bluuebunny/crossref_metadata_2025 huggingface dataset:
Presence of additionalP. vivaxmalaria in Duffy negative individuals from Southwestern Nigeria
Authors: Oboh Mary Aigbiremo , Singh Upasana Shyamsunder , Nidaye Daouda , Badiane Aida S. , Ali Anwar , Bharti Praveen Kumar , Das Aparup
Published: October 2019

Malaria in sub-Saharan Africa (sSA) is thought to be hugely caused byPlasmodium falciparumand very infrequently byP. ovale, P. malariae, withP. vivaxnot even being considered to be of any significant role. However, with the availability of very sensitive diagnostic tool, it has become more clear that, the percentage of non-falciparum malaria in this sub-region has been underestimated.P. vivaxwas historically thought to be absent in sSA due to the high prevalence of the Duffy null antigen in individuals residing here. Nevertheless, recent studies reporting the detection of vivax malaria in Duffy-negative individuals challenges this notion. Following our earlier report ofP. vivaxin Duffy-negative individuals, we have re-assessed all previous samples following the classical PCR method and sequencing to confirm both single/mixed infections as well as the Duffy status of the individuals.

Interestingly, fifteen additionalPlasmodiuminfections were detected, representing 5.9% in prevalence from our earlier work. In addition,P. vivaxrepresents 26.7% (4/15) of the new isolates collected in Nigeria. Sequencing results confirmed, all vivax isolates as truly vivax malaria and their Duffy status to be that of the Duffy-negative genotype. The identification of more vivax isolates among these Duffy-negative individuals from Nigeria, substantiate the expanding body of evidence of the ability ofP. vivaxto infect RBCs that do not express the DARC gene. Hence, such geno-epidemiological study should be conducted at the national level in order to evaluate the actual burden ofP. vivaxin the country.
Localization of BCR-ABL to stress granules contributes to its oncogenic function
Authors: Kashiwagi Sayaka , Fujioka Yoichiro , Kondo Takeshi , Satoh Aya O. , Yoshida Aiko , Fujioka Mari , Sasajima Hitoshi , Amano Maho , Teshima Takanori , Ohba Yusuke
Published: October 2019

The oncogenic tyrosine kinase BCR-ABL activates a variety of signaling pathways and plays a causative role in the pathogenesis of chronic myelogenous leukemia (CML); however, the subcellular distribution of this chimeric protein remains controversial. Here, we report that BCR-ABL is localized to stress granules and that its granular localization contributes to BCR-ABL-dependent leukemogenesis. BCR-ABL-positive granules were not colocalized with any markers for membrane-bound organelles but were colocalized with HSP90a, a component of RNA granules. The number of such granules increased with thapsigargin treatment, confirming that the granules were stress granules. Given that treatment with the ABL kinase inhibitor imatinib and elimination of the N-terminal region of BCR-ABL abolished granule formation, kinase activity and the coiled-coil domain are required for granule formation. Whereas wild-type BCR-ABL rescued the growth defect in IL-3-depleted Ba/F3 cells, mutant BCR-ABL lacking the N-terminal region failed to do so. Moreover, forced tetramerization of the N-terminus-deleted mutant could not restore the growth defect, indicating that granule formation, but not tetramerization, through its N-terminus is critical for BCR-ABL-dependent oncogenicity. Our findings together provide new insights into the pathogenesis of CML by BCR-ABL and open a window for developing novel therapeutic strategies for this disease.
Opening Pandora’s Box: Distribution of Plasmodium gametocytes in bloodstream
Authors: Pigeault R. , Isaïa J. , Yerbanga R. S. , Kounbobr R. D. , Ouedraogo J.B. , Cohuet A. , Lefèvre T. , Christe P.
Published: October 2019

Malaria, a vector borne disease caused by Plasmodium spp., remains a major global cause of morbidity and mortality. Optimization of the disease control strategies requires a thorough understanding of the fundamental processes underlying parasite transmission. Although the number of transmissible stages of Plasmodium (gametocyte) in human blood is frequently used as an indicator of human-to-mosquito transmission potential, this relationship is not always clear. Important efforts have been made to develop molecular tools to fine-tune gametocyte densities estimation and therefore improve the prediction of mosquito infection rates, but a significant level of uncertainty around this estimate remains. Here we show with both human and avian malaria system that the within-vertebrate host distribution of gametocytes could explain much of this uncertainty. By comparing gametocyte densities in bloodstream between different body parts, we found a difference by nearly 50% in humans and by more than 15% in birds. An estimation of gametocyte density from only one blood sample, as is usually the case, could therefore drastically over- or underestimated the infectivity of gametocyte carriers. This might have important consequences on the epidemiology of the disease since we show, using the avian malaria system, that this variation influences the transmission of the parasite to the mosquito vector. In the light of our results, we argue that it is essential to consider the heterogeneous distribution of gametocyte to improve human diagnosis, identify infectious reservoirs and to test new malaria control strategies.
p38-mitogen activated kinases mediate a developmental regulatory response to amino acid depletion and associated oxidative stress in mouse blastocyst embryos
Authors: Bora Pablo , Thamodaran Vasanth , Šušor Andrej , Bruce Alexander W.
Published: October 2019

