bluuebunny/crossref_metadata_2025 huggingface dataset:
Toxoplasmainfection alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease
Authors: Cromar Graham L. , Epp Jonathan , Popovic Ana , Gu Yusing , Ha Violet , Walters Brandon , St. Pierre James , Xiong Xuejian , Howland John , Josselyn Sheena , Parkinson John , Frankland Paul W.
Published: August 2021

Toxoplasma gondiiis a single celled parasite thought to infect 1 in 3 worldwide. During chronic infection,T. gondiican migrate to the brain where it promotes low-grade neuroinflammation with the capacity to induce changes in brain morphology and behavior. Consequently, infection withT. gondiihas been linked with a number of neurocognitive disorders including schizophrenia (SZ), dementia, and Parkinson’s disease. Beyond neuroinflammation, infection withT. gondiican modulate the production of neurotransmitters, such as dopamine. To further dissect these pathways and examine the impact of altered dopaminergic sensitivity inT. gondii-infected mice on both behavior and gene expression, we developed a novel mouse model, based on stimulant-induced (cocaine) hyperactivity. Employing this model, we found that infection withT. gondiidid not alter fear behavior but did impact motor activity and neuropsychiatric-related behaviurs. While both behaviors may help reduce predator avoidance, consistent with previous studies, the latter finding is reminiscent of neurocognitive disorders. Applying RNASeq to two relevant brain regions, striatum and hippocampus, we identified a broad upregulation of immune responses. However, we also noted significant associations with more meaningful neurologically relevant terms were masked due to the sheer number of terms incorporated in multiple testing correction. We therefore performed a more focused analysis using a curated set of neurologically relevant terms revealing significant associations across multiple pathways. We also found thatT. gondiiand cocaine treatments impacted the expression of similar functional pathways in the hippocampus and striatum although, as indicated by the low overlap among differentially expressed genes, largely via different proteins. Furthermore, while most differentially expressed genes reacted to a single condition and were mostly upregulated, we identified gene expression patterns indicating unexpected interactions betweenT. gondiiinfection and cocaine exposure. These include sets of genes which responded to cocaine exposure but not upon cocaine exposure in the context ofT. gondiiinfection, suggestive of a neuroprotective effect advantageous to parasite persistence. Given its ability to uncover such complex relationships, we propose this novel model offers a new perspective to dissect the molecular pathways by whichT. gondiiinfection contributes to neuropsychiatric disorders such as schizophrenia.
C2cd6-encoded CatSperτ Targets Sperm Calcium Channel to Ca2+Signaling Domains in the Flagellar Membrane
Authors: Hwang Jae Yeon , Wang Huafeng , Lu Yonggang , Ikawa Masahito , Chung Jean-Ju
Published: August 2021

In mammalian sperm cells, regulation of spatiotemporal Ca2+signaling relies on the quadrilinear Ca2+signaling nanodomains in the flagellar membrane. The sperm-specific, multi-subunit CatSper Ca2+channel, which is crucial for sperm hyperactivated motility and male fertility, organizes the nanodomains. Here, we report CatSperτ, theC2cd6-encoded membrane-associating C2 domain protein, can independently migrate to the flagella and serve as a major targeting component of the CatSper channel complex. CatSperτ loss-of-function in mice demonstrates that it is essential for sperm hyperactivated motility and male fertility. CatSperτ targets the CatSper channel into the quadrilinear nanodomains in the flagella of developing spermatids, whereas it is dispensable for functional channel assembly. CatSperτ interacts with ciliary trafficking machinery in a C2-dependent manner. These findings provide insights into the CatSper channel trafficking to the Ca2+signaling nanodomains and the shared molecular mechanisms of ciliary and flagellar membrane targeting.

Highlights

CatSperτ encoded byC2cd6is a C2 membrane-associating domain containing protein

CatSperτ loss-of-function impairs sperm hyperactivation and male fertility

CatSperτ adopts ciliary trafficking machineries for flagellar targeting via C2 domain

CatSperτ targets the CatSper channel into nanodomains of developing sperm flagella
HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities
Authors: Kalmar Lajos , Gupta Srishti , Kean Iain R. L. , Ba Xiaoliang , Hadjirin Nazreen , Lay Elizabeth , de Vries Stefan P.W. , Bateman Michael , Bartlett Harriett , Hernandez-Garcia Juan , Tucker Alexander W. , Restiff Olivier , Stevens Mark P , Wood James , Maskell Duncan J , Grant Andrew J , Holmes Mark A
Published: August 2021

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli.

