bluuebunny/crossref_metadata_2025 huggingface dataset:
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
Authors: Thomasen F. Emil , Skaalum Tórur , Kumar Ashutosh , Srinivasan Sriraksha , Vanni Stefano , Lindorff-Larsen Kresten
Published: May 2023

Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is diffcult. We have previously shown that the coarse-grained model, Martini 3, produces too compact ensembles in solution, that may in part be remedied by strengthening protein–water interactions. Here, we show that decreasing the strength of protein–protein interactions leads to improved agreement with experimental data on a wide set of systems. We show that the ‘symmetry’ between rescaling protein–water and protein–protein interactions breaks down when studying interactions with or within membranes; rescaling protein-protein interactions better preserves the binding specificity of proteins with lipid membranes, whereas rescaling protein-water interactions preserves oligomerization of transmembrane helices. We conclude that decreasing the strength of protein–protein interactions improves the accuracy of Martini 3 for IDPs and multidomain proteins, both in solution and in the presence of a lipid membrane.
Chronic high-sugar diet in adulthood protectsCaenorhabditis elegansfrom 6-OHDA induced dopaminergic neurodegeneration
Authors: Morton Katherine S. , Hartman Jessica H. , Heffernan Nathan , Ryde Ian T. , Kenny-Ganzert Isabel W. , Meng Lingfeng , Sherwood David R. , Meyer Joel N.
Published: May 2023

Background

Diets high in saturated fat and sugar, termed ‘western diets’, have been associated with several negative health outcomes, including increased risk for neurodegenerative disease. Parkinson’s Disease (PD) is the second most prevalent neurodegenerative disease and is characterized by the progressive death of dopaminergic neurons in the brain. We build upon previous work characterizing the impact of high sugar diets inCaenorhabditis elegansto mechanistically evaluate the relationship between high sugar diets and dopaminergic neurodegeneration.

Results

Adult high glucose and fructose diets, or exposure from day 1-5 of adulthood, led to increased lipid content and shorter lifespan and decreased reproduction. However, in contrast to previous reports, we found that adult chronic high-glucose and high-fructose diets did not induce dopaminergic neurodegeneration alone and were protective from 6-hydroxydopamine (6-OHDA) induced degeneration. Neither sugar altered baseline electron transport chain function, and both increased vulnerability to organism-wide ATP depletion when the electron transport chain was inhibited, arguing against energetic rescue as a basis for neuroprotection. The induction of oxidative stress by 6-OHDA is hypothesized to contribute to its pathology, and high sugar diets prevented this increase in the soma of the dopaminergic neurons. However, we did not find increased expression of antioxidant enzymes or glutathione levels. Instead, we found evidence suggesting downregulation of the dopamine reuptake transporterdat-1that could result in decreased 6-OHDA uptake.

Conclusion

Our work uncovers a neuroprotective role for high sugar diets, despite concomitant decreases in lifespan and reproduction. Our results support the broader finding that ATP depletion alone is insufficient to induce dopaminergic neurodegeneration, whereas increased neuronal oxidative stress may drive degeneration. Finally, our work highlights the importance of evaluating lifestyle by toxicant interactions.
Altered methionine metabolism impacts phenylpropanoid production and plant development inArabidopsis thaliana
Authors: Shin Doosan , Perez Veronica C. , Dickinson Gabriella K. , Zhao Haohao , Dai Ru , Tomiczek Breanna , Cho Keun Ho , Zhu Ning , Koh Jin , Grenning Alexander , Kim Jeongim
Published: May 2023

Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine-ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear.

Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants,ref2andref5. REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities.ref2andref5mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx respectively, it was assumed thatref2accumulates AAOx, not IAOx. Our study indicates thatref2accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid production inref2, but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity inref2were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation.

