bluuebunny/crossref_metadata_2025 huggingface dataset:
Motor and cognitive deficits limit the ability to flexibly modulate spatiotemporal gait features in older adults with mild cognitive impairment
Authors: Rosenberg Michael C. , Slusarenko Alexandra , Cao Ke , McKay J. Lucas , Emmery Laura , Kesar Trisha M. , Hackney Madeleine E.
Published: September 2022

Introduction

Dance-based therapies are an emerging form of movement therapy aiming to improve motor and cognitive function in older adults with mild cognitive impairments (MCIs). Despite promising effects of dance-based therapies on function, it remains unclear how age-related declines in motor and cognitive function affect movement capacity and influence which movements and rhythms maximize dance therapy efficacy. Here, we evaluated the effects of age and MCI on the ability to accurately modulate spatial (i.e., joint kinematics), temporal (i.e., step timing), and spatiotemporal features of gait to achieve spatial and temporal targets during walking.

Methods

We developed novel rhythmic movement sequences - nine spatial, nine temporal, and four spatiotemporal - that deviated from typical spatial and temporal features of walking. Healthy young adults (HYA), healthy older adults (HOA), and adults with MCI were trained on each gait modification before performing the modification overground, with kinematic data recorded using wearable sensors.

Results

HOA performed spatial (p = 0.010) and spatiotemporal (p = 0.048) gait modifications less accurately than HYA. Individuals with MCI performed spatiotemporal gait modifications less accurately than HOA (p = 0.017). Spatial modifications to the swing phase of gait (p = 0.006, Cohen’sd= -1.3), and four- and six-stepDuplerhythms during temporal modifications (p<0.030, Cohen’sd>0.9) elicited the largest differences in gait performance in HYA vs. HOA and HOA vs. MCI, respectively.

Discussion

These findings suggest that age-related declines in strength and balance reduce the ability to accurately modulate spatial gait features, while declines in working memory in individuals with MCI may reduce the ability to perform longer temporal gait modification sequences.

Differences in rhythmic movement sequence performance highlight motor and cognitive factors potentially underlying deficits in gait modulation capacity, which may guide therapy personalization and provide more sensitive indices to track intervention efficacy.
Heterogeneous migration of neuronal progenitors to the insula shapes the human brain
Authors: Mallela Arka N. , Deng Hansen , Gholipour Ali , Warfield Simon K , Goldschmidt Ezequiel
Published: September 2022

The human cerebrum consists of a precise and stereotyped arrangement of lobes, gyri, and connectivity that underlies human cognition. The development of this arrangement is less clear. Current models of radial glial cell migration explain individual gyral formation but fail to explain the global configuration of the cerebral lobes. Moreover, the insula, buried in the depths of the Sylvian fissure, belies conventional models. Here, we show that the insula has unique morphology in adults, that insular morphology and slow volumetric growth emerge during fetal development, and that a novel theory of curved migration is required to explain these findings. We calculated morphologic data in the insula and other lobes in adults (N=107) and in anin uterofetal brain atlas (N=81 healthy fetuses).In utero, the insula grows an order of magnitude slower than the other lobes and demonstrates shallower sulci, less curvature, and less surface complexity both in adults and progressively throughout fetal development. Novel spherical projection analysis demonstrates that the lenticular nuclei obstruct 60-70% of radial pathways from the ventricular zone (VZ) to the insula, forcing a curved migration path to the insula in contrast to a direct radial pathway. Using fetal diffusion tractography, we identify streams of putative progenitor cells that originate from the VZ and migrate tangentiallyaroundthe lenticular nuclei to form the insula. These results challenge existing models of radial migration to the cortex, provide an alternative model for insular and cerebral development, and lay the groundwork to understand cerebral malformations, insular functional connectivity, and insular pathologies.
Unsupervised Restoration of a Complex Learned Behavior After Large-Scale Neuronal Perturbation
Authors: Wang Bo , Torok Zsofia , Duffy Alison , Bell David , Wongso Shelyn , Velho Tarciso , Fairhall Adrienne , Lois Carlos
Published: September 2022

Reliable execution of behaviors requires that brain circuits correct for variations in neuronal dynamics. Genetic perturbation of the majority of excitatory neurons in a brain region involved in song production in adult songbirds with stereotypical songs triggered severe degradation of their songs. The song fully recovered within two weeks, and substantial improvement occurred even when animals were prevented from singing during the recovery period, indicating that offline mechanisms enable recovery in an unsupervised manner. Song restoration was accompanied by increased excitatory synaptic inputs to unmanipulated neurons in the same region. A model inspired by the behavioral and electrophysiological findings suggests that a combination of unsupervised single-cell and population-level homeostatic plasticity rules can support the observed functional restoration after large-scale disruption of networks implementing sequential dynamics. In the model the sequence is restored through a parallel homeostatic process, rather than regrown serially, and predicts that sequences should recover in a saltatory fashion. Correspondingly, we observed such recovery in the songs of manipulated animals, with syllables that rapidly alternate between abnormal and normal durations from rendition to rendition until eventually they permanently settled into their original length. These observations indicate the existence of cellular and systems-level restorative mechanisms that ensure behavioral resilience.
SPECC1L binds MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin
Authors: Mehta V , Decan N , Gaudreau-Lapierre A , Copeland JW , Trinkle-Mulcahy L
Published: September 2022

