bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational Space Profile Enhances Generic Molecular Representation Learning
Authors: Wang Lin , Wang Shihang , Yang Hao , Li Shiwei , Wang Xinyu , Zhou Yongqi , Tian Siyuan , Liu Lu , Bai Fang
Published: December 2023

The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, that carries the potential to be applied across a wide scope of drug discovery scenarios. However, current molecular representation models have been limited to 2D or static 3D structures, overlooking the dynamic nature of small molecules in solution and their ability to adopt flexible conformational changes crucial for drug-target interactions. To address this limitation, we propose a novel strategy that incorporates the conformational space profile into molecular representation learning. By capturing the intricate interplay between molecular structure and conformational space, our strategy enhances the representational capacity of our model named GeminiMol. Consequently, when pre-trained on a miniaturized molecular dataset, the GeminiMol model demonstrates a balanced and superior performance not only on traditional molecular property prediction tasks but also on zero-shot learning tasks, including virtual screening and target identification. By capturing the dynamic behavior of small molecules, our strategy paves the way for rapid exploration of chemical space, facilitating the transformation of drug design paradigms.
Deep MALDI-MS Spatial ‘Omics guided by Quantum Cascade Laser Mid-infrared Imaging Microscopy
Authors: Gruber Lars , Schmidt Stefan , Enzlein Thomas , Vo Huong Giang , Cairns James Lucas , Ucal Yasemin , Keller Florian , Abu Sammour Denis , Rudolf Rüdiger , Eckhardt Matthias , Iakab Stefania Alexandra , Bindila Laura , Hopf Carsten
Published: December 2023

In spatial ‘omics, highly confident molecular identifications are indispensable for the investigation of complex biology and for spatial biomarker discovery. However, current mass spectrometry (MS)-based spatial ‘omics must compromise between data acquisition speed and biochemical profiling depth, thus often leading to only “putative” molecular identifications. Here, we introduce fast quantum cascade laser mid-infrared imaging microscopy to guide MS imaging to confined tissue areas of high interest,e.g.,multicellular spheroid cores or kidney glomeruli, for spatial lipidomics profiling at maximized analytical depth utilizing magnetic resonance-MS imaging at >106resolution or prm-PASEF-MS2fragmentation imaging. Instigating selective sulfatide accumulation in arylsulfatase A-deficient mice as ground truth concept, we demonstrate that deep QCL-infrared-guidedon-tissuespatial ‘omics unequivocally identifies 120 sulfatides. This approach enables identifications of odd-chain sulfatides and studies of structure-ion mobility-relationships that provide chemical rationales for improvements to current ion mobility prediction algorithms. Workflows and data processing tools are provided as community resources.
Ecological histories determine the success of social exploitation
Authors: Schaal Kaitlin A. , Manhes Pauline , Velicer Gregory J.
Published: December 2023

Ecological context often modifies biotic interactions, yet effects of ecological history are poorly understood. In experiments with the bacteriumMyxococcus xanthus, resource-level histories of genotypes interacting during cooperative multicellular development were found to strongly regulate social fitness. Yet how developmental spore production responded to variation in resource-level histories between interactants differed greatly between cooperators and cheaters; relative-fitness advantages gained by cheating after high-resource growth were generally reduced or absent if one or both parties experienced low-resource growth. Low-resource growth also eliminated facultative exploitation in some pairwise mixes of cooperation-proficient natural isolates that occurs when both strains have grown under resource abundance. Our results contrast with previous studies in which cooperator fitness correlated positively with resource level and suggest that resource-level variation may be important in regulating whether exploitation of cooperators occurs in a natural context.
Connecting species-specific extents of genome reduction in mitochondria and plastids
Authors: Giannakis Konstantinos , Richards Luke , Dauda Kazeem A. , Johnston Iain G.
Published: December 2023

Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types has been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and chloroplast genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that mtDNA and ptDNA gene retention are related across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and non-algal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.
Scalable, Robust, High-throughput Expression, Purification & Characterization of Nanobodies Enabled by 2-Stage Dynamic Control
Authors: Hennigan Jennifer N. , Menacho-Melgar Romel , Sarkar Payel , Lynch Michael D.
Published: December 2023

Nanobodies are single-domain antibody fragments that have garnered considerable use as diagnostic and therapeutic agents as well as research tools. However, obtaining pure VHHs, like many proteins, can be laborious and inconsistent. High level cytoplasmic expression inE. colican be challenging due to improper folding and insoluble aggregation caused by reduction of the conserved disulfide bond. We report a systems engineering approach leveraging engineered strains ofE. coli, in combination with a two-stage process and simplified downstream purification, enabling improved, robust soluble cytoplasmic nanobody expression, as well as rapid cell autolysis and purification. This approach relies on the dynamic control over the reduction potential of the cytoplasm, in combination with dynamic expression of chaperones and lysis enzymes needed for purification. Collectively, the engineered system results in more robust growth and protein expression, enabling efficient scalable nanobody production, and purification from high throughput microtiter plates, to routine shake flask cultures and larger instrumented bioreactors. We expect this system will expedite VHH development.
Magnetogenetic stimulation inside MRI induces spontaneous and evoked changes in neural circuits activity in rats
Authors: Chuang Kai-Hsiang , Qian Chunqi , Gilad Assaf , Pelled Galit
Published: December 2023

