bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-alcoholic steatohepatitis disrupts diurnal liver transcriptome rhythms in mice
Authors: de Assis Leonardo Vinicius Monteiro , Demir Münevver , Oster Henrik
Published: January 2023

Background & Aims

The liver ensures organismal homeostasis through modulation of physiological functions over the course of the day. How liver diseases such as non-alcoholic steatohepatitis (NASH) affects daily transcriptome rhythms in the liver remains elusive. To start closing this gap, we evaluated the impact of NASH on the diurnal regulation of the liver transcriptome in mice. Along this, we investigated how stringent consideration of circadian rhythmicity affects the outcomes of NASH transcriptome analyses.

Approach & Results

Comparative rhythm analysis of the liver transcriptome from diet-induced NASH and control mice revealed an almost 3h phase advance in global gene expression rhythms. Rhythmically expressed genes associated with DNA repair and cell cycle regulation showed increased overall expression and circadian amplitude. In contrast, lipid and glucose metabolism associated genes showed loss of circadian amplitude, reduced overall expression, and phase advances in NASH livers. Comparison of NASH-induced liver transcriptome responses between published studies revealed little overlap (12%) in differentially expressed genes (DEGs). However, by controlling for sampling time and using circadian analytical tools, a 7-fold increase in DEG detection was achieved compared to methods without time control.

Conclusions

NASH had a strong effect on circadian liver transcriptome rhythms with phase- and amplitude-specific effects for key metabolic and cell repair pathways, respectively. Accounting for circadian rhythms in NASH transcriptome studies markedly improves DEGs detection and enhances reproducibility.
Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer
Authors: Verma Taru , Hendiani Saghar , Moral Carlota Carbajo , Andersen Sandra B. , Hammarlund Emma , Burmølle Mette , Sand Karina K.
Published: January 2023

Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Mineral surfaces are, however, known to preserve DNA in the environment, and sedimentary ancient DNA studies have solidified that there are considerable amounts of fragmented DNA stored in sediments world-wide. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we highlight that fragmented ancient DNA can be fueling the evolution of contemporary bacteria and advocate to consider this route for genetic variation in evolutionary history. We show thatAcinetobacter baylyican incorporate 60 bp DNA fragments adsorbed to a wide range of common sedimentary minerals and that the transformation frequencies scale with the mineral surface properties. Further, our results point to interfacial geochemical and sedimentologic processes as facilitators of evolutionary innovation where DNA-molecules are specific to the environment and the processes providing new DNA molecules may also provide the need to evolve. In contrast to heritable stochastic mutations as proposed by Darwin, the access by which bacteria acquire new genomic material at times with increased stress and also needs, would indicate a non-random mechanism that may propel evolution in a non-stochastic manner.
Telomerase reactivation induces progression of mouse BrafV600E-driven thyroid cancers without telomere lengthening
Authors: Landa Iñigo , Thornton Caitlin EM , Xu Bin , Haase Jacob , Krishnamoorthy Gnana P. , Hao Jingzhu , Knauf Jeffrey A , Herbert Zachary T , Blasco María A , Ghossein Ronald , Fagin James A
Published: January 2023

Mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the paradigm of a cross-cancer alteration in a non-coding region.TERTpromoter mutations (TPMs) are biomarkers of poor prognosis in several tumors, including thyroid cancers. TPMs enhanceTERTtranscription, which is otherwise silenced in adult tissues, thus reactivating abona fideoncoprotein. To studyTERTderegulation and its downstream consequences, we generated aTertmutant promoter mouse model via CRISPR/Cas9 engineering of the murine equivalentlocus(Tert-123C>T) and crossed it with thyroid-specific BrafV600E-mutant mice. We also employed an alternative model ofTertoverexpression (K5-Tert). Whereas all BrafV600Eanimals developed well-differentiated papillary thyroid tumors, 29% and 36% of BrafV600E+Tert-123C>Tand BrafV600E+K5-Tert mice progressed to poorly differentiated thyroid cancers at week 20, respectively. Braf+Tert tumors showed increased mitosis and necrosis in areas of solid growth, and older animals from these cohorts displayed anaplastic-like features, i.e., spindle cells and macrophage infiltration. MurineTertpromoter mutation increasedTerttranscriptionin vitroandin vivo, but temporal and intra-tumoral heterogeneity was observed. RNA-sequencing of thyroid tumor cells showed that processes other than the canonical Tert-mediated telomere maintenance role operate in these specimens. Pathway analysis showed that MAPK and PI3K/AKT signaling, as well as processes not previously associated with this tumor etiology, involving cytokine and chemokine signaling, were overactivated. Braf+Tert animals remained responsive to MAPK pathway inhibitors. These models constitute useful pre-clinical tools to understand the cell-autonomous and microenvironment-related consequences of Tert-mediated progression in advanced thyroid cancers and other aggressive tumors carrying TPMs.
Healthy aging and cognitive impairment alter EEG functional connectivity in distinct frequency bands
Authors: Kumar Wupadrasta Santosh , Ray Supratim
Published: January 2023