The subcellular localization, activity and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit (PP1 cat) is mediated through its dynamic association with regulatory subunits in holoenzyme complexes. While some functional overlap is observed for the three human PP1cat isoforms, they also show distinct targeting based on relative preferences for specific regulatory subunits. A well-known example is the preferential association of MYPT1 with PP1β in the myosin phosphatase complex. In smooth muscle, MYPT1/ PP1β counteracts the muscle contraction induced by phosphorylation of the light chains of myosin by the myosin light chain kinase. This phosphatase complex is also found in non-muscle cells, where it is targeted to both myosin and non-myosin substrates and contributes to regulation of the balance of cytoskeletal structure and motility during cell migration and division. Although it remains unclear how MYPT1/PP1β traffics between microtubule- and actin-associated substrates, our identification of the microtubule- and actin-binding protein SPECC1L in both the PP1β and MYPT1 interactomes suggested that it may be the missing link. Validation of their association, together with the strong overlap that we observed for the SPECC1L and MYPT1 interactomes, suggested that they exist in a stable complex in the cell. We further showed that SPECC1L binds MYPT1 directly, and that it can impact the balance of the distribution of the MYPT1/ PP1β complex between the microtubule and filamentous actin networks.
Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under lowS-adenosylmethionine
Authors: Haws Spencer A. , Miller Lillian J. , Rojas La Luz Diego , Kuznetsov Vyacheslav I. , Trievel Raymond C. , Craciun Gheorghe , Denu John M.
Published: September 2022

S-adenosylmethionine (SAM) is the methyl donor for site-specific methylation reactions on histone proteins, imparting key epigenetic information. During SAM-depleted conditions that can arise from dietary methionine restriction, lysine di- and tri-methylation are reduced while sites such as Histone-3 lysine-9 (H3K9) are actively maintained, allowing cells to restore higher-state methylation upon metabolic recovery. Here, we investigated if the intrinsic catalytic properties of H3K9 histone methyltransferases (HMTs) contribute to this epigenetic persistence. We employed systematic kinetic analyses and substrate binding assays using four recombinant H3K9 HMTs (i.e., EHMT1, EHMT2, SUV39H1, and SUV39H2). At both high and low (sub-saturating) [SAM], all HMTs displayed the highest catalytic efficiency (kcat/KM) for monomethylation compared to di- and trimethylation on H3 peptide substrates. The favored monomethylation reaction was also reflected inkcatvalues, apart from SUV39H2 which displayed a similarkcatregardless of substrate methylation state. Using differentially-methylated nucleosomes as substrates, kinetic analyses of EHMT1 and EHMT2 revealed similar catalytic preferences. Orthogonal binding assays revealed only small differences in substrate affinity across methylation states, suggesting that catalytic steps dictate the monomethylation preferences of EHMT1, EHMT2, and SUV39H1. To linkin vitrocatalytic rates with nuclear methylation dynamics, we built a mathematical model incorporating measured kinetic parameters and a time course of mass spectrometry-based H3K9 methylation measurements following cellular SAM depletion. The model revealed that the intrinsic kinetic constants of the catalytic domains could recapitulatein vivoobservations. Together, these results suggest catalytic discrimination by H3K9 HMTs maintain nuclear H3K9me1, ensuring epigenetic persistence after metabolic stress.
Transcription and DNA methylation signatures of paternal behavior in hippocampal dentate gyrus of prairie voles
Authors: Waddell Nicholas J. , Liu Yan , Chitaman Javed M. , Kaplan Graham J. , Wang Zuoxin , Feng Jian
Published: September 2022

In socially monogamous prairie voles (Microtus ochrogaster), parental behaviors not only occur in mothers and fathers, but also exist in some virgin males. In contrast, the other virgin males display aggressive behaviors towards conspecific pups. However, little is known about the molecular underpinnings of this behavioral dichotomy, such as gene expression changes and their regulatory mechanisms. To address this, we profiled the transcriptome and DNA methylome of hippocampal dentate gyrus of four prairie vole groups, namely attacker virgin males, parental virgin males, fathers, and mothers. While we found a concordant gene expression pattern between parental virgin males and fathers, the attacker virgin males have a more deviated transcriptome. Moreover, numerous DNA methylation changes were found in pair-wise comparisons among the four groups. We found some of these DNA methylation changes correlate with transcription differences, particularly at genes with extreme expression changes. Furthermore, the gene expression changes and methylome alterations are selectively enriched in certain biological pathways, such as Wnt signaling, which suggest a canonical transcription regulatory role of DNA methylation in paternal behavior. Therefore, our study presents an integrated view of prairie vole dentate gyrus transcriptome and epigenome that provides a DNA epigenetic based molecular insight of paternal behavior.
PI 4-kinases promote cell surface expansion and facilitate tissue morphogenesis during Drosophila cellularization and gastrulation
Authors: Chen Wei , Bergstein Victoria , He Bing
Published: September 2022

