bluuebunny/crossref_metadata_2025 huggingface dataset:
A Syx-RhoA-Dia1 signaling axis regulates cell cycle progression, DNA damage, and therapy resistance in glioblastoma
Authors: Lin Wan-Hsin , Feathers Ryan W. , Cooper Lisa M. , Lewis-Tuffin Laura J. , Sarkaria Jann N. , Anastasiadis Panos Z.
Published: December 2021

Glioblastomas (GBM) are aggressive tumors that lack effective treatments. Here, we show that the Rho family guanine nucleotide exchange factor Syx promotes GBM cell growth both in vitro and in orthotopic GBM patient-derived xenografts. Growth defects upon Syx depletion are attributed to prolonged mitosis, increased DNA damage, G2/M cell cycle arrest, and cell apoptosis, mediated by altered mRNA and protein expression of various cell cycle regulators. These effects are phenocopied by depletion of the Rho downstream effector Dia1 and are due at least in part to increased cytoplasmic retention and reduced activity of the YAP/TAZ transcriptional coactivators. Further, targeting Syx signaling cooperates with radiation treatment and temozolomide (TMZ) to decrease viability in GBM cells irrespective of their inherent response to TMZ. Taken together, the data indicate that a Syx-RhoA-Dia1-YAP/TAZ signaling axis regulates cell cycle progression, DNA damage, and therapy resistance in GBM and argue for its targeting for cancer treatment.

One Sentence Summary

Syx promotes growth and therapy resistance in glioblastoma.
RORA regulates neutrophil migration and activation in zebrafish
Authors: Hsu Alan Y. , Wang Tianqi , Syahirah Ramizah , Liu Sheng , Li Kailing , Zhang Weiwei , Wang Jiao , Cao Ziming , Tian Simon , Matosevic Sandro , Staiger Chris , Wan Jun , Deng Qing
Published: December 2021

Neutrophil migration and activation are essential for defense against pathogens. However, this process may also lead to collateral tissue injury. We used microRNA overexpression as a platform and discovered protein-coding genes that regulate neutrophil migration. Here we show that miR-99 decreased the chemotaxis of zebrafish neutrophils and human neutrophil-like cells. In zebrafish neutrophils, miR-99 directly targets the transcriptional factorRAR-related orphan receptor alpha (roraa). Inhibiting RORα, but not the closely related RORγ, reduced chemotaxis of zebrafish and primary human neutrophils without causing cell death, and increased susceptibility of zebrafish to bacterial infection. Expressing a dominant-negative form of Rorα or disrupting theroraalocus specifically in zebrafish neutrophils reduced cell migration. At the transcriptional level, RORα regulates transmembrane signaling receptor activity and protein phosphorylation pathways. Our results, therefore, reveal previously unknown functions of miR- 99 and RORα in regulating neutrophil migration and anti-microbial defense.
Thermal asymmetries influence effects of warming on stage and size-dependent predator-prey interactions
Authors: Pepi Adam , Hayes Tracie , Lyberger Kelsey
Published: December 2021

Climate warming directly influences the developmental and feeding rates of organisms. Changes in these rates are likely to have consequences for species interactions, particularly for organisms affected by stage- or size-dependent predation. However, because of differences in species-specific responses to warming, predicting the impact of warming on predator and prey densities can be difficult. We present a general model of stage-dependent predation with temperature-dependent vital rates to explore the effects of warming when predator and prey have different thermal optima. We found that warming generally favored the interactor with the higher thermal optimum. Part of this effect occurred due to the stage-dependent nature of the interaction, and part due to thermal asymmetries. Furthermore, large differences in thermal optima between predators and prey (i.e., a high degree of asymmetry) led to a weaker interaction. Interestingly, below the predator and prey thermal optima, warming caused prey densities to decline, even as increasing temperature improved prey performance. We also parameterize our model using values from a well-studied system,Arctia virginalisandFormica lasioides, in which the predator has a warmer optimum. Overall, our results provide a general framework for understanding stage- and temperature-dependent predator-prey interactions, and illustrate that the thermal niche of both predator and prey are important to consider when predicting the effects of climate warming.
Transcriptional shift and metabolic adaptations during Leishmania quiescence using stationary-phase and drug pressure as models
Authors: Jara Marlene , Barrett Michael , Maes Ilse , Regnault Clement , Imamura Hideo , Domagalska Malgorzata Anna , Dujardin Jean-Claude
Published: December 2021

Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavourable conditions. Quiescent cells are characterized by slow or non-proliferation and deep down-regulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but molecular and metabolic features enabling its maintenance are unknown. Here we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components such as amastins and GP63 or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. Noteworthy, among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers affords novel insights into cell regulation and shows commonly modulated features across stimuli and stages.
Protein length distribution is remarkably consistent across Life
Authors: Nevers Yannis , Glover Natasha , Dessimoz Christophe , Lecompte Odile
Published: December 2021

