bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre-assembled Cas9 ribonucleoprotein-mediated gene deletion identifies the carbon catabolite repressor and its target genes in Coprinopsis cinerea
Authors: Pareek Manish , Hegedüs Botond , Hou Zhihao , Csernetics Árpád , Wu Hongli , Virágh Máté , Sahu Neha , Liu Xiao-Bin , Nagy László G.
Published: June 2022

Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. This gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in-vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9-RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor encoding genes, among others. Our results support the notion that, similarly to reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented in this paper expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation.

Importance

Mushroom-forming fungi include some of the most efficient degraders of lignocellulosic plant biomass. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulation of these metabolic enzymes is known as carbon catabolite repression, which is orchestrates by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g. glucose) are not available. Here, we identified the Cre1 ortholog in a litter-decomposer Agaricomycete, Coprinopsis cinerea, knocked it out and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
No Semantic Information is Necessary to Evoke General Neural Signatures of Face Familiarity - Evidence from Cross-Experiment Classification
Authors: Dalski Alexia , Kovács Gyula , Ambrus Géza Gergely
Published: June 2022

Recent theories on the neural correlates of face identification stressed the importance of the available identity-specific semantic and affective information. However, whether such information is essential for the emergence of neural signal of familiarity has not yet been studied in detail.

Here, we explored the shared representation of face familiarity between perceptually and personally familiarized identities. We applied a cross-experiment multivariate pattern classification analysis (MVPA), to test if EEG patterns for passive viewing of personally familiar and unfamiliar faces are useful in decoding familiarity in a matching task where familiarity was attained thorough a short perceptual task. Importantly, no additional semantic, contextual, or affective information was provided for the familiarized identities during perceptual familiarization. Although the two datasets originate from different sets of participants who were engaged in two different tasks, familiarity was still decodable in the sorted, same identity matching trials.

This finding indicates that the visual processing of the faces of personally familiar and purely perceptually familiarized identities involve similar mechanisms, leading to cross-classifiable neural patterns.
Cortical activity during naturalistic music listening reflects short-range predictions based on long-term experience
Authors: Kern Pius , Heilbron Micha , de Lange Floris P. , Spaak Eelke
Published: June 2022

Expectations shape our experience of music. However, the internal model upon which listeners form melodic expectations is still debated. Do expectations stem from Gestalt-like principles or statistical learning? If the latter, does long-term experience play an important role, or are short-term regularities sufficient? And finally, what length of context informs contextual expectations? To answer these questions, we presented human listeners with diverse naturalistic compositions from Western classical music, while recording neural activity using MEG. We quantified note-level melodic surprise and uncertainty using various computational models of music, including a state-of-the-art transformer neural network. A time-resolved regression analysis revealed that neural activity over fronto-temporal areas tracked melodic surprise particularly around 200 ms and 300–500 ms after note onset. This neural surprise response was dissociated from sensory-acoustic and adaptation effects. Neural surprise was best predicted by computational models that incorporated long-term statistical learning – rather than by simple, Gestalt-like principles. Yet, intriguingly, the surprise reflected primarily short-range musical contexts of less than ten notes. We present a full replication of our novel MEG results in an openly available EEG dataset. Together, these results elucidate the internal model that shapes melodic predictions during naturalistic music listening.
Genomic instability in patients with sex determination defects and germ cell cancer
Authors: Krivega Maria , Zimmer Jutta , Slezko Anna , Frank-Herrmann Petra , Rehnitz Julia , Hohenfellner Markus , Bettendorf Markus , Luzarowski Marcin , Strowitzki Thomas
Published: June 2022

The ability to transmit genetic information through generations depends on preservation of genome integrity. Genetic abnormalities affect cell differentiation, causing tissue specification defects and cancer. We addressed genomic instability in individuals with Differences of Sex Development (DSD), characterized by gonadal dysgenesis, infertility, high susceptibility for different types of cancer, especially Germ Cell Tumors (GCT), and in men with testicular GCTs. Whole proteome analysis of leukocytes, supported by specific gene expression assessment, and dysgenic gonads characterization, uncovered DNA damage phenotypes with altered innate immune response and autophagy. Further examination of DNA damage response revealed a reliance on deltaTP53, which was compromised by mutations in the transactivation domain in DSD-patients with GCT. Accordingly, drug-induced rescue of DNA damage was achieved by autophagy inhibition but not by stabilization of TP53 in DSD-patients’ blood in vitro. This study elucidates possibilities for prophylactic treatments of DSD patients as well as new diagnostic approaches of GCT.

