bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary unique mechanistic framework of clathrin-mediated endocytosis in plants
Authors: Narasimhan Madhumitha , Johnson Alexander , Prizak Roshan , Kaufmann Walter Anton , Casillas-Pérez Barbara , Friml Jiří
Published: September 2019

In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME follows the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the surface but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.
Color-specific porosity in double pigmented natural 3d-nanoarchitectures of blue crab shell
Authors: Nekvapil Fran , Cintă Pinzaru Simona , Barbu–Tudoran Lucian , Suciu Maria , Glamuzina Branko , Tamaş Tudor , Chiş Vasile
Published: September 2019

3D-engineered nanoarchitectures with various functionalities are still difficult to obtain and translate for real-world applications. However, such nanomaterials are naturally abundant and yet wasted, but could trigger huge interest for blue bioeconomy, provided that our understanding of their ultrastructure-function is achieved. To date, the Bouligand pattern in crustaceans shell structure is believed to be unique. Here we demonstrated that in blue crab Callinectes sapidus, the 3D-nanoarchitecture is color-specific, while the blue and red-orange pigments interplay in different nano-sized channels and pores. Thinnest pores of about 20 nm are found in blue shell. Additionally, the blue pigment co-existence in specific Bouligand structure is proved for the green crab Carcinus aestuarii, although the crab does not appear blue. The pigments interplay, simultaneously detected in color-specific, native crab shells overturns our understanding in crustaceans coloration and may trigger the selective use of particular colored natural nanoarchitectures for biomolecular loading and slow release, infectious barriers, bioremediation, translational diffusivity and many others.
The positive role of noise for information acquisition in biological signaling pathways
Authors: Azpeitia Eugenio , Wagner Andreas
Published: September 2019

All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways, which rely on interactions between molecules that detect and transmit the presence of an extracellular cue or signal to the cell’s interior. Such interactions are inherently stochastic and thus noisy. In classical information theory, a noisy communication channel degrades the amount of transmissible information relative to a noise-free channel. For this reason, one would expect that the kinetic parameters that determine a pathway’s operation minimize noise. We show that this is not the case under a wide range of biologically sensible parameter values. Specifically, we perform computational simulations of simple signaling systems, which show that a noisy molecular interaction dynamics is a necessary condition for information acquisition. Moreover, we show that optimal information acquisition, where a system reacts most sensitively to changes in the environment, can be obtained close to the maximal attainable level of noise in the system. Our work highlights the positive role that noise can have in biological information processing.

Author summary

The acquisition of information is fundamental for living systems, because the decisions they take based on such information directly affect survival and reproduction. The molecular mechanisms used by cells to acquire information are signaling pathways. The molecular interactions of signaling pathways, such as the binding of a signal to a receptor, are by nature noisy. This is important, because noise disrupts information. Hence, to maximize the acquisition of information, signaling pathways should minimize the noise of their molecular interactions. Here we show that a noisy dynamic of the molecular interactions can improve the acquisition of information, and that the maximal capacity to acquire information can be obtained with a close-to-maximal level of noise in a signaling pathway. Thus, contrary to expectations, noise can improve the acquisition of information in living systems.
Co-circulation of Dengue Virus Serotypes 1 and 3 during the 2019 epidemic in Dar es Salaam, Tanzania
Authors: Mwanyika Gaspary , Mboera Leonard E.G. , Rugarabamu Sima , Lutwama Julius , Sindato Calvin , Paweska Janusz T. , Misinzo Gerald
Published: September 2019

Background

Dengue is an important mosquito-borne viral disease in tropical and sub-tropical countries. In this study molecular characterization was carried out to determine dengue viruses circulating among patients at health facilities during 2019 epidemic in Dar es Salaam, Tanzania.

Methods

The study involved outpatients seeking care for febrile illness at four health facilities in Kinondoni and Ilala Districts of Dar es Salaam City in Tanzania. A total of 45 sera from the outpatients were confirmed dengue-positive for dengue virus (DENV) non-structural protein 1 (NS1) antigen and/or NS1-IgG/IgM antibodies using on-site rapid test. The presence of the virus was detected by reverse-transcription polymerase chain reaction (RT-PCR) method. Of the 45 sera, 20 samples were selected randomly for identification of specific dengue virus serotypes using RT-PCR followed by evaluation of resulting amplicons on agarose gel electrophoresis.

Findings and significance

Both Dengue virus serotypes 1 (DENV-1) and 3 (DENV-3) were detected in the samples tested with the former being dominant. We present the first evidence of dengue virus co-infection of DENV-1 and DENV-3 serotypes in Tanzania. The emergence of DENV-1 indicates the possibility of importation of the virus to Tanzania from endemic countries. Due to DENV serotype co-circulation, there is an increased risk of severe dengue in future epidemics. Our findings advocate the importance of genomic-based surveillance to provide rapid evidence of dengue virus emergence/re-emergence and spread.

