bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites
Authors: Aida Honoka , Uchida Keisuke , Nagai Motoki , Hashizume Takamasa , Masuo Shunsuke , Takaya Naoki , Ying Bei-Wen
Published: February 2023

The medium composition was crucial for achieving the best performance of synthetic construction. What and how medium components determined the production of the synthetic construction remained poorly investigated. To address the questions, a comparative survey with two genetically engineeredEscherichia colistrains was performed. As a case study, the strains carried the synthetic pathways for producing the aromatic compounds of 4APhe or Tyr, which were common in the upstream but differentiated in the downstream metabolism. Bacterial growth and compound production were examined in hundreds of medium combinations that comprised 48 pure chemicals. The resultant data sets linking the medium composition to bacterial growth and production were subjected to machine learning for improved production. Intriguingly, the primary medium components determining the production of 4PheA and Tyr were differentiated, which were the initial resource (glucose) of the synthetic pathway and the inducer (IPTG) of the synthetic construction, respectively. Fine-tuning of the primary component significantly increased the yields of 4APhe and Tyr, indicating that a single component could be crucial for the performance of synthetic construction. Transcriptome analysis observed the local and global changes in gene expression for improved production of 4APhe and Tyr, respectively, revealing divergent metabolic strategies for producing the foreign and native metabolites. The study demonstrated that ML-assisted medium optimization could provide a novel point of view on how to make the synthetic construction meet the original design.
Transposon accumulation at xenobiotic gene family loci: a comparative genomic analysis in aphids
Authors: Baril Tobias , Pym Adam , Bass Chris , Hayward Alex
Published: February 2023

The evolution of resistance is a major challenge for the sustainable control of pests and pathogens. Thus, a deeper understanding of the evolutionary and genomic mechanisms underpinning resistance evolution is required to safeguard health and food production. Several studies have implicated transposable elements (TEs) in xenobiotic resistance evolution in insects. However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid genomes, considering major subsets of XGFs involved in metabolic resistance to insecticides: Cytochrome P450s, glutathione S-transferases, esterases, UDP-glucuronosyltransferases, and ABC transporters. We find that TEs are significantly enriched at XGFs compared to other genes. XGFs show similar levels of TE enrichment to housekeeping genes. But unlike housekeeping genes, XGFs are not constitutively expressed in germline cells, supporting the selective enrichment of TEs at XGFs, rather than enrichment due to chromatin availability. Hotspots of extreme TE enrichment occur around certain XGFs. In aphids of agricultural importance, we find particular enrichment of TEs around cytochrome P450 genes with known functions in the detoxification of synthetic insecticides. Our results provide evidence supporting a general role for TEs as a source of genomic variation at host XGFs, and highlight the existence of considerable variability in TE content across XGFs and host species. These findings demonstrate the need for detailed functional verification analyses to clarify the significance of individual TE insertions and elucidate underlying mechanisms at TE-XGF hotspots.
Biophysical characterization and modeling ofSCN1Again-of-function predicts interneuron hyperexcitability and a predisposition to network instability through homeostatic plasticity
Authors: Berecki Géza , Bryson Alexander , Polster Tilman , Petrou Steven
Published: February 2023

SCN1Again-of-function variants are associated with early onset developmental and epileptic encephalopathies (DEEs) that possess distinct clinical features compared to Dravet syndrome caused bySCN1Aloss-of-function. However, it is unclear howSCN1Again-of-function may predispose to cortical hyper-excitability and seizures. Here, we first report the clinical features of a patient carrying ade novo SCN1Avariant (T162I) associated with neonatal-onset DEE, and then characterize the biophysical properties of T162I and three otherSCN1Avariants associated with neonatal-onset or early infantile DEE (I236V, P1345S, R1636Q). In voltage clamp experiments, three variants (T162I, P1345S and R1636Q) exhibited changes in activation and inactivation properties that enhanced window current, consistent with gain-of-function. Dynamic action potential clamp experiments utilising model neurons incorporating Nav1.1. channels supported a gain-of-function mechanism for all four variants. Here, the T162I, I236V, P1345S, and R1636Q variants exhibited higher peak firing rates relative to wild type and the T162I and R1636Q variants produced a hyperpolarized threshold and reduced neuronal rheobase. To explore the impact of these variants upon cortical excitability, we used a spiking network model containing an excitatory pyramidal cell (PC) and parvalbumin positive (PV) interneuron population.SCN1Again-of-function was modeled by enhancing the excitability of PV interneurons and then incorporating three simple forms of homeostatic plasticity that restored pyramidal cell firing rates. We found that homeostatic plasticity mechanisms exerted differential impact upon network function, with changes to PV- to-PC and PC-to-PC synaptic strength predisposing to network instability. Overall, our findings support a role forSCN1Again-of-function and inhibitory interneuron hyperexcitability in early onset DEE. We propose a mechanism through which homeostatic plasticity pathways can predispose to pathological excitatory activity and contribute to phenotypic variability inSCN1Adisorders.
OPTIMAL: An OPTimised Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data exploration
Authors: Hunter Bethany , Nicorescu Ioana , Foster Emma , McDonald David , Hulme Gillian , Fuller Andrew , Thomson Amanda , Goldsborough Thibaut , Hilkens Catharien M.U. , Majo Joaquim , Milross Luke , Fisher Andrew , Bankhead Peter , Wills John , Rees Paul , Filby Andrew , Merces George
Published: February 2023