Significance Statement

Aliphatic aldoximes are precursors of various specialized metabolites including defense compounds. This study reveals that aliphatic aldoximes repress phenylpropanoid production and that altered methionine metabolism affects plant growth and development. As phenylpropanoids include vital metabolites such as lignin, a major sink of fixed carbon, this metabolic link may contribute to available resource allocation during defense.
Neuroimaging Signatures of Metacognitive Improvement in Sensorimotor Timing
Authors: Bader Farah , Wiener Martin
Published: May 2023

Error monitoring is an essential human ability underlying learning and metacognition. In the time domain, humans possess a remarkable ability to learn and adapt to temporal intervals, yet the neural mechanisms underlying this are not well understood. Recently, we demonstrated that humans exhibit improvements in sensorimotor time estimates when given the chance to incorporate feedback from a previous trial (Bader and Wiener 2021), suggesting that humans are metacognitively aware of their own timing errors. To test the neural basis of this metacognitive ability, human participants of both sexes underwent fMRI while they performed a visual temporal reproduction task with randomized suprasecond intervals (1-6s). Crucially, each trial was repeated following feedback, allowing a “re-do” to learn from the successes or errors in the initial trial. Behaviorally, we replicated our previous finding that subjects improve their performance on re-do trials despite the feedback being temporally uninformative (i.e. early or late). For neuroimaging, we observed a dissociation between estimating and reproducing time intervals, with the former more likely to engage regions associated with the default mode network (DMN), including the superior frontal gyri, precuneus, and posterior cingulate, whereas the latter activated regions associated traditionally with the “Timing Network” (TN), including the supplementary motor area (SMA), precentral gyrus, and right supramarginal gyrus. Notably, greater DMN involvement was observed in Re-do trials. Further, the extent of the DMN was greater on re-do trials, whereas for the TN it was more constrained. Finally, Task-based connectivity between these networks demonstrated higher inter-network correlation on initial trials, but primarily when estimating trials, whereas on re-do trials communication was higher during reproduction. Overall, these results suggest the DMN and TN work in concert to mediate subjective awareness of one’s sense of time for the purpose of improving timing performance.

Significance Statement

A finely tuned sense of time perception is imperative for everyday motor actions (e.g., hitting a baseball). Timing self-regulation requires correct assessment and updating duration estimates if necessary. Using a modified version of a classical task of time measurement, we explored the neural regions involved in error detection, time awareness, and learning to time. Reinforcing the role of the SMA in measuring temporal information and providing evidence of co-activation with the DMN, this study demonstrates that the brain overlays sensorimotor timing with a metacognitive awareness of its passage.
An Open-Source Tool for Automated Human-Level Circling Behavior Detection
Authors: Stanley O.R. , Swaminathan A. , Wojahn E. , Ahmed Z. M. , Cullen K. E.
Published: May 2023

Quantifying behavior and relating it to underlying biological states is of paramount importance in many life science fields. Although barriers to recording postural data have been reduced by progress in deep-learning-based computer vision tools for keypoint tracking, extracting specific behaviors from this data remains challenging. Manual behavior coding, the present gold standard, is labor-intensive and subject to intra-and inter-observer variability. Automatic methods are stymied by the difficulty of explicitly defining complex behaviors, even ones which appear obvious to the human eye. Here, we demonstrate an effective technique for detecting one such behavior, a form of locomotion characterized by stereotyped spinning, termed ’circling’. Though circling has an extensive history as a behavioral marker, at present there exists no standard automated detection method. Accordingly, we developed a technique to identify instances of the behavior by applying simple postprocessing to markerless keypoint data from videos of freely-exploring (Cib2-/-;Cib3-/-) mutant mice, a strain we previously found to exhibit circling. Our technique agrees with human consensus at the same level as do individual observers, and it achieves >90% accuracy in discriminating videos of wild type mice from videos of mutants. As using this technique requires no experience writing or modifying code, it also provides a convenient, noninvasive, quantitative tool for analyzing circling mouse models. Additionally, as our approach was agnostic to the underlying behavior, these results support the feasibility of algorithmically detecting specific, research-relevant behaviors using readily-interpretable parameters tuned on the basis of human consensus.
Rescue of secretion of a rare-disease associated mis-folded mutant glycoprotein inUGGT1knock-out mammalian cells
Authors: Tax Gábor , Guay Kevin P. , Soldà Tatiana , Hitchman Charlie J. , Hill Johan C. , Vasiljević Snežana , Lia Andrea , Modenutti Carlos P. , Straatman Kees R. , Santino Angelo , Molinari Maurizio , Zitzmann Nicole , Hebert Daniel N. , Roversi Pietro , Trerotola Marco
Published: May 2023