Author Summary

Antimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.
In vitro coinfection by influenza A virus and respiratory syncytial virus generates hybrid viral particles with altered structure and tropism
Authors: Haney Joanne , Vijayakrishnan Swetha , Streetley James , Dee Kieran , Goldfarb Daniel Max , Clarke Mairi , Mullin Margaret , Carter Stephen D , Bhella David , Murcia Pablo R
Published: August 2021

Interactions between respiratory viruses impact viral transmission dynamics and clinical outcomes. To identify and characterize virus-virus interactions at the cellular level, we coinfected human lung cells with influenza A virus (IAV) and respiratory syncytial virus (RSV). Super-resolution microscopy, live-cell imaging, scanning electron microscopy, and cryo-electron tomography revealed extracellular and membrane-associated filamentous structures consistent with hybrid viral particles (HVPs). We show that HVPs harbor surface glycoproteins and ribonucleoproteins of IAV and RSV, and use the RSV fusion glycoprotein to evade anti-IAV neutralising antibodies and to infect and spread among cells lacking IAV receptors. Finally, we show evidence of IAV and RSV coinfection within cells of the bronchial epithelium, with viral proteins from both viruses co-localising at the apical surface. Our observations have profound implications for infection biology as they define a previously unknown interaction between respiratory viruses that might affect virus pathogenesis by expanding virus tropism and facilitating immune evasion.
RSC and GRFs confer promoter directionality by limiting divergent noncoding transcription
Authors: Wu Andrew , Vivori Claudia , Patel Harshil , Sideri Theodora , Moretto Fabien , van Werven Folkert
Published: August 2021

The directionality of gene promoters - the ratio of protein-coding over divergent noncoding transcription - is highly variable and regulated. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus a decrease in promoter directionality. We find that RSC facilitates nucleosome positioning upstream in promoters at the sites of divergent transcription. These highly directional promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription. We propose that any DNA binding factor, when stably associated with cryptic transcription start sites, form barriers for repressing divergent transcription. Our study provides an explanation as to why certain promoters are more directional than others.
Haploinsufficiency of the mouse Tshz3 gene leads to kidney dysfunction
Authors: Sanchez-Martin Irene , Magalhães Pedro , Fatmi Ahmed , Richard Fabrice , Vu Manh Thien Phong , Saurin Andy , Feuillet Guylène , Denis Colette , Schanstra Joost P. , Zürbig Petra , Caubit Xavier , Fasano Laurent
Published: August 2021

Renal tract defects and autism spectrum disorder (ASD) deficits represent the phenotypic core of the 19q12 deletion syndrome caused by the loss of one copy of the TSHZ3 gene. While a proportion of Tshz3 heterozygous (Tshz3+/lacZ) mice display ureteral defects, no kidney defects have been reported in these mice. The purpose of this study was to characterize the expression of Tshz3 in adult kidney as well as the renal physiological consequences of embryonic haploinsufficiency of Tshz3 by analyzing the morphology and function of Tshz3 heterozygous adult kidney. Here, we described Tshz3 expression in the smooth muscle and stromal cells lining the renal pelvis, the papilla and glomerular endothelial cells (GEnCs) of the adult kidney. Histological analysis showed that Tshz3+/lacZ adult kidney had an average of 29% fewer glomeruli than wild type kidney. Transmission electron microscopy (TEM) of Tshz3+/lacZ glomeruli revealed ultrastructural defects. Compared to wild type, Tshz3+/lacZ mice showed no difference in their urine parameters but lower blood urea, phosphates, magnesium and potassium at 2 months of age. At the molecular level, transcriptome analysis identified differentially expressed genes related to inflammatory processes in Tshz3+/lacZ compare to wild type (WT; control) adult kidneys. Lastly, analysis of the urinary peptidome revealed 33 peptides associated with Tshz3+/lacZ adult mice. These results provide the first evidence that in the mouse Tshz3 haploinsufficiency leads to cellular, molecular and functional abnormalities in the adult mouse kidney.
Functional Connectivity of the World’s Protected Areas
Authors: Brennan A. , Naidoo R. , Greenstreet L. , Mehrabi Z. , Ramankutty N. , Kremen C.
Published: August 2021