In every living species, the function of a protein depends on its organisation of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species. Here we evaluated this diversity by comparing protein length distribution across 2,326 species (1,688 bacteria, 153 archaea and 485 eukaryotes). We found that proteins tend to be on average slightly longer in eukaryotes than in bacteria or archaea, but that the variation of length distribution across species is low, especially compared to the variation of other genomic features (genome size, number of proteins, gene length, GC content, isoelectric points of proteins). Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting the actual variation of protein length distribution across species is even smaller. These results open the way for developing a genome annotation quality metric based on protein length distribution to complement conventional quality measures. Overall, our findings show that protein length distribution between living species is more consistent than previously thought, and provide evidence for a universal purifying selection on protein length, whose mechanism and fitness effect remain intriguing open questions.
Anti-inflammatory compounds improve spiral ganglion neuron survival after aminoglycoside-induced hair cell loss in rats
Authors: Rahman Muhammad T. , Bailey Erin M. , Gansemer Benjamin M. , Pieper Andrew , Manak J. Robert , Green Steven H.
Published: December 2021

Abstract

Spiral ganglion neurons (SGNs) relay auditory information from cochlear hair cells to the central nervous system. After hair cells are destroyed by aminoglycoside antibiotics, SGNs gradually die. However, the reasons for this cochlear neurodegeneration are unclear. We used microarray gene expression profiling to assess transcriptomic changes in the spiral ganglia of kanamycin-deafened and age-matched control rats and found that many of the genes upregulated after deafening are associated with immune/inflammatory responses. In support of this, we observed increased numbers of macrophages in the spiral ganglion of deafened rats. We also found, via CD68 immunoreactivity, an increase in activated macrophages after deafening. An increase in CD68-associated nuclei was observed by postnatal day 23, a time before significant SGN degeneration is observed. Finally, we show that the immunosuppressive drugs dexamethasone and ibuprofen, as well as the NAD salvage pathway activator P7C3, provide at least some neuroprotection post-deafening. Ibuprofen and dexamethasone also decreased the degree of macrophage activation. These results suggest that activated macrophages specifically, and perhaps a more general neuroinflammatory response, are actively contributing to SGN degeneration after hair cell loss.
Role of glycine-N-methyl transferase in human and murine nonalcoholic steatohepatitis
Authors: Quinn Connor R. , Rico Mario C. , Merali Carmen , Merali Salim
Published: December 2021

Non-alcoholic fatty liver disease (NAFLD) has become one of the most prominent forms of chronic liver disease worldwide, mirroring the obesity epidemic. NAFLD is the number one cause of chronic liver disease worldwide, with 25% of these patients developing nonalcoholic steatohepatitis (NASH). This significantly increases the risk of cirrhosis and decompensated liver failure. Past studies in rodent models have shown that the knockout of glycine-N-methyltransferase (GNMT) is associated with steatosis, fibrosis, and hepatocellular carcinoma. However, the attenuation of GNMT in subjects with NASH and the molecular basis for its impact on the disease process have yet to be elucidated. To address this knowledge gap, we show the reduction of GNMT protein levels in the liver of NASH subjects compared to healthy controls. To gain insight into the impact of decreased GNMT in the disease process, we performed global label-free proteome studies on the livers from a murine Western diet-based model of NASH. We identified the differential expression of essential proteins involved in hallmark NASH pathogenesis, including lipid metabolism, inflammation, and fibrosis. Significantly, the downregulation of GNMT, the prominent regulator of S-adenosylmethionine (AdoMet), was identified as a contributing factor to these networks, increasing fourfold in AdoMet levels. AdoMet is an essential metabolite for transmethylation reactions and a substrate for polyamine synthesis, and its levels can impact polyamine flux and generate oxidative stress. Therefore, we performed targeted proteome and metabolomics studies to show a decrease in GNMT transmethylation, an increase in flux through the polyamine pathway, and increased oxidative stress.

Abstract Figure
Epigenetic and Transcriptional Dysregulation in CD4+ T cells of Patients with Atopic Dermatitis
Authors: Eapen Amy A. , Parameswaran Sreeja , Forney Carmy , Edsall Lee E. , Miller Daniel , Donmez Omer , Dunn Katelyn , Lu Xiaoming , Granitto Marissa , Rowden Hope , Magier Adam Z. , Pujato Mario , Chen Xiaoting , Kaufman Kenneth , Bernstein David I , Devonshire Ashley L. , Rothenberg Marc E. , Weirauch Matthew T. , Kottyan Leah
Published: December 2021

Atopic dermatitis (AD) is one of the most common skin disorders in children. Disease etiology involves genetic and environmental factors, with the 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated epigenetic mechanisms that may account for genetic susceptibility in CD4+ T cells. To understand gene regulatory activity differences in peripheral blood T cells in AD, we measured chromatin accessibility (ATAC-seq), NFKB1 binding (ChIP-seq), and gene expression (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD and age-matched, non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of AD risk loci overlapping with AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NFκB DNA binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD-specific or Control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NFκB DNA binding motifs. Surprisingly, Control-specific NKFB1 ChIP-seq peaks were not enriched for NFKB1 motifs, instead containing motifs for other classes of human TFs, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of genotype-dependent chromatin accessibility at 36 AD risk variants (30% of AD risk loci) that could lead to genotype-dependent expression at these loci. We propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease and genotype-dependent chromatin accessibility involving NFKB binding.

