bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel antidepressant actingviaallosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons
Authors: Zhang Jilin , Duan Jinjin , Ye Luyu , Li Wei , Zhou Haitao , Liu Fang , Xiaoting Tian , Xie Yang , Huang Yiming , Sun Yidi , Zhou Hu , Huang Chenggang , Li Yang , Zhu Shujia , Guo Fei
Published: November 2022

N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated calcium-permeable excitatory channels. They have attracted great interest as potential targets for the treatment of depression in recent years. NMDARs typically assemble as heterotetramers composed of two GluN1 and two alternative GluN2 (2A-2D) subunits, the latter of which endow various subtypes with diverse gating and pharmacological properties. To date, limited molecules with GluN2 specificity have been identified to show antidepressant effects. Here, we identify a compound termed YY-23 extracted fromRhizoma Anemarrhenaeallosterically inhibited the channel activities of GluN2C- or GluN2D-incorporated NMDARs, an effect that was presumably influenced by the S2 segment in the ligand-binding domain of the GluN2 subunit. We found that prefrontal GluN2D-containing NMDARs were predominantly expressed at GABAergic interneurons rather than pyramidal neurons. Furthermore, we revealed that YY-23 suppressed the activity of GluN2D-containing NMDARs and GABAergic neurotransmission in the medial prefrontal cortex (mPFC). As a consequence, this GABAergic disinhibition facilitated the excitatory transmission. Behavioural experiments showed that YY-23 acted as a rapid antidepressant in both stress-naïve and stressed animal models, which was abolished inGrin2d-knockoutmice. Together, our findings suggest that GluN2D-incorporated NMDARs on GABAergic interneurons might be promising therapeutic targets for the treatment of depression.
The SspB adaptor drives structural changes in the AAA+ClpXP protease during ssrA-tagged substrate delivery
Authors: Ghanbarpour Alireza , Fei Xue , Baker Tania A. , Davis Joseph H. , Sauer Robert T.
Published: November 2022

Energy-dependent protein degradation by the AAA+ClpXP protease helps maintain protein homeostasis in organisms ranging from simple bacteria to humans. InE. coliand many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structures reveal that binding of the substrate•adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ClpX hexamer and its interaction with the ClpP tetradecamer.

SIGNIFICANCE

Intercellular proteases, including ClpXP, degrade damaged or unneeded proteins. Peptide tags allow specific protein substrates to be recognized by the ClpX unfoldase/translocase component of ClpXP and by an adaptor, SspB, which tethers itself to ClpX and enhances ClpXP degradation of the tagged protein. Our cryo-EM structure of ClpXP bound to SspB and a tagged substrate shows that SspB and ClpX simultaneously contact the degradation tag and reveal changes in the structure of ClpX and its interaction with ClpP. These structural changes appear to be a prelude to an initial ClpX translocation step that pulls the substrate away from SspB and initiates degradation by allowing substrate unfolding and further translocation of the unfolded substrate into the proteolytic chamber of ClpP.
Vitamin-B12 enrichment in tempeh by co-culture withPropionibacterium freudenreichiiduring fermentation
Authors: He Meng Tian , Howell Kate S.
Published: November 2022

Vitamin-B12, or cobalamin, is an essential human vitamin and most commonly acquired in the diet through consumption of animal products. Acquisition of the vitamin for people who follow strict plant-based diets is limited to supplementation via tablets or consumption of fortified foods. Tempeh — an Indonesian food of soybeans fermented with a filamentous fungi,Rhizopussp. is a potential dietary source of cobalamin, but its presence is under question based on difficult quantification of this trace vitamin. This study tested the presence and concentration of vitamin-B12 in commercially available tempeh and tempeh produced with deliberate inoculation of various bacteria and moulds. Vitamin-B12 was not detected in any commercially available tempeh. Tempeh made with filamentous fungi andPropionibacterium freudenreichii(ATCC 9617) consistently produced detectable levels of cobalamin.P. freudenreichiico-fermented withRhizopus oligosporus(ATCC 22959) produced the highest concentration of cobalamin at 8.26 ± 0.13 μg/100g of wet weight of tempeh. Co-fermentation with a different tempeh mould significantly reduced the amount of cobalamin (P= 0.008). Results from this study suggest that incorporating nutrient-enhancing microbes into an existing fermentation stage of a product is an effective method to increase the nutritional density of food. The results of this study suggest that cheap, safe and easily cultured microbes can contribute to the nutritional diversity of people following plant-only diets.
Integrative single-cell characterization of hypothalamus sex-differential and obesity-associated genes and regulatory elements
Authors: Nguyen Hai P. , Chan Candace S.Y , Cintron Dianne Laboy , Sheng Rory , Harshman Lana , Nobuhara Mai , Ushiki Aki , Biellak Cassidy , An Kelly , Gordon Gracie M. , Mifsud Francois , Blake Abbey , Huang Eric J. , Hemberg Martin , Vaisse Christian , Ahituv Nadav
Published: November 2022