Rapid environmental change threatens to isolate the world’s wildlife populations and intensify biodiversity loss. Global policies have called for expanding and connecting the world’s protected areas (PAs) to curtail the crisis, yet how well PA networks currently support wildlife movement, and where connectivity conservation or restoration is most critical, have never been mapped globally. Here, we map the functional connectivity (how animals move through landscapes) of the world’s terrestrial PAs for the first time. Also, going beyond existing global connectivity indices, we quantify national PA-connectedness using an approach that meaningfully represents animal movement through anthropogenic landscapes. We find that reducing the human footprint may improve national PA-connectivity more than adding new PAs; however, both strategies are critical for improving and preserving connectivity in places where the predicted flow of animal movement is highly concentrated. We show that the majority of critical connectivity areas (CCAs) (defined as globally important areas of concentrated animal movements) remain unprotected. Of these, 72% overlap with previously-identified global conservation priority areas, while 3% of CCAs occur within moderate to heavily modified lands. Conservation and restoration of CCAs could safeguard connectivity of the world’s PAs, and dovetail with previously identified global conservation priorities.
Caracterization of Am –A genomes chromosomes in diploid wheat, polyploid wheat and triticales by marker cytogenetic
Authors: Dounia Hammouda Bousbia , Abdelkader Benbelkacem
Published: August 2021

The distribution and Caracterization of constitutive heterochromatin in A-Am genomes of diploid wheat (progenitor), polyploid wheat (hybrids) and triticales (primary and secondary) are analyzed and compared by C-bands. The Comparison of zones rich in highly repeated DNA sequences marked by C bands on the all chromosomes of Am - A genomes revealed an important structural heterogeneity. Four chromosomes of Triticum monococcum (1Am-3Am-4Am-5Am) are almost similar to their homologues in wheat (Triticum durum , Triticum aestivum ) and triticale, by the presence or absence of C bands. Contrary to the chromosomes 2Am (rich in heterochromatin), 6Am-7Am (absence of C bands) show a great differentiation compared to their homologues of Triticum durum and Triticum aestivum and x-Triticosecale Wittmack. In the triticales, A genome chromosomes are richer in heterochromatin compared to theirs homologous of polyploid wheats. This is explained by a "genome shock The confrontation of C- bands genome (Triticum monococcum) with a C+ bands genome (durum wheat / or common wheat) produces an interspecific hybrid which at the sixth generation reveals C+ bands (triticales). The variations observed in our vegetal material indicated the existence of an intervarietal and interspecific heterochromatic polymorphism. The presence of B chromosomes in triticales, could be explained as a manifestation of their adaptation.
Columnar localization and laminar origin of cortical surface electrical potentials
Authors: Baratham Vyassa L. , Dougherty Maximilian E. , Ledochowitsch Peter , Maharbiz Michel M. , Bouchard Kristofer E.
Published: August 2021

Electrocorticography (ECoG) methodologically bridges basic neuroscience and understanding of human brains in health and disease. However, the localization of ECoG signals across the surface of the brain and the spatial distribution of their generating neuronal sources are poorly understood. To address this gap, we recorded from rat auditory cortex using customized μECoG, and simulated cortical surface electrical potentials with a full-scale, biophysically detailed cortical column model. Experimentally, μECoG-derived auditory representations were tonotopically organized and signals were anisotropically localized to ≤±200 μm, i.e., a single cortical column. Biophysical simulations reproduce experimental findings, and indicate that neurons in cortical layers V and VI contribute ∼85% of evoked high-gamma signal recorded at the surface. Cell number and synchronicity were the primary biophysical properties determining laminar contributions to evoked μECoG signals, while distance was only a minimal factor. Thus, evoked μECoG signals primarily originate from neurons in the infragranular layers of a single cortical column.

In Brief

Baratham et al., investigated the localization and origins of sensory evoked ECoG responses. They experimentally found that ECoG responses were anisotropically localized ≤±200 μm, i.e., a single cortical column. Biophysically detailed simulations revealed that neurons in layers V &VI were the primary sources of evoked ECoG responses, in contrast to common thinking.

Highlights

Evoked μECoG signals are localized on the surface to a cortical column.

Neurons in cortical layers V and VI constitute the vast majority of the signal recorded at the surface.

Different laminar contributions to ECoG signal are driven by cell density and synchronicity.
Third-order motifs are sufficient to fully and uniquely characterize spatiotemporal neural network activity
Authors: Deshpande Sarita S. , Smith Graham A. , van Drongelen Wim
Published: August 2021