During epithelial morphogenesis, dynamic cell shape change driven by intrinsic or extrinsic forces requires prompt regulation of cell surface area. Using Drosophila ventral furrow formation as a model, we identified the PI 4-kinase Fwd as an important regulator for apical constriction-mediated cell shape changes. These morphological changes involve prompt lateral surface expansion in the constricting cells and apical surface expansion in the non-constricting cells adjacent to the constriction domain, both of which are impeded upon depletion of Fwd. Computer modeling demonstrates that restricting apical and lateral cell surface expansion will result in specific tissue-level morphological abnormalities during furrow formation, which well predicts the phenotypes observed in the fwd deficient embryos. Fwd also promotes cell surface expansion during cellularization, but this function is largely redundant with another PI 4-kinase, PI4KIIα. Together, our findings uncover an important role of Fwd in facilitating cell surface expansion in support of dynamic epithelial remodeling.
Structural insights into the organization and channel properties of human Pannexin isoforms 1 and 3
Authors: Hussain Nazia , Apotikar Ashish , Pidathala Shabareesh , Mukherjee Sourajit , Burada Ananth Prasad , Sikdar Sujit Kumar , Kutti Vinothkumar R. , Penmatsa Aravind
Published: September 2022

Pannexins are single-membrane large-pore ion channels that release ATP upon activation. Three isoforms of pannexins, 1, 2, and 3, perform diverse cellular roles, including inflammation, differentiation, neuropathic pain, and ATP release. In this study, we report the cryoEM structure of pannexin 3 at 3.9 Å and characterize the structural differences with pannexin isoforms 1 and 2. We observe the organization of the Pannexin 3 vestibule into two distinct chambers with a wider pore radius in comparison to both PANX1 and 2 isoforms. We further report the structure of pannexin1 congenital mutant R217H in the resolution range of 3.9 Å. The congenital mutant R217H in transmembrane helix3 (TM3), R217H induce structural changes that leads to a partially closed pore and altered ATP interaction propensities. The channel conductance of the congenital mutant displays weakened voltage sensitivity. The results showcase a complete comparison of the three pannexin isoform structures that along with the structure of Pannexin 1 congenital mutant highlight distinct structural features of pannexin isoforms and the allosteric role of distant substitutions in dictating channel behavior in Pannexin 1.
Insights into the activation of Kinesin1 from the molecular characterisation of JIP3/4 binding to Kif5b
Authors: Vilela Fernando , Chenon Mélanie , Velours Christophe , Andreani Jessica , Llinas Paola , Ménétrey Julie
Published: September 2022

Whereas our understanding of kinesin auto-inhibition mechanisms is improving faster, important insights into kinesin activation mechanisms such as those controlled by cargo-motor adaptors are still missing. JIP3 and JIP4 are versatile motor-cargo adaptors for kinesin1 and dynein-dynactin motors enabling bi-directional transport on microtubules. JIP3 activates kinesin1 heavy chains, independently of kinesin1 light chains. In this report, we characterize the molecular details of the binding of the kinesin1 heavy chain, Kif5b to the motor-cargo adaptors, JIP3 and JIP4, using biophysical approaches. The definition of the exact binding site of Kif5b, as well as the specificity of interaction between JIP3 and JIP4 provide new insights into kinesin1 activation.
Remodelling of carbon metabolism during sulfoglycolysis inEscherichia coli
Authors: Mui Janice W.-Y. , De Souza David P. , Saunders Eleanor C. , McConville Malcolm J. , Williams Spencer J.
Published: September 2022

Sulfoquinovose (SQ) is a major metabolite in the global sulfur cycle produced by nearly all photosynthetic organisms. One of the major pathways involved in the catabolism of SQ in bacteria, such asEscherichia coli, is a variant of the glycolytic Embden-Meyerhof-Parnas (EMP) pathway termed the sulfoglycolytic EMP (sulfo-EMP) pathway, which leads to consumption of three of the six carbons of SQ and excretion of 2,3-dihydroxypropanesulfonate (DHPS). Comparative metabolite profiling of aerobically Glc-grown and SQ-grownE. coliwas undertaken to identify the metabolic consequences of switching from glycolysis to sulfoglycolysis. Sulfoglycolysis was associated with the diversion of triose-phosphates to synthesize sugar phosphates (gluconeogenesis), and an unexpected accumulation of trehalose and glycogen storage carbohydrates. Sulfoglycolysis was also associated with global changes in central carbon metabolism, as indicated by changes in levels of intermediates in the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway (PPP), polyamine metabolism, pyrimidine metabolism and many amino acid metabolic pathways. Upon entry into stationary phase and depletion of SQ,E. coliutilize their glycogen, indicating a reversal of metabolic fluxes to allow glycolytic metabolism.