Functional connectivity (FC) indicates the interdependencies between brain signals recorded from spatially distinct locations in different frequency bands, which is modulated by cognitive tasks and is known to change with aging and cognitive disorders. Recently, the power of narrow-band gamma oscillations induced by visual gratings has been shown to reduce with both healthy aging and in subjects with mild cognitive impairment (MCI). However, the impact of aging/MCI on stimulus-induced gamma FC has not been well studied. We recorded electroencephalogram (EEG) from a large cohort (N=229) of elderly subjects (>49 years) while they viewed large cartesian gratings to induce gamma oscillations and studied changes in alpha and gamma FC with healthy aging (N=218) and MCI (N=11). Surprisingly, we found that aging and disease changed power and FC in different ways. With healthy aging, alpha power did not change but FC decreased significantly. MCI reduced gamma but not alpha FC significantly compared with age and gender matched controls, even when power was matched between the two groups. Overall, our results show distinct effects of aging and disease on EEG power and FC, suggesting different mechanisms and the potential to use EEG stimulus-induced FC along with power for early diagnosis of Alzheimer’s Disease.
Circadian oscillation in primary cilium length by clock genes regulate fibroblast cell migration
Authors: Nakazato Ryota , Matsuda Yuki , Ijaz Faryal , Ikegami Koji
Published: January 2023

Various mammalian cells have autonomous cellular clocks that are produced by the transcriptional cycle of clock genes. Cellular clocks provide circadian rhythms for cellular functions via transcriptional and cytoskeletal regulation. The vast majority of mammalian cells possess a primary cilium, an organelle protruding from the cell surface. Here, we investigated the little-known relationship between circadian rhythm and primary cilia. The length and number of primary cilia showed circadian dynamics both in vitro and in vivo. The circadian rhythm of primary cilium length was abolished by SR9011 and Bmal1 knockout. A centrosomal protein, pericentrin, transiently accumulates in centriolar satellites, the base of primary cilia at the shortest cilia phase, and induces elongation of primary cilia at the longest cilia phase in the circadian rhythm of primary cilia. In addition, rhythmic cell migration during wound healing depends on the length of primary cilia and affects the rate of wound healing. Our findings demonstrate that the circadian dynamics of primary cilia length by clock genes control fibroblast migration and could provide new insights into chronobiology.
USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC
Authors: Zheng Jingyi , Wu Shasha , Tang Mao , Xi Shaoyan , Wang Yanchen , Ren Jun , Luo Hao , Hu Pengchao , Sun Liangzhan , Du Yuyang , Yang Hui , Wang Fenfen , Gao Han , Dai Ziwei , Ou Xijun , Li Yan
Published: January 2023

Abnormal alternative splicing (AS) caused by alterations in spliceosomal factors is implicated in cancers. Standard models posit that splice site selection is mainly determined by early spliceosomal U1, U2 snRNPs. Whether and how other mid/late-acting spliceosome components such as USP39 modulate tumorigenic splice site choice remain largely elusive. We observed that hepatocyte-specific knock-in of USP39 promoted hepatocarcinogenesis and potently regulated splice site selection. In human liver cancer cells, USP39 promoted tumor proliferation in a spliceosome-dependent manner. USP39 depletion deregulated hundreds of AS events, including the oncogenic splice-switching of KANK2. Mechanistically, we developed a novel RBP-motif enrichment analysis and found that USP39 modulated exon inclusion/exclusion by interacting with SRSF6/HNRNPC in both humans and mice. Our data represent a paradigm for the control of splice site selection by mid/late-acting spliceosome proteins and their interacting RBPs. USP39 and possibly other mid/late-acting spliceosome proteins may represent potential prognostic biomarkers and targets for cancer therapy.