Neuroscientific analyses balance between capturing the brain’s complexity and expressing that complexity in meaningful and understandable ways. Here we present a novel approach that fully characterizes neural network activity and does so by uniquely transforming raw signals into easily interpretable and biologically relevant metrics of network behavior. We first prove that third-order, or triple, correlation describes network activity in its entirety using the triple correlation uniqueness (TCU) theorem. Triple correlation quantifies the relationships among three events separated by spatial and temporal lags, which are triplet motifs. Classifying these motifs by their event sequencing leads to fourteen qualitatively distinct motif classes that embody well-studied network behaviors such as synchrony, feedback, feedforward, convergence, and divergence. Within these motif classes, the summed triple correlations provide novel metrics of network behavior, as well as being inclusive of commonly used analyses. We demonstrate the power of this approach on a range of networks with increasingly obscured signals, from ideal noiseless simulations to noisy experimental data. This approach can be easily applied to any recording modality, so existing neural datasets are ripe for reanalysis. Triple correlation is an accessible signal processing tool with a solid theoretical foundation capable of revealing previously elusive information within recordings of neural networks.
Fission and PINK-1-mediated mitophagy are required for Insulin/IGF-1 signaling mutant reproductive longevity
Authors: Cota Vanessa , Murphy Coleen T.
Published: August 2021

Women’s reproductive cessation is the earliest sign of human aging and is caused by decreasing oocyte quality. Similarly, C. elegans’ reproduction declines with age and is caused by oocyte quality decline. Aberrant mitochondrial dynamics are a hallmark of age-related dysfunction, but the role of mitochondrial morphology in reproductive aging is largely unknown. We examined the requirements for mitochondrial fusion and fission in oocytes of both wild-type worms and the long-lived, long-reproducing insulin-like receptor mutant daf-2. We find that normal reproduction requires both fusion and fission. By contrast, daf-2 mutants require fission, but not fusion, for reproductive span extension. daf-2 mutant oocytes’ mitochondria are punctate (fissioned) and may be primed for mitophagy, as loss of the mitophagy regulator PINK-1 shortens daf-2’s reproductive span. Our data suggest that daf-2 maintain oocyte mitochondria quality with age via a shift toward punctate mitochondrial morphology and mitophagy to extend reproductive longevity.
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks
Authors: Zhang Pan , Zheng Shuangjia , Chen Jianwen , Zhou Yaoqi , Yang Yuedong
Published: August 2021

Motivation

Antibodies are a type of important biomolecules in the humoral immunity system, which can bind tightly to potential antigens with high affinity and specificity. An accurate identification of the paratope, the binding sites with antigens, is crucial for antibody mechanistic research and design. Although many methods have been developed for paratope prediction, further improvement of their accuracy is necessary.

Results

In this study, we concatenated the sequences of Complementarity Determining Regions (CDRs) within a single antibody to better capture nonlocal interactions between different CDRs and loop type-specific features for improving paratope prediction. We further integrated BiLSTM and transformer networks to gain the dependencies among the residues within the concatenated CDR sequences and to increase the interpretability of the model. The new method called DeepANIS (Antibody Interacting Site prediction) outperforms other antibody paratope prediction methods compared.

Availability

The DeepANIS method is freely available as a webserver at https://biomed.nscc-gz.cn:9094/apps/DeepANIS and for download at https://github.com/HideInDust/DeepANIS

Contact

yangyd25@mail.sysu.edu.cn or zhouyq@szbl.ac.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida
Authors: Ballesteros Jesús A. , Santibáñez-López Carlos E. , Baker Caitlin M. , Benavides Ligia R. , Cunha Tauana J. , Gainett Guilherme , Ontano Andrew Z. , Setton Emily V.W. , Arango Claudia P. , Gavish-Regev Efrat , Harvey Mark S. , Wheeler Ward C. , Hormiga Gustavo , Giribet Gonzalo , Sharma Prashant P.
Published: August 2021

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
Collective computation and the emergence of hunter-gatherer small-worlds
Authors: Hamilton Marcus J.
Published: August 2021

Two defining features of human sociality are large brains with neurally-dense cerebral cortices and the propensity to form complex social networks with non-kin. Large brains and the social networks in which they are embedded facilitate flows of fitness-enhancing information at multiple scales, but are also energetically expensive. In this paper, we consider how flows of energy and information interact to shape the macroscopic features of hunter-gatherer socioecology. Collective computation is the processing of information by complex adaptive systems to generate inferences in order to solve adaptive problems. In hunter-gatherer societies the adaptive problem is how to maximize fitness by optimizing information processing given the energy constraints of complex environments. The solution is the emergent macroscopic structure of the socioecology. Here we show how computation is extended across social networks to form the decentralized knowledge systems characteristic of hunter-gatherer societies. Data show that hunter-gatherer bands of co-residing families constitute computationally powerful networks that are embedded within hierarchically modular social networks that form complex metapopulations bound by fission-fusion dynamics at multiple scales facilitating the flow of information far beyond local interactions. These dynamics lead to the emergence of hunter-gatherer small-worlds where highly clustered local interactions are embedded within much larger, but sparsely connected metapopulations. Hunter-gatherers optimize local energy budgets in small groups but maintain interactions with much larger social networks while avoiding many of the ecological costs.
SNARE-dependent mitochondria-lysosome contacts regulate glial mitochondrial dynamics and dopaminergic neuron survival
Authors: Wang Honglei , Wang Linfang , Yi Shuanglong , Zhang Shiping , Ho Margaret S.
Published: August 2021