Analysis of Imaging Mass Cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single cell segmentation and sub-optimal approaches for data visualisation and exploration. This can lead to inaccurate identification of cell phenotypes, states or spatial relationships compared to reference data from single cell suspension technologies. To this end we have developed the “OPTIMAL” framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualisation/clustering and spatial neighbourhood analysis. Using a panel of 27 metal-tagged antibodies recognising well characterised phenotypic and functional markers to stain the same FFPE human tonsil sample Tissue Microarray (TMA) over 12 temporally distinct batches we tested several cell segmentation models, a range of differentarcsinhcofactor parameter transformation values, five different dimensionality reduction algorithms and two clustering methods. Finally we assessed the optimal approach for performing neighbourhood analysis. We found that single cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using “classical” bi-variate data display techniques. The optimalarcsinhcofactor for parameter transformation was 1 as it maximised the statistical separation between negative and positive signal distributions and a simple Z-score normalisation step afterarcsinhtransformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing Phenograph in terms of cell type identification. We also found that neighbourhood analysis was influenced by the method used for finding neighbouring cells with a “disc” pixel expansion outperforming a “bounding box” approach combined with the need for filtering objects based on size and image-edge location. Importantly OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output, allows for single cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.
Markerless motion capture estimates of lower extremity kinematics and kinetics are comparable to marker-based across 8 movements
Authors: Song Ke , Hullfish Todd J. , Silva Rodrigo Scattone , Silbernagel Karin Grävare , Baxter Josh R.
Published: February 2023

Motion analysis is essential for assessing in-vivo human biomechanics. Marker-based motion capture is the standard to analyze human motion, but the inherent inaccuracy and practical challenges limit its utility in large-scale and real-world applications. Markerless motion capture has shown promise to overcome these practical barriers. However, its fidelity in quantifying joint kinematics and kinetics has not been verified across multiple common human movements. In this study, we concurrently captured marker-based and markerless motion data on 10 healthy subjects performing 8 daily living and exercise movements. We calculated the correlation (Rxy) and root-mean-square difference (RMSD) between markerless and marker-based estimates of ankle dorsi-plantarflexion, knee flexion, and three-dimensional hip kinematics (angles) and kinetics (moments) during each movement. Estimates from markerless motion capture matched closely with marker-based in ankle and knee joint angles (Rxy≥ 0.877, RMSD ≤ 5.9°) and moments (Rxy≥ 0.934, RMSD ≤ 2.66 % height × weight). High outcome comparability means the practical benefits of markerless motion capture can simplify experiments and facilitate large-scale analyses. Hip angles and moments demonstrated more differences between the two systems (RMSD: 6.7° – 15.9° and up to 7.15 % height × weight), especially during rapid movements such as running. Markerless motion capture appears to improve the accuracy of hip-related measures, yet more research is needed for validation. We encourage the biomechanics community to continue verifying, validating, and establishing best practices for markerless motion capture, which holds exciting potential to advance collaborative biomechanical research and expand real-world assessments needed for clinical translation.
Ubiquinone deficiency drives reverse electron transport to disrupt hepatic metabolic homeostasis in obesity
Authors: Goncalves Renata L.S. , Wang Zeqiu Branden , Inouye Karen E. , Lee Grace Yankun , Fu Xiaorong , Saksi Jani , Rosique Clement , Parlakgul Gunes , Arruda Ana Paula , Hui Sheng Tony , Loperena Mar Coll , Burgess Shawn C. , Graupera Isabel , Hotamisligil Gökhan S.
Published: February 2023

Mitochondrial reactive oxygen species (mROS) are central to physiology. While excess mROS production has been associated with several disease states, its precise sources, regulation, and mechanism of generationin vivoremain unknown, limiting translational efforts. Here we show that in obesity, hepatic ubiquinone (Q) synthesis is impaired, which raises the QH2/Q ratio, driving excessive mROS production via reverse electron transport (RET) from site IQin complex I. Using multiple complementary genetic and pharmacological modelsin vivowe demonstrated that RET is critical for metabolic health. In patients with steatosis, the hepatic Q biosynthetic program is also suppressed, and the QH2/Q ratio positively correlates with disease severity. Our data identify a highly selective mechanism for pathological mROS production in obesity, which can be targeted to protect metabolic homeostasis.
Evolutionary changes in germ granule mRNA content are driven by multiple mechanisms inDrosophila
Authors: Doyle Dominique A. , Burian Florencia N. , Aharoni Benjamin , Klinder Annabelle J. , Menzel Melissa M. , Nifras Gerard Carlo C. , Shabazz-Henry Ahad L. , Palma Bianca Ulrich , Hidalgo Gisselle A. , Sottolano Christopher J. , Ortega Bianca M. , Niepielko Matthew G.
Published: February 2023