Author Summary

Dengue viruses are the most important mosquito-borne pathogens that pose a serious global health threat. Tanzania has reported several dengue virus epidemics since 2010 with the majority of the epidemics occurring in Dar-es-Salaam city. Until August 2019, a total of 6,859 dengue cases have been confirmed in the country. We performed molecular characterization of dengue viruses (DENV) circulating during the 2019 epidemic phase. It was found that DENV-1 serotype was dominant during the epidemic and two samples of the tested sera were co-infected by DENV-1 and DENV-3 serotypes. These findings emphasize the importance of genomic-based surveillance of dengue viruses in Tanzania to guide strategies for appropriate interventions.
Adaptive iron utilization compensates for the lack of an inducible uptake system inNaegleria fowleriand represents a potential target for therapeutic intervention
Authors: Arbon Dominik , Ženíšková Kateřina , Mach Jan , Grechnikova Maria , Malych Ronald , Talacko Pavel , Sutak Robert
Published: September 2019

Warm fresh water is a natural habitat for many single-celled organisms, including protozoan parasites such as the infamous brain-eating amoeba,Naegleria fowleri,which can become pathogenic for mammals, including humans. The condition caused byN. fowleriis known as primary amoebic meningoencephalitis, which is a generic and usually fatal infection of the brain with rapid onset. One of the important factors influencing a wide spectrum of pathogens, includingN. fowleri, is the bioavailability of iron in the environment. The strategy of withholding iron evolved in mammalian hosts, and the different strategies of pathogens to obtain it are an important part of host-parasite interactions.

In the present study, we employ different biochemical and analytical methods to explore the effect of decreased iron availability on the cellular processes ofN. fowleri. We show that under iron starvation, nonessential, iron-dependent, mostly cytosolic pathways inN. fowleriare downregulated, while the metal is utilized in the mitochondria to maintain vital respiratory processes. Surprisingly,N. fowlerifails to respond to acute shortages of iron by the induction of a reductive iron uptake system that seems to be the main iron-obtaining strategy of the parasite. Our work aims to demonstrate the importance of mitochondrial iron in the biology ofN. fowleriand to explore the plausibility of exploiting it as a potential target for therapeutic interference.

Author Summary

Naegleria fowleriis undoubtedly one of the deadliest parasites of humans, hence the name “brain-eating amoeba”. Being dangerous, but rare, it may be regarded as a highly understudied pathogen of humans. Unfortunately, the symptoms of primary amoebic meningoencephalitis may be confused with much more common bacterial meningoencephalitis; therefore, it is quite probable that many infections caused byN. fowlerihave been misdiagnosed as bacterial infections without further inquiry. In many cases, fast diagnosis is vital for commencing the correct therapy, and even then, complete success of the treatment is very rare. Our laboratory focuses on the uptake and intracellular metabolism of metals in unicellular eukaryotes, so we decided to explore the biology ofN. fowlerifrom this aspect. Changes in the proteome, as a direct effect of iron-deficient conditions, were described, and these data were used to further explore the ways in whichN. fowleriresponds to these conditions on a cellular level and how its biology changes. Based on these findings, we propose that the struggle ofN. fowlerito obtain iron from its host could be exploited for therapeutic interference purposes in primary amoebic meningoencephalitis patients.
BWGS: a R package for genomic selection and its application to a wheat breeding programme
Authors: Charmet Gilles , Tran Louis Gautier , Auzanneau Jérôme , Rincent Renaud , Bouchet Sophie
Published: September 2019

We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates of Breeding values (GEBV) for genomic selection. BWGS relies on existing R-libraries, all freely available from CRAN servers. The two main functions enable to run 1) replicated random cross validations within a training set of genotyped and phenotyped lines and 2) GEBV prediction, for a set of genotyped-only lines. Options are available for 1) missing data imputation, 2) markers and training set selection and 3) genomic prediction with 15 different methods, either parametric or semi-parametric.

The usefulness and efficiency of BWGS are illustrated using a population of wheat lines from a real breeding programme. Adjusted yield data from historical trials (highly unbalanced design) were used for testing the options of BWGS. On the whole, 760 candidate lines with adjusted phenotypes and genotypes for 47 839 robust SNP were used. With a simple desktop computer, we obtained results which compared with previously published results on wheat genomic selection. As predicted by the theory, factors that are most influencing predictive ability, for a given trait of moderate heritability, are the size of the training population and a minimum number of markers for capturing every QTL information. Missing data up to 40%, if randomly distributed, do not degrade predictive ability once imputed, and up to 80% randomly distributed missing data are still acceptable once imputed with Expectation-Maximization method of package rrBLUP. It is worth noticing that selecting markers that are most associated to the trait do improve predictive ability, compared with the whole set of markers, but only when marker selection is made on the whole population. When marker selection is made only on the sampled training set, this advantage nearly disappeared, since it was clearly due to overfitting. Few differences are observed between the 15 prediction models with this dataset. Although non-parametric methods that are supposed to capture non-additive effects have slightly better predictive accuracy, differences remain small. Finally, the GEBV from the 15 prediction models are all highly correlated to each other. These results are encouraging for an efficient use of genomic selection in applied breeding programmes and BWGS is a simple and powerful toolbox to apply in breeding programmes or training activities.
Glucose availability impacts proteotoxic stress in Caenorhabditis elegans
Authors: Gatrell Landon , Wilkins Whitney , Rana Priya , Farris Mindy
Published: September 2019

