bluuebunny/crossref_metadata_2025 huggingface dataset:
Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India
Authors: Woodworth Michael H. , Dynerman David , Crawford Emily D. , Li Lucy M. , Doernberg Sarah B. , Ramirez-Avila Lynn , Serpa Paula Hayakawa , Nichols Amy , Lyden Amy , Tato Cristina M. , Miller Steve , Derisi Joseph L. , Langelier Charles
Published: April 2019

Candida auris is an emerging multidrug-resistant yeast with high mortality. We report the sentinel C. auris case on the United States West Coast in a patient who relocated from India. We identified close phylogenetic relatedness to the South Asia clade and ERG11 Y132F and FKS1 S639Y mutations potentially explaining antifungal resistance.
In situstructure of rotavirus VP1 RNA-dependent RNA polymerase
Authors: Jenni Simon , Salgado Eric N. , Herrmann Tobias , Li Zongli , Grant Timothy , Grigorieff Nikolaus , Trapani Stefano , Estrozi Leandro F. , Harrison Stephen C.
Published: April 2019

Rotaviruses, like other non-enveloped, double-strand RNA (dsRNA) viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the “double-layer particle” or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each fivefold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRpin situ, by local reconstruction of density around individual fivefold positions. We have analyzed intact virions (“triple-layer particles” or TLPs), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA,in vitroas well asin vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosyl methionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, dsRNA genome.
Deleterious Mutation Accumulation and the Long-Term Fate of Chromosomal Inversions
Authors: Berdan Emma L. , Blanckaert Alexandre , Butlin Roger K. , Bank Claudia
Published: April 2019

Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.

Author Summary

A chromosomal inversion is a segment of the chromosome that is flipped (inverted arrangement) relative to the normal orientation (standard arrangement). Such structural mutations may facilitate evolutionary processes such as adaptation and speciation, because reduced recombination in inverted regions allows beneficial combinations of alleles to behave as a “single unit”. This locally reduced recombination can have major consequences for the evolution of the allelic content inside the inversion. We used simulations to investigate some of these consequences. Inverted regions tended to accumulate more deleterious recessive mutations than the rest of the genome, which decreased the fitness of homokarotypes (individuals with two copies of the same arrangement). This led to a strong selective advantage for heterokaryotypes (individuals with one copy of each arrangement), maintaining the inversion polymorphism in the population. The accumulation of deleterious mutations also resulted in strong divergence between arrangements. We occasionally observed an arrangement that diverged into a small number of highly differentiated haplotypes, stopping the fitness decrease in homokaryotypes. Our results highlight the dynamic features of inversions by showing how the evolution of allelic content can greatly affect the fate of an inversion.
Inflammasome-independent role for NLRP3 in controlling innate anti-helminth immunity and tissue repair in the lung
Authors: Chenery AL , Alhallaf R , Agha Z , Ajendra J , Parkinson JE , Cooper MM , Chan BHK , Eichenberger RM , Dent LA , Robertson AAB , Kupz A , Brough D , Loukas A , Sutherland TE , Allen JE , Giacomin PR
Published: April 2019

Alternatively activated macrophages are essential effector cells during type 2 immunity and tissue repair following helminth infections. We previously showed that Ym1, an alternative activation marker, can drive innate IL-1R-dependent neutrophil recruitment during infection with the lung-migrating nematode, Nippostrongylus brasiliensis suggesting a potential role for the inflammasome in the IL-1-mediated innate response to infection. While inflammasome proteins such as NLRP3 have important pro-inflammatory functions in macrophages, their role during type 2 responses and repair are less defined. We therefore infected Nlrp3−/− mice with N. brasiliensis. Unexpectedly, compared to WT mice, infected Nlrp3−/− mice had increased neutrophilia and eosinophilia, correlating with enhanced worm killing but at the expense of increased tissue damage and delayed lung repair. Transcriptional profiling showed that infected Nlrp3−/− mice exhibited elevated type 2 gene expression compared to WT mice. Notably, inflammasome activation was not evident early post-infection with N. brasiliensis and in contrast to Nlrp3−/− mice, anti-helminth responses were unaffected in caspase-1/11 deficient or WT mice treated with the NLRP3-specific inhibitor MCC950. Together these data suggest that NLRP3 can constrain lung neutrophilia and helminth killing and negatively regulate type 2 immune responses in an inflammasome-independent manner.
Generation of viral vectors specific to neuronal subtypes of targeted brain regions by Enhancer-Driven Gene Expression (EDGE)
Authors: Nair Rajeevkumar Raveendran , Blankvoort Stefan , Lagartos Maria Jose , Kentros Cliff
Published: April 2019