The co-packaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to post-transcriptionally regulate mRNAs that function in germline development and maintenance. InD. melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates that contain multiple transcripts from a specific gene. Nucleated by Oskar (Osk), homotypic clusters inD. melanogasterare generated through a stochastic seeding and self-recruitment process that requires the 3’ UTR of germ granule mRNAs. Interestingly, the 3’ UTR belonging to germ granule mRNAs, such asnanos(nos), have considerable sequence variations amongDrosophilaspecies. Thus, we hypothesized that evolutionary changes in the 3’ UTR influences germ granule development. To test our hypothesis, we investigated the homotypic clustering ofnosandpolar granule component(pgc) in fourDrosophilaspecies and concluded that homotypic clustering is a conserved developmental process used to enrich germ granule mRNAs. Additionally, we discovered that the number of transcripts found innosand/orpgcclusters could vary significantly among species. By integrating biological data with computational modeling, we determined that multiple mechanisms underlie naturally occurring germ granule diversity, including changes innos,pgc,osklevels, and/or homotypic clustering efficacy. Finally, we found that thenos3’ UTR from different species can alter the efficacy ofnoshomotypic clustering, resulting in germ granules with reducednosaccumulation. Our findings highlight the impact that evolution has on the development of germ granules and may provide insight into processes that modify the content of other classes of biomolecular condensates.
Signalling-dependent refinement of cell fate choice during tissue remodelling
Authors: Herszterg Sophie , de Gennes Marc , Cicolini Simone , Huang Anqi , Alexandre Cyrille , Smith Matthew , Araujo Helena , Vincent Jean-Paul , Salbreux Guillaume
Published: February 2023

How biological form emerges from cell fate decisions and tissue remodelling is a fundamental question in development biology. However, an understanding of how these processes operate side-by-side to set precise and robust patterns is largely missing. Here, we investigate this interplay during the process of vein refinement in theDrosophilapupal wing. By following reporters of signalling activity dynamically, together with tissue flows, we show that longitudinal vein refinement arises from a combination of local tissue deformation and cell fate adjustments controlled by a signalling network involving Notch, Dpp, and EGFR. Perturbing large-scale convergence and extension tissue flows does not affect vein refinement, showing that pre-patterned vein domains are able to intrinsically refine to the correct width. A minimal biophysical description taking into account key signalling interactions recapitulates the intrinsic tissue ability to establish a thin, regular vein independently of large-scale tissue flows. Supporting this prediction, artificial proveins optogenetically generated orthogonal to the axis of wing elongation refine against large-scale flows. Overall, we find that signalling-mediated updating of cell fate is a key contributor to reproducible patterning.
The use of DNA barcoding for the identification of giant hogweeds in the European North-East of Russia
Authors: Shadrin D.M. , Dalke I.V. , Zakhozhiy I.G. , Shilnikov D.S. , Kozhin M.N. , Chadin I.F.
Published: February 2023

Qualitative differences in the nrDNA ITS and ETS sequences in the total sample were determined to allow identification of the following groups of samples:H. mantegazzianum, H. cf.sosnowskyi, H. cf.mantegazzianumandH. cf.sosnowskyi×H. cf.mantegazzianumamong other representatives of theHeracleumgenus presented in the genetic databases. The study revealed the absence of correlation between a sample type in the groupH. mantegazzianum, H. cf.sosnowskyi, H. cf.mantegazzianumandH. cf.sosnowskyi×H. cf.mantegazzianumand qualitative transformations in the ITS and ETS sequences. The qualitative analysis of the rbcL, matK, rps16 intron, intergenic spacers psbA-trnH, trnQ-rps16, rps16-trnK and rpl32-trnL cpDNA sequences for the samples identified asHeracleum mantegazzianum,H. cf.sosnowskyi,H. cf.mantegazzianumandH. cf.sosnowskyi×H. cf.mantegazzianumdemonstrated no correlation between them as well.
Interferon inhibits a model RNA virus via a limited set of inducible effector genes
Authors: McDougal Matthew B. , De Maria Anthony M. , Ohlson Maikke B. , Kumar Ashwani , Xing Chao , Schoggins John W.
Published: February 2023

Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon-stimulated genes (ISGs). The field has mostly focused on identifying individual antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is not known how many ISGs are required to protect cells from a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, we used CRISPR-based loss-of-function screens to identify a markedly limited set of ISGs that confer interferon-mediated suppression of a model alphavirus, Venezuelan equine encephalitis virus (VEEV). We show via combinatorial gene targeting that three antiviral effectors – ZAP, IFIT3, and IFIT1 – together constitute the majority of interferon-mediated restriction of VEEV, while accounting for less than 0.5% of the interferon-induced transcriptome. Together, our data suggests a refined model of the antiviral interferon response in which a small subset of “dominant” ISGs may confer the bulk of the inhibition of a given virus.
Androgen Receptor driven gene score identifies tumors with Epithelial to Mesenchymal Transition features in triple negative breast cancer
Authors: Rajarajan Savitha , Snijesh VP , Anupama CE , Nair Madhumathy G , Apoorva D , Chandrakala M , Patil Sharada , Nimbalkar Vidya P , Alexander Annie , Pillai Maalavika , Jolly Mohit Kumar , Sabarinathan Radhakrishnan , Ramesh Rakesh S , Srinath BS , Prabhu Jyothi S
Published: February 2023