AUTHOR SUMMARY

Stimulated CD4+ T cells from patients with atopic dermatitis have disease-dependent regulation of how gene expression is regulated. This regulation is disease dependent and the way the DNA is accessible and the transcription factor NFKB1 binds is enriched for genetic risk variants. Clinically, the CD4+ T cells in the peripheral blood of patients with AD respond to stimulation in a disease and genotype-dependent manner.
Harzianic Acid has multi-target antimicrobial activity against Gram-Positive Bacteria
Authors: Ouyang Xudong , Hoeksma Jelmer , Beenker Wouter A.G. , van der Beek Samantha , den Hertog Jeroen
Published: December 2021

The thermophilic fungus Oidiodendron flavum is a saprobe that is commonly isolated from soil. Here, we identified a Gram-positive bacteria-selective antimicrobial secondary metabolite from this fungal species, harzianic acid (HA). Using Bacillus subtilis strain 168 combined with several assays, we found that HA targeted the cell membrane, though only at high concentrations. To further study the antimicrobial activity of HA, we isolated an HA-resistant strain, Bacillus subtilis strain M9015, and discovered that the mutant has more translucent colonies, has cross resistance to rifampin, and harbors five mutations in the coding region of four distinct genes. Further analysis of these genes indicated that the mutation in atpE might be responsible for the translucency of the colony, and mutation in yusO for resistance to both HA and rifampin. We conclude that HA is a multi-target antimicrobial agent against Gram-positive bacteria.
Lateral plate mesoderm cell-based organoid system for NK cell regeneration from human pluripotent stem cells
Authors: Huang Dehao , Li Jianhuan , Hu Fangxiao , Weng Qitong , Wang Tongjie , Peng Huan , Wu Bingyan , Xia Chengxiang , Wu Hongling , Xiong Jiapin , Lin Jiali , Lin Yunqing , Wang Yao , Zhang Qi , Liu Xiaofei , Liu Lijuan , Zheng Xiujuan , Qiu Haiyan , Geng Yang , Du Xin , Wang Lei , Hao Jie , Wang Jinyong
Published: December 2021

Human pluripotent stem cell (hPSC)-induced NK (iNK) cells are a promising “off-the-shelf” cell product for universal immune therapy. Conventional methods for iNK cell regeneration from hPSCs include embryonic body-formation and feeder-based expansion steps, which bring instability, time-consuming, and high costs for manufacture. In this study, we develop an embryonic body-free, organoid aggregate method for NK cell regeneration from hPSCs. In a short time window of 27-day induction, millions of hPSC input can produce over billions of iNK cells without the necessity of NK cell-expansion feeders. The iNK cells highly express classical toxic granule proteins, apoptosis-inducing ligands, as well as abundant activating and inhibitory receptors. Functionally, the iNK cells eradicate human tumor cells by mechanisms of direct cytotoxity, apoptosis, and antibody-dependent cellular cytotoxicity. This study provides a reliable scale-up method for regenerating human NK cells from hPSCs, which promotes the universal availability of NK cell products for immune therapy.
A wipe-based stool collection and preservation kit for microbiome community profiling
Authors: Hua Hui , Meydan Cem , Afshin Evan E. , Lili Loukia , D’Adamo Christopher R. , Dudley Joel , Price Nathan D. , Zhang Bodi , Mason Christopher E.
Published: December 2021

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
A dynamic antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors
Authors: Carobbi Andrea , Di Nepi Simone , Fridman Chaya M. , Dar Yasmin , Ben-Yaakov Rotem , Barash Isaac , Salomon Dor , Sessa Guido
Published: December 2021

The type VI secretion system (T6SS) is deployed by numerous Gram-negative bacteria to deliver toxic effectors into neighboring cells. The genome of Pantoea agglomerans pv. betae (Pab) phytopathogenic bacteria contains a gene cluster (T6SS1) predicted to encode a complete T6SS. Using secretion and competition assays, we found that T6SS1 in Pab is a functional antibacterial system that allows this pathogen to outcompete rival plant-associated bacteria found in its natural environment. Computational analysis of the T6SS1 gene cluster revealed that antibacterial effector and immunity proteins are encoded within three dynamic genomic islands that harbor arrays of orphan immunity genes or toxin and immunity cassettes. Functional analysis demonstrated that the specialized antibacterial effector VgrG contains a C-terminal catalytically active glucosaminidase domain that is used to degrade prey peptidoglycan. Moreover, we confirmed that a bicistronic unit at the end of the T6SS1 cluster encodes a novel antibacterial T6SS effector and immunity pair. Together, these results demonstrate that Pab T6SS1 is an antibacterial system delivering a lysozyme-like effector to eliminate competitors, and indicate that this bacterium contains novel T6SS effectors.