Graphic Abstract
Towards Analyzing the Reclassification Dynamics of ClinVar Variants
Authors: Ruscheinski Andreas , Reimler Anna Lena , Ewald Roland , Uhrmacher Adelinde M.
Published: January 2023

ClinVar aggregates information about genetic variants and their relation to human diseases and forms a valuable resource for clinical diagnostics. The assessment of variants, e.g., as being benign or pathogenetic, changes over time. We collected variant classification histories of ClinVar releases and used those to derive discrete-time Markov chains to investigate the reclassification dynamics of variants in ClinVar in terms of transition probabilities between ClinVar releases and reclassifications.
Transformation of primary murine peritoneal mast cells by constitutive KIT activation as a result of lostCdkn2a/Arfexpression
Authors: Capellmann Sandro , Sonntag Roland , Schüler Herdit , Meurer Steffen K , Gan Lin , Kauffmann Marlies , Horn Katharina , Königs-Werner Hiltrud , Weiskirchen Ralf , Liedtke Christian , Huber Michael
Published: January 2023

Mast cells (MCs) are immune cells of the myeloid lineage distributed in tissues throughout the body. Phenotypically, they are a heterogeneous group characterized by different protease repertoires stored in secretory granules and differential presence of receptors. To adequately address aspects of MC biology either primary MCs isolated from human or mouse tissue or different human MC lines, like HMC-1.1 and -1.2, or rodent MC lines like L138.8A or RBL-2H3 are frequently used. Nevertheless, cellular systems to study MC functions are very limited. We have generated a murine connective tissue-like MC line, termed PMC-306, derived from primary peritoneal MCs (PMCs), which spontaneously transformed. We analyzed PMC-306 cells regarding MC surface receptor expression, effector functions and respective signaling pathways, and found that the cells reacted very similar to primary wildtype (WT) PMCs. In this regard, stimulation with MAS-related G-protein-coupled receptor member B2 (MRGPRB2) ligands induced respective signaling and effector functions. Furthermore, PMC-306 cells revealed significantly accelerated cell cycle progression, which however was still dependent on IL-3 and stem cell factor (SCF). Phenotypically, PMC-306 cells adopted an immature connective tissue-like MCs appearance. The reason for immortalization most likely is the loss of the two critical cell cycle regulatorsCdkn2a/INK4A andArf/p19, respectively. The loss ofCdkn2aandArfexpression could be mimicked in primary bone marrow-derived mast cells (BMMCs) by SCF supplementation strongly arguing for an involvement of KIT activation in the transformation process. Hence, this new cell line might be a useful tool to study further aspects of PMC function and to address tumorigenic processes associated with MC leukemia.
From breast cancer cell homing to the onset of early bone metastasis: dynamic bone (re)modeling as a driver of metastasis
Authors: Young Sarah A. E. , Heller Anna-Dorothea , Garske Daniela S. , Rummler Maximilian , Qian Victoria , Ellinghaus Agnes , Duda Georg N. , Willie Bettina M. , Grüneboom Anika , Cipitria Amaia
Published: January 2023

Breast cancer often metastasizes to bone causing osteolytic lesions. Structural and biophysical changes are rarely studied, yet are hypothesized to influence metastatic progression. Here, we developed a mouse model of early bone metastasis and multimodal 3D imaging to quantify cancer cell homing, dynamic bone (re)modeling and onset of bone metastasis. Using 3D light sheet fluorescence microscopy, we show eGFP+cancer cells and small clusters in 3D (intact) bones. We detect early bone lesions using time-lapsein vivomicroCT and reveal altered bone (re)modeling in absence of detectable lesions. With a new microCT image analysis tool, we detect and track the growth of early bone lesions over time. We show that cancer cells home in all bone compartments, while osteolytic lesions are only detected in the metaphysis, a region of high (re)modeling. Our study provides novel insights of dynamic bone (re)modeling as a driver during the early phase of metastasis.
Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures
Authors: Yi Xu , Fritzsching Keith J. , Rogawski Rivkah , Xu Yunyao , McDermott Ann E.
Published: January 2023

While low temperature NMR holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) inE. coliDHFR at 105K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of Ni+1to Ψi. With selective15N and13C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in13C’-15N correlation spectrum. For this unique amide we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin 114 ± 7 for the major peak, and 150 ± 8 and 164 ± 16° for the minor peak as contrasted with 118 for the X-ray crystal structure (and 118-130 for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low temperature NMR spectra.

Significance Statement

Understanding protein conformational flexibility is essential for insights into the molecular basis of protein function and the thermodynamics of proteins. Here we investigate the ensemble of protein backbone conformations in a frozen protein freezing, which is likely a close representation for the ensemble in rapid equilibrium at room temperature. Various conformers are spectrally resolved due to the exquisite sensitivity of NMR shifts to local conformations, and NMR methods allow us to directly probe the torsion angles corresponding to each band of chemical shifts.
DOT1L deletion impairs the development of cortical Parvalbumin-expressing interneurons
Authors: Cheffer Arquimedes , Garcia-Miralles Marta , Maier Esther , Akol Ipek , Franz Henriette , Vedartham Srinivasan Vandana Shree , Vogel Tanja
Published: January 2023