Maternal starvation coincident with preimplantation development has profound consequences for placental-foetal development, with various identified pathologies persisting/manifest in adulthood; the ‘Developmental Origin of Health and Disease’ (DOHaD) hypothesis/model. Despite evidence describing DOHaD-related incidence, supporting mechanistic and molecular data relating to preimplantation embryos themselves are comparatively meagre. We recently identified the classically recognised stress-related p38-mitogen activated kinases (p38-MAPK) as regulating formation of the extraembryonic primitive endoderm (PrE) lineage within mouse blastocyst inner cell mass (ICM). Thus, we wanted to assay if PrE differentiation is sensitive to amino acid availability, in a manner regulated by p38-MAPK. Although blastocysts appropriately mature, without developmental/morphological or cell fate defects, irrespective of amino acid supplementation status, we found the extent of p38-MAPK inhibition induced phenotypes was more severe in the absence of amino acid supplementation. Specifically, both PrE and epiblast (EPI) ICM progenitor populations remained unspecified and there were fewer cells and smaller blastocyst cavities. Such phenotypes could be ameliorated, to resemble those observed in groups supplemented with amino acids, by addition of the anti-oxidant NAC (N-acetyl-cysteine), although PrE differentiation deficits remained. Therefore, p38-MAPK performs a hitherto unrecognised homeostatic early developmental regulatory role (in addition to direct specification of PrE), by buffering blastocyst cell number and ICM cell lineage specification (relating to EPI) in response to amino acid availability, partly by counteracting induced oxidative stress; with clear implications for the DOHaD model.
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM
Authors: Uchański Tomasz , Masiulis Simonas , Fischer Baptiste , Kalichuk Valentina , Wohlkönig Alexandre , Zögg Thomas , Remaut Han , Vranken Wim , Aricescu A. Radu , Pardon Els , Steyaert Jan
Published: October 2019

Nanobodies (Nbs) are popular and versatile tools for structural biology because they have a compact single immunoglobulin domain organization. Nbs bind their target proteins with high affinities while reducing their conformational heterogeneity, and they stabilize multi-protein complexes. Here we demonstrate that engineered Nbs can also help overcome two major obstacles that limit the resolution of single-particle cryo-EM reconstructions: particle size and preferential orientation at the water-air interface. We have developed and characterised novel constructs, termed megabodies, by grafting Nbs into selected protein scaffolds to increase their molecular weight while retaining the full antigen binding specificity and affinity. We show that the megabody design principles are applicable to different scaffold proteins and recognition domains of compatible geometries and are amenable for efficient selection from yeast display libraries. Moreover, we used a megabody to solve the 2.5 Å resolution cryo-EM structure of a membrane protein that suffers from severe preferential orientation, the human GABAAβ3 homopentameric receptor bound to its small-molecule agonist histamine.
Increased expression of genetically-regulatedFLT3implicated in Tourette’s Syndrome
Authors: Liao Calwing , Vuokila Veikko , Catoire Hélène , Akçimen Fulya , Ross Jay P. , Bourassa Cynthia V. , Dion Patrick A. , Meijer Inge A. , Rouleau Guy A.
Published: October 2019

Tourette’s Syndrome (TS) is a neurodevelopmental disorder that is characterized by motor and phonic tics. A recent TS genome-wide association study (GWAS) identified a genome-wide significant locus. However, determining the biological mechanism of GWAS signals remains difficult. Here, we conduct a TS transcriptome-wide association study (TWAS) consisting of 4,819 cases and 9,488 controls and found that increased expression ofFLT3in the dorsolateral prefrontal cortex (DLPFC) is associated with TS. We further showed that there is global dysregulation ofFLT3across several brain regions and probabilistic causal fine-mapping of the TWAS signal prioritizesFLT3with a posterior inclusion probability of 0.849. We validated the gene’s expression in 100 lymphoblastoid cell lines, establishing that TS cells had a 1.72 increased fold change compared to controls. A phenome-wide association study points towardsFLT3having links with immune-related pathways such as monocyte count. We also identify several splicing events inMPHOSPH9, CSGALNACT2andFIP1L1associated with TS, which are also implicated in immune function. This analysis of expression and splicing begins to explore the biology of TS GWAS signals.
A transcription start site map in human pancreatic islets reveals functional regulatory signatures
Authors: Varshney Arushi , Kyono Yasuhiro , Elangovan Venkateswaran Ramamoorthi , Wang Collin , Erdos Michael R. , Narisu Narisu , Albanus Ricardo D’Oliveira , Orchard Peter , Stitzel Michael L. , Collins Francis S. , Kitzman Jacob O. , Parker Stephen C. J.
Published: October 2019