Background

Androgen receptor (AR) is considered marker associated with better prognosis within hormone receptor positive tumors. Its role in triple negative tumors however is controversial showing both better and worse prognosis and different methods are used for identification of AR driven tumors. Conflicting results could be due to intrinsic molecular differences or scoring method for AR positivity. We attempted to develop an AR driven gene score and examined its utility in subtypes of breast cancer (BC).

Methods

A bioinformatic pipeline was constructed and applied on publicly available microarray data sets obtained from AR positive BC cell lines treated with dihydrotestosterone (DHT). Expression levels of genes identified through the pipeline along with set of epithelial mesenchymal transition (EMT) markers, proliferation associated genes and enzymes involved in intracrinal androgen metabolism was evaluated in a cohort of Indian Breast cancer patients. Tumors were divided into AR high and low based on the gene score and association with clinical parameters, circulating androgens, disease free survival, proliferation and EMT markers were examined, all results were further validated in external public datasets.

Results

AR driven gene score was calculated as average expression of the 6 genes selected through bioinformatic analysis. 53% (133/249) tumors were classified as AR high by the gene score and had significantly better clinical parameters such as higher age, smaller tumor size, lower grade and lower proliferation. Tumors with high AR driven gene score had significantly better disease-free survival (mean survival time of 86.13 vs 72.69 months, log rank p=0.032) when compared to the AR low tumors. A subset analysis within TNBC (N=66) showed 36% (24/66) were AR high and had significantly higher expression of EMT markers (p=0.024). Though circulating levels of total testosterone was not different between the groups, intratumoral levels of 5 alfa reductase (SRD5A1) was significantly high in tumors with high AR driven score.

Conclusion

Role of AR in breast cancer is debatable and difficult to decipher with protein detection alone. Our results support the context dependent function of AR in driving better prognosis, while identifying its role in driving EMT within TNBC tumors.
Immunostimulatory effects ofBacillus coagulansSANK70258
Authors: Ikeda Yuki , Ito Naoto , Yamashita Niya , Minamikawa Natsuki , Nagata Kazuki , Yashiro Takuya , Aida Masanori , Yamada Ryouichi , Hachisu Masakazu , Nishiyama Chiharu
Published: February 2023

Specific intestinal bacteria modulate immunoresponses through various pathways, and several probiotic bacteria have been identified as immunostimulants by screening. In the present study, we evaluated the immunomodulating effects ofBacillus coagulansSANK70258 (B. coagulansSANK70258), a spore-forming and lactic acid-producing bacterium usable as food supplement for human and animals. We found that treatment of mouse splenocytes with γ-ray irradiatedB. coagulansSANK70258 induced high amount of IFN-γ in comparison with 7 kinds of typical lactic acid bacteria. Further analyses using splenocytes revealed that NK cell is a major source of IFN-γ, andB.coagulansSANK70258-induced IFN-γ production was inhibited by neutralization of IL-12 or IL-23, depletion of CD11c+cells, and inhibition of NFκB.B. coagulansSANK70258 also induced release of IFN-γ from activated CD8+T cells, and increased expression of chemokine receptors in CD8+T cells.B. coagulansSANK70258-treatment induced production of cytokines from bone marrow-derived dendritic cells, which is reduced by knockdown ofTlr2andNod2. B. coagulansSANK70258-treatment also induced IgA production from Peyer’s patch cells with high level among tested lactic bacteria. The oral intake of γ-ray irradiatedB. coagulansSANK70258 significantly increased intestinal IgA levels and IgA-expressing B cells in the Peyer’s patch of mice. Taken together, we conclude thatB. coagulansSANK70258 possesses high activity as immunostimulant inducing production of IFN-γ and IgA.
Increased cortical inhibition immediately following brief motor memory reactivation supports reconsolidation and overnight offline learning gains
Authors: Eisenstein Tamir , Furman-Haran Edna , Tal Assaf
Published: February 2023

Practicing motor skills stabilizes and strengthens motor memories by repeatedly reactivating and reconsolidating them. The conventional view, by which a repetitive practice is required for substantially improving skill performance, has been recently challenged by behavioral experiments, in which even brief reactivations of the motor memory have led to significant improvements in skill performance. However, the mechanisms which facilitate brief reactivation-induce skill improvements remain elusive. While initial memory consolidation has been repeatedly associated with increased neural excitation and dis-inhibition, reconsolidation has been shown to involve a poorly-understood mixture of both excitatory and inhibitory alterations.

