bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-cost, open-access refractive index mapping of algal cells using the transport of intensity equation
Authors: Grant Stephen , Richford Kyle , Burdett Heidi , McKee David , Patton Brian R. 
Published: May 2019

AbstractPhase contrast microscopy allows stain free imaging of transparent biological samples. One technique, using the transport of intensity equation (TIE), can be performed without dedicated hardware by simply processing pairs of images taken at known spacings within the sample. The resulting TIE images are quantitative phase maps of unstained biological samples. Therefore, spatially resolved refractive index information can also be determined.Using low-cost, open-source hardware, we applied the TIE to living algal cells to measure their refractive index. We obtained refractive index values that were repeatable within species and differed by distinct amounts depending on the species being measured. We suggest TIE imaging as a method of discrimination between different algal species and, potentially, non-biological materials, based on refractive index. Potential applications in biogeochemical modelling and climate sciences are suggested.
Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual
Authors: Sanderson Brian J. , Park Sunchung , Jameel M. Inam , Kraft Joshua C. , Thomashow Michael F. , Schemske Douglas W. , Oakley Christopher G. 
Published: May 2019

ABSTRACTPremise of the studyDespite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Sweden and Italy provides the essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress.MethodsHere we examine the consequences of a naturally occurring loss of function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing of the Italian CBF2 allele, and two were created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression both before and after cold acclimation.Key resultsFreezing tolerance was greater in the Swedish (72%) compared to the Italian (11%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified ten genes for which all CBF2 LOF lines and the IT ecotype showed similar patterns of reduced cold responsive expression compared to the SW ecotype.ConclusionsWe identified ten genes that are at least partially regulated by CBF2 that may contribute to the differences in cold acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.
Liraglutide improves hepatic steatosis and metabolic dysfunctions in a 3-week dietary mouse model of non-alcoholic steatohepatitis
Authors: Duparc Thibaut , Briand François , Trenteseaux Charlotte , Mérian Jules , Combes Guillaume , Najib Souad , Sulpice Thierry , Martinez Laurent O. 
Published: May 2019

ABSTRACTAimNon-alcoholic steatohepatitis (NASH) is an emerging health problem worldwide. However, efficacious pharmacological treatment for NASH is lacking. A major issue for preclinical evaluation of potential therapeutics for NASH is the limited number of appropriate animal models, i.e., models that do not require long-term dietary intervention and adequately mimic disease progression in humans. The present study aimed to evaluate a 3-week dietary mouse model of NASH and to validate it by studying the effects of liraglutide, a compound in advanced clinical development for NASH.MethodsC57BL6/J mice were fed a diet high in fat (60%), cholesterol (1.25%) and cholic acid (0.5%) along with 2% hydroxypropyl-β-cyclodextrin in drinking water (HFCC-CDX diet). Histological and biological parameters were measured at 1 and 3 weeks. Following 1-week diet induction, liraglutide was administrated daily for 2 weeks, and then NASH-associated phenotypic aspects were evaluated in comparison with control mice.ResultsPrior to treatment with liraglutide, mice fed the HFCC-CDX diet for 1 week developed liver steatosis and had increased levels of oxidative-stress markers and hepatic and systemic inflammation. For mice not treated with liraglutide, these aspects were even more pronounced after 3 weeks of the dietary period, with additional liver insulin resistance and fibrosis. Liraglutide treatment corrected the diet-induced alterations in glucose metabolism and significantly reduced hepatic steatosis and inflammation.ConclusionThis study provides a novel 3-week dietary model of mice that rapidly develop NASH features, and this model will be suitable for evaluating the therapeutic efficacy of compounds in preclinical drug development for NASH.
Increasing cerebral blood flow improves cognition into late stages in Alzheimer’s disease mice
Authors: Bracko Oliver , Njiru Brendah N. , Swallow Madisen , Ali Muhammad , Schaffer Chris B. 
Published: May 2019