Teaser

DNA damage phenotypes accompany aneuploidy of sex chromosomes and link to infertility and high propensity to germ cell tumor development.
Strategies of developmental vestibular plasticity after unilateral embryonic ear removal in Xenopus laevis
Authors: Gordy Clayton , Straka Hans
Published: June 2022

Appropriate gaze control mechanisms rely on bilateral mirror-symmetric vestibular endorgans, central circuits, and extraocular motor effectors. Embryonic removal of one inner ear prior to the formation of these structures was used to evaluate the extent to which animals can develop appropriate motor outputs in the presence of only a singular inner ear. Near-congenital one-eared tadpoles subjected to separate or combinatorial visuo-vestibular motion stimulation exhibited vestibular-ocular reflexes, though smaller in gain compared to controls, whereas isolated visuo-motor responses remained largely unaltered. Surprisingly, direction-specific responses in one-eared tadpoles revealed a spectrum of vestibulo-ocular reflex performance, where in many cases rather robust responses were observed during head motion towards the missing ear. Rotation toward the remaining ear elicited eye movements which were often severely attenuated. This suggests that embryonically generated one-eared animals develop bidirectional vestibular signal detection and downstream processing capacities that allow activation of robust compensatory eye movements. However, this capability seems to occur at the expense of performance of vestibular reflexes during motion in the canonical activation direction of the singular ear. Consequently, the development of central vestibulo-motor circuits in one-eared animals likely relies on strategies in which the outcome for gaze stabilization is driven by balanced homeostatic levels and individual temporal tuning of abducens motoneuron activity. Despite the lack of bilateral symmetric vestibular afferent input, the developing central nervous system is capable of creating a framework for symmetric sensorimotor transformations.
Co-occurrence of past and present shifts current neural representations and mediates serial biases
Authors: Zhang Huihui , Luo Huan
Published: June 2022

The regularities of the world render an intricate interplay between past and present. Even across independent trials, current-trial perception can be automatically shifted by preceding trials, namely the ‘serial bias’. Meanwhile, the neural implementation of the spontaneous shift of present by past that operates on multiple features remains unknown. In two auditory categorization experiments with human electrophysiology recordings, we demonstrate that serial bias arises from the co-occurrence of past-trial neural reactivation and the neural encoding of current-trial features. The meeting of past and present shifts the neural representation of current-trial features and modulates serial bias behavior. Critically, past-trial features (i.e., pitch, category, motor response) that constitute an ‘event-file’ keep their respective identities in working memory and are only reactivated by the corresponding features in the current trial, giving rise to dissociated feature-specific serial biases. This ’event-file’ reactivation might constitute a fundamental mechanism for adaptive past-to-present generalizations over multiple features.
“Genetic and chemical disruption of Amyloid Precursor Protein processing impairs zebrafish sleep maintenance”
Authors: Özcan Güliz Gürel , Lim Sumi , Canning Thomas , Tirathdas Lavitasha , Donnelly Joshua , Kundu Tanushree , Rihel Jason
Published: June 2022

Amyloid precursor protein (APP) is a brain-rich, single pass transmembrane protein that is proteolytically processed into multiple products, including Amyloid-beta (Aβ), a major driver of Alzheimer’s disease (AD). Although both over-expression of APP, as in mouse models used to study AD, and exogenously delivered Aβ lead to changes in sleep behaviors, whether APP processing plays an endogenous role in regulating sleep is unknown. Here, we demonstrate that APP processing into Aβ40 and Aβ42 is conserved in zebrafish and then describe sleep/wake phenotypes in loss of functionappaandappbmutants. Larvae with mutations inappahad reduced waking activity but normal sleep patterns, while larvae that lackedappbhad shortened sleep bout durations at night. Treatment with the γ-secretase inhibitor DAPT also shortened sleep bouts at night, while the BACE-1 inhibitor lanabecestat lengthened sleep bouts. Since both drugs fail to further alter sleep inappbmutants, and intraventricular injection of the App cleavage product P3 also shortens night-time sleep bouts, we conclude that the proper balance of Appb proteolytic processing is required for normal sleep maintenance in zebrafish.
Alterations in neural stem cell quiescence and activation in the 3xTG-AD model of Alzheimer’s Disease
Authors: Liu Yubing , Fong Bensun C. , Harris Richard A. , McNicoll Marie-Michelle , Abdi Amaal A. , Cuthbert Jacob B. , Cook David P. , Figeys Daniel , Wang Jing , Vanderhyden Barbara C. , Slack Ruth S.
Published: June 2022