Understanding brain function requires understanding neural circuits at the level of specificity at which they operate. While recent years have seen the development of a variety of remarkable molecular tools for the study of neural circuits, their utility is currently limited by the inability to deploy them in specific elements of native neural circuits, i.e. particular neuronal subtypes. One can obtain a degree of specificity with neuron-specific promoters, but native promoters are almost never sufficiently specific restricting this approach to transgenic animals. We recently showed that one can obtain transgenic mice with augmented anatomical specificity in targeted brain regions by identifyingcis-regulatory elements (i.e. enhancers) uniquely active in those brain regions and combining them with a heterologous promoter, an approach we call EDGE (Enhancer-Driven Gene Expression). Here we extend this strategy to the generation of viral (rAAV) vectors, showing that when combined with the right minimal promoter they largely recapitulate the specificity seen in the corresponding transgenic lines in wildtype animals, even of another species. Because active enhancers can be identified in any tissue sample, this approach promises to enable the kind of circuit-specific manipulations in any species. This should not only greatly enhance our understanding of brain function, but may one day even provide novel therapeutic avenues to correct the imbalances in neural circuits underlying many disorders of the brain.
The Role of the Subthalamic Nucleus in Inhibitory Control of Oculomotor Behavior in Parkinson’s Disease
Authors: Bakhtiari Shahab , Altinkaya Ayca , Pack Christopher C. , Sadikot Abbas F.
Published: April 2019

The ability to inhibit an inappropriate action in a context is an important part of the human cognitive repertoire, and deficiencies in this ability are common in neurological and psychiatric disorders. An anti-saccade is a simple experimental task within the oculomotor repertoire that can be used to test this ability. The task involves an inhibition of a saccade to the peripheral target (pro-saccade) and generation of a voluntary eye movement toward the mirror position (anti-saccade). Previous studies provide evidence for a possible contribution from the basal ganglia in anti-saccade behavior. However, the precise role of different components in generation of anti-saccade behavior is still uncertain. Parkinson’s disease patients with implanted deep brain stimulation (DBS) in subthalamic nucleus (STN) provide us with a unique opportunity to investigate the role of STN in anti-saccade behavior. Previous attempts to show the effect of STN DBS on anti-saccades have produced conflicting observations. For example, the effect of STN DBS on anti-saccade error rate is not yet clear. Part of this inconsistency may be related to differences in dopaminergic states in different studies. Here, we tested Parkinson’s disease patients on anti- and pro-saccade tasks ON and OFF STN DBS and ON and OFF dopaminergic medication. We made three main observations. First, STN DBS increases the anti-saccade error rate while patients are OFF dopamine replacement therapy. Second, there is an interaction between dopamine replacement therapy and STN DBS. More specifically, L-dopa reduces the effect of STN DBS on anti-saccade error rate. Third, STN DBS can induce different effects on pro- and anti-saccades in different patients. These observations provide evidence for an important role for the STN in the circuitry underlying context-dependent modulation of visuomotor action selection.
Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific
Authors: de Barros Dantas Luíza Lane , Almeida-Jesus Felipe Marcelo , de Lima Natalia Oliveira , Alves-Lima Cícero , Nishiyama Milton Yutaka , Carneiro Monalisa Sampaio , Souza Glaucia Mendes , Hotta Carlos Takeshi
Published: April 2019

We investigated whether different specialized organs in field-grown sugarcane follow the same temporal rhythms in transcription. We assayed the transcriptomes of three organs during the day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the two internodes were more similar to each other than to those of the leaves. More transcripts were rhythmic under field conditions than under circadian conditions and most of their peaks were during the day. Among the transcripts that were considered expressed in all three organs, only 7.4% showed the same rhythmic time course pattern. The central oscillators of these three organs — the networks that generate circadian rhythms — had similar dynamics with different amplitudes. The differences between the rhythmic transcriptomes in circadian conditions and field conditions highlight the importance of field experiments to understand the plant circadian clock in natura. The highly specialized nature of the rhythmic transcriptomes in sugarcane organs probably arises from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues.