The ability to modulate specific neural circuits and simultaneously visualize and measure brain activity with MRI would greatly impact understanding brain function in health and disease. The combination of neurostimulation methods and MRI in animal models have already shown promise in elucidating fundamental mechanisms associated with brain activity. We developed an innovative magnetogenetics neurostimulation technology that can trigger neural activity through magnetic fields. Similar to other genetic-based neuromodulation methods, magnetogenetics offers cell-, area- and temporal- specific control of neural activity. However, the magnetogenetics protein (Electromagnetic Preceptive Gene (EPG)) are activated by non-invasive magnetic fields, providing a unique way to target neural circuits by the MRI gradients while simultaneously measure their effect on brain activity. EPG was expressed in rat’s visual cortex and the amplitude of low-frequency fluctuation (fALFF), resting-state functional connectivity (FC), and sensory activation was measured using a 7T MRI. The results demonstrate that EPG-expressing rats had significantly higher signal fluctuations in the visual areas and stronger FC in sensory areas consistent with known anatomical visuosensory and visuomotor connections. This new technology complements the existing neurostimulation toolbox and provides a mean to study brain function in a minimally-invasive way which was not possible previously.
The 2-oxoglutarate/malate carrier extends the family of mitochondrial carriers capable of FA-activated proton transport
Authors: Žuna Kristina , Tyschuk Tatyana , Beikbaghban Taraneh , Sternberg Felix , Kreiter Jürgen , Pohl Elena E.
Published: December 2023

Metabolic reprogramming in cancer cells has been linked to the mitochondrial dysfunction. Recent studies have suggested the mitochondrial 2-oxoglutarate/malate carrier (OGC) as a potential target for preventing cancer progression. Although OGC is known to be a part of the malate/aspartate shuttle, its exact role in cancer metabolism remains unclear. In this study, we investigated the contribution of recombinant murine OGC to the proton transport by measuring the conductance (Gm) of planar lipid bilayer membranes reconstituted with OGC. Our results show that OGC significantly increases Gmonly in the presence of free fatty acids (FAs) and 2,4-dinitrophenol, demonstrating for the first time its involvement in proton transport. We found that (i) the increase in OGC activity directly correlates with the increase in the number of unsaturated bonds of FAs, and (ii) OGC substrates and inhibitors compete with FAs for the same binding site. In addition, we have identified R90 as a crucial amino acid of the binding site for FAs, ATP, 2-oxoglutarate, and malate, which is a first step towards understanding the OGC-mediated proton transport mechanism. Elucidating the contribution of OGC to the uncoupling will be crucial in the design of targeted drugs for the treatment of cancer and other metabolic diseases.
Precipitation and Extraction Methods for Protein Purification: A Meta-Analysis of Purification Performance and Cost-Effectiveness
Authors: Decker John S. , Yano Utsuki , Melgar Romel Menacho , Lynch Michael D.
Published: December 2023

For protein drug purification, packed-bed chromatography often remains both the predominant method and a bottleneck for cost and scalability. Accordingly, extensive efforts have been made to develop alternatives, such as precipitation and liquid-liquid extraction. Despite decades of development, such methods have been slow to see adoption in commercial processes. To diagnose the key barriers to implementation and guide future work, we have systematically reviewed studies of protein precipitation and liquid-liquid extraction. We classify the products, methods, and results of 168 publications representing 290 unique purification operations and analyze these operations in terms of both process economics and purification performance. Whereas it is generally assumed that precipitation and extraction methods will have lower costs than chromatography, we find that this is only the case under specific process conditions such as at a large manufacturing scale and low initial sample purity. Furthermore, we find that only a small number of the many precipitation and extraction methods reported to date have shown readiness for implementation in protein drug purification processes. Finally, we identify key factors governing both the economic and purification performance of this class of methods: first, that operating costs are almost entirely predictable by the ratio between the mass of phase-forming materials used and the mass of product protein yielded; second, that use of modern optimization techniques such as Design of Experiments is associated with significantly better purification performance and cost-effectiveness.

Highlights

Alternative separation purification methods are not always cheaper than chromatography

The use of a combination of phase separating agents remains largely underexplored/underutilized

Lower initial purity and increasing production scale favor phase-separation over chromatography

The direct material usage rate is an important predictor of alternative separation cost-effectiveness

Current alternative separation method development has largely ignored optimization of direct material usage rate
Curcumin alleviates Arsenic trioxide-induced behavioural impairment, oxidative damage & morphological alterations in striatal region of mice brain
Authors: Pandey Kamlesh Kumar , Mehta Kamakshi , Kaur Balpreet , Dhar Pushpa , Kaler Saroj
Published: December 2023

Arsenic-induced neurotoxicity is well-documented in literature and reported to have dose-dependent damaging effects in the mice brain. Curcumin, a cost-effective plant polyphenol, safely demonstrates protective effects against arsenic-induced neurotoxicity by modifying oxidative stress, apoptosis, and neurochemistry in rodents’ brain.