Endoplasmic reticulum (ER) retention of mis-folded glycoproteins is mediated by the ER- localised eukaryotic glycoprotein secretion checkpoint, UDP-glucose glycoprotein glucosyl-transferase (UGGT). The enzyme recognises a mis-folded glycoprotein and flags it for ER retention by reglucosylating one of its N-linked glycans. In the background of a congenital mutation in a secreted glycoprotein gene, UGGT-mediated ER retention can cause rare disease even if the mutant glycoprotein retains activity (“responsive mutant”). Here, we investigated the subcellular localisation of the human Trop-2 Q118E variant, which causes gelatinous drop- like corneal dystrophy (GDLD). Compared with the wild type Trop-2, which is correctly localised at the plasma membrane, the Trop-2-Q118E variant is found to be heavily retained in the ER. Using Trop-2-Q118E, we tested UGGT modulation as a rescue-of-secretion therapeutic strategy for congenital rare disease caused by responsive mutations in genes encoding secreted glycoproteins. We investigated secretion of a EYFP-fusion of Trop-2-Q118E by confocal laser scanning microscopy. As a limiting case of UGGT inhibition, mammalian cells harbouring CRISPR/Cas9-mediated inhibition of theUGGT1and/orUGGT2gene expressions were used. The membrane localisation of the Trop-2-Q118E-EYFP mutant was successfully rescued inUGGT1-/-andUGGT1/2-/-cells. UGGT1 also efficiently reglucosylated Trop-2-Q118E-EYFPin cellula. The study supports the hypothesis that UGGT1 modulation constitutes a novel therapeutic strategy for the treatment of Trop-2-Q118E associated GDLD, and it encourages the testing of modulators of ER glycoprotein folding Quality Control (ERQC) as broad-spectrum rescue- of-secretion drugs in rare diseases caused by responsive secreted glycoprotein mutants.

Synopsis

Deletion of theUGGT1andUGGT1/2genes in HEK 293T cells rescues secretion of an EYFP-fusion of the human Trop-2-Q118E glycoprotein mutant. The mutant is retained in the secretory pathway in wild type cells and it localises to the cell membrane inUGGT1-/-single andUGGT1/2-/-double knock-out cells. The Trop-2-Q118E glycoprotein disease mutant is efficiently glucosylated by UGGT1 in human cells demonstrating that it is abona fidecellular UGGT1 substrate.
Reconstructing stochastic cell population trajectories reveals regulators and heterogeneity of endothelial flow-migration coupling driving vascular remodelling
Authors: Giese Wolfgang , Rosa André , Baumann Elisabeth , Oppenheim Olya , Akmeric Emir B. , Andrade Santiago , Hollfinger Irene , Bartels-Klein Eireen , Alt Silvanus , Gerhardt Holger
Published: May 2023

Emerging concepts of developmental vascular remodelling recently identified that selectively labelled sprouting tip cells and/or venous endothelial cells (ECs) accumulate in developing arteries, suggesting directional migration of specific ECs drives artery formation. However, a general population analysis and detailed quantitative investigation of migratory mechanisms is so far lacking. Here, we developed a universally applicable quantitative approach and a computational model allowing to track and simulate stochastically labelled EC populations irrespective of labelling density and origin. Dynamic mapping of EC distributions in a bespoke coordinate system revealed how ECs move during the most active remodelling phases in the mouse retina. Simulation and parameter sensitivity analysis illustrated that the population shift from veins to arteries cannot be explained by random walk, but best fits to a tuneable dual force-field between shear-force induced directionality against blood flow, and hypoxia mediated VEGFA-gradients. High migration rates require only weak flow-migration coupling, whereas low migration rates require strong coupling to the flow direction. Functional analysis identified Cdc42 as the critical mediator of overall population movement from veins to arteries, yet with surprising heterogeneity suggesting the existence of distinct cell populations. This new quantitative understanding will enable future tailored intervention and tuning of the remodelling process.
Structural evidence for MADS-box type I family expansion seen in new assemblies ofA. arenosaandA. lyrata
Authors: Bramsiepe Jonathan , Krabberød Anders K. , Bjerkan Katrine N. , Alling Renate M. , Johannessen Ida M. , Hornslien Karina S. , Miller Jason R. , Brysting Anne K. , Grini Paul E.
Published: May 2023

