bluuebunny/crossref_metadata_2025 huggingface dataset:
Post-Exposure Effects of Vaccines on Infectious Diseases
Authors: Gallagher Tara , Lipsitch Marc
Published: July 2019

Many available vaccines have demonstrated post-exposure effectiveness, but no published systematic reviews have synthesized these findings. We searched the PubMed database for clinical trials and observational human studies concerning the post-exposure vaccination effects, targeting infections with an FDA-licensed vaccine plus dengue, hepatitis E, malaria, and tick borne encephalitis, which have licensed vaccines outside of the U.S. Studies concerning animal models, serologic testing, and pipeline vaccines were excluded. Eligible studies were evaluated by definition of exposure, and their attempt at distinguishing pre- and post-exposure effects was rated on a scale of 1-4. We screened 4518 articles and ultimately identified 14 clinical trials and 31 observational studies for this review, amounting to 45 eligible articles spanning 7 of the 28 vaccine-preventable diseases. For secondary attack rate, this body of evidence found the following medians for post-exposure vaccination effectiveness: hepatitis A: 85% (IQR: 28; 5 sources), hepatitis B: 85% (IQR: 22; 5 sources), measles: 83% (IQR: 21; 8 sources), varicella: 67% (IQR: 48; 9 sources), smallpox: 45% (IQR: 39; 4 sources), and mumps: 38% (IQR: 7; 2 sources). For case fatality proportions resulting from rabies and smallpox, the vaccine efficacies had medians of 100% (IQR: 0; 6 sources) and 63% (IQR: 50; 8 sources) post-exposure. Although mainly used for preventive measures, many available vaccines can modify or preclude disease if administered after exposure. This post-exposure effectiveness could be important to consider during vaccine trials and while developing new vaccines.
Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues
Authors: Muse Meghan E. , Titus Alexander J. , Salas Lucas A. , Wilkins Owen M. , Mullen Chelsey , Gregory Kelly J. , Schneider Sallie S. , Crisi Giovanna M. , Jarwale Rahul M. , Otis Christopher N. , Christensen Brock C. , Arcaro Kathleen F.
Published: July 2019

Background

Emerging work has demonstrated that histologically normal (non-tumor) tissue adjacent to breast tumor tissue shows evidence of molecular alterations related to tumorigenesis, referred to as field cancerization effects. Although changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumor DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumor.

Methods

Matched tumor, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select breast epithelial cells from normal tissues, and neoplastic cells from tumor specimens for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array.

Results

We identified substantially more CpG loci that were differentially methylated between contralateral-normal breast and tumor tissue (63,271 CpG loci q < 0.01), than between ipsilateral-normal tissue and tumor (38,346 CpG loci q < 0.01). In addition, we identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). Hypomethylated loci in ipsilateral normal relative to contralateral were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3. Hypermethylated loci in ipsilateral-normal relative to contralateral-normal tissue were significantly enriched for CpG island shore regions.

Conclusions

Our results indicate that early hypermethylation events in breast carcinogenesis are more likely to occur in the regions immediately surrounding CpG islands than CpG islands per se, reflecting a field effect of the tumor on surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk.
Cryo-EM structure of the completeE. coliDNA Gyrase nucleoprotein complex
Authors: Broeck Arnaud Vanden , Ortiz Julio , Lamour Valérie
Published: July 2019

