bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units
Authors: de Siqueira Guilherme Marcelino Viana , Pereira-dos-Santos Felipe Marcelo , Silva-Rocha Rafael , Guazzaroni Maria-Eugenia
Published: May 2021

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units from a hospital in Brazil. While our results point that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.
DynamicRunx1chromatin boundaries affect gene expression in hematopoietic development
Authors: Owens Dominic D.G. , Anselmi Giorgio , Oudelaar A. Marieke , Downes Damien J. , Cavallo Alessandro , Harman Joe R. , Schwessinger Ron , Bucakci Akin , Greder Lucas , de Ornellas Sara , Jeziorska Danuta , Telenius Jelena , Hughes Jim R. , de Bruijn Marella F.T.R.
Published: May 2021

The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia.Runx1is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation ofRunx1in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures.Runx1resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility,Runx1enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increased in the TAD, along with initiation ofRunx1expression from the P2 promoter. Differentiation to hematopoietic progenitor cells was associated with the formation of tissue-specific sub-TADs overRunx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from bothRunx1promoters. Deletions of promoter-proximal CTCF sites at the sub-TAD boundaries had no obvious effects on E-P interactions but led to partial loss of domain structure, mildly affected gene expression, and delayed hematopoietic development. Together, our analyses of gene regulation at a large multi-promoter developmental gene revealed that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.
Intraneuronal chloride levels encode tiredness in cortex
Authors: Alfonsa Hannah , Brodersen Paul , Newey Sarah E. , Yamagata Tomoko , Panayi Marios C. , Bannerman David M. , Vyazovskiy Vladyslav V. , Akerman Colin J.
Published: May 2021

Continuous periods of wakefulness are associated with reduced performance levels due to the build-up of sleep pressure in active regions of the brain. These effects manifest as use-dependent changes in cortical network activity and the mechanisms underlying these changes represent targets for overcoming the cognitive effects of tiredness. Here we reveal a central role for intraneuronal chloride levels, which increase in a use-dependent manner during waking, and reduce the strength of local synaptic inhibition in mouse cortex. Activity-dependent increases in chloride account for spatial and temporal features of sleep pressure, they underlie cortical network oscillations in the sleep-deprived state, and targeting chloride regulation in cortex can rescue performance levels when tired. These findings provide a missing link between sleep-wake history, synaptic transmission and cortical dynamics.

One-Sentence Summary

The effects of sleep pressure on cortical function are caused by use-dependent changes in chloride-mediated synaptic inhibition.
Transcriptome analysis reveals higher levels of mobile element-associated abnormal gene transcripts in temporal lobe epilepsy patients
Authors: Hu Kai , Liang Ping
Published: May 2021

Objective

To determine role of abnormal splice variants associated with mobile elements in epilepsy.

Methods

Publicly available human RNA-seq-based transcriptome data for laser-captured dentate granule cells of post-mortem hippocampal tissues from temporal lobe epilepsy patients with (TLE, N=14 for 7 subjects) and without hippocampal sclerosis (TLE-HS, N=8 for 5 subjects) and healthy individuals (N=51), surgically resected bulk neocortex tissues from TLE patients (TLE-NC, N=17). For each individual sample, de novo transcriptome assembly was performed followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts) to compare the ME-transcript frequency across the sample groups. Enrichment analysis for genes associated with ME-transcripts and detailed sequence examination for representative epileptic genes were performed to analyze the pattern and mechanism of ME-transcripts on gene function.

Results

We observed significantly higher levels of ME-transcripts in the hippocampal tissues of epileptic patients, particularly in TLE-HS. Among ME classes, SINEs were shown to be the most frequent contributor to ME-transcripts followed by LINEs and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences, leading abnormal splicing variants. For protein coding genes, ME sequences were mostly found in the 3’-UTR regions, with a significant portion also in the coding sequences (CDS) leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for involvement in the mRNA splicing process in all sample groups, with bias towards neural and epilepsy-associated genes in the epileptic transcriptomes.

Significance

Our data suggest that abnormal splicing involving MEs, leading to loss of function in critical genes, plays a role in epilepsy, particularly in TLE-HS, providing a novel insight on the molecular mechanisms underlying epileptogenesis.

Key points box

Significantly higher rates of abnormal splicing variants involving mobile elements (MEs) were observed in the hippocampal tissues of epilepsy patients.

SINEs/Alus are most frequently observed in ME-transcripts followed by LINEs and DNA transposons.