Arabidopsis thalianadiverged fromA. arenosaandA. lyrataat least 6 million years ago and are identified by genome-wide polymorphisms or morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based in the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors are specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for a high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using twode-novoassembled and annotated chromosome-level genomes ofA. arenosaandA. lyratassp.petraeawe analyzed the MADS-box type I gene family inArabidopsisto predict orthologs, copy number and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression betweenA. arenosaandA. lyratassp.petraeain the endosperm, suggesting a genetic cause for the endosperm-based hybridization barrier inA. arenosaandA. lyratassp.petraeahybrid seeds.
OAS3 and RNase L integrate into higher-order antiviral condensates
Authors: Cusic Renee , Burke James M.
Published: May 2023

Oligoadenylate synthetase 3 (OAS3) and Ribonuclease L (RNase L) are components of a mammalian RNA decay pathway that is critical for combating viral infection. Nevertheless, the subcellular localization of OAS3 and RNase L during the antiviral response has remained elusive. Herein, we show that upon activation in response to double-stranded RNA or viral infection, OAS3 and RNase L integrate into higher-order cytoplasmic assemblies distinct from stress granules (SGs), RNase L-induced bodies (RLBs), or processing bodies (P-bodies). We identified these assemblies as double-stranded RNA-induced foci (dRIF), which also contain activated protein kinase R (PKR). We observed incorporation of RNase L, OAS3, and PKR in dRIFs during Zika virus and dengue virus infection. Our data support that condensation of dsRNA, OAS3 and RNase L at dRIFs promotes the homodimerization and oligomerization of RNase L required for its rapid activation, demonstrating a fundamental role for biological condensates in activating antiviral signaling.
In-cell structural insight into the stability of sperm microtubule doublet
Authors: Tai Linhua , Yin Guoliang , Huang Xiaojun , Zhu Yun , Sun Fei
Published: May 2023

The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of sperm DMT remains elusive. Here, byin situcryo-electron tomography, we solved the in-cell structure of mouse sperm DMT up to 3.6 Å resolution and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of sperm DMT that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
The variation and evolution of complete human centromeres
Authors: Logsdon Glennis A. , Rozanski Allison N. , Ryabov Fedor , Potapova Tamara , Shepelev Valery A. , Mao Yafei , Rautiainen Mikko , Koren Sergey , Nurk Sergey , Porubsky David , Lucas Julian K. , Hoekzema Kendra , Munson Katherine M. , Gerton Jennifer L. , Phillippy Adam M. , Alexandrov Ivan A. , Eichler Evan E.
Published: May 2023

We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that centromere single-nucleotide variation can increase by up to 4.1-fold relative to other genomic regions, with the caveat that up to 45.8% of centromeric sequence, on average, cannot be reliably aligned with current methods due to the emergence of new α-satellite higher-order repeat (HOR) structures and two to threefold differences in the length of the centromeres. The extent to which this occurs differs depending on the chromosome and haplotype. Comparing the two sets of complete human centromeres, we find that eight harbor distinctly different α-satellite HOR array structures and four contain novel α-satellite HOR variants in high abundance. DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by at least 500 kbp—a property not readily associated with novel α-satellite HORs. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan, and macaque genomes. Comparative analyses reveal nearly complete turnover of α-satellite HORs, but with idiosyncratic changes in structure characteristic to each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the p- and q-arms of human chromosomes and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
Exogenous Recombinant N-Acetylgalactosamine-4-Sulfatase (Arylsulfatase B; ARSB) Inhibits Progression of B16F10 Cutaneous Melanomas and Modulates Cell Signaling
Authors: Bhattacharyya Sumit , O-Sullivan Insug , Tu Jieqi , Chen Zhengjia , Tobacman Joanne K.
Published: May 2023

In the syngeneic, subcutaneous B16F10 mouse model of malignant melanoma, treatment with exogenous ARSB markedly reduced tumor size and extended survival.In vivoexperiments showed that local treatment with exogenous N-acetylgalactosamine-4-sulfatase (Arylsulfatase B; ARSB) led to reduced tumor growth over time (p<0.0001) and improved the probability of survival up to 21 days (p=0.0391). Tumor tissue from the treated mice had lower chondroitin 4-sulfate (C4S) content and lower sulfotransferase activity. The free galectin-3 declined, and the SHP2 activity increased, due to altered binding with chondroitin 4-sulfate. These changes induced effects on transcription, which were mediated by Sp1, phospho-ERK1/2, and phospho-p38 MAPK. Reduced mRNA expression of chondroitin sulfate proteoglycan 4 (CSPG4), chondroitin sulfotransferase 15 (N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase), and matrix metalloproteinases 2 and 9 resulted. Experiments in the human melanoma cell line A375 demonstrated similar responses to exogenous ARSB as in the tumors, and inverse effects followed RNA silencing. ARSB, which removes the 4-sulfate group at the non-reducing end of C4S, acts as a tumor suppressor, and treatment with exogenous ARSB impacts on vital cell signaling and reduces the expression of critical genes associated with melanoma progression.