Over 500 noncoding genomic loci are associated with obesity. The majority of these loci reside near genes that are expressed in the hypothalamus in specific neuronal subpopulations that regulate food intake, hindering the ability to identify and functionally characterize them. Here, we carried out integrative single-cell analysis (RNA/ATAC-seq) on both mouse and human male and female hypothalamus to characterize genes and regulatory elements in specific cell subpopulations. Utilizing both transcriptome and regulome data, we identify over 30 different neuronal and non-neuronal cell subpopulations and a shared core of transcription factors that regulate cell cluster-specific genes between mice and humans. We characterize several sex-specific differentially expressed genes and the regulatory elements that control them in specific cell subpopulations. Overlapping cell-specific scATAC peaks with obesity-associated GWAS variants, identifies potential obesity-associated regulatory elements. Using reporter assays and CRISPR editing, we show that many of these sequences, including the top obesity-associated loci (FTOandMC4R), are functional enhancers whose activity is altered due to the obesity-associated variant and regulate known obesity genes. Combined, our work provides a catalog of genes and regulatory elements in hypothalamus cell subpopulations and uses obesity to showcase how integrative single-cell sequencing can identify functional variants associated with hypothalamus-related phenotypes.
Regenerative Agriculture Augments Bacterial Community Structure for a Healthier Soil and Agriculture
Authors: Singh Indira , Hussain Meeran , G Manjunath , Chandra Nagasuma , G Ravikanth
Published: November 2022

Use of chemical fertilization and pesticides not only harm the environment but also have detrimental consequences on human health. In recent years, there has been a major emphasis worldwide on natural agriculture methods. Regenerative agriculture is known across the world as a combination of nature-friendly farming practices such as no-till, cover cropping, crop-rotation, agro-forestry and use of organic home-based/farm-based ingredients to revive soil health. In India, a number of farmers are slowly adopting these practices using home-based mixtures and farmyard manure for soil rejuvenation and pest management. In order to evaluate the efficacy of the regenerative agriculture practices, this study compared conventional and regenerative agriculture plots for their soil bacterial and nutrient profiles. Two crops - ragi and vegetable (tomato/beans), and different lengths (≤3 and >5 years) of regenerative practices were additional metrics considered to understand variabilities due to crop-type and period of application. We found that all regenerative practices were effective in bringing about an enrichment for soil bacteria with a more heterogeneous composition. Additionally, the regenerative vegetable (RV) plots had an enhanced representation ofActinobacteriota, Chloroflexi, CyanobacteriaandPatescibacteriain comparison to conventional vegetable (CV) plots and Barren land (BL). Similarly, the regenerative ragi (RR) plots saw higher representation ofFirmicutesandActinobacteriotain comparison to conventional ragi (CR) plots and BL. The RV plots were also found to be enriched for Plant Growth Promoting Rhizobacteria (PGPRs) -Pseudomonas sp., and RR plots were enriched forBacillus sp., andMesorhizobium sp., which are known to play significant roles in vegetable and ragi growth respectively. Interestingly, long-term regenerative agriculture was able to support good nutrient composition while enhancing Soil Organic Carbon (SOC) levels. In all, the regenerative agriculture practices were found to be effective in improving bacterial community structure and simultaneously improving soil health. We found that BL soil with eucalyptus plantation showed least bacterial diversity suggesting detrimental impact on soil health.
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Authors: Jorstad Nikolas L. , Close Jennie , Johansen Nelson , Yanny Anna Marie , Barkan Eliza R. , Travaglini Kyle J. , Bertagnolli Darren , Campos Jazmin , Casper Tamara , Crichton Kirsten , Dee Nick , Ding Song-Lin , Gelfand Emily , Goldy Jeff , Hirschstein Daniel , Kroll Matthew , Kunst Michael , Lathia Kanan , Long Brian , Martin Naomi , McMillen Delissa , Pham Trangthanh , Rimorin Christine , Ruiz Augustin , Shapovalova Nadiya , Shehata Soraya , Siletti Kimberly , Somasundaram Saroja , Sulc Josef , Tieu Michael , Torkelson Amy , Tung Herman , Ward Katelyn , Callaway Edward M. , Hof Patrick R. , Keene C. Dirk , Levi Boaz P. , Linnarsson Sten , Mitra Partha P. , Smith Kimberly , Hodge Rebecca D. , Bakken Trygve E. , Lein Ed S.
Published: November 2022