AbstractAlzheimer’s disease (AD) is associated with a 20-30% reduction in cerebral blood flow. In the APP/PS1 mouse model of AD, inhibiting neutrophil adhesion using an antibody against the neutrophil specific protein Ly6G was recently shown to drive rapid improvements in cerebral blood flow that was accompanied by an improvement in performance on short-term memory tasks. Here, in a longitudinal aging study, we assessed how far into disease development a single injection of anti-Ly6G can acutely improve memory function. We found that APP/PS1 mice as old as 15-16 months had improved performance on the object replacement and Y-maze tests of short-term memory, measured at one day after anti-Ly6G treatment. APP/PS1 mice 17-18 months of age or older did not show acute improvements in cognitive performance, although we did find that cerebral blood flow was still increased by 17% in 21-22 months old APP/PS1 mice given anti-Ly6G. These data add to the growing body of evidence suggesting that cerebral blood flow reductions are an important contributing factor to the cognitive dysfunction associated with neurodegenerative disease.
Shift in bacterial taxa precedes morphological plasticity in a larval echinoid
Authors: Carrier Tyler J. , Reitzel Adam M. 
Published: May 2019

AbstractMorphological plasticity is an adaptive response to heterogenous environments when a fitness advantage is conferred. Larval sea urchins, for example, increase individual fitness in dilute feeding environments by elongating their feeding structure. Morphological plasticity for larval sea urchins is also coupled with significant shifts in the associated bacterial community, but whether this response occurs before, during, or following the expression of plasticity is unclear. Using the sea urchinLytechinus variegatus, we define the temporal pattern of the associated bacterial community throughout the expression of morphological plasticity. From prefeeding through plasticity, we observed thatL. variegatuslarvae exhibit a four-stage successional pattern and the relatedness of the larval-associated bacterial community directly reflects morphological plasticity and does so prior to expression of the environmental-specific morphology. Based on the structure of the larval-associated bacterial communities, the expression of morphological plasticity correlates short-arm larvae deviating from the microbial trajectory of pre-plastic siblings. Taken together, these data suggest that a holobiont may exhibit shifts in the associated bacterial community corresponding with the environmental variation in absence or anticipation of morphological plasticity.
Individual differences in stereotypy and neuron subtype translatome with TrkB deletion
Authors: Engeln Michel , Song Yang , Chandra Ramesh , La Ashley , Evans Brianna , Fox Megan E. , Thomas Shavin , Francis T. Chase , Hertzano Ronna , Lobo Mary Kay 
Published: May 2019

AbstractMotor stereotypies occurring in early-onset neuropsychiatric diseases are associated with dysregulated basal ganglia direct-pathway activity. Disruptions in network connectivity through impaired neuronal structure have been implicated in both rodents and humans. However, the neurobiological mechanisms leading to direct-pathway neuron disconnectivity in stereotypy remain poorly understood. We have a mouse line with Tropomyosin receptor kinase B (TrkB) receptor deletion from D1-expressing cells (D1-Cre-flTrkB) in which a subset of animals shows repetitive rotations and head tics with juvenile onset. Here we demonstrate these behaviors may be associated with abnormal direct-pathway activity by reducing rotations using chemogenetic inhibition of dorsal striatum D1-medium spiny neurons (D1-MSNs) in both juvenile and young adult mice. Taking advantage of phenotypical differences in animals with similar genotype, we then interrogated the D1-MSN specific translatome associated with repetitive behavior by using RNA-sequencing of ribosome-associated mRNA. Detailed translatome analysis followed by multiplexed gene expression assessment revealed profound alterations in neuronal projection and synaptic structure related genes in stereotypy mice. Examination of neuronal morphology demonstrated dendritic atrophy and dendritic spine loss in dorsal striatum D1-MSNs from mice with repetitive behavior. Together, our results uncover phenotype-specific molecular alterations in D1-MSNs that relate to morphological adaptations in mice displaying stereotypy behavior.
Identification of pathogenic variant enriched regions across genes and gene families
Authors: Pérez-Palma Eduardo , May Patrick , Iqbal Sumaiya , Niestroj Lisa-Marie , Du Juanjiangmeng , Heyne Henrike , Castrillon Jessica , O’Donnell-Luria Anne , Nürnberg Peter , Palotie Aarno , Daly Mark , Lal Dennis 
Published: May 2019

