bluuebunny/crossref_metadata_2025 huggingface dataset:
Error quantification in multi-parameter mapping facilitates robust estimation and enhanced group level sensitivity
Authors: Mohammadi Siawoosh , Streubel Tobias , Klock Leonie , Lutti Antoine , Pine Kerrin , Weber Sandra , Edwards Luke , Scheibe Patrick , Ziegler Gabriel , Gallinat Jürgen , Kühn Simone , Callaghan Martina F. , Weiskopf Nikolaus , Tabelow Karsten
Published: January 2022

Multi-Parameter Mapping (MPM) is a comprehensive quantitative neuroimaging protocol that enables estimation of four physical parameters (longitudinal and effective transverse relaxation rates R1 and , proton density PD, and magnetization transfer saturation MTsat) that are sensitive to microstructural tissue properties such as iron and myelin content. Their capability to reveal microstructural brain differences, however, is tightly bound to controlling random noise and artefacts (e.g. caused by head motion) in the signal. Here, we introduced a method to estimate the local error of PD, R1 and MTsat maps that captures both noise and artefacts on a routine basis without requiring additional data. To investigate the method’s sensitivity to random noise, we calculated the model-based signal-to-noise ratio (mSNR) and showed in measurements and simulations that it correlated linearly with an experimental raw-image-based SNR map. We found that the mSNR varied with MPM protocols, magnetic field strength (3T vs. 7T) and MPM parameters: it halved from PD to R1 and decreased from PD to MTsat by a factor of 3-4. Exploring the artefact-sensitivity of the error maps, we generated robust MPM parameters using two successive acquisitions of each contrast and the acquisition-specific errors to down-weight erroneous regions. The resulting robust MPM parameters showed reduced variability at the group level as compared to their single-repeat or averaged counterparts. The error and mSNR maps may better inform power-calculations by accounting for local data quality variations across measurements. Code to compute the mSNR maps and robustly combined MPM maps is available in the open-source hMRI toolbox.
Sri Lankan Footprint in Global Aquatic Science Research: A Scientometric Analysis
Authors: Bandara Tharindu
Published: January 2022

The present study summarizes the research productivity and international collaboration in aquatic studies conducted by Sri Lankan scholars during 2000-2019. The study was based on the SCOPUS®database. R programming language, packagebibliometrixand Vosviewer software were employed in the analysis. Results of the present study indicate that increasing growth trend in the annual number of publications. A significant correlation (p<0.05) between the number of articles and per capita GDP (Gross Domestic Production) was also observed. Senior authors dominated in terms of the article count, citation count,hindex, and other author productivity indices. Journal of the National Science Foundation of Sri Lanka had the highest article count (n=33). Aquatic studies in Sri Lanka were more locally funded. Sri Lanka had strong research collaborations with Japan, South Korea and Australia. During 2000-2019, the transition of aquatic studies from lacustrine field studies to molecular lab-based studies were observed. The findings of the present study may provide a comprehensive understanding on the current context and future directions of aquatic studies in Sri Lanka.
Rational design yields molecular insights on leaf binding of the anchor peptide Macaque Histatin
Authors: Dittrich Jonas , Brethauer Christin , Goncharenko Liudmyla , Bührmann Jens , Zeisler-Diehl Viktoria , Pariyar Shyam , Jakob Felix , Kurkina Tetiana , Schreiber Lukas , Schwaneberg Ulrich , Gohlke Holger
Published: January 2022

1

In times of a constantly growing world population and increasing demand for food, sustainable agriculture is crucial. To reduce the amount of applied nutrients, herbicides, and fungicides, the rainfastness of plant protection agents is of pivotal importance. As a result of protective agent wash-off, plant protection is lost, and soils and groundwater are severely polluted. To date, rainfastness of plant protection products is achieved by adding polymeric adjuvants to the agrochemicals. However, polymeric adjuvants will be regarded as microplastics in the future, and environmentally friendly alternatives are needed. Anchor peptides (APs) are promising biobased and biodegradable adhesion promoters. While the adhesion of anchor peptides to artificial surfaces, such as polymers, has already been investigated in theory and experimentally, exploiting the adhesion to biological surfaces remains challenging. The complex nature and composition of biological surfaces such as plant leaf and fruit surfaces complicate the generation of accurate models. Here, we present the first detailed three-layered atomistic model of the surface of apple leaves and use it to compute free energy profiles of the adhesion and desorption of APs to and from that surface. Our model is validated by a novel fluorescence-based MTP assay that mimicks these complex processes and allows quantifying them. For the AP Macaque Histatin, we demonstrate that aromatic and positively charged amino acids are essential for binding to the waxy apple leaf surface. The established protocols should generally be applicable for tailoring the binding properties of APs to biological interfaces.
Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances
Authors: Hera Mahmudur Rahman , Pierce-Ward N. Tessa , Koslicki David
Published: January 2022