The cortical plate is composed of excitatory and inhibitory neurons, the latter of which originate in the ganglionic eminences. From their origin in the ventral telencephalon, interneuron precursors migrate during embryonic development over some distance to reach their final destination in the cortical plate. The histone methyltransferase DOT1L is necessary for proper cortical plate development and layer distribution of glutamatergic neurons, however, its specific role on cortical interneuron development has not yet been explored. Here, we demonstrate that DOT1L affects interneuron development in a cell-autonomous manner. Deletion ofDot1lin MGE-derived interneuron precursor cells results in an overall reduction and altered distribution of GABAergic interneurons in the cortical plate at postnatal day (P) 0. Furthermore, we observed an altered proportion of GABAergic interneurons in the cortex and striatum at P21 with a significant decrease in Parvalbumin (PVALB)-expressing interneurons. Altogether, our results indicate that reduced numbers of cortical interneurons upon DOT1L deletion results from altered post-mitotic differentiation/maturation.
ZMYM2 controls human transposable element transcription through distinct co-regulatory complexes
Authors: Owen Danielle , Aguilar-Martinez Elisa , Ji Zongling , Li Yaoyong , Sharrocks Andrew D.
Published: January 2023

ZMYM2 is a zinc finger transcriptional regulator that plays a key role in promoting and maintaining cell identity. It has been implicated in several diseases such as congenital anomalies of the kidney where its activity is diminished and cancer where it participates in oncogenic fusion protein events. ZMYM2 is thought to function through promoting transcriptional repression and here we provide more evidence to support this designation. Here we studied ZMYM2 function in human cells and demonstrate that ZMYM2 is part of distinct chromatin-bound complexes including the established LSD1-CoREST-HDAC1 corepressor complex. We also identify new functional and physical interactions with ADNP and TRIM28/KAP1. The ZMYM2-TRIM28 complex forms in a SUMO-dependent manner and is associated with repressive chromatin. ZMYM2 and TRIM28 show strong functional similarity and co-regulate a large number of genes. However, there are no strong links between ZMYM2-TRIM28 binding events and nearby individual gene regulation. Instead, ZMYM2-TRIM28 appears to regulate genes in a more regionally defined manner within TADs where it can directly regulate co-associated retrotransposon expression. We find that different types of ZMYM2 binding complex associate with and regulate distinct subclasses of retrotransposons, with ZMYM2-ADNP complexes at SINEs and ZMYM2-TRIM28 complexes at LTR elements. We propose a model whereby ZMYM2 acts directly through retrotransposon regulation, which may then potentially affect the local chromatin environment and associated coding gene expression.

Genome browser session

UCSC browser session containing the peak tracks:http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:18,078,462-18,084,961&hide=all&hgct_customText=http://bartzabel.ls.manchester.ac.uk/sharrockslab/yaoyong/ZNF198/index_file_hg19_chipSeq_ZMYM2_final.txt

Original ChIP-seq and ATAC-seq data from U2OS cells can be viewed On ArrayExpress at: E-MTAB-12292 (ADNP and TRIM28 ChIP-seq), E-MTAB-12293 (SUMO ChIP-seq) and E-MTAB-12294 (ATAC-seq)
Hatchling fish disperse using an efficient multisensory strategy
Authors: Lin Allia , Álvarez-Salvado Efrén , Milicic Nikola , Pujara Nimish , Ehrlich David E.
Published: January 2023

Animals improve fitness by choosing when and where to disperse in the environment using sensory cues. In freshwater habitats subject to flood and drought, dispersal can urgently challenge newly hatched fish. Here we manipulated rearing environment and sensory systems to reveal an adaptive sensorimotor strategy for dispersal. If we constrained hatchlings or blocked feedback about motion by simultaneously impairing the lateral line and vision, they gulped air and elevated their buoyancy to passively sail on faster surface waters. In stagnant water, hatchlings then covered more ground with hyperstable swimming, tightly steering based on graviception. In hydrodynamic simulations, these adaptations nearly tripled diffusivity and made dispersal robust to local conditions. Through combined use of three senses, hatchlings adapt their behavior to flexibly and efficiently disperse.
Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing and metagenomics
Authors: Hernández Marcela , Roy Shamik , Keevil C. William , Dumont Marc G.
Published: January 2023

Background

In this study, we aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil, by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled “heavy” and the unlabelled “light” SIP fractions were sequenced.

Results

After incubations, an increase of the 16S rRNA copy numbers in the “heavy” fractions of the treatments with18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) are highly abundant after two days of incubation with antibiotics. Several Pseudomonadota (formally Proteobacteria) includingStenotrophomonaswere prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genusStenotrophomonas(90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. On the other hand, only two ARGs from the unbinned-assembled light fractions were identified.