The present study determined the neuroprotective potential of curcumin (CUR) on adverse effects induced by arsenic trioxide (As2O3) in mice striatal region. Healthy adult male mice were chronically administered with varying concentrations of As2O3(2, 4 & 8 mg/kg bw) alone and along with CUR (100 mg/kg bw) via oral route for 45 days. Towards the end of experimental period, the animals were subjected to behavioural paradigm including open field task, novel object recognition, rota-rod and morris water maze. Fresh striatal tissues were collected from the animals on day 46 for biochemical analysis such as MDA, GPx and GSH. While perfusion fixed brains were processed for morphological observations.

Behavioural study showed an apparent decrease in certain cognitive functions (learning and memory) and locomotor activity in mice exposed to As2O3compared to controls. Simultaneous treatment of As2O3(2, 4 & 8 mg/kg bw) and curcumin (100 mg/kg bw) alleviated theAs-induced locomotor and cognitive deficits. As2O3alone exposure also exhibited a significant increase in oxidative stress marker (MDA) and decrease in antioxidant enzyme levels (GPx, GSH). Morphological alterations were noted in mice subjected to elevated doses of As2O3(4 & 8 mg/kg bw). However, these changes were reversed in mice who received As2O3+ CUR co-treatment. Together, our findings provide preliminary evidence that curcumin protects mice striatal region from As2O3-induced behavioral, biochemical and morphological alterations.
GlnA3Mtis able to glutamylate spermine but it is not essential for the detoxification of spermine inMycobacterium tuberculosis
Authors: Krysenko Sergii , Emani Carine Sao , Bäuerle Moritz , Oswald Maria , Kulik Andreas , Meyners Christian , Hillemann Doris , Merker Matthias , Wohlers Inken , Hausch Felix , Brötz-Oesterhelt Heike , Mitulski Agnieszka , Reiling Norbert , Wohlleben Wolfgang
Published: December 2023

Mycobacterium tuberculosisis well adapted to survive and persist in the infected host, escaping the host immune response. Since polyamines, which are synthesized by infected macrophages are able to inhibit the growth ofM. tuberculosis, the pathogen needs strategies to cope with toxic spermine. The actinomyceteStreptomyces coelicolor, closely related toM. tuberculosismakes use of a gamma-glutamylation pathway to functionally neutralize spermine. We therefore considered whether a similar pathway would be functional inM. tuberculosis. In the current study we demonstrated thatM. tuberculosisgrowth was inhibited by the polyamine spermine. Using a glutamine synthetase-basedin vitroenzymatic activity assay we determined that GlnA3Mt(Rv1878) is a gamma-glutamylspermine synthetase. In anin vitrophosphate release assay we showed that purified His-Strep-GlnA3Mtas well as native GlnA3Mtprefer spermine as a substrate to putrescine, cadaverine, spermidine or other monoamines and amino acids, suggesting that GlnA3Mtmay play a specific role in the detoxification of the polyamine spermine. However, the deletion of theglnA3gene inM. tuberculosisdid not result in growth inhibition or enhanced sensitivity ofM. tuberculosisin the presence of high spermine concentrations. Subsequent RNAsequencing ofM. tuberculosisbacteria revealed that the gene cluster consisting of the efflux pump-encodingrv3065-rv3066-rv3067genes is upregulated upon spermine treatment, suggesting its involvement in bacterial survival under elevated spermine concentrations.

IMPORTANCE

Antibiotics for the treatment ofMycobacterium tuberculosisinfections attack classical bacterial targets, such as the cell envelope or the ribosome. UponM. tuberculosisinfection macrophages synthesize the polyamine spermine which - at elevated concentrations - is toxic forM. tuberculosis. Based on our investigations of spermine resistance in the closely related actinomyceteStreptomyces coelicolor, we hypothesized that the glutamyl-sperminesynthetase GlnA3 may be responsible for resistance against toxic spermine. Here we show that the mycobacterial glutamyl-sperminesynthetase indeed can inactivate spermine by glutamylation. However, GlnA3 is probably not the only resistance mechanism since aglnA3mutant ofM. tuberculosiscan survive under spermine stress. Gene expression studies suggest that an efflux pump may participate in resistance. The functional role of GlnA3Mtas well as of the spermine transporter in the pathogenicity ofM. tuberculosisis of special interest for their validation as new targets of novel anti-tubercular drugs.
Dysregulation of innate immune signaling in animal models of Spinal Muscular Atrophy
Authors: Garcia Eric L. , Steiner Rebecca E. , Raimer Amanda C. , Herring Laura E. , Matera A. Gregory , Spring Ashlyn M.
Published: December 2023

Background

Spinal Muscular Atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the Survival Motor Neuron (SMN) protein. SMA presents across broad spectrum of disease severity. Unfortunately, vertebrate models of intermediate SMA have been difficult to generate and are thus unable to address key aspects of disease etiology. To address these issues, we developed aDrosophilamodel system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes.