One sentence summary

The rhythmic transcriptome of field-grown sugarcane is highly organ-specific.
Aging induces Nlrp3 inflammasome dependent adipose B cell expansion to impair metabolic homeostasis
Authors: Camell Christina D. , Lee Aileen , Günther Patrick , Goldberg Emily L. , Spadaro Olga , Youm Yun-Hee , Bartke Andrzej , Hubbard Gene B. , Ikeno Yuji , Ruddle Nancy H. , Schultze Joachim , Dixit Vishwa Deep
Published: April 2019

Visceral adiposity in elderly is associated with alterations in adipose tissue immune cells leading to inflammation and metabolic dysfunction. The Nlrp3 inflammasome is a critical regulator of macrophage activation, inflammation, and immunometabolism in visceral adipose tissue during aging; however, the potential contribution of adipose tissue B cells is unexplored. Here, we show that aging expands adipose-resident B cells and fat-associated lymphoid clusters (FALCs) in visceral white adipose tissue. Adipose tissue B cells exhibit a memory-like B cell profile similar to the phenotype of aged B cells that are increased in spleen of old mice. Mechanistically, the age-induced FALC formation and adipose B cell expansion, but not B cell transcriptional program, is dependent on the Nlrp3 inflammasome. Furthermore, B cell depletion in aged mice restores lipolysis and defense against loss of core body temperature during cold stress. These data reveal that inhibiting Nlrp3-dependent B cell accumulation can be targeted to reverse metabolic impairment in aging adipose tissue.

Highlights

- Adipose-resident aged B cells are increased in fat-associated lymphoid clusters (FALC)

- FALC formation and adipose-resident B cell expansion during aging are regulated by the Nlrp3 inflammasome

- Nlrp3 and B cell depletion in aging restores lipolysis and improves cold tolerancea
An analytical theory of balanced cellular growth
Authors: Dourado Hugo , Lercher Martin J.
Published: April 2019

The biological fitness of unicellular organisms is largely determined by their balanced growth rate, i.e., by the rate with which they replicate their biomass composition. Natural selection on this growth rate occurred under a set of physicochemical constraints, including mass conservation, reaction kinetics, and limits on dry mass per volume; mathematical models that maximize the balanced growth rate while accounting explicitly for these constraints are inevitably nonlinear and have been restricted to small, non-realistic systems. Here, we lay down a general theory of balanced growth states, providing explicit expressions for protein concentrations, fluxes, and the growth rate. These variables are functions of the concentrations of cellular components, for which we calculate marginal fitness costs and benefits that can be related to metabolic control coefficients. At maximal growth rate, the net benefits of all concentrations are equal. Based solely on physicochemical constraints, the growth balance analysis (GBA) framework introduced here unveils fundamental quantitative principles of cellular growth and leads to experimentally testable predictions.
Mapping-based Genome Size Estimation
Authors: Natarajan Shakunthala , Gehrke Jessica , Pucker Boas
Published: April 2019

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses ofArabidopsis thalianaandBeta vulgarisdata sets are presented to show the impact of different parameters.Oryza sativa, Brachypodium distachyon,Solanum lycopersicum,Vitis vinifera, andZea mayswere also analyzed to demonstrate the broad applicability of this approach. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub:https://github.com/bpucker/MGSE.
Motto: Representing motifs in consensus sequences with minimum information loss
Authors: Wang Mengchi , Wang David , Zhang Kai , Ngo Vu , Fan Shicai , Wang Wei
Published: April 2019

Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, representing motifs by wildcard-style consensus sequences is compact and sufficient for interpreting the motif information and search for motif match. Based on mutual information theory and Jenson-Shannon Divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus sequences. We name this representation as sequence Motto and have implemented an efficient algorithm with flexible options for converting motif PWMs into Motto from nucleotides, amino acids, and customized alphabets. Here we show that this representation provides a simple and efficient way to identify the binding sites of 1156 common TFs in the human genome. The effectiveness of the method was benchmarked by comparing sequence matches found by Motto with PWM scanning results found by FIMO. On average, our method achieves 0.81 area under the precision-recall curve, significantly (p-value < 0.01) outperforming all existing methods, including maximal positional weight, Douglas and minimal mean square error. We believe this representation provides a distilled summary of a motif, as well as the statistical justification.

