bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling plastics exposure for the marine biota: Risk maps for fin whales in the Pelagos Sanctuary (North-Western Mediterranean)
Authors: Guerrini Federica , Mari Lorenzo , Casagrandi Renato
Published: February 2019

The Mediterranean basin is among the most impacted marine ecoregions globally, being at the same time semi-enclosed by densely populated countries and crossed by trafficked maritime routes. Such anthropogenic pressure threatens both the qual-ity of its waters and the high biodiversity living in them, making the role of Marine Protected Areas (MPAs) crucial for pre-serving species suitable habitats. Under the European Union Marine Strategy Framework Directive, marine litter has been recognized as one of the principal causes of marine pollution, and public awareness on its environmental and biological impacts is raising. Using a quantitative and data-driven modelling approach, here we assess the presence of plastic waste within the feeding grounds of the fin whale Balaenoptera physalus, an endangered cetacean for which there is increasing evidence of impacts due to microplastic ingestion. To this end, we analyze a decade (2000 - 2010) of advection patterns of marine plastic litter, modelled with a Lagrangian approach. Particles are released in the MPA Pelagos, the International Sanctuary for the Protection of Mediterranean Marine Mammals (North-Western Mediterranean, between France, Italy and Monaco), from different sources (i.e., untreated waste along coasts, plastic discharged from rivers and plastic pollution released along maritime shipping routes). Risk of exposure of fin whales to microplastic pollution is evaluated by interlacing plastic litter distribution maps obtained through modelling with maps of suitable habitats obtained from the elaboration of satellite chlorophyll-a data in species-specific visited areas. Our modelling results show that all the three main sources of plastic litter taken into account clearly contribute to impacting cetaceans in the Sanctuary, yet in a different manner. The procedure formalized here can be extended to assess the risk caused by plastic pollution in other MPAs as well as to evaluate possible impacts on other taxa, thus informing targeted actions to tackle the complex issue of marine litter.
Analysis of solid-state heparin samples by ATR-FTIR spectroscopy
Authors: Devlin Anthony , Mycroft-West Courtney J. , Guerrini Marco , Yates Edwin A. , Skidmore Mark A.
Published: February 2019

The widely used anticoagulant pharmaceutical, heparin, is a polydisperse, heterogeneous polysaccharide. Heparin is one of the essential medicines defined by the World Health Organisation but, during 2007-2008, was the subject of adulteration. The intrinsic heterogeneity and variability of heparin makes it a challenge to monitor its purity by conventional means. This has led to the adoption of alternative approaches for its analysis and quality control, some of which are based on multivariate analysis of 1H NMR spectra, or exploit correlation techniques. Such NMR spectroscopy-based analyses, however, require costly and technically demanding NMR instrumentation. Here, an alternative approach based on the use of attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR) combined with multivariate analysis is proposed. FTIR-ATR employs more affordable and easy-to-use technology and, when combined with multivariate analysis of the resultant spectra, readily differentiates between glycosaminoglycans of different types, between heparin samples of distinct animal origins and enables the detection of both known heparin contaminants, such as over-sulphated chondroitin sulfate (OSCS), as well as other alien sulphated polysaccharides in heparin samples to a degree of sensitivity comparable to that achievable by NMR. The approach will permit the rapid and cost-effective monitoring of pharmaceutical heparin at any stage of the production process and indeed, in principle, the quality control of any heterogeneous or variable material.
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota
Authors: Aranda-Díaz Andrés , Obadia Benjamin , Thomsen Tani , Hallberg Zachary F. , Tüzün Güvener Zehra , Casey Huang Kerwyn , Ludington William B.
Published: February 2019

Despite decades of investigation into how antibiotics affect isolated bacteria, it remains highly challenging to predict consequences for communities in complex environments such as the human intestine. Interspecies interactions can impact antibiotic activity through alterations to the extracellular environment that change bacterial physiology. By measuring key metabolites and environmental pH, we determined that metabolic cross-feeding among members of the fruit fly gut microbiota drives changes in antibiotic sensitivityin vitro. Co-culturing ofLactobacillus plantarumwithAcetobacterspecies induced tolerance to rifampin. Mechanistically, we found that acetobacters counter the acidification driven byL. plantarumproduction of lactate, and that pH shifts during stationary phase were sufficient to drive rifampin tolerance inL. plantarummonocultures. The keyLactobacillusphysiological parameter related to tolerance was a reduction in lag time exiting stationary phase, opposite to a previously identified mode of tolerance to ampicillin inE. coli. Lactobacillustolerance to erythromycin also depended on growth status and pH, suggesting that our findings generalize to other antibiotics. Finally, tolerance ofL. plantarumto rifampin varied spatially across the fruit fly gut. This mechanistic understanding of the coupling among interspecies interactions, environmental pH, and antibiotic tolerance enables future predictions of growth and the effects of antibiotics in more complex communities and within hosts.
Structural and binding studies of human CAMKK2 kinase domain bound to small molecule ligands
Authors: Profeta Gerson S. , dos Reis Caio V. , Godoi Paulo H. C. , Fala Angela M. , Sartori Roger , Salmazo Anita P. T. , Ramos Priscila Z. , Massirer Katlin B. , Elkins Jonathan M. , Drewry David H. , Gileadi Opher , Couñago Rafael M.
Published: February 2019