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validate transcriptional enhancer activity (5% FDR) for 2,279 of 3,378 (~68%) tested islet CAGE elements. TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting functional enhancers at GWAS loci.
Striatal iron content is linked to reduced fronto-striatal brain function under working memory load
Authors: Rodrigue Karen M. , Daugherty Ana M. , Foster Chris M. , Kennedy Kristen M.
Published: October 2019

Non-heme iron accumulation contributes to age-related decline in brain structure and cognition via a cascade of oxidative stress and inflammation, although its effect on brain function is largely unexplored. Thus, we examine the impact of striatal iron on dynamic range of BOLD modulation to working memory load. N=166 healthy adults (age 20-94) underwent cognitive testing and an imaging session including n-back (0-, 2-, 3-, and 4-back fMRI), R2*-weighted imaging, and pcASL to measure cerebral blood flow. A statistical model was constructed to predict voxelwise BOLD modulation by age, striatal iron content and an age × iron interaction, controlling for cerebral blood flow, sex, and task response time. A significant interaction between age and striatal iron content on BOLD modulation was found selectively in the putamen, caudate, and inferior frontal gyrus. Greater iron was associated with reduced modulation to difficulty, particularly in middle-aged and younger adults with greater iron content. Further, iron-related decreases in modulation were associated with poorer executive function in an age-dependent manner. These results suggest that iron may contribute to differences in functional brain activation prior to older adulthood, highlighting the potential role of iron as an early factor contributing to trajectories of functional brain aging.
Identification of drug modifiers for RYR1 related myopathy using a multi-species discovery pipeline
Authors: Volpatti Jonathan , Endo Yukari , Groom Linda , Brennan Stephanie , Noche Ramil , Zuercher William , Roy Peter , Dirksen Robert T. , Dowling James J.
Published: October 2019

Ryanodine receptor type I-related myopathies (RYR1-RMs) represent the largest group of non-dystrophic myopathies. RYR1-RMs are associated with severe disabilities and early mortality; despite these facts, there are currently no available treatments. The goal of this study was to identify new therapeutic targets for RYR1-RMs. To accomplish this, we developed a novel discovery pipeline using nematode, zebrafish, and mammalian cell models of the disease. We first performed large-scale drug screens inC. elegansand zebrafish. 74 positive hits were identified inC. elegans, while none were uncovered in the zebrafish. Targeted testing of these hits in zebrafish yielded positive results for two compounds. We examined these compounds using newly createdRyr1knockout C2C12 cells, and found that p38 inhibition impaired caffeine-induced Ca2+release. Lastly, we tested one p38 inhibitor in myotubes fromRyr1Y524S/+(YS) mice, and demonstrated that it blunts the aberrant temperature-dependent increase in resting Ca2+in these cells. In all, we developed a unique platform for RYR1-RM therapy development that is potentially applicable to a broad range of neuromuscular disorders.
The interplay of top-down focal attention and the cortical tracking of speech
Authors: Lesenfants D , Francart T
Published: October 2019

Abstract

Many active neuroimaging paradigms rely on the assumption that the participant sustains attention to a task. However, in practice, there will be momentary distractions, potentially influencing the results. We investigated the effect of focal attention, objectively quantified using a measure of brain signal entropy, on cortical tracking of the speech envelope. The latter is a measure of neural processing of naturalistic speech. We let participants listen to 44 minutes of natural speech, while their electroencephalogram was recorded, and quantified both entropy and cortical envelope tracking. Focal attention affected the later brain responses to speech, between 100 and 300 ms latency. By only taking into account periods with higher attention, the measured cortical speech tracking improved by 47%. This illustrates the impact of the participant’s active engagement in the modeling of the brain-speech response and the importance of accounting for it. Our results suggests a cortico-cortical loop that initiates during the early-stages of the auditory processing, then propagates through the parieto-occipital and frontal areas, and finally impacts the later-latency auditory processes in a top-down fashion. The proposed framework could be transposed to other active electrophysiological paradigms (visual, somatosensory, etc) and help to control the impact of participants’ engagement on the results.
Scale-resolved analysis of brain functional connectivity networks with spectral entropy
Authors: Nicolini Carlo , Forcellini Giulia , Minati Ludovico , Bifone Angelo
Published: October 2019

Functional connectivity is derived from inter-regional correlations in spontaneous fluctuations of brain activity, and can be represented in terms of complete graphs with continuous (real-valued) edges. The structure of functional connectivity networks is strongly affected by signal processing procedures to remove the effects of motion, physiological noise and other sources of experimental error. However, in the absence of an established ground truth, it is difficult to determine the optimal procedure, and no consensus has been reached on the most effective approach to remove nuisance signals without unduly affecting the network intrinsic structural features. Here, we use a novel information-theoretic approach, based on von Neumann entropy, which provides a measure of information encoded in the networks at different scales. We also define a measure of distance between networks, based on information divergence, and optimal null models appropriate for the description of functional connectivity networks, to test for the presence of nontrivial structural patterns that are not the result of simple local constraints. This formalism enables a scale-resolved analysis of the distance between an empirical functional connectivity network and its maximally random counterpart, thus providing a means to assess the effects of noise and image processing on network structure.