For protein coding genes, MEs mostly locate in 3’ UTR, but also in coding regions, causing open reading frame disruption, with a bias for neural and epileptic genes.

Abnormal splicing involving MEs may be a contributing factor in epileptogenesis.
Non-destructive Chemical Imaging of Bone Tissue for Intraoperative and Diagnostic Applications
Authors: Shin Kseniya S. , Men Shuaiqian , Wong Angel , Cobb-Bruno Colburn , Chen Eleanor , Fu Dan
Published: May 2021

Bone is difficult to image using traditional histopathological methods, leading to challenges in intraoperative consultations needed in orthopedic oncology. However, intraoperative pathological evaluation is critical in guiding surgical treatment. In this study, we demonstrate that a multimodal imaging approach that combines stimulated Raman scattering (SRS) microscopy, two-photon fluorescence (TPF) microscopy, and second harmonic generation (SHG) microscopy can provide useful diagnostic information regarding intact bone tissue fragments from surgical excision or biopsy specimens. We imaged bone samples from 14 patient cases and performed comprehensive chemical and morphological analyses of both mineral and organic components of bone. Our main findings show that carbonate content combined with morphometric analysis of bone organic matrix can separate several major classes of bone cancer associated diagnostic categories with an average accuracy of >90%. This proof-of-principle study demonstrate that multimodal imaging and machine learning-based analysis of bony tissue can provide crucial diagnostic information for guiding clinical decisions in orthopedic oncology.
The Age-Dependent Decline in Neuron Growth Potential in the CNS is Associated with an Age-Related Dysfunction of Neuronal Mitochondria
Authors: Sutherland Theresa C. , Sefiani Arthur , Horvat Darijana , Huntington Taylor E. , Lei Yuanjiu , West A. Phillip , Geoffroy Cédric G.
Published: May 2021

The age of incidence of Spinal Cord Injury (SCI) and the average age of people living with SCI is continuously increasing. In contrast, SCI is extensively modelled in young adult animals, hampering translation of research to clinical application. While there has been significant progress in manipulating axon growth after injury, how it is impacted by aging impacts this is still unknown. Aging is associated with a decline in mitochondrial functions, whereas mitochondria are essential to successful neurite and axon growth. Using isolation and culture of adult cortical neurons, we have analyzed mitochondrial changes in 2-, 6-, 12- and 18-month mice. We observed reduced neurite growth in older neurons. Older neurons also showed dysfunctional respiration, reduced membrane potential, and altered mitochondrial membrane transport proteins; however mitochondrial DNA (mtDNA) abundance and cellular ATP were increased. Taken together, these data suggest dysfunctional mitochondria in older neurons are involved in the age-dependent reduction in neuron growth. Both normal aging and traumatic injury are associated with mitochondrial dysfunction, posing a challenge for an aging SCI population as the two elements can compound one another to worsen injury outcomes. The results of this study highlight this as an area of great interest in CNS trauma.
Exceptionally high sequence-level variation in the transcriptome ofPlasmodium falciparum
Authors: Dave Bruhad , Kanyal Abhishek , Mamatharani DV , Karmodiya Krishanpal
Published: May 2021

Single-nucleotide variations in RNA (hereafter referred to simply as SNVs), arising from co- and post-transcriptional phenomena including transcription errors and RNA editing, are well studied in organisms ranging from bacteria to humans. In the malaria parasitePlasmodium falciparum, stage-specific and non-specific gene-expression variations are known to accompany the parasite’s array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite’s transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the transcriptome of theP. falciparum. We show that these SNVs cover most of the parasite’s transcriptome. SNV rates for theP. falciparumlines we assayed, as well as for publicly availableP. vivaxandP. falciparumclinical isolate datasets were of the order of 10−3per base, about tenfold higher than rates we calculated for bacterial datasets. These SNVs may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution ofP. falciparumand parasite biology more broadly, and we anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.
Extended interval BNT162b2 vaccination enhances peak antibody generation in older people
Authors: Parry H , Bruton R , Stephens C , Brown K , Amirthalingam G , Hallis B , Otter A , Zuo J , Moss P
Published: May 2021

Objectives

To assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination.

Design

Population based cohort study comparing immune responses 2 weeks after the second vaccine, with appropriate time-matched samples in participants who received standard or extended interval double vaccination.

Setting

Primary care networks, Birmingham, UK. December 2020 to April 2021.