Sketching methods offer computational biologists scalable techniques to analyze data sets that continue to grow in size. MinHash is one such technique to estimate set similarity that has enjoyed recent broad application. However, traditional MinHash has previously been shown to perform poorly when applied to sets of very dissimilar sizes.FracMinHashwas recently introduced as a modification of MinHash to compensate for this lack of performance when set sizes differ. This approach has been successfully applied to metagenomic taxonomic profiling in the widely used toolsourmash gather. While experimental evidence has been encouraging, FracMinHash has not yet been analyzed from a theoretical perspective. In this paper, we perform such an analysis to derive various statistics of FracMinHash, and prove that while FracMinHash is not unbiased (in the sense that its expected value is not equal to the quantity it attempts to estimate), this bias is easily corrected for both the containment and Jaccard index versions. Next, we show how FracMinHash can be used to compute point estimates as well as confidence intervals for evolutionary mutation distance between a pair of sequences by assuming a simple mutation model. We also investigate edge cases where these analyses may fail, to effectively warn the users of FracMinHash indicating the likelihood of such cases. Our analyses show that FracMinHash estimates the containment of a genome in a large metagenome more accurately and more precisely when compared to traditional MinHash, and the point estimates and confidence intervals perform significantly better in estimating mutation distances.
PEGPH20, a PEGylated Human Hyaluronidase, Induces Radiosensitization by Reoxygenation In Pancreatic Cancer Xenografts. A Molecular Imaging Study
Authors: Seki Tomohiro , Saida Yu , Kishimoto Shun , Lee Jisook , Otowa Yasunori , Yamamoto Kazutoshi , Chandramouli Gadisetti VR , Devasahayam Nallathamby , Mitchell James B. , Brender Jeffery R. , Krishna Murali C.
Published: January 2022

PEGylated human hyaluronidase (PEGPH20) enzymatically depletes hyaluronan, an important component of the extracellular matrix, in tumors. The resultant improvement in vascular patency and perfusion has been shown to increase the delivery of therapeutic molecules. We show that PEGPH20 also improves the efficacy of radiation therapy in a human pancreatic adenocarcinoma BxPC3 mouse model overexpressing hyaluronan synthase 3 (BxPC3-HAS3) while exerting little effect on the corresponding wild type tumors. Mice overexpressing HAS3 developed fast growing, radiation resistant tumors that became rapidly more hypoxic as time progressed. Treatment with PEGPH20 increased survival times when used in combination with radiation therapy, significantly more than either radiation therapy or PEGPH20 alone. Radiosensitization in BxPC3-HAS3 tumors was attributed to an increase in local pO2as studied by by EPR imaging. No effect on survival, radiation treatment, or pO2was seen in wild type tumors after PEGPH20 treatment. Dynamic contrast enhanced (DCE) MRI and MRI based blood volume imaging showed improved perfusion/permeability and local blood volume, respectively, in BxPC3-HAS3 tumors after PEGPH20 treatment, accounting for the increase in tumor oxygenation. Photoacoustic imaging indicated immediate changes in tumor oxygenation after treatment. Metabolic MRI using hyperpolarized [1-13C] pyruvate suggested a metabolic shift towards decreased glycolytic flux after PEGPH20 treatment. In summary, the results showed that PEGPH20 may be useful for radiosensitization of pancreatic cancer but only in the subset of tumors with substantial hyaluronan accumulation and the response of the treatment may potentially be monitored non-invasive imaging of the hemodynamic and metabolic changes in the tumor microenvironment.
Reciprocal epigenetic Sox2 regulation by SMAD1-SMAD3 is critical for anoikis resistance and metastasis in cancer
Authors: Shonibare Zainab , Monavarian Mehri , O’ Connell Kathleen , Altomare Diego , Shelton Abigail , Mehta Shubham , Jaskula-Sztul Renata , Phaeton Rebecca , Starr Mark D. , Whitaker Regina , Berchuck Andrew , Nixon Andrew B , Arend Rebecca , Lee Nam Y , Miller C. Ryan , Hempel Nadine , Mythreye Karthikeyan
Published: January 2022

Growth factors in the tumor environment are key regulators of cell survival and metastasis. Here we reveal, dichotomy between TGF-β superfamily growth factors BMP and TGF-β/activin, and their downstream SMAD effectors. Gene expression profiling uncovered Sox2 as a key signaling node regulated in an opposing manner by anoikis-promoting BMP2, 4 and 9, and anoikis-suppressing TGF-β and activin A. We find that Sox2 repression by BMPs robustly inhibits intraperitoneal tumor burden and increases survival in multiple ovarian cancer models. Repression of Sox2 is driven by SMAD1 dependent histone H3K27me3 recruitment and DNA methylation at SOX2’s promoter. Conversely, TGF-β and activin A promote Sox2 expression, and anoikis resistance by SMAD3 mediated histone H3K4me3 recruitment. We find that balancing Sox2 levels is critical for anoikis, as transcriptomics reveals regulation of key cell death pathways. Moreover, BMP-driven SMAD1 signaling can override TGF-β and activin’s effect on Sox2, which has clinical significance due to the high levels of TGF-β we find in ovarian cancer patients. Together, our findings identify Sox2 as a contextual and contrastingly regulated key node, downstream of TGF-β superfamily members controlling anoikis and metastasis in ovarian cancers.