Alterations in protein folding may lead to aggregation of misfolded proteins, which is strongly correlated with neurotoxicity and cell death. Protein aggregation has been shown as a normal consequence of aging, but it is largely associated with age-related disease, particularly neurodegenerative diseases like Huntington disease (HD). Huntington disease is caused by a CAG repeat expansion in the huntingtin gene and serves as a useful model for neurodegeneration due to its strictly genetic origin. Research in the model organism Caenorhabditis elegans suggests that glucose protects against cell stress, including proteotoxicity related to aggregation, despite the well-known, lifespan-shortening effects of glucose. We hypothesized that glucose could be beneficial by alleviating energy deficiency, a well-characterized phenomenon in HD, or by upregulating stress resistance pathways. We used C. elegans expressing polyglutamine repeats to quantify lifespan, motility, reproduction, learning, and activity of succinate dehydrogenase (SDH), with and without glucose, to identify the role of glucose in proteotoxicity and neuroprotection. Our data show HD worms on glucose plates exhibited shorter lifespans, no change in motility, learning, or SDH product formation, but had altered reproductive phenotypes similar to dietary restriction. Additionally, worms expressing toxic polyglutamine repeats were unable to learn association of food with a neutral odorant. We also observed tissue-specific differences; polyglutamine appeared to be slightly more toxic to muscle cells than neurons. Rather than increasing energy production, glucose appeared to decrease mitochondrial metabolism, as SDH formation decreases with added glucose. Future work investigating glucose-mediated neuroprotection should focus on connecting metabolism, sirtuin activation, and DAF-16 activation.
ASK1/p38-mediated NLRP3 inflammasome signaling pathway contributed to aberrant retinal angiogenesis in diabetic retinopathy
Authors: Zou Wenjun , Zhang Zhengwei , Luo Shasha , Cheng Libo , Huang Xiaoli , Ding Nannan , Yu Jinjin , Pan Ying , Wu Zhifeng
Published: September 2019

Abstracts

Diabetic retinopathy is the leading cause of blindness in the working-age population in many countries. Despite the available treatments, some patients present late in the course of the disease when treatment is more difficult. Hence, it is crucial that the new targets are found and utilized in clinical therapy of diabetic retinopathy. In this study, we constructed the DR animal model and the high model in HRMEC cell to investigate the relationship between ASK1/p38 and NLRP3 in DR. The results showed that DR could cause the inflammatory response and microvascular proliferation. NLRP3 contributed to DR-mediated inflammatory development and progression, which promoted the inflammatory related cytokine expression. Meanwhile, it could promote the tube formation of retinal microvascular endothelial and angiogenesis. Moreover, further research showed that NLRP3 mediated aberrant retinal angiogenesis in diabetic retinopathy was regulated by ASK1 and p38. It suggested that ASK1/p38 could become a new target in DR treatment.
Root production in a subtropical pasture is mediated by cultivar and defoliation severity
Authors: Wilson Chris H. , Vendramini Joao M. , Sollenberger Lynn E. , Flory S. Luke
Published: September 2019

Background

Grasslands occupy significant land area and account for a large proportion of the global soil carbon stock, yet the direct effects of grazing and genotypic composition on relationships between shoot and root production are poorly resolved. This lack of understanding hinders the development of models for predicting root production in managed grasslands, a critical variable for determining soil carbon stocks.

Methods

We quantified the effects of season-long defoliation treatments on both shoot and root production across four cultivars of a widely-planted pasture grass species (Paspalum notatum Fluegge) in a common garden setting in South Florida, USA.

Results

We found that infrequently applied (4 week) severe defoliation (to 5 cm) substantially enhanced shoot production for all cultivars, while severe defoliation reduced root production across cultivars, regardless of frequency. Overall, cultivars varied substantially in root production across the range of defoliation treatments in our study. However, there was no significant relationship between shoot and root production.

