bluuebunny/crossref_metadata_2025 huggingface dataset:
Optically active, paper-based scaffolds for 3D cardiac tissue engineering
Authors: Guo F. , Jooken S. , Ahmad A. , Yu W. , Deschaume O. , Thielemans W. , Bartic C.
Published: March 2024

In this work, we report the design and fabrication of a light-addressable, paper-based, nanocomposite scaffold for optical modulation and read-out of in vitro grown cardiac tissue. The scaffold consists of paper cellulose microfibers functionalized with gold nanorods (GNRs) and semiconductor quantum dots (QDs), embedded into a cell-permissive collagen matrix. The GNRs enable cardiomyocyte activity modulation through local temperature gradients induced by near-infrared (NIR) laser illumination, with the local temperature changes reported by the temperature-dependent QD photoluminescence (PL). The micrometer size paper fibers promote the tubular organization of HL-1 cardiac muscle cells, while the NIR plasmonic stimulation modulates reversibly their activity. Given its high spatial resolution, NIR modulation offers an excellent alternative to electrode-based methods for cell activity modulation and is more compatible with 3D tissue constructs. As such, optical platforms based on nanocomposite scaffolds will have a significant impact on the progress of drug screening, toxicity studies, and heart disease modeling.
The Spx stress regulator confers high-level β-lactam resistance and decreases susceptibility to last-line antibiotics in methicillin resistantStaphylococcus aureus
Authors: Nielsen Tobias Krogh , Petersen Ida Birkjær , Xu Lijuan , Barbuti Maria Disen , Mebus Viktor , Justh Anni , Alqarzaee Abdulelah Ahmed , Jacques Nicolas , Oury Cécile , Thomas Vinai , Kjos Morten , Henriksen Camilla , Frees Dorte
Published: March 2024

Infections caused by methicillin resistantStaphylococcus aureus(MRSA) are a leading cause of mortality worldwide. MRSA have acquired resistance to next generation β-lactam antibiotics through the horizontal acquisition of themecAresistance gene. Development of high resistance is, however, often associated with additional mutations in a set of chromosomal core genes, known as potentiators which through poorly described mechanisms enhance resistance. TheyjbHgene was recently identified as a hot spot for adaptive mutations during severe infections. Here, we show that inactivation ofyjbHincreased β-lactam MICs up to 16-folds and transformed MRSA cells with low level of resistance to being homogenously highly resistant to β-lactams. TheyjbHgene encodes an adaptor protein that targets the transcriptional stress regulator Spx for degradation by the ClpXP protease. Using CRISPRi to knock downspxtranscription, we unambiguously linked hyper-resistance to accumulation of Spx. Spx was previously proposed to be essential, however, our data indicate that Spx is dispensable for growth at 37°C but becomes essential in the presence of antibiotics with various targets. On the other hand, high Spx levels bypassed the role of PBP4 in β-lactam resistance and broadly decreased MRSA susceptibility to compounds targeting the cell wall or the cell membrane including vancomycin, daptomycin, and nisin. Strikingly, Spx potentiated resistance independently of its redox sensing switch. Collectively, our study identifies a general stress pathway that, in addition to promoting the development of high-level, broad-spectrum β-lactam resistance, also decreases MRSA susceptibility to critical antibiotics of last resort.
Comparison of CcrM-dependent methylation inCaulobacter crescentusandBrucella abortusby nanopore sequencing
Authors: Campbell Maxwell , Barton Ian Scott , Roop R. Martin , Chien Peter
Published: March 2024

Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order,Caulobacter crescentus, relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such asBrucella abortus, depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation inCaulobacterand show excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation inBrucella abortusfor the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on theBrucellamethylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen.

Importance

DNA methylation plays an important role in bacteria to maintain genome integrity and regulate of gene expression. We used nanopore sequencing to directly measure methylated bases inCaulobacter crescentusandBrucella abortus. InCaulobacter, we showed that stabilization of the CcrM methyltransferase upon loss of the Lon protease results in prolific methylation and discovered that the putative methylase AlkB is unlikely to have a global physiological effect. We measured genome-wide methylation in Brucella for the first time, revealing a similar role for CcrM in cell-cycle methylation but a more complex regulation by the Lon protease than in Caulobacter. Finally, we show how the virulence factor MucR impacts DNA methylation patterns inBrucella.
Dark-based Optical Sectioning assists Background Removal in Fluorescence Microscopy
Authors: Cao Ruijie , Li Yaning , Wang Wenyi , Zhang Guoxun , Wang Gang , Sun Yu , Ren Wei , Sun Jing , Hou Yiwei , Xu Xinzhu , Hu Jiakui , Lu Yanye , Li Changhui , Wu Jiamin , Li Meiqi , Qu Junle , Xi Peng
Published: March 2024