Highlights

Sox2 is a key node for anoikis resistance in cancer

Sox2 is differentially regulated by TGF-β/activin and BMPs in broad cancers

BMP9 is a robust metastasis suppressor by lowering Sox2

Sox2 regulation is contextual, epigenetic and at the transcriptional level
Effect of cannabidiol on apoptosis and cellular interferon and interferon-stimulated gene responses to the SARS-CoV-2 genes ORF8, ORF10 and M protein
Authors: Fernandes Maria Fernanda , Chan John Zewen , Hung Chia Chun Joey , Tomczewski Michelle Victoria , Duncan Robin Elaine
Published: January 2022

Aims

To study effects on cellular innate immune responses to novel genes ORF8 and ORF10, and the more conserved Membrane protein (M protein) from the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, either alone, or in combination with cannabidiol (CBD).

Main Methods

HEK293 cells were transfected with a control plasmid, or plasmids expressing ORF8, ORF10, or M protein, and assayed for cell number and markers of apoptosis at 24 h, and expression of interferon and interferon-stimulated genes at 14 h.

Key findings

A significant reduction in cell number, and increase in early and late apoptosis, was found after 24 h in cells where expression of viral genes was combined with 1-2 μM CBD treatment, but not in control-transfected cells treated with CBD, or in cells expressing viral genes but treated only with vehicle. CBD (2 μM) augmented expression of IFNγ, IFNλ1 and IFNλ2/3, as well as the 2’-5’-oligoadenylate synthetase (OAS) family members OAS1, OAS2, OAS3, and OASL, in cells expressing ORF8, ORF10, and M protein. CBD also augmented expression of these genes in control cells not expressing viral genes, without enhancing apoptosis.

Significance

Our results demonstrate a poor ability of HEK293 cells to respond to SARS-CoV-2 genes alone, but suggest an augmented innate anti-viral response to these genes in the presence of CBD. Furthermore, our results indicate that CBD may prime components of the innate immune system, increasing readiness to respond to viral infection without activating apoptosis, and therefore could be studied for potential in prophylaxis.
Structural and functional impact by SARS-CoV-2 Omicron spike mutations
Authors: Zhang Jun , Cai Yongfei , Lavine Christy L. , Peng Hanqin , Zhu Haisun , Anand Krishna , Tong Pei , Gautam Avneesh , Mayer Megan L. , Rits-Volloch Sophia , Wang Shaowei , Sliz Piotr , Wesemann Duane R. , Yang Wei , Seaman Michael S. , Lu Jianming , Xiao Tianshu , Chen Bing
Published: January 2022

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein, but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.
A Longitudinal Study of Dominant E. coli Lineages and Antimicrobial Resistance in the Gut of Children Living in an Upper Middle-income Country
Authors: Calderón Diana , Cárdenas Paúl A. , Prado Belen , Graham Jay P. , Trueba Gabriel
Published: January 2022

The gastrointestinal tract constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem, nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. In this prospective study, a fresh fecal sample was obtained from children longitudinally over one year (30 fecal samples at sampling period 1 and 22 fecal samples at sampling periods 2 and 3). From each stool sample, five E. coli colonies were randomly selected (n = 405 E. coli isolates total) in order to characterize the genotype and phenotypic antimicrobial resistance patterns. We found that all numerically dominant E. coli lineages in children’s intestines were transient colonizers, and antimicrobial resistance phenotypes of these strains varied significantly over time without any apparent selective force. Whole-genome sequencing of 3 isolates belonging to ST131 found in one child during the sampling period I and II indicated that isolates were three different ST 131 clones that carried extended-spectrum β-lactamase (ESBL) genes.

IMPORTANCE

The length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance in a community. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine. We found that E. coli lineages in the children's gut change considerably and rapidly over time. This study suggests that some phenotypic resistance patterns may result from the random distribution of genes in E. coli populations over time and may not be associated with differential exposure to antimicrobials.
RNA-based therapy for Cryptosporidium parvum infection: proof-of-concept studies
Authors: Castellanos-Gonzalez A , Sadiqova A , Ortega-Mendez J , White AC
Published: January 2022

Cryptosporidium is a leading cause of moderate-to-severe diarrhea in children. Nitazoxanide, the only FDA-approved treatment for cryptosporidiosis, has limited efficacy in those at highest risk for sequelae. RNA-argonaute (Ago) complexes to Cryptosporidium nucleoside diphosphate kinase (cpNDK) decreased the Cryptosporidium parvum mRNA by 95% in infected cells in vitro. Treatment of mice by oral gavage with ssRNA/Ago complexes encapsulated in lipid nanoparticles led to delivery of the complexes into intestinal epithelial cells. Treatment of C. parvum infected mice with ssRNA/Ago complexes targeting cpNDK led to the resolution of oocyst shedding in 4/5 SCID/beige mice. These results confirm the potential use of antisense therapy as an alternative approach to cryptosporidiosis treatment.
Fibromodulin Ablation Exacerbates the Severity of Acute DSS Colitis
Authors: Halasi Mariana , Grinstein Mor , Adini Avner , Adini Irit
Published: January 2022

