bluuebunny/crossref_metadata_2025 huggingface dataset:
Rosai-Dorfman Disease of the Breast With Variable IgG4+ Plasma Cells
Authors: Hoffmann Jenny C. , Lin Chieh-Yu , Bhattacharyya Siddhartha , Weinberg Olga K. , Chisholm Karen M. , Bayerl Michael , Cascio Michael , Venkataraman Girish , Allison Kimberly , Troxell Megan , Chang Chung-Che , Bagg Adam , George Tracy I. , O’Malley Dennis , Ohgami Robert S.
Published: August 2019

Rosai-Dorfman disease (RDD) is an uncommon disorder, characterized by an atypical expansion of histiocytes which classically shows emperipolesis and immunoreactivity with S-100 protein. RDD affects the lymph nodes as well as extranodal sites; however, RDD of the breast is exceptionally rare. Herein, we describe the histopathologic features of 22 cases of RDD occurring in the breast, with an emphasis on the differential diagnosis. All cases were notable for an exuberant lymphocytic infiltrate with and without germinal center formation, and the majority (19/22) showed numerous plasma cells: 5 to 132/high-power field (HPF). IgG and IgG4 immunohistochemical stains were available for 13 cases; in no instance were criteria for IgG4-related sclerosing disease met, though in a single case the IgG4/IgG ratio was increased to 25%. Sclerosis was present in the majority of cases (18/22), and was frequently prominent. RDD cells showing emperipolesis were present in all cases (22/22), and ranged from rare (<1/50 HPF) to numerous (>50/50 HPF). Two of the cases in our series were initially misdiagnosed as inflammatory myofibroblastic tumor and plasma cell mastitis with granulomatous inflammation. As emperipolesis can be indistinct, the presence of stromal fibrosis and a prominent lymphoplasmacytic inflammatory infiltrate should prompt a careful search for the characteristic histiocytes, which can be aided by the use of S-100 immunohistochemistry.
Health literacy, cognitive ability and self-reported diabetes in the English Longitudinal Study of Ageing
Authors: Fawns-Ritchie Chloe , Price Jackie , Deary Ian J
Published: August 2019

Objective

To examine the association of health literacy and cognitive ability with risk of diabetes.

Research Design and Methods: Participants were 8,669 English Longitudinal Study of Ageing participants (mean age 66.7 years, SD 9.7) who completed health literacy and cognitive ability tests at wave 2 (2004-2005), and who answered a self-reported question on whether a doctor had ever diagnosed them with diabetes. Logistic regression was used to examine the cross-sectional associations of health literacy and cognitive ability with diabetes status. In those without diabetes at wave 2, Cox regression was used to test the associations of health literacy and cognitive ability with risk of diabetes over a median of 9.5 years follow-up (n=6,961).

Results

Adequate (compared to limited) health literacy (OR 0.72, 95% CI 0.61-0.84) and higher cognitive ability (OR per 1 SD 0.73, CI 0.67-0.80) were both associated with lower odds of self-reported diabetes. Adequate health literacy (HR 0.64; CI 0.53-0.77) and higher cognitive ability (HR 0.77, CI 0.69-0.85) were also associated with lower risk of self-reporting diabetes during follow-up. When both health literacy and cognitive ability were added to the same model, these associations were slightly attenuated. Additional adjustment for health behaviours, education and social class attenuated associations further, and neither health literacy nor cognitive ability were significantly associated with diabetes.

Conclusions

Adequate health literacy and better cognitive ability were associated with reduced risk of diabetes. These associations were independent of each other, but not of other health- and socioeconomic-related variables.
Research on Artificial Intelligence and Primary Care: A Scoping Review
Authors: Kueper Jacqueline K. , Terry Amanda L. , Zwarenstein Merrick , Lizotte Daniel J.
Published: August 2019

Objective

The purpose of this study was to assess the nature and extent of the body of research on artificial intelligence (AI) and primary care.

Methods

We performed a scoping review, searching 11 published and grey literature databases with subject headings and key words pertaining to the concepts of 1) AI and 2) primary care: MEDLINE, EMBASE, Cinahl, Cochrane Library, Web of Science, Scopus, IEEE Xplore, ACM Digital Library, MathSciNet, AAAI, arXiv. Screening included title and abstract and then full text stages. Final inclusion criteria: 1) research study of any design, 2) developed or used AI, 3) used primary care data and/or study conducted in a primary care setting and/or explicit mention of study applicability to primary care; exclusion criteria: 1) narrative, editorial, or textbook chapter, 2) not applicable to primary care population or settings, 3) full text inaccessible in the English Language. We extracted and summarized seven key characteristics of included studies: overall study purpose(s), author appointments, primary care functions, author intended target end user(s), target health condition(s), location of data source(s) (if any), subfield(s) of AI.

Results

Of 5,515 non-duplicate documents, 405 met our eligibility criteria. The body of literature is primarily focused on creating novel AI methods or modifying existing AI methods to support physician diagnostic or treatment recommendations, for chronic conditions, using data from higher income countries. Meaningfully more studies had at least one author with a technology, engineering, or math appointment than with a primary care appointment (57 (14%) compared to 217 (54%)). Predominant AI subfields were supervised machine learning and expert systems.

Discussion

Overall, AI research associated with primary care is at an early stage of maturity with respect to widespread implementation in practice settings. For the field to progress, more interdisciplinary research teams with end-user engagement and evaluation studies are needed.