A fundamental challenge in fluorescence microscopy is the defocused background caused by scattering light, optical aberration, or limited axial resolution. Severe defocus backgrounds will submerge the in-focus information and cause artifacts in the following processing. Here, we leverage a priori knowledge about dark channels of biological structures and dual frequency separation to develop a single-frame defocus removal algorithm. It stably improves the signal-to-background ratio and structural similarity index measure of images by approximately 10-fold, and recovers in-focus signal with 85% accuracy, even when the defocus background is 50 times larger than in-focus information. Our Dark-based optical sectioning approach (Dark sectioning) is fully compatible with various microscopy techniques, such as wide-filed microscopy, polarized microscopy, laser-scanning / spinning-disk confocal microscopy, stimulated emission depletion microscopy, lightsheet microscopy, and light-field microscopy. It also complements reconstruction or processing algorithms such as deconvolution, structure illumination microscopy, and super-resolution optical fluctuation imaging.
Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase
Authors: Dadi Pavani , Pauling Clint W. , Shrivastava Abhishek , Shah Dhara D.
Published: March 2024

Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbeBacteroides fragilisforms multiple neuromodulatory molecules such as γ-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and β-alanine. We evolvedBfGAD and doubled its taurine productivity. Additionally, we increased its specificity towards the substrate L-glutamate. Here, we provide a chemical strategy via which theBfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.
Structural insights into sphingosine 1-phosphate receptor 4 activation
Authors: Gao Wei , Gan Shiyi , Zhang Mengting , Inoue Asuka , Xie Mengting , He Huan , Zhu Huan , Guo Shanshan , Qiu Chen , Chang Di , Yu Jinling , Deng Zhuo , Ye Fang , Li Shiliang , Zhang Jian , Zhao Zhenjiang , Xue Mengzhu , Ofosuhene Bernard , Xu Yufang , Lin Honghuang , Qian Xuhong , Zhu Lili , Du Yang , Li Honglin
Published: March 2024

S1PR4 is one of five subtypes of sphingosine 1-phosphate receptors (S1PRs) that regulate immune cell functioning, with functional distinctions to other subtypes. S1PR1-targeted modulators caused serious cardiac and vascular adverse effects because S1PR1 was expressed throughout the whole body. Since S1PR4 was only expressed in lung and lymphoid cells, S1PR4-targeted modulators might not trigger these side effects. However, the development of S1PR4-specific agonists is greatly hindered because of the lack of activated S1PR4 structure. Here, we resolved cryo-EM structures of activated S1PR4 and revealed the structural mechanism of ligand recognition, receptor activation, and Gαicoupling. Our results offered structural templates for the development of selective S1PR4 agonists with improved safety profiles.
Structure-guided aminoacylation and assembly of chimeric RNAs
Authors: Radakovic Aleksandar , Lewicka Anna , Todisco Marco , Aitken Harry R. M. , Weiss Zoe , Kim Shannon , Bannan Abdullah , Piccirilli Joseph A. , Szostak Jack W.
Published: March 2024

Coded ribosomal peptide synthesis could not have evolved unless its sequence and amino acid specific aminoacylated tRNA substrates already existed. We therefore wondered whether aminoacylated RNAs might have served some primordial function prior to their role in protein synthesis. Here we show that specific RNA sequences can be nonenzymatically aminoacylated and ligated to produce amino acid-bridged stem-loop RNAs. We used deep sequencing to identify RNAs that undergo highly efficient glycine aminoacylation followed by loop-closing ligation. The crystal structure of one such glycine-bridged RNA hairpin reveals a compact internally stabilized structure with the same eponymous T-loop architecture found in modern tRNA. We demonstrate that the T-loop assisted amino acid bridging of RNA oligonucleotides enables the rapid template-free assembly of a chimeric version of an aminoacyl-RNA synthetase ribozyme. We suggest that the primordial assembly of such chimeric ribozymes would have allowed the greater functionality of amino acids to contribute to enhanced ribozyme catalysis, providing a driving force for the evolution of sequence and amino acid specific aminoacyl-RNA synthetase enzymes prior to their role in protein synthesis.
Molecular mechanism of Mad2 conformational conversion promoted by the Mad2-interaction motif of Cdc20
Authors: Yu Conny W.H. , Fischer Elyse S. , Greener Joe G. , Yang Jing , Zhang Ziguo , Freund Stefan M.V. , Barford David
Published: March 2024