Epidemiological studies have associated pigment production with protection against certain human diseases. In contrast to African Americans, European descendants are more likely to suffer from angiogenesis-dependent and inflammatory diseases, such as wet age-related macular degeneration (ARMD) and ulcerative colitis (UC), respectively. In this study, albino mice that produced high levels of fibromodulin (FMOD) developed less severe acute colitis compared with mice lacking in FMOD as assessed by clinical symptoms and histopathological changes. In a mouse model of dextran sodium sulfate (DSS)-induced acute colitis, FMOD depletion affected the expression and localization of tight junction proteins, contributing to the destruction of the epithelial barrier. Furthermore, this study revealed a stronger inflammatory response after DSS treatment in the absence of FMOD, where FMOD depletion led to an increase in activated T cells, plasmacytoid dendritic cells (pDCs), and type I IFN production. These findings point to FMOD as a potential biomarker of disease severity in UC among light-skinned individuals of European descent.
Hippocampal protein aggregation signatures fully distinguish pathogenic and wildtypeUBQLN2in amyotrophic lateral sclerosis
Authors: Thumbadoo Kyrah M. , Dieriks Birger V. , Murray Helen C. , Swanson Molly E. V. , Yoo Ji Hun , Mehrabi Nasim F. , Turner Clinton , Dragunow Michael , Faull Richard L. M. , Curtis Maurice A. , Siddique Teepu , Shaw Christopher E. , Henden Lyndal , Williams Kelly L. , Nicholson Garth A. , Scotter Emma L.
Published: January 2022

Mutations in theUBQLN2gene cause X-linked dominant amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD) characterised by ubiquilin 2 aggregates in neurons of the motor cortex, hippocampus, and spinal cord. However, ubiquilin 2 neuropathology is also seen in sporadic and familial ALS or FTD cases not caused byUBQLN2mutations, particularlyC9orf72-linked cases. This makes the mechanistic role of ubiquilin 2 mutations and the value of ubiquilin 2 pathology for predicting genotype unclear. Here we examine a cohort of 41 genotypically diverse ALS cases with or without FTD, including five cases withUBQLN2variants (resulting in p.S222G, p.P497H, p.P506S, and two cases with p.T487I). Using multiplexed (5-label) fluorescent immunohistochemistry, we mapped the co-localisation of ubiquilin 2 with phosphorylated TDP-43 (pTDP-43), dipeptide repeat aggregates, and p62, in the hippocampus of controls (n=5), or ALS with or without FTD in sporadic (n=20), unknown familial (n=3),SOD1-linked (n=1),FUS-linked (n=1),C9orf72-linked (n=5), andUBQLN2-linked (n=5) cases. We differentiate between i) ubiquilin 2 aggregation together with pTDP-43 or dipeptide repeat proteins, and ii) ubiquilin 2 self-aggregation promoted byUBQLN2gene mutations that cause ALS/FTD. Overall, we describe a hippocampal protein aggregation signature that fully distinguishes mutant from wildtype ubiquilin 2 in ALS with or without FTD, whereby mutant ubiquilin 2 is more prone than wildtype to aggregate independently of driving factors. This neuropathological signature can be used to assess the pathogenicity ofUBQLN2gene variants and to understand the mechanisms ofUBQLN2-linked disease.
BECN1 F121A mutation increases autophagic flux in aged mice and improves aging phenotypes in an organ-dependent manner
Authors: Sebti Salwa , Zou Zhongju , Shiloh Michael U.
Published: January 2022

Autophagy is necessary for lifespan extension in multiple model organisms and autophagy dysfunction impacts age-related phenotypes and diseases. Introduction of an F121A mutation into the essential autophagy protein BECN1 constitutively increases basal autophagy in young mice and reduces cardiac and renal age-related changes in longer-livedBecn1F121Amutant mice. However, both autophagic and lysosomal activity have been described to decline with age. Thus, whether autophagic flux is maintained during aging and whether it is enhanced inBecn1F121Amice is unknown. Here we demonstrate that old wild type mice maintained functional autophagic flux in heart, kidney and skeletal muscle but not liver, and oldBecn1F121Amice had increased autophagic flux in those same organs compared to wild type. In parallel,Becn1F121Amice were not protected against age-associated hepatic phenotypes but demonstrated reduced skeletal muscle fiber atrophy. These findings identify an organ-specific role for the ability of autophagy to impact organ aging phenotypes.
How salience enhances inhibitory control: An analysis of electro-cortical mechanisms
Authors: Kenemans J. Leon , Schutte Iris , Van Bijnen Sam , Logemann H. N. Alexander
Published: January 2022

Stop-signal tasks (SSTs) combined with human electro-cortical recordings (Event-Related Potentials, ERPs) have revealed mechanisms associated with successful stopping (relative to failed), presumably contributing to inhibitory control. The corresponding ERP signatures have been labeled stop N1 (+/- 100-ms latency), stop N2 (200 ms), and stop P3 (160-250 ms), and argued to reflect more proactive (N1) versus more reactive (N2, P3) mechanisms. However, stop N1 and stop N2, as well as latencies of stop-P3, appear to be quite inconsistent across studies. The present work addressed the possible influence of stop-signal salience, expecting high salience to induce clear stop N1s but reduced stop N2s, and short-latency stop P3s.

