualizes CRISPR-induced chromosomal alterations in living animals. This enabled comprehensive screening of more than 2000 sgRNAs clustered in 525 quadruple arrays across 21 megabases of genomic DNA, revealing remarkably high on-target activity (100%, 82/82) and undetectable off-target cutting (0%, 0/443). Quantitative side-by-side comparisons with a current Cas9-based system targeting over 100 genes demonstrates that multiplexed Cas12a-mediated gene targeting achieves superior performance and reveals phenotypes missed by established methods. This highly efficient and specific system provides a framework for reliable functional genomics studies across diverse organisms.
Unveiling the native architecture of adult cardiac tissue using the 3D-NaissI method
Authors: Pataluch Nicolas , Guilbeau-Frugier Céline , Pons Véronique , Wahart Amandine , Karsenty Clément , Sénard Jean-Michel , Galés Céline
Published: November 2024

Abstract

Accurately imaging adult cardiac tissue in its native state is essential for regenerative medicine and understanding heart disease. Current fluorescence methods encounter challenges with tissue fixation. Here, we introduce the 3D-NaissI (3D-Native Tissue Imaging) method, enabling rapid, cost-effective imaging of fresh cardiac tissue samples in their closest native state, that we also extended to other tissues.

We validated 3D-NaissI’s efficacy in preserving cardiac tissue integrity using small biopsies under hypothermic conditions in phosphate-buffered saline, offering unparalleled resolution in confocal microscopy for imaging fluorescent-small molecules/-antibodies. Compared to conventional histology, 3D-NaissI preserves cardiac tissue architecture and native protein epitopes, facilitating the use of a wide range of commercial antibodies without unmasking strategies. We successfully identified specific cardiac protein expression patterns in cardiomyocytes (CMs) from rodents and humans, including for the first time ACE2 localization in the lateral membrane/T-Tubules and SGTL2 in the sarcoplasmic reticulum. These findings shed light on COVID-19-related cardiac complications and suggest novel explanations for iSGLT2 therapeutic benefits in HFpEF patients. Additionally, we challenge the notion of "connexin-43 lateralization” in heart pathology, suggesting it may be an artifact of cardiac fixation, as 3D-NaissI clearly revealed native connexin-43 expression at the lateral membrane of healthy CMs. We also discovered previously undocumented periodic ring-like 3D structures formed by pericytes covering CMs’ lateral surfaces. These structures, positive for laminin-2, delineate a specific spatial architecture of laminin-2 receptors at the CM surface, highlighting the pivotal role of pericytes in CM function. Lastly, 3D-NaissI facilitates mapping native human protein expression in fresh cardiac autopsies, providing insights into both pathological and non-pathological contexts.

Hence, 3D-NaissI offers unparalleled insights into native cardiac tissue biology and promises to advance our understanding of physiology and pathophysiology, surpassing standard histology in resolution and accuracy.
The Rho effector ARHGAP18 coordinates a Hippo pathway feedback loop through YAP and Merlin to regulate the cytoskeleton and epithelial cell polarity
Authors: Murray Emma C. , Hodge Gilian M. , Lee Leighton S. , Mitchell Cameron A.R. , Lombardo Andrew T.
Published: November 2024

The organization of the cell’s cytoskeletal filaments is coordinated through a complex symphony of signaling cascades originating from internal and external cues. Two major actin regulatory pathways are signal transduction through Rho family GTPases and growth and proliferation signaling through the Hippo pathway. These two pathways act to define the actin cytoskeleton, controlling foundational cellular attributes such as morphology and polarity. In this study, we use human epithelial cells to investigate the interplay between the Hippo and Rho Family signaling pathways, which have predominantly been characterized as independent actin regulatory mechanisms. We identify that the RhoA effector, ARHGAP18, forms a complex with the Hippo pathway transcription factor YAP to address a long-standing enigma in the field. Using super resolution STORM microscopy, we characterize the changes in the actin cytoskeleton, on the single filament level, that arise from CRISPR/Cas9 knockout of ARHGAP18. We report that the loss of ARHGAP18 results in alterations of the cell that derive from both aberrant RhoA signaling and inappropriate nuclear localization of YAP. These findings indicate that the Hippo and Rho family GTPase signaling cascades are coordinated in their temporal and spatial control of the actin cytoskeleton.
Drone-Based Identification of Flood-Tolerant Maize via Multispectral Imaging: A Real-World Case Study
Authors: Mitchell Madison , Sidberry Grace , Mathison Morgan , DeSalvio Aaron J. , Kick Daniel , Washburn Jacob D.
Published: November 2024