During mitosis, unattached kinetochores trigger the spindle assembly checkpoint by promoting assembly of the mitotic checkpoint complex, a heterotetramer comprising Mad2, Cdc20, BubR1 and Bub3. Critical to this process is the kinetochore-mediated catalysis of an intrinsically slow conformational conversion of Mad2 from an open (O-Mad2) inactive state to a closed (C-Mad2) active state bound to Cdc20. These Mad2 conformational changes involve substantial remodelling of the N-terminal β1 strand and C-terminal β7/β8 hairpin.In vitro, the Mad2- interaction motif (MIM) of Cdc20 (Cdc20MIM) triggers rapid conversion of O- to C-Mad2, effectively removing the kinetic barrier for MCC assembly. How Cdc20MIMdirectly induces Mad2 conversion remains unclear. In this study we demonstrate that the Cdc20MIM-binding site is inaccessible in O-Mad2. Time-resolved NMR and molecular dynamics simulations show how Mad2 conversion involves sequential conformational changes of flexible structural elements in O-Mad2, orchestrated by Cdc20MIM. Conversion is initiated by the β7/β8 hairpin of O-Mad2 transiently unfolding to expose a nascent Cdc20MIM-binding site. Engagement of Cdc20MIMto this site promotes release of the β1 strand. We propose that initial conformational changes of the β7/β8 hairpin allows binding of Cdc20MIMto a transient intermediate state of Mad2, thereby lowering the kinetic barrier to Mad2 conversion.
Role of protein-protein interactions on model chromatin organization
Authors: Swain Pinaki , Choubey Sandeep , Vemparala Satyavani
Published: March 2024

The three-dimensional organization of chromatin is influenced by DNA-binding proteins, through specific and non-specific interactions. However, the role of DNA sequence and interaction between binding proteins in influencing chromatin structure is not yet fully understood. By employing a simple polymer-based model of chromatin, that explicitly considers sequence-dependent binding of proteins to DNA and protein-protein interactions, we elucidate a mechanism for chromatin organization. We find that: (1) Tuning of protein-protein interaction and protein concentration is sufficient to either promote or inhibit the compartmentalization of chromatin. (2) The presence of chromatin acts as a nucleating site for the condensation of the proteins at a density lower than in isolated protein systems. (3) The exponents describing the spatial distance between the different parts of the chromatin, and their contact probabilities are strongly influenced by both sequence and the protein-protein attraction. Our findings have the potential application of re-interpreting data obtained from various chromosome conformation capture technologies, thereby laying the groundwork for advancing our understanding of chromatin organization.
Cellular mechanotransduction of human osteoblasts in microgravity
Authors: Wubshet Nadab H. , Cai Grace , Chen Samuel J. , Sullivan Molly , Reeves Mark , Mays David , Harrison Morgan , Varnado Paul , Yang Benjamin , Arreguin-Martinez Esmeralda , Qu Yunjia , Lin Shan-Shan , Duran Pamela , Aguilar Carlos , Giza Shelby , Clements Twyman , Liu Allen P.
Published: March 2024

Astronauts experience significant and rapid bone loss as a result of an extended stay in space, making the International Space Station (ISS) the perfect laboratory for studying osteoporosis due to the accelerated nature of bone loss on the ISS. This prompts the question, how does the lack of load due to zero-gravity propagate to bone-forming cells, human fetal osteoblasts (hFOBs), altering their maturation to mineralization? Here, we aim to study the mechanotransduction mechanisms by which bone loss occurs in microgravity. Two automated experiments, 4 microfluidic chips capable of measuring single-cell mechanics of hFOBs via aspiration and cell spheroids incubated in pressure-controlled chambers, were each integrated into a CubeLab deployed to the ISS National Laboratory. For the first experiment, we report protrusion measurements of aspirated cells after exposure to microgravity at the ISS and compare these results to ground control conducted inside the CubeLab. Our analysis revealed slightly elongated protrusions for space samples compared to ground samples indicating softening of hFOB cells in microgravity. In the second experiment, we encapsulated osteoblast spheroids in collagen gel and incubated the samples in pressure-controlled chambers. We found that microgravity significantly reduced filamentous actin levels in the hFOB spheroids. When subjected to pressure, the spheroids exhibited increased pSMAD1/5/9 expression, regardless of the microgravity condition. Moreover, microgravity reduced YAP expression, while pressure increased YAP levels, thus restoring YAP expression for spheroids in microgravity. Our study provides insights into the influence of microgravity on the mechanical properties of bone cells and the impact of compressive pressure on cell behavior and signaling in space.
The p90 Ribosomal S6 Kinases 2 and 4 promote Prostate Cancer cell proliferation in androgen-dependent and independent ways
Authors: Cronin Ryan , Azadova Aygun , Marco Antonio , Laissue Philippe P. , Brooke Greg N. , Prischi Filippo
Published: March 2024