Three SST varieties were combined with high-resolution EEG. An imperative visual (go) stimulus was occasionally followed by a subsequent (stop) stimulus that signalled to withhold the just initiated response. Stop-Signal Reaction Times (SSRTs) decreased linearly from visual-low to visual-high-salience to auditory. Auditory Stop N1 was replicated. A C1-like visual evoked potential (latency < 100 ms) was observed only with high salience, but not robustly associated with successful versus failed stops. Using the successful-failed contrast a visual stop-N1 analogue (112-156 ms post-stop-signal) was identified, as was right-frontal stop N2, but neither was sensitive to salience. Stop P3 had shorter latency for high than for low salience, and the extent of the early high-salience stop P3 correlated inversely with SSRT. These results suggest that salience-enhanced inhibitory control as manifest in SSRTs is associated with reactive rather than proactive electrocortical mechanisms.
Potentiation of drug toxicity through virus latency reversal promotes preferential elimination of HIV infected cells
Authors: Truong Thanh Tung , Hayn Manuel , Frich Camilla Kaas , Ladefoged Lucy Kate , Olesen Morten T. Jarlstad , Jakobsen Josefine H. , Lunabjerg Cherie K. , Schiøtt Birgit , Münch Jan , Zelikin Alexander N.
Published: January 2022

Eliminating latently infected cells is a highly challenging, indispensable step towards the overall cure for HIV/AIDS. We recognized that the unique HIV protease cut site (Phe-Pro) can be reconstructed using a potent toxin, monomethyl auristatin F (MMAF), which features Phe at its C-terminus. We hypothesized that this presents opportunities to design prodrugs that are specifically activated by the HIV protease. To investigate this, a series of MMAF derivatives was synthesized and evaluated in cell culture using latently HIV-infected cells. Cytotoxicity of compounds was enhanced upon latency reversal by up to 11-fold. In a mixed cell population, nanomolar concentrations of the lead compound depleted predominantly the HIV-infected cells and in doing so markedly enriched the pool with the uninfected cells. Despite expectation, mechanism of action of the synthesized toxins was not as HIV protease-specific prodrugs, but likely through the synergy of toxicities between the toxin and the reactivated virus.
Precise Transcript Reconstruction with End-Guided Assembly
Authors: Schon Michael A. , Lutzmayer Stefan , Hofmann Falko , Nodine Michael D.
Published: January 2022

Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.

Summary statement

Bookend is a generalized framework that utilizes RNA 5′ and 3′ end information hidden in RNA-seq datasets to accurately reconstruct transcriptomes including those from single cells.
Efficient generation of lower induced Motor Neurons by coupling Ngn2 expression with developmental cues
Authors: Limone Francesco , Mitchell Jana M. , San Juan Irune Guerra , Smith Janell L. M. , Raghunathan Kavya , Couto Alexander , Ghosh Sulagna Dia , Meyer Daniel , Mello Curtis J. , Nemesh James , Smith Brittany M. , McCarroll Steven , Pietiläinen Olli , Nehme Ralda , Eggan Kevin
Published: January 2022

Human pluripotent stem cells (hPSCs) are a powerful tool for disease modelling and drug discovery, especially when access to primary tissue is limited, such as in the brain. Current neuronal differentiation approaches use either small molecules for directed differentiation or transcription-factor-mediated programming. In this study we coupled the overexpression of the neuralising transcription factor Neurogenin2 (Ngn2) with small molecule patterning to differentiate hPSCs into lower induced Motor Neurons (liMoNes). We showed that this approach induced activation of the motor neuron (MN) specific transcription factor Hb9/MNX1, using anHb9::GFP-reporter line, with up to 95% of cells becoming Hb9::GFP+. These cells acquired and maintained expression of canonical early and mature MN markers. Molecular and functional profiling revealed that liMoNes resembled bona fide hPSC-derived MN differentiated by conventional small molecule patterning. liMoNes exhibited spontaneous electrical activity, expressed synaptic markers and formed contacts with muscle cells in vitro. Pooled, multiplex single-cell RNA sequencing on 50 cell lines revealed multiple anatomically distinct MN subtypes of cervical and brachial, limb-innervating MNs in reproducible quantities. We conclude that combining small molecule patterning with Ngn2 can facilitate the high-yield, robust and reproducible production of multiple disease-relevant MN subtypes, which is fundamental in the path to propel forward our knowledge of motoneuron biology and its disruption in disease.
Optimized Multicolour Immunofluorescence Panel for Cattle T Cell Phenotyping by an 8-Colour, 10-Parameter Panel
Authors: Roos Eduard O. , Mwangi William , Gerner Wilhelm , Waters Ryan , Hammond John A.
Published: January 2022