Calcium/Calmodulin-dependent Protein Kinase Kinase 2 (CAMKK2) acts as a signaling hub, receiving signals from various regulatory pathways and decoding them via phosphorylation of downstream protein kinases - such as AMPK (AMP-activated protein kinase) and CAMK types I and IV. CAMKK2 relevance is highlighted by its constitutive activity being implicated in several human pathologies. However, at present, there are no specific small-molecule inhibitors available for this protein kinase. Moreover, CAMKK2 and its closest human homologue, CAMKK1, are thought to have overlapping biological roles. Here we present six novel co-structures of CAMKK2 bound to potent ligands identified from a library of ATP-competitive kinase inhibitors. Isothermal titration calorimetry (ITC) revealed that binding to some of these molecules is enthalpy driven. We expect our results to further advance current efforts to discover small molecule kinase inhibitors specific to each human CAMKK.
Structure-based methyl resonance assignment with MethylFLYA
Authors: Pritišanac Iva , Würz Julia , Alderson T. Reid , Güntert Peter
Published: February 2019

Methyl groups provide crucial NMR probes for investigating protein structure, dynamics and mechanisms in systems that are too large for NMR with uniform isotope labeling. This requires the assignment of methyl signals in the NMR spectra to specific methyl groups in the protein, an expensive and time-consuming endeavor that limits the use of methyl-based NMR for large proteins. To resolve this bottleneck, several methyl resonance assignment methods have been developed. These approaches remain limited with regard to complete automation and/or the extent and accuracy of the assignments. Here, we present the completely automated MethylFLYA method for the assignment of methyl groups. MethylFLYA requires as input exclusively methyl-methyl nuclear Overhauser effect spectroscopy (NOESY) peak lists. The algorithm was applied to five proteins of 28–358 kDa mass with a total of 708 isotope-labeled methyl groups. Manually made 1H/13C reference assignments were available for 674 methyls. The available experimental peak lists contained NOESY cross peaks for 614 methyls. MethylFLYA confidently assigned 488 methyls, i.e. 79% of those with NOESY data. Of these assignments, 460 agreed with the reference, 5 were different (and 23 concerned methyls without reference assignment). For three proteins of 28, 81, and 358 kDa, all confident assignments by MethylFLYA were correct. We furthermore show that, for high-quality NOESY spectra, automatic picking of NOE signals followed by resonance assignment with MethylFLYA can yield results that are comparable to those obtained for manually prepared peak lists, indicating the feasibility of unbiased, fully automatic methyl resonance assignment starting directly from the NMR spectra. This renders MethylFLYA an advantageous alternative to existing approaches for structure-based methyl assignment. MethylFLYA assigns, for most proteins, significantly more methyl groups than other algorithms, has an average error rate of 1%, modest runtimes of 0.4–1.2 h for the five proteins, and flexibility to handle arbitrary isotope labeling patterns and include data from other types of NMR spectra.
Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins
Authors: Zhang Haiyang , Petrie Meghan V. , He Yiwei , Peace Jared M. , Chiolo Irene E. , Aparicio Oscar M.
Published: February 2019

Chromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. Sites undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. InS. cerevisiae, replication origins occupy characteristic subnuclear localizations that anticipate their initiation timing during S phase. Here, we link localization of replication origins in G1 phase with Fkh1 activity, which is required for their early replication timing. Using a Fkh1-dependent origin relocalization assay, we determine that execution of Dbf4-dependent kinase function, including Cdc45 loading, results in dynamic relocalization of a replication origin from the nuclear periphery to the interior in G1 phase. Origin mobility increases substantially with Fkh1-driven relocalization. These findings provide novel molecular insight into the mechanisms that govern dynamics and spatial organization of DNA replication origins and possibly other functional DNA elements.
Impaired M-current in KCNQ2 Encephalopathy Evokes Dyshomeostatic Modulation of Excitability
Authors: Simkin Dina , Searl Timothy J. , Piyevsky Brandon N. , Forrest Marc , Williams Luis A. , Joshi Vaibhav , Zhang Hongkang , Ryan Steven J. , Schwake Michael , Robertson Gabriella L. , Penzes Peter , Laux Linda C. , McManus Owen B. , Dempsey Graham T. , Millichap John J. , George Alfred. L. , Kiskinis Evangelos
Published: February 2019