DNA Gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, the detailed architecture of DNA Gyrase from the model genetic organismE. coli, is still missing, impeding structure-function analysis ofE. coli-specific catalytic regulation and limiting the study of conformational intermediates of this highly flexible macromolecule. Herein, we determined the complete molecular structure of theE. coliDNA Gyrase bound to a 180 bp DNA and the antibiotic Gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil with unprecedented details the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of closed and pre-opening states of the DNA-binding domain provides a better understanding of the allosteric movements of the enzyme complex. In this region, the local atomic resolution reaching up to 3.0 Å enables the identification of the antibiotic density in the DNA complex. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates. The type 2A DNA topoisomerases (Top2) are nanomachines that control DNA topology during multiple cellular processes such as replication, transcription and cell division1-4. These enzymes catalyze the transport of a DNA duplex through a double strand break to perform DNA relaxation, decatenation and unknotting. DNA Gyrase plays a vital role in the compaction of the bacterial genome and is the sole type 2 topoisomerase able to introduce negative supercoils into DNA, a reaction coupled to ATP hydrolysis5.
Limited recognition ofMycobacterium tuberculosis-infected macrophages by polyclonal CD4 and CD8 T cells from the lungs of infected mice
Authors: Patankar Yash R. , Sutiwisesak Rujapak , Boyce Shayla , Lai Rocky , Arlehamn Cecilia S. Lindestam , Sette Alessandro , Behar Samuel M.
Published: July 2019

Immune responses followingMycobacterium tuberculosis(Mtb) infection or vaccination are frequently assessed by measuring T cell recognition of crude Mtb antigens, recombinant proteins, or peptide epitopes. We previously showed that not all Mtb-specific T cells recognize Mtb-infected macrophages. Thus, an important question is what proportion of T cells elicited by Mtb infection recognize Mtb-infected macrophages. We answer this question by developing a modified elispot assay using viable Mtb-infected macrophages, a low multiplicity of infection and purified T cells. In C57BL/6 mice, CD4 and CD8 T cells were classically MHC restricted. Comparable frequencies of T cells that recognize Mtb-infected macrophages were determined using interferon-γ elispot and intracellular cytokine staining, and lung CD4 T cells more sensitively recognized Mtb-infected macrophages than lung CD8 T cells. Compared to the numbers of Mtb antigen-specific T cells for antigens such as ESAT-6 and TB10.4, low frequencies of pulmonary CD4 and CD8 T cells elicited by aerosolized Mtb infection recognize Mtb-infected macrophages. Finally, we demonstrate that BCG vaccination elicits T cells that recognize Mtb-infected macrophages. We propose that the frequency of T cells that recognize infected macrophages could correlate with protective immunity and may be an alternative approach to measuring T cell responses to Mtb antigens.
UK-Biobank Whole Exome Sequence Binary Phenome Analysis with Robust Region-based Rare Variant Test
Authors: Zhao Zhangchen , Bi Wenjian , Zhou Wei , VandeHaar Peter , Fritsche Lars G. , Lee Seunggeun
Published: July 2019

In biobank data analysis, most binary phenotypes have unbalanced case-control ratios, which can cause inflation of type I error rates. Recently, a saddlepoint approximation (SPA) based single variant test has been developed to provide an accurate and scalable method to test for associations of such phenotypes. For gene- or region-based multiple variant tests, a few methods exist which adjust for unbalanced case-control ratios; however, these methods are either less accurate when case-control ratios are extremely unbalanced or not scalable for large data analyses. To address these problems, we propose SKAT/SKAT-O type region-based tests, where the single-variant score statistic is calibrated based on SPA and Efficient Resampling (ER). Through simulation studies, we show that the proposed method provides well-calibrated p-values. In contrast, the unadjusted approach has greatly inflated type I error rates (90 times of exome-wideα=2.5×10-6) when the case-control ratio is 1:99. Additionally, the proposed method has similar computation time as the unadjusted approaches and is scalable for large sample data. Our UK Biobank whole exome sequence data analysis of 45,596 unrelated European samples and 791 PheCode phenotypes identified 10 rare variant associations with p-value < 10-7, including the associations betweenJAK2and myeloproliferative disease,TNCand large cell lymphoma andF11and congenital coagulation defects. All analysis summary results are publicly available through a web-based visual server.
First report of Telenomus remus parasitizing Spodoptera frugiperda and its natural parasitism in South China
Authors: Liao Yong-Lin , Yang Bin , Xu Miao-Feng , Lin Wei , Wang De-Sen , Chen Ke-wei , Chen Hua-Yan
Published: July 2019