Alzheimer’s Disease (AD) is the most common form of dementia with progressive cognitive deficits and mood disorders (Knopman et al., 2021). Recent studies have associated AD pathology with the impairment of adult neurogenesis, as indicated by impaired neural stem cell (NSCs) homeostasis (Bond et al., 2015). Recent work has further associated AD progression with a decline in the number and maturation of adult-born neurons in the SGZ, distinct from typical age-related decline (Moreno-Jiménez et al., 2019). In 3xTG-AD mice, a well-established mouse model of AD, our and other groups have demonstrated impairments to NSC pool and neural progenitor proliferation, as well as adult-born neurons, before the onset of Aβ plaques and NFTs (Hamilton et al., 2010, 2015; Rodríguez et al., 2008, 2009). However, the regulatory mechanisms underlying the functional impairment of adult NSCs remain to be resolved. Here, we employ single-cell RNA-Seq to establish population-specific defects in the 3xTG-AD mouse model during adult SGZ neurogenesis. Relative to control mice, we observe a dramatic AD-induced decrease in the primed and activated NSC population, which results in a progressive loss of cells committed to neurogenesis. Transcriptome measurements suggest that 3xTG-AD NSCs and their progeny represent enhanced ribosomal and mitochondrial biogenesis, and disturbed Notch signaling pathway. RNA velocity analysis reveals reduced NSC activation as evidenced by a large fraction of Ascl1-postive cells, instead of entering cell cycle, returning to the primed and quiescent state. This is further supported by reduced numbers of Lpar1-expressing cells, a marker of neural progenitor cells, in the SGZ. Our work explores, at a stage-specific resolution, changes in the regulatory networks guiding adult neurogenesis, and identifies niche disturbances in the regulation of NSC quiescence and activation. These NSC deficits underlying impaired neurogenesis identified in AD mice, may be key contributors underlying the compromised hippocampal function in AD.
Binding and unbinding pathways of peptide substrate on SARS-CoV-2 3CL protease
Authors: Moritsugu Kei , Ekimoto Toru , Ikeguchi Mitsunori , Kidera Akinori
Published: June 2022

Based on many crystal structures of ligand complexes, much study has been devoted to understanding the molecular recognition of SARS-CoV-2 3C-like protease (3CLpro), a potent drug target for COVID-19. In this research, to extend this present static view, we examined the kinetic process of binding/unbinding of an eight-residue substrate peptide to/from 3CLpro by evaluating the path ensemble with the weighted ensemble simulation. The path ensemble showed the mechanism of how a highly flexible peptide folded into the bound form. At the early stage, the dominant motion was the diffusion on the protein surface showing a broad distribution, whose center was led into the cleft of the Chymotrypsin fold. We observed a definite sequential formation of the hydrogen bonds at the later stage occurring in the cleft, initiated between Glu166 (3CLpro) and P3_Val (peptide), followed by binding to the oxyanion hole and completed by the sequencespecific recognition at P1_Gln.
Cancers adapt to their mutational load by buffering protein misfolding stress
Authors: Tilk Susanne , Frydman Judith , Curtis Christina , Petrov Dmitri
Published: June 2022

In asexual populations that don’t undergo recombination, such as cancer, deleterious mutations are expected to accrue readily due to genome-wide linkage between mutations. Despite this mutational load of often thousands of deleterious mutations, many tumors thrive. How tumors survive the damaging consequences of this mutational load is not well understood. Here, we investigate the functional consequences of mutational load in 10,295 human tumors by quantifying their phenotypic response through changes in gene expression. Using a generalized linear mixed model (GLMM), we find that high mutational load tumors up-regulate proteostasis machinery related to the mitigation and prevention of protein misfolding. We replicate these expression responses in cancer cell lines and show that the viability in high mutational load cancer cells is strongly dependent on complexes that degrade and refold proteins. This indicates that upregulation of proteostasis machinery is causally important for high mutational burden tumors and uncovers new therapeutic vulnerabilities.

Statement of Significance

Cancers can successfully survive an accumulation of thousands of protein-damaging mutations. Here, we show that high mutational load tumors mitigate these damaging consequences by up-regulating complexes that buffer against protein misfolding stress – providing novel therapeutic vulnerabilities and suggesting that disruption of proteostasis is a hallmark of somatic evolution.
C-terminal disulfide bond in SUN2 regulate dynamic remodeling of LINC complexes at the nuclear envelope
Authors: Sharma Rahul , Hetzer Martin W.
Published: June 2022

The LINC complex tethers the cell nucleus to the cytoskeleton to regulate mechanical forces during cell migration, differentiation, and diseases. The function of LINC complexes relies on the interaction between highly conserved SUN and KASH proteins that form higher-order assemblies capable of load bearing. These structural details have emerged from in vitro assembled LINC complexes however, the principles of in vivo assembly remain obscure. Here, we report a conformation-specific SUN2 antibody as a tool to visualize LINC complex dynamics in situ. Using imaging, biochemical and cellular methods, we find that conserved cysteines in SUN2 undergo KASH dependent inter- and intra- molecular disulfide bond rearrangements. Disruption of the SUN2 terminal disulfide bond compromises SUN2 localization, turnover, LINC complex assembly as well as cytoskeletal organization and cell migration. Moreover, using pharmacological and genetic interventions, we identify components of the ER lumen as SUN2 cysteines redox state regulators. Overall, we provide evidence for SUN2 disulfide bond rearrangement as a physiologically relevant structural modification that regulates LINC complex functions.
Mechanical properties of breast, kidney, and thyroid tumours measured by AFM: relationship with tissue structure
Authors: Levillain A. , Confavreux C.B. , Decaussin-Petrucci M. , Durieux E. , Paparel P. , Le-Bail Carval K. , Maillard L. , Bermond F. , Mitton D. , Follet H.
Published: June 2022