Mutations in KCNQ2, which encodes a pore-forming K+ channel subunit responsible for neuronal M-current, cause neonatal epileptic encephalopathy, a complex disorder presenting with severe early-onset seizures and impaired neurodevelopment. The condition is exceptionally difficult to treat, partially because the effects of KCNQ2 mutations on the development and function of human neurons are unknown. Here, we used induced pluripotent stem cells and gene editing to establish a disease model, and measured the functional properties of patient-derived neurons using electrophysiological and optical approaches. We find that while patient-derived excitatory neurons exhibit reduced M-current early, they develop intrinsic and network hyperexcitability progressively. This hyperexcitability is associated with faster action potential repolarization, larger afterhyperpolarization, and a functional enhancement of large conductance Ca2+-activated K+ (BK) channels. These properties facilitate a burst-suppression firing pattern that is reminiscent of the interictal electroencephalography pattern in patients. Importantly, we were able to phenocopy these excitability features in control neurons only by chronic but not acute pharmacological inhibition of M-current. Our findings suggest that dyshomeostatic mechanisms compound KCNQ2 loss-of-function and lead to alterations in the neurodevelopmental trajectory of patient-derived neurons. Our work has therapeutic implications in explaining why KCNQ2 agonists are not beneficial unless started at an early disease stage.
Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly
Authors: Comerci Colin J. , Herrmann Jonathan , Yoon Joshua , Jabbarpour Fatemeh , Zhou Xiaofeng , Nomellini John F. , Smit John , Shapiro Lucy , Wakatsuki Soichi , Moerner W.E.
Published: February 2019

Bacteria assemble the cell envelope using localized enzymes to account for growth and division of a topologically complicated surface1–3. However, a regulatory pathway has not been identified for assembly and maintenance of the surface layer (S-layer), a 2D crystalline protein coat surrounding the curved 3D surface of a variety of bacteria4,5. By specifically labeling, imaging, and tracking native and purified RsaA, the S-layer protein (SLP) fromC. crescentus, we show that protein self-assembly alone is sufficient to assemble and maintain the S-layerin vivo. By monitoring the location of newly produced S-layer on the surface of living bacteria, we find that S-layer assembly occurs independently of the site of RsaA secretion and that localized production of new cell wall surface area alone is insufficient to explain S-layer assembly patterns. When the cell surface is devoid of a pre-existing S-layer, the location of S-layer assembly depends on the nucleation characteristics of SLP crystals, which grow by capturing RsaA molecules freely diffusing on the outer bacterial surface. Based on these observations, we propose a model of S-layer assembly whereby RsaA monomers are secreted randomly and diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated into growing 2D S-layer crystals. The complicated topology of the cell surface enables formation of defects, gaps, and grain boundaries within the S-layer lattice, thereby guiding the location of S-layer assembly without enzymatic assistance. This unsupervised mechanism poses unique challenges and advantages for designing treatments targeting cell surface structures or utilizing S-layers as self-assembling macromolecular nanomaterials. As an evolutionary driver, 2D protein self-assembly rationalizes the exceptional S-layer subunit sequence and species diversity6.
Lead optimisation of dehydroemetine for repositioned use in malaria
Authors: Panwar Priyanka , Burusco Kepa K. , Abubaker Muna , Matthews Holly , Gutnov Andrey , Fernández-Álvaro Elena , Bryce Richard A. , Wilkinson James , Nirmalan Niroshini
Published: February 2019

Drug repositioning offers an effective alternative tode novodrug design to tackle the urgent need for novel anti-malarial treatments. The anti-amoebic compound, emetine dihydrochloride, has been identified as a potentin-vitroinhibitor of the multi-drug resistant strain K1 ofPlasmodium falciparum(IC50: 47 nM + 2.1 nM). 2,3-dehydroemetine, a synthetic analogue of emetine dihydrochloride has been claimed to have less cardiotoxic effects than emetine. The structures of two diastereoisomers of 2,3-dehydroemetine were modelled on the reported emetine binding site on cryo-EM structure 3J7A and it was found that(-)-R,S-dehydroemetine mimicked the bound pose of emetine more closely than(-)-S,S-dehydroisoemetine.(-)-R,S-dehydroemetine was also found to be highly potent against the multi-drug resistant K1 strain ofP. falciparumin comparison with(-)-S,S-dehydroisoemetine, which loses its potency due to the change of configuration at C-1’. In addition to its effect on the asexual erythrocytic stages ofP. falciparum, the compounds exhibited gametocidal properties with no cross-resistance against any of the multi-drug resistant strains tested. Drug interaction studies showed(-)-R,S-dehydroemetine to have synergistic antimalarial activity with atovaquone and proguanil. Emetine dihydrochloride, and(-)-R,S-dehydroemetine failed to show any inhibition of the hERG potassium channel and displayed atovoquone-like activity on the mitochondrial membrane potential.
Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids
Authors: Huang Qin , Chan Ken Y. , Tobey Isabelle G. , Chan Yujia Alina , Poterba Tim , Boutros Christine L. , Balazs Alejandro B. , Daneman Richard , Bloom Jonathan M. , Seed Cotton , Deverman Benjamin E.
Published: February 2019