Excess moisture (flooding, water logging, etc.) is a major source of crop damage causing catastrophic monetary losses to farmers around the world. Losses from excess water are often more common and costly than those from too little water (i.e., drought). Extreme weather patterns are predicted to increase, increasing the expected frequency of excess moisture events to farmers across the Midwest. Despite its importance, studying the impacts of flooding in the field is challenging due to unpredictability of flooding and fields being rendered inaccessible during flooding. Here, we took advantage of a natural flood experiment to examine the responses, damage, and recovery of diverse maize hybrids. Using drones, we monitored the hybrids before, during, and after flooding and examined the spatial and genetic components associated with post-flood survival.
Successful establishment of an exogenous gene expression system inChlamydomnaschloroplast based on viral replication elements
Authors: Jiang Yanan , Zhang Guiying , Wang Song , Raza Ali , Liu Xiang , Guo Chunli , Wu Sha , Luo Jixu , Lie Yihao , Liu Yingqi , Jia Bin , Hu Zhangli
Published: November 2024

Currently, transformation in unicellular green alga (Chlamydomonas reinhardtii) chloroplast is hindered by a low yield of target products, possibly due to the heterogeneity of the chloroplast genome. In this study, an expression platform was established inC. reinhardtiiby leveraging replicative elements from beet curly top geminivirus, which led to a high level of heterologous gene expression, as previously reported inNicotiana tabacum. Platform performance was verified by the successful expression of a linearizedmvenuscassette, achieving a higher expression level than that obtained using the homologous-recombination-based approach. This study provides a new strategy in microalgae synthetic biology and opens new avenue for accumulating valuable bioproducts at high concentrations.
Degradation of intrinsically disordered proteins using proteolysis targeting nanobody conjugate
Authors: Sun Xiaofeng , Wu Donglian , Zhou Chengjian , Xia Simin , Chen Xi
Published: November 2024

Intrinsically disordered proteins (IDPs) play crucial roles in diverse cellular processes and are implicated in numerous diseases. However, due to the inherently unstructured nature, it is challenging to modulate their function using small molecule degraders or inhibitors. To address this, we introduced proteolysis targeting nanobody conjugate (PROTNC) composed of a nanobody that binds to an IDP, an E3 ligase ligand, and a cyclic cell-penetrating peptide for efficient intracellular delivery. We first showed a general-purpose PROTNC system capable to degrade different endogenous IDPs based on a co-condensate formation mechanism. We also introduced a straightforward strategy to degrade individual IDPs using specific PROTNCs equipped with a nanobody recognizing that particular IDP. Notably, we demonstrated the degradation of TPX2 which is an undruggable oncogenic IDP responsible for microtubule nucleation. This targeted degradation effectively inhibited cancer cell proliferation by disrupting bipolar mitotic spindle assembly in metaphase and directed cells to apoptotic pathway.
Ciliopathy interacts with neonatal anesthesia to cause non-apoptotic caspase-mediated motor deficits
Authors: Sarić Nemanja , Atak Zeynep , Sade Courtni Foster , Reddy Nikita , Bell Gabrielle , Tolete Christina , Rajtboriraks May T. , Hashimoto-Torii Kazue , Jevtović-Todorović Vesna , Haydar Tarik F. , Ishibashi Nobuyuki
Published: November 2024