We apply this novel approach to address a few open questions in the analysis of brain functional connectivity networks. Specifically, we demonstrate a strongly beneficial effect of network sparsification by removal of the weakest links, and the existence of an optimal threshold that maximizes the ability to extract information on large-scale network structures. Additionally, we investigate the effects of different degrees of motion at different scales, and compare the most popular processing pipelines designed to mitigate its deleterious effect on functional connectivity networks.
Q203 containing fully intermittent oral regimens exhibited high sterilizing activity against Mycobacterium ulcerans in mice
Authors: Chauffour Aurélie , Robert Jérôme , Veziris Nicolas , Aubry Alexandra , Pethe Kevin , Jarlier Vincent
Published: October 2019

Buruli ulcer (BU), caused by Mycobacterium ulcerans is currently treated by a daily combination of rifampin and either injectable streptomycin or oral clarithromycin. An intermittent oral regimen would facilitate the treatment supervision. We first evaluated the bactericidal activity of newer antimicrobials against M. ulcerans using a BU animal model. The imidazopyridine amine Q203 exhibited high bactericidal activity whereas tedizolid (oxazolidinone close to linezolid), selamectine and ivermectine (avermectine compound) and the benzothiazinone PBTZ169 were not active. Consequently, Q203 was evaluated for its bactericidal and sterilizing activities in combined intermittent regimens. Q203 given twice a week in combination with one of the other long half-life compounds, rifapentine or bedaquiline, sterilized the mice footpads in 8 weeks, i.e. after a total of only 16 doses, and prevented relapse during a period of 20 weeks after stopping the treatment. These results are very promising for future intermittent oral regimens which would greatly simplify BU treatments in the field.

Author summary

The current treatment of Buruli ulcer (BU), infection caused by Mycobacterium ulcerans is based on a daily antibiotic combination of rifampin associated with streptomycin or clarithromycin. A shorter or intermittent treatment without an injectable drug would clearly simplify the management on the field. We evaluated the bactericidal activity of several new antimicrobials drugs in a mice model of BU and found that the Q203 exhibited the highest bactericidal effect. We subsequently identified new antibiotic combinations containing Q203 with high sterilizing activity when administrated twice a week for 8 weeks.
Championing Health Promotion through Group Patient and Family Education Activities in the Outpatient Department of a Tertiary Care Hospital
Authors: Almahameed Mahmoud Ibrahim , Kakish Shadi F. , Abu-Shaheen Amani
Published: October 2019

Background

Health education involves not only providing relevant information but also facilitating health-related behavior change. Patient education during the waiting period plays an essential role in promoting health and improving patient satisfaction rates.

Objective

To promote health by educating patients and their companions during their waiting period at the King Fahad Medical City (KFMC) Hospital, Riyadh, with the help of nurses and assess their satisfaction rate.

Methods

A cross-sectional study, including patients and their companions in the waiting rooms of the various OPD’s, was conducted. Group teaching sessions were conducted, followed by the assessment of patient and nurse satisfaction rate, and compliance rate using evaluation forms. Pre-implementation surveys were conducted to assess the drawbacks, based on which procedure was modified, and feedback was recorded using an electronic iPad. Data were collected with the help of questionnaires filled at the end of each teaching session and analyzed using descriptive analysis. Results of both the assessment and re-assessment were compared in terms of the number of attendees.

Results

There was an improvement in number of attendees (4362 vs. 3392), patient satisfaction rate (90% vs. 78%), nurse satisfaction rate (83.09% vs. 33.18%) and compliance rate (100% vs. 65%) post-modifications. Few loopholes in terms of inappropriate environment and time of the lecture were also observed.

Conclusion

The health educators can assist people in achieving their health goals by organizing structured health education activities, providing appropriate health education materials, and effective training. However, the satisfaction rates of people and health educators should be assessed by conducting routine feedback surveys.
The origin and diversification of pteropods predate past perturbations in the Earth’s carbon cycle
Authors: Peijnenburg Katja T.C.A. , Janssen Arie W. , Wall-Palmer Deborah , Goetze Erica , Maas Amy , Todd Jonathan A. , Marlétaz Ferdinand
Published: October 2019

Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification (OA). Their thin aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in Earth’s carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset incorporating 21 new species and new fossil evidence. In agreement with traditional taxonomy, we recovered the first molecular support for a division between sea butterflies (Thecosomata: mucus-web feeders) and sea angels (Gymnosomata: active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled and unshelled groups, diverged in the mid to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene Eocene Thermal Maximum (PETM), which is the closest analogue to modern-day ocean acidification and warming. Our findings indicate that aragonitic calcifiers have been resilient to extreme perturbations in the Earth’s carbon cycle over evolutionary timescales.
Interactions of a bacterial RND transporter with a transmembrane small protein in a lipid environment
Authors: Du Dijun , Neuberger Arthur , Orr Mona Wu , Newman Catherine E. , Hsu Pin-Chia , Samsudin Firdaus , Szewczak-Harris Andrzej , Ramos Leana M. , Debela Mekdes , Khalid Syma , Storz Gisela , Luisi Ben F.
Published: October 2019