Conclusions

Our results find that aboveground and belowground productivity are only weakly coupled, suggesting caution against use of simple aboveground proxies to predict variations in root production in grasslands. More broadly, our results demonstrate that improved modeling and management of grasslands for belowground ecosystem services, including soil carbon sequestration/stocks, will need to account for intraspecific genetic variations and responses to defoliation management.
Baobab Diversity, Seed Germination and Early Growth
Authors: Egbadzor Kenneth F.
Published: September 2019

The diversity in baobab was studied on 75 trees located at Adaklu District and Ho and Hohoe Municipalities. Thirteen morphological traits were used in the characterisation based on Bioversity descriptors for baobab. GenStat edition 12 was used to analyse the diversity as well as germination and growth data. Group average hierarchical clustering with Jaccard similarity coefficient discriminated among most of the baobab trees. Clustering was not based on location although few trees that were not discriminated were from the same communities. The clustering can be used in selecting trees for further studies and domestication. Germination tests were conducted with soaked, boiled and sulphuric acid treated seeds. Only the sulphuric acid treated seeds had germination significantly higher than the control. More studies should be done to find easier way of breaking seed dormancy of baobab. There were significant differences in 100 seed weight, seed length and thickness among seeds from three different trees. However, there were no significant difference in seed width of the same sample. Seed size traits should be considered in selecting baobab for domestication because of the high variability revealed. Observation on seedling growth revealed less than 10 leaves in the first month and increased to about 20 in the fourth month. Growth in girth was 5mm and 8mm in the first and fourth months respectively. Seedling height of 17cm in the first month reached 40cm in four months. Information from this research is valuable for further work on domestication of baobab.
Gnrh1-induced responses are indirect in female medaka Fsh cells
Authors: Hodne Kjetil , Fontaine Romain , Ager-Wick Eirill , Weltzien Finn-Arne
Published: September 2019

Reproductive function in vertebrates is stimulated by gonadotropin-releasing hormone (GnRH) that controls the synthesis and release of the two pituitary gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH). FSH and LH, which regulates different stages of gonadal development, are produced by two different cell types in the fish pituitary, in contrast to mammals and birds, thus allowing the investigation of their differential regulation. In the present work, we show by fluorescentin situhybridization that Lh cells in adult female medaka express Gnrh receptors, whereas Fsh cells do not. This is confirmed by patch clamp recordings and cytosolic Ca2+measurements on dispersed pituitary cells, where Lh cells, but not Fsh cells, respond to Gnrh1 by increased action potential frequencies and cytosolic Ca2+levels. In contrast, both Fsh and Lh cells are able to respond electrically and by elevating the cytosolic Ca2+levels to Gnrh1 in brain-pituitary tissue slices. Using Ca2+uncaging in combination with patch clamp recordings and cytosolic Ca2+measurements, we show that Fsh and Lh cells form homo- and heterotypic networks in the pituitary. Taken together, these results show that the effects of Gnrh1 on Fsh release in adult female medaka is indirect, likely mediated via Lh cells.
The structure of the iron-catecholate transporter Fiu suggests substrate import occurs via a 2-step mechanism
Authors: Grinter Rhys , Lithgow Trevor
Published: September 2019

The Ferric Iron Uptake (Fiu) transporter fromEscherichia colifunctions in the transport of iron-catecholate complexes across the bacterial outer membrane, providing the bacterium with iron which is an essential element for growth. Recently, it became clear that Fiu also represents a liability: its activity allows the import of antimicrobial compounds that have evolved to mimic catecholate. In this work we have determined the structure of Fiu and analyzed its function to address how Fiu and related transporters from other bacterial species can bind catecholate in a surface-exposed cavity. In addition, the crystal structure of Fiu reveals the presence of a large, selectively gated cavity in the interior of this transporter. This chamber is large enough to accommodate the Fiu substrate and may act to regulate substrate import. These data provide insight into the mechanism of substrate uptake by Fiu and related transporters identified inPseudomonas aeruginosaandAcinetobacter baumannii. As Fiu and its homologues are the targets of substrate mimicking antibiotics, these data will assist in the development of antibiotics that target these receptors for cell entry.
Canine sense of quantity: evidence for numerical ratio-dependent activation in parietotemporal cortex
Authors: Aulet Lauren S. , Chiu Veronica C. , Prichard Ashley , Spivak Mark , Lourenco Stella F. , Berns Gregory S.
Published: September 2019

The approximate number system, which supports the rapid estimation of quantity, emerges early in human development and is widespread across species. Neural evidence from both human and non-human primates suggests the parietal cortex as a primary locus of numerical estimation, but it is unclear whether the numerical competencies observed across non-primate species are subserved by similar neural mechanisms. Moreover, because studies with non-human animals typically involve extensive training, little is known about the spontaneous numerical capacities of non-human animals. To address these questions, we examined the neural underpinnings of number perception using awake canine functional magnetic resonance imaging. Dogs passively viewed dot arrays that varied in ratio and, critically, received no task-relevant training or exposure prior to testing. We found evidence of ratio-dependent activation, which is a key feature of the approximate number system, in canine parietotemporal cortex in the majority of dogs tested. This finding is suggestive of a neural mechanism for quantity perception that has been conserved across mammalian evolution.
LAB-AID (Laboratory Automated Interrogation of Data): an interactive web application for visualization of multi-level data from biological experiments
Authors: Kozic Zrinko , Booker Sam , Dando Owen , Hardingham Giles , Kind Peter
Published: September 2019