Mitochondria are dynamic organelles that undergo fission and fusion, enabling swift structural modification to adapt cellular needs. Disturbances in mitochondrial dynamics, frequently defects ascribed to neurons, have been associated with pathological contexts such as neurodegeneration in Parkinson’s disease. Nonetheless, the mechanism of glial mitochondrial dynamics contributing to neurodegeneration remains unclear. Here we present evidence that the Drosophila R-SNARE VAMP7 regulates glial mitochondrial dynamics and dopaminergic neuron survival via modulating the dynamic of mitochondria-lysosome contact, which determines the mitochondrial fission site. Independent of its characterized role in autophagosome-lysosome fusion, glial VAMP7 depletion causes mitochondrial elongation and dysfunction, increased ROS levels, and production of lipid droplets. These conferred changes in glia in turn affects nearby dopaminergic neuron survival. Glial VAMP7 genetically interacts with the mitochondrial fission/fusion factors Drp1 and Marf1 and controls glial mitochondrial dynamics via regulating the frequency and duration of mitochondria-lysosome contact. Our findings indicate that SNARE proteins, although not direct mediators on mitochondrial fusion, provide spatial cues to modulate glial mitochondrial fission via organelle contacts, impacting on neuron survival in a non-cell-autonomous manner.
The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS
Authors: Lao Hiu-Yin , Ng Timothy Ting-Leung , Wong Ryan Yik-Lam , Wong Celia Sze-Ting , Chan Chloe Toi-Mei , Wong Denise Sze-Hang , Lee Lam-Kwong , Jim Stephanie Hoi-Ching , Leung Jake Siu-Lun , Lo Hazel Wing-Hei , Wong Ivan Tak-Fai , Yau Miranda Chong-Yee , Lam Jimmy Yiu-Wing , Wu Alan Ka-Lun , Siu Gilman Kit-Hang
Published: August 2021

Bacterial pathogens that cannot be identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming and low-throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests, which are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by respective built-in analysis programs (MiSeq Reporter Software and Epi2me) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a comparatively higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of optimized Nanopore 16S was 96.36%, which was identical to Sanger 16S and was better than Illumina 16S (71.52%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78h and 8.25h, respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.
Spatiotemporally Resolved Multivariate Pattern Analysis for M/EEG
Authors: Higgins Cameron , Vidaurre Diego , Kolling Nils , Liu Yunzhe , Behrens Tim , Woolrich Mark
Published: August 2021

An emerging goal in neuroscience is tracking what information is represented in brain activity over time as a participant completes some task. Whilst EEG and MEG offer millisecond temporal resolution of how activity patterns emerge and evolve, standard decoding methods present significant barriers to interpretability as they obscure the underlying spatial and temporal activity patterns. We instead propose the use of a generative encoding model framework that simultaneously infers the multivariate spatial patterns of activity and the variable timing at which these patterns emerge on individual trials. An encoding model inversion allows predictions to be made about unseen test data in the same way as in standard decoding methodology. These SpatioTemporally Resolved MVPA (STRM) models can be flexibly applied to a wide variety of experimental paradigms, including classification and regression tasks. We show that these models provide insightful maps of the activity driving predictive accuracy metrics; demonstrate behaviourally meaningful variation in the timing of pattern emergence on individual trials; and achieve predictive accuracies that are either equivalent or surpass those achieved by more widely used methods. This provides a new avenue for investigating the brain’s representational dynamics and could ultimately support more flexible experimental designs in future.

HIGHLIGHTS

We introduce SpatioTemporally Resolved MVPA (STRM), an approach that explicitly models how successive stages of stimulus processing are distributed in both space and time in M/EEG data.

We show that STRM is broadly applicable to diverse types of M/EEG data and outputs meaningful and interpretable maps of how neural representations evolve in space and time at millisecond resolution.

The trial-specific deviations in activity pattern timings identified by STRM are not random, but vary systematically with inter-trial differences in behavioural, cognitive and physiological variables.