The small protein AcrZ inEscherichia coliinteracts with the transmembrane portion of the multidrug efflux pump AcrB and increases the resistance of the bacterium to a subset of the antibiotic substrates of that transporter. It is not clear how the physical association of the two proteins selectively changes activity of the pump for defined substrates. Here, we report cryo-EM structures of AcrB and the AcrBZ complex in lipid environments, and comparisons suggest that conformational changes occur in the drug binding pocket as a result of AcrZ binding. Simulations indicate that cardiolipin preferentially interacts with the AcrBZ complex, due to increased contact surface, and we observe that the drug sensitivity of bacteria lacking AcrZ is exacerbated when combined with cardiolipin deficiency. Taken together, the data suggest that AcrZ and lipid cooperate to allosterically modulate the activity of AcrB. This mode of regulation by a small protein and lipid may occur for other membrane proteins.
Genomic evidence for a hybrid origin of the yeast opportunistic pathogenCandida albicans
Authors: Mixão Verónica , Gabaldón Toni
Published: October 2019

Opportunistic yeast pathogens are of increasing medical concern.Candida albicans, the species with the highest incidence, is a natural commensal of humans that can adopt a pathogenic behaviour. This species is highly heterozygous, is an obligate diploid, and cannot undergo meiosis, adopting instead a parasexual cycle. The origin of these traits is unknown and we hypothesize they could result from ancestral hybridization. We tested this idea by analyzing available genomes ofC. albicansisolates and comparing them to those of hybrid and non-hybrid strains of otherCandidaspecies. Our results show compelling evidence thatC. albicansis an evolved hybrid, with levels and patterns of ancestral heterozygosity that cannot be fully explained under the paradigm of vertical evolution. Although the level of inferred divergence between the putative parental lineages (2.8%) is not clearly beyond current species boundaries in Saccharomycotina, we show here that all analyzedC. albicansstrains derive from a single hybrid ancestor, which diverged by extensive loss of heterozygosis. This finding has important implications for our understanding ofC. albicansevolution, including the loss of the sexual cycle, the origin of the association with humans, and the evolution of virulence traits.
Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau
Authors: Tong Chao , Li Miao , Tang Yongtao , Zhao Kai
Published: October 2019

Comparative genomics has elucidate the molecular footprints of adaptations to extreme environments at high altitude including hypoxia, but insight into the genomic basis of saline and alkaline adaptation in highland fish has rarely been provided. The increasing of water salinization is a growing threat to Tibetan endemic fish species. Here we performed one of the first comparative genomics studies and began to characterize genomic signature of alkaline adaptation in a Schizothoracine fish inhabiting soda lake on the Tibetan Plateau. We found that expansions of lineage-specific genes associated with ion transport and transmembrane functions, genome-wide elevated rate of molecular evolution in Schizothoracine fishes relative to other lowland teleost fish species. In addition, we found specific changes in the rate of molecular evolution between G. p. kelukehuensis and other teleost fishes for ion transport-related genes. Furthermore, we identified a set of genes associated with ion transport and energy metabolism underwent positive selection. Using tissue-transcriptomics, we found that most REGs and PSGs in G. p. kelukehuensis were broadly expressed across three tissues and significantly enriched for ion transport functions. Finally, we identified a set of ion transport-related genes with evidences for both selection and co-expressed which contributed to alkaline tolerance in G. p. kelukehuensis. Altogether, our study identified putative genomic signature and potential candidate genes contributed to ongoing alkaline adaptation in Schizothoracine fish.
Prophase removal of chromosome-associated RNAs facilitates anaphase chromosome segregation
Authors: Sharp Judith A. , Wang Wei , Blower Michael D.
Published: October 2019

During mitosis, the genome is transformed from a decondensed, transcriptionally active state to a highly condensed, transcriptionally inactive state. Mitotic chromosome reorganization is marked by the general attenuation of transcription on chromosome arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation and nuclear envelope breakdown is unknown. SAF-A/hnRNPU is an abundant nuclear protein with RNA-to-DNA tethering activity, coordinated by two spatially distinct nucleic acid binding domains. Here we show that RNA is evicted from prophase chromosomes through Aurora-B-dependent phosphorylation of the SAF-A DNA-binding domain; failure to execute this pathway leads to accumulation of SAF-A:RNA complexes on mitotic chromosomes and elevated rates of anaphase segregation defects. This work reveals a role for Aurora-B in removing chromatin-associated RNAs during prophase, and demonstrates that Aurora-B dependent relocalization of SAF-A during cell division contributes to the fidelity of chromosome segregation.
A microtranslatome coordinately regulates sodium and potassium currents in the heart
Authors: Eichel Catherine A. , Ríos-Pérez Erick B. , Liu Fang , Jameson Margaret B. , Jones David K. , Knickelbine Jennifer J. , Robertson Gail A.
Published: October 2019