Here, we followed a three-day reactivation-reconsolidation framework, to examine whether the excitatory/inhibitory mechanisms which underlie brief reactivation and repetitive practice differ. Healthy volunteers practiced a motor sequence learning task using either brief reactivation or repetitive practice and were assessed using ultra-high field (7T) magnetic resonance spectroscopy at the primary motor cortex (M1). We found that increased inhibition (GABA concentrations) and decreased excitation/inhibition (glutamate/GABA ratios) immediately following the brief reactivation were associated with overnight offline performance gains. These gains were on-par with those exhibited following repetitive practice, where no correlations with inhibitory or excitatory changes were observed. Our findings suggest that brief reactivation and repetitive practice depend on fundamentally different neural mechanisms, and that early inhibition – and not excitation – is particularly important in supporting the learning gains exhibited by brief reactivation.
Design, evaluation and implementation of synthetic isopentyldiol pathways inEscherichia coli
Authors: Liu Yongfei , Chen Lin , Liu Pi , Yuan Qianqian , Ma Chengwei , Wang Wei , Zhang Chijian , Ma Hongwu , Zeng An-Ping
Published: February 2023

Isopentyldiol (IPDO) is an important raw material in cosmetic industry. So far IPDO is exclusively produced through chemical synthesis. Growing interest in natural personal care products has inspired the quest to develop a bio-based process. We previously reported a biosynthetic route that produces IPDO via extending leucine catabolism (route A), the efficiency of which, however, is not satisfactory. To address this issue, we computational designed a novel non-natural IPDO synthesis pathway (Route B) using RetroPath RL, the state of art tool for bio-retrosynthesis based on Artificial Intelligence methods. We compared this new pathway with route A and another two intuitively designed routes for IPDO biosynthesis from various aspects. Route B, which exhibits the highest thermodynamic driving force, least non-native reaction steps and lowest energy requirements appeared to hold the greatest potential for IPDO production. All three newly designed routes were then implemented inE. coliBL21(DE3) strain. Results show that the computationally designed route B can produce 2.2 mg/L IPDO from glucose, whereas no IPDO production from routes C and D. These results highlight the importance and usefulness ofin silicodesign and comprehensive evaluation of the potential efficiencies of candidate pathways in constructing novel non-natural pathways for the production of biochemicals.
Exploratory mass cytometry analysis reveals immunophenotypes of cancer treatment-related pneumonitis
Authors: Yanagihara Toyoshi , Hata Kentaro , Matsubara Keisuke , Kunimura Kazufumi , Suzuki Kunihiro , Tsubouchi Kazuya , Ikegame Satoshi , Baba Yoshihiro , Fukui Yoshinori , Okamoto Isamu
Published: February 2023

Anti-cancer treatments can result in various adverse effects, including infections due to immune suppression/dysregulation and drug-induced toxicity in the lung. One of the major opportunistic infections isPneumocystis jiroveciipneumonia (PCP), which can cause severe respiratory complications and high mortality rates. Cytotoxic drugs and immune-checkpoint inhibitors (ICIs) can induce interstitial lung diseases (ILDs). Nonetheless, the differentiation of these diseases can be difficult, and the pathogenic mechanisms of such diseases are not yet fully understood. To better comprehend the immunophenotypes, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid from patients with PCP, cytotoxic drug-induced ILD (DI-ILD), and ICI-associated ILD (ICI-ILD) using two panels containing 64 markers. In PCP, we observed an expansion of the CD16+T cell population, with the highest CD16+T proportion in a fatal case. In ICI-ILD, we found an increase in CD57+CD8+T cells expressing immune checkpoints (TIGIT+LAG3+TIM-3+PD-1+), FCRL5+B cells, and CCR2+CCR5+CD14+monocytes. These findings uncover the diverse immunophenotypes and possible pathomechanisms of cancer treatment-related pneumonitis.
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Authors: Choudhury Subham , Narayanan Bharath , Moret Michael , Hatzimanikatis Vassily , Miskovic Ljubisa
Published: February 2023

Generating large omics datasets has become routine practice to gain insights into cellular processes, yet deciphering such massive datasets and determining intracellular metabolic states remains challenging. Kinetic models of metabolism play a critical role in integrating omics data, as they provide explicit connections between metabolite concentrations, metabolic fluxes, and enzyme levels. Nevertheless, the challenges associated with determining the kinetic parameters that underlie cellular physiology pose significant obstacles to the broader acceptance and adoption of these models within the research community. Here, we present RENAISSANCE, a generative machine learning framework for efficiently parameterizing large-scale kinetic models with dynamic properties matching experimental observations. Through seamless integration and consolidation of diverse omics data and other relevant information, like extracellular medium composition, physicochemical data, and expertise of domain specialists, we show that the proposed framework accurately characterizes unknown intracellular metabolic states, including metabolic fluxes and metabolite concentrations inE. coli’s metabolic network. Moreover, we show that RENAISSANCE successfully estimates missing kinetic parameters and reconciles them with sparse and noisy experimental data, resulting in a substantial reduction in parameter uncertainty and a notable improvement in the accuracy and reliability of the parameter estimates. The proposed framework will be invaluable for researchers who seek to analyze metabolic variations involving changes in metabolite and enzyme levels and enzyme activity in health and biotechnological studies.
CD99 Promotes Self-renewal in Hematopoietic Stem Cells and Leukemia Stem Cells by Regulating Protein Synthesis
Authors: Huang Yi , Kapti Eda Gozel , Ji Yuanyuan , Thomas Toby , Dempsey Jebrail , Mims Karin , Berezniuk Iryna , Guo Liang , Kroger Benjamin , Hu Wenhuo , Park Christopher Y. , Chung Stephen S.
Published: February 2023