Oncogenic activation of the phosphatidylinositol-3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways are frequent events in Prostate Cancer (PCa) that have been correlated to tumour formation, disease progression and therapeutic resistance. At the intersection of these two pathways lies the p90 ribosomal S6 kinase (RSKs) family, which regulates many proteins involved in cell survival, growth and proliferation. As such, deregulated RSKs activity has been associated with multiple cancer types, including PCa. However, the full extent of the RSKs involvement in prostate tumorigenesis remains to be determined. Here we have shown that RSKs levels are increased in PCa samples and cell lines. The RSKs were found to enhance Androgen Receptor (AR) activity, the key oncogenic driver in PCa. Indeed, all RSKs were found to interact in close proximity to the AR. However, RSK2/4, but not RSK1/3, showed changes in cell localisation following AR nuclear translocation. Consistently, silencing of RSK2/4, but not RSK1/3, inhibited PCa proliferation in an androgen-dependent and independent manner, respectively, and induced different signaling events downstream of the AR. The data suggests that RSK2 and RSK4 activity is required for PCa cell proliferation, but they are likely regulating growth via different mechanisms.
In Vitro Budding and Floatation based Enrichment of Mitochondria-derived Vesicles for Proteomics from Rat Heart
Authors: Nair Nidhi , Ramesh Lariza , Marib Areeba , Rajeev Thejaswitha , Johnson John B , Sundararaman Ananthalakshmy
Published: March 2024

Mitochondria-derived vesicles (MDVs) are a novel class of vesicles whose biogenesis and trafficking are poorly characterized. Here, we describe the protocol toin vitrogenerate MDVs from mitochondria isolated from animal heart tissues. The protocol can be coupled with Transmission Electron Microscopy (TEM), proteomics or western blotting as final readouts. The protocol is optimized to improve the yield and purity of vesicles for downstream proteomics and facilitates selection of key regulators to be validated within cells.

Graphical abstract

The protocol has been adapted and further modified from (Soubannier et al., 2012).
Axonal Injury, Sleep Disturbances, and Memory following Traumatic Brain Injury
Authors: Tinney Emma M. , España-Irla Goretti , Warren Aaron E.L. , Whitehurst Lauren N. , Stillman Alexandra M , Hillman Charles H. , Morris Timothy P. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: March 2024

Objectives

Traumatic brain injury (TBI) is associated with sleep deficits, but it is not clear why some report sleep disturbances and others do not. The objective of this study was to assess the associations between axonal injury, sleep, and memory in chronic and acute TBI.

Methods

Data were acquired from two independent datasets which included 156 older adult veterans (69.8 years) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) with prior moderate-severe TBIs and 90 (69.2 years) without a TBI and 374 participants (39.6 years) from Transforming Research and Clinical Knowledge in TBI (TRACK-TBI) with a recent mild TBI (mTBI) and 87 controls (39.6 years), all who completed an MRI, memory assessment, and sleep questionnaire.

Results

Older adults with a prior TBI had a significant association between axial diffusivity in the left anterior internal capsule (ALIC) and sleep disturbances [95% CI(5.0e+07, 1.7e+08), p ≤ .01]. This association was significantly different [95% CI(6.8e+07,2.2e+08), p=.01] from controls. ALIC predicted changes in memory over one-year in TBI [95% CI(−1.8e+08,-2.7e+07), p=.03]. We externally validated those findings in TRACK-TBI where ALIC axial diffusivity within two-weeks after injury was significantly associated with higher sleep disturbances in the TBI group at two-weeks [95% CI(−7.2e-06, −1.9e-04), p=0.04], six-months [95% CI(−4.2e-06,-1.3e-04), p≤ .01] and 12-months post-injury [95% CI(−5.2e-06, −1.2e-04), p=0.03]. These associations not seen in controls.

Interpretations

Axonal injury to the ALIC is robustly associated with sleep disturbances in multiple TBI populations. Early assessment of ALIC damage following mTBI could identify those at risk for persistent sleep disturbances following injury.
Structural characterization of a polymorphic repeat at the CACNA1C schizophrenia locus
Authors: Moya Raquel , Wang Xiaohan , Tsien Richard W , Maurano Matthew T
Published: March 2024

Genetic variation within intron 3 of the CACNA1C calcium channel gene is associated with schizophrenia and bipolar disorder, but analysis of the causal variants and their effect is complicated by a nearby variable-number tandem repeat (VNTR). Here, we used 155 long-read genome assemblies from 78 diverse individuals to delineate the structure and population variability of the CACNA1C intron 3 VNTR. We categorized VNTR sequences into 7 Types of structural alleles using sequence differences among repeat units. Only 12 repeat units at the 5′ end of the VNTR were shared across most Types, but several Types were related through a series of large and small duplications. The most diverged Types were rare and present only in individuals with African ancestry, but the multiallelic structural polymorphism Variable Region 2 was present across populations at different frequencies, consistent with expansion of the VNTR preceding the emergence of early hominins. VR2 was in complete linkage disequilibrium with fine-mapped schizophrenia variants (SNPs) from genome-wide association studies (GWAS). This risk haplotype was associated with decreased CACNA1C gene expression in brain tissues profiled by the GTEx project. Our work suggests that sequence variation within a human-specific VNTR affects gene expression, and provides a detailed characterization of new alleles at a flagship neuropsychiatric locus.
An Allosteric Cholesterol Site in Glycine Receptors Characterized Through Molecular Simulations
Authors: Jalalypour Farzaneh , Howard Rebecca J , Lindahl Erik
Published: March 2024

Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear--in particular for cholesterol. To identify such interactions, here we report on coarse-grained simulations in a model neuronal membrane for three zebrafish glycine-receptor structures, representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions, and observe cholesterol bound to the receptor at an outer-leaflet intersubunit site in a state-dependent manner, indicating that it can bias receptor function. Finally, using a modified perturbation-response scanning approach, we applied short atomistic simulations to identify amino-acid translations correlated with gating conformational changes. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of heteromeric glycine receptors, including specific amino-acid contacts applicable to biophysical modeling and pharmaceutical design.
Sorting at ciliary base and ciliary entry of BBSome, IFT-B and IFT-A
Authors: Mitra Aniruddha , Gioukakis Evangelos , Mul Wouter , Peterman Erwin J.G.
Published: March 2024

Summary/Abstract

Anterograde intraflagellar transport (IFT) trains, composed of IFT-B, IFT-A and BBSome subcomplexes, are responsible for transporting ciliary proteins into the cilium. How IFT subcomplexes reach the ciliary base and assemble into IFT trains is poorly understood. Here, we perform quantitative single-molecule imaging inC. eleganschemosensory cilia to uncover how IFT subcomplexes arrive at the base, organize in IFT trains, and enter the cilium. We find that BBSomes reach the base via diffusion where they either associate with assembling IFT trains or with the membrane surrounding the base. In contrast, IFT-B and IFT-A reach the base via directed transport on vesicles that stop at distinct locations near the base. Individual subcomplexes detach from the vesicles into a diffusive pool and associate to assembling trains. Our results indicate that the assembly of IFT trains is a step-wise process involving the subsequent incorporation of first IFT-B, then IFT-A and finally BBSomes.
Overlapping binding sites underlie TF genomic occupancy
Authors: Khetan Shubham , Bulyk Martha L.
Published: March 2024

Sequence-specific DNA binding by transcription factors (TFs) is a crucial step in gene regulation. However, current high-throughputin vitroapproaches cannot reliably detect lower affinity TF-DNA interactions, which play key roles in gene regulation. Here, we developed PADIT-seq (proteinaffinity toDNA byin vitrotranscription and RNAsequencing) to assay TF binding preferences to all 10-bp DNA sequences at far greater sensitivity than prior approaches. The expanded catalogs of low affinity DNA binding sites for the human TFs HOXD13 and EGR1 revealed that nucleotides flanking high affinity DNA binding sites create overlapping lower affinity sites that together modulate TF genomic occupancyin vivo. Formation of such extended recognition sequences stems from an inherent property of TF binding sites to interweave each other and expands the genomic sequence space for identifying noncoding variants that directly alter TF binding.

One-Sentence Summary

Overlapping DNA binding sites underlie TF genomic occupancy through their inherent propensity to interweave each other.
Contact behaviour before, during and after the COVID-19 pandemic in the Netherlands: evidence from contact surveys in 2016-2017 and 2020-2023
Authors: Backer Jantien A. , Vos Eric R. A. , den Hartog Gerco , van Hagen Cheyenne C. E. , de Melker Hester E. , van der Klis Fiona R. M. , Wallinga Jacco
Published: March 2024

Background

The first wave of the COVID-19 pandemic in 2020 was largely mitigated by reducing contacts in the general population. In 2022 most contact-reducing measures were lifted.

Aim

We assess whether the population has reverted to pre-pandemic contact behaviour and how this would affect the transmission potential of a newly emerging pathogen.

Methods

The PIENTER Corona study was held every 2-6 months in the Netherlands from April 2020, as a follow-up on the 2016-2017 PIENTER3 study. In both studies, participants (ages 1-85) reported the number and age group of all face-to-face persons contacted on the previous day. The contact behaviour during and after the COVID-19 pandemic was compared to the pre-pandemic baseline. The transmission potential was examined using the Next Generation Matrix approach.

Results

We found an average of 15.4 (14.3-16.4, 95% CI) community contacts per person per day in the post-pandemic period, which is 13% lower than the baseline value of 17.8 (17.0-18.5). Children have the highest number of contacts as before the pandemic. Mainly adults aged 20-59 have not reverted to their pre-pandemic behaviour, possibly because this age group works more often from home. Although the number of contacts is structurally lower compared to the pre-pandemic period, the effect on the transmission potential of a newly emerging respiratory pathogen is limited if all age groups were equally susceptible.