Results

Here, we carried out transcriptomic and proteomic profiling of mild and intermediateDrosophilamodels of SMA to elucidate molecules and pathways that contribute to the disease. Using this approach, we elaborated a role for the SMN complex in the regulation of innate immune signaling. We find that mutation or tissue-specific depletion of SMN induces hyperactivation of the Immune Deficiency (IMD) and Toll pathways, leading to overexpression of antimicrobial peptides (AMPs) and ectopic formation of melanotic masses in the absence of an external challenge. Furthermore, knockdown of downstream targets of these signaling pathways reduced melanotic mass formation caused by SMN loss. Importantly, we identify SMN as a negative regulator of an ubiquitylation complex that includes Traf6, Bendless and Diap2, and plays a pivotal role in several signaling networks.

Conclusions

In alignment with recent research on other neurodegenerative diseases, these findings suggest that hyperactivation of innate immunity contributes to SMA pathology. This work not only provides compelling evidence that hyperactive innate immune signaling is a primary effect of SMN depletion, but it also suggests that the SMN complex plays a regulatory role in this processin vivo. In summary, immune dysfunction in SMA is a consequence of reduced SMN levels and is driven by cellular and molecular mechanisms that are conserved between insects and mammals.
Sporadic phage defense in epidemicVibrio choleraemediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic
Authors: Patel Kishen M. , Seed Kimberley D.
Published: December 2023

Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogenVibrio choleraeharboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system’s impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinicalV. choleraeisolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance ofV. choleraeand its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.

Importance

The global bacterial pathogenVibrio choleraecauses an estimated 1 to 4 million cases of cholera each year. Thus, studying the factors that influence its persistence as a pathogen is of great importance. One such influence is the lytic phage ICP1, as once infected by ICP1,V. choleraeis destroyed. To date, we have observed that the phage ICP1 shapesV. choleraeevolution through the flux of anti-phage bacterial immune systems. Here, we probe clinicalV. choleraeisolates for novel anti-phage immune systems that can inhibit ICP1 and discover the toxin-antitoxin system DarTG as a potent inhibitor. Our results underscore the importance ofV. choleraeand ICP1 surveillance to elaborate novel means by whichV. choleraecan persist in both the human host and aquatic reservoir in the face of ICP1.
GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology
Authors: DiCesare Sophia M. , Ortega Antonio J. , Collier Gracen E. , Daniel Steffi , Thompson Krista N. , McCoy Melissa K. , Posner Bruce A. , Hulleman John D.
Published: December 2023

Malattia Leventinese/Doyne Honeycomb Retinal Dystrophy (ML/DHRD) is an age-related macular degeneration (AMD)-like retinal dystrophy caused by an autosomal dominant R345W mutation in the secreted glycoprotein, fibulin-3 (F3). To identify new small molecules that reduce F3 production from retinal pigmented epithelium (RPE) cells, we knocked-in a luminescent peptide tag (HiBiT) into the endogenous F3 locus which enabled simple, sensitive, and high throughput detection of the protein. The GSK3 inhibitor, CHIR99021 (CHIR), significantly reduced F3 burden (expression, secretion, and intracellular levels) in immortalized RPE and non-RPE cells. Low-level, long-term CHIR treatment promoted remodeling of the RPE extracellular matrix (ECM), reducing sub-RPE deposit-associated proteins (e.g., amelotin, complement component 3, collagen IV, and fibronectin), while increasing RPE differentiation factors (e.g., tyrosinase, and pigment epithelium derived factor). In vivo, treatment of 8 mo R345W+/+knockin mice with CHIR (25 mg/kg i.p., 1 mo) was well tolerated and significantly reduced R345W F3-associated AMD-like basal laminar deposit number and size, thereby preventing the main pathological feature in these mice. This is the first demonstration of small molecule-based prevention of AMD-like pathology in ML/DHRD mice and may herald a rejuvenation of interest in GSK3 inhibition for the treatment of neurodegenerative diseases, including, potentially AMD itself.
Advancing mRNA subcellular localization prediction with graph neural network and RNA structure
Authors: Li Fuyi , Bi Yue , Guo Xudong , Tan Xiaolan , Wang Cong , Pan Shirui
Published: December 2023

Motivation

The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNA’s secondary structure.

Results

In this study, we propose Allocator, a multi-view parallel deep learning framework that seamlessly integrates the RNA sequence-level and structure-level information, enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocator’s superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations.