Blood production is sustained by hematopoietic stem cells (HSCs), which are typically the only blood cells capable of long-term self-renewal. Acute myeloid leukemia (AML) is initiated by aberrantly self-renewing malignant stem cells termed leukemia stem cells (LSCs). HSCs exhibit and depend on low levels of protein synthesis to self-renew. However, the mechanisms by which HSCs regulate protein synthesis to maintain their capacity for self-renewal in the setting of proliferative stress and leukemogenesis remain unknown. Here we show CD99, a cell surface protein upregulated in LSCs, is required for self-renewal of proliferating HSCs and LSCs. We found that loss of CD99 in HSCs and LSCs leads to increased protein synthesis and that their self-renewal capacity can be restored by translation inhibition. These data demonstrate a functional role for CD99 in constraining protein synthesis, which may promote the clonal expansion of HSCs and LSCs that leads to AML. Furthermore, they show that similar to HSCs, LSCs depend on regulated protein synthesis.
Manipulating single-unit theta phase-locking with PhaSER: An open-source tool for real-time phase estimation and manipulation
Authors: Christenson Wick Zoé , Philipsberg Paul A , Lamsifer Sophia I , Kohler Cassidy , Katanov Elizabeth , Feng Yu , Humphrey Corin , Shuman Tristan
Published: February 2023

The precise timing of neuronal spiking relative to the brain’s endogenous oscillations (i.e., phase-locking or spike-phase coupling) has long been hypothesized to coordinate cognitive processes and maintain excitatory-inhibitory homeostasis. Indeed, disruptions in theta phase-locking have been described in models of neurological diseases with associated cognitive deficits and seizures, such as Alzheimer’s disease, temporal lobe epilepsy, and autism spectrum disorders. However, due to technical limitations, determining if phase-locking causally contributes to these disease phenotypes has not been possible until recently. To fill this gap and allow for the flexible manipulation of single-unit phase-locking to on-going endogenous oscillations, we developed PhaSER, an open-source tool that allows for phase-specific manipulations. PhaSER can deliver optogenetic stimulation at defined phases of theta in order to shift the preferred firing phase of neurons relative to theta in real-time. Here, we describe and validate this tool in a subpopulation of inhibitory neurons that express somatostatin (SOM) in the CA1 and dentate gyrus (DG) regions of the dorsal hippocampus. We show that PhaSER is able to accurately deliver a photo-manipulation that activates opsin+ SOM neurons at specified phases of theta in real-time in awake, behaving mice. Further, we show that this manipulation is sufficient to alter the preferred firing phase of opsin+ SOM neurons without altering the referenced theta power or phase. All software and hardware requirements to implement real-time phase manipulations during behavior are available online (https://github.com/ShumanLab/PhaSER).
Beak morphometry and morphogenesis across avian radiations
Authors: Mosleh Salem , Choi Gary P. T. , Musser Grace M. , James Helen F. , Abzhanov Arhat , Mahadevan L.
Published: February 2023

Adaptive avian radiations associated with the diversification of bird beaks into a multitude of forms enabling different functions are exemplified by Darwin’s finches and Hawaiian honeycreepers. To elucidate the nature of these radiations, we quantified beak shape and skull shape using a variety of geometric measures that allowed us to collapse the variability of beak shape into a minimal set of geometric parameters. Furthermore, we find that just two measures of beak shape, the ratio of the width to length and the normalized sharpening rate (increase in the transverse beak curvature near the tip relative to that at the base of the beak), are both strongly correlated with diet, and thus indicative of how bite forces are correlated with beak shape. Finally, by considering how transverse sections to the beak centerline evolve with distance from the tip, we show that a simple geometry-driven growth law termed “modified mean curvature flow” captures the beak shapes of Darwin’s finches and Hawaiian honeycreepers. A surprising consequence of the simple growth law is that beak shapes that are not allowed based on the developmental program of the beak are also not observed in nature, suggesting a link between evolutionary morphology and development in terms of growth-driven developmental constraints.
Elevational Range Sizes of Woody plants Increase with Climate Variability in the Tropical Andes
Authors: Montaño-Centellas Flavia , Fuentes Alfredo F. , Cayola Leslie , Macía Manuel J. , Arellano Gabriel , Loza M. Isabel , Nieto-Ariza Beatriz , Tello J. Sebastián
Published: February 2023

Aim

The climate variability hypothesis proposes that species subjected to wide variation in climatic conditions will evolve wider niches, resulting in larger distributions. We test this hypothesis in tropical plants across a broad elevational gradient; specifically, we use a species-level approach to evaluate whether elevational range sizes are explained by the levels of thermal variability experienced by species.