Participants

172 people aged over 80 years of age. All donors received the BNT162b2 Pfizer/BioNTech vaccination and were vaccinated with either a standard 3 week interval between doses or an extended interval schedule.

Main outcome measures

Peak quantitative spike-specific antibody and cellular immune responses.

Results

In donors without evidence of previous infection the peak antibody response was 3.5-fold higher in donors who had undergone delayed interval vaccination. Cellular immune responses were 3.6-fold lower.

Conclusion

Peak antibody responses after the second BNT162b2 vaccine are markedly enhanced in older people when this is delayed to 12 weeks although cellular responses are lower. Extended interval vaccination may therefore offer the potential to enhance and extend humoral immunity. Further follow up is now required to assess long term immunity and clinical protection.

What is already known on this topic

The BNT162b2 vaccine is highly effective against Covid-19 infection and was delivered with a 3-week time interval in registration studies. However, this interval has been extended in many countries in order to extend population coverage with a single vaccine. It is not known how immune responses after the second dose are influenced by delaying the second vaccine.

What this study adds

We provide the first assessment of immune responses in the first 14 weeks after standard or extended interval BNT162b2 vaccination and show that delaying the second dose acts to strongly boost the peak antibody response in older people. The extended interval vaccination may offer a longer period of clinical protection. This information will be of value in optimizing vaccine regimens and help guide guide vaccination policies.
In vivo macromolecular crowding is differentially modulated by Aquaporin 0 in zebrafish lens: insights from a nano-environment sensor and spectral imaging
Authors: Vorontsova Irene , Vallmitjana Alexander , Torrado Belén , Schilling Thomas , Hall James E. , Gratton Enrico , Malacrida Leonel
Published: May 2021

Macromolecular crowding is crucial for cellular homeostasis. In vivo studies of macromolecular crowding and ultimately water-dynamics are needed to understand their role in cellular fates. The macromolecular crowding in the lens is essential for understanding normal optics of the lens, and moreover for understanding and prevention of cataract and presbyopia. Here we combine the use of the water nano-environmentally sensitive sensor (6-acetyl-2-dimethylaminonaphthalene, ACDAN) with in vivo studies of Aquaporin zero zebrafish mutants to understand the lens macromolecular crowding. Spectral phasor analysis of ACDAN fluorescence reveal the extent of water dipolar relaxation and demonstrate that the mutations in the duplicated zebrafish Aquaporin 0s, Aqp0a and Aqp0b, alter the water state and macromolecular crowding in the living zebrafish lens. Our results provide in vivo evidence that Aqp0a promotes fluid influx in the deeper lens cortex, whereas Aqp0b facilitates fluid efflux. This work opens new perspectives for in vivo studies on macromolecular crowding.

Teaser

In this study we uncover the roles of Aquaporin 0 in macromolecular crowding required for lens development and vision.
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar
Authors: Sun Hequan , Jiao Wen-Biao , Campoy José A. , Krause Kristin , Goel Manish , Folz-Donahue Kat , Kukat Christian , Huettel Bruno , Schneeberger Korbinian
Published: May 2021

Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ using high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, almost 50% of the genome were found to be identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving around 20% of the genome. Among 38,214 genes, only 54% were present in four haplotypes with an average of 3.2 copies per gene. Analyzing the leaf transcriptome as example, we found that 11% of the genes featured differently expressed alleles in at least one of the haplotypes, of which 25% are likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.
Noncanonical Wnt/Ror2 signaling regulates cell-matrix crosstalk to prompt directional tumor cell invasion and dissemination in breast cancer
Authors: Si Hongjiang , Zhao Na , Pedroza Andrea , Rosen Jeffrey M. , Creighton Chad J. , Roarty Kevin
Published: May 2021

Bidirectional cell-extracellular matrix (ECM) interactions represent fundamental exchanges during tumor progression. We demonstrate the noncanonical Wnt receptor, Ror2, regulates tumor cell-driven matrix remodeling in models of breast cancer. Wnt/Ror2 loss-of-function triggers tumor cell invasion, accompanied by changes in actin cytoskeleton, adhesion, and collagen crosslinking gene expression programs. E-cadherin levels decline upon Ror2 depletion, and spatially, we pinpoint the upregulation and redistribution of α5 and β3 integrins together with the production of fibronectin in areas of invasion. Wnt/β-catenin-dependent and Wnt/Ror2 alternative Wnt signaling appear to regulate distinct functions for tumor cells regarding their ability to modify cell-ECM exchanges during invasion. Furthermore, blocking either integrin or focal adhesion kinase (FAK), a downstream mediator of integrin-mediated signal transduction, abrogates the enhanced migration observed upon Ror2 loss. These results reveal a critical function for the alternative Wnt receptor, Ror2, as a determinant of reciprocal communication between tumor cells and ECM during cancer invasion and metastasis.
Uncertainty in denoising of MRSI using low-rank methods
Authors: Clarke William T , Chiew Mark
Published: May 2021