AVAILABILITY

Motto is freely available at http://wanglab.ucsd.edu/star/motto.
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
Authors: Cernilogar Filippo M. , Hasenöder Stefan , Wang Zeyang , Scheibner Katharina , Burtscher Ingo , Sterr Michael , Smialowski Pawel , Groh Sophia , Evenroed Ida M. , Gilfillan Gregor D. , Lickert Heiko , Schotta Gunnar
Published: April 2019

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.
Individual differences in the influence of mental imagery on conscious perception
Authors: Dijkstra N. , Hinne M. , Bosch S.E. , van Gerven M.A.J.
Published: April 2019

Mental imagery and visual perception rely on similar neural mechanisms, but the function of this overlap remains unclear. One idea is that imagery can influence perception. Previous research has shown that imagining a stimulus prior to binocular presentation of rivalling stimuli increases the chance of perceiving the imagined stimulus. In this study we investigated how this effect interacts with bottom-up sensory input by comparing psychometric response curves for congruent and incongruent imagery in humans. A Bayesian hierarchical model was used, allowing us to simultaneously study group-level effects as well as effects for individual participants. We found strong effects of both imagery as well as its interaction with sensory evidence within individual participants. However, the direction of these effects were highly variable between individuals, leading to weak effects at the group level. This highlights the heterogeneity of conscious perception and emphasizes the need for individualized investigation of such complex cognitive processes.
Phylogenetic and Spatial Distribution of Evolutionary Isolation and Threat in Turtles and Crocodilians (Non-Avian Archosauromorphs)
Authors: Colston Timothy J. , Kulkarni Pallavi , Jetz Walter , Pyron R. Alexander
Published: April 2019

The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and ~360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with machine learning algorithms to present a phylogenetically-informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. In contrast to other terrestrial vertebrates and their own diversity in the fossil record, extant turtles and crocodilians have not experienced any mass extinctions or shifts in diversification rate, or any significant jumps in rates of body-size evolution over time. We predict threat for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened crocodile and turtle species in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies.
MerMAIDs: A novel family of metagenomically discovered, marine, anion-conducting and intensely desensitizing channelrhodopsins
Authors: Oppermann Johannes , Fischer Paul , Silapetere Arita , Liepe Bernhard , Rodriguez-Rozada Silvia , Flores-Uribe José , Peter Enrico , Keidel Anke , Vierock Johannes , Kaufmann Joel , Broser Matthias , Luck Meike , Bartl Franz , Hildebrandt Peter , Wiegert J. Simon , Béjà Oded , Hegemann Peter , Wietek Jonas
Published: April 2019

Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. We describe a novel, metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of further novel optogenetic tools from metagenomic databases and enhance general understanding of ChR function.
Yorkie and JNK revert syncytial muscles into myoblasts during Org-1 dependent lineage reprogramming
Authors: Schaub Christoph , Rose Marcel , Frasch Manfred
Published: April 2019

Lineage reprogramming has become a prominent focus in research since it was demonstrated that lineage restricted transcription factors can be used in vitro for direct reprogramming [1]. Recently, we reported that the ventral longitudinal musculature (VLM) of the adult Drosophila heart arises in vivo by direct lineage reprogramming from alary muscles (AM), a process which starts with dedifferentiation and fragmentation of syncytial alary muscles into mononucleate myoblasts. Central upstream activators of the genetic program regulating the development of VLMs from alary muscles are the T-box factor Org-1 (Drosophila Tbx1) and the LIM homeodomain factor Tup (Drosophila Islet1) [2]. However, the events downstream of Org-1 and Tup that exert dedifferentiation and fragmentation of alary muscles have been unknown. In the present report, we shed light on the initiation of this first step of transdifferentiation and show that AM lineage specific activation of Yorkie (Yki), the transcriptional co-activator of the transcription factor Scalloped (Sd), has a key role in initiating AM lineage reprogramming. An additional necessary input comes from active dJNK signaling, which contributes to the inactivation of the Hippo kinase cascade upstream of Yki and furthermore activates dJun. The synergistic activities of the Yki/Sd and dJun/dFos (AP-1) transcriptional activator complexes in the absence of Hippo activity initiate AM dedifferentiation and lead to the expression of Myc and piwi, which are crucial for different aspects of AM transdifferentiation. Our results provide new insights into the mechanisms that mediate muscle lineage plasticity during a cellular reprogramming process occurring in vivo.