Increasing evidence suggests that anesthesia may induce developmental neurotoxicity, yet the influence of genetic predispositions associated with congenital anomalies on this toxicity remains largely unknown. Children with congenital heart disease often exhibit mutations in cilia-related genes and ciliary dysfunction, requiring sedation for their catheter or surgical interventions during the neonatal period. Here we demonstrate that briefly exposing ciliopathic neonatal mice to ketamine causes motor skill impairments, which are associated with a baseline deficit in neocortical layer V neuron apical spine density and their altered dynamics during motor learning.. These neuromorphological changes were linked to augmented non-apoptotic neuronal caspase activation. Neonatal caspase suppression rescued the spine density and motor deficits, confirming the requirement for sublethal caspase signaling in appropriate spine formation and motor learning. Our findings suggest that ciliopathy interacts with ketamine to induce motor impairments, which is reversible through caspase inhibition. Furthermore, they underscore the potential for ketamine- induced sublethal caspase responses in shaping neurodevelopmental outcomes.
Piezo2 in sensory neurons influences systemic and adipose tissue metabolism
Authors: Passini Fabian S. , Bornstein Bavat , Rubin Sarah , Kuperman Yael , Krief Sharon , Masschelein Evi , Mehlman Tevie , Brandis Alexander , Addadi Yoseph , Shalom Shira Huri-Ohev , Richter Erik A. , Yardeni Tal , Tirosh Amir , De Bock Katrien , Zelzer Elazar
Published: November 2024

Systemic metabolism ensures energy homeostasis through inter-organ crosstalk regulating thermogenic adipose tissue. Unlike the well-described inductive role of the sympathetic system, the inhibitory signal ensuring energy preservation remains poorly understood. Here, we show that, via the mechanosensor Piezo2, sensory neurons regulate morphological and physiological properties of brown and beige fat and prevent systemic hypermetabolism. Targeting Runx3/PV sensory neurons in independent genetic mouse models resulted in a systemic metabolic phenotype characterized by reduced body fat and increased insulin sensitivity and glucose tolerance. Deletion of Piezo2 in PV sensory neurons reproduced the phenotype, protected against high-fat diet-induced obesity and caused adipose tissue browning and beiging, likely driven by elevated norepinephrine levels. Finding that brown and beige fat are innervated by Runx3/PV sensory neurons expressing Piezo2, suggests a model where mechanical signals sensed by Piezo2 in sensory neurons protect energy storages and prevent a systemic metabolic phenotype.

Highlights

Lack of Runx3/PV sensory neurons reduces body fat and fasting glucose levels and increases glucose tolerance in mice

Mechanosensitive ion channel PIEZO2 in PV sensory neurons plays an important role in systemic metabolism under physiological and pathological conditions

PIEZO2 in PV sensory neurons regulates thermogenic programs and glucose uptake in brown and beige adipose tissues

Brown and beige adipose tissues are innervated by Runx3/PV sensory neurons
UniSPAC: A Unified Segmentation Framework for Proofreading and Annotation in Connectomics
Authors: Deng Juntao , Wu Jiamin , Chen Changmin , Zheng Qihao , Zhang Zhaoxiang , Wu Jingpeng , Ouyang Wanli , Song Chunfeng
Published: November 2024

Reconstructing dense neuronal connections from volume electron microscopy (vEM) images is a critical challenge in neuroscience, driving the development of various automatic neuron segmentation methods. Although current state-of-the-art automated segmentation methods can achieve high segmentation accuracy, they still require substantial manual proofreading and rely heavily on labeled datasets, which are often scarce, particularly for non-model organisms. Here, we introduce a Unified Segmentation framework for Proofreading and Annotation in Connectomics (UniSPAC) by providing the interactive segmentation model in 2D-level and the neuron tracing model in 3D-level. UniSPAC-2D allows users to correct its segmentation errors through point-based prompts, combining segmentation and proofreading in a single framework. UniSPAC-3D automatically traces neurons segmented by UniSPAC-2D across image slices, significantly reducing human involvement. Furthermore, UniSPAC-2D and UniSPAC-3D models can facilitate the semi-automatic generation of labeled data for new species, eliminating the need for external annotation tools. The fresh annotated data generated during proofreading in turn optimizes the interactive model through an online learning strategy, reducing the labeling effort for novel species over time. UniSPAC outperforms the start-of-the-art Segment Anything Model (SAM) in Drosophila segmentation, achieving 47x higher efficiency, and surpasses ACRLSD in cross-species segmentation on zebra finch data.
Glycocalyx-induced formation of membrane tubes
Authors: Xiao Ke , Rangamani Padmini
Published: November 2024