Location

Central Andes

Time period

Present day

Major taxa studied

Woody plants

Methods

Combining data from 479 forest plots, we determined the elevational distributions of nearly 2300 species along an elevational gradient (∼209 – 3800 m). For each species, we calculated the maximum annual variation in temperature experienced across its elevational distribution. We used phylogenetic generalized least square models to evaluate the effect of thermal variability on range size. Our models included additional covariates that might affect range size: body size, local abundance, mean temperature and total precipitation. We also considered interactions between thermal variability and mean temperature or precipitation. To account for geometric constraints, we repeated our analyses with a standardized measure of range size, calculated by comparing observed range sizes with values obtained from a null model.

Results

Our results supported the main prediction of the climate variability hypothesis. Thermal variability had a strong positive effect on the range size, with species exposed to higher thermal variability having broader elevational distributions. Body size and local abundance also had positive, yet weak effects, on elevational range size. Furthermore, there was a strong positive interaction between thermal variability and mean annual temperature.

Main conclusions

Thermal variability had an overriding importance in driving elevational range sizes of woody plants in the Central Andes. Moreover, the relationship between thermal variability and range size might be even stronger in warmer regions, underlining the potential vulnerability of tropical montane floras to the effects of global warming.
Hypoxia dampens innate immune signalling at early time points and increases Zika virus replication in iPSC-derived macrophages
Authors: Schilling Mirjam , Vaughan-Jackson Alun , James William , McKeating Jane A
Published: February 2023

Type I interferons (IFNs) are the major host defence against viral infection and are induced following activation of cell surface or intracellular pattern recognition receptors, including retinoic-acid-inducible gene I (RIGI)-like receptors (RLRs). All cellular processes are shaped by the microenvironment and one important factor is the local oxygen tension. The majority of published studies on IFN signalling are conducted under atmospheric (18%) oxygen conditions, that do not reflect the physiological oxygen levels in most organs (1-5% O2). We studied the effect of low oxygen on IFN induction and signalling in induced Pluripotent Stem Cell (iPSC)-derived macrophages as a model for tissue-resident macrophages and assessed the consequence for Zika virus (ZIKV) replication. Hypoxic conditions dampened the expression of interferon-stimulated genes (ISGs) following RLR stimulation or IFN treatment at early time points. RNA-sequencing and bio-informatic analysis uncovered several pathways including changes in transcription factor availability, the presence of HIF binding sites in promoter regions, and CpG content that may contribute to the reduced ISG expression. Importantly, hypoxic conditions increased ZIKV replication at early time points, emphasizing the importance of understanding how low oxygen conditions in the local microenvironment affect pathogen sensing and host defence.
Shear-induced phenotypic transformation of microgliain vitro
Authors: Park Eunyoung , Ahn Song Ih , Park Jin-Sung , Shin Jennifer H.
Published: February 2023

Brain cells are influenced by continuous fluid shear stress driven by varying hydrostatic and osmotic pressure conditions, depending on the brain’s pathophysiological conditions. While all brain cells are sensitive to the subtle changes in various physicochemical factors in the microenvironment, microglia, the resident brain immune cells, exhibit the most dramatic morphodynamic transformation. However, little is known about the phenotypic alterations in microglia in response to the changes in fluid shear stress. In this study, we first established a flow-controlled microenvironment to investigate the effects of shear flow on microglial phenotypes, including morphology, motility, and activation states. Microglia exhibited two distinct morphologies with different migratory phenotypes in a static condition: bipolar cells that oscillate along their long axis and unipolar cells that migrate persistently. When exposed to flow, a significant fraction of bipolar cells showed unstable oscillation with an increased amplitude of oscillation and a decreased frequency, which consequently led to the phenotypic transformation of oscillating cells into migrating cells. Interestingly, the level of pro-inflammatory genes increased in response to shear stress, while there were no significant changes in the level of anti-inflammatory genes. Our findings suggest that an interstitial fluid-level stimulus can cause a dramatic phenotypic shift in microglia toward pro-inflammatory states, shedding light on pathological outbreaks of severe brain diseases. Given that the fluidic environment in the brain can be locally disrupted in pathological circumstances, the mechanical stimulus by a fluid flow should also be considered a crucial element in regulating the immune activities of the microglia in brain diseases.