Highlights

Direct lineage reprogramming of alary muscles depends on Yorkie and JNK

Yorkie and JNK mediate reversal of syncytial muscle cell fate

Yki/Sd and AP-1 induce alary muscle dedifferentiation synergistically

Yki dependent Myc induces and Piwi mediates reprogramming of alary muscles
Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda
Authors: Zhang Dong , Zou Hong , Hua Cong-Jie , Li Wen-Xiang , Mahboob Shahid , Al-Ghanim Khalid Abdullah , Al-Misned Fahad , Jakovlić Ivan , Wang Gui-Tang
Published: April 2019

The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different datasets often producing starkly incongruent phylogenetic hypotheses. We hypothesised that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different datasets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artefacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artefacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements can produce major compositional biases even on short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
Correlation of mRNA delivery timing and protein expression in lipid-based transfection
Authors: Reiser A. , Woschée D. , Mehrotra N. , Krzysztoń R. , Strey H. H. , Rädler J. O.
Published: April 2019

Non-viral gene delivery is constrained by the dwell time that most synthetic nucleic acid nanocarriers spend inside endosomal compartments. In order to overcome this endosomal-release bottleneck, methods are required that measure nanocarrier uptake kinetics and transfection efficiency simultaneously. Here, we employ live-cell imaging on single-cell arrays (LISCA) to study the delivery-time distribution of lipid-based mRNA complexes under varied serum conditions. By fitting a translation-maturation model to hundreds of individual eGFP reporter fluorescence time courses, the protein expression onset times and the expression rates after transfection are determined. Using this approach, we find that delivery timing and protein expression rates are not intrinsically correlated at the single-cell level, even though population-averaged values of both parameters conjointly change as a function of increasing external serum protein fraction. Lipofectamine mediated delivery showed decreased transfection efficiency and longer delivery times with increasing serum protein concentration. This is in contrast to ionizable lipid nanoparticles (LNPs) mediated transfer, which showed increased efficiency and faster uptake in the presence of serum. In conclusion, the interdependences of single-cell expression rates and onset timing provide additional clues on uptake and release mechanisms, which are useful for improving nucleic acid delivery.
Targeted sequence capture outperforms RNA-Seq and degenerate-primer PCR cloning for sequencing the largest mammalian multi-gene family
Authors: Yohe Laurel R. , Davies Kalina T. J. , Simmons Nancy B. , Sears Karen E. , Dumont Elizabeth R. , Rossiter Stephen J. , Dávalos Liliana M.
Published: April 2019

Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for both sequencing and downstream analyses. Focusing on the common vampire bat,Desmodus rotundus, we evaluated how different sequencing approaches performed in recovering the largest mammalian protein-coding multigene family:olfactory receptors(OR). Using the common vampire bat genome as a reference, we determined the proportion of putatively protein-coding receptors recovered by: 1) amplicons from degenerate primers sequenced via Sanger technology, 2) RNA-Seq of the main olfactory epithelium, and 3) those genes “captured” with probes designed from transcriptomes of closely-related species. Our initial re-annotation of the high-quality vampire bat genome resulted in >400 intactORgenes, more than double the number based on original estimates. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomicORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all putative receptors in the genome. Therefore, variation among assemblies was caused by low coverage of some receptors, rather than high rates of assembly error. Given this variability, we caution against using the counts of number of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes.
Shared genetic etiology between obsessive-compulsive disorder, obsessive-compulsive symptoms in the population, and insulin signaling
Authors: Bralten Janita , Widomska Joanna , De Witte Ward , Yu Dongmei , Mathews Carol A. , Scharf Jeremiah M. , Buitelaar Jan , Crosbie Jennifer , Schachar Russell , Arnold Paul , Lemire Mathieu , Burton Christie L. , Franke Barbara , Poelmans Geert
Published: April 2019

Objective

Obsessive-compulsive symptoms (OCS) in the population have been linked to obsessive-compulsive disorder (OCD) in genetic and epidemiological studies. Insulin signaling has been implicated in OCD. We extend previous work by assessing genetic overlap between OCD, population-based OCS, and central nervous system (CNS) and peripheral insulin signaling.