Conclusions

The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil, and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.
Membrane-dependent actin polymerization mediated by theLegionella pneumophilaeffector protein MavH
Authors: Zhang Qing , Wan Min , Mao Yuxin
Published: January 2023

L. pneumophilapropagates in eukaryotic cells within a specialized niche, theLegionella-containing vacuole (LCV). The infection process is controlled by over 330 effector proteins delivered through the type IV secretion system. In this study, we report that theLegionellaMavH effector harbors a lipid-binding domain that specifically recognizes PI(3)P (phosphatidylinositol 3-phosphate) and localizes to endosomes when ectopically expressed. We show that MavH recruits host actin capping proteins (CP) and actin to the endosome via its CP interacting (CPI) motif and WH2-like actin-binding domain, respectively. In vitro assays revealed that MavH stimulates robust actin polymerization only in the presence of PI(3)P-containing liposomes and the recruitment of CP by MavH negatively regulates F-actin density at the membrane. Furthermore, inL. pneumophila-infected cells, MavH can be detected around the LCV at the very early stage of infection. Together, our results reveal a novel mechanism of membrane-dependent actin polymerization catalyzed by MavH that may play a role at the early stage ofL. pneumophilainfection by regulating host actin dynamics.
Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse
Authors: Brown Anthony , Pan Qingfei , Fan Li , Indersie Emilie , Tian Cheng , Timchenko Nikolai , Li Liyuan , Hansen Baranda S. , Tan Haiyan , Lu Meifen , Peng Junmin , Pruett-Miller Shondra M. , Yu Jiyang , Cairo Stefano , Zhu Liqin
Published: January 2023

Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 (RRM2) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit,RRM2B. Computational analysis revealed distinct signaling networks RRM2 andRRM2Bwere involved in HB patient tumors, with RRM2 supporting cell proliferation andRRM2Bparticipating heavily in stress response pathways. Indeed,RRM2Bupregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during whichRRM2Bwas gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.
The effects of repeated intraperitoneal administration of the GABABreceptor agonist baclofen on body weight in rats maintained on a restricted feeding schedule
Authors: Ebenezer Ivor S.
Published: January 2023

It has previously been shown that chronic systemic administration of the GABABagonist, baclofen, reduces body weight in free feeding rats but has no effect on long-term food intake. The present study was conducted to extend these observations by investigating the effects of baclofen on body weight, food intake and water consumption in rats maintained on a restricted feeding schedule. The rats were allowed free access to food for 3 hours each day and injected intraperitoneally (i.p) once daily over a period of 11 days with baclofen (4 mg / kg; n=8) or saline (Control Group; n=8) immediately after each feeding session. Baclofen treatment produced small decreases in food intake on Days 2, 4 and 5 (P<0.05) compared with control animals but there were no differences between the 2 groups on Days 6 to 11. Baclofen did not affect prandial water intake. However, baclofen significantly decreased body weight gain of the animals (F(1,14)= 22.0,P< 0.01) starting 3 days after the initiation of treatment. During the subsequent 9 days both groups received no treatments. However, the “Baclofen Group” continued displaying significant reductions in body weight gain (F(1,14)= 8.47 p<0.01) but there were no significant differences in food and water consumption between the 2 groups of animals. The results of this study indicate that repeated administration of baclofen to food-restricted rats for 11 days reduces body weight and that the effects persist when the drug is withdrawn. While it is possible that the decrease in food intake during the early period of the experiment may have been partly responsible for the reduction in body weight in the baclofen-treated animals, the observation that these rats displayed reduction in body weight during the latter part of the study when there was no significant differences in food intake between the 2 groups, suggests that the drug decreases body weight independently of its effects on food consumption.
Temporal variability and cell mechanics control robustness in mammalian embryogenesis
Authors: Fabrèges Dimitri , Murtra Bernat Corominas , Moghe Prachiti , Kickuth Alison , Ichikawa Takafumi , Iwatani Chizuru , Tsukiyama Tomoyuki , Daniel Nathalie , Gering Julie , Stokkermans Anniek , Wolny Adrian , Kreshuk Anna , Duranthon Véronique , Uhlmann Virginie , Hannezo Edouard , Hiiragi Takashi
Published: January 2023

How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet open question in biology. Here, we establish a quantitative morphomap of pre-implantation embryogenesis in mouse, rabbit and monkey embryos, which reveals that although blastomere divisions desynchronise passively without compensation, 8-cell embryos still display robust 3D structure. Using topological analysis and genetic perturbations in mouse, we show that embryos progressively change their cellular connectivity to a preferred topology, which can be predicted by a simple physical model where noise and actomyosin-driven compaction facilitate topological transitions lowering surface energy. This favours the most compact embryo packing at the 8- and 16-cell stage, thus promoting higher number of inner cells. Impairing mitotic desynchronisation reduces embryo packing compactness and generates significantly more cell mis-allocation and a lower proportion of inner-cell-mass-fated cells, suggesting that stochasticity in division timing contributes to achieving robust patterning and morphogenesis.
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins
Authors: Singleton Marc , Eisen Michael
Published: January 2023

Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexiblek-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic HMM. In making the latter, we also wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotatedDrosophilagenomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction
Authors: Zheng Julia , Nishida Yuya , Okrasińska Alicja , Bonito Gregory M. , Heath-Heckman Elizabeth A.C. , Liu Kevin J.
Published: January 2023

Abstract

Just as a phylogeny encodes the evolutionary relationships among a group of organisms, a cophylogeny represents the coevolutionary relationships among symbiotic partners. Both are widely used to investigate a range of topics in evolutionary biology and beyond. Both are also primarily reconstructed using computational analysis of biomolecular sequence data as well as other biological character data. The most widely used cophylogenetic reconstruction methods utilize an important simplifying assumption: species phylogenies for each set of coevolved taxa are required as input and assumed to be correct. Many theoretical and experimental studies have shown that this assumption is rarely – if ever – satisfied, and the consequences for cophylogenetic studies are poorly understood. To address this gap, we conduct a comprehensive performance study that quantifies the relationship between species tree estimation error and downstream cophylogenetic estimation accuracy. The study includes performance benchmarking usingin silicomodel-based simulations. Our investigation also includes assessments of cophylogenetic reproducibility using genomic sequence datasets sampled from two important models of symbiosis: soil-associated fungi and their endosymbiotic bacteria, and bobtail squid and their bioluminescent bacterial symbionts. Our findings conclusively demonstrate the major impact that upstream phylogenetic estimation error has on downstream cophylogenetic reconstruction quality.
Investigating the Complexity of Gene Co-expression Estimation for Single-cell Data
Authors: Zhang Jiaqi , Singh Ritambhara
Published: January 2023

Abstract

With the rapid advance of single-cell RNA sequencing (scRNA-seq) technology, understanding biological processes at a more refined single-cell level is becoming possible. Gene co-expression estimation is an essential step in this direction. It can annotate functionalities of unknown genes or construct the basis of gene regulatory network inference. This study thoroughly tests the existing gene co-expression estimation methods on simulation datasets with known ground truth co-expression networks. We generate these novel datasets using two simulation processes that use the parameters learned from the experimental data. We demonstrate that these simulations better capture the underlying properties of the real-world single-cell datasets than previously tested simulations for the task. Our performance results on tens of simulated and eight experimental datasets show that all methods produce estimations with a high false discovery rate potentially caused by high-sparsity levels in the data. Finally, we find that commonly used pre-processing approaches, such as normalization and imputation, do not improve the co-expression estimation. Overall, our benchmark setup contributes to the co-expression estimator development, and our study provides valuable insights for the community of single-cell data analyses.
Systematic Analysis of Network-driven Adaptive Resistance to CDK4/6 and Estrogen Receptor Inhibition using Meta-Dynamic Network Modelling
Authors: Hart Anthony , Shin Sung-Young , Nguyen Lan K.
Published: January 2023

Drug resistance inevitably emerges during the treatment of cancer by targeted therapy. Adaptive resistance is a major form of drug resistance, wherein the rewiring of protein signalling networks in response to drug perturbation allows the drug-targeted protein’s activity to recover, despite the continuous presence of the drug, enabling the cells to survive/grow. Simultaneously, molecular heterogeneity enables the selection of drug-resistant cancer clones that can survive an initial drug insult, proliferate, and eventually cause disease relapse. Despite their importance, the link between heterogeneity and adaptive resistance, specifically how heterogeneity influences protein signalling dynamics to drive adaptive resistance, remains poorly understood. Here, we have explored the relationship between heterogeneity, protein signalling dynamics and adaptive resistance through the development of a novel modelling technique coined Meta Dynamic Network (MDN) modelling. We use MDN modelling to characterise how heterogeneity influences the drug-response signalling dynamics of the proteins that regulate early cell cycle progression and demonstrate that heterogeneity can robustly facilitate adaptive resistance associated dynamics for key cell cycle regulators. We determined the influence of heterogeneity at the level of both protein interactions and protein expression and show that protein interactions are a much stronger driver of adaptive resistance. Owing to the mechanistic nature of the underpinning ODE framework, we then identified a full spectrum of subnetworks that drive adaptive resistance dynamics in the key early cell cycle regulators. Finally, we show that single-cell dynamic data supports the validity of our MDN modelling technique and a comparison between our predicted resistance mechanisms and known CDK4/6 and Estrogen Receptor inhibitor resistance mechanisms suggests MDN can be deployed to robustly predict network-level resistance mechanisms for novel drugs and additional protein signalling networks.
Alteration of neural network and hippocampal slice activation through exosomes derived from 5XFAD nasal lavage fluid
Authors: Kim Sang Seong , Jeon Jae Kyong , Ganbat Dulguun , Kim Taewoon , Shin Kyusoon , Hong Sungho , Hong Jong Wook
Published: January 2023