These methods result in predictive accuracy metrics that are mostly equivalent to, or a modest improvement on, conventional methods.
MTORC2 is a physiological hydrophobic motif kinase of S6 Kinase 1
Authors: Majeed Sheikh Tahir , Majeed Rabiya , Malik Aijaz A , Zargar Muhammad Afzal , Andrabi Khurshid Iqbal
Published: August 2021

Ribosomal protein S6 kinase 1 (S6K1), a major downstream effector molecule of mTORC1, regulates cell growth and proliferation by modulating protein translation and ribosome biogenesis. We have recently identified eIF4E as an intermediate in transducing signals from mTORC1 to S6K1 and further demonstrated that the role of mTORC1 is restricted to inducing eIF4E phosphorylation and interaction with S6K1. This interaction relieves S6K1 auto-inhibition and facilitates its hydrophobic motif (HM) phosphorylation and activation as a consequence. These observations underscore a possible involvement of mTORC1 independent kinase in mediating HM phosphorylation. Here, we report mTORC2 as an in-vivo/physiological HM kinase of S6K1. We show that rapamycin-resistant S6K1 truncation mutant ΔNHΔCT continues to display HM phosphorylation with selective sensitivity toward Torin-1. We also show that HM phosphorylation of wildtype S6K1and ΔNHΔCT depends on the presence of mTORC2 regulatory subunit-rictor. Furthermore, truncation mutagenesis and molecular docking analysis reveal the involvement of a conserved 19 amino acid stretch of S6K1 in mediating interaction with rictor. We finally show that deletion of the 19 amino acid region from wild type S6K1 results in loss of interaction with rictor, with a resultant loss of HM phosphorylation regardless of the presence of functional TOS motif. Our data demonstrate that mTORC2 acts as a physiological HM kinase that can activate S6K1 after its auto-inhibition is overcome by mTORC1. We, therefore, propose a novel mechanism for S6K1 regulation where mTOR complex 1 and 2 act in tandem to activate the enzyme.
The NADPH Oxidase A of Verticillium dahliae is Essential for Pathogenicity, Normal Development, and Stress Tolerance, and it Interacts with Yap1 to Regulate Redox Homeostasis
Authors: Vangalis Vasileios , Papaioannou Ioannis A. , Markakis Emmanouil A. , Knop Michael , Typas Milton A.
Published: August 2021

Maintenance of redox homeostasis is vital for aerobic organisms and particularly relevant to plant pathogens. These need to balance between endogenous ROS production that is required for their development and pathogenicity, and host-derived oxidative stress. Endogenous ROS in fungi are generated by the membrane-bound NADPH oxidase (NOX) complexes and the mitochondrial respiratory chain, while the transcription factor Yap1 is a major regulator of the antioxidant response. Here we investigated the roles of NoxA and Yap1 in fundamental biological processes of the important plant pathogen Verticillium dahliae. Deletion of noxA impaired growth and morphogenesis, compromised formation of hyphopodia, diminished penetration ability and pathogenicity, increased sensitivity against antifungal agents, and dysregulated expression of antioxidant genes. On the other hand, deletion of yap1 resulted in defects in conidial and microsclerotia formation, increased sensitivity against oxidative stress, and down-regulated antioxidant genes. Localized accumulation of ROS was observed before conidial fusion and during the heterokaryon incompatibility reaction upon nonself fusion. The frequency of inviable fusions was not affected by deletion of Yap1. Analysis of a double knockout mutant revealed an epistatic relationship between noxA and yap1. Our results collectively reveal instrumental roles of NoxA and ROS homeostasis in the biology of V. dahliae.
Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans
Authors: Rajaei Moein , Saxena Ayush Shekhar , Johnson Lindsay M. , Snyder Michael C. , Crombie Timothy A. , Tanny Robyn E. , Andersen Erik C. , Joyner-Matos Joanna , Baer Charles F.
Published: August 2021

Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the laboratory as in nature. The base-substitution spectrum differs betweenC. eleganslaboratory mutation accumulation (MA) experiments and the standing site-frequency spectrum, which has been argued to be in part owing to increased oxidative stress in the laboratory environment. Using genome sequence data fromC. elegansMA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased oxidative stress, we find the base-substitution spectrum is similar betweenmev-1, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). Conversely, the rate of short insertions is greater inmev-1, consistent with studies in other organisms in which environmental stress increased the rate of insertion–deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are different from those of nonmononucleotide sequence, both for indels and base-substitutions, and whereas the nonmononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different, with a greater frequency of A:T → T:A transversions and an increased proportion of ±1-bp indels. The discrepancy in mutational spectra between laboratory MA experiments and natural variation is likely owing to a consistent (but unknown) effect of the laboratory environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.
Blockchain in the accounting, auditing and accountability fields: a bibliometric and coding analysis
Authors: Secinaro Silvana , Dal Mas Francesca , Brescia Valerio , Calandra Davide
Published: August 2021

Purpose

This study aims to offer a bibliometric and coding analysis of blockchain articles published in the accounting, auditing and accountability fields.