Variation in cortical cytoarchitecture is the basis for histology-based definition of cortical areas, such as Brodmann areas. Single cell transcriptomics enables higher-resolution characterization of cell types in human cortex, which we used to revisit the idea of the canonical cortical microcircuit and to understand functional areal specialization. Deeply sampled single nucleus RNA-sequencing of eight cortical areas spanning cortical structural variation showed highly consistent cellular makeup for 24 coarse cell subclasses. However, proportions of excitatory neuron subclasses varied strikingly, reflecting differences in intra- and extracortical connectivity across primary sensorimotor and association cortices. Astrocytes and oligodendrocytes also showed differences in laminar organization across areas. Primary visual cortex showed dramatically different organization, including major differences in the ratios of excitatory to inhibitory neurons, expansion of layer 4 excitatory neuron types and specialized inhibitory neurons. Finally, gene expression variation in conserved neuron subclasses predicts differences in synaptic function across areas. Together these results provide a refined cellular and molecular characterization of human cortical cytoarchitecture that reflects functional connectivity and predicts areal specialization.
Malonyl-CoA is an ancient physiological ATP-competitive mTORC1 inhibitor
Authors: Nicastro Raffaele , Brohée Laura , Alba Josephine , Nüchel Julian , Figlia Gianluca , Kipschull Stefanie , Gollwitzer Peter , Romero-Pozuelo Jesus , Fernandes Stephanie A. , Lamprakis Andreas , Vanni Stefano , Teleman Aurelio A. , De Virgilio Claudio , Demetriades Constantinos
Published: November 2022

Cell growth is regulated primarily by the mammalian/mechanistic Target of Rapamycin Complex 1 (mTORC1) that functions both as a nutrient sensor and a master controller of virtually all biosynthetic pathways1. This ensures that cells are metabolically active only when conditions are optimal for growth. Notably, although mTORC1 is known to regulate fatty acid (FA) biosynthesis, how and whether the cellular lipid biosynthetic capacity signals back to fine-tune mTORC1 activity remains poorly understood. Here, we show that mTORC1 senses the capacity of a cell to synthesize FAs by detecting the levels of malonyl-CoA, an intermediate of this biosynthetic pathway. We find that, in both yeast and mammalian cells, this regulation is very direct, with malonyl-CoA binding to the mTOR catalytic pocket and acting as a specific ATP-competitive inhibitor. When ACC1 (acetyl-CoA carboxylase 1) is hyperactive or FASN (fatty acid synthase) is downregulated/inhibited, elevated malonyl-CoA levels are channelled to proximal mTOR molecules that form direct protein-protein interactions with ACC1 and FASN. Our findings represent a conserved, unique, homeostatic mechanism whereby impaired FA biogenesis leads to reduced mTORC1 activity to coordinatively link this metabolic pathway to the overall cellular biosynthetic output. Moreover, they reveal the first-described example of a physiological metabolite that directly inhibits the activity of a signalling kinase by competing with ATP for binding.
Partial Mimicry of the Microtubule Binding of Tau by Its Membrane Binding
Authors: MacAinsh Matthew , Zhou Huan-Xiang
Published: November 2022

Tau, as typical of intrinsically disordered proteins (IDPs), binds to multiple targets including microtubules and acidic membranes. The latter two surfaces are both highly negatively charged, raising the prospect of mimicry in their binding by tau. The tau-microtubule complex was recently determined by cryo-EM. Here we used molecular dynamics simulations to characterize the dynamic binding of tau K19 to an acidic membrane. This IDP can be divided into three repeats, each containing an amphipathic helix. The three amphipathic helices, along with flanking residues, tether the protein to the membrane interface. The separation between and membrane positioning of the amphipathic helices in the simulations are validated by published EPR data. The membrane contact probabilities of individual residues in tau show both similarities to and distinctions from native contacts with microtubules. In particular, a Lys that is conserved among the repeats forms similar interactions with membranes and with microtubules, as does a conserved Val. This partial mimicry facilitates both the membrane anchoring of microtubules by tau and the transfer of tau from membranes to microtubules.
Express visuomotor responses reflect knowledge of both target location and conscious intent during reaches of different amplitudes
Authors: Contemori Samuele , Loeb Gerald E. , Corneil Brian D. , Wallis Guy , Carroll Timothy J.
Published: November 2022

When humans reach to visual targets, extremely rapid (~90 ms) bursts of activity can be observed on task-relevant proximal muscles. Such express visuomotor responses are inflexibly locked in time and space to the target and have been proposed to reflect rapid visuomotor transformations conveyed subcortically via the tecto-reticulo-spinal pathway. Previously, we showed that express visuomotor responses are sensitive to explicit cue-driven information about the target, suggesting that the express pathway can be modulated by cortical signals affording contextual pre-stimulus expectations. Here, we show that the express visuomotor system incorporates information about the veridical target-directed reaching metrics and contextual instructions during visuospatial tasks requiring different movement amplitudes. In one experiment, we recorded the activity from two shoulder muscles as participants reached toward targets that appeared at different distances. Longer hand-to-target distances led to larger and more prevalent express visuomotor responses than short-reach targets. This suggests that both the direction and distance of veridical hand-to-target reaches are encoded along the putative subcortical express pathway. In a second experiment, we modulated the movement amplitude by asking the participants to deliberately undershoot, overshoot, or stop (control) at the target. The overshoot and undershoot tasks impaired the generation of large and frequent express visuomotor responses, consistent with the inability of the express pathway to generate responses directed toward non-veridical targets (e.g. anti-reach tasks). Our findings appear to reflect strategic, cortically-driven modulation of the express visuomotor circuit to facilitate rapid and effective response initiation during target-directed actions.