AbstractMissense variant interpretation is challenging. Essential regions for protein function are conserved among gene family members, and genetic variants within these regions are potentially more likely to confer risk to disease. Here, we generated 2,871 gene family protein sequence alignments involving 9,990 genes and performed missense variant burden analyses to identify novel essential protein regions. We mapped 2,219,811 variants from the general population into these alignments and compared their distribution with 65,034 missense variants from patients. With this gene family approach, we identified 398 regions enriched for patient variants spanning 33,887 amino acids in 1,058 genes. As a comparison, testing the same genes individually we identified less patient variant enriched regions involving only 2,167 amino acids and 180 genes. Next, we selectedde novovariants from 6,753 patients with neurodevelopmental disorders and 1,911 unaffected siblings, and observed a 5.56-fold enrichment of patient variants in our identified regions (95% C.I. =2.76-Inf, p-value = 6.66×10−8). Using an independent ClinVar variant set, we found missense variants inside the identified regions are 111-fold more likely to be classified as pathogenic in comparison to benign classification (OR = 111.48, 95% C.I = 68.09-195.58, p-value < 2.2e−16). All patient variant enriched regions identified (PERs) are available online through a user-friendly platform for interactive data mining, visualization and download athttp://per.broadinstitute.org. In summary, our gene family burden analysis approach identified novel patient variant enriched regions in protein sequences. This annotation can empower variant interpretation.
A cytomegalovirus immunevasin triggers integrated stress response-dependent reorganization of the endoplasmic reticulum
Authors: Zhang Hongbo , Read Clarissa , Nguyen Christopher C. , Siddiquey Mohammed N.A. , Shang Chaowei , Hall Cameron M. , von Einem Jens , Kamil Jeremy P. 
Published: May 2019

ABSTRACTHuman cytomegalovirus (HCMV) encodes an ER-resident glycoprotein, UL148, which activates the unfolded protein response (UPR) but is fully dispensable for viral replication in cultured cells. Hence, its previously ascribed roles in immune evasion and modulation of viral cell tropism are hypothesized to cause ER stress. Here, we show that UL148 is necessary and sufficient to drive the formation of large ER-derived structures that occupy up to 7% of the infected cell cytosol. The structures are found to be sites where UL148 coalesces with cellular proteins involved in ER quality control, such as Hrd1 and EDEM1. Transmission electron microscopy analyses reveal the structures to be comprised of tortuous, densely packed and apparently collapsed ER membranes that connect to distended cisternae. During induced ectopic expression of UL148-GFP fusion protein, punctate signals traffic to accumulate at prominent structures that exhibit poor recovery of fluorescence after photobleaching. Small molecule blockade of the integrated stress response (ISR) prevents the formation of puncta, leading to a uniform reticular fluorescent signal. Accordingly, ISR inhibition during HCMV infection abolishes the coalescence of UL148 and Hrd1 into discrete structures, which argues that UL148 requires the ISR to cause ER reorganization. Given that UL148 stabilizes immature forms of a receptor binding subunit for a viral envelope glycoprotein complex important for HCMV infectivity, our results imply that stress-dependent ER remodeling contributes to viral cell tropism.IMPORTANCEPerturbations to ER morphology occur during infection with various intracellular pathogens and in certain genetic disorders. We identify that an HCMV gene product, UL148, profoundly reorganizes the ER during infection, and is sufficient to do so when expressed on its own. Our results reveal that UL148-dependent reorganization of the ER is a prominent feature of HCMV infected cells. Moreover, we find that this example of virally induced organelle remodeling requires the integrated stress response (ISR), a stress adaptation pathway that contributes to a number of disease states. Since ER reorganization accompanies the roles of UL148 in HCMV cell tropism and intracellular retention of the immune cell co-stimulatory ligand CD58, our results may have implications for understanding the mechanisms involved. Furthermore, our findings provide a basis to utilize UL148 as a tool to investigate organelle responses to stress and to identify novel drugs targeting the ISR.
Accuracy, Robustness and Scalability of Dimensionality Reduction Methods for Single Cell RNAseq Analysis
Authors: Sun Shiquan , Zhu Jiaqiang , Ma Ying , Zhou Xiang 
Published: May 2019