Tubular membrane structures are ubiquitous in cells and in the membranes of intracellular organelles such as the Golgi complex and the endoplasmic reticulum. Tubulation plays essential roles in numerous biological processes, including filopodia growth, trafficking, ion transport, and cellular motility. Understanding the fundamental mechanism of the formation of membrane tubes is thus an important problem in the fields of biology and biophysics. Though extensive studies have shown that tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins, little is known about how membrane tubes are induced by glycocalyx, a sugar-rich layer at the cell surface. In this work, we develop a biophysical model that combines polymer physics theory and the Canham-Helfrich membrane theory to investigate how the glycocalyx generates cylindrical tubular protrusions on the cell membrane. Our results show that the glycocalyx alone can induce the formation of tubular membrane structures. This tube formation involves a first-order shape transition without any externally applied force or other curvature-inducing mechanisms. We also find that critical values of glycocalyx grafting density and glycopolymer length are needed to induce the formation of tubular structures. The presence of vertical actin force, line tension, and spontaneous curvature reduces the critical grafting density and length of polymer that triggers the formation of membrane tube, which suggests that the glycocalyx makes tube formation energetically more favorable when combined with an actin force, line tension, and spontaneous curvature.

Significance Statement

In many cells, the existence of glycocalyx, a thick layer of polymer meshwork comprising proteins and complex sugar chains coating the outside of the cell membrane, regulates the formation of membrane tubes. Here, we propose a theoretical model that combines polymer physics theory and the Canham-Helfrich membrane theory to study the formation of cylindrical tubular protrusions induced by the glycocalyx. Our findings indicate that glycocalyx plays an important role in the formation of membrane tubes. We find that there exists critical grafting density and length of polymer that triggers the formation of membrane tubes, and the glycocalyx-induced tube formation is facilitated when combined with actin forces, line tension, and spontaneous curvature. Our theoretical model has implications for understanding how biological membranes may form tubular structures.
Disordered Hippocampal Reactivations Predict Spatial Memory Deficits in a Mouse Model of Alzheimer’s Disease
Authors: Shipley S. , Abrate M.P. , Hayman R. , Chan D. , Barry C.
Published: November 2024

Alzheimer’s disease (AD) is characterised by progressive memory decline associated with hippocampal degeneration. However, the specific physiological mechanisms underlying hippocampal dysfunction in AD remain poorly understood and improved knowledge may aid both diagnosis and help identify new avenues for therapeutic intervention. We investigated how disruptions in hippocampal reactivations relate to place cell stability and spatial memory deficits in an AD mouse model. Using the APP knock-in mouse model ‘NL-G-F’, we conducted simultaneous behavioural and electrophysiological recordings in a radial arm maze. NL-G-F mice exhibited significant impairments in memory performance, demonstrated by an increased propensity to revisit arms, compared to wild-type controls. These memory deficits were associated with a reduction in the stability of hippocampal place cells, which occurred over short timescales and was accentuated across rest. While the rate of hippocampal reactivation events during rest was unchanged, the structure of these events was significantly degraded in NL-G-F mice. The decreased structure of reactivations was predictive of decreased stability in place cell firing. These findings suggest that disrupted reactivation sequences may act as a mechanism of memory disorder in AD.
Visuo-Vestibular Integration for Self-Motion: Human Cortical Area V6 Prefers Forward and Congruent Stimuli
Authors: Marchand Sarah , Balcou Marine , Picher Philippine , Rosito Maxime , Mateo Damien , Vayssiere Nathalie , Durand Jean-Baptiste , Severac Cauquil Alexandra
Published: November 2024

BACKGROUND

The integration of visual and vestibular input is crucial for self-motion. Information from both sensory systems merges early in the central nervous system. Among the numerous cortical areas involved in processing this information, some (V6 and VIP) respond specifically to vestibular anteroposterior information.

OBJECTIVE

To further understand the involvement of these and other areas in self-motion processing when vestibular and visual information are combined with varying congruence and direction parameters.