SIGNIFICANCE STATEMENT

Express(~90 ms) arm muscle responses that are consistently tuned toward the location of visual stimuli suggest a subcortical contribution to target-directed visuomotor behaviour in humans, potentially via the tecto-reticulo-spinal pathway. This study shows that express muscle responses are modulated appropriately to reach targets at different distances, but generally suppressed when the task required non-veridical responses to overshoot/undershoot the real target. The data suggest that the tecto-reticulo-spinal pathway can be exploited strategically by the cerebral cortex to facilitate rapid initiation of effective responses during a visuospatial task.
Positive associations matter: microbial relationships drive tick microbiome composition
Authors: Fountain-Jones Nicholas M. , Khoo Benedict S. , Rau Austin , Berman Jesse D. , Burton Erin N. , Oliver Jonathan D.
Published: November 2022

Untangling how factors such as environment, host, associations between species and dispersal predict microbial dynamics is a fundamental challenge. In this study, we use a robust sampling design coupled with complementary machine-learning approaches to quantify the relative role of these factors in shaping microbiome variation of the blacklegged tickIxodes scapularis. I. scapularisis the most important vector forBorrelia burgdorferi. (the causative agent for Lyme disease) in the U.S as well as a range of other important zoonotic pathogens. Yet the relative role of the interactions between pathogens and symbionts compared to other ecological forces is unknown. We found that positive associations between microbes where the occurrence of one microbe increases the probability of observing another, including between both pathogens and symbionts, was by far the most important factor shaping the tick microbiome. Microclimate and host factors played an important role for a subset of the tick microbiome includingBorrelia(Borreliella) andRalstonia, but for the majority of microbes, environmental and host variables were poor predictors at a regional scale. This study provides new hypotheses on how pathogens and symbionts might interact within tick species, as well as valuable predictions for how some taxa may respond to changing climate.
Biophysical modeling of actin-mediated structural plasticity reveals mechanical adaptation in dendritic spines
Authors: Bonilla-Quintana M. , Rangamani P.
Published: November 2022

Synaptic plasticity is important for learning and memory formation; it describes the strengthening or weakening of connections between synapses. The postsynaptic part of excitatory synapses resides in dendritic spines, which are small protrusions on the dendrites. One of the key features of synaptic plasticity is its correlation with the size of these spines. A long-lasting synaptic strength increase (long-term potentiation, LTP) is only possible through the reconfiguration of the actin spine cytoskeleton. Here, we develop an experimentally-informed three-dimensional computational model in a moving boundary framework to investigate this reconfiguration. Our model describes the reactions between actin and actin-binding proteins (ABPs) leading to the cytoskeleton remodeling and their effect on the spine membrane shape to examine the spine enlargement upon LTP. Moreover, we find that the incorporation of perisynaptic elements enhances spine enlargement upon LTP, exhibiting the importance of accounting for these elements when studying structural LTP. Our model shows adaptation to repeated stimuli resulting from the interactions between spine proteins and mechanical forces.

Significance Statement

Dendritic spines are small protrusions that receive stimulation from presynaptic neurons. Upon stimulation, the dendritic spines change their size, an important feature of synaptic plasticity. This change is achieved by modifications to the actin cytoskeleton and mediated by many actin-binding proteins. To investigate the fundamental mechanics of spine expansion, we developed a 3D biophysical model that accounts for the dynamics of cytoskeleton-membrane interactions. Our simulations predict that spine expansion due to actin remodeling can be enhanced by including the interaction with perisynaptic elements that affect the spine’s mechanical properties. We also found that mechanical properties can control spine expansion after repeated stimuli, which ensures physiological size. Thus, we predict that spine growth is regulated by its mechanical properties.
The soil microbiome reduces Striga infection of sorghum by modulation of host-derived signaling molecules and root development
Authors: Kawa Dorota , Thiombiano Benjamin , Shimels Mahdere , Taylor Tamera , Walmsley Aimee , Vahldick Hannah E , Leite Marcio FA , Musa Zayan , Bucksch Alexander , Dini-Andreote Francisco , Chen Alexander J , Daksa Jiregna , Etalo Desalegn , Tessema Taye , Kuramae Eiko E , Raaijmakers Jos M , Bouwmeester Harro , Brady Siobhan M
Published: November 2022