Catastrophic arrhythmias and sudden cardiac death can occur with even a small imbalance between inward sodium currents and outward potassium currents, but mechanisms establishing this critical balance are not understood. Here, we show that mRNA transcripts encoding INa and IKr channels (SCN5A and hERG, respectively) are associated in defined complexes during protein translation. Using biochemical, electrophysiological and single-molecule fluorescence localization approaches, we find that roughly half the hERG translational complexes contain SCN5A transcripts. Moreover, the transcripts are regulated in a way that alters functional expression of both channels at the membrane. Association and coordinate regulation of transcripts in discrete “microtranslatomes” represents a new paradigm controlling electrical activity in heart and other excitable tissues.
Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 inhibitor AtSCS
Authors: Tarnowski Krzysztof , Klimecka Maria , Ciesielski Arkadiusz , Goch Grażyna , Kulik Anna , Fedak Halina , Poznański Jarosław , Lichocka Małgorzata , Pierechod Marcin , Engh Richard A. , Dadlez Michał , Dobrowolska Grażyna , Bucholc Maria
Published: October 2019

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. InArabidopsis thaliana, the use of alternative transcription start sites located withinAtSCSgene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing35S::AtSCS-A-c-mycor35S::AtSCS-B-c-mycin thescs-1knockout mutant revealed thatin plantaboth forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.

One sentence Summary

Two isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.
Identification of chloroplast envelope proteins with critical importance for cold acclimation
Authors: Trentmann Oliver , Mühlhaus Timo , Zimmer David , Sommer Frederik , Schroda Michael , Haferkamp Ilka , Keller Isabel , Pommerrenig Benjamin , Neuhaus H. Ekkehard
Published: October 2019

The ability of plants to cope with cold temperatures relies on their photosynthetic activity. This already demonstrates that the chloroplast is of utmost importance for cold acclimation and acquisition of freezing tolerance. During cold acclimation, the properties of the chloroplast change markedly. To provide the most comprehensive view of the protein repertoire of chloroplast envelope, we analysed this membrane system in Arabidopsis thaliana using MS-based proteomics. Profiling chloroplast envelope membranes was achieved by a cross comparison of protein intensities across plastid and the enriched membrane fraction both under normal and cold conditions. Multivariable logistic regression models the probabilities for the classification problem to address envelop localization. In total, we identified 38 envelope membrane intrinsic or associated proteins exhibiting altered abundance after cold acclimation. These proteins comprise several solute carries, such as the ATP/ADP antiporter NTT2 (substantially increased abundance) or the maltose exporter MEX1 (substantially decreased abundance). Remarkably, analysis of the frost recovery of ntt loss-of-function and mex1 overexpressor mutants confirmed that the comparative proteome is well suited to identify novel key factors involved in cold acclimation and acquisition of freezing tolerance. Moreover, for proteins with known physiological function we propose scenarios explaining their possible role in cold acclimation. Furthermore, spatial proteomics introduces a novel layer of complexity and enabled the identification of proteins differentially localized at the envelope membrane under the changing environmental regime.
Ascorbate deficiency does not limit non-photochemical quenching in Chlamydomonas reinhardtii
Authors: Vidal-Meireles André , Tóth Dávid , Kovács László , Neupert Juliane , Tóth Szilvia Z.
Published: October 2019

Ascorbate (vitamin C) plays essential roles in development, signaling, hormone biosynthesis, regulation of gene expression, stress resistance and photoprotection. In vascular plants, violaxanthin de-epoxidase (VDE) requires ascorbate (Asc) as reductant, thereby it is required for the energy-dependent component of non-photochemical quenching (NPQ). In order to assess the role of Asc in NPQ in green algae, which are known to contain low amounts of Asc, we searched for an insertional Chlamydomonas reinhardtii mutant affected in the VTC2 gene, essential for Asc biosynthesis. The Crvtc2-1 knockout mutant was viable and, depending on the growth conditions, it contained 10 to 20% Asc relative to its wild type. When Chlamydomonas was grown photomixotrophically at moderate light, the zeaxanthin-dependent component of NPQ emerged upon strong red illumination both in the Crvtc2-1 mutant and in its wild type. Deepoxidation was unaffected by Asc deficiency, demonstrating that the Chlorophycean VDE found in Chlamydomonas does not require Asc as a reductant. The rapidly induced, energy-dependent NPQ component, characteristic of photoautotrophic Chlamydomonas cultures grown at high light, was not limited by Asc deficiency either. On the other hand, a reactive oxygen species-induced photoinhibitory NPQ component was greatly enhanced upon Asc deficiency, both under photomixotrophic and photoautotrophic conditions. These results demonstrate that Asc has distinct roles in NPQ formation in Chlamydomonas than in vascular plants.