Importance

The sulfosugar sulfoquinovose is estimated to be produced on a scale of 10 billion tonnes per annum, making it a major organosulfur species in the biosulfur cycle. Microbial degradation of sulfoquinovose through sulfoglycolysis allows utilization of its carbon content and contributes to biomineralization of its sulfur. However, the metabolic consequences of microbial growth on sulfoquinovose are unclear. We use metabolomics to identify the metabolic adaptations thatEscherichia coliundergoes when grown on sulfoquinovose versus glucose. This revealed increased flux into storage carbohydrates through gluconeogenesis, and reduced flux of carbon into the TCA cycle and downstream metabolism. These changes are relieved upon return to stationary phase growth and reversion to glycolytic metabolism. This work provides s new insights into the metabolic consequences of microbial growth on an abundant sulfosugar.
High-resolution volumetric imaging constrains compartmental models to explore synaptic integration and temporal processing by cochlear nucleus globular bushy cells
Authors: Spirou George A. , Kersating Matthew G. , Carr Sean , Razzaq Bayan , Alves-Pinto Carolyna Y. , Dawson Mariah , Ellisman Mark H. , Manis Paul B.
Published: September 2022

Globular bushy cells (GBCs) of the cochlear nucleus play central roles in the temporal processing of sound. Despite investigation over many decades, fundamental questions remain about their dendrite structure, afferent innervation, and integration of synaptic inputs. Here, we use volume electron microscopy (EM) to construct synaptic maps that precisely specify convergence ratios and synaptic weights for auditory- nerve innervation and accurate surface areas of all postsynaptic compartments. Detailed biophysically-based compartmental models can help develop hypotheses regarding how GBCs integrate inputs to yield their recorded responses to sound. We established a pipeline to export a precise reconstruction of auditory nerve axons and their endbulb terminals together with high-resolution dendrite, soma, and axon reconstructions into biophysically-detailed compartmental models that could be activated by a standard cochlear transduction model. With these constraints, the models predict auditory nerve input profiles whereby all endbulbs onto a GBC are subthreshold (coincidence detection mode), or one or two inputs are suprathreshold (mixed mode). The models also predict the relative importance of dendrite geometry, soma size, and axon initial segment length in setting action potential threshold and generating heterogeneity in sound-evoked responses, and thereby propose mechanisms by which GBCs may homeostatically adjust their excitability. Volume EM also reveals new dendritic structures and dendrites that lack innervation. This framework defines a pathway from subcellular morphology to synaptic connectivity, and facilitates investigation into the roles of specific cellular features in sound encoding. We also clarify the need for new experimental measurements to provide missing cellular parameters, and predict responses to sound for furtherin vivostudies, thereby serving as a template for investigation of other neuron classes.
Evolutionary and cellular analysis of the dark pseudokinase PSKH2
Authors: Byrne Dominic P , Shrestha Safal , Daly Leonard A , Marensi Vanessa , Ramakrishnan Krithika , Eyers Claire E , Kannan Natarajan , Eyers Patrick A
Published: September 2022

Pseudokinases, so named because they lack one or more conserved canonical amino acids that define their catalytically-active relatives, have evolved a variety of biological functions in both prokaryotic and eukaryotic organisms. Human PSKH2 is closely related to the canonical kinase PSKH1, which maps to the CAMK family of protein kinases. Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue. Although the biological role(s) of vertebrate PSKH2’s remains unclear, we previously identified species-level adaptions in PSKH2 that have led to the appearance of kinase or pseudokinase variants in vertebrate genomes alongside a canonical PSKH1 paralog. In this paper we confirm that, as predicted, PSKH2 lacks detectable protein phosphotransferase activity, and exploit structural informatics, biochemistry and cellular proteomics to begin to characterise vertebrate PSKH2 orthologues. AlphaFold 2-based structural analysis predicts functional roles for both the PSKH2 N- and C-regions that flank the pseudokinase domain core, and cellular truncation analysis confirms that the N-terminal domain, which contains a conserved myristoylation site, is required for both stable human PSKH2 expression and localisation to a membrane-rich subcellular fraction containing mitochondrial proteins. Using mass spectrometry-based proteomics, we confirm that human PSKH2 is part of a cellular mitochondrial protein network, and that its expression is regulated through client-status within the HSP90/Cdc37 molecular chaperone system. HSP90 interactions are mediated through binding to the PSKH2 C-terminal tail, leading us to predict that this region might act as both a cis and trans regulatory element, driving outputs linked to the PSKH2 pseudokinase domain that are important for functional signalling.
Sialidases and Fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria
Authors: Shuoker Bashar , Pichler Michael J. , Jin Chunsheng , Hiroka Sakanaka , Wu Haiyang , Martínez Gascueña Ana , Liu Jining , Nielsen Tine Sofie , Holgersson Jan , Nordberg Karlsson Eva , Juge Nathalie , Meier Sebastian , Morth Jens Preben , Karlsson Niclas G. , Abou Hachem Maher
Published: September 2022