Design/methodology/approach

The data were collected using the Scopus database and a bibliometric and qualitative coding analysis with the keywords “blockchain” and “accounting” or “auditing” or “accountability.” Of the 514 initial sources, 93 peer-reviewed papers, book chapters and conference proceedings in the areas of business, management and accounting were finally selected. Nonscientific sources such as nonpeer-reviewed books and white papers were excluded.

Findings

This study reveals a promising and multidisciplinary field of research dominated by scholars and less by practitioners. Qualitative research, especially discourse analysis, is the most used method among authors. This study gives some useful insights about blockchain's definition and characteristics, business models, processes involved, connection with other technologies and relationships with accounting theories. Among the most interesting insights, the results confirm that technology as an external force can create an intersection among several research areas: accounting, auditing, accountability, business, management, computer science and engineering fields. Finally, in terms of research themes, although blockchain has a clear effect on auditing accounting, the links with the area of accountability are less clear and validated.

Originality/value

This study highlights the current state of the field, combining methodological approaches and providing valuable future research insights. Additionally, it is also a starting point for professionals to fully understand blockchain's characteristics and potential with a constructive and systemic approach.
Food choice drivers of potential lab-grown meat consumers in Australia
Authors: Garcez de Oliveira Padilha Lívia , Malek Lenka , Umberger Wendy J.
Published: August 2021

Purpose

To examine the market potential for lab-grown meat (LGM) in Australia by: (1) determining consumers' willingness to consume LGM; (2) exploring heterogeneity in both consumers' willingness to consume LGM and food choice values; and (3) characterizing unique consumer clusters (segments) using socio-demographic, behavioral and psychosocial factors.

Design/methodology/approach

Latent class cluster analysis was conducted using online survey data obtained from a nationally representative sample of 1,078 Australian food shoppers.

Findings

Six consumer clusters were identified, each distinct in their degree of willingness to consume LGM and in their food choice values. Three clusters (49% of consumers) indicated some willingness to consume LGM. One segment, “Prospective LGM eaters” (12%), appeared “very willing” to consume LGM. These consumers were more likely to be younger (<35 years); university-educated; have greater prior awareness of LGM; stronger beliefs regarding the potential self- and society-related benefits of growing demand for LGM; and higher trust in diverse information sources.

Practical implications

Insights on the characteristics of each cluster provide useful information for the industry on how to tailor product development and marketing strategies to address the needs of consumers with the greatest potential to consume LGM.

Originality/value

This is the first consumer research on the topic of LGM to explore market opportunities for LGM in Australia using a nationally representative consumer sample.
Re-defining open government data standards for smart cities’ websites: a case study of selected cities
Authors: Lnenicka Martin , Saxena Stuti
Published: August 2021

Purpose

The purpose of this paper is to study the select Smart Cities of Czech and Indian counterparts and assess the extent to which open government data (OGD) standards are being adhered to using select indicators.

Design/methodology/approach

This study integrates the benchmarking frameworks provided in literature on OGD and apply them to evaluate the OGD standards of the Smart Cities’ websites.

Findings

Whereas the Czech Smart Cities are relatively more advanced in their OGD initiatives, the Indian counterpart is far lagging behind in their endeavors.

Originality/value

While there are many studies on OGD and Smart Cities, there has been no study which seeks to appreciate if the OGD initiatives are being adhered to by the Smart Cities.
Couple stress-based unsymmetric 8-node planar membrane elements with good tolerances to mesh distortion
Authors: Shang Yan , Wu Huanpu
Published: August 2021

Purpose

The paper aims to propose two new 8-node quadrilateral membrane elements with good distortion tolerance for the modified couple stress elasticity based on the unsymmetric finite element method (FEM).

Design/methodology/approach

The nodal rotation degrees of freedom (DOFs) are introduced into the virtual work principle and constrained by the penalty function for approximating the test functions of the physical rotation and curvature. Therefore, only the C0 continuity instead of C1 continuity is required for the displacement during the element construction. The first unsymmetric element assumes the test functions of the displacement and strain using the standard 8-node isoparametric interpolations, while these test functions in the second model are further enhanced by the nodal rotation DOFs. Besides, the trial functions in these two elements are constructed based on the stress functions that cana priorisatisfy related governing equations.