Availability

The webserver of Allocator is available athttp://Allocator.unimelb-biotools.cloud.edu.au; the source code and datasets are available athttps://github.com/lifuyi774/Allocator
CCT3 drives Sorafenib resistance by inhibiting TFRC-mediated iron uptake in HCC
Authors: Zhu Huihui , Liu Qiuhong , Meng Qinna , Zhang Linjian , Lan Jiaheng , Zhu Danhua , Chen Yonxia , Aishan Nadire , Ouyang Xiaoxi , Zhang Sainan , Jin Lidan , Xiao Lanlan , Wang Linbo , Li Lanjuan , Ji Feiyang
Published: December 2023

Sorafenib is commonly utilized in the management of advanced hepatocellular carcinoma (HCC). However, its efficacy in extending patients’ survival is hindered by the development of drug resistance. By employing protein posttranslational modification (PTM) omics, including acetylome, phosphoproteome, and ubiquitinome, in conjunction with genome-wide CRISPR/Cas9 knockout library screening, we have successfully identified chaperonin containing TCP1 subunit 3 (CCT3) as a key factor contributing to Sorafenib resistance. Furthermore, we observed a reduction in the ubiquitination of CCT3 at lysine 21 (K21) subsequent to Sorafenib treatment. This study provides evidence that CCT3 hinders the recycling of transferrin receptor protein 1 (TFRC) by interacting with alpha-actinin-4 (ACTN4), which is influenced by K6-linked ubiquitination on K21. Depleting CCT3 increased the susceptibility of cells to Sorafenib-induced ferroptosis, while reintroducing CCT3 through transfection restored resistance to ferroptosis. Additionally, impairing ACTN4 or TFRC depletion compromised CCT3’s ability to inhibit Sorafenib-induced ferroptosis. In summary, targeting CCT3 presents a potential strategy for overcoming Sorafenib resistance in HCC.
Metabolic sensing in AgRP regulates sucrose preference and dopamine release in the nucleus accumbens
Authors: Reichenbach Alex , Dempsey Harry , Andrews Zane B.
Published: December 2023

Hunger increases the motivation for calorie consumption, often at the expense of low taste appeal. However, the neural mechanisms integrating calorie-sensing with increased motivation for calorie consumption remain unknown. Agouti-related peptide neurons in the arcuate nucleus of the hypothalamus sense hunger, and the ingestion of caloric solutions promote dopamine release in the absence of sweet taste perception. Therefore, we hypothesized that metabolic-sensing of hunger by AgRP neurons would be essential to promote dopamine release in the nucleus accumbens in response to caloric, but not non-caloric solutions. Moreover, we examined whether metabolic sensing in AgRP neurons affected taste preference to bitter solutions under conditions of energy need. Here we show that impaired metabolic sensing in AgRP neurons attenuated nucleus accumbens dopamine release in response to sucrose, but not saccharin, consumption. Further, metabolic sensing in AgRP neurons was essential to distinguish nucleus accumbens dopamine response to sucrose consumption when compared with saccharin. Under conditions of hunger, metabolic sensing in AgRP neurons increased the preference of sucrose solutions laced with the bitter tastant, quinine, to ensure calorie consumption whereas mice with impaired metabolic sensing in AgRP neurons maintained a strong aversion to sucrose/quinine solutions despite ongoing hunger. In conclusion, we demonstrate normal metabolic sensing in AgRP neurons drives the preference for calorie consumption, primarily when needed, by engaging dopamine release in nucleus accumbens.
scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data
Authors: Vanderaa Christophe , Gatto Laurent
Published: December 2023

Analysing mass spectrometry (MS)-based single-cell proteomics (SCP) data is challenging. The data analysis must address numerous problems that are inherent to both MS-based proteomics technologies and single-cell experiments. This has led to the development of complex and divergent data processing workflows within the field. In this work, we present scplainer, a principled and standardised approach for extracting meaningful insights from SCP data. The approach relies on minimal data processing combined with linear modelling. The approach is a simple yet powerful approach for exploring and interpreting various types of SCP data. scplainer performs variance analysis, differential abundance analysis and component analysis while streamlining the visualization of the results. This thorough exploration enhances our capacity to gain a deeper understanding of the biological processes hidden in the data. Finally, we demonstrate that scplainer corrects for technical variability, and even enables the integration of data sets from different SCP experiments. The approach effectively generates high-quality data that are amenable to perform downstream analyses. In conclusion, this work reshapes the analysis of SCP data by moving efforts from dealing with the technical aspects of data analysis to focusing on answering biologically relevant questions.
NMDAR Phosphoproteome Controls Synaptic Growth and Learning
Authors: Funahashi Yasuhiro , Ahammad Rijwan Uddin , Zhang Xinjian , Hossen Emran , Kawatani Masahiro , Nakamuta Shinichi , Yoshimi Akira , Wu Minhua , Wang Huanhuan , Wu Mengya , Li Xu , Faruk Md. Omar , Shohag Md Hasanuzzaman , Lin You-Hsin , Tsuboi Daisuke , Nishioka Tomoki , Kuroda Keisuke , Amano Mutsuki , Noda Yukihiko , Yamada Kiyofumi , Sakimura Kenji , Nagai Taku , Yamashita Takayuki , Uchino Shigeo , Kaibuchi Kozo
Published: December 2023