Purpose

Low-rank denoising of MRSI data results in an apparent increase in spectral SNR. However, it is not clear if this translates to a lower uncertainty in metabolite concentrations after spectroscopic fitting. Estimation of the true uncertainty after denoising is desirable for downstream analysis in spectroscopy.

In this work the uncertainty reduction from low-rank denoising methods based on spatio-temporal separability and linear predictability in MRSI are assessed. A new method for estimating metabolite concentration uncertainty after denoising is proposed. Finally, automatic rank threshold selection methods are assessed in simulated low SNR regimes.

Methods

Assessment of denoising methods is conducted using Monte Carlo simulation of proton MRSI data, and by reproducibility of repeated in vivo acquisitions in five subjects.

Results

In simulated and in vivo data, spatio-temporal based denoising is shown to reduce the concentration uncertainty, but linear prediction denoising increases uncertainty. Uncertainty estimates provided by fitting algorithms after denoising consistently under-estimate actual metabolite uncertainty. However, the proposed uncertainty estimation, based on an analytical expression for entry-wise variance after denoising, is more accurate. Finally, it is shown automated rank threshold selection using Marchenko-Pastur distribution can bias the data in low SNR conditions. An alternative soft-thresholding function is proposed.

Conclusion

Low-rank denoising methods based on spatio-temporal separability do reduce uncertainty in MRS(I) data. However, thorough assessment is needed as assessment by SNR measured from residual baseline noise is insufficient given the presence of non-uniform variance. It is also important to select the right rank thresholding method in low SNR cases.
Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics
Authors: Harris Julian A. , Faust Bryan , Gondin Arisbel B. , Dämgen Marc André , Suomivuori Carl-Mikael , Veldhuis Nicholas A. , Cheng Yifan , Dror Ron O. , Thal David M. , Manglik Aashish
Published: May 2021

The neuropeptide Substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via Gqand Gsproteins. Neurokinin A also activates NK1R, but leads to selective Gqsignaling. How two stimuli yield distinct G-protein signaling at the same G-protein-coupled-receptor remains unclear. We determined cryo-EM structures of active NK1R bound to SP or the Gq-biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent Gssignaling but not Gqsignaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility deep in the NK1R pocket. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G-protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.
Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations
Authors: Othman Houcemeddine , da Rocha Jorge , Hazelhurst Scott
Published: May 2021

Pharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequencing showed that a large proportion of the variants for these genes are rare in African populations. This study investigates the impact of such variants on protein structure to assess their functional importance. We use genetic data of CYP3A5 from 458 individuals from sub-Saharan Africa to conduct a structural bioinformatics analysis. Five missense variants were modeled and microsecond scale molecular dynamics simulations were conducted for each, as well as for the CYP3A5 wildtype, and the Y53C variant, which has a known deleterious impact on enzyme activity. The binding of ritonavir and artemether to CYP3A5 variant structures was also evaluated. Our results showed different conformational characteristics between all the variants. No significant structural changes were noticed. However, the genetic variability acts on the plasticity of the protein. The impact on drug binding may be drug dependant. We conclude that rare variants hold relevance in determining the pharmacogenomics properties of populations. This could have a significant impact on precision medicine applications in sub-Saharan Africa.
Activation of thalamo-cortical circuits with posterior hypothalamic nucleus deep brain stimulation
Authors: Young Calvin K. , Bland Brian H.
Published: May 2021