Highlights:

Exogenous ARSB reduced tumor size and increased survival

Chondroitin 4-sulfate increased, leading to increased free galectin-3

mRNA expression of CSPG4 and CHST15 declined following ARSB treatment

mRNA expression of MMP9 and pro-MMP2 declined following ARSB treatment

Active SHP2 increased, leading to declines in phospho-ERK1/2 and phospho-p38 MAPK
Human amygdala volumetric patterns convergently evolved in cooperatively breeding and domesticated species
Authors: Cerrito Paola , Burkart Judith M.
Published: May 2023

Purpose

The amygdala is a hub in brain networks that supports social life and fear processing. Compared to other apes, humans have a relatively larger lateral nucleus of the amygdala, which is consistent with both the self-domestication and the cooperative breeding hypothesis of human evolution.

Methods

Here, we take a comparative approach to the evolutionary origin of the relatively larger lateral amygdala nucleus in humans. We carry out phylogenetic analysis on a sample of 17 mammalian species for which we acquired single amygdala nuclei volumetric data.

Results

Our results indicate that there has been convergent evolution toward larger lateral amygdala nuclei in both domesticated and cooperatively breeding mammals.

Conclusion

These results suggest that changes in processing fearful stimuli to reduce fear-induced aggression, which are necessary for domesticated and cooperatively breeding species alike, tap into the same neurobiological proximate mechanism. However, humans show not only changes in processing fearful stimuli but also in prosociality. Since cooperative breeding, but not domestication, is also associated with prosociality, a prominent role of the former during human evolution is more parsimonious, whereas self-domestication may have been involved as an additional stepping stone.
Bioluminescence imaging ofCyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung
Authors: Veland Nicolas , Gleneadie Hannah J , Brown Karen E , Sardini Alessandro , Pombo Joaquim , Dimond Andrew , Burns Vanessa , Sarkisyan Karen , Schiering Chris , Webster Zoe , Merkenschlager Matthias , Fisher Amanda G
Published: May 2023

Aryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such asCyp1a1. To dynamically visualise AHR activityin vivo,we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenousCyp1a1locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal andCyp1a1expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustainedCyp1a1expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespokeCyp1a1-Flucreporters to longitudinally monitor AHR activityin vivo.
Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth
Authors: Summers Jody A. , Jones Kenneth L.
Published: May 2023

Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.
Retracing the evolution of a modern periplasmic binding protein
Authors: Michel Florian , Romero-Romero Sergio , Höcker Birte
Published: May 2023

Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimerin vitroandin-cell. The X-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.
The oncogene cyclin D1 promotes bipolar spindle integrity under compressive force
Authors: Sutanto Renaldo , Neahring Lila , Marques Andrea Serra , Kilinc Seda , Goga Andrei , Dumont Sophie
Published: May 2023

The mitotic spindle is the bipolar, microtubule-based structure that segregates chromosomes at each cell division. Aberrant spindles are frequently observed in cancer cells, but how oncogenic transformation affects spindle mechanics and function, particularly in the mechanical context of solid tumors, remains poorly understood. Here, we constitutively overexpress the oncogene cyclin D1 in human MCF10A cells to probe its effects on spindle architecture and response to compressive force. We find that cyclin D1 overexpression increases the incidence of spindles with extra poles, centrioles, and chromosomes. However, it also protects spindle poles from fracturing under compressive force, a deleterious outcome linked to multipolar cell divisions. Our findings suggest that cyclin D1 overexpression may adapt cells to increased compressive stress, contributing to its prevalence in cancers such as breast cancer by allowing continued proliferation in mechanically challenging environments.
A high-content screen reveals new regulators of nuclear membrane stability
Authors: Gunn Amanda L. , Yashchenko Artem I. , Dubrulle Julien , Johnson Jodiene , Hatch Emily M.
Published: May 2023