ABSTRACTBackgroundDimensionality reduction (DR) is an indispensable analytic component for many areas of single cell RNA sequencing (scRNAseq) data analysis. Proper DR can allow for effective noise removal and facilitate many downstream analyses that include cell clustering and lineage reconstruction. Unfortunately, despite the critical importance of DR in scRNAseq analysis and the vast number of DR methods developed for scRNAseq studies, however, few comprehensive comparison studies have been performed to evaluate the effectiveness of different DR methods in scRNAseq.ResultsHere, we aim to fill this critical knowledge gap by providing a comparative evaluation of a variety of commonly used DR methods for scRNAseq studies. Specifically, we compared 18 different DR methods on 30 publicly available scRNAseq data sets that cover a range of sequencing techniques and sample sizes. We evaluated the performance of different DR methods for neighborhood preserving in terms of their ability to recover features of the original expression matrix, and for cell clustering and lineage reconstruction in terms of their accuracy and robustness. We also evaluated the computational scalability of different DR methods by recording their computational cost.ConclusionsBased on the comprehensive evaluation results, we provide important guidelines for choosing DR methods for scRNAseq data analysis. We also provide all analysis scripts used in the present study atwww.xzlab.org/reproduce.html. Together, we hope that our results will serve as an important practical reference for practitioners to choose DR methods in the field of scRNAseq analysis.
Rotational Dynamics Reduce Interference Between Sensory and Memory Representations
Authors: Libby Alexandra , Buschman Timothy J. 
Published: May 2019

AbstractSensory stimuli arrive in a continuous stream. By learning statistical regularities in the sequence of stimuli, the brain can predict future stimuli (Xu et al. 2012; Gavornik and Bear 2014; Maniscalco et al. 2018; J. Fiser and Aslin 2002). Such learning requires associating immediate sensory information with the memory of recently encountered stimuli (Ostojic and Fusi 2013; Kiyonaga et al. 2017). However, new sensory information can also interfere with short-term memories (Parthasarathy et al. 2017). How the brain prevents such interference is unknown. Here, we show that sensory representations rotate in neural space over time, to form an independent memory representation, thus reducing interference with future sensory inputs. We used an implicit learning paradigm in mice to study how statistical regularities in a sequence of stimuli are learned and represented in primary auditory cortex. Mice experienced both common sequences of stimuli (e.g. ABCD) and uncommon sequences (e.g. XYCD). Over four days of learning, the neural population representation of commonly associated stimuli (e.g. A and C) converged. This facilitated the prediction of upcoming stimuli, but also led unexpected sensory inputs to overwrite the sensory representation of previous stimuli (postdiction). Surprisingly, we found the memory of previous stimuli persisted in a second, orthogonal dimension. Unsupervised clustering of functional cell types revealed that the emergence of this second memory dimension is supported by two separate types of neurons; a ‘stable’ population that maintained its selectivity throughout the sequence and a ‘switching’ population that dynamically inverted its selectivity. This combination of sustained and dynamic representations produces a rotation of the encoding dimension in the neural population. This rotational dynamic may be a general principle, by which the cortex protects memories of prior events from interference by incoming stimuli.
Antibiotic interactions shape short-term evolution of resistance in E. faecalis
Authors: Dean Ziah , Maltas Jeff , Wood Kevin B. 
Published: May 2019