The gut mucolytic specialist Akkermansia muciniphila is strongly associated with the integrity of the mucus layer. Mucin glycan utilization requires the removal of diverse protective caps, notably, fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those with double sulphated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the exclusive sialyl T-antigen specificity of a sialidase of a previously unknown family and catalytic apparatus. Key cell attached sialidases and fucosidases conferred mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, the sialic acid fucose did not contribute to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unique mechanistic insight into the initiation of mucin O-glycan degradation by A. muciniphila and the nutrient sharing between key mucus-associated bacteria.
ARHGEF18 is a flow-responding exchange factor controlling endothelial tight junctions and vascular leakage
Authors: Batta Surya Prakash Rao , Rio Marc , Lebot Corentin , Baron-Menguy Céline , Moutaoukil Reda , Le Ruz Robin , Loirand Gervaise , Vion Anne-Clémence
Published: September 2022

The shear stress resulting from blood flow is a major regulator of endothelial cell (EC) biology and morphology. Rho protein-mediated cytoskeleton remodeling is an early and essential step of EC responses to flow. However, how Rho protein signaling is controlled by shear stress remains unclear. Here we demonstrate that phosphorylation, activity and expression of the Rho nucleotide exchange factor (RhoGEF) ARHGEF18 in ECs are modulated by the magnitude of shear stress. ARHGEF18 interacts with tight junctions, participates in ECs elongation and alignment and allows the maintenance of the endothelial barrier under physiological flow conditions. ARHGEF18 also promotes EC adhesion and migration by controlling focal adhesion formation.In vivo, ARHGEF18 is involved in flow response of ECs and in the control of vascular permeability in mice. Together, our results identified ARHGEF18 as the first flow-sensitive RhoGEF in ECs, whose activity is essential for the maintenance of intercellular junctions and the control of vascular permeabilityin vivo.
Mapping the glial transcriptome in Huntington’s disease using snRNAseq: Selective disruption of glial signatures across brain regions
Authors: Bøstrand Sunniva M. K. , Seeker Luise A. , Kazakou Nina-Lydia , Bestard-Cuche Nadine , Jäkel Sarah , Kenkhuis Boyd , Henderson Neil C. , de Bot Susanne T. , van Roon-Mom Willeke , Priller Josef , Williams Anna
Published: September 2022

Huntington’s disease (HD) is a severely debilitating, autosomal dominant neurodegenerative disease with a fatal outcome. There is accumulating evidence of a prominent role of glia in the pathology of HD, and we investigated this by conducting single nuclear RNA sequencing (snRNAseq) of human post mortem brain in four differentially affected regions; caudate nucleus, frontal cortex, hippocampus and cerebellum. Across 127,205 nuclei from people with HD, and age/sex matched controls, we found heterogeneity of glia which is altered in HD. We describe prominent changes in the abundance of certain subtypes of astrocytes, microglia, oligodendrocyte precursor cells and oligodendrocytes between HD and control samples, and these differences are widespread across brain regions. Furthermore, we highlight two possible mechanisms that characterise the glial contribution to disease pathology. Firstly, we show that upregulation of molecular chaperones represents a cross-glial signature in HD, which likely reflects an adaptive response to the accumulation of mutant Huntingtin (mHTT). Secondly, we show an oligodendrocyte-specific upregulation of the calmodulin-dependent 3’,5’-cyclic nucleotide phosphodiesterase 1A (PDE1A) in HD brain compared to controls, which may cause dysfunction of key cellular functions due to the downregulation of the important second messengers cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Our results support the hypothesis that glia have an important role in the pathology of HD, and show that all types of glia are affected in the disease. As glia are more tractable to treat than neurons, our findings may be of therapeutic relevance.
Postsynaptic receptors regulate presynaptic transmitter stability through trans-synaptic bridges
Authors: Godavarthi Swetha K. , Hiramoto Masaki , Ignatyev Yuri , Levin Jacqueline B. , Li Hui-quan , Pratelli Marta , Borchardt Jennifer , Czajkowski Cynthia , Borodinsky Laura N. , Sweeney Lora , Cline Hollis T. , Spitzer Nicholas C.
Published: September 2022

Stable matching of neurotransmitters with their receptors is fundamental to synapse function, to achieve reliable and robust communication in neural circuits. Presynaptic neurotransmitters regulate selection of postsynaptic transmitter receptors. However, whether postsynaptic receptors regulate selection of presynaptic transmitters is unknown. Here we show that blockade of postsynaptic acetylcholine receptors at the neuromuscular junction leads to loss of the cholinergic phenotype in motor neurons and stabilization of an earlier, developmentally transient glutamatergic phenotype. Exogenous postsynaptic expression of GABAAreceptors leads to the stabilization of an earlier, developmentally transient GABAergic motor neuron phenotype. Both acetylcholine receptors and GABA receptors are linked to presynaptic neurons through trans-synaptic bridges. Knock-down of different components of these trans-synaptic bridges prevents stabilization of the cholinergic and GABAergic phenotypes. We conclude that this bidirectional communication enforces a match between transmitter and receptor and ensures the fidelity of synaptic transmission. Our findings suggest a role of dysfunctional transmitter receptors in neurological disorders that involve the loss of the presynaptic transmitter.
The mobility of the cap domain is essential for the substrate promiscuity of a family IV esterase from sorghum rhizosphere microbiome
Authors: Distaso Marco , Cea-Rama Isabel , Coscolín Cristina , Chernikova Tatyana N. , Tran Hai , Ferrer Manuel , Sanz-Aparicio Julia , Golyshin Peter N.
Published: September 2022

Metagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of theSorghum bicolorrhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the eDNA was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0(Topt, 50 °C; Tm, 55.7 °C; pHopt, 9.5) was stable in the presence of 10-20% v/v organic solvents and exhibited hydrolytic activity againstp-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg−1), and a large battery of 69 structurally different esters (up to 30.2 U mg−1), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg−1). This broad substrate specificity contrasts with the fact that EH0showed a long and narrow catalytic tunnel, whose access appears to be hindered by a thigth folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, that altogether allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be immobile elements that contain hydrophobic patches involved in substrate pre-recognition and in turn substrate specificity within family IV esterases.

IMPORTANCE

A better understanding of structure–function relationships of enzymes allows revealing key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of theSorghum bicolorrhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilicParvibaculumandErythrobacterspp. and hyperthermophilicPyrobaculumandSulfolobusspp. and had a very narrow, single-entry access tunnel to the active site, access which is controlled by a capping domain that includes a number of not conserved proline residues. These structural markers, distinct from those of other substrate promiscuous esterases, can help tuning substrate profiles beyond tunnel and active site engineering.
SETD2 deficiency promotes renal fibrosis through the TGF-β/Smad signaling pathway in the absence of VHL
Authors: Liu Changwei , Li Xiaoxue , Zhu Yiwen , Feng Wenxin , Zhang Wei , Ma Chunxiao , Xu Yue , Gui Liming , Aji Rebiguli , Gao Wei-Qiang , Li Li
Published: September 2022

Renal fibrosis is the final development pathway and the most common pathological manifestation of chronic kidney disease. An important intrinsic cause of renal fibrosis is epigenetic alterations. SET domain–containing 2 (SETD2) is the sole histone H3K36 trimethyltransferase, catalyzing H3K36 dimethylation to trimethylation. There is evidence that SETD2-mediated epigenetic alterations are implicated in many diseases. However, it is unclear what role SETD2 plays in the development of renal fibrosis. Clinical data indicate that SETD2 is lowly expressed in patients with renal fibrosis. Here, we established genetically engineered mice with SETD2 and VHL deficiency. SETD2 deficiency leads to severe renal fibrosis in VHL-deficient mice. Mechanically, SETD2 maintains the transcriptional level of Smad7, a negative feedback factor of the TGF-β/Smad signaling pathway, thereby preventing the activation of the TGF-β/Smad signaling pathway. Deletion of SETD2 leads to reduced smad7 expression, which results in activation of the TGF-β/Smad signaling pathway and ultimately fibrosis in the absence of VHL. Our findings reveal the role of SETD2-mediated H3K36me3 of Smad7 in regulating the TGF-β/Smad signaling pathway in renal fibrogenesis. Thus, our study provides innovative insights into SETD2 as a potential therapeutic target for the treatment of renal fibrosis.
Germplasm Collections and Morphological Studies of Andropogon gayanus-Andropogon tectorum Complex in Southwestern Nigeria
Authors: Ojo Funmilola Mabel , Nwokeocha Chinyere Constance , Faluyi Julius Olaoye
Published: September 2022

Morphological studies were carried out on collections of Andropogon gayanus-Andropogon tectorum complex from Southwestern Nigeria. This is with the view to providing full characterization of the accession of the two species of Andropogon and elucidating their population dynamics.

Morphological data from selected accessions of A. gayanus and A. tectorum from different parts of Southwestern Nigeria were collected and characterized using an adaptation of the Descriptors for Wild and Cultivated Rice (Oryza spp), Biodiversity International. Preliminary morphological description of the accessions were carried out at the point of collection. Garden populations were raised from the vegetative parts of some accessions and maintained in Botanical Garden of the Obafemi Awolowo University, Ile-Ife. The data obtained were subjected to inferential tests and Duncan’s multiple range test.

The results revealed a distinct distribution pattern of the two species of Andropogon in the area of study which suggests a south-ward migration of Andropogon gayanus, that is from the northern vegetational zones of Nigeria to the southern ecological zones. The migration of A. gayanus around Igbeti with occasional occurrence of A. tectorum along the roadsides without any distinct phenotypic hybrid, and Budo-Ode in Oyo State is established as the southern limit of the spread of A. gayanus. This migration of A. gayanus to the South is not an invasion but a slow process. There was no A. gayanus encountered in Osun, Ondo, Ekiti and Ogun States. Andropogon gayanus and Andropogon tectorum do not only emerge from the rootstocks rapidly but can also produce independent propagules by rooting at some nodes. The plants can spread by means of these propagules even if it does not produce sexual or apomictic seeds. This potential for vegetative propagation in addition to the perennial habit confer considerable advantage for colonization by the Andropogon gayanus-Andropogon tectorum complex.
A small dynamic leaf-level model predicting photosynthesis in greenhouse tomatoes
Authors: Joubert D , Zhang N , Berman S.R. , Kaiser E , Molenaar J , Stigter J.D.
Published: September 2022

The conversion of supplemental greenhouse light energy into biomass is not always optimal. Recent trends in global energy prices and discussions on climate change highlight the need to reduce our energy footprint associated with the use of supplemental light in greenhouse crop production. This can be achieved by implementing “smart” lighting regimens which in turn rely on a good understanding of how fluctuating light influences photosynthetic physiology.