SUMMARY BOXES

Section 1: What is already known on this topic

Advancements in technology and the availability of health data have increased opportunities for artificial intelligence to be used for primary care purposes.

No comprehensive review of research on artificial intelligence associated with primary care has been performed.

Section 2: What this study adds

The body of research on artificial intelligence and primary care is driven by authors without appointments in primary care departments and is focused on developing artificial intelligence methods to support diagnostic and treatment decisions.

There is a need for more interdisciplinary research teams and evaluation of artificial intelligence projects in ‘real world’ practice settings.
Candidate molecular predictors of outcome after aneurysmal subarachnoid haemorrhage: a systematic review of haemoglobin metabolism, inflammation and oxidative injury pathways
Authors: Gaastra Ben , Galea Ian
Published: August 2019

Aneurysmal subarachnoid haemorrhage (aSAH) is a devastating form of stroke associated with significant morbidity and mortality. Very little is known about the predictors of poor outcome and the pathophysiological mechanisms underlying neurological injury following aSAH. Three molecular pathways have been shown to be important: haemoglobin metabolism, inflammation and oxidative injury. The aim of this review is to use a systematic approach to identify a panel of key genes within these three pathways in order to focus future studies investigating predictors of poor outcome and the mechanisms of neurological injury following aSAH. Manual searching and bioinformatic mining tools were used. Studies of experimental or human SAH were included, and outcome was broadly defined to include all encountered readouts such as mortality, neurological scores, and neuropathological markers of tissue damage. If two or more molecules belonged to the same biochemical pathway, this pathway was examined in detail to identify all its components, which were then searched individually for any evidence of association with outcome using the same broad definition as before. This resulted in the identification of 58 candidate genes within the three pathways of interest (haemoglobin metabolism, inflammation and oxidative injury) potentially linked to outcome after aSAH.
Evolution of a novel and adaptive floral scent in wild tobacco
Authors: Guo Han , Lackus Nathalie D. , Köllner Tobias G. , Li Ran , Bing Julia , Wang Yangzi , Baldwin Ian T. , Xu Shuqing
Published: August 2019

Many plants emit diverse floral scents that mediate plant-environment interactions and attain reproductive success. However, how plants evolve novel adaptive floral volatiles remains unclear. Here, we show that in the wild tobacco, Nicotiana attenuata, a dominant species-specific floral volatile (benzyl acetone, BA) that attracts pollinators and deters florivore is synthesized by phenylalanine ammonia-lyase 4 (NaPAL4), isoflavone reductase 3 (NaIFR3), and chalcone synthase 3 (NaCHAL3). Transient expression of NaFIR3 alone in N. attenuata leaves is sufficient and necessary for ectopic foliar BA emissions, and the BA emission level is increased by co-expressing NaIFR3 with NaPAL4 and NaCHAL3. Independent changes in transcription in all three genes contributed to intraspecific variations of floral BA emission. However, among species, the gain-of-expression in NaIFR3 resulted in the biosynthesis of BA that was only found in N. attenuata. This study suggests that novel metabolic pathways associated with adaptation can arise via re-configurations of gene expression.
Machine-driven parameter optimisation of biochemical reactions
Authors: Poulain Stéphane , Arnaud Ophélie , Kato Sachi , Chen Iris , Ishida Hiro , Carninci Piero , Plessy Charles
Published: August 2019

The development of complex, multi-step methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where an optimum is sought in a multidimensional parameter space through step-by-step optimisations. The difficulty of miniaturising reactions under the microliter volumes usually handled in multiwell plates by robots, plus the cost of the experiments, limit the number of parameters and the dynamic ranges that can be explored. Nevertheless, because of non-linearities of the response of biochemical systems to their reagent concentrations, broad dynamic ranges are necessary. Here we use a high-performance nanoliter handling platform and computer generation of liquid transfer programs to explore in quadruplicates more than 600 combinations of 4 parameters of a biochemical reaction, the reverse-transcription, which lead us to uncover non-linear responses, parameter interactions and novel mechanistic insights. With the increased availability of computer-driven laboratory platforms for biotechnology, our results demonstrate the feasibility and advantage of methods development based on reproducible, computer-aided exhaustive characterisation of biochemical systems.
Regulation of circular RNA circNFATc3 in cancer cells alters proliferation, migration and oxidative phosphorylation
Authors: Karedath Thasni , Al-Dasim Fatima M. , Ahmed Ikhlak , Al-Qurashi Albandary , Raza Afsheen , Andrews Simeon S. , Ahmed Ayeda Abdulsalam , Mohamoud Yasmin Ali , Dermime Said , Malek Joel A.
Published: August 2019

Circular RNAs were once considered artifacts of transcriptome sequencing but have recently been identified as functionally relevant in multiple cancers. Although there is still no clear main function of circRNAs, several studies have revealed that circRNAs are expressed in a variety of eukaryotic organisms, demonstrate conservation across species, and are expressed in a regulated manner often independent of their parental linear isoforms. circNFATC3, an abundant and uncharacterized circular isoform of NFATC3 gene (which is formed form backsplicing of exon 2 and 3) in solid tumors was identified from transcriptomic data. Here we show that circNFATC3 gain of and loss of function experiments using RNAi mediated circRNA silencing and circular mini vector-mediated overexpression of circularized constructs in breast and ovarian cancer cell lines affects molecular phenotypes. Knockdown of circNFATC3 induces a reduction in cell proliferation, invasion, migration, and oxidative phosphorylation. Gain of function of circNFATc3 in MDA-MB -231 cells and SKOV3 cells shows a significant increase in cell proliferation, migration, and respiration. The above results suggest that circNFATC3 is a functionally relevant circular RNA in cancer
Brunner Syndrome associated MAOA dysfunction in human induced dopaminergic neurons results in dysregulated NMDAR expression and increased network activity
Authors: Shi Y. , van Rhijn J.R. , Bormann M. , Mossink B. , Frega M. , Hakobjan M. , Kittel-Schneider S. , Schubert D. , Brunner H. , Franke B. , Kasri N. Nadif
Published: August 2019