Significance Statement

In this work, we describe the identification of a Pantoea agglomerans T6SS as an antibacterial determinant used by this phytopathogen to outcompete bacterial rivals. Furthermore, we provide an in-depth analysis of the T6SS gene cluster and the putative effector and immunity genes that comprise it, and we propose explanations for its dynamic evolution and effector diversification in Pantoea strains. Lastly, we experimentally validate two predicted effector and immunity pairs, and we demonstrate that one is a potent lysozyme-like toxin.
c-MAF maintains the transcriptional program of enterocyte zonation and the balance of absorptive/intestinal secretory cell types
Authors: González-Loyola Alejandra , Wyss Tania , Munoz Olivia , Prat-Luri Borja , Delorenzi Mauro , Verdeil Gregory , Petrova Tatiana V.
Published: December 2021

Small intestinal villi are structural and functional units uniquely adapted to the nutrient absorption in higher vertebrates. Villus enterocytes are organized in spatially resolved “zones” dedicated to specialized tasks such anti-bacterial protection, and absorption of amino-acids, carbohydrates and lipids. The molecular mechanisms specifying villus zonation are incompletely understood. We report that inactivation of transcription factor c-MAF, highly expressed in mature lower and mid-villus enterocytes, perturbed the entire villus zonation program, by increasing the expression of regulators of carbohydrate and bile acid metabolism and transport, while suppressing genes related to amino acid and lipid absorption. Maf inactivation under homeostatic conditions expanded tuft cells and led to compensatory gut lengthening, preventing body weight loss. However, delayed enterocyte maturation in the absence of Maf impaired body weight recovery after acute intestinal injury, resulting in reduced survival. Our results identify c-MAF as a novel regulator of small intestinal villus zonation program, while highlighting the importance of coordination between stem/progenitor and differentiation programs for intestinal regeneration.

c-MAF is expressed in differentiated enterocytes. c-MAF loss alters enterocyte zonation leading to a compensatory gut remodelling and tuft cell expansion. Upon acute intestinal injury mice deficient for c-MAF cannot recover due to lack of nutrient transport and compensatory lengthening.
The structure of HiSiaQM defines the architecture of tripartite ATP-independent periplasmic (TRAP) transporters
Authors: Peter Martin F. , Depping Peer , Schneberger Niels , Severi Emmanuele , Gatterdam Karl , Tindall Sarah , Durand Alexandre , Heinz Veronika , Koenig Paul-Albert , Geyer Matthias , Ziegler Christine , Thomas Gavin H. , Hagelueken Gregor
Published: December 2021

Tripartite ATP-independent periplasmic (TRAP) transporters are widespread in bacteria and archaea and provide important uptake routes for many metabolites 1–3. They consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains) that form a functional unit 4. While the structures of the P-domains are well-known, an experimental structure of any QM-domain has been elusive. HiSiaPQM is a TRAP transporter for the monocarboxylate sialic acid, which plays a key role in the virulence of pathogenic bacteria 5. Here, we present the first cryo-electron microscopy structure of the membrane domains of HiSiaPQM reconstituted in lipid nanodiscs. The reconstruction reveals that TRAP transporters consist of 15 transmembrane helices and are structurally related to elevator-type transporters, such as GltPh and VcINDY 6, 7. Whereas the latter proteins function as multimers, the idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. Structural and mutational analyses together with an AlphaFold 8 model of the tripartite (PQM) complex reveal the structural and conformational coupling of the substrate-binding protein to the transporter domains. Furthermore, we characterize high-affinity VHHs that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake in vivo. Thereby, they also confirm the orientation of the protein in the membrane. Our study provides the first structure of any binding-protein dependent secondary transporter and provides starting points for the development of specific inhibitors.
Characterization of the hepatitis E virus replicase
Authors: Metzger Karoline , Bentaleb Cyrine , Hervouet Kévin , Alexandre Virginie , Montpellier Claire , Saliou Jean-Michel , Ferrié Martin , Camuzet Charline , Rouillé Yves , Lecoeur Cécile , Dubuisson Jean , Cocquerel Laurence , Aliouat-Denis Cécile-Marie
Published: December 2021