Here, a simple fit-for-purpose dynamic model is presented. It accurately predicts net leaf photosynthesis under natural fluctuating light. It comprises two ordinary differential equations predicting: 1) the total stomatal conductance to CO2 diffusion and 2) the CO2 concentration inside a leaf. It contains elements of the Farquhar-von Caemmerer-Berry model and the successful incorporation of this model suggests that for tomato (Solanum lycopersicum L.), it is sufficient to assume that Rubisco remains activated despite rapid fluctuations in irradiance. Furthermore, predictions of the net photosynthetic rate under both 400ppm and enriched 800ppm ambient CO2 concentrations indicate a strong correlation between the dynamic rate of photosynthesis and the rate of electron transport. Finally, we are able to indicate whether dynamic photosynthesis is Rubisco or electron transport rate limited.

Author summary

The cultivation of greenhouse crops under optimised conditions will become increasingly important, with supplemental lighting playing a vital role. However, converting light energy into plant photosynthesis is not always optimal. A potential venue that may lead to the efficient conversion of light energy involves a model-based implementation of “smart” lighting control strategy. This approach does however necessitate a good understanding of how plants harness light energy under natural fluctuating irradiance. Accordingly, as a first step, we have developed a small leaf-level model that predicts dynamic photosynthesis in natural fluctuating light. It may potentially be used in future supplemental light control applications.
FGF signaling regulates salivary gland branching morphogenesis by modulating cell adhesion
Authors: Ray Ayan T. , Soriano Philippe
Published: September 2022

Loss of FGF signaling leads to defects in salivary gland branching, but the mechanisms underlying this phenotype remain largely unknown. We disrupted expression of Fgfr1 and Fgfr2 in salivary gland epithelial cells and find that both receptors function coordinately in regulating branching. Strikingly, branching morphogenesis in double knockouts is restored by Fgfr1/2 knockin alleles incapable of engaging canonical RTK signaling, suggesting that additional FGF dependent mechanisms play a role during salivary gland branching. Fgfr1/2 conditional null mutants showed defective cell-cell and cell-matrix adhesion, both of which have been shown to play instructive roles in salivary gland branching. Loss of FGF signaling led to disordered cellbasement membrane interactions in vivo as well as in organ culture. This was partially restored upon introducing Fgfr1/2 wild type or signaling alleles incapable of eliciting canonical intracellular signaling. Together, our results identify non-canonical FGF signaling mechanisms that regulate branching morphogenesis through cell adhesion processes.
The effects of acute Methylene Blue administration on cerebral blood flow and metabolism in humans and rats
Authors: Singh Nisha , MacNicol Eilidh , DiPasquale Ottavia , Randall Karen , Lythgoe David , Mazibuko Ndabezinhle , Simmons Camilla , Selvaggi Pierluigi , Stephenson Stephanie , Turkheimer Federico E , Cash Diana , Zelaya Fernando , Colasanti Alessandro
Published: September 2022

Methylene Blue (MB) is a brain-penetrating drug with putative neuroprotective, antioxidant and metabolic enhancing effects. In vitro studies suggest that MB enhances mitochondrial complexes activity. However, no study has directly assessed the haemodynamic and metabolic effects of MB in the human brain.

We used in vivo neuroimaging to measure the effect of MB on cerebral blood flow (CBF) and brain metabolism in humans and in rats. Two doses of MB (0.5 and 1 mg/kg in humans; 2 and 4 mg/kg in rats; iv) induced reductions in global cerebral blood flow (CBF) in humans (F(1.74, 12.17)5.82, p=0.02) and rats (F(1,5)26.04, p=0.0038). Human cerebral metabolic rate of oxygen (CMRO2) was also significantly reduced (F(1.26, 8.84)8.01, p=0.016), as was the rat cerebral metabolic rate of glucose (CMRglu) (t=2.6(16) p=0.018).