The engineered AAV-PHP.B family of adeno-associated virus efficiently delivers genes throughout the mouse central nervous system. To guide their application across disease models, and to inspire the development of translational gene therapy vectors useful for targeting neurological diseases in humans, we sought to elucidate the host factors responsible for the CNS tropism of AAV-PHP.B vectors. Leveraging CNS tropism differences across mouse strains, we conducted a genome-wide association study, and rapidly identified and verified LY6A as an essential receptor for the AAV-PHP.B vectors in brain endothelial cells. Importantly, this newly discovered mode of AAV binding and transduction is independent of other known AAV receptors and can be imported into different cell types to confer enhanced transduction by the AAV-PHP.B vectors.
A primal role for balance in the development of coordinated locomotion
Authors: Ehrlich David E. , Schoppik David
Published: February 2019

Mature locomotion requires that animal nervous systems coordinate distinct groups of muscles. The pressures that guide the development of coordination are not well understood. We studied vertical locomotion in developing zebrafish to understand how and why coordination might emerge. We found that zebrafish used their pectoral fins and bodies synergistically to climb. As they developed, zebrafish came to coordinate their fins and bodies to climb with increasing postural stability. Fin-body synergies were absent in mutants with-out vestibular sensation, linking balance and coordination. Similarly, synergies were systematically altered following cerebellar lesions, identifying a neural substrate regulating fin-body coordination. Computational modeling illustrated how coordinated climbing could improve balance as zebrafish mature. Together these findings link the sense of balance to the maturation of coordinated locomotion. As they develop, zebrafish improve postural stability by optimizing fin-body coordination. We therefore propose that the need to balance drives the development of coordinated locomotion.
MAGMA: inference of sparse microbial association networks
Authors: Cougoul Arnaud , Bailly Xavier , Wit Ernst C.
Published: February 2019

Microorganisms often live in symbiotic relationship with their environment and they play a central role in many biological processes. They form a complex system of interacting species. Within the gut micro-biota these interaction patterns have been shown to be involved in obesity, diabetes and mental disease. Understanding the mechanisms that govern this ecosystem is therefore an important scientific challenge. Recently, the acquisition of large samples of microbiota data through metabarcoding or metagenomics has become easier.

Until now correlation-based network analysis and graphical modelling have been used to identify the putative interaction networks formed by the species of microorganisms, but these methods do not take into account all features of microbiota data. Indeed, correlation-based network cannot distinguish between direct and indirect correlations and simple graphical models cannot include covariates as environmental factors that shape the microbiota abundance. Furthermore, the compositional nature of the microbiota data is often ignored or existing normalizations are often based on log-transformations, which is somewhat arbitrary and therefore affects the results in unknown ways.

We have developed a novel method, called MAGMA, for detecting interactions between microbiota that takes into account the noisy structure of the microbiota data, involving an excess of zero counts, overdispersion, compositionality and possible covariate inclusion. The method is based on Copula Gaus-sian graphical models whereby we model the marginals with zero-inflated negative binomial generalized linear models. The inference is based on an efficient median imputation procedure combined with the graphical lasso.

We show that our method beats all existing methods in recovering microbial association networks in an extensive simulation study. Moreover, the analysis of two 16S microbial data studies with our method reveals interesting new biology.

MAGMA is implemented as an R-package and is freely available at https://gitlab.com/arcgl/rmagma, which also includes the scripts used to prepare the material in this paper.
MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction
Authors: Fields Bryden , Moeskjær Sara , Friman Ville-Petri , Andersen Stig U. , Young J. Peter W.
Published: February 2019

Background

Sequencing and PCR errors are a major challenge when characterising genetic diversity using high-throughput amplicon sequencing (HTAS).

Results

We have developed a multiplexed HTAS method, MAUI-seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. We show that two main advantages of this approach are efficient elimination of chimeric and other erroneous reads, outperforming DADA2 and UNOISE3, and the ability to confidently recognise genuine alleles that are present at low abundance or resemble chimeras.

Conclusions

The method provides sensitive and flexible profiling of diversity and is readily adaptable to most HTAS applications, including microbial 16S rRNA profiling and metabarcoding of environmental DNA.
Identification of genes with enriched expression in early developing mouse cone photoreceptors
Authors: Buenaventura Diego F. , Corseri Adrianne , Emerson Mark M.
Published: February 2019

Cone photoreceptors are the critical first cells that mediate high acuity vision. Despite their importance and their potential use in cell-based therapies for retinal diseases, there is a lack of knowledge about the early developmental stages of these cells. Here we characterize the expression of the homeobox transcription factor Lhx4 as an early and enriched cone photoreceptor expressed gene in both chicken and mouse. A Lhx4 GFP reporter mouse was found to recapitulate this early cone photoreceptor expression and was used to purify and profile embryonic mouse cone photoreceptors by single cell RNA sequencing. This enrichment in cone photoreceptors allowed for the robust identification of genes associated with the early cone transcriptome and also identified subpopulations of these cells. A comparison to previously reported datasets allowed the classification of genes according to developmental timing, cell type specificity, and whether they were regulated by the rod transcription factor Nrl. This analysis has extended the set of known early cone enriched genes and identified those that are regulated independently of Nrl. This report furthers our knowledge of the transcriptional events that occur in early cone photoreceptors.
DNA Nanostructures Coordinate Gene Silencing in Mature Plants
Authors: Zhang Huan , Demirer Gozde S. , Zhang Honglu , Ye Tianzheng , Goh Natalie S. , Aditham Abhishek J. , Cunningham Francis J. , Fan Chunhai , Landry Markita P.
Published: February 2019