Hepatitis E virus (HEV) is the major cause of acute hepatitis worldwide. HEV is a positive-sense RNA virus expressing 3 open reading frames (ORFs). ORF1 encodes the ORF1 non– structural polyprotein, the viral replicase which transcribes the full-length genome and a subgenomic RNA that encodes the structural ORF2 and ORF3 proteins. The present study is focused on the replication step with the aim to determine whether the ORF1 polyprotein is processed during the HEV lifecycle and to identify where the replication takes place inside the host cell. As no commercial antibody recognizes ORF1 in HEV-replicating cells, we aimed at inserting epitope tags within the ORF1 protein without impacting the virus replication efficacy. Two insertion sites located in the hypervariable region were thus selected to tolerate the V5 epitope while preserving HEV replication efficacy. Once integrated into the infectious full-length Kernow C-1 p6 strain, the V5 epitopes did neither impact the replication of genomic nor the production of subgenomic RNA. Also, the V5-tagged viral particles remained as infectious as the wildtype particles to Huh-7.5 cells. Next, the expression pattern of the V5-tagged ORF1 was compared in heterologous expression and replicative HEV systems. A high molecular weight protein (180 kDa) that was expressed in all 3 systems and that likely corresponds to the unprocessed form of ORF1 was detected up to 25 days after electroporation in the p6 cell culture system. Additionally, less abundant products of lower molecular weights were detected in both in cytoplasmic and nuclear compartments. Concurrently, the V5-tagged ORF1 was localized by confocal microscopy inside the cell nucleus but also as compact perinuclear substructures in which ORF2 and ORF3 proteins were detected. Importantly, using in situ hybridization (RNAScope®), positive and negative-strand HEV RNAs were localized in the perinuclear substructures of HEV-producing cells. Finally, by simultaneous detection of HEV genomic RNAs and viral proteins in these substructures, we identified candidate HEV factories.
A spatiotemporally resolved single cell atlas of the Plasmodium liver stage
Authors: Afriat Amichay , Zuzarte-Luís Vanessa , Halpern Keren Bahar , Buchauer Lisa , Marques Sofia , Lahree Aparajita , Amit Ido , Mota Maria M. , Itzkovitz Shalev
Published: December 2021

Malaria infection involves an obligatory, yet clinically silent liver stage1,2. Hepatocytes operate in repeating units termed lobules, exhibiting heterogeneous gene expression patterns along the lobule axis3, but the effects of hepatocyte zonation on parasite development have not been molecularly explored. Here, we combine single-cell RNA sequencing4 and single-molecule transcript imaging5 to characterize the host’s and parasite’s temporal expression programs in a zonally-controlled manner for the rodent malaria parasite Plasmodium berghei ANKA. We identify differences in parasite gene expression in distinct zones, and a sub-population of periportally-biased hepatocytes that harbor abortive infections associated with parasitophorous vacuole breakdown. These ‘abortive hepatocytes’ up-regulate immune recruitment and key signaling programs. They exhibit reduced levels of Plasmodium transcripts, perturbed parasite mRNA localization, and may give rise to progressively lower abundance of periportal infections. Our study provides a resource for understanding the liver stage of Plasmodium infection at high spatial resolution and highlights heterogeneous behavior of both the parasite and the host hepatocyte.
Ubiquitin Ligase SmDDA1b of Eggplant (Solanum melongena) Enhances Bacterial Wilt Resistance via SmNAC Degradation
Authors: Wang Yixi , Yan Shuangshuang , Yu Bingwei , Gan Yuwei , Lei Jiangjun , Chen Changming , Zhu Zhangsheng , Qiu Zhengkun , Cao Bihao
Published: December 2021

Bacterial wilt (BW) is a soil-borne disease that severely impacts plant growth and productivity globally. Ubiquitination plays a crucial role in disease resistance. Our previous research indicated that NAC transcription factor SmNAC negatively regulates BW resistance in eggplant (Solanum melongena). However, whether the ubiquitin/26S proteasome system (UPS) participates in this regulation is unknown.

This study used SmNAC as a bait to screen eggplant cDNA library and obtained SmDDA1b, an E3 ubiquitin ligase. Subcellular location and bimolecular fluorescence complementation assays revealed that SmDDA1b could interact with SmNAC in the nucleus. The in vivo and in vitro ubiquitination experiments indicated that SmDDA1b can degrade SmNAC through UPS. However, the discovery of negative regulation of SmDDA1b expression by SmNAC showed that there was a negative feedback loop between SmNAC and SmDDA1b in eggplant.

The SmDDA1b-overexpressed lines showed a higher BW resistance associated with high expression levels of salicylic acid (SA)-related genes and SA content than the wild-type lines. However, SmDDA1b-silencing lines showed the opposite results, indicating that SmDDA1b is a positive regulatory gene for BW resistance.

This study provides a candidate gene that can enhance BW resistance in eggplants. In addition, it provides insight into a mechanism that promotes plant disease resistance via the SmDDA1b-SmNAC-SA pathway.
Plasmodium SAS4/CPAP is a flagellum basal body component during male gametogenesis, but is not essential for parasite transmission
Authors: Zeeshan Mohammad , Brady Declan , Markus Robert , Vaughan Sue , Ferguson David , Holder Anthony A. , Tewari Rita
Published: December 2021