One-sentence summary

In Chlamydomonas -in contrast to seed plants-, ascorbate is not required for violaxanthin deepoxidation and energy-dependent non-photochemical quenching but it mitigates photoinhibitory quenching.
A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and response
Authors: Fu Jing , Liu Jiaming , Gao Xudong , Zhang Xinglin , Bai Juan , Hao Yueling , Cui Hongchang
Published: October 2019

Root growth relies on both cell division and elongation, which occur in the meristem and elongation zones respectively. SCARECROW (SCR) is a GRAS family gene essential for root growth and radial patterning in the Arabidopsis root. Previous studies showed that SCR promotes root growth by suppressing cytokinin response in the meristem, but there is also evidence that SCR expressed beyond the meristem is required as well for root growth. Here we report that SCR promotes root growth by promoting cell elongation through suppression of oxidative stress response and maintenance of redox homeostasis in the elongation zone. In the scr root, a higher level of hydrogen peroxide was detected, which can be attributed to down-regulation of peroxidase gene 3. When stress response was blocked or redox status was ameliorated by the aba2 or upb1 mutation, the scr mutant produced a significantly longer root with longer cells and a larger and mitotically more active meristem, even though the stem cell and radial patterning defects still persisted. We showed that WRKY15, an oxidative responsive gene, was a direct target of SCR down-regulated in the scr mutant, which suggests that SCR has an active role in suppressing oxidative stress response. Since hydrogen peroxide and peroxidases are essential for endodermal differentiation, these results suggest that SCR plays a central role in coordinating cell elongation, endodermal differentiation, redox homeostasis, and oxidative stress response in plant root.

One sentence summary

This study reveals a novel mechanism of root growth regulation, which involves a previously unrecognized role of SCR in regulating cell elongation, endodermal differentiation, and redox homeostasis.
BTB-TAZ domain protein MdBT2 modulates malate accumulation by targeting a bHLH transcription factor for degradation in response to nitrate
Authors: Zhang Quan-Yan , Gu Kai-Di , Cheng Lailiang , Wang Jia-Hui , Yu Jian-Qiang , Wang Xiao-Fei , You Chun-Xiang , Hu Da-Gang , Hao Yu-Jin
Published: October 2019

Excessive application of nitrate, an essential macronutrient and a signal regulating diverse physiological processes, decreases malate accumulation in apple fruit, but the underlying mechanism remains poorly understood. Here, we show that an apple BTB/TAZ protein MdBT2 is involved in regulating malate accumulation and vacuolar pH in response to nitrate.In vitroandin vivoassays indicate that MdBT2 interacts directly with and ubiquitinates a bHLH transcription factor, MdCIbHLH1, via the ubiquitin/26S proteasome pathway in response to nitrate. This ubiquitination results in the degradation of MdCIbHLH1 protein and reduces the transcription of MdCIbHLH1-targeted genes involved in malate accumulation and vacuolar acidification includingMdVHA-Aencoding a vacuolar H+-ATPase gene, andMdVHP1encoding a vacuolar H+-pyrophosphatase gene, as well asMdALMT9encoding a aluminum-activated malate transporter gene. A series of transgenic analyses in apple materials including fruits, plantlets and calli demonstrate that MdBT2 controls nitrate-mediated malate accumulation and vacuolar pH at least partially, if not completely, via regulating the MdCIbHLH1 protein level. Taken together, these findings reveal that MdBT2 regulates the stability of MdCIbHLH1 via ubiquitination in response to nitrate, which in succession transcriptionally reduces the expression of malate-associated genes, thereby controlling malate accumulation and vacuolar acidification in apples under high nitrate supply.
The Arp2/3 complex and the formin, Diaphanous, are both required to regulate the size of germline ring canals in the developing egg chamber
Authors: Thestrup Josephine , Tipold Marina , Kindred Alexandra , Stark Kara , Curry Travis , Lewellyn Lindsay
Published: October 2019

Intercellular bridges are an essential structural feature found in both germline and somatic cells throughout the animal kingdom. Because of their large size, the germline intercellular bridges, or ring canals, in the developing fruit fly egg chamber are an excellent model to study the formation, stabilization, and expansion of these structures. Within the egg chamber, the germline ring canals connect 15 supporting nurse cells to the developing oocyte, facilitating the transfer of materials required for successful oogenesis. The ring canals are derived from a stalled actomyosin contractile ring; once formed, additional actin and actin-binding proteins are recruited to the ring to support the 20-fold expansion that accompanies oogenesis. These behaviors provide a unique model system to study the actin regulators that control incomplete cytokinesis, intercellular bridge formation, and expansion. By temporally controlling their expression in the germline, we have demonstrated that the Arp2/3 complex and the formin, Diaphanous (Dia), coordinately regulate ring canal size and expansion throughout oogenesis. Dia is required for successful incomplete cytokinesis and the initial stabilization of the germline ring canals. Once the ring canals have formed, the Arp2/3 complex and Dia cooperate to determine ring canal size and maintain their stability. Our data suggest that the nurse cells must maintain a precise balance between the activity of these two nucleators during oogenesis.
Hippocampal hub neurons maintain unique functional properties throughout their lifetime
Authors: Bocchio Marco , Gouny Claire , Angulo-Garcia David , Toulat Tom , Tressard Thomas , Baude Agnès , Cossart Rosa
Published: October 2019