Conclusion

Continuous monitoring of contacts can signal changes in contact patterns and can provide a ‘new normal’ baseline. Both aspects are needed to be prepared for a future pandemic.
Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain
Authors: Agostini Francesco , Pereyra Leonardo , Dale Justin , Yambire King Faisal , Maglioni Silvia , Schiavi Alfonso , Ventura Natascia , Milosevic Ira , Raimundo Nuno
Published: March 2024

Mitochondria and lysosomes are two organelles that carry out both signaling and metabolic roles in the cells. Recent evidence has shown that mitochondria and lysosomes are dependent on one another, as primary defects in one cause secondary defects in the other. Nevertheless, the signaling consequences of primary mitochondrial malfunction and of primary lysosomal defects are not similar, despite in both cases there are impairments of mitochondria and of lysosomes. Here, we used RNA sequencing to obtain transcriptomes from cells with primary mitochondrial or lysosomal defects, to identify what are the global cellular consequences that are associated with malfunction of mitochondria or lysosomes. We used these data to determine what are the pathways that are affected by defects in both organelles, which revealed a prominent role for the cholesterol synthesis pathway. This pathway is transcriptionally up-regulated in cellular and mouse models of lysosomal defects and is transcriptionally down-regulated in cellular and mouse models of mitochondrial defects. We identified a role for post-transcriptional regulation of the transcription factor SREBF1, a master regulator of cholesterol and lipid biosynthesis, in models of mitochondrial respiratory chain deficiency. Furthermore, the retention of Ca2+in the lysosomes of cells with mitochondrial respiratory chain defects contributes to the differential regulation of the cholesterol synthesis pathway in the mitochondrial and lysosomal defects tested. Finally, we verifiedin vivo, using models of mitochondria-associated diseases in C.elegans, that normalization of lysosomal Ca2+levels results in partial rescue of the developmental arrest induced by the respiratory chain deficiency.
MYT1L deficiency impairs excitatory neuron trajectory during cortical development
Authors: Yen Allen , Chen Xuhua , Skinner Dominic D. , Leti Fatjon , Crosby MariaLynn , Hoisington-Lopez Jessica , Wu Yizhe , Chen Jiayang , Mitra Robi D. , Dougherty Joseph D.
Published: March 2024

Mutations that reduce the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder. Furthermore, MYT1L is routinely used as a proneural factor in fibroblast-to-neuron transdifferentiation. MYT1L has been hypothesized to play a role in the trajectory of neuronal specification and subtype specific maturation, but this hypothesis has not been directly tested, nor is it clear which neuron types are most impacted by MYT1L loss. In this study, we profiled 313,335 nuclei from the forebrains of wild-type and MYT1L-deficient mice at two developmental stages: E14 at the peak of neurogenesis and P21, when neurogenesis is complete, to examine the role of MYT1L levels in the trajectory of neuronal development. We found that MYT1L deficiency significantly disrupted the relative proportion of cortical excitatory neurons at E14 and P21. Significant changes in gene expression were largely concentrated in excitatory neurons, suggesting that transcriptional effects of MYT1L deficiency are largely due to disruption of neuronal maturation programs. Most effects on gene expression were cell autonomous and persistent through development. In addition, while MYT1L can both activate and repress gene expression, the repressive effects were most sensitive to haploinsufficiency, and thus more likely mediate MYT1L syndrome. These findings illuminate the intricate role of MYT1L in orchestrating gene expression dynamics during neuronal development, providing insights into the molecular underpinnings of MYT1L syndrome.
Comparing the limbic-frontal connectome across the primate order: conservation of connections and implications for translational neuroscience
Authors: Folloni Davide , Roumazeilles Lea , Bryant Katherine L , Manger Paul R , Bertelsen Mads F , Khrapitchev Alexandre A , Rudebeck Peter H , Mars Rogier B
Published: March 2024

The interaction of the limbic system and frontal cortex of the primate brain is important in many affective behaviors. For this reason, it is heavily implicated in a number of psychiatric conditions. This system is often studied in the macaque monkey, the most largely-used non-human primate model species. However, how evolutionary conserved this system is and how well results obtained in any model species translate to the human can only be understood by studying its organization across the primate order. Here, we present an investigation of the topology of limbic-frontal connections across seven species, representing all major branches of the primate family tree. We show that dichotomous organization of amydalofugal and uncinate connections with frontal cortex is conserved across all species. Subgenual connectivity of the cingulum bundle, however, seems less prominent in prosimian and New World monkey brains. These results inform both translational neuroscience and primate brain evolution.
Adaptation of a methanogen to the constructed environment
Authors: Kawaichi Satoshi , Kotoky Rhitu , Fiutowski Jacek , Rotaru Amelia-Elena
Published: March 2024

Due to unique genomic adaptations, Methanococcus maripaludis Mic1c10 exhibits severe corrosive behavior when in direct contact with Fe0. These adaptations are linked to attachment and effective growth on constructed surfaces. One such adaptation is that of a specific [NiFe]-hydrogenase that may anchor on the cell surface via glycosyl-glycosyl interactions to receive Fe0-electrons directly. Such an evolutionary response to constructed environments requires us to rethink methane cycling in human-altered ecosystems.
Nano-scale viscometry reveals an inherent mucus defect in cystic fibrosis
Authors: Ponomarchuk Olga , Boudreault Francis , Gryczynski Ignacy , Dzyuba Sergei V. , Fudala Rafal , Gryczynski Zygmunt , Hanrahan John W. , Grygorczyk Ryszard
Published: March 2024