In the mammalian brain, NMDA receptors (NMDARs) activation triggers a calcium-dependent signal transduction cascade resulting in postsynaptic remodeling and behavioral learning. However, the phosphoprotein signal flow through this transduction network is poorly understood. Here, we show that NMDAR-dependent phosphorylation drives the assembly of protein signaling complexes that regulate synaptic morphology and behavior. We performed large-scale phosphoproteomic analyses of protein kinase target proteins in successive layers of the signaling network in mouse striatal/accumbal slices. NMDARs activation resulted in the phosphorylation of 194 proteins, including Rho GTPase regulators. CaMKII-mediated phosphorylation of ARHGEF2 increased its RhoGEF activity, thereby activating the RhoA-Rho-kinase pathway. Subsequent phosphoproteomics of Rho-kinase revealed 221 protein targets, including SHANK3. Experimental validation revealed a pathway from NMDAR-dependent calcium influx through CaMKII, ARHGEF2, Rho-kinase, and SHANK3 to coordinate assembly of an actin-tethered postsynaptic complex of SHANK3/NMDAR/PSD95/DLGAP3 for spine growth and aversive learning. These findings show that NMDARs initiate metabolic phosphorylation for learning.
MeXpose - A modular imaging pipeline for the quantitative assessment of cellular metal bioaccumulation
Authors: Braun Gabriel , Schaier Martin , Werner Paulina , Theiner Sarah , Zanghellini Jürgen , Wisgrill Lukas , Fyhrquist Nanna , Koellensperger Gunda
Published: December 2023

We introduce MeXpose, an imaging pipeline for single-cell metallomics by laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOFMS). MeXpose is designed for mechanistic studies on metal exposure unravelling cellular phenotypes and tissue level characteristics of metal bioaccumulation. MeXpose leverages the high-resolution capabilities of low-dispersion laser ablation setups, a standardised approach to quantitative bioimaging, and the toolbox of immunohistochemistry using metal-labelled antibodies for cellular phenotyping. MeXpose further offers the full scope of single-cell metallomics via an extended mass range accessible through ICP-TOFMS instrumentation (covering isotopes from m/z 14-256) and integration of a complete image analysis workflow. This enables studying quantitative metal accumulation in phenotypically characterized tissue at cellular resolution. Metal amounts in the sub-fg range per cell can be absolutely quantified. As a showcase, anex vivohuman skin model exposed to cobalt chloride (CoCl2) was investigated. Metal permeation was studied for the first time at single-cell resolution, showing high bioaccumulation in the epidermal layers and especially in mitotic cells, accumulating cobalt (Co) in the low fg range per cell. In this cellular phenotype, Co accumulation was correlated to DNA damage. While the amount of cobalt was significantly lower in the collagenous matrix of the dermal layer, cells in the vicinity of blood vessels and smooth muscle showed significant Co deposits as well. MeXpose provides unprecedented insights into metal bioaccumulation with the ability to explore novel relationships between metal exposure and cellular responses on a single-cell level, paving the way for advanced toxicological and therapeutic studies.

Graphical abstract
Fine tuning of Rpb4 phosphorylation modulates Rpb4/7 stoichiometry within yeast RNA polymerase II and regulates gene expression
Authors: González-Jiménez Araceli , González-Jiménez María del Carmen , Jordán-Pla Antonio , Medina Ithaisa , Alfonso Manuel J. , Richard Stephen , Fernández-Tornero Carlos , Choder Mordechai , Calvo Olga
Published: December 2023

RNA polymerase II (RNAPII) consists of 12 subunits, including Rpb4 and Rpb7, which form a heterodimeric stalk domain. In yeast, assembly of Rpb4/7 with the 10-subunit “core” is substoichiometric. Aside from its role in transcription, Rpb4/7 also binds to mRNAs co-transcriptionally (mRNA imprinting), exits the nucleus together with the mRNA, and modulates subsequent cytoplasmic processes like translation and degradation. However, the mechanisms underlying Rpb4/7 functions and its association with RNAPII remain poorly understood. In this study, we identify five phosphorylation sites in Rpb4 that regulate various steps of mRNA and snoRNA biogenesis, including transcription elongation and the polyadenylation step. We also provide evidence that the kinase Hrr25 and the phosphatase Fcp1, known to target the carboxyl-terminal domain (CTD) of Rpb1 and participate in processes at gene 3′-ends, coordinate Rpb4 phosphorylation. Inefficient Rpb4 phosphorylation leads to increased Rpb4 association with RNAPII, particularly at gene 3′-ends, suggesting that Rpb4-P promotes stalk dissociation from RNAPII either before or during transcription termination. Collectively, our findings underscore the pivotal role of dynamic Rpb4 phosphorylation in regulating Rpb4/7 stoichiometry as well as transcription elongation and termination, with an impact on mRNA imprinting.
Learning regular cross-trial shifts of the target location in serial search involves awareness – an eye-tracking study
Authors: Yu Hao , Allenmark Fredrik , Müller Hermann J. , Shi Zhuanghua
Published: December 2023