The posterior hypothalamic nucleus (PH) has extensive anatomical connections to motor, cognitive, visceral, and homeostatic areas of the brain and serves as a crucial subcortical modulator of behaviour. Previous studies have demonstrated that deep brain stimulation (DBS) of this area can lead to powerful activation of motor behaviour, overcoming two rodent models of parkinsonian akinesia by increasing neocortical excitability. However, it is unclear how the PH may mediate this increase in neocortical excitability. In the present study, we examined the role of the thalamus in the PH-DBS mediated increase in neocortical excitability. In urethane anaesthetized animals, we demonstrate that PH-DBS elicits increased spiking activity in the motor thalamus (VL) that receives direct afferents from the PH that precedes the increase in spiking activity in the corresponding motor cortex. In contrast, in the somatosensory thalamus (VPM) where PH afferents are sparse at best, PH-DBS did not elicit an increase in thalamic activity despite of a slight increase in the corresponding somatosensory cortical spiking. Current source density analyses suggest a thalamo-cortical mechanism for motor cortex activation whereas a cortico-cortical activation mechanism is involved in somatosensory cortical activation. Inactivation of the VL resulted in the abolition of motor cortex spiking despite of the persistence of desynchronized field potential activity. Collectively, these data suggest indirect orthodromic activation of PH output fibres to the thalamus mediates increased neocortical excitation, which may spread through cortico-cortical connections and lead to an increase in integrated, non-stereotypical motor behaviour.
Metabolic Dynamics inEscherichia coli-based Cell-Free Systems
Authors: Miguez April M. , Zhang Yan , Piorino Fernanda , Styczynski Mark P.
Published: May 2021

The field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metabolic activity that is poorly understood yet has a significant impact on CFE productivity. Here, we use metabolomics to characterize the temporal metabolic changes in CFE systems and their constituent components, including significant metabolic activity in central carbon and amino acid metabolism. We find that while changing the reaction starting state via lysate pre-incubation impacts protein production, it has a comparatively small impact on metabolic state. We also demonstrate that changes to lysate preparation have a larger effect on protein yield and temporal metabolic profiles, though general metabolic trends are conserved. Finally, while we improve protein production through targeted supplementation of metabolic enzymes, we show that the endogenous metabolic activity is fairly resilient to these enzymatic perturbations. Overall, this work highlights the robust nature of CFE reaction metabolism as well as the importance of understanding the complex interdependence of metabolites and proteins in CFE systems to guide optimization efforts.

Abstract Figure

Abstract Figure
Arp2/3 mediated dynamic lamellipodia of the hPSC colony edges promote liposome-based DNA delivery
Authors: Surma Michelle , Anbarasu Kavitha , Das Arupratan
Published: May 2021

Cationic liposome-mediated delivery of drugs, DNA, or RNA plays a pivotal role in small molecule therapy, gene editing, and immunization. However, our current knowledge regarding the cellular structures that facilitate this process remains limited. Here, we used human pluripotent stem cells (hPSCs), which form compact colonies consisting of dynamically active cells at the periphery and epithelial-like cells at the core. We discovered that cells at the colony edges selectively got transfected by cationic liposomes through Arp2/3 dependent dynamic lamellipodia, which is augmented by myosin II inhibition. Conversely, cells at the core establish tight junctions at their apical surfaces, impeding liposomal access to the basal lamellipodia and thereby inhibiting transfection. In contrast, liposomes incorporating mannosylated lipids are internalized throughout the entire colony via receptor-mediated endocytosis. These findings contribute a novel mechanistic insight into enhancing therapeutic delivery via liposomes, particularly in cell types characterized by dynamic lamellipodia, such as immune cells, or those comprising the epithelial layer.

Significance Statement

Drug or gene delivery to human cells is essential for effective treatment. Cationic liposomes provide a safe delivery vehicle compared to viruses. However, the cellular structures required for internalizing liposomes are not yet fully understood. Using human stem cells which grow in compact colonies with more dynamic cells at the periphery and epithelial like cells at the center, here we discovered that Arp2/3 dependent dynamic lamellipodia promotes cationic liposome delivery in dynamic cells while receptor mediated endocytosis is required for epithelial cells. This is significant as it provides mechanisms for enhancing liposome delivery to both migratory and epithelial cells in our body.

Abstract Figure

Graphical Abstract

Mechanisms for liposome transfection to the lamellipodial or epithelial cells.