The mechanical properties of the extracellular matrix are essential for regulating cancer cell behaviour, but how they change depending on tumour type remains unclear. The aim of the current study was to determine how the mechanical properties of tumours that frequently metastasize to bones were affected depending on histological type. Human breast, kidney, and thyroid specimens containing tumour and normal tissue were collected during surgery. The elastic modulus and elastic fraction of each sample were characterised using atomic force microscopy and compared with histopathological markers. We observed that tumour mechanical properties were differentially affected depending on organ and histological type. Indeed, clear cell renal carcinoma and poorly differentiated thyroid carcinoma displayed a decrease in the elastic modulus compared to their normal counterpart, while breast tumours, papillary renal carcinoma and fibrotic thyroid tumours displayed an increase in the elastic modulus. Elastic fraction decreased only for thyroid tumour tissue, indicating an increase in the viscosity. These findings suggest a unique mechanical profile associated with each subtype of cancer. Therefore, viscosity could be a discriminator between tumour and normal thyroid tissue, while elasticity could be a discriminator between the subtypes of breast, kidney and thyroid cancers.

Graphical abstract
Gene structure heterogeneity drives transcription noise within human chromosomes
Authors: Chiang Michael , Brackley Chris A. , Naughton Catherine , Nozawa Ryu-Suke , Battaglia Cleis , Marenduzzo Davide , Gilbert Nick
Published: June 2022

Classical observations have long suggested there is a link between 3D gene structure and transcription1–4. However, due to the many factors regulating gene expression, and to the challenge of visualizing DNA and chromatin dynamics at the same time in living cells, this hypothesis has been difficult to quantitatively test experimentally. Here we take an orthogonal approach and use computer simulations, based on the known biophysical principles of genome organisation5–7, to simultaneously predict 3D structure and transcriptional output of human chromatin genome wide. We validate our model by quantitative comparison with Hi-C contact maps, FISH, GRO-seq and single-cell RNA-seq data, and provide the 3DGene resource to visualise the panoply of structures adopted by any active human gene in a population of cells. We find transcription strongly correlates with the formation of protein-mediated microphase separated clusters of promoters and enhancers, associated with clouds of chromatin loops, and show that gene noise is a consequence of structural heterogeneity. Our results also indicate that loop extrusion by cohesin does not affect average transcriptional patterns, but instead impacts transcriptional noise. These findings provide a functional role for intranuclear microphase separation, and an evolutionary mechanism for loop extrusion halted at CTCF sites, to modulate transcriptional noise.
ARF6 is a host factor for SARS-CoV-2 infectionin vitro
Authors: Mirabelli C. , Sherman E.J. , Cunha J. Bragazzi , Wotring J.W. , El Saghir J. , Harder J. , Kretzler M. , Sexton J.Z. , Emmer B.T. , Wobus C.E.
Published: June 2022

SARS-CoV-2 is a newly emerged beta-coronavirus that enter cells via two routes, direct fusion at the plasma membrane or endocytosis followed by fusion with the late endosome/lysosome. While the viral receptor, ACE2, multiple entry factors, and the mechanism of fusion of the virus at the plasma membrane have been extensively investigated, viral entry via the endocytic pathway is less understood. By using a human hepatocarcinoma cell line, Huh-7, which is resistant to the antiviral action of the TMPRSS2 inhibitor camostat, we discovered that SARS-CoV-2 entry is not dependent on dynamin but dependent on cholesterol. ADP-ribosylation factor 6 (ARF6) has been described as a host factor for SARS-CoV-2 replication and it is involved in the entry and infection of several pathogenic viruses. Using CRISPR-Cas9 genetic deletion, we observed that ARF6 is important for SARS-CoV-2 uptake and infection in Huh-7. This finding was corroborated using a pharmacologic inhibitor, whereby the ARF6 inhibitor NAV-2729 showed a dose-dependent inhibition of viral infection. Importantly, NAV-2729 reduced SARS-CoV-2 viral loads also in more physiologic models of infection: Calu-3 and kidney organoids. This highlighted the importance of ARF6 in multiple cell contexts. Together, these experiments points to ARF6 as a putative target to develop antiviral strategies against SARS-CoV-2.
Glutamine metabolism modulates chondrocyte inflammatory response
Authors: Arra Manoj , Swarnkar Gaurav , Adapala Naga Suresh , Naqvi Syeda Kanwal , Cai Lei , Rai Farooq , Mbalaviele Gabriel , Brophy Robert , Abu-Amer Yousef
Published: June 2022