Sorghum bicoloris one of the most important cereals in the world and a staple crop for smallholder famers in sub-Saharan Africa. However approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the root parasitic weedStriga hermonthica.Existing Striga management strategies often show an inconsistent to low efficacy. Hence, novel and integrated approaches are needed as an alternative strategy. Here, we demonstrate that the soil microbiome suppresses Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation, and depletion of haustorium inducing factors (HIFs), root exudate compounds that are critical for the initial stages of Striga infection. We further identify microbial taxa associated with reduced Striga infection with concomitant changes in root cellular anatomy and differentiation as well as HIF degradation. Our study describes novel microbiome-mediated mechanisms of Striga suppression, encompassing repression of haustorium formation and induction of physical barriers in the host root tissue. These findings open new avenues to broaden the effectiveness of Striga management practices.
PKM2-mediated epigenetic reprogramming regulates hypoxic expression ofPFKFB3to promote breast cancer progression
Authors: Pandkar Madhura R. , Raveendran Adarsh , Biswas Kajal , Mutnuru Srinivas Abhishek , Mishra Jharna , Samaiya Atul , Sharan Shyam K. , Shukla Sanjeev
Published: November 2022

The hypoxic milieu is a critical modulator of aerobic glycolysis, yet the regulatory mechanisms existing between the key glycolytic enzymes in hypoxic cancer cells are largely unexplored. In particular, M2 isoform of pyruvate kinase (PKM2) − the ratelimiting enzyme of glycolysis, is well-known to confer adaptive advantages under hypoxia. Herein, we report a non-canonical role of PKM2 in functioning as a co-activator of HIF-1α to govern the transcription of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Nuclear PKM2 enhances HIF-1α and p300 occupancy atPFKFB3hypoxia responsive elements (HREs) resulting in its upregulation. Consequently, absence of nuclear PKM2 fails to recruit HIF-1α which activates an opportunistic occupancy of HIF-2α atPFKFB3HREs. Enhanced binding of HDAC3 also occurs in the absence of PKM2 which prevents HIF-2α from efficiently inducing PFKFB3 to hamper proliferation of hypoxic breast cancer cells. In addition, clinical relevance of the study has been investigated by demonstrating that Shikonin blocks nuclear translocation of PKM2 to suppressPFKFB3expression. Furthermore, MCF7 cells-derived xenograft tumors in mice exhibited substantial tumor growth inhibition when treated with shikonin, highlighting the vitality of targeting PKM2. Taken in concert, this work provides novel insights into contributions of PKM2 in modulating hypoxic transcriptome and a previously unreported molecular axis exhibited by the hypoxic breast cancer cells for ensuring the maintenance of PFKFB3 expression essential for achieving high glycolytic flux.

Statement of significance

Nuclear PKM2 orchestrates the binding of histone modifiers to epigenetically alter PFKFB3 promoter and affects the binding of HIF-2α. Notably, targeting this axis attenuates proliferation of hypoxic breast cancer cells.
Alpha and beta-diversities performance comparison between different normalization methods and centered log-ratio transformation in a microbiome public dataset
Authors: Bars-Cortina David
Published: November 2022

Microbiome data obtained after ribosomal RNA or shotgun sequencing represent a challenge for their ecological and statistical interpretation. Microbiome data is compositional data, with a very different sequencing depth between sequenced samples from the same experiment and harboring many zeros. To overcome this scenario, several normalizations and transformation methods have been developed to correct the microbiome data’s technical biases, statistically analyze these data more optimally, and obtain more confident biological conclusions. Most existing studies have compared the performance of different normalization methods mainly linked to microbial differential abundance analysis methods but without addressing the initial statistical task in microbiome data analysis: alpha and beta-diversities. Furthermore, most of the studies used simulated microbiome data. The present study attempted to fill this gap. A public whole shotgun metagenomic sequencing dataset from a USA cohort related to gastrointestinal diseases has been used. Moreover, the performance comparison of eleven normalization methods and the transformation method based on the centered log ratio (CLR) has been addressed. Two strategies were followed to attempt to evaluate the aptitude of the normalization methods between them: the centered residuals obtained for each normalization method and their coefficient of variation. Concerning alpha diversity, the Shannon-Weaver index has been used to compare its output to the normalization methods. Regarding beta-diversity (multivariate analysis), it has been explored three types of analysis: principal coordinate analysis (PCoA) as an exploratory method; distance-based redundancy analysis (db-RDA) as interpretative analysis; and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) as machine learning discriminatory multivariate method. Moreover, other microbiome statistical approaches were compared along the normalization and transformation methods: permutational multivariate analysis of variance (PERMANOVA), analysis of similarities (ANOSIM), beta-dispersion and multi-level pattern analysis in order to associate specific species to each type of diagnosis group in the dataset used. The GMPR (geometric mean of pairwise ratios) normalization method presented the best results regarding the dispersion of the new matrix obtained after being scaled. For the case ofαdiversity, no differences were detected among the normalization methods compared. In terms ofβdiversity, the db-RDA and the sPLS-DA analysis have allowed us to detect the most meaningful differences between the normalization methods. The CLR transformation method was the most informative in biological terms, allowing us to make more predictions. Nonetheless, it is important to emphasize that the CLR method and the UQ normalization method have been the only ones that have allowed us to make predictions from the sPLS-DA analysis, so their use could be more encouraged.
Charge-voltage curves of Shaker potassium channel are not hysteretic at steady state
Authors: Cowgill John , Chanda Baron
Published: November 2022