Methods

We conducted genome-wide association studies (GWASs) in the population-based Philadelphia Neurodevelopmental Cohort (PNC, 650 children and adolescents) of the total OCS score and six OCS factors from an exploratory factor analysis of 22 questions. Subsequently, we performed polygenic risk score (PRS) analysis to assess shared genetic etiologies between clinical OCD (using GWAS data from the Psychiatric Genomics Consortium), the total OCS score and OCS factors. We then performed gene-set analyses with a set of OCD-linked genes centered around CNS insulin-regulated synaptic function and PRS analyses for five peripheral insulin signaling-related traits. For validation purposes, we explored data from the independent Spit for Science population cohort (5047 children and adolescents).

Results

In the PNC, we found a shared genetic etiology between OCD and ‘impairment’, ‘contamination/cleaning’ and ‘guilty taboo thoughts’. In the Spit for Science cohort, we were able to validate the finding for ‘contamination/cleaning’, and additionally observed genetic sharing between OCD and ‘symmetry/counting/ordering’. The CNS insulin-linked gene-set associated with ‘symmetry/counting/ordering’. We also identified genetic sharing between peripheral insulin signaling-related traits (type 2 diabetes and the blood levels of HbA1C, fasting insulin and 2 hour glucose) and OCD as well as certain OCS.

Conclusions

OCD, OCS in the population and insulin-related traits share genetic risk factors, indicating a common etiological mechanism underlying somatic and psychiatric disorders.
Pericytes enable effective angiogenesis in the presence of pro-inflammatory signals
Authors: Kang Tae-Yun , Bocci Federico , Jolly Mohit Kumar , Levine Herbert , Onuchic José Nelson , Levchenko Andre
Published: April 2019

Angiogenesis frequently occurs in the context of acute or persistent inflammation. The complex interplay of pro-inflammatory and pro-angiogenic cues is only partially understood. Using a new experimental model permitting exposure of developing blood vessel sprouts to multiple combinations of diverse biochemical stimuli and juxtacrine cell interactions, we present evidence that a pro-inflammatory cytokine, tumor necrosis factor (TNF), can have both pro- and anti-angiogenic effects, depending on the dose and the presence of pericytes. In particular, we find that pericytes can rescue and enhance angiogenesis in the presence of otherwise inhibitory high TNF doses. This sharp switch from pro- to anti-angiogenic effect of TNF observed with an escalating dose of this cytokine, as well as the effect of pericytes are explained by a mathematical model trained on the biochemical data. Furthermore, this model was predictive of the effects of diverse combinations of pro-and anti-inflammatory cues, and variable pericyte coverage. The mechanism supports the effect of TNF and pericytes as modulating signaling networks impinging in Notch signaling and specification of the Tip and Stalk phenotypes. This integrative analysis elucidates the plasticity of the angiogenic morphogenesis in the presence of diverse and potentially conflicting cues, with immediate implications for many physiological and pathological settings.
PyRates – A Python Framework for rate-based neural Simulations
Authors: Gast Richard , Rose Daniel , Möller Harald E. , Weiskopf Nikolaus , Knösche Thomas R.
Published: April 2019

In neuroscience, computational modeling has become an important source of insight into brain states and dynamics. A basic requirement for computational modeling studies is the availability of efficient software for setting up models and performing numerical simulations. While many such tools exist for different families of neural models, there is a lack of tools allowing for both a generic model definition and efficiently parallelized simulations. In this work, we present PyRates, a Python framework that provides the means to build a large variety of neural models as a graph. PyRates provides intuitive access to and modification of all mathematical operators in a graph, thus allowing for a highly generic model definition. For computational efficiency and parallelization, the model graph is translated into atensorflow-based compute graph. Using the example of two different neural models belonging to the family of rate-based population models, we explain the mathematical formalism, software structure and user interfaces of PyRates. We then show via numerical simulations that the behavior shown by the model implementations in PyRates is consistent with the literature. Finally, we demonstrate the computational capacities and scalability of PyRates via a number of benchmark simulations of neural networks differing in size and connectivity.
Inhibiting fibroblast aggregation in skin wounds unlocks developmental pathway to regeneration
Authors: Seifert Ashley W. , Cook Adam B. , Shaw Douglas
Published: April 2019