A key step in understanding the results of biological experiments is visualization of the data. Many laboratory experiments contain a range of measurements that exist within a hierarchy of interdependence. An automated way to visualise and interrogate experimental data would: 1) lead to improved understanding of the results, 2) help to determine which statistical tests should be performed, and 3) easily identify outliers and sources of batch effects. Unfortunately, existing graphing solutions often demand expertise in programming, require considerable effort to import and examine such multi-level data, or are unnecessarily complex for the task at hand. Here we present LAB-AID (Laboratory Automated Interrogation of Data), an interactive tool specifically designed to automatically visualize and query hierarchical data resulting from biological experiments.
Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation
Authors: Kabelka Ivo , Pachler Michael , Prévost Sylvain , Letofsky-Papst Ilse , Lohner Karl , Pabst Georg , Vácha Robert
Published: September 2019

We studied the synergistic mechanism of equimolar mixtures of magainin 2 (MG2a) and PGLa in phosphatidylethanolamine/phosphatidylglycerol mimics of Gram-negative cytoplasmic membranes. In a preceding paper [Pachler et al., Biophys. J. 2019 xxx], we reported on the early onset of parallel heterodimer formation of the two antimicrobial peptides already at low concentrations and the resulting defect formation in membranes. Here, we focus on the structures of the peptide/lipid aggregates occurring in the synergistic regime at elevated peptide concentrations. Using a combination of calorimetric, scattering, electron microscopic andin silicotechniques, we demonstrate that the two peptides, even if applied individually, transform originally large unilamellar vesicles into multilamellar vesicles, with a collapsed interbilayer spacing resulting from peptide induced adhesion. Interestingly, the adhesion does not lead to a peptide induced lipid separation of charged and charge neutral species. In addition to this behavior, equimolar mixtures of MG2a and PGLa formed surface-aligned fibril-like structures, which induced adhesion zones between the membranes and the formation of transient fusion stalks in molecular dynamics simulations and a coexisting sponge phase observed by small-angle X-ray scattering. The previously reported increased leakage of lipid vesicles of identical composition in the presence of MG2a/PGLa mixtures is therefore related to a peptide-induced cross-linking of bilayers.

STATEMENT OF SIGNIFICANCE

We demonstrate that the synergistic activity of the antimicrobial peptides MG2a and PGLa correlates to the formation of surface-aligned fibril-like peptide aggregates, which cause membrane adhesion, fusion and finally the formation of a sponge phase.
A low dose of simvastatin enhanced the therapeutic efficacy of mesenchymal stem cell (MSC) transplantation in skin wound healing in diabetic mice associated with increases in pAkt, SDF-1, and angiogenesis
Authors: Sukpat Supakanda , Israsena Nipan , Wongphoom Jutamas , Ingrungruanglert Praewphan , Sim Tao Ming , Patumraj Suthiluk
Published: September 2019

Purpose

We aimed to determine the possible mechanisms of underlying the effects of low dose simvastatin on enhancing the therapeutic efficacy of MSC transplantation in diabetic wound healing.

Methods

Balb/c nude mice were divided into five groups:- control mice (CON), diabetic mice (DM), diabetic mice pretreated with low-dose simvastatin (DM+SIM), diabetic mice implanted with MSCs (DM+MSCs) and diabetic mice pretreated with low-dose simvastatin and implanted with MSCs (DM+MSCs+SIM). Seven days before wound induction, low dose simvastatin was orally administered to the DM+SIM and DM+MSCs+SIM groups. Eleven weeks after the induction of diabetes, all mice were given bilateral full-thickness excisional back skin wounds.

Results

By comparing the DM+MSCs+SIM and DM+MSCs groups, the results showed that on day 14; the wound closure (%WC) and capillary vascularity (%CV) in the DM+MSCs+SIM group were significantly increased compared to those in the DM+MSCs group. In addition, by using immunohistochemical techniques, it was also shown that the expression of SDF-1, a chemotactic factor regulating the migration of stem cells, in the DM+SIM+MSCs group was increased compared with that in the DM+MSCs group. Furthermore, using phospho-Akt (S473) Pan Specific DuoSet IC ELISA (R&D Systems, USA) kits, the increased tissue Akt levels were found in the DM+SIM+MSCs group but not in the other groups.