Findings

The benchmark tests show that both the two elements can efficiently simulate the size-dependent plane problems, exhibiting good numerical accuracies and high distortion tolerances. In particular, they can still exactly reproduce the constant couple stress state when the element shape deteriorates severely into the degenerated triangle. Moreover, it can also be observed that the second element model, in which the linked interpolation technique is used, has better performance than the first one, especially in capturing the steep gradients of the physical rotations.

Originality/value

As the proposed new elements use only three DOFs per node, they can be readily incorporated into the existing finite element (FE) programs. Thus, they are of great benefit to analysis of size-dependent membrane behaviors of micro/nano structures.
When the beans got spilled: the tragic case of cafe coffee day
Authors: Jalan Akanksha
Published: August 2021

Learning outcomes

The learning outcomes of this paper are as follows: to understand the language of accounting, to interpret financial statements to understand beyond what’s reported and to predict the financial health of a company before it is too late.

Case overview/synopsis

The case revolves around the Indian coffee retail giant - Café Coffee Day (hereafter, CCD). Coffee Day Global Limited of which CCD is a part, is the largest producer of Arabica beans in India. The case goes on to discuss the life and profile of VG Siddhartha (hereafter, VGS), whose leadership and farsightedness made coffee a household name in India, traditionally a tea-drinking country. Within just a year or two after its Initial Public Offering in November 2015, the company’s financial and legal troubles began to surface. The worst blow came when VGS, the 60-year-old founder and CEO committed suicide on July 29, 2019. His group’s mounting debt and impending doom had propelled him to take his own life. Today, the future of CCD remains hanging in the balance, with creditors ready and willing to take the firm into bankruptcy.

Complexity academic level

Under-graduates and above.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 1: Accounting and Finance.
Understanding “Riba” (interest): the religious and the rational
Authors: Azmat Saad , Bhatti Ayesha , Hassan M. Kabir
Published: August 2021

Learning outcomes

The case explores Ayesha’s reasoning, who is also a financial expert, regarding how she approaches the question of Riba (interest) so that she can maximize her financial returns and remain true to her religious identity. The discussion in the case revolves around alternate rationalizations as to why Riba (interest) continues to remain important for many Islamic investors.

Case overview/synopsis

Historically, the prohibition of Riba (interest) prevented the exploitation of the poor borrower who was charged exorbitant interest rates by wealthy lenders. In the modern day, a banking system which operates in a regulated setup and charges market-based interest rates, the rationale regarding the exploitation of the poor seems less compelling. Furthermore, other economic realities such as inflation and currency fluctuations further lend support to protecting one’s investments through prudent financial decisions. In this case the authors approach this decision regarding the prohibition of Riba (interest) in Islam from the point of view of the protagonist, Ayesha Bhatti, who is religiously conscious and is faced with certain personal investment choices.

Complexity academic level

The case focuses on one of the core issues of Islamic finance (IF), that of the prohibition of charging Riba (interest) on debt and the reasons behind this ruling. The relevance of this prohibition to modern day financial markets is essential to understand IF.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 1: Accounting and Finance.
Ultra-high-net-worth individuals: self-presentation and luxury consumption on Instagram
Authors: Michaelidou Nina , Christodoulides George , Presi Caterina
Published: August 2021

Purpose

Limited research has examined the segment of ultra-high-net-worth individuals (UHNWIs). This study aims to explore how this segment self-presents with regard to luxury on Instagram.

Design/methodology/approach

We use a qualitative research approach to content-analyze 815 publicly available photos on Instagram. The analytical approach involves multiple stages and yields three key themes.

Findings

Through Instagram images, UHNWIs engage in inconspicuous consumption via subtle displays of luxury possessions and more cues that indicate luxury experiences, power and social connections. The results further identify four dimensions of self-presentation in luxury consumption on social media: ostentatious, humble, revealed and hidden.

Research limitations/implications

The study adopts an inductive approach to identify themes related to UHNWIs’ self-presentation on Instagram. Other research could adopt a quantitative approach to identify drivers of the various themes. In addition, the unit of analysis was the photo posted by the UHNWI rather than the UHNWI himself or herself. Further research might explicitly consider the overall profile of each UHNWI and their holistic approach to posting with a view to developing a typology of UHNWIs based on the way they self-present and portray their luxury consumption.

Practical implications

Luxury marketers should focus on inconspicuous products and experiences that allow the UHNWIs to decelerate and spend time with their loved ones, access rare experiences and demonstrate power via their networks.

Originality/value

We extend prior research on self-presentation on Instagram. The authors focus on UHNWIs, a neglected yet significant segment of the luxury market.