Data shown here suggest cationic liposomes fuse with the negatively charged dynamic lamellipodia membrane in an Arp2/3 dependent manner and the process is enhanced by Myosin II inhibition, such as with the stem cell colony edge cells. However, cells more epithelial in nature such as those inside the stem cell colony center do not possess dynamic lamellipodia at the apical surface, rather they form tight junctions which inhibit cationic liposome transfection. Epithelial cells rely on receptor mediated endocytosis in both Myosin II dependent and independent manners to internalize liposomes with lipids that contain ligands for cell surface receptors such as mannose.
Restoration of DNA Integrity and Cell Cycle by Electric Stimulation in Planarian Tissues Damaged by Ionizing Radiation
Authors: Davidian Devon , LeGro Melanie , Barghouth Paul G. , Rojas Salvador , Ziman Benjamin , Maciel Eli Isael , Ardell David , Escobar Ariel L. , Oviedo Néstor J.
Published: May 2021

Exposure to high levels of ionizing γ-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally γ-irradiated tissues of the planarian flatwormSchmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse damaging effects of high dose γ-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.
High-throughput Raman-activated cell sorting in the fingerprint region
Authors: Lindley Matthew , de Pablo Julia Gala , Peterson Jorgen Walker , Isozaki Akihiro , Hiramatsu Kotaro , Goda Keisuke
Published: May 2021

Cell sorting is the workhorse of biological research and medicine. Cell sorters are commonly used to sort heterogeneous cell populations based on their intrinsic features. Raman-activated cell sorting (RACS) has recently received considerable interest by virtue of its ability to discriminate cells by their intracellular chemical content, in a label-free manner. However, broad deployment of RACS beyond lab-based demonstrations is hindered by a fundamental trade-off between throughput and measurement bandwidth (i.e., cellular information content). Here we overcome this trade-off and demonstrate broadband RACS in the fingerprint region (300 − 1,600 cm−1) with a record high throughput of ~50 cells per second. This represents a 100× throughput increase compared to previous demonstrations of broadband fingerprint-region RACS. To show the utility of our RACS, we demonstrate real-time label-free sorting of microalgal cells based on their accumulation of carotenoids and polysaccharide granules. These results hold promise for medical, biofuel, and bioplastic applications.
Lipid Bilayer Induces Contraction of the Denatured State Ensemble of a Helical-Bundle Membrane Protein
Authors: Gaffney Kristen A. , Guo Ruiqiong , Bridges Michael D. , Chen Daoyang , Muhammednazaar Shaima , Kim Miyeon , Yang Zhongyu , Schilmiller Anthony L. , Faruk Nabil F. , Peng Xiangda , Jones A. Daniel , Sun Liangliang , Hubbell Wayne L. , Sosnick Tobin R. , Hong Heedeok
Published: May 2021

Defining the denatured state ensemble (DSE) and intrinsically disordered proteins is essential to understanding protein folding, chaperone action, degradation, translocation and cell signaling. While a majority of studies have focused on water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we reconstituted the DSE of a helical-bundle membrane protein GlpG of Escherichia coli in native lipid bilayers and measured the DSE’s conformation and compactness. The DSE was obtained using steric trapping, which couples spontaneous denaturation of a doubly biotinylated GlpG to binding of two bulky monovalent streptavidin molecules. Using limited proteolysis and mass spectrometry, we mapped the flexible regions in the DSE. Using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy, we determined the dimensions of the DSE. Finally, we employed our Upside model for molecular dynamics simulations to generate the DSE including the collapsed and fully expanded states in a bilayer. We find that the DSE is highly dynamic involving the topology changes of transmembrane segments and their unfolding. The DSE is expanded relative to the native state, but only to 55–90% of the fully expanded condition. The degree of expansion depends on the chemical potential with regards to local packing and the lipid composition. Our result suggests that the E. coli’s native lipid bilayer promotes the association of helices in the DSE of membrane proteins and, probably in general, facilitating interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.

Significance

Here, we delineate the conformation of the denatured state ensemble (DSE) of a membrane protein confined in a native lipid bilayer and assay whether the bilayer permits full expansion or nonspecific collapse of the DSE. Using the intramembrane protease GlpG as a model, we find that the denatured state is a dynamic ensemble involving topological changes and local unfolding of transmembrane segments. The bilayer tends to contract the DSE relative to the fully lipid-solvated, expanded conformations while the degree of compactness is determined by the balance between protein-lipid, lipid-lipid and protein-protein interactions. These findings provide new insights into the lipid bilayer as a solvent that mediates folding, chaperone action, turnover and protein-protein interactions in cell membranes.
Biochar alters soil properties, microbial community diversity, and enzyme activities, while decreasing conifer performance
Authors: Nash Jake , Miesel Jessica , Bonito Gregory , Sakalidis Monique , Ren Han , Warnock Daniel , Tiemann Lisa
Published: May 2021