The fall armyworm, Spodoptera frugiperda, is a lepidopteran pest that feeds on many economically important cereal crops such as corn, rice, sorghum, and sugarcane. Native to the Americas, it has become a serious invasive pest in Africa and Asia. Recently, this pest was found invaded China and has spread exceptionally fast across the country. As S. frugiperda will most likely become a major pest in China, Integrated Pest Management strategies, including biological control methods, should be developed to win the battle against it. Here, we report the detection of Telenomus remus parasitizing S. frugiperda eggs in cornfields in South China based on morphological and molecular evidence. Our preliminary surveys indicated that the natural parasitism rates of T. remus on S. frugiperda could reach 30% and 50% for egg masses and per egg mass, respectively. Further application of T. remus against S. frugiperda in biological control programs are discussed.
Differential impact on motility and biofilm dispersal of closely related phosphodiesterases in Pseudomonas aeruginosa
Authors: Cai Yu-Ming , Hutchin Andrew , Craddock Jack , Walsh Martin A. , Webb Jeremy Stephen , Tews Ivo
Published: July 2019

Bacteria typically occur either as free-swimming planktonic cells or within a sessile, biofilm mode of growth. In Pseudomonas aeruginosa, the transition between these lifestyles is known to be modulated by the intracellular secondary messenger cyclic dimeric-GMP (c-di-GMP). We are interested in the control of distinct biofilm-relevant phenotypes in P. aeruginosa through the modulation of intracellular c-di-GMP. Here, we characterise motility and associated biofilm formation and dispersal in two pairs of related multi-domain proteins with putative c-di-GMP turnover domains, selected to contain additional PAS (Per-Arnt-Sim) homology domains known for their ability to process environmental stimuli. The enzymes PA0861 (RbdA) and PA2072 have distinct functions despite their similar domain structures. The ΔrbdA deletion mutant showed significantly increased biofilm formation while biofilm formation was impaired in ΔPA2072. Using a GFP transcriptional reporter fused to the cyclic di-GMP-responsive cdrA promoter, we show correlation between biofilm phenotype and c-di-GMP levels. Both proteins are shown to play a role in nitric oxide (NO) induced biofilm dispersal. We further studied pseudo-enzymes of similar architecture. PA5017 (DipA) is an inactive cyclase, and PA4959 (FimX) is described here as an inactive cyclase/phosphodiesterase. Loss of swimming and twitching motilities, respectively, is observed in deletion variants, which correlated with NO-induced biofilm dispersal phenotypes, as ΔdipA dispersed less well while ΔfimX dispersed better than wild type. The study highlights how Pseudomonas differentiates c-di-GMP output – in this case motility – using structurally very similar proteins and underlines a significant role for pseudo-enzymes in motility regulation and associated biofilm dispersal.

Importance

Bacterial biofilms exert pervasive economic and societal impact across a range of environmental, engineered and clinical contexts. The secondary messenger cyclic guanosine di-phosphate, c-di-GMP, is known to control the ability of many bacteria to form biofilms. The opportunistic human pathogen Pseudomonas aeruginosa PAO1 has 38 putative enzymes that can regulate c-di-GMP turnover, and these proteins modulate various cellular functions and influence bacterial lifestyle. The specific protein sensory domains and mechanisms of motility that lead to biofilm dispersal remain to be fully understood. Here we studied multi-domain proteins with the PAS (Per-Arnt-Sim) homology domains, these being classic sensors to environmental stimuli. Our study demonstrates the significant roles for the pseudo-enzymes PA4959 (FimX) and PA5017 (DipA) in regulation of biofilm phenotype and motility. Further, enzymes with highly homologous structures, such as PA0861 (RbdA) and PA2072, have almost orthogonal function in biofilm and motility control.
Photorhabdus LuminescensToxin complex (TCC) a recombinant injection nano-machine – delivery of recombinantYersinia enterocoliticaYopT
Authors: Ng’ang’a Peter , Ebner Julia K. , Plessner Matthias , Aktories Klaus , Schmidt Gudula
Published: July 2019