Purpose and appropriate sample types

This multiplex staining panel was developed to differentiate cattle T cells into conventional (CD4 and CD8) and unconventional (γδ-TCR) subsets as well as their stage of differentiation and activation. The combination of CD45RO and CD62L allows the identification of naïve (TNaïve), central memory (TCM), effector memory (TEM) and terminal effector (TTE) T cells. Activated cattle T cells (TAV) can be identified by the cell surface expression of CD25. This panel was developed using cryopreserved cattle peripheral blood mononuclear cells (PBMCs) and tested on fresh as well as stimulated PBMCs. Therefore, this 8-colour, 10-parameter flow cytometry panel simultaneously identifies cattle TNaïve, TAV, TCM, TEM, TTE and γδ-TCR cells. This panel will improve our ability to examine T cell response to pathogens and vaccines in cattle including the potential to identify previously undescribed subpopulations. Furthermore, this panel can be readily optimised for other bovid species as many of these reagents are likely to cross react.
Comparative transcriptome investigation of Nosema ceranae infecting eastern honeybee workers
Authors: Fan Yuanchan , Wang Jie , Yu Kejun , Zhang Wende , Cai Zongbin , Sun Minghui , Hu Ying , Zhao Xiao , Xiong Cuiling , Niu Qingsheng , Chen Dafu , Guo Rui
Published: January 2022

Apis cerana is the original host for Nosema ceranae, a widespread fungal parasite resulting in bee nosemosis, which leads to severe losses for apiculture industry throughout the world. However, knowledge of N. ceranae infecting eastern honeybees is extremely limited. Currently, the mechanism underlying N. ceranae infection is still largely unknown. Based on our previously gained high-quality transcriptome datasets, comparative transcriptomic investigation was conducted in this work, with a focus on virulence factor-associated differentially expressed genes (DEGs). Microscopic observation showed that A. c. cerana workers’ midguts were effectively infected after inoculation with clean spores of N. ceranae. Totally, 1411, 604, and 38 DEGs were identified from NcCK vs. NcT1, NcCK vs. NcT2 and NcT1 vs. NcT2 comparison groups. Venn analysis showed that ten up-regulated genes and nine down-regulated ones were shared by aforementioned comparison groups. GO category indicated these DEGs were involved in a series of functional terms relevant to biological process, cellular component, and molecular function, such as metabolic process, cell part, and catalytic activity. Additionally, KEGG pathway analysis suggested that the DEGs were engaged in an array of pathways of great importance, such as metabolic pathway, glycolysis, and biosynthesis of secondary metabolites. Further, expression clustering analysis demonstrated that majority of genes encoding virulence factors such as ricin B lectins and polar tube proteins displayed apparent up-regulation, whereas a few virulence factor-associated genes such as hexokinase gene and 6-phosphofructokinase gene presented down-regulation during the fungal infection. Finally, the expression trend of 14 DEGs was confirmed by RT-qPCR, validating the reliability of our transcriptome datasets. These results together demonstrated that an overall alteration of the transcriptome of N. ceranae occurred during the infection of A. c. ceranae workers, and most of virulence factor-related genes were induced to activation to promote the fungal invasion. Our findings not only lay a foundation for clarifying the molecular mechanism underlying N. ceranae infection of eastern honeybee workers, but also shed light on developing novel targets for microsporidiosis control.
Label-free sensing of cells with fluorescence lifetime imaging: the quest for metabolic heterogeneity
Authors: Shirshin Evgeny A. , Shirmanova Marina V. , Gayer Alexey V. , Lukina Maria M. , Nikonova Elena E. , Yakimov Boris P. , Budylin Gleb S. , Dudenkova Varvara V. , Ignatova Nadezhda I. , Komarov Dmitry V. , Yakovlev Vladislav , Becker Wolfgang , Zagaynova Elena V. , Shcheslavskiy Vladislav I. , Scully Marlan O.
Published: January 2022

Molecular, morphological and physiological heterogeneity is the inherent property of cells, which governs differences in their response to external influence. The tumor cells metabolic heterogeneity is of a special interest due to its clinical relevance to the tumor progression and therapeutic outcomes. Rapid, sensitive and non-invasive assessment of metabolic heterogeneity of cells is of a great demand for biomedical sciences. Fluorescence lifetime imaging (FLIM), which is an all-optical technique is an emerging tool for sensing and quantifying cellular metabolism by measuring fluorescence decay parameters (FDPs) of endogenous fluorophores, such as NAD(P)H. To achieve the accurate discrimination between metabolically diverse cellular subpopulations, appropriate approaches to FLIM data collection and analysis are needed. In this report, the unique capability of FLIM to attain the overarching goal of discriminating metabolic heterogeneity has been demonstrated. This has been achieved using a novel approach to data analysis based on the non-parametric analysis, which revealed a much better sensitivity to the presence of metabolically distinct subpopulations as compare more traditional approaches of FLIM measurements and analysis. The new approach was further validated for imaging cultured cancer cells treated with chemotherapy. Those results pave the way for an accurate detection and quantification of cellular metabolic heterogeneity using FLIM, which will be valuable for assessing therapeutic vulnerabilities and predicting clinical outcomes.
Approximated Gene Expression Trajectories (AGETs) for Gene Regulatory Network Inference on Cell Tracks
Authors: Spiess Kay , Taylor Shannon E. , Fulton Timothy , Toh Kane , Saunders Dillan , Hwang Seongwon , Wang Yuxuan , Paige Brooks , Steventon Benjamin , Verd Berta
Published: January 2022