Osteoarthritis is the most common joint disease in the world with significant societal consequences, but lacks effective disease modifying interventions. The pathophysiology consists of a prominent inflammatory component that can be targeted to prevent cartilage degradation and structural defects. Intracellular metabolism has emerged as a culprit of the inflammatory response in chondrocytes, with both processes co-regulating each other. The role of glutamine metabolism in chondrocytes, especially in the context of inflammation, lacks a thorough understanding and is the focus of this work. We display that chondrocytes utilize glutamine for energy production and anabolic processes. Furthermore, we show that glutamine deprivation itself causes metabolic reprogramming and decreases the inflammatory response of chondrocytes through inhibition of NF-κB activity. Finally, we display that glutamine deprivation promotes autophagy and that ammonia is an inhibitor of autophagy. Overall, we identify a relationship between glutamine metabolism and inflammatory signaling and display the need for increased study of chondrocyte metabolic systems.
Identification of a small chemical as a lysosomal calcium mobilizer and characterization of its ability to inhibit autophagy and viral infection
Authors: Zhang Kehui , Huang Lihong , Chen Nanjun , Yue Jianbo
Published: June 2022

We previously identified GADPH as one of the cyclic adenosine diphosphoribose (cADPR)’s binding proteins and found that GADPH participates in cADPR-mediated Ca2+ release from ER via RyRs. Based on the simulated cADPR-GAPDH complex structure, we performed the structure-based drug screening, identified several small chemicals with high docking scores to cADPR’s binding pocket in GAPDH, and showed that two of these compounds, C244 and C346, are potential cADPR antagonists. We further synthesized several analogs of C346, and found that its analog, G42, also mobilized Ca2+ release from lysosomes. G42 alkalized lysosomal pH, and inhibited autophagosome-lysosome fusion. Moreover, G42 markedly inhibited Zika virus (ZIKV, a flavivirus) or murine hepatitis virus (MHV, a β-coronavirus) infections of host cells. These results suggest that G42 inhibits virus infection, likely by triggering lysosomal Ca2+ mobilization and inhibiting autophagy.
PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni
Authors: Blouin Michael S. , Bollmann Stephanie R. , Tennessen Jacob A.
Published: June 2022

Background

Biomphalaria glabrata is a snail intermediate host for Schistosoma mansoni, a trematode responsible for human schistosomiasis. BS90 is one of the most well studied strains of B. glabrata owing to its high resistance to infection by most strains of S. mansoni. An F2 mapping study from 1999 identified two RAPD markers that associated with what appeared to be single-locus, dominant resistance by the BS90 population relative to the susceptible M-line population. One marker cannot be mapped, but the other, OPM-04, maps to within 5 Mb of PTC2, a region we recently showed has a very large effect on resistance within another snail population challenged by the same strain of parasite (PR1). Here we tested the hypothesis that the PTC2 region contains the causal gene/s that explain the iconic resistance of BS90 snails.

Methods

We used marker-assisted backcrossing to drive the BS90 version of the PTC2 region (+/-∼ 1 Mb on either side) into an M-line (susceptible strain) genetic background, and the M-line version into a BS90 genetic background. We challenged the offspring with PR1-strain schistosomes and tested for effects of allelic variation in the PTC2 region in a common genetic background.

Results

Relative to M-line haplotypes, the BS90 haplotype actually confers enhanced susceptibility. So we reject our original hypothesis. One possible explanation for our result was that the causal gene linked to OPM-04 is near, but not in the PTC2 block that we introgressed into each line. So we used an F2 cross to independently test the effects of the PTC2 and OPM-04 regions in a randomized genetic background. We confirmed that the BS90 haplotype confers increased susceptibility, and we see a similar, although non-significant effect at OPM-04. We discuss possible reasons why our results differed so dramatically from those of the 1999 study. We also present PacBio assemblies of the PTC2 and flanking region in BS90 and M-line, compare with previously published PTC2 haplotypes, and discuss candidate genes that might be behind the enhanced susceptibility of the BS90 haplotype.
Decreasing photosystem antenna size: a double-edged sword for canopy photo-synthetic efficiency
Authors: Mao Linxiong , Song Qingfeng , Li Ming , Liu Xinyu , Shi Zai , Chen Faming , Chen Gen-yun , Zhu Xin-Guang
Published: June 2022