The centriole/basal body (CBB) is an evolutionarily conserved organelle acting as a microtubule organising centre (MTOC) to nucleate cilia, flagella and the centrosome. SAS4/CPAP is a conserved component associated with BB biogenesis in many model flagellated cells. Plasmodium, a divergent unicellular eukaryote and causative agent of malaria, displays an atypical closed mitosis with an MTOC, reminiscent of the acentriolar MTOC, embedded in the nuclear membrane at most proliferative stages. Mitosis during male gamete formation is accompanied by flagellum formation: within 15 minutes, genome replication (from 1N to 8N) and three successive rounds of mitosis without nuclear division occur, with coordinated axoneme biogenesis in the cytoplasm resulting in eight flagellated gametes. There are two MTOCs in male gametocytes. An acentriolar MTOC located with the nuclear envelope and a centriolar MTOC (basal body) located within the cytoplasm that are required for flagellum assembly. To study the location and function of SAS4 during this rapid process, we examined the spatial profile of SAS4 in real time by live cell imaging and its function by gene deletion. We show its absence during asexual proliferation but its presence and coordinated association and assembly of SAS4 with another basal body component, kinesin8B, which is involved in axoneme biogenesis. In contrast its separation from the nuclear kinetochore marker NDC80 suggests that SAS4 is part of the basal body and outer centriolar MTOC residing in the cytoplasm. However, deletion of the SAS4 gene produced no phenotype, indicating that it is not essential for male gamete formation or parasite transmission through the mosquito.
LINE-1 activation in the cerebellum drives ataxia
Authors: Takahashi Takehiro , Kudo Eriko , Song Eric , Carvalho Fernando , Yasumoto Yuki , Kong Yong , Park Annsea , Stoiljkovic Milan , Gao Xiao-Bing , Shanabrough Marya , Szigeti-Buck Klara , Liu Zhong-Wu , Zhang Yalan , Sulkowski Parker , Glazer Peter M. , Kaczmarek Leonard K. , Horvath Tamas L. , Iwasaki Akiko
Published: December 2021

Previous studies have revealed that dysregulation of long interspersed nuclear element 1 (LINE-1), a dominant class of transposable elements in the human genome, correlates with neurodegeneration1–3. Yet whether LINE-1 dysregulation is causal to disease pathogenesis has not been proven directly. Here, we demonstrate that expression of evolutionarily younger LINE-1 families is elevated in the cerebella of ataxia telangiectasia (AT) patients, which was correlated with extensive downregulation of epigenetic silencers. To examine whether LINE-1 activation causes neurologic disease, we established an approach to directly target and activate the promoter of a young family of LINE-1 in mice. LINE-1 activation in the cerebellum was sufficient to lead to robust progressive ataxia. Purkinje cells in the diseased mice exhibited marked electrophysiological dysfunctions and degeneration with a significant accumulation of cytoplasmic ribonucleoprotein LINE-1Orf1p aggregates, endoplasmic reticulum (ER) stress, and DNA damage. Treatment with lamivudine, a nucleoside reverse transcriptase inhibitor, blunted the disease progression by reducing DNA damage, attenuating gliosis and interferon gene signature, and recovering the loss of key functional molecules for calcium homeostasis in Purkinje cells. This study provides direct evidence that young LINE-1 activation drives ataxia phenotype, and points to its pleiotropic effects leading to DNA damage, inflammation, and dysfunction and degeneration of neurons.
Drosophila renal stem cells enhance fitness by delayed remodeling of adult Malpighian tubules
Authors: Wang Chenhui , Spradling Allan C.
Published: December 2021

Drosophila renal stem cells (RSCs) contradict the common expectation that stem cells maintain tissue homeostasis. RSCs are abundant, quiescent and confined to the peri-ureter region of the kidney-like Malpighian tubules (MTs). Although derived during pupation like intestinal stem cells, RSCs initially remodel the larval MTs only near the intestinal junction. However, following adult injury to the ureter by xanthine stones, RSCs remodel the damaged region in a similar manner. Thus, RSCs represent stem cells encoding a developmental redesign. The remodeled tubules have a larger luminal diameter and shorter brush border, changes linked to enhanced stone resistance. However, RSC-mediated modifications also raise salt sensitivity and reduce fecundity. Our results suggest that RSCs arose by arresting developmental progenitors to preserve larval physiology until a time in adulthood when it becomes advantageous to complete development by RSC activation.

One-Sentence Summary

Activated Drosophila renal stem cells rebuild the adult Malphigian tubules using a less efficient but more stone-resistant design.
Progressive polysomal association of Upf1, Upf2, and Upf3 as ribosomes traverse mRNA coding regions
Authors: Ganesan Robin , Mangkalaphiban Kotchaphorn , Baker Richard E. , He Feng , Jacobson Allan
Published: December 2021

Upf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.
Striatum-projecting prefrontal cortex neurons support working memory maintenance
Authors: Chernysheva Maria , Sych Yaroslav , Fomins Aleksejs , Alatorre Warren José Luis , Lewis Christopher , Capdevila Laia Serratosa , Boehringer Roman , Amadei Elizabeth A. , Grewe Benjamin F. , O’Connor Eoin C. , Hall Benjamin J. , Helmchen Fritjof
Published: December 2021