ABSTRACTAntibiotic combinations are increasingly used to combat bacterial infections. Multidrug therapies are a particularly important treatment option for E. faecalis, an opportunistic pathogen that contributes to high-inoculum infections such as infective endocarditis. While numerous synergistic drug combinations for E. faecalis have been identified, much less is known about how different combinations impact the rate of resistance evolution. In this work, we use high-throughput laboratory evolution experiments to quantify adaptation in growth rate and drug resistance of E. faecalis exposed to drug combinations exhibiting different classes of interactions, ranging from synergistic to suppressive. We identify a wide range of evolutionary behavior, including both increased and decreased rates of growth adaptation, depending on the specific interplay between drug interaction and cross resistance. For example, selection in a dual-lactam combination leads to accelerated growth adaptation compared to selection with the individual drugs, even though the resulting resistance profiles are nearly identical. On the other hand, populations evolved in an aminoglycoside and -lactam combination exhibit decreased growth adaptation and resistant profiles that depend on the specific drug concentrations. We show that the main qualitative features of these evolutionary trajectories can be explained by simple rescaling arguments that correspond to geometric transformations of the two-drug growth response surfaces measured in ancestral cells. The analysis also reveals multiple examples where resistance profiles selected by drug combinations correspond to (nearly) optimized linear combinations of those selected by the component drugs. Our results highlight trade-offs between drug interactions and collateral effects during the evolution of multi-drug resistance and emphasize evolutionary benefits and disadvantages of particular drug pairs targeting enterococci.
Tracking of quiescence inLeishmaniaby quantifying the expression of GFP in the ribosomal DNA locus
Authors: Jara Marlene , Maes Ilse , Imamura Hideo , Domagalska Malgorzata A. , Claude Dujardin Jean , Arevalo Jorge 
Published: May 2019

ABSTRACTUnder stressful conditions some microorganisms adopt a reversible non or slow proliferative quiescent stage that allows their survival. Although quiescence has been described broadly in bacteria, this phenotype has been only recently discovered inLeishmania. In the present work we developed a biosensor of quiescence that allows to monitor the physiological stage of the parasite at population and single cell levels. We inserted a GFP gene into the ribosomal DNA locus and followed the expression of this reporter gene, driven by the ribosomal promotor (rGFP expression). We showed that rGFP expression decreased significantly and rapidly during thein vitrotransition from extracellular promastigotes to intracellular amastigotes ofL. mexicanaanL. braziliensisand that the decrease in rGFP expression was coupledin vitrowith a decrease in replication as measured by BrdU incorporation. Quiescence was not only observed in reference laboratory strains, but also among clinical isolates. We found that quiescence was reversible as the parasites could rapidly resume their metabolically active and proliferative stage when they were put back in an optimal environment for growth. We demonstrated for the first time in live cells that amastigotes are a heterogeneous population in which shallow and deep quiescent stages may coexist. Finally, we showed that rGFP expression could be monitoredin vivoand that quiescent amastigotes could reside in tissues of animals with latent infections ofL. braziliensisorL. mexicana. We propose rGFP expression as a simple parameter to define quiescent cells and further characterize them.IMPORTANCEQuiescence is a physiological diversification that allows pathogens to overcome chemotherapy without the development of drug resistance and to be invisible to the immune system of their host. Quiescent pathogens can cause latent infections and (re-) emerge in an unpredictable time during the lifetime of the individual. The phenomenon was recently described inLeishmaniain which it could explain several clinical and sub-clinical features, like therapeutic failure, reactivation of the disease and asymptomatic infections. However, a simple biosensor of quiescence forLeishmaniais not yet available. We show for the first time that the integration of GFP within the rDNA locus and the subsequent quantification of its expression can be used as a biosensor to distinguish quiescent subpopulations among live amastigotes. Moreover, we show quiescence is quickly reversible bothin vivoandin vitro. We offer a tool that will allow the further molecular characterization of quiescent parasites.