Optimization of antenna size of photosynthetic systems is one strategy to increase plant canopy photosynthesis and crop yield potential. The relationship between antenna size and photosynthesis rate has been extensively studied recently. However, conflicting results have been obtained. Here we show that the extent of decrease in antenna size is a major factor determining the consequences of decreasing antenna on photosynthesis and growth-related parameters. Specifically, we constructed transgenic rice lines with artificial microRNA (amiRNA) targeting to Chlorophyll Synthesis (YGL1) to generate transgene heterozygous and homozygous lines with different leaf chlorophyll contents and antenna sizes. We found that canopy photosynthesis (Ac), biomass and grain yield of the heterozygote were not significantly different from those of WT while the Ac, biomass and grain yield of the homozygote were lower than those of WT. Further, when the maximal quantum yield of photosystem II (Fv/Fm) was larger than 0.8, decreasing antenna size by reducing chlorophyll biosynthesis did not affect leaf photosynthesis; but when Fv/Fm was lower than 0.8, there is a positive relationship between antenna size and leaf photosynthesis. There is large variation in both leaf chlorophyll content and antenna size in elite rice cultivars, suggesting that there is a large scope to decrease leaf chlorophyll content to increase nitrogen use efficiency as long as the quantum yield of PSII is not compromised.
The Cdc42 effector and non-receptor tyrosine kinase, ACK defines a distinct STAT5 transcription signature in a chronic myeloid leukaemia cell model
Authors: Corry Jessica , Jachimowicz Daniel , Keith Benjamin , Vicente-Garcia Jose Julio , Mott Helen R. , Wickson Kate , Owen Darerca
Published: June 2022

Activated Cdc42-associated kinase (ACK) is a Rho family effector that is widely implicated in cancer. Here, we describe new roles for ACK in transcriptional regulation mediated by its relationship with the signal transducer and activators of transcription (STAT) family. We show that ACK can interact with STAT3, STAT5A and STAT5B, and augments phosphorylation at the conserved activation tyrosine on these STAT members. ACK stimulates oncogenic STAT nuclear relocation and transcriptional activation. We also identify endogenous relationships between ACK and STAT family members in haematopoietic disease cell lines. In the K562 chronic myeloid leukaemia cell line, we confirm that ACK contributes to the pool of active, nuclear STAT5. By interrogating ACK knock out cells we describe an ACK-driven STAT5 transcriptional signature in K562s. We propose ACK as a contributor to hyperactivated STAT5 signalling in this CML cell line and reveal a new route for therapeutic intervention.
Human sperm TMEM95 binds eggs and facilitates membrane fusion
Authors: Tang Shaogeng , Lu Yonggang , Skinner Will M. , Sanyal Mrinmoy , Lishko Polina V. , Ikawa Masahito , Kim Peter S.
Published: June 2022

Tmem95 encodes a sperm acrosomal membrane protein, whose knockout has a male-specific sterility phenotype in mice. How TMEM95 plays a role in membrane fusion of sperm and eggs has remained elusive. Here, we utilize a sperm penetration assay as a model system to investigate the function of human TMEM95. We show that human TMEM95 binds to hamster egg membranes, providing evidence for a TMEM95 receptor on eggs. Using X-ray crystallography, we reveal an evolutionarily conserved, positively charged region of TMEM95 as a putative receptor-binding surface. Amino-acid substitutions within this region of TMEM95 ablate egg-binding activity. We identify monoclonal antibodies against TMEM95 that reduce the number of human sperm fused with hamster eggs in sperm penetration assays. Strikingly, these antibodies do not block binding of sperm to eggs. Taken together, these results provide strong evidence for a specific, receptor-mediated interaction of sperm TMEM95 with eggs and suggest that this interaction may have a role in facilitating membrane fusion.

Significance statement

Membrane fusion of sperm and eggs is pivotal in sexual reproduction. Tmem95 knockout mice show male-specific sterility, but it was unknown how sperm TMEM95 facilitates membrane fusion with eggs. We show here that human TMEM95 binds eggs. Our crystal structure of TMEM95 suggests a region where this binding may occur. We develop monoclonal antibodies against TMEM95 that impair sperm-egg fusion but do not block sperm-egg binding. Thus, we propose that there is a receptor-mediated interaction of sperm TMEM95 with eggs, and that this interaction may have a direct role in membrane fusion. Our work suggests avenues for the identification of the TMEM95 egg receptor and may enable the development of infertility treatments and contraceptives for humans.
Cis-membrane association of human ATG8 proteins N-terminus mediates autophagy
Authors: Zhang Wenxin , Nishimura Taki , Gahlot Deepanshi , Saito Chieko , Davis Colin , Jefferies Harold B. J. , Schreiber Anne , Thukral Lipi , Tooze Sharon A.
Published: June 2022