Plant bioengineering may generate high yielding and stress-resistant crops amidst a changing climate and a growing global population (1–3). However, delivery of biomolecules to plants relies onAgrobacteriuminfection (4) or biolistic particle delivery (5), the former of which is only amenable to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall which is absent in mammalian cells and poses the dominant physical barrier to exogenous biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells, however, nanoparticle-mediated delivery remains unexplored for passive biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver small interfering RNAs (siRNAs), and effectively silence a constitutively-expressed gene inNicotiana benthamianaleaves. We show that nanostructure internalization into plant cells and the corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies, but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures, and details both the design parameters of importance for plant cell internalization, and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
Single cell profiling of CRISPR/Cas9-induced OTX2 deficient retinas reveals fate switch from restricted progenitors
Authors: Ghinia Tegla Miruna G. , Buenaventura Diego F. , Kim Diana Y. , Thakurdin Cassandra , Gonzalez Kevin C. , Emerson Mark M.
Published: February 2019

Development of the vertebrate eye, like many developmental systems, depends on genes that are used iteratively in multiple distinct processes. The OTX2 transcription factor is one such gene, with a requirement for eye formation, photoreceptor formation, and retinal pigment epithelium specification, among others. Recent evidence has suggested that OTX2 is also expressed in subsets of retinal progenitor cells with restricted fate choices. However, given the multiple roles for OTX2 and limitations of conventional conditional knockout strategies, the functional significance of this expression is unknown. Here we use CRISPR/Cas9 gene editing to produce mutations of OTX2, identifying similar phenotypes to those observed in human patients. In addition, we use single cell RNA sequencing to determine the functional consequences of OTX2 gene editing by CRISPR/Cas9 on the population of cells derived from OTX2-expressing retinal progenitor cells. We not only confirm that OTX2 is required for the generation of photoreceptors, but also for maintaining the proliferative potential of cells and suppressing the formation of specific retinal fates. These include subtypes of retinal ganglion and horizontal cells normally associated with these progenitor types, suggesting that in this context OTX2 functions to repress sister cell fate choices. Upregulation of key transcription factors involved in the formation of these cells was observed suggesting that OTX2 is upstream of critical nodes of gene regulatory networks of these alternative fates.
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
Authors: Portik Daniel M. , Wiens John J.
Published: February 2019

Phylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large-scale trees are based on a “supermatrix” approach, which involves amalgamating thousands of published sequences for a group. Constructing up-to-date supermatrices can be challenging, especially as new sequences may become available almost constantly. Additionally, genomic datasets (composed of thousands of loci) are becoming common in phylogenetics and phylogeography, and present novel challenges for constructing such datasets.

Here we present SuperCRUNCH, a Python toolkit for assembling large phylogenetic datasets. It can be applied to GenBank sequences, unpublished sequences, or combinations of GenBank and unpublished data. SuperCRUNCH constructs local databases and uses them to conduct rapid searches for user-specified sets of taxa and loci. Sequences are parsed into putative loci and passed through rigorous filtering steps. A post-filtering step allows for selection of one sequence per taxon (i.e. species-level supermatrix) or retention of all sequences per taxon (i.e. population-level dataset). Importantly, SuperCRUNCH can generate “vouchered” population-level datasets, in which voucher information is used to generate multi-locus phylogeographic datasets. SuperCRUNCH offers many options for taxonomy resolution, similarity filtering, sequence selection, alignment, and file manipulation.

We demonstrate the range of features available in SuperCRUNCH by generating a variety of phylogenetic datasets. Output datasets include traditional species-level supermatrices, large-scale phylogenomic matrices, and phylogeographic datasets. Finally, we briefly compare the ability of SuperCRUNCH to construct species-level supermatrices to alternative approaches. SuperCRUNCH generated a large-scale supermatrix (1,400 taxa and 66 loci) from 16GB of GenBank data in ∼1.5 hours, and generated population-level datasets (<350 samples, <10 loci) in <1 minute. It outperformed alternative methods for supermatrix construction in terms of taxa, loci, and sequences recovered.