Conclusions

Our study suggests that a low dose of simvastatin enhanced the therapeutic efficacy of MSCs in diabetic wound healing, and this effect was associated with increases in pAkt levels, SDF-1 levels, and angiogenesis, and improved wound closure.
CNS Glycosylphosphatidylinositol Deficiency Results in Delayed White Matter Development, Ataxia, and Premature Death in a Novel Mouse Model
Authors: Lukacs Marshall , Stottmann Rolf W.
Published: September 2019

The Glycosylphosphatidylinositol (GPI) anchor is a post-translational modification added to approximately 150 different proteins to facilitate proper membrane anchoring and trafficking to lipid rafts. Biosynthesis and remodeling of the GPI anchor requires the activity of over twenty distinct genes. Defects in the biosynthesis of GPI anchors in humans leads to Inherited Glycosylphosphatidylinositol Deficiency (IGD). IGD patients display a wide range of phenotypes though the central nervous system (CNS) appears to be the most commonly affected tissue. A full understanding of the etiology of these phenotypes has been hampered by the lack of animal models due to embryonic lethality of GPI biosynthesis gene null mutants. Here we model IGD by genetically ablating GPI production in the CNS with a conditional mouse allele of phosphatidylinositol glycan anchor biosynthesis, class A (Piga) and Nestin-Cre. We find that the mutants do not have structural brain defects but do not survive past weaning. The mutants show progressive decline with severe ataxia consistent with defects in cerebellar development. We show the mutants have reduced myelination and defective Purkinje cell development. Surprisingly we found Piga was expressed in a fairly restricted pattern in the early postnatal brain consistent with the defects we observed in our model. Thus, we have generated a novel mouse model of the neurological defects of IGD which demonstrates a critical role for GPI biosynthesis in cerebellar and white matter development.
Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)
Authors: Bangs Max R. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E.
Published: September 2019

The delimitation of species-boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life-histories co-distributed in the highly modified Colorado River (i.e., Flannelmouth Sucker,Catostomus latipinnis; Bluehead Sucker,C. Pantosteus discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction-site associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in Bluehead Sucker, supporting elevation ofC. P. virescensto species-status, and recognizingC. P. discobolus yarrowi(Zuni Bluehead Sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate Flannelmouth Sucker lineages as ESUs (Evolutionarily Significant Units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the alignment of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolationversussecondary contact.
Muscle function and homeostasis require macrophage-derived cytokine inhibition of AKT activity in Drosophila
Authors: Kierdorf Katrin , Hersperger Fabian , Sharrock Jessica , Vincent Crystal M. , Ustaoglu Pinar , Dou Jiawen , Gyoergy Attila , Groß Olaf , Siekhaus Daria E. , Dionne Marc S.
Published: September 2019

Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK-STAT signaling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signaling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signaling activity in the absence of any immune challenge. Macrophages are the source of much of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal from macrophages to muscle that controls AKT activity and metabolic homeostasis.
A versatile bulk electrotransfection protocol for mouse embryonic fibroblast and iPS cells
Authors: Eghbalsaied Shahin , Hyder Iqbal , Kues Wilfried A.
Published: September 2019

A square-wave pulsing protocol was developed using OptiMEM-GlutaMAX for high efficient transfection of mouse embryonic fibroblast (MEF) and induced pluripotency stem (iPS) cells. An electrotransfection efficiency of > 95% was repeated for both MEF and iPS cells using reporter-encoding plasmids. The protocol was very efficient for plasmid size ranging from 6.2 to 13.5 kb. A high rate of targeted gene knockout (> 95 %) was produced in Venus transgenic cells using indels formation. Targeted deletions in the Venus transgene were performed by co-electroporation of two gRNA-encoding plasmids. In conclusion, this plasmid electrotransfection protocol is straight-forward, cost-effective, and efficient for CRISPRing mouse primary cells.
Human microbiome sequences in the light of the Nubeam
Authors: Dai Hang , Guan Yongtao
Published: September 2019

We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and based on which assigns numbers to reads. Nubeam capitalizes on the non-commutative property of matrix multiplication, such that different reads are assigned different numbers, and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam can account for GC bias and nucleotide quality, and is computationally efficient; the K-mer method is a special case of Nubeam, but without those benefits. As a reference-free approach, Nubeam avoids reference bias and mapping bias and can work with organisms without reference genomes. Thus, Nubeam is ideal to analyze datasets from metagenomic whole-genome sequencing, where the amount of unmapped reads is substantial. When applied to human microbiome sequencing, Nubeam recapitulated findings made by mapping-based methods, and shed lights on contributions of unmapped reads. In particular, body habitats dominate clustering of unmapped pseudo-samples; there are more outliers in skin whole samples than the skin mapped pseudo-samples; and analysis of unmapped reads suggested that the sequencing depth is far from sufficient for urogenital samples.
How to Pare a Pair: Topology Control and Pruning in Intertwined Complex Networks
Authors: Kramer Felix , Modes Carl D.
Published: September 2019