Monoamine oxidase A (MAOA) is an enzyme that catalyzes the degradation of dopamine, noradrenaline, and serotonin. Regulation of monoamine neurotransmitter abundance through MAOA activity strongly affects motor control, emotion, and cognitive function. Mutations in MAOA cause Brunner Syndrome, which is characterized by impulsive aggressive behavior and mild intellectual disability (ID). The impaired MAOA activity in Brunner Syndrome patients results in bioamine aberration, but it is currently unknown how this affects neuronal function. MAOA is highly expressed in serotonergic and dopaminergic neurons, and dysfunction of both neurotransmission systems is associated with aggressive behavior in mice and humans. Research has so far mainly focused on the serotonergic system. Here, we generated human induced pluripotent stem cell-derived induced dopaminergic neurons (iDANs) from individuals with known MAOA mutations, to investigate MAOA-dependent effects on dopamine neuronal function in the context of Brunner Syndrome. We assessed iDAN lines from three patients and combined data from morphological analysis, gene expression, single-cell electrophysiology, and network analysis using micro-electrode arrays (MEAs). We observed mutation-dependent functional effects as well as overlapping changes in iDAN morphology. The most striking effect was a clear increase in N-methyl-D-aspartate (NMDA) receptor mRNA expression in all patient lines. A marked increase was also seen in coordinated network activity (network bursts) on the MEA in all patient lines, while single-cell intrinsic properties and spontaneous excitatory postsynaptic currents activity appeared normal. Together, our data indicate that dysfunction of MAOA leads to increased coordinated network activity in iDANs, possibly caused by increased synaptic NMDA receptor expression.
AttenuatedSalmonellatyphimurium cancer therapy has direct effects on the tumor epithelium in colorectal cancer
Authors: Maslowski Kendle M. , Takahashi Masumi , Nakanishi Yumiko , Mackie Gillian M. , Everard Isabel , Copland Alastair , Oda Hirotsugu , Kanaya Takashi , Ohno Hiroshi
Published: August 2019

Bacterial cancer therapy (BCT) shows great promise for treatment of solid tumors, yet basic mechanisms of bacterial-induced tumor suppression remain undefined. The intestinal epithelium is the natural route of infection forSalmonellaand thus harbors innate immune defenses which protect against infection. Attenuated strains ofSalmonella entericaserovar Typhimurium (STm) have commonly been used in mouse models of BCT, largely with the use of xenograft and orthotopic transplant cancer models. We aimed to better understand the tumor epithelium-targeted mechanisms of BCT by using mouse models of intestinal tumorigenesis and tumor organoid cultures to assess the effectiveness and mechanisms of treatment with aromatase A-deficientSTm (STmΔaroA).STmΔaroAdelivered by oral gavage could significantly reduce tumor burden and tumor load in both a colitis-associated colon cancer model (CAC) and in a spontaneous intestinal cancer model,Apcmin/+mice.STmΔaroAcolonization of tumors caused alterations in transcription of mRNAs associated with epithelial–mesenchymal transition as well as metabolic and cell cycle-related transcripts. Metabolomic analysis of tumors demonstrated alteration in the metabolic environment ofSTmΔaroA-treated tumors, suggestingSTmΔaroAimposes metabolic competition on the tumor. Use of tumor organoid culturesin vitrodemonstrated thatSTmΔaroAcan directly affect the tumor epithelium with alterations in transcripts and metabolites similar toin vivo-treated tumors. Thereby, we demonstrate that bacterial cancer therapy is efficacious in autochthonous intestinal cancer models, that BCT imposes metabolic competition, and that BCT has direct effects on the tumor epithelium, which have not previously been appreciated.

One Sentence Summary

AttenuatedSalmonella entericaserovar Typhimurium can home to gastrointestinal tumors and directly affect the tumor epithelium, inducing transcriptional and metabolic changes that lead to reduced tumor burden in mice.
The evolution of parental effects when selection acts on fecundity versus viability
Authors: Kuijper Bram , Johnstone Rufus A.
Published: August 2019