Autophagy is an essential catabolic pathway which sequesters and engulfs cytosolic substrates via autophagosomes, unique double-membraned structures. ATG8 proteins are ubiquitin-like proteins recruited to autophagosome membranes by lipidation at the C-terminus. ATG8s recruit substrates, such as p62, and play an important role in mediating autophagosome membrane expansion. However, the precise function of lipidated ATG8 in expansion remains obscure. Using a real-timein vitrolipidation assay, we revealed that the N-termini of lipidated human ATG8s (LC3B and GABARAP) are highly dynamic and interact with the membrane. Moreover, atomistic MD simulation and FRET assays indicate that N-termini of LC3B and GABARAP associatein cison the membrane. Thecis-membrane association of the N-terminus is critical to maintain membrane expansion and the size of autophagosomes in cells, consequently, mediating the efficient degradation of p62. Our study provides fundamental molecular insights into autophagosome membrane expansion, revealing the critical and unique function of lipidated ATG8.
Optimized dCas9 Programmable Transcriptional Activators for Plants
Authors: Zinselmeier Matthew H , Casas-Mollano J. Armando , Cors Jonathan , Sychla Adam , Heinsch Stephen C , Voytas Daniel F , Smanski Michael J
Published: June 2022

Understanding how gene expression impacts plant development and physiology is important for rationally engineering improved crops. Programmable Transcriptional Activators (PTAs), including CRISPR-Cas activators, have traditionally relied on a limited number of transcriptional activation domains. Usually the VP64 domain, derived from human herpes simplex virus, is fused to a DNA-binding domain to activate target gene expression. We reasoned there was considerable space for PTA improvement by replacing VP64 with a plant-derived activation domain. To address this, we designed, built, and tested a PTA library of 38 putative plant transcriptional activation domains. Domains fromHSFA6b, AvrXa10, DOF1, DREB1, andDREB2genes function as strong activators inSetaria viridisandArabidopsis thalianain protoplast assays and in transgenic plants. Overexpression of multiple endogenous genes (FT, PAP1, WUS) reached levels similar to the highly expressed housekeeping gene,PP2A, regardless of basal expression level. Further, these domains were effective in different PTA architectures, including the dCas9-SunTag, dCas9-Moontag, and TALE-SunTag systems. Lastly, we demonstrate the ability of these improved PTAs to map enhancer regions that promote gene expression in plants. This work demonstrates the effective and flexible nature of PTAs to activate target genes in plants, providing tools that can be used to improve agronomically relevant traits of interest.
Cultivate customer loyalty in national culture: a meta-analysis of electronic banking customer loyalty
Authors: Zhang Liming , Yi Yuxin , Zhou Guichuan
Published: June 2022

Purpose

This paper presents a meta-analysis of the electronic banking (e-banking) customer loyalty literature in the last 10 years. The study investigated the moderating role of national culture in the relationship between e-banking customer loyalty and its antecedents.

Design/methodology/approach

Using a meta-analysis of customer loyalty in 19 countries, the authors incorporated national culture scores based on Hofstede's cultural dimensions to explore how the relative importance of e-banking customer loyalty antecedents varies across cultures.

Findings

The study revealed that national culture moderates the relationship between e-banking customer loyalty and its seven antecedents for four cultural dimensions, yet there was no significant moderation for satisfaction.

Research limitations/implications

This study reviewed the relationships in the literature on customer loyalty in e-banking contexts, extending and enriching the current knowledge. However, some specific limitations, such as the non-use of qualitative studies and the clipping of adverse concepts, exist in the secondary data and should be considered.

Practical implications

The results show that the seven antecedents affect e-banking customer loyalty to different degrees. Managers should incorporate cultural factors in e-banking customer management.

Originality/value

Only a few studies have assessed cultural differences in relation to e-banking customer loyalty. The authors address this need by offering deeper insights into how cultural dimensions moderate the relationships between e-banking customer loyalty and its antecedents through a meta-analytical review. The study findings offer managers a new perspective of leveraging the benefits of cultural differences, enhancing their decision-making in international business.
Corporate social responsibility and customer-citizenship behaviors: the role of customer–company identification
Authors: Fatma Mobin , Khan Imran , Kumar Vikas , Shrivastava Avinash Kumar
Published: June 2022

Purpose

This study aims to analyse a proposed model depicting the direct and indirect relationship between consumer perceptions of corporate social responsibility (CSR) and customer citizenship behaviour (CCB) in the banking industry.

Design/methodology/approach

In this study, data was collected from banking consumers in India. The final sample included 505 responses. The hypotheses were tested using structural equation modelling.

Findings

The findings suggest that consumer perceptions of CSR are positively related to consumer identification with the company and CCB. Also, the relationship between consumer perception of CSR and CCB is mediated through consumer–company identification. This suggests that CSR activities are positively related with the consumer identification with their company, which encourages CCB.

Originality/value

This study contributes empirically and theoretically to expand the limited knowledge about the cognitive link between CSR and consumer behaviour. This study provides new insights about the proposed relationships related to the effects of consumer perception of CSR on CCB.
The development of perception scale of gender role in disaster management and the examination with related factors
Authors: Onal Ebru Inal , Soysal  Sümeyra , Paksoy Erbaydar Nüket
Published: June 2022

Purpose

This study aims to develop a perception scale of gender role in disaster management and examine related factors.