SuperCRUNCH is a modular bioinformatics toolkit that can be used to assemble datasets for any taxonomic group and scale (kingdoms to individuals). It allows rapid construction of supermatrices, greatly simplifying the process of updating large phylogenies with new data. It is also designed to produce population-level datasets. SuperCRUNCH streamlines the major tasks required to process phylogenetic data, including filtering, alignment, trimming, and formatting. SuperCRUNCH is open-source, documented, and available at https://github.com/dportik/SuperCRUNCH.
Quantitative analysis of the ThrbCRM1-centered gene regulatory network
Authors: Souferi Benjamin , Emerson Mark M.
Published: February 2019

Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as close to an in vivo context as possible. Here we use electroporation of plasmid reporters to define critical parameters of a specific cis-regulatory element, ThrbCRM1, during retinal development. ThrbCRM1 is associated with cone photoreceptor genesis and activated in a subset of developing retinal cells that co-express the Otx2 and Onecut1 (OC1) transcription factors. Variation of reporter plasmid concentration was used to generate dose response curves and revealed an effect of binding site availability on the number and strength of cells with reporter activity. Critical sequence elements of the ThrbCRM1 element were defined using both mutagenesis and misexpression of the Otx2 and OC1 transcription factors in the developing retina. Additionally, these experiments suggest that the ThrbCRM1 element is co-regulated by Otx2 and OC1 even under conditions of sub-optimal binding of OC1.

Summary Statement

Systematic variation of the levels of a transcriptional reporter plasmid, its trans-acting factors, and transcription factor binding sites reveals properties of a retinal enhancer during development.
OsCYP71D8L as a key regulator involved in growth and stress response by mediating gibberellins and cytokinins homeostasis in rice
Authors: Zhou Jiahao , Li Zeyu , Xiao Guiqing , Huang Rongfeng , Zhang Haiwen
Published: February 2019

Phytohormones are pivotal in the regulation of plant growth and development, and acclimation to adverse environments. Multiple cytochrome P450 monooxygenases (CYP450s) are involved in the biosynthesis and catabolism of phytohormones. Here, we reported that a CYP450 member of CYP71 clan, OsCYP71D8L, participated in the control of multiple agronomic traits and abiotic stress responses by affecting gibberellin (GA) and cytokinin (CK) homeostasis in rice. We found that its gain-of-function mutant (cyp71d8l) and transgenic plants overexpressing OsCYP71D8L (OsCYP71D8L-OE) displayed similar phenotypes such as dwarfed plant, reduced panicle length and grain number per panicle. In OsCYP71D8L-OE seedlings, endogenous GAs and CKs was notably decreased and increased as compared with wild type (WT), respectively. Correspondingly, the dwarfed plant and less developed root of cyp71d8l and OsCYP71D8L-OE seedlings could be rescued by exogenous GA3, but more exacerbated by exogenous 6-BA. Importantly, cyp71d8l and OsCYP71D8L-OE seedlings maintained high chlorophyll contents and low reactive oxygen species level, and showed significantly enhanced tolerances to drought and high salt compared with WT. Thus, our results suggest that OsCYP71D8L plays roles in regulating rice growth and stress responses by coordinating GAs and CKs homeostasis, and it is useful to engineer stress-tolerant rice.
C. eleganssynMuv B proteins regulate spatial and temporal chromatin compaction during development
Authors: Costello Meghan E. , Petrella Lisa N.
Published: February 2019

Tissue-specific establishment of repressive chromatin through creation of compact chromatin domains during development is necessary to ensure proper gene expression and cell fate.C. eleganssynMuv B proteins are important for the soma/germline fate decision and mutants demonstrate ectopic germline gene expression in somatic tissue, especially at high temperature. We show thatC. eleganssynMuv B proteins regulate developmental chromatin compaction and that timing of chromatin compaction is temperature sensitive in both wild-type and synMuv B mutants. Chromatin compaction in mutants is delayed into developmental time-periods when zygotic gene expression is upregulated and demonstrates an anterior-to-posterior pattern. Loss of this patterned compaction coincides with the developmental time-period of ectopic germline gene expression that leads to a developmental arrest in synMuv B mutants. Thus, chromatin organization throughout development is regulated both spatially and temporally by synMuv B proteins to establish repressive chromatin in a tissue-specific manner to ensure proper gene expression.
Unveiling the transcriptome complexity of the High- and Low- Zinc & Iron accumulating Indian wheat (Triticum aestivum L.) cultivars
Authors: Mishra Vinod Kumar , Gupta Saurabh , Chand Ramesh , Yadav Punam Singh , Singh Satish Kumar , Joshi Arun Kumar , Varadwaj Pritish Kumar
Published: February 2019