Biochars are porous charcoal-like materials that can enhance soil health and plant growth, but its use has not been adequately evaluated in woody cropping systems. We set up an experimental Christmas tree plantation on a Marlette series soil amended with two types of biochar and conducted two studies on the impacts of biochar on the agroecosystem over three years following establishment. The first study investigated the effects of biochar on plant performance, soil physicochemical properties and extracellular enzyme activities, while the second investigated the response of the root-associated fungal community. Both biochars stimulated five extracellular enzyme activities, with increases of between 67% and 446%. Structural equation modelling identified increases to dissolved organic carbon and soil moisture as potential mechanisms of biochar’s effects on enzyme activities. Tree growth and survival were negatively affected by biochar application, depending on the tree species and biochar applied, which may have been due to induced nitrogen limitation. High-throughput sequencing showed that biochar decreased the diversity of root-associated fungal communities, with the ectomycorrhizal species Wilcoxina mikolae reaching levels of hyper-dominance on balsam fir in response to one of the biochars. Further studies should investigate how biochar can be harnessed to remediate specific soil quality issues or restructure soil ecosystems in ways that improve crop performance.
M-GAN-XGBOOST model for sales prediction and precision marketing strategy making of each product in online stores
Authors: Wang Song , Yang Yang
Published: May 2021

Purpose

The rapid development of e-commerce has brought not only great convenience to people but a great challenge to online stores. Phenomenon such as out of stock and slow sales has been common in recent years. These issues can be managed only when the occurrence of the sales volume is predicted in advance, and sufficient warnings can be executed in time. Thus, keeping in mind the importance of the sales prediction system, the purpose of this paper is to propose an effective sales prediction model and make digital marketing strategies with the machine learning model.

Design/methodology/approach

Based on the consumer purchasing behavior decision theory, we discuss the factors affecting product sales, including external factors, consumer perception, consumer potential purchase behavior and consumer traffic. Then we propose a sales prediction model, M-GNA-XGBOOST, using the time-series prediction that ensures the effective prediction of sales about each product in a short time on online stores based on the sales data in the previous term or month or year. The proposed M-GNA-XGBOOST model serves as an adaptive prediction model, for which the instant factors and the sales data of the previous period are the input, and the optimal computation is based on the proposed methodology. The adaptive prediction using the proposed model is developed based on the LSTM (Long Short-Term Memory), GAN (Generative Adversarial Networks) and XGBOOST (eXtreme Gradient Boosting). The model inherits the advantages among the algorithms with better accuracy and forecasts the sales of each product in the store with instant data characteristics for the first time.

Findings

The analysis using Jingdong dataset proves the effectiveness of the proposed prediction method. The effectiveness of the proposed method is enhanced and the accuracy that instant data as input is found to be better compared with the model that lagged data as input. The root means squared error and mean absolute error of the proposed model are found to be around 11.9 and 8.23. According to the sales prediction of each product, the resource can be arranged in advance, and the marketing strategy of product positioning, product display optimization, inventory management and product promotion is designed for online stores.

Originality/value

The paper proposes and implements a new model, M-GNA-XGBOOST, to predict sales of each product for online stores. Our work provides reference and enlightenment for the establishment of accurate sales-based digital marketing strategies for online stores.
A BIM-lean framework for digitalisation of premanufacturing phases in offsite construction
Authors: Barkokebas Beda , Khalife Salam , Al-Hussein Mohamed , Hamzeh Farook
Published: May 2021

Purpose

The research introduces means for improving premanufacturing processes (design, procurement and bidding) by leveraging digitalisation in offsite construction. Specifically, this paper proposes a framework that provides measures for the planning and implementation of digitalisation in offsite construction by positioning building information modelling (BIM) as the key technology and lean principles to add value and reduce waste.

Design/methodology/approach

The paper follows the design science research approach to develop the proposed framework and attain the aforementioned objective. The developed framework includes data collection, value-stream mapping and simulation to assess current processes, develop and propose improvements. An empirical implementation is employed to demonstrate the applicability of both the framework and the measures used to evaluate the outcomes.

Findings

The application of the proposed three-stage framework resulted in 9.45%–23.33%-time reduction per year for the various improvement categories in premanufacturing phases. Employing simulation and applying the developed measures provide incentive for upper management to adopt the suggested improvements. Additionally, while the empirical implementation was tested on a modular construction company, the methods used indicate that the framework, with its generic guidelines, could be applied and customized to any offsite company.