People can learn, and utilize, not only static but also dynamic (cross-trial) regularities in the positioning oftargetitems in parallel, ‘pop-out’ visual search. However, while static target-location learning also works in serial search, acquiring dynamic regularities seems prevented by the demands imposed by item-by-item scanning. Also, questions have been raised regarding a role of explicit awareness for utilizing (at least) dynamic regularities to optimize performance. The present study re-investigated whether dynamic regularities may be learned in serial search when regular shifts of the target location occur frequently, and whether such learning would correlate with awareness of the dynamic rule. To this end, we adopted the same regularity used by Yu et al. (2023) to demonstrate dynamic learning in parallel search: a cross-trial shift of the target location in, e.g., clockwise direction within a circular array in 80% of the trials, which was compared to irregular shifts in the opposite (e.g., counterclockwise; 10%) or some other, random direction (10%). The results showed that ⅔ of participants learned the dynamic regularity, with their performance gains correlating with awareness: the more accurately they estimated how likely the target shifted in the frequent direction, the greater their gains. Importantly, part of the gains accrued already early during search: a large proportion of the very first and short-latency eye movements was directed to the predicted location, whether or not the target appeared there. We discuss whether this rule-driven behavior is causally mediated by conscious control. (248 words).
Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space
Authors: Akpinaroglu Deniz , Seki Kosuke , Guo Amy , Zhu Eleanor , Kelly Mark J. S. , Kortemme Tanja
Published: December 2023

Machine learning has revolutionized computational protein design, enabling significant progress in protein backbone generation and sequence design. Here, we introduce Frame2seq, a structure-conditioned masked language model for protein sequence design. Frame2seq generates sequences in a single pass, achieves 49.1% sequence recovery on the CATH 4.2 test dataset, and accurately estimates the error in its own predictions, outperforming the autoregressive ProteinMPNN model with over six times faster inference. To probe the ability of Frame2seq to generate novel designs beyond the native-like sequence space it was trained on, we experimentally test 26 Frame2seq designs for de novo backbones with low identity to the starting sequences. We show that Frame2seq successfully designs soluble (22/26), monomeric, folded, and stable proteins (17/26), including a design with 0% sequence identity to native. The speed and accuracy of Frame2seq will accelerate exploration of novel sequence space across diverse design tasks, including challenging applications such as multi-objective optimization.
Curvature-induced lipid sorting beyond the critical packing parameter
Authors: König M. , de Vries R. , Grünewald F. , Marrink S.J. , Pezeshkian W.
Published: December 2023

Over the last few decades, the spatial organization of biomembranes has received a lot of attention. With the fluid mosaic model, Singer and Nicolson proposed that biomembranes behave as two-dimensional fluids, allowing proteins and lipids to diffuse freely and thus react to external stimuli. Biological functionality and membrane organization are intricately linked to each other, however, how these organizations emerge is yet to be established. Here we use coarse-grained molecular dynamics simulations to explore the relationship between membrane shape and lateral organization at the nanoscale for a broad range of lipid mixtures. Our results illustrate that membrane curvature and lateral organization are intimately linked at the nanoscale and the relationship is much more complicated compared to the traditional views, in particular the lipid shape concept. Furthermore, we show that large membrane curvature can disrupt phase separation, line tension, and interleaflet coupling leading to non-intuitive lipid sorting. Our findings highlight how curvature-driven sorting can alter the phase behavior of lipid mixtures, which could be crucial for cellular functionality.
An RNAi screen to identify proteins required for cohesion rejuvenation during meiotic prophase in Drosophila oocytes
Authors: Haseeb Muhammad A. , Bernys Alana C. , Dickert Erin E. , Bickel Sharon E.
Published: December 2023