Exosomes contain various intracellular biomarkers reflecting the condition of cells, organs, and subjects. Under neurodegenerative conditions, they contrive in detrimental neuronal communications leading to the initiation and propagation of neurodegenerative symptoms. Since the exosomes in olfactory fluid are readily accessible to collect in ample amount noninvasively and highly enriched in neural biomarkers, they can be a primary biomarker if we can verify precise pathophysiological information from them. Here we show that exosomes from nasal lavage fluid (NLF) of the neurodegeneration model animal, 5XFAD mice, induce the pathological network activity in neuronal cultures. We separated intact NLF exosomes from the 5XFAD and wild-type mice via a high-efficacy microfluidic system and applied them to the primary cortical neurons and organotypic hippocampal slice cultures (OHSC), whose neuronal activities were monitored by a high-density microelectrode array system. We found that NLF exosomes from 5XFAD mice increased the firing rate of neuronal spikes with augmentation of neuronal connectivity similar to the effect of pathological amyloid beta oligomer treatment. Furthermore, the current source densities, computed from the local field potentials, were elevated in OHSCs incubated with the exosomes, suggesting a pathological shift in synaptic and membrane currents. Those results demonstrate that NLF exosomes from neurodegeneration model can effectively modify neuronal networks and suggest that this property can serve as a functional biomarker for Alzheimer’s disease.
Stereoinversion via alcohol dehydrogenases enables complete catabolism of β-1-type lignin-derived aromatic isomers
Authors: Kato Ryo , Maekawa Kodai , Kobayashi Shota , Hishiyama Shojiro , Katahira Rui , Nambo Miki , Higuchi Yudai , Kuatsjah Eugene , Beckham Gregg T. , Kamimura Naofumi , Masai Eiji
Published: January 2023

Sphingobiumsp. SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism oferythro-DGPD was reported in SYK-6, but the catabolic pathway forthreo-DGPD was heretofore unknown. Here we elucidated the catabolism ofthreo-DGPD, which proceeds through conversion toerythro-DGPD. Whenthreo-DGPD was incubated with SYK-6, the Cα alcohol groups ofthreo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD+-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced toerythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase andldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated thatldpCandldpBare predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα alcohol group ofthreo-DGPD with a net stereoinversion using multiple dehydrogenases.

IMPORTANCE

In many catalytic depolymerization processes of lignin polymers, aryl–ether bonds are selectively cleaved, leaving carbon–carbon bonds between aromatic units intact, including dimers and oligomers with β-1 linkages. Therefore, elucidating the catabolic system of β-1-type lignin-derived compounds will aid in the establishment of biological funneling of heterologous lignin-derived aromatic compounds to value-added products. In this work, we found thatthreo-DGPD was converted by successive stereoselective oxidation and reduction at the Cα-position by multiple alcohol dehydrogenases toerythro-DGPD, which is further catabolized. This system is very similar to that developed to obtain enantiopure alcohols from racemic alcohols by artificially combining two enantiocomplementary alcohol dehydrogenases. The results presented here demonstrate that SYK-6 has evolved to catabolize all four stereoisomers of DGPD by incorporating this stereoinversion system into its native β-1-type dimer catabolic system.
A role for Toll-like receptor 3 in lung vascular remodeling associated with SARS-CoV-2 infection
Authors: Farkas Daniela , Bogamuwa Srimathi , Piper Bryce , Newcomb Geoffrey , Gunturu Pranav , Bednash Joseph S. , Londino James D. , Elhance Ajit , Nho Richard , Mejia Oscar Rosas , Yount Jacob S. , Horowitz Jeffrey C. , Goncharova Elena A. , Mallampalli Rama K. , Robinson Richard T. , Farkas Laszlo
Published: January 2023