Development of Zinc (Zn), Iron (Fe) and other minerals rich grains along with various stress tolerance and susceptible (STR) wheat genotype, will help to reduce globally spread malnutrition problem. Current study deals with transcriptome profiling of 4 high- and 3 low- Zn & Fe accumulating wheat genotypes (HZFWGs) and (LZFWGs). Functional characterization of expressed and high and low specific genes, accompanied by metabolic pathways analysis reveals, phenylpropanoid biosynthesis, and other associated pathways are mainly participating in plant stress defense mechanism in both genotypes. Chlorophyll synthesis, Zn & Fe binding, metal ion transport, and ATP-Synthase coupled transport mechanism are highly active in HZFWGs while in LZFWGs ribosomal formation, biomolecules binding activities and secondary metabolite biosynthesis. Transcripts accountable for minerals uptake and purine metabolism in HZFWGs are highly enriched. Identified transcripts may be used for marker-assisted selection and breeding to develop minerals rich crops.
SHIV.CH505-infected infant and adult rhesus macaques exhibit similar HIV Env-specific antibody kinetics, despite distinct T-follicular helper (Tfh) and germinal center B cell landscapes
Authors: Nelson Ashley N. , Goswami Ria , Dennis Maria , Tu Joshua , Mangan Riley J. , Saha Pooja T. , Cain Derek W. , Shen Xiaoying , Shaw George M. , Bar Katharine , Hudgens Michael , Pollara Justin , Paris Kristina De , Van Rompay Koen K.A. , Permar Sallie R.
Published: February 2019

Pediatric HIV infection remains a large global health concern despite the widespread use of antiretroviral therapy (ART). Thus, global elimination of pediatric HIV infections will require the development of novel immune-based approaches, and understanding infant immunity to HIV is critical to guide the rational design of these intervention strategies. Despite their immunological immaturity, HIV-infected children develop broadly neutralizing antibodies (bnAbs) more frequently and earlier than adults do. Furthermore, T-follicular helper (Tfh) cells have been associated with bnAb development in HIV-infected children and adults. To further our understanding of age-related differences in the development of HIV-specific immunity, we evaluated the generation of virus-specific humoral immune responses in infant (n=6) and adult (n=12) rhesus macaques (RMs) infected with a transmitted/founder (T/F) simian-human immunodeficiency virus (SHIV.C.CH505). The plasma HIV envelope-specific IgG antibody kinetics were similar in SHIV-infected infant and adult RMs, with no significant differences in the magnitude or breadth of these responses. Interestingly, autologous tier 2 virus neutralization responses also developed with similar frequency and kinetics in infant and adult RMs, despite infants exhibiting significantly higher Tfh and germinal center B cell frequencies compared to adults. Our results indicate that the humoral immune response to SHIV infection develops with similar kinetics among infant and adult RMs, suggesting that the early life immune system is equipped to respond to HIV-1 and promote the production of neutralizing HIV antibodies.

Importance

There is a lack of understanding on how the maturation of the infant immune system influences immunity to HIV infection, or how these responses differ from those of adults. Improving our knowledge of infant HIV immunity will help guide antiviral intervention strategies that take advantage of the unique infant immune environment to successfully elicit protective immune responses. We utilized a rhesus macaque model of SHIV infection as a tool to distinguish the differences in HIV humoral immunity in infants versus adults. Here, we demonstrate that the kinetics and quality of the infant humoral immune response to HIV are highly comparable to that of adults during the early phase of infection, despite distinct differences in their Tfh responses, indicating that slightly different mechanisms may drive infant and adult humoral immunity.
Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure
Authors: Gustavsen Julia A. , Suttle Curtis A.
Published: February 2019

Marine microbes including viruses are an essential part of the marine ecosystem that forms the base of the foodweb, and drives biogeochemical cycles. Marine viral communities display repeatable changes in abundance and community composition throughout time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. Changes in the taxonomic composition within DNA bacteriophages related to T4-like viruses and marnavirus-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were examined using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomes, respectively. The results showed that for both viral marker genes, the dominant groups of phylogenetically-related viruses shifted over time and contained many transient taxa and few persistent taxa; yet, different community structures were observed in these different viral communities. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities.

Importance

Using high-throughput sequencing of coastal seawater collected every two weeks for one year, the dynamics of two groups of ecologically important groups of viruses were described in the context of their putative hosts and the environment. There was a large diversity of viruses and putative hosts in this study, and groups of phylogenetically-related viruses showed temporal dynamics in dominance. Examining the richness of viruses by phylogenetic groups showed different dynamics of either boom-bust or continued persistence. At the OTU-level, some members of these related groups persisted throughout time, while others were more ephemeral. These findings were put in context of potential quasispecies behaviour, and the dynamics of putative hosts. These results showed that temporal dynamics of viral communities have a phylogenetic signal which is important for understanding the ecology of these viruses since it elucidated one of the drivers of the community structure.
Transketolase is involved in the control of Sigma B during chronic infection byStaphylococcus aureus
Authors: Tan Xin , Ramond Elodie , Jamet Anne , Decaux-Tramoni Baptiste , Dupuis Marion , Euphrasie Daniel , Tros Fabiola , Nemazanyy Ivan , Ziveri Jason , Nassif Xavier , Charbit Alain , Coureuil Mathieu
Published: February 2019