Recent work on self-organized remodeling of vasculature in slime-mold, leaf venation systems and vessel systems in vertebrates has put forward a plethora of potential adaptation mechanisms. All these share the underlying hypothesis of a flow-driven machinery, meant to alter rudimentary vessel networks in order to optimize the system’s dissipation, flow uniformity, or more, with different versions of constraints. Nevertheless, the influence of environmental factors on the long-term adaptation dynamics as well as the networks structure and function have not been fully understood. Therefore, interwoven capillary systems such as found in the liver, kidney and pancreas, present a novel challenge and key opportunity regarding the field of coupled distribution networks. We here present an advanced version of the discrete Hu–Cai model, coupling two spatial networks in 3D. We show that spatial coupling of two flow-adapting networks can control the onset of topological complexity in concert with short-term flow fluctuations. We find that both fluctuation-induced and spatial coupling induced topology transitions undergo curve collapse obeying simple functional rescaling. Further, our approach results in an alternative form of Murray’s law, which incorporates local vessel interactions and flow interactions. This geometric law allows for the estimation of the model parameters in ideal Kirchhoff networks and respective experimentally acquired network skeletons.
Multiplexed Nanometric 3D Tracking of Microbeads using a FFT-Phasor Algorithm
Authors: Brouwer T. B. , Hermans N. , van Noort J.
Published: September 2019

Many single-molecule biophysical techniques rely on nanometric tracking of microbeads to obtain quantitative information about the mechanical properties of biomolecules such as chromatin fibers. Their three-dimensional position can be resolved by holographic analysis of the diffraction pattern in wide-field imaging. Fitting this diffraction pattern to Lorentz Mie scattering theory yields the bead position with nanometer accuracy in three dimensions but is computationally expensive. Real-time multiplexed bead tracking therefore requires a more efficient tracking method. Here, we introduce 3D phasor tracking, a fast and robust bead tracking algorithm with nanometric localization accuracy in a z-range of over 10 µm. The algorithm is based on a 2D cross-correlation using Fast Fourier Transforms with computer-generated reference images, yielding a processing rate of up to 10.000 regions of interest per second. We implemented the technique in magnetic tweezers and tracked the 3D position of over 100 beads in real-time on a generic CPU. Its easy implementation, efficiency, and robustness can improve multiplexed biophysical bead tracking applications, especially where high throughput is required.

Significance

Microbeads are often used in biophysical single-molecule manipulation experiments and accurately tracking their position in 3 dimensions is key for quantitative analysis. Holographic imaging of these beads allows for multiplexing bead tracking but image analysis can be a limiting factor. Here we present a 3D tracking algorithm based on Fast Fourier Transforms that is fast, has nanometric precision, is robust against common artifacts and is accurate over 10’s of micrometers. We show its real-time application for magnetic tweezers based force spectroscopy on more than 100 chromatin fibers in parallel, but we anticipate that many other bead-based biophysical essays can benefit from this simple and robust 3 phasor algorithm.
Lipids in xylem sap of woody plants across the angiosperm phylogeny
Authors: Schenk H. Jochen , Michaud Joseph M. , Mocko Kerri , Espino Susana , Melendres Tatiana , Roth Mary R. , Welti Ruth , Kaack Lucian , Jansen Steven
Published: September 2019

Lipids have been observed attached to lumen-facing surfaces of mature xylem conduits of several plant species, but there has been little research on their functions or effects on water transport, and only one lipidomic study of the xylem apoplast. Therefore, we conducted lipidomic analyses of xylem sap from woody stems of seven plants representing six major angiosperm clades, including basal magnoliids, monocots, and eudicots, to characterize and quantify phospholipids, galactolipids, and sulfolipids in sap using mass spectrometry. Locations of lipids in vessels ofLaurus nobiliswere imaged using TEM and confocal microscopy. Xylem sap contained the galactolipids di- and mono-galactosyldiacylglycerol (DGDG and MGDG), as well as all common plant phospholipids, but only traces of sulfolipids, with total lipid concentrations in extracted sap ranging from 0.18 to 0.63 nmol / mL across all seven species. Contamination of extracted sap from lipids in cut living cells was found to be negligible. Lipid composition of sap was compared to wood in two species and was largely similar, suggesting that sap lipids, including galactolipids, originate from cell content of living vessels. Seasonal changes in lipid composition of sap were observed for one species. Lipid layers coated all lumen-facing vessel surfaces ofLaurus nobilis, and lipids were highly concentrated in inter-vessel pits. The findings suggest that apoplastic, amphiphilic xylem lipids are a universal feature of angiosperms. The findings require a reinterpretation of the cohesion-tension theory of water transport to account for the effects of apoplastic lipids on dynamic surface tension and hydraulic conductance in xylem.
Glioma-induced alterations in neuronal activity and neurovascular coupling during disease progression
Authors: Montgomery Mary Katherine , Kim Sharon H. , Dovas Athanassios , Patel Kripa , Mela Angeliki , Humala Nelson , Zhao Hanzhi T. , Thibodeaux David N. , Shaik Mohammed , Ma Ying , Grinband Jack , Chow Daniel S. , Schevon Catherine , Hillman Elizabeth M. C. , Canoll Peter
Published: September 2019