Cardiovascular sequelae of severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) disease 2019 (COVID-19) contribute to the complications of the disease. One potential complication is lung vascular remodeling, but the exact cause is still unknown. We hypothesized that endothelial TLR3 insufficiency contributes to lung vascular remodeling induced by SARS-CoV-2. In the lungs of COVID-19 patients and SARS-CoV-2 infected Syrian hamsters, we discovered thickening of the pulmonary artery media and microvascular rarefaction, which were associated with decreased TLR3 expression in lung tissue and pulmonary artery endothelial cells (ECs).In vitro, SARS-CoV-2 infection reduced endothelial TLR3 expression. Following infection with mouse-adapted (MA) SARS-CoV-2, TLR3 knockout mice displayed heightened pulmonary artery remodeling and endothelial apoptosis. Treatment with the TLR3 agonist polyinosinic:polycytidylic acid reduced lung tissue damage, lung vascular remodeling, and endothelial apoptosis associated with MA SARS-CoV-2 infection. In conclusion, repression of endothelial TLR3 is a potential mechanism of SARS-CoV-2 infection associated lung vascular remodeling and enhancing TLR3 signaling is a potential strategy for treatment.
Coronaviruses use ACE2 monomers as entry receptors
Authors: Eiring Patrick , Klein Teresa , Backes Simone , Streit Marcel , Doose Sören , Beliu Gerti , Sauer Markus
Published: January 2023

The angiotensin-converting enzyme 2 (ACE2) has been identified as entry receptor on cells enabling binding and infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via trimeric spike (S) proteins protruding from the viral surface1,2. It has been suggested that trimeric S proteins preferably bind to plasma membrane areas with high concentrations of preferably multimeric ACE2 receptors to achieve a higher binding and infection efficiency1,3. However, our current knowledge about the influence of ACE2 expression and organization in the plasma membrane on SARS-CoV-2 infection efficiency remains elusive. Here we useddirectstochastic optical reconstruction microscopy (dSTORM) in combination with different labeling approaches to visualize the distribution and quantify the expression of ACE2 on different cells. Our results reveal that endogenous ACE2 receptors are present as monomers in the plasma membrane with densities of only 1-2 receptors μm-2. In addition, binding of trimeric S proteins does not induce clustering of ACE2 receptors in the plasma membrane. Supported by infection studies using vesicular stomatitis virus (VSV) particles bearing S proteins our data demonstrate that a single S protein interaction per virus particle with a monomeric ACE2 receptor is sufficient for infection which attests SARS-CoV-2 a high infectivity.
A ROS-based hybrid algorithm for the UAV path planning problem
Authors: Canpolat Tosun Demet , Işık Yasemin
Published: January 2023

Purpose

It is possible with classical path planning algorithms to plan a path in a static environment if the instant position of the vehicle is known and the target and obstacle positions are constant. In a dynamic case, these methods used for the static environment are insufficient. The purpose of this study is to find a new method that can provide a solution to the four-rotor unmanned aerial vehicle (UAV) path planning problem in static and dynamic environments.

Design/methodology/approach

As a solution to the problem within the scope of this study, there is a new hybrid method in which the global A* algorithm and local the VFH+ algorithm are combined.

Findings

The performance of the designed algorithm was tested in different environments using the Gazebo model of a real quadrotor and the robot operating system (ROS), which is the widely used platform for robotic applications. Navigation stacks developed for mobile robots on the ROS platform were also used for the UAV, and performance benchmarks were carried out. From the proposed hybrid algorithm, remarkable results were obtained in terms of both planning and implementation time compared to ROS navigation stacks.

Originality/value

This study proposes a new hybrid approach to the path planning problem for UAVs operating in both static and dynamic environments.
The role of purchasing in raising the maturity of smart maintenance management
Authors: Johannes Koos , Voordijk Hans , Aranda-Mena Guillermo
Published: January 2023

Purpose

The aim of this study is to provide insights into how the purchasing function can increase the maturity of smart maintenance management (SMM) in construction clients by (1) assessing current SMM maturity and (2) developing an adapted service triad for purchasing's meaningful involvement in SMM.

Design/methodology/approach

A multiple case research design was used, and data were collected from four higher education institutes in the Netherlands through an assessment of their current SMM maturity. Coding and a cross-case analysis were used to qualitatively analyze the data to identify roles and value chain integration factors as intermediate steps in adapting the service triad to a service hexad.

Findings

Within construction client organizations, collaboration between maintenance management, project management and ICT services requires improvement. The proposed service hexad redefines the client's SMM roles with the aim of improving collaboration. The authors discuss how this enables a transition to higher levels of SMM maturity.

Research limitations/implications

The findings were derived from a particular class of construction clients: higher education institutes that operate owner-occupied properties. Although the service hexad could be adapted, to owner-occupied multi-user properties, further research is necessary to assess its relevance for investor-owned properties.

Practical implications

Implementing the service hexad provides construction clients with a stronger position in supply networks. It clarifies the briefing process in construction management and emphasizes the data supply responsibilities of construction management professionals.

Originality/value

The study draws on the service triads and meaningful involvement concepts from the purchasing literature and applies them to SMM.