Most predictions on the evolution of adaptive parental effects and phenotypic memory exclusively focus on the role of the abiotic environment. How parental effects are affected by population demography and life history is less well understood. To overcome this, we use an analytical model to assess whether selection acting on fecundity versus viability affects the evolution of parental effects in a viscous population experiencing a spatiotemporally varying environment. We find that parental effects commonly evolve in regimes of viability selection, but are less likely to evolve in regimes of fecundity selection. In regimes of viability selection, an individual’s phenotype becomes correlated with its local environment during its lifetime, as those individuals with a locally adapted phenotype are more likely to survive until parenthood. Hence, a parental phenotype rapidly becomes an informative cue about its local environment, favoring the evolution of parental effects. By contrast, in regimes of fecundity selection, locally maladapted and adapted parents survive at equal rates, so that the parental phenotype, by itself, is not informative about the local environment. Correlations between phenotype and environment still arise, but only when more fecund, locally adapted individuals leave more successfully established offspring to the local patch. Hence, correlations take at least two generations to develop, making them more sensitive to distortion by environmental change or competition with immigrant offspring. Hence, we conclude that viability selection is most conducive to the evolution of adaptive parental effects in spatially structured populations.
Molecular profiling of driver events and tumor-infiltrating lymphocytes in metastatic uveal melanoma
Authors: Karlsson Joakim , Nilsson Lisa M. , Forsberg Elin MV , Mitra Suman , Alsén Samuel , Shelke Ganesh , Sah Vasu R , Stierner Ulrika , All-Eriksson Charlotta , Einarsdottir Berglind , Jespersen Henrik , Ny Lars , Lindnér Per , Larsson Erik , Bagge Roger Olofsson , Nilsson Jonas A.
Published: August 2019

Uveal melanoma (UM) is a rare form of melanoma with a genetics and immunology that is different from skin melanoma. Previous studies have identified genetic driver events of early stage disease when the tumor is confined to the eye. However due to lack of a clinical rationale to biopsy metastatic disease, access to tumor material to perform molecular profiling of metastases has been limited. In this study, we have characterized genomic events in UM metastases using whole-genome sequencing of fresh frozen biopsies from thirty-two patients and profiled the transcriptomes of individual tumor infiltrating lymphocytes in eight patients by single-cell sequencing. We find that 91% of the patients have metastases carrying inactivating events in the tumor suppressor BAP1 and this coincided with somatic alterations in GNAQ, GNA11, CYSLTR2, PLCB4, SF3B1 and/or CDKN2A. Mutational signature analysis revealed a rare subset of tumors with prominent signs of UV damage, associated with outlier mutational burden. We study copy number variations (CNV) and find overrepresented events, some of which were not altered in matched primary eye tumors. A focused siRNA screen identified functionally significant genes of some of the segments recurrently gained. We reintroduced a functional copy of BAP1 into a patient-derived BAP1 deficient tumor cell line and found broad transcriptomic changes of genes associated with subtype distinction and prognosis in primary UM. Lastly, our analysis of the immune microenvironments of metastases revealed a presence of tumor-reactive T cells. However, a majority expressed the immune checkpoint receptors TIM-3, LAG3 and TIGIT, and to a lesser extent PD-1. These results provide an updated view of genomic events represented in metastatic UM and immune interactions in advanced lesions.
Nutrient regulation of the islet epigenome controls adaptive insulin secretion
Authors: Wortham Matthew , Liu Fenfen , Fleischman Johanna Y. , Wallace Martina , Mulas Francesca , Vinckier Nicholas K. , Harrington Austin R. , Cross Benjamin R. , Chiou Joshua , Patel Nisha A. , Sui Yinghui , Jhala Ulupi S. , Shirihai Orian S. , Huising Mark O. , Gaulton Kyle J. , Metallo Christian M. , Sander Maike
Published: August 2019

Adaptation of the islet β-cell insulin secretory response to changing insulin demand is critical for blood glucose homeostasis, yet the mechanisms underlying this adaptation are unknown. Here, we show that nutrient-stimulated histone acetylation plays a key role in adapting insulin secretion through regulation of genes involved in β-cell nutrient sensing and metabolism. Nutrient regulation of the epigenome occurs at sites occupied by the chromatin-modifying enzyme Lsd1 in islets. We demonstrate that β-cell-specific deletion ofLsd1leads to insulin hypersecretion, aberrant expression of nutrient response genes, and histone hyperacetylation. Islets from mice adapted to chronically increased insulin demand exhibited similar epigenetic and transcriptional changes. Moreover, genetic variants associated with fasting glucose and type 2 diabetes are enriched at LSD1-bound sites in human islets, suggesting that interpretation of nutrient signals is genetically determined. Our findings reveal that adaptive insulin secretion involves Lsd1-mediated coupling of nutrient state to regulation of the islet epigenome.
Controlling the Mitochondrial Protonmotive Force with Light to Impact Cellular Stress Resistance
Authors: Berry Brandon J. , Trewin Adam J. , Milliken Alexander S. , Baldzizhar Aksana , Amitrano Andrea M. , Kim Minsoo , Wojtovich Andrew P.
Published: August 2019

Mitochondrial respiration generates an electrochemical proton gradient across the mitochondrial inner membrane called the protonmotive force (PMF) to drive diverse functions and make ATP. Current techniques to manipulate the PMF are limited to its dissipation; there is no precise, reversible method to increase the PMF. To address this issue, we used an optogenetic approach and engineered a mitochondria-targeted light-activated proton pumping protein we called mitochondria-ON (mtON) to selectively increase the PMF. Here, mtON increased the PMF light dose-dependently, supported ATP synthesis, increased resistance to mitochondrial toxins, and modulated energy-sensing behavior in Caenorhabditis elegans. Moreover, transient mtON activation during hypoxia prevented the well-characterized adaptive response of hypoxic preconditioning. Our novel optogenetic approach demonstrated that a decreased PMF is both necessary and sufficient for hypoxia-stimulated stress resistance. Our results show that optogenetic manipulation of the PMF is a powerful tool to modulate metabolic and cell signaling outcomes.
Runx3 prevents spontaneous colitis by directing differentiation of anti-inflammatory mononuclear phagocytes
Authors: Hantisteanu Shay , Dicken Joseph , Negreanu Varda , Goldenberg Dalia , Brenner Ori , Leshkowitz Dena , Lotem Joseph , Levanon Ditsa , Groner Yoram
Published: August 2019

RUNX3 is one of three mammalian Runt-domain transcription factors (TFs) that regulate gene expression in several types of immune cells. Runx3-deficiency in mice is associated with a multitude of defects in the adaptive and innate immunity systems, including the development of early onset colitis. Our study reveals that conditional deletion of Runx3 specifically in mononuclear phagocytes (MNP) (MNPRunx3−/−) but not in T cells, recapitulates the early onset spontaneous colitis seen in Runx3−/− mice.