Design/methodology/approach

A total of 1,167 individuals were reached in the main trial. Exploratory and confirmatory factor analyses were applied to test the validity of the final scale form, respectively.

Findings

The scale was developed as unidimensional with two positive items and 17 negative items. The mean scores of the participants were in the positive perception group. The 19-item model is a reliable and valid instrument for measuring the perception of gender role specific to disaster management.

Practical implications

Determining the perceptions of the people will guide the policies related to gender equity and equality and activities to be carried out in the disaster management field. This tool can be used to raise awareness related to gender perceptions in the disaster preparedness activities.

Originality/value

The “Perception Scale of Gender Role in Disaster Management” which is a reliable and robust tool to determine the perception of gender role specific to the disaster management was developed in this study. This tool can contribute to address the needs and capacities and provide influencive strategy development through gender analysis.
Green pride in sustainable versus premium brand decisions
Authors: Souto Maior Cecilia , Mantovani Danielle , Pinto Diego Costa , Ferreira Mário Boto
Published: June 2022

Purpose

Earlier research indicates that brand choices may display different identity signals, such as altruism and benevolence for green brands or high status and exclusiveness for premium brands. This research adds to the literature by exploring how opting for green (vs premium) brands leads consumers to feel authentic (vs hubristic) pride.

Design/methodology/approach

Three experimental studies were conducted to test the hypotheses related to green versus premium choices (Studies 1–3), public accountability (Study 2) and the underlying process of anticipated judgment (Study 3).

Findings

The findings reveal that choosing a green (vs premium) brand results in higher authentic pride and lower hubristic pride. However, the green pride effects were only observed when consumers' brand choices were publicly accountable. Finally, anticipated judgment mediates changes in authentic pride driven by green (vs premium) brands.

Originality/value

The study findings contribute preponderantly to the green consumer behavior literature and practice by providing primary evidence that green (vs premium) branding can trigger distinct patterns of pride in comparative decisions.
Flow of two immiscible non-Newtonian fluids in an elastic tube
Authors: Sreedharamalle Sreenadh , Baina Sumalatha , A.N.S. Srinivas
Published: June 2022

Purpose

This paper aims to investigate the flow of two-layered non-Newtonian fluids with different viscosities in an axisymmetric elastic tube.

Design/methodology/approach

A mathematical model was considered for this study to describe the flow characteristics of two-layered non- Newtonian Jeffrey fluids in an elastic tube. Because Jeffrey fluid model is a better model for the description of physiological fluid motion. Further, this model is a significant generalization of Newtonian fluid model. Analytical expressions for flux, stream functions, velocities and interface velocity have been derived in terms of elastic parameters, inlet, outlet and external pressures. The effects of various pertinent parameters on the flow behavior have been studied.

Findings

The volumetric flow rate was calculated by different models of Mazumdar (1992) and Rubinow and Keller (1972); from this it was found that the flux of Jeffrey fluid is more in the case of Rubinow and Keller model than Mazumdar. A comparative study is made between single-fluid and two-fluid models of Jeffrey fluid flows and it was observed that more flux and higher velocities were observed in the case of two-fluid model rather than single-fluid model. Furthermore, when both the Jeffrey parameter tends to zero and ratios of viscosities and radii are unity, the results in this study agree with those of Rubinow and Keller (1972).

Originality/value

To describe the fluid flow in an elastic tube with two-layered systems, the models and solutions developed here are very important. These results will be highly suitable in analyzing the rheological characteristics of blood flow in a small blood vessel because of their elastic nature.
Joint one‐dimensional inversion of magnetotelluric data and surface‐wave dispersion curves using correspondence maps
Authors: Aquino M. , Marquis G. , Vergne J.
Published: June 2022

We use a correspondence map to jointly invert surface‐wave dispersion curves and magnetotelluric data for subsurface shear velocity and resistivity but also for a possible relationship between them. Our first experiments consist of inversions of synthetic data computed from models linked by first‐ and second‐order polynomial relationships. Our methodology produces joint inversion model pairs from which 100% fit the ‘observed’ parameter relationship within a 5% error vs only 15% of the separate inversion pairs for the degree 1 relationship experiment. For the degree 2 relationship synthetic test, 80% of the joint inversion model pairs fit the ‘observed’ relationship within a 5% error while 45% of the separate inversion pairs. This reduces the number of acceptable models without compromising the data fit (‘reduction of non‐uniqueness'). The next experiment involves synthetic data from models of known physical properties, taken from well logs, but without a known relationship. We show how to select an appropriate polynomial degree for joint inversion when the relationship is unknown. Having validated the approach with synthetic cases, we apply our methodology to field data. We compare separate and joint inversions, and we find that the one‐dimensional subsurface models retrieved from joint inversions are more similar to previous models documented in the area than the separate inversion models.