Charged residues in transmembrane segments of voltage-gated ion channels (VGICs) sense and respond to changes in the electric field. The movement of these gating charges underpins voltage-dependent activation and is also a direct metric of the net free-energy of channel activation. However, for most voltage-gated ion channels, the charge-voltage (Q-V) curves appear to be dependent on initial conditions. For instance, Q-V curves of Shaker potassium channel obtained by hyperpolarizing from 0 mV is left shifted compared to those obtained by depolarizing from a holding potential of -80 mV. This hysteresis in Q-V curves is a common feature of channels in the VGIC superfamily and raises profound questions about channel energetics because the net free-energy of channel gating is a state function and should be path independent. Due to technical limitations, conventional gating current protocols are limited to test pulse durations of<500 ms which raises the possibility that the dependence of Q-V on initial conditions reflects a lack of equilibration. Others have suggested that the hysteresis is fundamental thermodynamic property of voltage-gated ion channels and reflects energy dissipation due to measurements under non-equilibrium conditions inherent to rapid voltage jumps (Villalba-Galea, 2017). Using an improved gating current and voltage-clamp fluorometry protocols, we show that the gating hysteresis arising from different initial conditions in Shaker potassium channel is eliminated with ultra-long (18-25 second) test pulses. Our study identifies a modified gating current recording protocol to obtain steady state Q-V curves of a voltage-gated ion channel. Above all, these findings demonstrate that the gating hysteresis in Shaker channel is a kinetic phenomenon rather than a true thermodynamic property of the channel and the charge-voltage curve is a true measure of the net-free energy of channel gating.
Temporal inhibition of electron transport chain attenuates stress-induced cellular senescence by prolonged disturbance of proteostasis in human fibroblasts
Authors: Takenaka Yasuhiro , Inoue Ikuo , Hirasaki Masataka , Ikeda Masaaki , Kakinuma Yoshihiko
Published: November 2022

We previously developed a stress-induced premature senescence (SIPS) model in which normal human fibroblast MRC-5 cells were treated with either the proteasome inhibitor MG132 or the V-ATPase inhibitor bafilomycin A1 (BAFA1). To elucidate the involvement of mitochondrial function in our SIPS model, we treated cells with an inhibitor of electron transport chain (ETC) complexes I, III, or a mitochondrial uncoupler reagent along with MG132 or BAFA1 and evaluated the induction of premature senescence. SIPS induced by MG132 or BAFA1 was partially attenuated by co-treatment with antimycin A (AA) and rotenone, but not carbonyl cyanide 3-chlorophenylhydrazone (CCCP), in which intracellular reactive oxygen species (ROS) levels, acute mitochondrial unfolded protein responses, and accumulation of protein aggregates were remarkably suppressed. Co-treatment with AA also reversed the temporal depletion of SOD2 in the mitochondrial fraction on day 1 of MG132 treatment. Furthermore, co-treatment with AA suppressed the induction of mitophagy in MG132-treated cells and enhanced mitochondrial biogenesis. These findings provide evidence that the temporal inhibition of mitochondrial respiration exerts protective effects against the progression of premature senescence caused by impaired proteostasis.

Graphical abstract

GRAPHICAL ABSTRACT

Cellular senescence is induced by prolonged inhibition of proteasome or lysosome function using MG132 and bafilomycin A1 (BAFA1), respectively. When cells were co-treated with a mitochondrial respiration inhibitor, antimycin A, and MG132 or BAFA1, oxidative stress, mitochondrial unfolded protein response (UPRmt), accumulation of protein aggregates, and mitophagy were suppressed whereas mitochondrial biogenesis was enhanced, resulting in the attenuation of stress-induced cellular senescence (SIPS).
Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking
Authors: Bianco Nicholas A. , Collins Steven H. , Liu Karen , Delp Scott L.
Published: November 2022