The study of pattern formation has greatly benefited from our ability to reverse-engineer gene regulatory network (GRN) structure from spatio-temporal quantitative gene expression data. Traditional approaches omit tissue morphogenesis, and focus on systems where the timescales of pattern formation and morphogenesis can be separated. In such systems, pattern forms as an emergent property of the underlying GRN and mechanistic insight can be obtained from the GRNs alone. However, this is not the case in most animal patterning systems, where patterning and morphogenesis are co-occurring and tightly linked. To address the mechanisms driving pattern formation in such systems we need to adapt our GRN inference methodologies to explicitly accommodate cell movements and tissue shape changes. In this work we present a novel framework to reverse-engineer GRNs underlying pattern formation in tissues undergoing morphogenetic changes and cell rearrangements. By integrating quantitative data from live and fixed embryos, we approximate gene expression trajectories (AGETs) in single cells and use a subset to reverse-engineer candidate GRNs using a Markov Chain Monte Carlo approach. GRN fit is assessed by simulating on cell tracks (live-modelling) and comparing the output to quantitative data-sets. This framework generates candidate GRNs that recapitulate pattern formation at the level of the tissue and the single cell. To our knowledge, this inference methodology is the first to integrate cell movements and gene expression data, making it possible to reverse-engineer GRNs patterning tissues undergoing morphogenetic changes.
Comparing the folding landscapes of evolutionarily divergent procaspase-3
Authors: Yao Liqi , Clark A. Clay
Published: January 2022

All caspases evolved from a common ancestor and subsequently developed into two general classes, inflammatory or apoptotic caspases. The caspase-hemoglobinase fold has been conserved throughout nearly one billion years of evolution and is utilized for both the monomeric and dimeric subfamilies of apoptotic caspases, called initiator and effector caspases, respectively. We compared the folding and assembly of procaspase-3b from zebrafish to that of human effector procaspases in order to examine the conservation of the folding landscape. Urea-induced equilibrium folding/unfolding of procaspase-3b showed a minimum three-state folding pathway, where the native dimer isomerizes to a partially folded dimeric intermediate, which then unfolds. A partially folded monomeric intermediate observed in the folding landscape of human procaspase-3 is not well-populated in zebrafish procaspase-3b. By comparing effector caspases from different species, we show that the effector procaspase dimer undergoes a pH-dependent conformational change, and that the conformational species in the folding landscape exhibit similar free energies. Together, the data show that the landscape for the caspase-hemoglobinase fold is conserved, yet it provides flexibility for species-specific stabilization or destabilization of folding intermediates resulting in changes in stability. The common pH-dependent conformational change in the native dimer, which yields an enzymatically inactive species, may provide an additional, albeit reversible, mechanism for controlling caspase activity in the cell.
Epac1 regulates cellular SUMOylation by promoting the formation of SUMO-activating nuclear condensates
Authors: Yang Wenli , Robichaux William G. , Mei Fang C. , Lin Wei , Li Li , Pan Sheng , White Mark A. , Chen Yuan , Cheng Xiaodong
Published: January 2022

Protein SUMOylation plays an essential role in maintaining cellular homeostasis when cells are under stress. However, precisely how SUMOylation is regulated, and a molecular mechanism linking cellular stress to SUMOylation remains elusive. Herein, we report that cAMP, a major stress-response second messenger, acts through Epac1 as a regulator of cellular SUMOylation. The Epac1-associated proteome is highly enriched with components of the SUMOylation pathway. Activation of Epac1 by intracellular cAMP triggers phase separation and the formation of nuclear condensates containing Epac1 and general components of the SUMOylation machinery to promote cellular SUMOylation. Furthermore, genetic knockout of Epac1 obliterates oxidized low-density lipoprotein induced cellular SUMOylation in macrophages, leading to suppression of foam cell formation. These results provide a direct nexus connecting two major cellular stress responses to define a molecular mechanism in which cAMP regulates the dynamics of cellular condensates to modulate protein SUMOylation.
Geometric control of Myosin-II orientation during axis elongation
Authors: Lefebvre M.F. , Claussen N.H. , Mitchell N.P. , Gustafson H.J. , Streichan S.J.
Published: January 2022

The actomyosin cytoskeleton is a crucial driver of morphogenesis. Yet how the behavior of large-scale cytoskeletal patterns in deforming tissues emerges from the interplay of geometry, genetics, and mechanics remains incompletely understood. Convergent extension flow inD. melanogasterembryos provides the opportunity to establish a quantitative understanding of the dynamics of anisotropic non-muscle myosin II. Cell-scale analysis of protein localization in fixed embryos suggests that there are complex rules governing how the control of myosin anisotropy is regulated by gene expression patterns. However, technical limitations have impeded quantitative and dynamic studies of this process at the whole embryo level, leaving the role of geometry open. Here we combinein totolive imaging with quantitative analysis of molecular dynamics to characterize the distribution of myosin anisotropy and corresponding genetic patterning. We found pair rule gene expression continuously deformed, flowing with the tissue frame. In contrast, myosin anisotropy orientation remained nearly static, aligned with the stationary dorsal-ventral axis of the embryo. We propose myosin recruitment by a geometrically defined static source, potentially related to the embryo-scale epithelial tension, and account for transient deflections by the interplay of cytoskeletal turnover with junction reorientation by flow. With only one parameter, this model quantitatively accounts for the time course of myosin anisotropy orientation in wild-type, twist, and even-skipped embryos as well as embryos with perturbed egg geometry. Geometric patterning of the cytoskeleton suggests a simple physical strategy to ensure a robust flow and formation of shape.
Theory for weakly polydisperse cytoskeleton filaments
Authors: Warshavsky Vadim , Marucho Marcelo
Published: January 2022