Engineering delivery systems for proteins and peptides into mammalian cells is an ongoing challenge for cell biological studies as well as for therapeutic approaches.Photorhabdus luminescenstoxin complex (PTC) is a heterotrimeric protein complex able to deliver diverse protein toxins into mammalian cells. We engineered the syringe like nano-machine for delivery of protein toxins from different species. Additionally, we loaded the highly active copepod luciferaseMetridia longaM-Luc7 for accurate quantification of injected molecules. We suggest that besides the size also the charge of the cargo defines the efficiency of packing and transport into mammalian cells. Our data show that thePhotorhabdus luminescenstoxin complex constitutes a powerful system to inject recombinant proteins, peptides and potentially other molecules like aptamers into mammalian cells. In contrast to other protein transporters based on pore formation, the cargo is protected from degradation. The system opens new perspectives for cell research and pharmacology.
Microbiota supplementation withBifidobacteriumandLactobacillusmodifies the preterm infant gut microbiota and metabolome
Authors: Alcon-Giner Cristina , Dalby Matthew J. , Caim Shabhonam , Ketskemety Jennifer , Shaw Alex , Sim Kathleen , Lawson Melissa , Kiu Raymond , Leclaire Charlotte , Chalklen Lisa , Kujawska Magdalena , Mitra Suparna , Fardus-Reid Fahmina , Belteki Gustav , McColl Katherine , Swann Jonathan R. , Kroll J. Simon , Clarke Paul , Hall Lindsay J.
Published: July 2019

Supplementation with members of the early-life microbiota or ‘probiotics’ is becoming increasingly popular to attempt to beneficially manipulate the preterm gut microbiota. We performed a large longitudinal study comprising two preterm groups; 101 orally supplemented withBifidobacteriumandLactobacillus(Bif/Lacto) and 133 non-supplemented (Control) matched by age, sex, birth-mode, and diet. 16S rRNA metataxonomic profiling on stool samples (n = 592) indicated a predominance ofBifidobacterium, and a reduction of pathobionts in the Bif/Lacto group. Metabolic phenotyping found a parallel increase in fecal acetate and lactate in the Bif/Lacto group compared to the Control group, which positively correlated withBifidobacteriumabundance consistent with the ability of the supplementedBifidobacteriumstrain to metabolize human milk oligosaccharides and reduced gut pH. This study demonstrates that microbiota supplementation can modify the preterm microbiome and the gastrointestinal environment to more closely resemble that of a full-term infant.
Factors affecting secondary sex characteristics in the yellowtail tetraAstyanax altiparanae
Authors: Siqueira-Silva Diógenes H. , Bertolini Rafaela M. , Pereira Nycolas L. , Nascimento Nivaldo F. , Senhorini José A. , Piva Lucas Henrique , Ferraz José Bento S. , Yasui George S.
Published: July 2019

This work aimed to analyze factors affecting secondary sexual characteristics in the yellowtail tetraAstyanax altiparanae.For this, seventy-five specimens were first separated into three different size classes (small, medium and large groups) between two seasons, summer and winter. In all groups, male fish were consistently bigger in the summer. On the other hand, females from both seasons presented in media the same length into the length classes. Afterwards, we performed histological analyses of the gonads to first confirm the genus and investigate the phase of maturation of each animal. During the winter, most of the small animals were males (22), most of the large animals, females (23), and the medium size animals followed a tendency of 1:1 ratio (9 male: 16 female). In the summer, male were the majority in both small (20) and medium (20) size. Larger-size animals were female (23). Then, in order to analyze the influence of genus, phase of maturation, season of the year, the number, and length of the animals spinelets, we diaphanized, counted, and measured them in each animal. Our results demonstrated that the spinelets are a sexual secondary characteristic of male genus independently of the size, season and phase of maturation. However, some tendencies were observed. Males bigger than 48 mm always presented spinelets; their size are in media the double in summer in comparison to winter; and summer males presents more rays with spinelets in the summer. Curiously, the larger specimen sampled was a female presenting spinelets in five rays. Lastly, we performed the gonadectomization of the animals and hypothesized that gonad hormones will directly influence this characteristic. The gonadectomization only initially influence on the size and number of spinelets in the anal fin rays, since the thirty-day-gonadectomized animals presented few and smaller spinelets against the control ones. However, the spinelets normalized in ninety-day-gonadectomized specimens. Such a work showed spinelets can be considered a secondary sexual characteristic to distinct male from female and can be used in the management in specimens bigger than 48 mm, but cannot indicate fish sterility.