Nuclear membrane rupture is a physiological response to multiplein vivoprocesses, such as cell migration, that can cause extensive genome instability and upregulate invasive and inflammatory pathways. However, the underlying molecular mechanisms of rupture are unclear and few regulators have been identified. In this study, we developed a reporter that is size excluded from re-compartmentalization following nuclear rupture events. This allows for robust detection of factors influencing nuclear integrity in fixed cells. We combined this with an automated image analysis pipeline in a high-content siRNA screen to identify new proteins that both increase and decrease nuclear rupture frequency in cancer cells. Pathway analysis identified an enrichment of nuclear membrane and ER factors in our hits and we demonstrate that one of these, the protein phosphatase CTDNEP1, is required for nuclear stability. Further analysis of known rupture contributors, including a newly developed automated quantitative analysis of nuclear lamina gaps, strongly suggests that CTDNEP1 acts in a new pathway. Our findings provide new insights into the molecular mechanism of nuclear rupture and define a highly adaptable program for rupture analysis that removes a substantial barrier to new discoveries in the field.
Visual deprivation during mouse critical period reorganizes network-level functional connectivity
Authors: Chen Siyu , Rahn Rachel M. , Bice Annie R. , Bice Seana H. , Padawer-Curry Jonah A. , Hengen Keith B. , Dougherty Joseph D. , Culver Joseph P.
Published: May 2023

A classic example of experience-dependent plasticity is ocular dominance (OD) shift, in which the responsiveness of neurons in the visual cortex is profoundly altered following monocular deprivation (MD). It has been postulated that OD shifts also modify global neural networks, but such effects have never been demonstrated. Here, we used longitudinal wide-field optical calcium imaging to measure resting-state functional connectivity during acute (3-day) MD in mice. First, delta GCaMP6 power in the deprived visual cortex decreased, suggesting that excitatory activity was reduced in the region. In parallel, interhemispheric visual homotopic functional connectivity was rapidly reduced by the disruption of visual drive through MD and was sustained significantly below baseline state. This reduction of visual homotopic connectivity was accompanied by a reduction in parietal and motor homotopic connectivity. Finally, we observed enhanced internetwork connectivity between visual and parietal cortex that peaked at MD2. Together, these findings support the hypothesis that early MD induces dynamic reorganization of disparate functional networks including association cortices.

Significance Statement

Monocular deprivation during the visual critical period triggers several plasticity mechanisms that collaborate to shift the excitability of neurons in the visual cortex. However, little is known about the impacts of MD on cortex-wide functional networks. Here, we measured cortical functional connectivity during short-term critical period MD. We demonstrate that critical period MD has immediate effects on functional networks beyond the visual cortex, and identify regions of substantial functional connectivity reorganization in response to MD.
Long-term structural plasticity of hippocampal dendritic spines following contextual fear memory reactivation
Authors: Medina Candela , Ramos Santiago Ojea , Miller Lucas Pozzo , Romano Arturo , de la Fuente Verónica
Published: May 2023

Dendritic spines are plastic structures exhibiting a high degree of morphological variability. Certain morphometric parameters, such as volume, positively correlate with the strength of the synapse in which they participate. Memories, too, are subject to change over time and with experiences. In particular, the presence of a reminder of a learning event can trigger the labilization of the memory trace, followed by a re-stabilization process termed reconsolidation. The underlying mechanisms behind the labilization/reconsolidation processes are of great interest, as they are thought of as possible targets for the treatment of post-traumatic stress disorders. Dendritic spines have long been considered the physical sites for memory formation and storage. Our work aimed at studying the long-term spine morphological plasticity associated with labilization/reconsolidation in the dorsal hippocampus, a brain region relevant for the formation of contextual memories. Our results suggest that labilization/reconsolidation does not affect spine density, but rather induces changes in spine morphology. Furthermore, we show that some of these changes are prevented by the inhibition of the transcription factor NF-κB inhibition. Finally, we found that NF-κB negative modulation also affects spine morphology in animals that were not exposed to recall but have undergone the training session, suggesting that there may be a late surge of NF-κB activity resulting from the consolidation itself.
Efficient taxa identification using a pangenome index
Authors: Ahmed Omar , Rossi Massimiliano , Boucher Christina , Langmead Ben
Published: May 2023