Abnormally viscous and thick mucus is a hallmark of cystic fibrosis (CF). How the genetic defect causes abnormal mucus in CF remains unanswered and a question of paramount interest. Mucus is produced by hydration of gel-forming mucin macromolecules that are stored in secretory granules prior to release. Current understanding of mucin/mucus structure before and after secretion remains limited and contradictory models exist. Here we used a molecular viscometer and fluorescence lifetime imaging of primary epithelial cells (Normal and CF) to measure nanometer-scale viscosity. We found significantly elevated intraluminal nanoviscosity in a population of CF mucin granules, indicating an intrinsic, pre-secretory, mucin defect. Validation experiments showed that high nanoviscosity in cellular environments is mainly due to the low mobility of water that hydrates macromolecules. Nanoviscosity influences protein conformational dynamics and function. Its elevation along the protein secretory pathway indicates molecular overcrowding and is expected to alter mucin’s post-translational processing, hydration, and mucus rheology after release. The nanoviscosity of extracellular CF mucus was elevated compared to non-CF mucus. Remarkably, it was higher after secretion than in granules, which suggests mucins have a weakly-ordered state in granules and adopt a highly-ordered, nematic crystalline structure extracellularly. This challenges the classical view of mucus as a porous agarose-like gel and suggests an alternative model for mucin organization before and after secretion. Our study also suggests that endoplasmic reticulum stress due to molecular overcrowding contributes to mucus pathogenesis in CF cells. It encourages the development of therapeutics that target pre-secretory mechanisms in CF and other muco-obstructive lung diseases.
Defining the EM-signature of successful cell-transfection
Authors: Pemberton Joshua G. , Tenkova Tatyana , Felgner Philip , Zimmerberg Josh , Balla Tamas , Heuser John
Published: March 2024

In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique ’inclusion-bodies.’ Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by ’annulate’ lamellae’ of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural ’signatures’ of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these ’signature’ cytoplasmic reactions.
Optimizing defect rework for a software start-up's schedule variation: a Six-Sigma-based approach
Authors: Mahato Satyajit , Roy Supriyo
Published: March 2024

Purpose

Managing project completion within the stipulated time is significant to all firms' sustainability. Especially for software start-up firms, it is of utmost importance. For any schedule variation, these firms must spend 25 to 40 percent of the development cost reworking quality defects. Significantly, the existing literature does not support defect rework opportunities under quality aspects among Indian IT start-ups. The present study aims to fill this niche by proposing a unique mathematical model of the defect rework aligned with the Six Sigma quality approach.

Design/methodology/approach

An optimization model was formulated, comprising the two objectives: rework “time” and rework “cost.” A case study was developed in relevance, and for the model solution, we used MATLAB and an elitist, Nondominated Sorting Genetic Algorithm (NSGA-II).

Findings

The output of the proposed approach reduced the “time” by 31 percent at a minimum “cost”. The derived “Pareto Optimal” front can be used to estimate the “cost” for a pre-determined rework “time” and vice versa, thus adding value to the existing literature.

Research limitations/implications

This work has deployed a decision tree for defect prediction, but it is often criticized for overfitting. This is one of the limitations of this paper. Apart from this, comparing the predicted defect count with other prediction models hasn’t been attempted. NSGA-II has been applied to solve the optimization problem; however, the optimal results obtained have yet to be compared with other algorithms. Further study is envisaged.

Practical implications

The Pareto front provides an effective visual aid for managers to compare multiple strategies to decide the best possible rework “cost” and “time” for their projects. It is beneficial for cost-sensitive start-ups to estimate the rework “cost” and “time” to negotiate with their customers effectively.

Originality/value

This paper proposes a novel quality management framework under the Six Sigma approach, which integrates optimization of critical metrics. As part of this study, a unique mathematical model of the software defect rework process was developed (combined with the proposed framework) to obtain the optimal solution for the perennial problem of schedule slippage in the rework process of software development.
Potential effects of nutrition‐induced alteration of gut microbiota on inflammatory bowel disease: A review
Authors: Tian Qi Bai , Chen Shui Jiao , Xiao Li Jun , Xie Jia Qi , Zhao Hong Bo , Zhang Xian
Published: March 2024