Salamanders are capable of full-thickness skin regeneration where removal of epidermis, dermis and hypodermis results in scar-free repair. What remains unclear is whether regeneration of these tissues recapitulates the cellular events of skin development or occurs through a process unique to regenerative healing. Unfortunately, information on the post-embryonic development of salamander skin is severely lacking, having focused on compartments or cell types, but never on the skin as a complete organ. By examining coordinated development of the epidermis and dermis in axolotls we establish six distinct stages of skin development (I-VI): I-V for normally paedomorphic adults and a sixth stage following metamorphosis. Raising animals either in isolation (zero density pressure) or in groups (density pressure) we find that skin development progresses as a function of animal size and that density directly effects developmental rate. Using keratins, p63, and proliferative markers, we show that although the epidermis lacks visible stratification at early stages of skin development, when the dermis transforms into the stratum spongiosum and stratum compactum keratinocytes differentiate into at least three distinct phenotypes that reveal a cryptic stratification program uncoupled from metamorphosis. Lastly, comparing skin regeneration to skin development, we find that dermal regeneration occurs through a unique process, relying heavily on remodeling of the wound extracellular matrix, rather than proceeding through direct development of a dermal lamella produced by the epidermis. By preventing fibroblast influx into the wound bed using beryllium nitrate, we show that in the absence of fibroblast generated ECM production skin regeneration occurs through an alternate route that recapitulates development.
Elementary Growth Modes provide a molecular description of cellular self-fabrication
Authors: de Groot Daan H. , Hulshof Josephus , Teusink Bas , Bruggeman Frank J. , Planqué Robert
Published: April 2019

A major aim of biology is to predict phenotype from genotype. Here we ask if we can describe all possible molecular states (phenotypes) for a cell that fabricates itself at a constant rate, given its enzyme kinetics and the stoichiometry of all reactions (the genotype). For this, we must understand the autocatalytic process of cellular growth which is inherently nonlinear: steady-state self-fabrication requires a cell to synthesize all of its components, including metabolites, enzymes and ribosomes, in the proportions that exactly match its own composition – the growth demand thus depends on the cellular composition. Simultaneously, the concentrations of these components should be tuned to accomplish this synthesis task – the cellular composition thus depends on the growth demand. We here derive a theory that describes all phenotypes that solve this circular problem; the basic equations show how the concentrations of all cellular components and reaction rates must be balanced to get a constant self-fabrication rate. All phenotypes can be described as a combination of one or more minimal building blocks, which we call Elementary Growth Modes (EGMs). EGMs can be used as the theoretical basis for all models that explicitly model self-fabrication, such as the currently popular Metabolism and Expression models. We then used our theory to make concrete biological predictions: we find that natural selection for maximal growth rate drives microorganisms to states of minimal phenotypic complexity: only one EGM will be active when cellular growth rate is maximised. The phenotype of a cell is only extended with one more EGM whenever growth becomes limited by an additional biophysical constraint, such as a limited solvent capacity of a cellular compartment. Our theory starts from basic biochemical and evolutionary considerations, and describes unicellular life, both in growth-promoting and in stress-inducing environments, in terms of EGMs, the universal building blocks of self-fabrication and a cell’s phenotype.
A generalized framework of AMOVA with any number of hierarchies and any level of ploidies
Authors: Huang Kang , Li Yuli , Dunn Derek W. , Zhang Pei , Li Baoguo
Published: April 2019

The analysis of molecular variance (AMOVA) is a widely used statistical model in the studies of population genetics and molecular ecology. The classical framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in contemporary species. The ploidy level may even vary within the same species, even within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for the multilocus genotypic and allelic phenotypic data. We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a software, POLYGENE, which is freely available athttps://github.com/huangkang1987/.
Spatial clustering of inhibition in mouse primary visual cortex
Authors: Bista Pawan , D’Souza Rinaldo D. , Meier Andrew M. , Ji Weiqing , Burkhalter Andreas
Published: April 2019