Originality/value

While several studies propose that BIM-Lean integration offers an advantage in the context of production systems, this paper focuses on the initial design and planning phases, which are mostly overlooked in the literature. Moreover, the present study provides quantitative evidence of the benefits of data integration through BIM technology.
Planet Abled: can it sustain its first-mover advantage and scale-up?
Authors: Sharma Anita , Ghuman Karminder
Published: May 2021

Learning outcomes

This paper aims to enable the application of Value Proposition Canvas and Business Model Canvas to evaluate an opportunity; understand the commonalities and differences between social and commercial enterprises; and recognize the challenges related to the paradox of the social mission and the financial/economic logic.

Case overview/synopsis

Neha Arora demonstrated exceptional capabilities of defying the social stigma associated with People with Disabilities (PwDs) to establish Planet Abled, a first in the world venture to provide accessible leisure excursions to PwDs. This entrepreneurial initiative enabling group and solo travel for PwDs as inclusive tourism has created the possibility of social sustainability by bringing change in the lives of PwDs and their family members by ignoring either the insensitive or overprotective societal attitudes and lack of infrastructure concerning travel for PwDs. Its potential growth qualifies for scaling-up, but it can also attract the existing big travel solution providers to enter this domain. Considering these facts, Neha faces multiple dilemmas: How can she sustain and scale up the early momentum created by her enterprise? How can she resolve the challenges related to the paradox of the social mission and the financial/ economic logic while scaling-up Planet Abled?

Complexity/Academic level

This case study is suitable for both undergraduate or graduate-level programs in the area of entrepreneurship.

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS 3: Entrepreneurship
Tourist purchases in a destination: what leads them to seek information from digital sources?
Authors: García-Milon Alba , Olarte-Pascual Cristina , Juaneda-Ayensa Emma , Pelegrín-Borondo Jorge
Published: May 2021

Purpose

In a context where retail stores are closing down and high streets are declining, the purpose of this paper is to analyse on-site shopping by tourists. This work identifies the drivers that lead tourists to use digital information sources at the beginning of the shopping process. Understanding these drivers can help destination managers and retailers encourage tourists to shop.

Design/methodology/approach

A personal survey was conducted in a Spanish city noted for its shopping facilities (Logroño), using a sample of 430 tourists with purchase intention. The survey was designed based on the extended unified theory of acceptance and use of technology (UTAUT2) model. A multivariate analysis, based on structural equation modelling, was carried out using partial least squares (PLS), based on variance.

Findings

The study’s finding is that performance expectancy, effort expectancy, social influence, facilitating conditions and habit influence intention to use digital sources of information to make purchases in a destination. Tourists prioritise utilitarian over hedonic motivations in the intention to use digital sources of information in tourist shopping.

Originality/value

It has been recognised that tourists are the perfect target to revitalise on-site shopping and, therefore, destinations must provide attractive shopping experiences from the outset. Prior to purchase, the search for available information is the first stage of the tourist shopping journey. Although many studies have analysed tourist shopping behaviour, none have focused, using the UTAUT2, on the digital information sources tourists consult pre-purchase. This research develops understanding of tourist shopping behaviour in this new technological context. This can help retailers/destinations provide better services and optimise the shopper's experience from the first stage of the process.
Navigating the logics of changing public facilities management
Authors: Svensson Ingrid , Löwstedt Martin
Published: May 2021

Purpose

The purpose of this paper is to explore how a multitude of demands and challenges faced by public facilities management organizations’ (PFMOs) particularly in relation to a large building stock in need of measures’ are acted upon and negotiated in practice. Specifically this study asks: What are the institutional logics (IL) that constitute the organizational context of PFMOs? How does an institutional worker navigate to create change in PFMOs?

Design/methodology/approach

Data were collected through a case study of a public facility management organization and include interviews, a questionnaire, observations and organizational documents. The analytical focus is the work of a single actor, a project manager portrayed as “the navigator” and his institutional work (IW) of developing and implementing new organizational practices, to meet current challenges and develop a more “strategic” facility management.

Findings

The complex institutional landscape faced by officials in PFMOs enforce officials responsible for implementing and developing new practices to become navigators.

Originality/value

The findings offer a rich practice-based account of the day-to-day IW carried out by actors that try to navigate complex institutional landscapes, consisting of multiple and, at times, conflicting IL. Current challenges for PFMOs are to be portrayed as multi-dimensional and the actual work to transform organizational practices in this context is highly complex, unordered and messy. The findings point towards a need for new competences and roles to tackle current challenges; geared towards integrating different logics and perspectives.