Staphylococcus aureusis a leading cause of both acute and chronic infections in humans. Its ability to persist within host cells is thought to play an important role in chronicity and treatment failures. The importance of the pentose phosphate pathway (PPP) duringS. aureuschronic infection is currently largely unexplored. Here, we focused on one key PPP enzyme, transketolase. We showed that inactivation of the unique gene encoding transketolase activity inS. aureusUSA300 (Δtkt) led to an impaired growth in broth. Using time-lapse video imaging, we correlated this phenotype with a defect in early intracellular proliferation compared to wild-type strain. As determined by metabolomic analysis,tktinactivation also had an important impact onS. aureusmetabolism. We then monitored long-term intracellular persistence over 10 days by counting of viable bacteria. Unexpectedly for such a slow-growing strain, the Δtktmutant was almost completely eliminated by endothelial cells after ten days, as opposed to a prototypical slow-growing ΔhemDBLmutant for which we recovered 1,000 fold more viable bacteria. We found that in infected cells, the transcriptional activity of the two master regulators Sigma B and RpiRc was drastically reduced in the Δtktmutant compared to wild-type strain. Concomitantly, RNAIII transcription was strongly increased. This transcriptional profile is likely to explain the inability of this slow-growing mutant to sustain long-term intracellular survival, suggesting that TKT -or a functional PPP-is required for intracellular bacteria to enable a transcriptional program geared towards persistence.

Importance

Staphylococcus aureusis a leading cause of severe bacterial infections. This bacterium is readily internalized by non-professional phagocytes and infected cells have been proposed to play an important role in chronic infections and treatment failures.

Here, we show the importance of the unique transketolase TKT ofS. aureusUSA300 in bacterial adaptation during chronic intracellular infection. We show that TKT is mandatory for the metabolomic homeostasis ofS. aureusduring intracellular persistence. This work unravels the critical role of TKT in the transcriptional regulation of the master regulators Sigma B, RpiRc and RNAIII linking the pentose phosphate pathway to the control of chronicS. aureusinfections.
Differences in Long-Chained Cuticular Hydrocarbons between Males and Gynes inCataglyphisDesert Ants
Authors: Inbar Shani , Privman Eyal
Published: February 2019

Cuticualar hydrocarbons play an important role in chemical communication in social insects, serving, among other things, as nestmate, gender, dominance and fertility recognition cues. In ants, however, very little is known about the precopulatory signals cuticular hydrocarbons carry. These signals may serve as affecting sex pheromones and aphrodisiacs or as reliable signals for idiosyncratic traits, which indirectly affect sexual selection. In this study, we examined, for the first time, in theCataglyphisgenus, sex-specific variability in cuticular hydrocarbons. We focused on a species that exhibits split sex-ratio and found significant quantitative differences between virgin queens and their potential mates. In an analyses of both absolute amounts and relative amounts, we found different compounds to be significantly displayed on gynes and drones, suggesting absolute and relative amounts may carry different signals influencing mating behavior and mate choice. We discuss the possible signals advertised by the non-polar fraction of these hydrocarbon profiles.
HydroShoot: a functional-structural plant model for simulating hydraulic structure, gas and energy exchange dynamics of complex plant canopies under water deficit - application to grapevine (Vitis vinifera L.)
Authors: Albasha Rami , Fournier Christian , Pradal Christophe , Chelle Michael , Prieto Jorge , Louarn Gaetan , Simonneau Thierry , Lebon Eric
Published: February 2019

This paper aims at presenting HydroShoot, a functional-structural plant model (FSPM) that is developed to simulate gas-exchange rates of complex plant canopies under water deficit conditions, by scaling up gas-exchange rates from the leaf to the canopy levels. The main hypothesis is that simulating both the hydraulic structure of the shoot together with the energy budget of individual leaves is the asset for successfully achieving this up-scaling task. HydroShoot was hence built as the ensemble of three interacting modules: hydraulic which calculates the distribution of xylem water potential across shoot hydraulic segments, energy which calculates the complete energy budget of individual leaves, and exchange which calculates net assimilation and transpiration rates of individual leaves. HydroShoot was coupled with irradiance interception and soil water balance models, and was evaluated on virtual and real grapevines having strongly contrasted canopies, under well-watered and water-deficit conditions. HydroShoot captured accurately the impact of canopy architecture and the varying soil water deficit conditions on plant-scale gas-exchange rates and leaf-scale temperature and water potential distributions. Both shoot hydraulic structure and leaf energy budget simulations were, as postulated, required to adequately scaling-up leaf to canopy gas-exchange rates. Notwithstanding, simulating the hydraulic structure of the shoot was found far more necessary to adequately performing this scaling task than simulating leaf energy balance. That is, the intra-canopy variability of leaf water potential was a better predictor of the reduction of whole plant gas-exchange rates under water deficit than the intra-canopy variability of leaf temperature. We conclude therefore that simulating the shoot hydraulic structure is a prerequisite if FSPM's are to be used to assess gas-exchange rates of complex plant canopies as those of grapevines. Finally HydroShoot is available through the OpenAlea platform (https://github.com/openalea/hydroshoot) as a set of reusable modules.