We show that Runx3 is expressed in colonic MNP, including resident macrophages (RM) and the dendritic cell cDC2 subsets and its loss results in impaired differentiation/maturation of both cell types. At the transcriptome level, loss of Runx3 in RM and cDC2 was associated with upregulation of pro-inflammatory genes similar to those in the early onset IBD murine model of RMIl10r−/−. The impaired RM maturation in the absence of Runx3 was associated with a marked decrease in expression of anti-inflammatory and TGFβ-regulated genes. Similarly, the decreased expression of β-catenin signaling associated genes in Runx3-deficient cDC2 indicates their impaired differentiation/maturation. Analysis of ChIP-seq data suggests that in both MNP cell types a significant fraction of these differentially expressed genes are high confidence Runx3 directly regulated genes. Interestingly, several of these putative Runx3 target genes harbor SNPs associated with IBD susceptibility in humans. Remarkably, the impaired maturation and pro-inflammatory phenotype of MNP lacking Runx3 was associated with a substantial reduction in the prevalence of colonic lamina propria Foxp3+ regulatory T cells and an increase in IFNγ-producing CD4+ T cells, underscoring Runx3 critical role in establishing tolerogenic MNP.

Together, these data emphasize the dual role of Runx3 in colonic MNP, as a transcriptional repressor of pro-inflammatory genes and an activator of maturation-associated genes including anti-inflammatory genes. Our study highlights the significance of the current MNPRunx3−/− model for understanding of human MNP-associated colitis. It provides new insights into the crucial involvement of Runx3 in intestinal immune tolerance by regulating colonic MNP maturation through TGFβR signaling and anti-inflammatory functions by Il10R signaling, befitting the identification of RUNX3 as a genome-wide associated risk gene for various immune-related diseases in humans including gastrointestinal tract diseases such as celiac and Crohn’s disease.
Megakaryocytes Display Innate Immune Cell Functions and Respond during Sepsis
Authors: Frydman Galit H. , Ellett Felix , Jorgensen Julianne , Marand Anika L. , Zukerberg Lawrence , Selig Martin , Tessier Shannon , Wong Keith H. K. , Olaleye David , Vanderburg Charles R. , Fox James G. , Tompkins Ronald G. , Irimia Daniel
Published: August 2019

Megakaryocytes (MKs) are precursors to platelets, the second most abundant cells in the peripheral circulation. However, while platelets are known participate in immune responses and play significant roles during infections, the role of MKs within the immune system has not been explored. Here we utilizein vitrotechniques to show that both cord blood-derived MKs (CB MKs) and MKs from a human megakaryoblastic leukemia cell line (Meg-01) chemotax towards pathogenic stimuli, phagocytose bacteria, and release chromatin webs in response to bacteria. Moreover, in patients with sepsis, we found that MK counts were significantly higher in the peripheral blood, and CD61+staining was increased in the kidneys and lungs, correlated with the development of organ dysfunction. Overall, our study suggests that MK cells display basic innate immune cell functions and respond during infections and sepsis.
Analysing complex metagenomic data with MicroWineBar
Authors: Klincke Franziska , Abel-Kistrup Martin , Saerens Sofie Maria Gilberte , Rasmussen Simon
Published: August 2019

An important step in metagenomics studies is to identify which species are present in a sample as well as to compare samples from different environments. Here we introduce MicroWineBar, a graphical tool for analyzing and comparing metagenomics samples. MicroWineBar can visualize the abundances of metagenomics samples in line and bar graphs, as well as analyse the richness and diversity. For a PCA as well as a differential abundance analysis, the abundance data is treated as compositional data and center log-ratio transformed. We use MicroWineBar to analyse two different years of wine fermentation as well as data from a human microbiome study of colorectal cancer. Importantly, MicroWineBar does not require any programming skills, is intuitive and user friendly. MicroWineBar is available athttps://github.com/klincke/MicroWineBarand as a python package from the Python Package Index.
Metal-Assisted and Microwave-Accelerated Germination
Authors: Aslan Kadir , Stevenson Monet , Guy Janelle , Bonyi Enock , Mohammed Muzaffer , Ozturk Birol , Drake Kyle , McLean Freeman , Souffrant Ashley , Bigio Amber
Published: August 2019