METHODS

Fifteen subjects underwent an MRI session while receiving visual (optic flow patterns) and galvanic vestibular stimuli mimicking six conditions: (1) visual forward, (2) visual backward, visual forward with (3) congruent or (4) incongruent vestibular information, visual backward with (5) congruent or (6) incongruent vestibular information.

RESULTS

The combination of concurrent vestibular stimulation and fully consistant optic flow patterns activated several bilateral cortical areas found predominantly in the insula. Among these vestibular areas and those previously defined in our initial study, the large majority do not show any specifity for the forward/backward direction or for the visuo-vestibular congruency. A notable exception was the parieto-occipital area V6, which showed a marked preference for congruent visuo-vestibular signals and for cues signaling forward motion.

CONCLUSIONS

By showing that V6 is more active when visuo-vestibular signals are more ecological (i.e.when both signals specify the most common self-motion direction), our results support the view that this area plays a crucial role in visuo-vestibular integration during self-motion.
Optimized directed evolution ofE. colileucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nε-acetyl-methyllysine
Authors: Ficaretta Elise D. , Yared Tarah J. , Bhattacharjee Subrata , Voss Lena A. , Huang Rachel L. , Chatterjee Abhishek
Published: November 2024

Site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in eukaryotes has predominantly relied on the pyrrolysyl-tRNA synthetase/tRNA pair. However, access to additional easily engineered pairs is crucial for expanding the structural diversity of the ncAA toolbox in eukaryotes. TheEscherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair presents a particularly promising alternative. This pair has been engineered to charge a small yet structurally diverse group of ncAAs in eukaryotic cells. However, expanding the substrate scope of EcLeuRS has been difficult due to the suboptimal yeast-based directed evolution platform used for its engineering. In this study, we address this limitation by optimizing the yeast-based directed evolution platform for efficient selection of ncAA-selective EcLeuRS mutants. Using the optimized selection system, we demonstrate rapid isolation of many novel EcLeuRS mutants capable of incorporating various ncAAs in mammalian cells, including ornithine and Nε-acetyl-methyllysine, a recently discovered post-translational modification in mammalian cells.
Enalapril mitigates aging by targeting antioxidative genes via phosphorylated Smad1/5/9
Authors: Lyu Wencong , Wang Haochen , Du Zhehao , Wei Ran , He Jianuo , Meng Fanju , Bi Jinlong , Zhang Lijun , Zhang Chao , Guan Yiting , Tao Wei
Published: November 2024

Aging increases the risk of a myriad of chronic diseases, which are expensive and difficult to treat owing to their various risk factors. Repurposing existing anti-aging medications has accelerated the development of therapies aimed at slowing aging. In this study, we revealed that enalapril, a drug widely prescribed for hypertension, can improve both cellular senescence and individual health. Mechanistically, phosphorylated Smad1/5/9 act as pivotal mediators of the anti-aging properties of enalapril. It stimulates downstream genes involved in cell cycle regulation and antioxidative defense, facilitating cell proliferation and diminishing the production of reactive oxygen species (ROS), thus increasing the antioxidative ability of enalapril. At the organismal level, enalapril has been shown to bolster the physiological performance of various organs; it notably enhances memory capacity and renal function and relieves lipid accumulation. Our work highlights the potential of enalapril to augment antioxidant defenses and combat the effects of aging, thereby indicating its promise as a treatment strategy for aging-associated diseases and its use for healthy aging.
A library of lineage-specific driver lines connects developing neuronal circuits to behavior in theDrosophilaVentral Nerve Cord
Authors: Soffers Jelly HM , Beck Erin , Sytkowski Daniel J. , Maughan Marianne E. , Devasi Devarakonda , Zhu Yi , Wilson Beth , David Chen Yu-Chieh , Erclik Ted , Truman James W. , Skeath James B. , Lacin Haluk
Published: November 2024