Cytoskeleton filaments have the extraordinary ability to change conformations dynamically in response to alterations of the number density of actins/tubulin, number density and type of binding agents, and electrolyte concentration. This property is crucial for eukaryotic cells to achieve specific biological functions in different cellular compartments. Conventional approaches on biopolymers solution break down for cytoskeleton filaments because they entail several approximations to treat their polyelectrolyte and mechanical properties. In this article, we introduce a novel density functional theory for polydisperse, semiflexible cytoskeleton filaments. The approach accounts for the equilibrium polymerization kinetics, length and orientation filament distributions, as well as the electrostatic interaction between filaments and the electrolyte. This is essential for cytoskeleton polymerization in different cell compartments generating filaments of different lengths, sometimes long enough to become semiflexible. We characterized the thermodynamics properties of actin filaments in electrolyte aqueous solutions. We calculated the free energy, pressure, chemical potential and second virial coefficient for each filament conformation. We also calculated the phase diagram of actin filaments solution and compared with the corresponding results in in-vitro experiments.
How does liability of origin influence cross-border acquisition completion? Evidence from Chinese firms
Authors: Jiang Tingting , Yang Buyun , Yang Bo , Wu Bo , Wan Guoguang
Published: January 2022

Purpose

The environment of international business (IB) and the capabilities of emerging market multinational enterprises (EMNEs) as well as their home countries have changed significantly, leading to some new features of liability of origin (LOR). This paper aims to extend the LOR literature by particularly focusing on the LOR of Chinese multinational enterprises (MNEs) and by taking into account the heterogeneity among industries and across individual MNEs.

Design/methodology/approach

Based on the stereotype content model and organizational legitimacy perspective, this study explores how LOR influences Chinese MNEs’ cross-border acquisition completions. Several hypotheses were tested by using a binary logistic regression model with panel data techniques based on data of 780 Chinese MNEs’ acquisition deals between 2008 and 2018.

Findings

The results of this study show that when the competence dimension of China’s LOR is perceived as high in the host country, Chinese MNEs are less likely to complete cross-border acquisitions. Moreover, deals are less likely to be completed when the warmth dimension of China’s LOR is perceived to be low. Global experience and the foreign-listed status of individual Chinese MNEs can alter the relationship between the LOR and deal completions.

Originality/value

This study advances and enriches the LOR research. It shows that a high level of competence in the home country has led to LOR for Chinese MNEs rather than the low level of competence proposed by existing LOR studies; and the LOR for Chinese MNEs is also determined by the perceived low level of warmth in the home country resulting from the geopolitical conflicts between two countries. In addition, the LOR suffered by EMNEs could vary based on certain industry- and firm-level characteristics. The findings of this study provide important practical implications for emerging economy governments and for firms intending to go abroad.
Dairy farmers’ knowledge and perception of climate change in the Eastern Cape province, South Africa
Authors: Diniso Yanga Simamkele , Zhou Leocadia , Jaja Ishmael Festus
Published: January 2022

Purpose

This study aims to evaluate the knowledge and attitudes of dairy farmers about climate change in dairy farms in the Eastern Cape province of South Africa.

Design/methodology/approach

The study was conducted following a cross-sectional research design (Bryman, 2012). The study was conducted mainly on dairy farms located on the south-eastern part of the Eastern Cape province in five districts out of the province’s six districts (Figure 1). These districts include Amathole, Chris Hani, OR Tambo and Cacadu; these regions were not included in a recent surveying study (Galloway et al., 2018).

Findings

In all, 71.7% of dairy farm workers heard about climate change from the television, and 60.4% of participants reported that they gathered information from radio. Eighty-two out of 106 (77.4%) correctly indicated that climate change is a significant long-term change in expected weather patterns over time, and almost 10% of the study participants had no clue about climate change. Approximately 63% of the respondents incorrectly referred to climate change as a mere hotness or coldness of the day, whereas the remainder of participants correctly refuted that definition of climate change. Most of the study participants correctly mentioned that climate change has an influence on dairy production (92.5%), it limits the dairy cows’ productivity (69.8%) and that dry matter intake of dairy cows is reduced under higher temperatures (75.5%).

Research limitations/implications

The use of questionnaire to gather data limits the study, as respondents relied on recall information. Also, the sample size and study area limits use of the study as an inference for the excluded parts of the Eastern Cape Province. Also, it focused only on dairy farm workers and did not request information from beef farmers.

Practical implications

This study imply that farmers without adequate knowledge of the impact of climate change keep complaining of a poor yield/ animal productivity and changing pattern of livestock diseases. Hence, a study such as the present one helps to bridge that gap and provide relevant governing authority the needed evidence for policy changes and intervention.

Social implications

Farmers will begin to get help from the government regarding climate change.

Originality/value

This a first study in South Africa seeking to document the knowledge of dairy farm workers about climate change and its impacts on productivity.