The medial prefrontal cortex (mPFC) and the dorsomedial striatum (dmStr) are linked to working memory (WM) but how striatum-projecting mPFC neurons contribute to WM encoding, maintenance, or retrieval remains unclear. Here, we probed mPFC→dmStr pathway function in freely-moving mice during a T-maze alternation test of spatial WM. Fiber photometry of GCaMP6m-labeled mPFC→dmStr projection neurons revealed strongest activity during the delay period that requires WM maintenance. Demonstrating causality, optogenetic inhibition of mPFC→dmStr neurons only during the delay period impaired performance. Conversely, enhancing mPFC→dmStr pathway activity—via pharmacological suppression of HCN1 or by optogenetic activation during the delay— alleviated WM impairment induced by NMDA receptor blockade. Consistently, cellular-resolution miniscope imaging resolved preferred activation of >50% mPFC→dmStr neurons during WM maintenance. This subpopulation was distinct from neurons showing preference for encoding and retrieval. In all periods, including the delay, neuronal sequences were evident. Striatum-projecting mPFC neurons thus critically contribute to spatial WM maintenance.
Social migratory connectivity: do birds that socialize in winter breed together?
Authors: Block Theadora A. , Lyon Bruce E. , Mikalonis Zachary , Chaine Alexis S. , Shizuka Daizaburo
Published: December 2021

Researching the complete life cycles of migratory animals is essential for understanding conservation and population dynamics. Many studies focus on the breeding season, but surviving winter is equally important. Living in groups during winter can play a vital role as social connections within groups can provide many benefits such as protection from predators and increased access to resources. However, it is often unknown how social connections change across seasons in migratory animals. We focus on social connections in a migratory bird and ask whether social connections in winter continue during breeding. Golden-crowned sparrows have distinct, stable winter communities which include both site and group fidelity across years: birds almost always rejoin the same social community each year. If these birds have social connectivity across migration, we would expect individuals that associate in winter would also associate together on their breeding grounds. Our small-scale GPS tagging study combined with intensive social behavior data revealed that sparrows in the same tightly-knit winter community migrated to highly disparate locations during summer, showing that social connections in winter do not continue in summer. This suggests that golden-crowned sparrows have entirely separate social structures across seasons and that long-term social memories allow them to reform stable groups each winter.
Verification of Hypsibius exemplaris Gąsiorek et al., 2018 (Eutardigrada; Hypsibiidae) application in anhydrobiosis research
Authors: Poprawa Izabela , Bartylak Tomasz , Kulpla Adam , Erdmann Weronika , Roszkowska Milena , Chajec Łukasz , Kaczmarek Łukasz , Karachitos Andonis , Kmita Hanna
Published: December 2021

Anhydrobiosis is considered to be an adaptation of important applicative implications because it enables resistance to the lack of water. The phenomenon is still not well understood at molecular level. Thus, a good model invertebrate species for the research is required. The best known anhydrobiotic invertebrates are tardigrades (Tardigrada), considered to be toughest animals in the world. Hypsibius. exemplaris is one of the best studied tardigrade species, with its name “exemplaris” referring to the widespread use of the species as a laboratory model for various types of research. However, available data suggest that anhydrobiotic capability of the species may be overestimated. Therefore, we determined anhydrobiosis survival by Hys. exemplaris specimens using three different anhydrobiosis protocols. We also checked ultrastructure of storage cells within formed dormant structures (tuns) that has not been studied yet for Hys. exemplaris. These cells are known to support energetic requirements of anhydrobiosis. The obtained results indicate that Hys. exemplaris appears not to be a good model species for anhydrobiosis research.
Volumetric assessment and longitudinal changes of brain structures in formalinized Beagle brains
Authors: Del Signore Francesca , Arribarat Germain , Della Salda Leonardo , Mogicato Giovanni , Deviers Alexandra , Cartiaux Benjamin , Vignoli Massimo , Peran Patrice , de Pasquale Francesco
Published: December 2021

High field MRI represents an advanced technique both for diagnostic and research purposes on animal models such as the Beagle dog. The increasing interest in non-invasive neuroscience, aging, and neuropathological research led to a need of reference values (in terms of volumetric assessment) for the typical brain structures involved and, nowadays, several canine brain MRI atlases have been provided. Since no reports are available regarding the measurements reproducibility and few information are available about formalin fixation effect on brain structures when applied to MRI segmentation, we assessed the segmentation variability of selected structures as a function of the operator (two operators segmented the same data) and their intrinsic variability within a sample of 11 Beagle dogs (9 females and 2 males, 1.6 ± 0.2 years). Then, we analyzed for one further Beagle dog (2 years old) the longitudinal changes in the brain segmentations of these structures corresponding four conditions: in vivo, post mortem (after euthanasia), ex vivo (brain extracted and studied after 1 month in formalin and after 11 months); all the MRI images were collected with a 3 T MRI scanner. Our findings suggest that the segmentation procedure can be considered overall reproducible since only slight statistical differences were detected, apart from the ventricles.