Inflammatory bowel disease (IBD), mainly comprising ulcerative colitis and Crohn's disease, is a group of gradually progressive diseases bringing significant mental anguish and imposes serious economic burdens. Interplay of genetic, environmental, and immunological factors have been implicated in its pathogenesis. Nutrients, as crucial environmental determinants, mainly encompassing carbohydrates, fats, proteins, and micronutrients, are closely related to the pathogenesis and development of IBD. Nutrition is essential for maintaining the dynamic balance of intestinal eco‐environments to ensure intestinal barrier and immune homeostasis, while this balance can be disrupted easily by maladjusted nutrition. Research has firmly established that nutrition has the potential to shape the composition and function of gut microbiota to affect the disease course. Unhealthy diet and eating disorders lead to gut microbiota dysbiosis and further destroy the function of intestinal barrier such as the disruption of membrane integrity and increased permeability, thereby triggering intestinal inflammation. Notably, appropriate nutritional interventions, such as the Mediterranean diet, can positively modulate intestinal microecology, which may provide a promising strategy for future IBD prevention. In this review, we provide insights into the interplay between nutrition and gut microbiota and its effects on IBD and present some previously overlooked lines of evidence regarding the role of derived metabolites in IBD processes, such as trimethylamine N‐oxide and imidazole propionate. Furthermore, we provide some insights into reducing the risk of onset and exacerbation of IBD by modifying nutrition and discuss several outstanding challenges and opportunities for future study.
The risk relationships between alcohol consumption, alcohol use disorder and alcohol use disorder mortality: A systematic review and meta‐analysis
Authors: Carr Tessa , Kilian Carolin , Llamosas‐Falcón Laura , Zhu Yachen , Lasserre Aurélie M. , Puka Klajdi , Probst Charlotte
Published: March 2024

Background and aims

Increasing levels of alcohol use are associated with a risk of developing an alcohol use disorder (AUD), which, in turn, is associated with considerable burden. Our aim was to estimate the risk relationships between alcohol consumption and AUD incidence and mortality.

Method

A systematic literature search was conducted, using Medline, Embase, PsycINFO and Web of Science for case–control or cohort studies published between 1 January 2000 and 8 July 2022. These were required to report alcohol consumption, AUD incidence and/or AUD mortality (including 100% alcohol‐attributable deaths). The protocol was registered with PROSPERO (CRD42022343201). Dose–response and random‐effects meta‐analyses were used to determine the risk relationships between alcohol consumption and AUD incidence and mortality and mortality rates in AUD patients, respectively.

Results

Of the 5904 reports identified, seven and three studies from high‐income countries and Brazil met the inclusion criteria for quantitative and qualitative syntheses, respectively. In addition, two primary US data sources were analyzed. Higher levels of alcohol consumption increased the risk of developing or dying from an AUD exponentially. At an average consumption of four standard drinks (assuming 10 g of pure alcohol/standard drink) per day, the risk of developing an AUD was increased sevenfold [relative risk (RR) = 7.14, 95% confidence interval (CI) = 5.13–9.93] and the risk of dying fourfold (RR = 3.94, 95% CI = 3.53–4.40) compared with current non‐drinkers. The mortality rate in AUD patients was 3.13 (95% CI = 1.07–9.13) per 1000 person‐years.

Conclusions

There are exponential positive risk relationships between alcohol use and both alcohol use disorder incidence and mortality. Even at an average consumption of 20 g/day (about one large beer), the risk of developing an alcohol use disorder (AUD) is nearly threefold that of current non‐drinkers and the risk of dying from an AUD is approximately double that of current non‐drinkers.
Shaping states into nations: The effects of ethnic geography on state borders
Authors: Müller‐Crepon Carl , Schvitz Guy , Cederman Lars‐Erik
Published: March 2024

Borders define states, yet little systematic evidence explains where they are drawn. Putting current challenges to state borders into perspective and breaking new methodological ground, this paper analyzes how ethnic geography and nationalism have shaped European borders since the 19th century. We argue that nationalism creates pressures to redraw political borders along ethnic lines, ultimately making states more congruent with ethnic groups. We introduce a Probabilistic Spatial Partition Model to test this argument, modeling state territories as partitions of a planar spatial graph. Using new data on Europe's ethnic geography since 1855, we find that ethnic boundaries increase the conditional probability that two locations they separate are, or will become, divided by a state border. Secession is an important mechanism driving this result. Similar dynamics characterize border change in Asia but not in Africa and the Americas. Our results highlight the endogenous formation of nation‐states in Europe and beyond.
Endogenous preferences, credible signaling, and the security dilemma: Bridging the rationalist–constructivist divide
Authors: Yoder Brandon , Haynes Kyle
Published: March 2024

How does the potential for socialization affect states' abilities to reassure each other and mitigate the security dilemma? Rationalist scholarship has identified numerous mechanisms by which states can credibly signal benign intentions. Yet it omits the possibility that states' interactions might endogenously shape their identities and domestic structures, and thus alter their basic preferences for or against cooperative outcomes. We present a formal model of the security dilemma that allows the sender's preferences to change endogenously as a function of the receiver's actions. The model yields several key results. First, the possibility of socialization generates incentives for benign actors to risk initiating cooperation, and even sustain cooperation in response to noncooperative signals in the hope of positively socializing the sender. However, conflict can still occur between mutually benign states through novel mechanisms not captured by standard models. These findings carry important implications for recent debates surrounding the US “engagement” strategy toward China.