Diffusely infiltrating gliomas are known to cause alterations in cortical function, vascular disruption and seizures. These neurological complications present major clinical challenges, yet their underlying mechanisms and causal relationships to disease progression are poorly characterized. Here, we followed glioma progression in awake Thy1-GCaMP6f mice using in-vivo wide-field optical mapping to monitor alterations in both neuronal activity and functional hemodynamics. The bilateral synchrony of spontaneous neuronal activity in glioma-infiltrated cortex gradually decreased, while neurovascular coupling was also progressively disrupted compared to uninvolved cortex. Over time, mice developed diverse patterns of high amplitude discharges and eventually generalized seizures that begin at the infiltrative margin of the tumors. Interictal and seizure events exhibited positive neurovascular coupling in uninfiltrated cortex, however glioma-infiltrated regions exhibited inverted hemodynamic responses driving seizure-evoked hypoxia. These results reveal a landscape of complex physiological interactions occurring during glioma progression and present new opportunities for exploring new biomarkers and therapeutic targets.

Highlights

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Glioma disrupts neural synchrony between bilateral cortical regions.

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WFOM reveals frequent interictal discharges and seizures during glioma progression.

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Tumor development is accompanied by local changes in neurovascular coupling.

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Altered neurovascular coupling drives hypoperfusion of the tumor during seizures.
High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns
Authors: Owen Lucy L. W. , Chang Thomas H. , Manning Jeremy R.
Published: September 2019

Our thoughts arise from coordinated patterns of interactions between brain structures that change with our ongoing experiences. High-order dynamic correlations in neural activity patterns reflect different subgraphs of the brain’s functional connectome that display homologous lower-level dynamic correlations. We tested the hypothesis that high-level cognition is reflected in high-order dynamic correlations in brain activity patterns. We developed an approach to estimating high-order dynamic correlations in timeseries data, and we applied the approach to neuroimaging data collected as human participants either listened to a ten-minute story or listened to a temporally scrambled version of the story. We trained across-participant pattern classifiers to decode (in held-out data) when in the session each neural activity snapshot was collected. We found that classifiers trained to decode from high-order dynamic correlations yielded the best performance on data collected as participants listened to the (unscrambled) story. By contrast, classifiers trained to decode data from scrambled versions of the story yielded the best performance when they were trained using first-order dynamic correlations or non-correlational activity patterns. We suggest that as our thoughts become more complex, they are reflected in higher-order patterns of dynamic network interactions throughout the brain.
Sex-specific transgenerational plasticity I: Maternal and paternal effects on sons and daughters
Authors: Hellmann Jennifer K , Bukhari Syed Abbas , Deno Jack , Bell Alison M
Published: September 2019

Transgenerational plasticity (TGP) or parental effects – when parental environments alter the phenotype of future generations – can influence how organisms cope with environmental change. An intriguing, underexplored possibility is that sex –of both the parent and the offspring – plays an important role in driving the evolution of transgenerational plasticity in both adaptive and nonadaptive ways.

Here, we evaluate the potential for sex-specific parental effects in a freshwater population of threespined sticklebacks (Gasterosteus aculeatus) by independently and jointly manipulating maternal and paternal experiences and separately evaluating their phenotypic effects in sons versus daughters. We tested the adaptive hypothesis that daughters are more responsive to cues from their mother, while sons are more responsive to cues from their father.

We exposed mothers, fathers, or both parents to visual cues of predation risk and measured offspring antipredator traits and brain gene expression.

Predator-exposed fathers produced sons that were more risk-prone, while predator-exposed mothers produced more anxious sons and daughters. Further, maternal and paternal effects on offspring survival were nonadditive: offspring with a predator-exposed father, but not two predator-exposed parents, had lower survival against live predators. There were also strong sex-specific effects on brain gene expression: exposing mothers versus fathers to predation risk activated different transcriptional profiles in their offspring, and sons and daughters strongly differed in the ways in which their brain gene expression profiles were influenced by parental experience.

We found little evidence to support the hypothesis that offspring prioritize their same-sex parent’s experience. Parental effects varied with both the sex of the parent and the offspring in complicated and nonadditive ways. Failing to account for these sex-specific patterns (e.g., by pooling sons and daughters) would have underestimated the magnitude of parental effects. Altogether, these results draw attention to the potential for sex to influence patterns of TGP and raise new questions about the interface between transgenerational plasticity and sex-specific selective pressures, sexual conflict, and sexual selection.