We report the proof-of-principle demonstration of a methodology, called Metal-Assisted and Microwave-Accelerated Germination, to modulate the germination of plant seeds and growth of plants using gold nanoparticles (Au NPs) and microwave heating. As a model plant seed, basil seeds were heated in a solution of 20 nm Au NPs using a microwave waveguide fiber connected to a solid-state microwave operating at 8 GHz at 20 W, which resulted in the development of longer basil gum as observed by optical microscopy. In control experiments, Au NPs or microwave heating was omitted to establish a baseline growth level under standard experimental conditions (no microwave heating or no Au NPs). Our results also show that hydroponic growth and soil growth of basil plants can be delayed with the use of 20 nm Au NPs at room temperature without microwave heating. The combined use of 20 nm Au NPs and microwave heating at 10 W for 6 minutes results in accelerated growth prolonged life of basil plants.
Labeling proteins withinDrosophilaembryos by combining FRET reporters, position-specific genomic integration, and GAL4-reponsive expression
Authors: Deng Tzyy-Chyn , Hsieh Chia-Jung , De Freitas Michael , Boulina Maria , Sharifai Nima , Samarajeewa Hasitha , Yanaba Tatsumi , Baker James D. , Kim Michael D. , Zusman Susan , Wan Kenneth H. , Yu Charles , Celniker Susan E. , Chiba Akira
Published: August 2019

Protein interaction network (PIN) or interactome has been mapped vigorously for the entire genome. We recognize, nonetheless, that such a map could illuminate profound insights had its context been revealed. We describe a scalable protein lableling method that could re-supply natural context back to the map of protein interactome. Genetically encoded fluorescent proteins, position-specific genomic integration and GAL4-responsive expression control enable labeling proteinsA, BandCeach with a either an eGFP, mCherry or NirFP in specified cells of optically transparent animals such asDrosophilaembryos. While following multiple proteins through development and behavior, these labels offer separable pairs of Förster resonance energy transfer between proteinsAandBand proteinsBandC. We test and observe FRET interactions between specific protein pairs controlling cytoskeleton, nuclear signaling and cell polarity. By using our protein labeling method, it will be possible to map protein interaction networkin situ— isPIN.
Reconstruction of the phase dynamics of the somitogenesis clock oscillator
Authors: Moya Lucas J. Morales , Dale J. Kim , Murray Philip J.
Published: August 2019

In this study we develop a computational framework for the reconstruction of the phase dynamics of the somitogenesis clock oscillator. Our understanding of the somitogenesis clock, a developmental oscillator found in the vertebrate embryo, has been revolutionised by the development of real time reporters of clock gene expression. However, the signals obtained from the real time reporters are typically noisy, nonstationary and spatiotemporally dynamic and there are open questions with regard to how post-processing can be used to both improve the insight gained from a given experiment and to constrain theoretical models. In this study we present a methodology, which is a variant of empirical mode decomposition, that reconstructs the phase dynamics of the somitogenesis clock. After validating the methodology using synthetic datasets, we define a set of metrics that use the reconstructed phase profiles to infer biologically meaningful quantities. We perform experiments in which the signal from a real time reporter of the somitogenesis clock is recorded and reconstruct the phase dynamics. Application of the defined metrics yields results that are consistent with previous experimental observations. Moreover, we extend previous work by developing a gradient descent method for defining automated kymographs and showing that boundary conditions are non-homogeneous. By studying phase dynamics along phase gradient descent trajectories, we show that, consistent with a previous theoretical model, the oscillation frequency is inversely correlated with the phase gradient but that the coefficient is not constant in time. The proposed methodology provides a tool kit for that can be used in the analysis of future experiments and the quantitative observations can be used to guide the development of future mathematical models.
Theory of microtubule length regulation in antiparallel overlaps
Authors: Kuan Hui-Shun , Betterton Meredith D.
Published: August 2019

During cell division, microtubules in the mitotic spindle form antiparallel overlaps near the center of the spindle. Kinesin motor proteins alter microtubule polymerization dynamics to regulate the length of these overlaps to maintain spindle integrity. Length regulation of antiparallel overlaps has been reconstituted with purified microtubules, crosslinkers, and motors. Here we develop a theory of steady-state overlap length which depends on the filament plus-end motor concentration, determined by a balance between motor arrival (motor binding and stepping in the overlap) and motor departure (motor unbinding from filament tips during depolymerization) in the absence of motor-driven sliding. Assuming that motors processively depolymerize and exhibit altered binding kinetics near MT plus-ends improves the agreement between theory and experiment. Our theory explains the origin of the experimentally observed critical concentration, a minimum motor concentration to observe a steady-state overlap length.
Rapidly Computing the Phylogenetic Transfer Index
Authors: Truszkowski Jakub , Gascuel Olivier , Swenson Krister M.
Published: August 2019

Given trees T and T* on the same taxon set, the transfer index ϕ(b, T*) is the number of taxa that need to be ignored so that the bipartition induced by branch b in T is equal to some bipartition in T*. Recently, Lemoine et al. [14] used the transfer index to design a novel bootstrap analysis technique that improves on Felsenstein’s bootstrap on large, noisy data sets. In this work, we propose an algorithm that computes the transfer index for all branches b ∈ T in O(n log3n) time, which improves upon the current O(n2)-time algorithm by Lin, Rajan and Moret [15]. Our implementation is able to process pairs of trees with hundreds of thousands of taxa in minutes and considerably speeds up the method of Lemoine et al. on large data sets. We believe our algorithm can be useful for comparing large phylogenies, especially when some taxa are misplaced (e.g. due to horizontal gene transfer, recombination, or reconstruction errors).
Phase variable glycosylation in non-typeableHaemophilus influenzae
Authors: Elango Danila , Schulz Benjamin L.
Published: August 2019