Understanding the developmental changes in neuronal lineages is crucial to elucidate how they assemble into functional neural networks. Studies investigating nervous system development in model systems have focused on only on a few regions of the central nervous system due to the limited availability of genetic drivers that target specific neuronal lineages throughout development and adult life. This has hindered our understanding of how distinct neuronal lineages interconnect to form neuronal circuits during development. Here, we present a split-GAL4 library composed of genetic driver lines, which we generated via editing the genomic locus of lineage-specific transcription factors and demonstrate that we can use this library to specifically target most individual neuronal hemilineages in theDrosophilaventral nerve cord (VNC) throughout development and into adulthood. Using these genetic driver lines, we found striking morphological changes in neuronal processes within a lineage during metamorphosis. We also demonstrated how neurochemical features of neuronal classes can be quickly assessed. Lastly, we documented behaviors elicited in response to optogenetic activation of individual neuronal lineages and generated a comprehensive lineage-behavior map of the entire fly VNC. Looking forward, this lineage-specific split-GAL4 driver library will provide the genetic tools needed to address the questions emerging from the analysis of the recent VNC connectome and transcriptome datasets.
Transcriptional Regulation of Mammary Alveolar Proliferation and Differentiation during Early Pregnancy
Authors: Vusich John , Garcia-Lerena Jesus , Schulte Anthony , Corfixsen Ryan , Andrechek Eran
Published: November 2024

Proliferation and differentiation of the mammary gland during pregnancy is regulated by a wide variety of factors. Using gene expression data, we have predicted that the E2F5 transcription factor has a role in the mammary gland during pregnancy. Using CUT&RUN for E2F5 in combination with gene expression data revealed that there were a number of E2F5 target genes associated with gene expression in early pregnancy, suggesting a critical role. This prediction was then functionally tested through analysis of mice with an ablation of E2F5 in the mouse mammary epithelium using a Floxed E2F5 in combination with MMTV-Cre. This revealed a striking delay in alveolar proliferation and differentiation at the early stages of pregnancy. The significance of this effect was lost in both a second pregnancy and by the mid-point of pregnancy in single parous females. Analysis of E2F5 targets revealed overlap but a slight divergence from the consensus E2F sequence and that E2F5 was bound to the promoter of many genes involved in cellular proliferation, including known regulators of pregnancy associated alveolar expansion such as Stat6. However, progesterone stimulation of cells in a reporter assay revealed that it counteracts the repression of Stat6 by E2F5, leading to expression of Stat6. Together these data reveal the complexity of the transcriptional regulation of alveolar proliferation in early pregnancy.
Circuit mechanisms underlying sexually dimorphic outcomes of early life stress
Authors: Jiang Cheng , Ruiz-Sanchez Ignacio , Mei Cindy , Pittenger Christopher
Published: November 2024

Stress during early life influences brain development and can affect social, motor, and emotional processes. We describe a striking sex difference in the effects of early life stress (ELS), which produces anhedonia and anxiety-like behaviors in female adolescent mice, as reported previously, but repetitive behavioral pathology and social deficits in male adolescent mice. Notably, this parallels sex differences seen in the prevalence of psychiatric symptoms: depression and anxiety disorders are more common in girls and women, whereas neurodevelopmental disorders like autism spectrum disorder and Tourette syndrome are markedly more common in boys and men. We characterized the effects of ELS on the medial prefrontal cortex (mPFC) and on its projections to the dorsal striatum (dStr) and lateral septum (LS). ELS males, but not females, developed hyperactivity in the cortico-striatal circuit and hypoactivity in the cortico-septal circuit. Chemogenetic manipulation of cortico-striatal projection neurons modulates repetitive behavioral pathology and social behaviors in stressed males, and anhedonia in stressed females. Activation of cortico-septal projection neurons rescues social deficits in stressed males. We conclude that early life stress produces sexually dimorphic behavioral effects, with potential relevance to human psychiatric symptoms, through its differential effects on cortico-striatal and cortico-septal circuits.
Non-targeted screening method for detecting temporal shifts in spectral patterns of Methicillin ResistanceStaphylococcus aureusand post-hoc description of peak features
Authors: Nichani Kapil , Uhlig Steffen , Martin Victor San , Hettwer Karina , Frost Kirstin , Steinacker Ulrike , Kaspar Heike , Gowik Petra , Kemmlein Sabine
Published: November 2024