This was contrary to our hypothesis that MB will increase CBF and energy metrics. Nevertheless, our results were reproducible across species and dose dependent. One possible explanation is that the concentrations used, although clinically relevant, reflect MB’s hormetic effects, i.e., higher concentrations produce inhibitory rather than augmentation effects on metabolism. Additionally, here we used healthy volunteers and healthy rats with normal cerebral metabolism where MB’s ability to enhance cerebral metabolism might be limited.
Rear cortex contraction aids in nuclear transit during confined migration by increasing pressure in the cell posterior
Authors: Keys Jeremy , Cheung Brian C.H. , Elpers Margaret A. , Wu Mingming , Lammerding Jan
Published: September 2022

As cells migrate through biological tissues, they must frequently squeeze through micron-sized constrictions in the form of interstitial pores between extracellular matrix fibers and/or other cells. Although it is now well recognized that such confined migration is limited by the nucleus, which is the largest and stiffest organelle, it remains incompletely understood how cells apply sufficient force to move their nucleus through small constrictions. Here, we report a mechanism by which contraction of the cell rear cortex pushes the nucleus forward to mediate nuclear transit through constrictions. Laser ablation of the rear cortex reveals that pushing forces behind the nucleus are the result of increased intracellular pressure in the rear compartment of the cell. The pushing forces behind the nucleus depend on accumulation of actomyosin in the rear cortex and require Rho-kinase (ROCK) activity. Collectively, our results suggest a mechanism by which cells generate elevated, intracellular pressure in the posterior compartment to facilitate nuclear transit through 3D constrictions. This mechanism may supplement or even substitute for other mechanisms supporting nuclear transit, ensuring robust cell migrations in confined 3D environments.
The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus
Authors: Godfroy Olivier , Zheng Min , Yao Haiqin , Henschen Agnes , Peters Akira F. , Scornet Delphine , Colin Sebastien , Ronchi Paolo , Hipp Katharina , Nagasato Chikako , Motomura Taizo , Cock J. Mark , Coelho Susana M.
Published: September 2022

The first mitotic division of the initial cell is a key event in all multicellular organisms and is usually concomitant with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular and independent generations, the sporophyte and the gametophyte. Each generation deploys a distinct developmental program autonomously from an initial cell, whose first cell division sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first division of the initial cell and subsequently failure to produce basal structures (rhizoids and prostrate filaments) during both generations of the life cycle. Cloning-by-sequencing revealed that BAS encodes a type B” regulatory subunit of protein phosphatase 2A, and transcriptomic analysis of early developmental stages uncovered potential effector genes involved in setting up basal cell fate in this organism. The bas mutant phenotype is very similar to that observed in the distag (dis) mutants, which lack a functional TBCCd1 protein, at both the cellular and morphological levels. The high level of similarity of the dis and bas mutant phenotypes indicate that TBCCd1 and PP2A are two critical components of the cellular machinery that regulates the division of the initial cell and mediates the establishment of basal cell fate in the developing thallus.
An ImageJ-based tool for three-dimensional registration between different types of microscopic images
Authors: Koyama Hiroshi , Kishi Kanae , Fujimori Toshihiko
Published: September 2022

Three-dimensional (3D) registration (i.e. alignment) between two microscopic images is substantially helpful to study tissues not adhere to substrates such as mouse embryos and organoids which are often three-dimensionally rotated during imaging. However, there is no 3D registration tool easily accessible for experimental biologists. Here we developed an ImageJ-based tool which achieves 3D registration accompanying both quantitative evaluation of the accuracy and reconstruction of 3D rotated images. In this tool, several landmarks are manually provided in two images to be aligned, and 3D rotation is computed so that the distances between the paired landmarks from the two images are minimized. By simultaneously providing multiple points (e.g. all nuclei in the regions of interest) other than the landmarks in the two images, the correspondence of each point between the two images is quantitatively explored: a certain nucleus in one image corresponds to which nucleus in another image. Furthermore, the 3D rotation is applied to one of the two images, resulting in reconstruction of 3D rotated images. We demonstrated that this tool successfully achieved 3D registration and reconstruction of images in mouse pre-implantation embryos, where one image was obtained during live imaging and another image from fixed embryos after live imaging. This approach provides a versatile tool applicable for various tissues and species.
Mutational Landscape of Cancer-Driver Genes Across Human Cancers
Authors: Sinkala Musalula
Published: September 2022

The cancer driver genes are involved in transforming healthy cells into cancerous cells. The molecular aberrations which lead to cancer involve gain and loss of function mutations in various cancer driver genes. Here, we examine the genome sequences of 20,066 primary tumours representing 43 distinct human cancers to identify and catalogue driver mutations in 729 known cancer genes. We show that the frequency of driver mutations in these genes varies significantly between cancer types. We find that the class of cancer driver genes most frequently mutated are the tumour suppressor genes (94%), followed by oncogenes (93%), transcription factors (72%), kinases (64%), cell surface receptors (63%), and phosphatases (22%). Furthermore, we identify the subset of these genes within which mutations exhibit a co-occurrence or mutually exclusive pattern. Interestingly, we find that patients with tumours with different combinations of driver gene mutation patterns tend to exhibit variable survival outcomes. Here, among the well-studied cancer genes, we showed that patients with tumours with KRAS and TP53 mutations are associated with the worst disease outcomes, and those with PI3KCA and BRAF mutations are associated with favourable survival outcomes. Besides providing new insights into cancer driver mutations, we unearth mutation patterns associated with disease outcomes and various hallmarks of cancer that bring us closer to fully understanding various forms of cancer.