Tools that classify sequencing reads against a database of reference sequences require efficient index data-structures. Ther-index is a compressed full-text index that answers substring presence/absence, count, and locate queries in space proportional to the amount of distinct sequence in the database:O(r)space, whereris the number of Burrows–Wheeler runs. To date, ther-index has lacked the ability to quickly classify matches according to which reference sequences (or sequence groupings, i.e., taxa) a match overlaps. We present new algorithms and methods for solving this problem. Specifically, given a collection D ofddocuments,D={T1,T2,…,Td}over an alphabet of size σ, we extend ther-index withO(rd)additional words to support document listing queries for a patternS[1..m]that occurs inndocdocuments in D inO(mlog⁡logw(σ+n/r)+ndoc)time andO(rd)space, wherewis the machine word size. Applied in a bacterial mock community experiment, our method is up to three times faster than a comparable method that uses the standardr-index locate queries. We show that our method classifies both simulated and real nanopore reads at the strain level with higher accuracy compared with other approaches. Finally, we present strategies for compacting this structure in applications in which read lengths or match lengths can be bounded.
Mediating roles of employee cynicism and workplace ostracism on the relationship between perceived organizational politics and counterproductive work behavior
Authors: Ugwu Fabian , Nwali Anthony C. , Ugwu Lawrence E. , Okafor Chiedozie O. , Ozurumba Keyna C. , Onyishi Ike E.
Published: May 2023

Purpose

This study investigated employee cynicism and workplace ostracism as pathways through which perceived organizational politics (POPs) is related to counterproductive work behavior (CWB) targeted at individual coworkers (CWB-I) and the organization (CWB-O).

Design/methodology/approach

Data were collected from 794 university employees in Southeastern, Nigeria at three-point of measurements.

Findings

Results of the Structural Equation Modelling showed that POPs positively predicted CWB-I but did not predict CWB-O directly. POPs positively predicted both employee cynicism and workplace ostracism. Employee cynicism did not predict CWB-I and CWB-O, but workplace ostracism positively predicted both CWB-I and CWB-O. Moreover, whilst POPs did not predict both CWB-I and CWB-O through employee cynicism; workplace ostracism partially mediated the relationship between POPs and the two dimensions of CWB.

Originality/value

The relationship between POPs and CWB has been documented in the literature, but whether affect-laden processes (employee cynicism and workplace ostracism) explain this relationship is new. Conducting the study in a context previously neglected extended our understanding of the indirect relationship between POPs and CWB.
A study of cash waqf contribution between millennials of Malaysia and Indonesia
Authors: Allah Pitchay Anwar , Sukmana Raditya , Ratnasari Ririn Tri , Abd Jalil Mohamad Isa
Published: May 2023

Purpose

This study aims to examine the determinants of motivation that influences Malaysian and Indonesian millennials to contribute cash waqf.

Design/methodology/approach

The present study used self-determination theory and 423 respondents, of which 205 respondents are from Malaysia and 218 from Indonesia. The study developed a self-administrative questionnaire, and it is distributed through an online survey method, and the data are analysed using SmartPLS partial least squares analysis.

Findings

The results show that perceived donor effectiveness and moral obligation factors influence both Malaysians and Indonesian millennials to make cash waqf contributions. Meanwhile, the face concern factor did not significantly affect millennials in Malaysia and Indonesia to contribute cash waqf. Furthermore, the sense of self-worth factor appears to significantly influence only Indonesian millennials but not Malaysian millennials.

Research limitations/implications

The research findings have significant theoretical and practical ramifications. Firstly, while face concern has a positive effect on millennials’ willingness to contribute cash to waqf, it is not statistically significant in Muslim populations. This implies that to persuade millennials to make cash waqf contributions, the face concern argument should be avoided.