Accurate chromosome segregation during meiosis requires maintenance of sister chromatid cohesion, initially established during premeiotic S phase. In human oocytes, DNA replication and cohesion establishment occur decades before chromosome segregation and deterioration of meiotic cohesion is one factor that leads to increased segregation errors as women age. Our previous work led us to propose that a cohesion rejuvenation program operates to establish new cohesive linkages during meiotic prophase in Drosophila oocytes and depends on the cohesin loader Nipped-B and the cohesion establishment factor Eco. In support of this model, we recently demonstrated that chromosome-associated cohesin turns over extensively during meiotic prophase and failure to load cohesin onto chromosomes after premeiotic S phase results in arm cohesion defects in Drosophila oocytes. To identify proteins required for prophase cohesion rejuvenation but not S phase establishment, we conducted a Gal4-UAS inducible RNAi screen that utilized two distinct germline drivers. Using this strategy, we identified 29 gene products for which hairpin expression during meiotic prophase, but not premeiotic S phase, significantly increased segregation errors. Prophase knockdown of Brahma or Pumilio, two positives with functional links to the cohesin loader, caused a significant elevation in the missegregation of recombinant homologs, a phenotype consistent with premature loss of arm cohesion. Moreover, fluorescence in situ hybridization confirmed that Brahma, Pumilio and Nipped-B are required during meiotic prophase for maintenance of arm cohesion. Our data support the model that Brahma and Pumilio regulate Nipped-B dependent cohesin loading during rejuvenation. Future analyses will better define the mechanism(s) that govern meiotic cohesion rejuvenation and whether additional prophase-specific positives function in this process.
Use it or lose it: fiscal year-end corporate investment around the world
Authors: Kim Yong H. , Li Bochen , Shin Hyun-Han , Wu Wenfeng
Published: December 2023

Purpose

It is documented that companies and government agencies in the USA invest more in the fourth fiscal quarter without having higher investment opportunities. While previous studies focus on the agency conflicts and information asymmetry within organizations, this study is motivated by Scharfstein and Stein's (2000) two-tiered agency model and aims to examine how firms' external business environment affects the “fourth quarter effect.”

Design/methodology/approach

The authors implement this study in a sample of 41 countries and observe similar seasonality in firm investment as documented in the US market.

Findings

More importantly, using country characteristics, this study finds that firms from countries with better investor rights and protection, and more developed financial markets show less severe over-investment in the fourth fiscal quarter.

Originality/value

This paper contributes to the literature of law and finance, and the internal capital market, by investigating the quarterly investment patterns of firms from 41 countries. The authors find that similar to the results in earlier studies on the US market, firms in the global market increase their capital expenditure in the fourth fiscal quarter, indicating that the internal agency conflicts between the headquarters and divisional managers are widespread across the world. The authors also find that firms that operate in countries with higher investor rights and protection, and more developed financial markets, tend to show less severe “fourth quarter effect”.
Gender-related effects of financial knowledge and confidence on preferences for ethical intermediaries and sustainable investments
Authors: Aristei David , Gallo Manuela
Published: December 2023

Purpose

This study analyses the role of individuals' objective financial knowledge in shaping preferences for ethical intermediaries and sustainable investments in Italy. Another goal of this study is to assess the impact of individuals' misperceptions about their own financial knowledge and to test for gender-related differences in attitudes towards socially responsible investing (SRI).

Design/methodology/approach

Using nationally representative microdata from the Bank of Italy’s “Italian Literacy and Financial Competence Survey” (IACOFI), the authors use probit models, extended to account for potential endogeneity issues, to assess the causal effects of financial knowledge and confidence on stated preferences for SRI. Empirical models also allow to explicitly assess the moderating role of gender on the effects of financial knowledge and confidence on attitudes towards sustainable investing.

Findings

Results indicate that individuals' preferences for sustainable finance significantly increase with financial knowledge, suggesting that inadequate financial competencies represent a barrier to participation in SRI. At the same time, lack of confidence in one’s own financial knowledge significantly hampers attitudes towards sustainable investments. Furthermore, the authors show that women have a greater preference for sustainable finance than men and point out that financial knowledge and confidence exert heterogenous effects on attitudes towards SRI.

Originality/value

This study provides several contributions to the literature on SRI. First, the authors give evidence of the causal effect of financial knowledge on preferences for both ethical financial intermediaries and sustainable investments. Moreover, this is the first study to investigate the role of financial underconfidence bias in shaping individuals' SRI attitudes. Finally, extending previous research, the authors assess differences in SRI preferences between women and men and provide novel evidence on gender-related heterogeneity in the effects of financial knowledge and underconfidence.
Intelligent algorithms applied to the prediction of air freight transportation delays
Authors: Mendonça Guilherme Dayrell , Oliveira Stanley Robson de Medeiros , Lima Jr Orlando Fontes , Resende Paulo Tarso Vilela de
Published: December 2023

Purpose

The objective of this paper is to evaluate whether the data from consignors, logistics service providers (LSPs) and consignees contribute to the prediction of air transport shipment delays in a machine learning application.

Design/methodology/approach

The research database contained 2,244 air freight intercontinental shipments to 4 automotive production plants in Latin America. Different algorithm classes were tested in the knowledge discovery in databases (KDD) process: support vector machine (SVM), random forest (RF), artificial neural networks (ANN) and k-nearest neighbors (KNN).

Findings

Shipper, consignee and LSP data attribute selection achieved 86% accuracy through the RF algorithm in a cross-validation scenario after a combined class balancing procedure.

Originality/value

These findings expand the current literature on machine learning applied to air freight delay management, which has mostly focused on weather, airport structure, flight schedule, ground delay and congestion as explanatory attributes.