Non-targeted methods (NTMs) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) show promise in bacterial resistance detection, yet temporal variations in spectral features pose significant challenges. These proteomic patterns, which characterize bacterial phenotypes and pathological functions, may vary over time due to bacterial adaptation, virulence, or resistance mechanisms, resulting in large prediction uncertainties and potentially degrading NTM performance. We present a comprehensive screening method to detect temporal changes in MALDI-TOF spectral patterns, demonstrated using methicillin-resistant and -susceptibleStaphylococcus aureus(MRSA/MSSA) isolates collected over several years. Our approach combines convolutional neural networks (CNN) with statistical methods, including significance testing, kernel density estimation, and receiver operating characteristics for dataset shift detection. We employ Gradient-weighted Class Activation Mapping (Gradcam) for post-hoc feature description, enabling biochemical characterization of temporal changes. This analysis reveals crucial insights into the dynamic relationship between spectral data patterns over time, addressing key challenges in developing robust NTMs for routine applications.
Sensing of extracellular L-Proline availability by the integrated stress response determines the outcome of cell competition
Authors: Krishnan Shruthi , Lima Ana , Low Ying Thong , Montero Salvador Perez , Tan Sizhe , Gregorio Aida Di , Barreto Adrian Perez , Bowling Sarah , Vousden Karen , Rodriguez Tristan A.
Published: November 2024

Cell competition is a quality control acting from development to the adult that eliminates cells that are less-fit than their neighbours. How winner cells induce the elimination of losers during this process is poorly understood. Here, we address this question by studying the onset of differentiation in mouse, where cell competition eliminates 35% of embryonic cells. These loser cells have mitochondrial dysfunction, and we find that this causes amino-acid deprivation and activation of the integrated stress response (ISR), a pathway essential for their survival. We show that L-Proline is a key amino-acid sensed by the ISR and that in a competitive environment, winner cells induce increased L-Proline uptake in loser cells. This causes ISR repression and their elimination. Our results imply that cell competition is acting as a nutrient sensor, eliminating dysfunctional cells when amino acids are plentiful but sparing them in nutrient poor environments.
What drives entrepreneurial intentions? Interplay between entrepreneurial education, financial support, role models and attitude towards entrepreneurship
Authors: Saoula Oussama , Abid Muhammad Farrukh , Ahmad Munawar Javed , Shamim Amjad
Published: November 2024

Purpose

This study aims to investigate the impact of entrepreneurial education (EE), financial support (FS) and role models (RMs) on one’s attitude towards entrepreneurship (ATE) and on entrepreneurial intention (EI) based on the theory of planned behaviour.

Design/methodology/approach

In this study, quantitative research design, a deductive approach and purposive sampling have been used to collect data from 352 individuals from various Malaysian higher education institutions. The data were analysed using partial least squares structural equation modelling.

Findings

The findings have provided interesting insights into how EE, FS and RMs have a significant impact on one’s ATE and their EI. Surprisingly, RMs did not emerge as a significant predictor of EI. However, it is worth noting that mediating relationships were of significance, indicating that one’s ATE plays a substantial mediating role between EE, FS, RMs and EIs.

Originality/value

To the best of the authors’ knowledge, this study is among the few that investigate the relationships between RMs, FS and EE in relation to enhancing EIs through the mediating role of one’s ATE in Malaysia. Based on the findings of this study, stakeholders in Malaysia’s education sector are being urged to develop policy guidelines for the designing and teaching of entrepreneurship education as well as to develop FS mechanisms for business start-ups. They are also being encouraged to expose students to entrepreneurial RMs to improve their ATE and their EIs.
Impact of technology adoption on livestock production efficiency incorporating grassland productivity
Authors: Huang Yi , Huang Zhipeng , Xu Gang , Zhang Yan
Published: November 2024

Purpose

Grassland degradation is a global ecological issue that inevitably leads to low livestock production efficiency (LPE). Adoption of appropriate technology is an effective way to improve productivity. However, the rate of technology adoption among herders in less developed pastoral areas is low. Therefore, it is critical to improve the level of technology adoption in order to increase LPE.

Design/methodology/approach

Based on remote sensing data and survey datasets of herder households in China’s Qinghai–Xizang Plateau, this paper innovatively constructs a stochastic production frontier model incorporating grassland productivity (i.e. grassland total net primary productivity) to accurately evaluate LPE and uses fractional regression models to determine the impact of technology adoption on LPE.