Furthermore, in the post mortem/ ex vivo comparison, the majority of the structures showed a higher contrast leading to more reproducible segmentations across operators and a net increase of volume of the studied structures; this could be justified by the intrinsic relaxation time changes observed as a consequence of formalin fixation, that led to an improvement of brain structures visualization and then segmentation.

To conclude, MRI based segmentation seems to be a useful and accurate tool that allows longitudinal studies, especially when applied to formalin fixed brains.
Age-related decline in function of ON and OFF visual pathways
Authors: Hathibelagal Amithavikram R , Prajapati Vishal , Jayagopi Indrani , Jalali Subhadra , Ganeshrao Shonraj Ballae
Published: December 2021

Purpose

Simple psychophysical paradigm is available as a digital application in iOS devices such as iPad to measure the function of ON and OFF visual pathways. However, an age-matched normative database is not readily available. The purpose of the study is to evaluate the response of ON and OFF visual pathways as a function of age.

Methods

158 normal healthy adults (84 males and 74 females) whose age ranged 18-80 years participated in the study. None of them had any ocular disease (except cataract of grade II or less) and visual acuity of ≤ 20/25. Monocular testing (only one eye) was performed on the ‘EyeSpeed’ application on an iPad at 40cm distance. The targets ranged between 1 to 3 light or dark squares presented randomly in a noise background and participants responded by indicating the number of squares by touching the screen as fast as possible. The main outcome variables are reaction time, accuracy and performance index (1 / speed * accuracy).

Results

The median reaction time was shorter (Median (IQR): 1.53s (0.49) [dark] Vs 1.76s (0.58) [light], p < 0.001) and accuracy was higher (97.21% (3.30) [dark] Vs 95.15% (5.10) [light], p < 0.001) for dark targets than the light targets. Performance index and reaction time for both target types significantly correlated with age (ρ = −0.41 to −0.43; p < 0.001).

Conclusions

This normative database will be useful to quantify disease-specific defects. More importantly, the ON pathway function can potentially serve as a surrogate for rod photoreceptor function.
The invigorating influence of relationship marketing on purchase intention in fine arts sector
Authors: Moslehpour Massoud , Song Chanho , Tran Anh Tung , Wong Wing-Keung , Enkhtaivan Ochirt
Published: December 2021

Purpose

This study aims to determine the influence of relationship marketing on consumer behavior in the fine arts sector. Specifically, it examines the relationship marketing dynamics that significantly impact art enthusiasts' intention to purchase and their satisfaction with the artist.

Design/methodology/approach

The proposed model was tested through the “structural equation modeling” technique to explain how and to what extent each variable affected purchase intention and satisfaction. Using a paper-based and online survey method to gather data, the authors analyzed 303 responses from art students, art collectors and art dealers in Mongolia. Eight hypotheses, including two mediating hypotheses, were developed and tested.

Findings

The results indicated that relationship investment and communication significantly influence trust, satisfaction and purchase intention, while trust significantly influences satisfaction and purchase intention. The study also assessed the vital role of trust as a mediator.

Practical implications

The study's results provide insights that may help artists, art collectors and art dealers promote and improve the sales of their art products. The interactions demonstrated between the construct reveal essential implications for art marketers interested in relationship marketing strategies.

Originality/value

This study is the first to explore the application of relationship marketing in the fine arts industry.
Key factors in tourism management to improve competitiveness in Latin America
Authors: Guaita Martínez José Manuel , Serdeira Azevedo Paula , Martín Martín José María , Puertas Medina Rosa María
Published: December 2021

Purpose

This paper analyzes tourism competitiveness in Latin America, providing a country-level ranking of tourism competitiveness. The study also identifies which areas of management to focus on in order to increase competitiveness in each case.

Design/methodology/approach

The study is based on the variables used by the World Economic Forum (WEF) to measure tourism competitiveness. The DP2 distance method is used to create a synthetic indicator. This method helps identify which areas best explain differences in competitiveness between countries.

Findings

In tourism, the most competitive Latin American countries are Costa Rica, Chile, Panama, Mexico and Uruguay. The areas that best explain the differences between countries relate to cultural and natural resources, the implementation of information and communication technologies (ICTs), international openness and transport infrastructure. These are therefore priority areas for tourism managers.

Practical implications

This paper provides detailed analysis for each country. The situation in each country is presented in terms of the key areas highlighted by the analysis. This approach can aid the individual decisions of companies and public managers, thus enhancing tourism competitiveness. This greater competitiveness can strengthen the tourism sector, which is crucial in uncertain times.

Originality/value

Based on a synthetic indicator, this research offers the first country-level analysis of tourism competitiveness in Latin America. The study is also novel in its ability to detect the areas where action should be taken to improve tourism competitiveness. This analysis offers an alternative to the WEF Travel and Tourism Competitiveness Index (TTCI), which has certain weaknesses. The results can help enhance tourism competitiveness in Latin American countries through the specific recommendations presented in this paper.