Walking balance is central to independent mobility, and falls due to loss of balance are a leading cause of death for people 65 years of age and older. Bipedal gait is typically unstable, but healthy humans use corrective torques to counteract perturbations and stabilize gait. Exoskeleton assistance could benefit people with neuromuscular deficits by providing stabilizing torques at lower-limb joints to replace lost muscle strength and sensorimotor control. However, it is unclear how applied exoskeleton torques translate to changes in walking kinematics. This study used musculoskeletal simulation to investigate how exoskeleton torques applied to the ankle and subtalar joints alter center of mass kinematics during walking. We first created muscle-driven walking simulations using OpenSim Moco by tracking experimental kinematics and ground reaction forces recorded from five healthy adults. We then used forward integration to simulate the effect of exoskeleton torques applied to the ankle and subtalar joints while keeping muscle excitations fixed based on our previous tracking simulation results. Exoskeleton torque lasted for 15% of the gait cycle and was applied between foot-flat and toe-off during the stance phase, and changes in center of mass kinematics were recorded when the torque application ended. We found that changes in center of mass kinematics were dependent on both the type and timing of exoskeleton torques. Plantarflexion torques produced upward and backward changes in velocity of the center of mass in mid-stance and upward and forward velocity changes near toe-off. Eversion and inversion torques primarily produced lateral and medial changes in velocity in mid-stance, respectively. Intrinsic muscle properties reduced kinematic changes from exoskeleton torques. Our results provide mappings between ankle plantarflexion and inversion-eversion torques and changes in center of mass kinematics which can inform designers building exoskeletons aimed at stabilizing balance during walking. Our simulations and software are freely available and allow researchers to explore the effects of applied torques on balance and gait.
Subcellular protein localisation ofTrypanosoma bruceibloodstream form-upregulated proteins maps stage-specific adaptations
Authors: Halliday Clare , Dean Samuel , Sunter Jack Daniel , Wheeler Richard John
Published: November 2022

Genome-wide subcellular protein localisation inTrypanosoma brucei, through our TrypTag project, has comprehensively dissected the molecular organisation of this important pathogen. Powerful as this resource is,T. bruceihas multiple developmental forms and we previously only analysed the procyclic form. This is an insect life cycle stage, leaving the mammalian bloodstream form unanalysed. The expectation is that between life stages protein localisation would not change dramatically (completely unchanged or shifting to analogous stage-specific structures). However, this has not been specifically tested. Similarly, which organelles tend to contain proteins with stage-specific expression can be predicted from known stage specific adaptations but has not been comprehensively tested. Here, we used endogenous tagging to determine the sub-cellular localisation of the majority of proteins encoded by transcripts significantly upregulated in the bloodstream form and compared them to the existing localisation data in procyclic forms. This confirmed the localisation of known and identified the localisation of novel stage-specific proteins, giving a map of which organelles tend to contain stage specific proteins: the mitochondrion for the procyclic form, and the endoplasmic reticulum, endocytic system and cell surface in the bloodstream form.
The Siglec-sialic acid-axis is a target for innate immunotherapy of glioblastoma
Authors: Schmassmann Philip , Roux Julien , Buck Alicia , Tatari Nazanin , Hogan Sabrina , Wang Jinyu , Lee Sohyon , Snijder Berend , Martins Tomás A. , Ritz Marie-Françoise , Shekarian Tala , Kaymak Deniz , McDaid Marta , Weller Michael , Weiss Tobias , Läubli Heinz , Hutter Gregor
Published: November 2022

Glioblastoma (GBM) is the most aggressive form of primary brain tumor, for which effective therapies are urgently needed. Cancer cells are capable of evading clearance by phagocytes such as microglia and monocyte-derived cells through engaging tolerogenic programs. Here, we found that high level of Siglec-9 expression correlates with reduced survival in GBM patients. Using conditional knockouts of Siglec-E, the murine functional homologue of Siglec-9, together with single-cell RNA sequencing, we demonstrated significant pro-phagocytosis effects in microglia and monocyte-derived cells in the absence of Siglec-E. Loss of Siglec-E on monocyte-derived cells enhances antigen cross-presentation and production of pro-inflammatory cytokines, resulting in more efficient T cell priming. This bridging of innate and adaptive responses delays tumor growth and results in prolonged survival. Further, we showed synergistic activity of Siglec-E blockade in combinatorial immunotherapies and demonstrate its translational potential against GBM.
Signatures of kin selection in a natural population of the bacteriaBacillus subtilis
Authors: Belcher Laurence J. , Dewar Anna E. , Hao Chunhui , Ghoul Melanie , West Stuart A.
Published: November 2022

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviours, which are favoured because they are directed towards relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations, because theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population ofBacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns, and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest cooperation favoured by kin selection, with an average relatedness ofr=0.77 between interacting individuals.
Structural Insights into Branch Site Proofreading by Human Spliceosome
Authors: Zhang Xiaofeng , Zhan Xiechao , Bian Tong , Yang Fenghua , Li Pan , Lu Yichen , Xing Zhihan , Zhang Qiangfeng Cliff , Shi Yigong
Published: November 2022