Non-typeableHaemophilus influenzae(NTHi) is a leading cause of respiratory tract infections worldwide and continues to be a global health burden. Adhesion and colonisation of host cells are crucial steps in bacterial pathogenesis, and in many strains of NTHi interaction with the host is mediated by the high molecular weight adhesins HMW1A and HMW2A. These adhesins areN-glycoproteins which are modified by cytoplasmic glycosyltransferases HMW1C and HMW2C. Phase variation in the number of short sequence repeats in the promoters ofhmw1Aandhmw2Adirectly affects their expression. Here, we report the presence of similar variable repeat elements in the promoters ofhmw1Candhmw2Cin diverse NTHi isolates. In anex vivoassay, we systematically altered substrate and glycosyltransferase expression and showed that both of these factors affected the site-specific efficiency of glycosylation on HMW-A. Glycosylation occupancy was incomplete at many sites, variable between sites, and generally lower close to the C-terminus of HMW-A. We investigated the causes of this variability. As HMW-C glycosylates HMW-A in the cytoplasm, we tested how secretion affected glycosylation on HMW-A and showed that retaining HMW-A in the cytoplasm indeed increased glycosylation occupancy across the full length of the protein. Site-directed mutagenesis showed that HMW-C had no inherent preference for glycosylating asparagines in NxS or NxT sequons. This work provides key insights into factors contributing to the heterogenous modifications of NTHi HMW-A adhesins, expands knowledge of NTHi population diversity and pathogenic capability, and is relevant to vaccine design for NTHi and related pathogens.
Dissecting the Roles of Kalirin-7/PSD95/GluN2B Interactions in Different Forms of Synaptic Plasticity
Authors: Yeh Mason L. , Yasko Jessica R. , Levine Eric S. , Eipper Betty A. , Mains Richard E.
Published: August 2019

Kalirin-7 (Kal7) is a Rac1/RhoG GEF and multidomain scaffold localized to the postsynaptic density which plays an important role in synaptic plasticity. Behavioral and physiological phenotypes observed in the Kal7 knockout mouse are quite specific: genetics of breeding, growth, strength and coordination are normal; Kal7 knockout animals self-administer cocaine far more than normal mice, show exaggerated locomotor responses to cocaine, but lack changes in dendritic spine morphology seen in wildtype mice; Kal7 knockout mice have depressed surface expression of GluN2B receptor subunits and exhibit marked suppression of long-term potentiation and depression in hippocampus, cerebral cortex, and spinal cord; and Kal7 knockout mice have dramatically blunted perception of pain. To address the underlying cellular and molecular mechanisms which are deranged by loss of Kal7, we administered intracellular blocking peptides to acutely change Kal7 function at the synapse, to determine if plasticity deficits in Kal7-/-mice are the product of developmental processes since conception, or could be detected on a much shorter time scale. We found that specific disruption of the interactions of Kal7 with PSD-95 or GluN2B resulted in significant suppression of long-term potentiation and long-term depression. Biochemical approaches indicated that Kal7 interacted with PSD-95 at multiple sites within Kal7.

Graphical Table of Contents

The postsynaptic density is an integral player in receiving, interpreting and storing signals transmitted by presynaptic terminals. The correct molecular composition is crucial for successful expression of synaptic plasticity. Key components of the postsynaptic density include ligand-gated ion channels, structural and binding proteins, and multidomain scaffolding plus enzymatic proteins. These studies address whether the multiple components of the synaptic density bind together in a static or slowly adapting molecular complex, or whether critical interactions are fluid on a minute-to-minute basis.
Antibody-induced crosslinking and cholesterol-sensitive, anomalous diffusion of nicotinic acetylcholine receptors
Authors: Mosqueira Alejo , Camino Pablo A. , Barrantes Francisco J.
Published: August 2019

Synaptic strength depends on the number of cell-surface neurotransmitter receptors in dynamic equilibrium with intracellular pools. Dysregulation of this homeostatic balance occurs e.g. in myasthenia gravis, an autoimmune disease characterized by a decrease in the number of postsynaptic nicotinic acetylcholine receptors (nAChRs). Monoclonal antibody mAb35 mimics this effect. Here we use STORM nanoscopy to characterize the individual and ensemble dynamics of mAb35-crosslinked receptors in the clonal cell line CHO-K1/A5, which robustly expresses adult muscle-type nAChRs. Antibody labeling of live cells results in 80% receptor immobilization. The remaining mobile fraction exhibits a heterogeneous combination of Brownian and anomalous diffusion. Single-molecule trajectories exhibit a two-state switching behavior between free Brownian walks and anticorrelated walks within confinement areas. The latter act as permeable fences (∼34 nm radius, ∼400 ms lifetime). Dynamic clustering, trapping and immobilization also occur in larger nanocluster zones (120-180 nm radius) with longer lifetimes (11 ± 1 s), in a strongly cholesterol-sensitive manner. Cholesterol depletion increases the size and average duration of the clustering phenomenon; cholesterol enrichment has the opposite effect. The disclosed high proportion of mAb35-crosslinked immobile receptors, together with their anomalous, cholesterol-sensitive diffusion and clustering, provides new insights into the antibody-enhanced antigenic modulation that leads to physiopathological internalization and degradation of receptors in myasthenia.