Statement of Significance

Cellular morphology and motility are important factors that encompass the alterations in protein and gene-level expressions within cells. In pathological conditions, microglia, the resident brain immune cells, are known to undergo morphodynamic transformations in response to various physicochemical stimuli. Besides the commonly known soluble biochemical factors in the microenvironment, the differential flow characteristics of ISF have been linked to several neurological diseases, such as Alzheimer’s, Parkinson’s, and brain tumors. Microglial cells, which are extremely sensitive to subtle changes in extracellular stimuli, have been identified as key players in these pathological conditions. Despite its importance, however, it has been challenging to study the sole effect of a shear flow on microglia. We investigated the morphodynamic features of microglia in response to precisely controlled interstitial-level fluid flow conditions using a microfluidic system in which isolated microglia are monitored in real-time while the undesirable effects from other extracellular factors are minimized.
A role for fibroblast-derived SASP factors in the activation of pyroptotic cell death in mammary epithelial cells
Authors: Hom Lisa M. , Sun Seunghoon , Campbell Jamie , Liu Pinyan , Culbert Shannon , Murphy Ireland M. , Schafer Zachary T.
Published: February 2023

In normal tissue homeostasis, bidirectional communication between different cell types can shape numerous biological outcomes. Many studies have documented instances of reciprocal communication between fibroblasts and cancer cells that functionally change cancer cell behavior. However, less is known about how these heterotypic interactions shape epithelial cell function in the absence of oncogenic transformation. Furthermore, fibroblasts are prone to undergo senescence, which is typified by an irreversible cell cycle arrest. Senescent fibroblasts are also known to secrete various cytokines into the extracellular space; a phenomenon that is termed the senescence-associated secretory phenotype (SASP). While the role of fibroblast derived SASP factors on cancer cells has been well studied, the impact of these factors on normal epithelial cells remains poorly understood. We discovered that treatment of normal mammary epithelial cells with conditioned media (CM) from senescent fibroblasts (SASP CM) results in a caspase-dependent cell death. This capacity of SASP CM to cause cell death is maintained across multiple senescence-inducing stimuli. However, the activation of oncogenic signaling in mammary epithelial cells mitigates the ability of SASP CM to induce cell death. Despite the reliance of this cell death on caspase activation, we discovered that SASP CM does not cause cell death by the extrinsic or intrinsic apoptotic pathway. Instead, these cells die by an NLRP3, caspase-1, and gasdermin D (GSDMD)-dependent induction of pyroptosis. Taken together, our findings reveal that senescent fibroblasts can cause pyroptosis in neighboring mammary epithelial cells, which has implications for therapeutic strategies that perturb the behavior of senescent cells.
Macroscale coupling between structural and effective connectivity in the mouse brain
Authors: Benozzo Danilo , Baron Giorgia , Coletta Ludovico , Chiuso Alessandro , Gozzi Alessandro , Bertoldo Alessandra
Published: February 2023

How the emergent functional connectivity (FC) relates to the underlying anatomy (structural connectivity, SC) is one of the biggest questions of modern neuroscience. At the macro-scale level, no one-to-one correspondence between structural and functional links seems to exist. And we posit that to better understand their coupling, two key aspects should be taken into account: the directionality of the structural connectome and the limitations of describing network functions in terms of FC. Here, we employed an accurate directed SC of the mouse brain obtained by means of viral tracers, and related it with single-subject effective connectivity (EC) matrices computed by applying a recently developed DCM to whole-brain resting-state fMRI data. We analyzed how SC deviates from EC and quantified their couplings by conditioning both on the strongest SC links and EC links. We found that when conditioning on the strongest EC links, the obtained coupling follows the unimodal-transmodal functional hierarchy. Whereas the reverse is not true, as there are strong SC links within high-order cortical areas with no corresponding strong EC links. This mismatch is even more clear across networks. Only the connections within sensory motor networks align both in terms of effective and structural strength.
A novel purity analysis method of bovine milk-derived exosomes by two-dimensional high-performance liquid chromatography
Authors: Lu Lu , Han Chunle , Zhang Quan , Wang Miao , Qi Dongli , Gao Mengya , Wang Na , Yin Jianxin , Dong Fengwei , Ge Xiaohu
Published: February 2023

Exosomes have been implicated in many biological processes as intercellular communication carriers. Because exosomes are increasingly explored as natural vehicles for cell and gene therapies, and drug delivery applications, it is critical to have high-quality samples. Protein:particle ratio, ELISA, western blotting, polymerase chain reaction, and size-exclusion high-performance liquid chromatography are the main methods that have been extensively applied to analyze exosomes purity in recent years. However, there is currently no well-established method that is convenient for routine quality analysis of small-size impurities in exosomes samples. Here, a size-exclusion high-performance liquid chromatography (SE-HPLC), an ion-exchange high-performance liquid chromatography (IEX-HPLC), and a novel two-dimensional high-performance liquid chromatography (2D-HPLC) method were used to detect the purity of bovine milk-derived exosomes with different processes of exosome isolation in detail. The results showed that the 2D-HPLC method could enhance the accuracy of detecting exosomal purity with higher precision and accuracy of instrumental, reduced personal error and experimental cost, shortened analysis time greatly, and more automation. The 2D-HPLC method is rapid, exhibits high selectivity, and has good sensitivity, thus making it well-suited for application in the pharmaceutical and toxicological analysis of exosomes.