Whether mouse visual cortex contains orderly feature maps is debated. The overlapping pattern of geniculocortical (dLGN) inputs with M2 muscarinic acetylcholine receptor-rich patches in layer 1 (L1) suggests a non-random architecture. Here, we found that L1 inputs from the lateral posterior thalamus (LP) avoid patches and target interpatches. Channelrhodopsin-assisted mapping of EPSCs in L2/3 shows that the relative excitation of parvalbumin-expressing interneurons (PVs) and pyramidal neurons (PNs) by dLGN, LP and cortical feedback are distinct and depend on whether the neurons reside in clusters aligned with patches or interpatches. Paired recordings from PVs and PNs shows that unitary IPSCs are larger in interpatches than patches. The spatial clustering of inhibition is matched by dense clustering of PV-terminals in interpatches. The results show that the excitation/inhibition balance across V1 is organized into patch and interpatch subnetworks which receive distinct long-range inputs and are specialized for the processing of distinct spatiotemporal features.
Effect of Electromagnetic Field (EMF) and Electric Field (EF) on Some Behavior of Honeybees (Apis melliferaL.)
Authors: Erdoğan Yaşar , Cengiz Mahir Murat
Published: April 2019

Geomagnetic field can be used by different magnetoreception mechanisms, for navigation and orientation by honeybees. The present study analyzed the effects of magnetic field on honeybees. This study was carried out in 2017 at the Bayburt University Beekeeping Application Station. In this study, the effect of Electro Magnetic field (EMF) and electric field (EF) on the time of finding the source of food of honeybees and the time of staying there were determined. The honeybees behaviors were analyzed in the presence of external magnetic fields generated by Helmholtz coils equipment. The Electro Magnetic field values of the coils were fixed to 0 μT (90mV/m), 50 μT (118 mV/m), 100 μT (151 mV/m), 150 μT (211 mV/m), 200 μT (264 mV/m). Petri dishes filled with sugar syrup were placed in the center of the coils. According to the study, honeybees visited at most U1 (mean =21.0±17.89 bees) and at least U5 (mean =10.82±11.77 bees). Honeybees waited for the longest time in U1 (mean =35.27±6.97 seconds) and at least in U5 (mean =12.28±5.58 seconds). According to the results obtained from this first study showed that honeybees are highly affected by electromagnetic radiation and electric field.

Honeybees uses the magnetic field of the earth to to determine their direction. Nowadays, the rapid spread of electrical devices and mobile towers leads to an increase in man-made EMF. This causes honeybees to lose their orientation and thus lose their hives.
A rapid and automated sample-to-result Candida auris real-time PCR assay for high-throughput testing of surveillance samples with BD MAX™ open system
Authors: Leach L. , Russell A. , Zhu Y. , Chaturvedi S. , Chaturvedi V.
Published: April 2019

The multidrug-resistant yeast pathogen Candida auris continues to cause outbreaks and clusters of clinical cases worldwide. Previously, we developed a real-time PCR assay for the detection of C. auris from surveillance samples (Leach et al. JCM. 2018: 56, e01223-17). The assay played a crucial role in the ongoing investigations of C. auris outbreak in New York City. To ease the implementation of the assay in other laboratories, we developed an automated sample-to-result real-time C. auris PCR assay using BD MAX™ open system. We optimized sample extraction at three different temperatures and four incubation periods. Sensitivity was determined using eight pools of patient samples, and specificity was calculated using four clades of C. auris, and closely and distantly related yeasts. Three independent extractions and testing of two patient sample pools in the quadruplicate yielded assay precision. BD MAX™ optimum assay conditions were: DNA extraction at 75°C for 20 min, and the use of PerfeCTa Multiplex qPCR ToughMix. The limit of detection (LOD) of the assay was one C. auris CFU/PCR reaction. We detected all four clades of C. auris without cross-reactivity to other yeasts. Of the 110 patient surveillance samples tested, 50 were positive for C. auris using the BD MAX™ System with 96% clinical sensitivity and 94% accuracy compared to the manual assay. BD MAX™ assay allows high-throughput C. auris screening of 180 surveillance samples in a 12-hour workday.