A preliminary version of this work has appeared in the biorXiv repository: https://www.biorxiv.org/content/10.1101/744664v1. The study was not pre-registered.
Interdimer “zipping” in the chemoreceptor signaling domain revealed by molecular dynamics simulations
Authors: Petukh Marharyta G. , Ortega Davi R. , Baudry Jerome , Zhulin Igor B.
Published: August 2019

Chemoreceptors are principal components of the bacterial sensory system that modulates cellular motility. They detect changes in the environment and transmit information to CheA histidine kinase, which ultimately controls cellular flagellar motors. The prototypical Tsr chemoreceptor in E. coli is a homodimer containing two principal functional modules: (i) a periplasmic ligand-binding domain and (ii) a cytoplasmic signaling domain. Chemoreceptor dimers are arranged into a trimer of dimers at the tip of the signaling domain comprising a minimal physical unit essential for enhancing the CheA activity several hundredfold. Trimers of dimers are arranged into highly ordered hexagon arrays at the cell pole; however, the mechanism underlying the trimer-of-dimer and higher order array formation remains unclear. Furthermore, molecular mechanisms of signal transduction that are likely to involve inter-dimer interactions are not fully understood. Here we apply all-atom, microsecond-time scale molecular dynamics simulations of the Tsr trimer of dimers atomic model in order to obtain further insight into potential interactions within the chemoreceptor signaling unit. We show extensive interactions between homodimers at the hairpin tip of the signaling domain, where strong hydrophobic interactions maintain binding. A subsequent zipping of homodimers is facilitated by electrostatic interactions, in particular by polar solvation energy and salt bridges that stabilize the final compact structure, which extends beyond the kinase interacting subdomain. Our study provides evidence that interdimer interactions within the chemoreceptor signaling domain are more complex than previously thought.
Crystal structure and Hirshfeld surface analysis of 4-(4-methylbenzyl)-6-phenylpyridazin-3(2H)-one
Authors: Daoui Said , Cinar Emine Berrin , El Kalai Fouad , Saddik Rafik , Karrouchi Khalid , Benchat Noureddine , Baydere Cemile , Dege Necmi
Published: August 2019

In this paper, we describe the synthesis of a new dihydro-2H-pyridazin-3-one derivative. The molecule, C18H16N2O, is not planar; the benzene and pyridazine rings are twisted with respect to each other, making a dihedral angle of 11.47 (2)°, and the toluene ring is nearly perpendicular to the pyridazine ring, with a dihedral angle of 89.624 (1)°. The molecular conformation is stabilized by weak intramolecular C—H...N contacts. In the crystal, pairs of N—H...O hydrogen bonds link the molecules into inversion dimers with anR22(8) ring motif. The intermolecular interactions were investigated using Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots, revealing that the most important contributions for the crystal packing are from H...H (56.6%), H...C/C...H (22.6%), O...H/H...O (10.0%) and N...C/C...N (3.5%) interactions.
Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices
Authors: Hill Shannon E. , Cho Hayeon , Raut Priyam , Lieberman Raquel L.
Published: August 2019

Olfactomedins are a family of modular proteins found in multicellular organisms that all contain five-bladed β-propeller olfactomedin (OLF) domains. In support of differential functions for the OLF propeller, the available crystal structures reveal that only some OLF domains harbor an internal calcium-binding site with ligands derived from a triad of residues. For the myocilin OLF domain (myoc-OLF), ablation of the ion-binding site (triad Asp, Asn, Asp) by altering the coordinating residues affects the stability and overall structure, in one case leading to misfolding and glaucoma. Bioinformatics analysis reveals a variety of triads with possible ion-binding characteristics lurking in OLF domains in invertebrate chordates such as Arthropoda (Asp–Glu–Ser), Nematoda (Asp–Asp–His) and Echinodermata (Asp–Glu–Lys). To test ion binding and to extend the observed connection between ion binding and distal structural rearrangements, consensus triads from these phyla were installed in the myoc-OLF. All three protein variants exhibit wild-type-like or better stability, but their calcium-binding properties differ, concomitant with new structural deviations from wild-type myoc-OLF. Taken together, the results indicate that calcium binding is not intrinsically destabilizing to myoc-OLF or required to observe a well ordered side helix, and that ion binding is a differential feature that may underlie the largely elusive biological function of OLF propellers.
Crystal structure of the N-terminal domain of the major virulence factor BB0323 from the Lyme disease agent Borrelia burgdorferi
Authors: Brangulis Kalvis , Akopjana Inara , Kazaks Andris , Tars Kaspars
Published: August 2019

Lyme disease is an infection caused by the spirochete Borrelia burgdorferi after it is transmitted to a mammalian organism during a tick blood meal. B. burgdorferi encodes at least 140 lipoproteins located on the outer or inner membrane, thus facing the surroundings or the periplasmic space, respectively. However, most of the predicted lipoproteins are of unknown function, and only a few proteins are known to be essential for the persistence and virulence of the pathogen. One such protein is the periplasmic BB0323, which is indispensable for B. burgdorferi to cause Lyme disease and the function of which is associated with cell fission and outer membrane integrity. After expression and transport to the periplasm, BB0323 is cleaved into C-terminal and N-terminal domains by the periplasmic serine protease BB0104. The resulting N-terminal domain is sufficient to ensure the survival of B. burgdorferi throughout the mouse–tick infection cycle. The crystal structure of the N-terminal domain of BB0323 was determined at 2.35 Å resolution. The overall fold of the protein belongs to the spectrin superfamily, with the characteristic interconnected triple-helical bundles known as spectrin repeats that function as linkers between different cell components in other organisms. Overall, the reported three-dimensional structure of the N-terminal domain of BB0323 not only reveals the molecular details of a protein that is essential for B. burgdorferi membrane integrity, cell fission and infectivity, but also suggests that spectrin repeats in bacteria are not limited to the EzrA proteins.