Originality/value

The comparative study between Malaysia and Indonesia adds new value to this study. These two Muslim majority countries have similar attributes in terms of religion, demography and race background. Furthermore, the focus of this study, which targets units of analysis from millennials, has received very little attention in the literature related to cash waqf.
Factors influencing SMEs’ intention to adopt electronic tendering: empirical evidence from an emerging African market
Authors: Nassir Souad , Lebdaoui Imane , Chetioui Youssef , Lebdaoui Hind
Published: May 2023

Purpose

Despite the digitalization reforms attempting to enhance public service quality, paper-based tendering is still widely used in a number of developing countries (i.e. Morocco). This has led to many issues including waste of time, higher costs as well as labor-intensive issues. E-tendering has been widely recommended as a key resolution. Still, both scholars and practitioners raised concerns related the readiness of small and medium enterprises (SMEs) to this digitalization process. The current research aims to investigate the key drivers of SMEs intention to adopt electronic tendering in the context of an emerging African market (i.e. Morocco). Specifically, the authors focus on SMEs contributing to the public procurement process and registered in the online portal recently created by the Moroccan government.

Design/methodology/approach

To achieve this goal, the authors proposed a conceptual model combining the unified theory of acceptance and use of technology (UTAUT) and technology acceptance model (TAM). Based on data collected from suppliers participating in Moroccan public tenders, the authors empirically tested the conceptual model using a partial least squares (PLS) estimation.

Findings

Facilitating conditions and social influence had a positive impact on SMEs intention to adopt electronic tendering. The study’s findings also convey a negative impact of effort expectancy on SMEs intent to adopt e-tendering. Unexpectedly, perceived performance had no significant impact on the intention to adopt electronic bidding among Moroccan SMEs.

Originality/value

This research filled the gap in the literature with regards to SMEs e-Tendering readiness in emerging markets. With the recent digitalization reforms of public tendering in many developing economies (i.e. Morocco), the study findings can be used to improve not only government implementation of electronic bidding but also SMEs' user experience.
Pedagogical considerations for enhancing peer support training in an online university environment
Authors: Witte Tricia H. , Mumba Mercy Ngosa , Jaiswal Jessica , Evans Teairra , Mugoya George C.T.
Published: May 2023

Purpose

Peer Support Specialists (PSS) play an integral role in substance use disorder treatment and aftercare services. PSS training programs vary in format and need to be evaluated for continued improvement. The purpose of this study was to gather feedback about course delivery and instruction from PSS trainees in a PSS training program in Alabama.

Design/methodology/approach

Focus groups were conducted with 15 PSS trainees after they completed two training courses delivered in an online university format. There were four men and 11 women. Four were black, 10 were white and one was Hispanic/Latinx. Participants ranged in age from 20 to 70.

Findings

Through content analysis of focus group content, four themes emerged: (1) issues with online navigation, (2) desire for an orientation to university-level education, (3) instructor qualities (e.g. approachability and availability) and (4) course structure considerations (e.g. balance between online and in-person learning, more frequent class meetings).

Originality/value

To the best of the authors’ knowledge, this study is the first to evaluate a new PSS training program in Alabama. Findings help inform future PSS training programs and assist in the development of best practices in PSS training.
Impact of Bitcoin mining and crypto market determinants on Bitcoin-based energy consumption
Authors: Sapra Nishant , Shaikh Imlak
Published: May 2023

Purpose

While Blockchain can serve us, Bitcoin threatens our survival. If Bitcoin is assumed to be a country, it will rank 38th globally for energy consumption. With 90.2 metric million tonnes of carbon dioxide, Bitcoin mining and trading has emerged as an environmental threat. The current study investigates how the trading-specific variables, the prices of Crypto Index and Ethereum, affect bitcoin-based energy consumption. Also, the role of mining-specific variables is analyzed.

Design/methodology/approach

The study uses monthly data from various sources collected from December 2018 to January 2023. The authors used the Autoregressive Distributed Lag (ARDL) Model to determine the short- and long-term relationships between variables. This study uses the Theory of Green Marketing and the Theory of Cross Elasticity of Demand as a theoretical lens.

Findings

The findings show that escalating crypto market index and Ethereum prices with a one-month lag increases bitcoin-specific electricity consumption and carbon emissions. Green investors may shift to cryptocurrencies based on consensus other than of Proof-of-Work. Ethereum behaves like a substitute for Bitcoin, reflected by the long-term positive relationship between Bitcoin's energy consumption and Ethereum prices.

Originality/value

The study analyses how the crypto market index and Ethereum price affect bitcoin-based energy use. The relationships identified are substantiated by the literature to provide suggestions to green investors and policymakers to mitigate the harmful impact of Bitcoin's colossal energy consumption on the natural environment.