Findings

The results show that grassland productivity is essential to estimating LPE, and failing to account for it will result in overestimation. Technology adopters have a technical advantage with respect to average LPE (0.596) when compared with non-adopters (0.540), and technology adoption positively contributes to LPE. Furthermore, compared with profit-seeking technology, pro-environmental technology contributes more to improving LPE, and the combined adoption of both technologies leads to a markedly greater enhancement in LPE.

Originality/value

Few studies have empirically analyzed the economic benefits of technologies that most smallholders can afford, and few measure LPE considering grassland productivity. This study fills these gaps, and the findings are highly relevant for policies aimed at encouraging technology adoption and facilitating more efficient livestock production.
Do the more women on the board, the higher the firm’s performance during a COVID-19 crisis? Evidence from ASEAN countries
Authors: Nadia Linda Putri , Sudirman Wahyu Febri Ramadhan , Pratiwi Anggun
Published: November 2024

Purpose

This study extends the literature on women directors and their impact on firm performance, focusing on developing countries and highlighting practices related to the role of gender diversity and inclusion in corporate governance, especially during a crisis like the COVID-19 pandemic.

Design/methodology/approach

We analyzed unbalanced panel data with five methods: OLS, fixed effect, random effect, two-stage least squares (2SLS) and the two-step system GMM. Using the Osiris database and annual reports from five Association of Southeast Asian Nations (ASEAN) countries covering 2010 to 2021, we analyzed 2,494 director-firm-year observations and 2,823 firm-year data on 305 firms.

Findings

We found a positive link between women on the board and firm performance. More women on the board enhance performance, particularly during crises, with a significant boost when three or more women are present. However, the positive impact weakens as the number of women surpasses this threshold.

Practical implications

This study’s finding can signal that women’s presence can bring better firm performance, although, in emerging economies, the growth of women’s presence on the board needs to be more inclusive. This condition becomes momentum for policymakers and practitioners or organizations to be more aware and count the women’s potential if they sit on the corporate board. These findings give implications and suggestions to the policymaker to make gender quotes at a high level, such as the board of directors under the critical mass theory, which is three women or one-third of the total board.

Originality/value

This research enhances understanding of how board gender diversity affects firm performance. Specifically, it examines the previously overlooked area of how diversity on boards impacts firms in developing countries facing crises.
Sanjeevani: replicating affordable child and maternal healthcare ecosystem for social transformation
Authors: Shroff Arvind , Shah Bhavin J.
Published: November 2024

Learning outcomes

The authors have discussed the importance of creating socially transformative health-care ecosystems in emerging economies like India. After completion of this case study and assignment questions, the students will be able to apply the case experience to comprehend the underlying factors influencing the decision of the implementation and replication of the Sanjeevani health-care service delivery model, understand the impact of free and subsidized health-care service delivery models on social transformation, evaluate the operational performance of health-care institutions using the balanced scorecard model and create practical relevance when implementing novel health-care solutions like Sanjeevani, which has been successful due to its singular pin-pointed focus on solving the issue of congenital heart diseases (CHDs).

Case overview/synopsis

Forty thousand surgeries against 0.3 million new CHD patients every year was the unbalanced equation of pediatric cardiac care in India. It also contributed to almost 46% of total CHD prevalence in the world. This case study explores the evolution of the affordable health-care ecosystem provided by Sri Sathya Sai Sanjeevani Hospital (Sanjeevani), Raipur, Chhattisgarh, which included services ranging from OPD to postoperative surgical care, including accommodation and food, completely free of cost. Over the past eight years, it had managed over 80,000 pediatric cardiac outpatients and performed over 9,000 surgeries. This case study also outlines the execution of Sanjeevani, as an affordable health venture aimed at producing social transformation. The pertinent question to be explored is, “Can the Sanjeevani healthcare ecosystem be replicated, both operationally and financially?”

Complexity academic level

This case study is suited to undergraduate Bachelor of Business Administration, Master of Business Administration (MBA) and executive MBA.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 2: Built Environment.