The temporal embryonic origins of cortical GABA neurons are critical for their specialization. In the neonatal hippocampus, GABA cells born the earliest (ebGABAs) operate as ‘hubs’ by orchestrating neuronal dynamics. However, their fate remains largely unknown. To fill this gap, we have examined CA1 ebGABAs using a combination of electrophysiology, neurochemical analysis, optogenetic connectivity mapping as well as ex vivo and in vivo calcium imaging. We show that CA1 ebGABAs not only operate as hubs during development, but also maintain distinct morpho-physiological and connectivity profiles, including a bias for long-range targets and local excitatory inputs. In vivo, ebGABAs signal a variety of network states, including the activation of local CA1 assemblies. Hence, ebGABAs are specified from birth to ensure unique functions throughout their lifetime. In the adult brain, this may take the form of a long-range hub role through the coordination of cell assemblies across distant regions.
The pheromone and pheromone receptor mating-type locus is involved in controlling uniparental mitochondrial inheritance inCryptococcus
Authors: Sun Sheng , Fu Ci , Ianiri Giuseppe , Heitman Joseph
Published: October 2019

Mitochondria are inherited uniparentally during sexual reproduction in the majority of eukaryotic species studied, including humans, mice, nematodes, as well as many fungal species. Mitochondrial uniparental inheritance (mito-UPI) could be beneficial in that it avoids possible genetic conflicts between organelles with different genetic backgrounds, as recently shown in mice; and it could prevent the spread of selfish genetic elements in the mitochondrial genome. Despite the prevalence of observed mito-UPI, the underlying mechanisms and the genes involved in controlling this non-mendelian inheritance are poorly understood in many species. InCryptococcus neoformans, a human pathogenic basidiomyceteous fungus, mating types (MATα andMATa) are defined by alternate alleles at the singleMATlocus that evolved from fusion of the twoMATloci (P/Rencoding pheromones and pheromone receptors,HDencoding homeodomain transcription factors) that are the ancestral state in the basidiomycota. Mitochondria are inherited uniparentally from theMATaparent inC. neoformansand this requires theSXI1α andSXI2aHD factors encoded byMAT. However, there is evidence additional genes contribute to control of mito-UPI inCryptococcus. Here we show that inCryptococcus amylolentus, a sibling species ofC. neoformanswith unlinkedP/RandHD MATloci, mitochondrial uniparental inheritance is controlled by theP/Rlocus, and is independent of theHDlocus. Consistently, by replacing theMATα alleles of the pheromones (MF) and pheromone receptor (STE3) with theMATaalleles, we show that theseP/Rlocus defining genes indeed affect mito-UPI inC. neoformansduring sexual reproduction. Additionally, we show that during early stages ofC. neoformanssexual reproduction, conjugation tubes are always produced by theMATα cells, resulting in unidirectional migration of theMATα nucleus into theMATacell during zygote formation. This process is controlled by theP/Rlocus and could serve to physically restrict movement ofMATα mitochondria in the zygotes, and thereby contribute to mito-UPI. We propose a model in which both physical and genetic mechanisms function in concert to prevent the coexistence of mitochondria from the two parents in the zygote and subsequently in the meiotic progeny, thus ensuring mito-UPI in pathogenicCryptococcus, as well as in closely related non-pathogenic species. The implications of these findings are discussed in the context of the evolution of mito-UPI in fungi and other more diverse eukaryotes.
A highly homogeneous expansion microscopy polymer composed of tetrahedron-like monomers
Authors: Gao Ruixuan , Yu Chih-Chieh (Jay) , Gao Linyi , Piatkevich Kiryl D , Neve Rachael L , Upadhyayula Srigokul , Boyden Edward S
Published: October 2019

Expansion microscopy (ExM) physically magnifies biological specimens to enable nanoscale-resolution imaging on conventional microscopes. Current ExM methods permeate biological specimens with free radical-polymerized polyacrylate hydrogels, whose network structure limits the microscopy resolution enabled by ExM. Here we report that ExM is possible using hydrogels with more homogeneous network structure, assembled via non-radical terminal linking of monomers of tetrahedral shape. As with earlier forms of ExM, such “tetra-gel”-embedded specimens can be iteratively expanded for greater physical magnification. Iterative tetra-gel expansion of herpes simplex virus type 1 (HSV-1) virions by ~10x in linear dimension results in a viral envelope deviation from sphericity of 9.2 nm, rather than the 14.3 nm enabled by free radical-polymerized hydrogels used in earlier versions of ExM. Thus, tetra-gel polymer chemistry may support new forms of ExM imaging that introduce fewer spatial errors than earlier versions, and raise the question of whether single biomolecule precision may be achievable.