Selection of the pre-mRNA branch site (BS) by U2 snRNP is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection; but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem loop (BSL) of U2 snRNA is shielded by the splicing factor TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2/BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA; the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection/proofreading by PRP5.
Understanding and leveraging phenotypic plasticity during metastasis formation
Authors: Shah Saumil , Philipp Lisa-Marie , Giaimo Stefano , Sebens Susanne , Traulsen Arne , Raatz Michael
Published: November 2022

Cancer metastasis is the process of detrimental systemic spread and the primary cause of cancer-related fatalities. Successful metastasis formation requires tumor cells to be proliferative and invasive; however, cells cannot be effective at both tasks simultaneously. Tumor cells compensate for this trade-off by changing their phenotype during metastasis formation through phenotypic plasticity. Given the changing selection pressures and competitive interactions that tumor cells face, it is poorly understood how plasticity shapes the process of metastasis formation. Here, we develop an ecology-inspired mathematical model with phenotypic plasticity and resource competition between phenotypes to address this knowledge gap. We find that phenotypically plastic tumor cell populations attain a stable phenotype equilibrium that maintains tumor cell heterogeneity. Considering treatment types inspired by chemo- and immunotherapy, we highlight that plasticity can protect tumors against interventions. Turning this strength into a weakness, we corroborate current clinical practices to use plasticity as a target for adjuvant therapy. We present a parsimonious view of tumor plasticity-driven metastasis that is quantitative and experimentally testable, and thus potentially improving the mechanistic understanding of metastasis and its treatment consequences.
Planning comprehensiveness and resource consumption in Chinese small enterprises
Authors: Rickards Robert C. , Ritsert Rolf
Published: November 2022

Purpose

This paper explores the comprehensiveness of management accountants’ planning and the resource consumption associated with it in Chinese small enterprises (SEs).

Design/methodology/approach

The methodology involves correlation and regression analyses of online survey responses.

Findings

The study findings are as follows: planning comprehensiveness and the resource consumption associated with it vary greatly across Chinese SEs; there is a trade-off between these two aspects of planning; and provision of linkages within and across plan types, employment of valuation analytics and the use of future-oriented techniques and tools, as well as joint venturing with a foreign partner explain roughly three-quarters of the observed differences in planning behavior.

Research limitations/implications

With no readily accessible source to ensure random selection of the units of analysis, this study relies on a convenience sample. Participants’ survey responses may contain a residual element of key informant bias.

Originality/value

This study uses primary data exclusively. It demonstrates a general trade-off between the comprehensiveness of management accountants’ planning and the associated resource consumption in Chinese SEs. Its novelty also derives from an approach that explains intercompany differences in the observed behavior via variables heretofore seldom used in empirical research.
Dynamic behavior analysis of cascaded buck converter and boost converter system
Authors: Xie Fan , Geng Xinyue , Li Guozheng , Ji Huayv , Luo Zhenxiong
Published: November 2022

Purpose

Cascaded DC-DC converters system is the main structure of distributed power system, and it has complex nonlinear phenomena during operation, which affect the power quality. Therefore, the dynamic behavior of the cascaded buck converter and boost converter system, as one of the typical cascaded DC-DC converters systems is analyzed.

Design/methodology/approach

Firstly, the studied cascaded system of the buck converter with peak current control and the boost converter with PI current control is introduced and its discrete modeling is built. Then, the Jacobian matrix of the cascaded system is calculated to research the stability when the parameter change. Finally, simulation by PSIM and experiments are carried out to verify the theoretical analysis.

Findings

The coexistence of fast and slow time scale bifurcations with the changes of reference current and input voltage are studied in the cascaded system, and using simulation analysis to further study the sensitivity of the inductor current of the front-stage converter and back-stage converter to different parameters.

Originality/value

A discrete model of the cascaded buck converter and boost converter system is established, and its dynamic behavior is analyzed in detail for the first time.
Empirical validation of IR sustainability model: leveraging on a PLS-SEM approach
Authors: Adam Usman Ahmed , Kaur Kiran
Published: November 2022

Purpose

This study aims to validate a proposed conceptual model for the implementation of sustainable institutional repositories (IRs) in Nigeria.

Design/methodology/approach

A quantitative approach shaped the survey research design. This study used structural equation modeling (SEM) analysis to evaluate the proposed model. The population of the study comprises 117 librarians, information technology staff and researchers knowledgeable about IR implementation status across 14 public universities in Nigeria. The data was collected using an online survey. The Smart-PLS v3.3 software was used to facilitate the analysis.

Findings

The findings indicate that the nine identified factors of the IR sustainability model have a significant influence on the implementation of sustainable IRs. This signified that the model has adequately depicted the relationship between the implementation of sustainable IRs and the identified factors.

Originality/value

This study provides an integrated synthesis of factors that influence the implementation of sustainable IRs. This study also presents the first-ever empirically validated model for sustainable IRs. The findings of this study addressed the challenge of implementing sustainable IRs and institutionalized the idea of IRs’ sustainability assessment.