Summary statement

This study elucidated whether the size, sex, environmental conditions, and gonadal development affect the development of spinelets, a bony structure presented in anal fins in mature fish. Additionally, gonadectomized fish were used to elucidate the effect of gonad on the rise of such structures. Interesting new data showed that such a secondary sex characteristic is influenced by sex, size, gonadal development, and season of the year, but spinelets arose even within gonadectomized fish; this suggests that such a structure is not indicative of sterility in this species.
A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a
Authors: Katzmeier Florian , Aufinger Lukas , Dupin Aurore , Quinteiro Jorge , Lenz Matthias , Bauer Ludwig , Klumpe Sven , Sherpa Dawafuti , Dürr Benedikt , Honemann Maximilian , Styazhkin Igor , Simmel Friedrich C. , Heymann Michael
Published: July 2019

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of ≈6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.
A synthetic metabolic network for physicochemical homeostasis
Authors: Pols Tjeerd , Sikkema Hendrik R. , Gaastra Bauke F. , Frallicciardi Jacopo , Śmigiel Wojciech M. , Singh Shubham , Poolman Bert
Published: July 2019

One of the grand challenges in chemistry is the construction of functional out-of-equilibrium networks, which are typical of living cells. Building such a system from molecular components requires control over the formation and degradation of the interacting chemicals and homeostasis of the internal physical-chemical conditions. The provision and consumption of ATP lies at the heart of this challenge. We report thein vitroconstruction in vesicles of a pathway for sustained ATP production that is maintained away from equilibrium by control of energy dissipation. We maintain a constant level of ATP with varying load on the system. The pathway enables us to control the transmembrane fluxes of osmolytes and to demonstrate basic physicochemical homeostasis. Our work demonstrates metabolic energy conservation and cell volume regulatory mechanisms in a cell-like system at a level of complexity minimally needed for life.
A positional information gradient of sonic hedgehog is required for flight feather formation in avian wings
Authors: Busby Lara , Aceituno Cristina , McQueen Caitlin , Rich Constance A. , Ros Maria A. , Towers Matthew
Published: July 2019

Flight is a triumph of evolution that enabled the radiation and success of birds. A crucial step was the development of forelimb flight feathers that may have evolved for courtship or territorial displays in ancestral theropod dinosaurs. Classical tissue recombination experiments performed in the chick embryo provide evidence that signals operating during early limb development specify the position and identity of feathers. Here we show that a positional information gradient of Sonic hedgehog (Shh) signalling in the embryonic chick wing bud specifies the pattern of adult flight feathers in a defined spatial and temporal sequence that reflects their different identities. We reveal that the Shh signalling gradient is interpreted into specific patterns of flight feather-associated gene expression. Our data suggests that flight feather evolution involved the co-option of the pre-existing digit patterning mechanism and therefore uncovers an embryonic process that played a fundamental step in the evolution of avian flight.
Migratory divides coincide with species barriers across replicated avian hybrid zones above the Tibetan Plateau
Authors: Scordato Elizabeth S.C. , Smith Chris C.R. , Semenov Georgy A. , Liu Yu , Wilkins Matthew R. , Liang Wei , Rubtsov Alexander , Sundev Gomboobaatar , Koyama Kazuo , Turbek Sheela P. , Wunder Michael B. , Stricker Craig A. , Safran Rebecca J.
Published: July 2019

Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, the relative contribution of migratory behavior to reproductive isolation is difficult to test. Comparing reproductive isolation in hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with an apparent migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridized extensively. Within migratory divides, migratory phenotype was associated with assortative mating, implicating a central contribution of divergent migratory behavior to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a longstanding hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.
Cognitive control of orofacial and vocal responses in the human frontal cortex
Authors: Loh Kep Kee , Procyk Emmanuel , Neveu Remi , Lamberton Franck , Hopkins William , Petrides Michael , Amiez Céline
Published: July 2019

The frontal cortical areas critical for human speech production, i.e. the ventrolateral frontal cortex (cytoarchitectonic areas 44 and 45; VLF) and the dorsomedial frontal cortex (DMF) comprising the mid-cingulate cortex (MCC) and the pre-supplementary motor area (preSMA), exist in non-human primates and are implicated in cognitive vocal control functions. The present functional neuroimaging study seeks to define the basic roles of these VLF-DMF network regions in primate vocal production and how they might have been adapted for human speech. We demonstrate that area 44 and the MCC are respectively involved in the cognitive selection of orofacial, non-speech vocal and verbal responses, and the feedback-driven adaptation of these responses – roles that are likely preserved across primates. In contrast, area 45 and preSMA have roles that are specific to human speech: area 45 contributes to active verbal retrieval during learning, while preSMA is involved in processing verbal feedback during orofacial/vocal adaptations.
The lipid transfer protein Saposin B does not directly bind CD1d for lipid antigen loading
Authors: Shamin Maria , Benedyk Tomasz H. , Graham Stephen C. , Deane Janet E.
Published: July 2019

Lipid antigens are presented on the surface of cells by the CD1 family of glycoproteins, which have structural and functional similarity to MHC class I molecules. The hydrophobic lipid antigens are embedded in membranes and inaccessible to the lumenal lipid-binding domain of CD1 molecules. Therefore, CD1 molecules require lipid transfer proteins for lipid loading and editing. CD1d is loaded with lipids in late endocytic compartments, and lipid transfer proteins of the saposin family have been shown to play a crucial role in this process. However, the mechanism by which saposins facilitate lipid binding to CD1 molecules is not known and is thought to involve transient interactions between protein components to ensure CD1-lipid complexes can be efficiently trafficked to the plasma membrane for antigen presentation. Of the four saposin proteins, the importance of Saposin B (SapB) for loading of CD1d is the most well-characterised. However, a direct interaction between CD1d and SapB has yet to be described. In order to determine how SapB might load lipids onto CD1d, we used purified, recombinant CD1d and SapB and carried out a series of highly sensitive binding assays to monitor direct interactions. Using equilibrium binding analysis, chemical cross-linking and co-crystallisation experiments, under a range of different conditions, we could not demonstrate a direct interaction. This work establishes comprehensively that the role of SapB in lipid loading does not involve direct binding to CD1d. We discuss the implication of this for our understanding of lipid loading of CD1d and propose several factors that may influence this process.
Non-genetic intra-tumor heterogeneity is a major predictor of phenotypic heterogeneity and ongoing evolutionary dynamics in lung tumors
Authors: Sharma Anchal , Merritt Elise , Hu Xiaoju , Cruz Angelique , Jiang Chuan , Sarkodie Halle , Zhou Zhan , Malhotra Jyoti , Riedlinger Gregory M , De Subhajyoti
Published: July 2019

Impacts of genetic and non-genetic intra-tumor heterogeneity (ITH) on tumor phenotypes and evolvability remain debated. We analyzed ITH in lung squamous cell carcinoma (LUSC) at the levels of genome, transcriptome, tumor-immune interactions, and histopathological characteristics by multi-region profiling and using single-cell sequencing data. Overall, in LUSC genomic heterogeneity alone was a weak indicator of intra-tumor non-genetic heterogeneity at immune and transcriptomic levels that impacted multiple cancer-related pathways including those related to proliferation and inflammation, which in turn contributed to intra-tumor regional differences in histopathology and subtype classification. Genome, transcriptome, and immune-level heterogeneity influenced different aspects of tumor evolution. Tumor subclones had substantial differences in proliferation score, suggestive of non-neutral clonal dynamics. Scores for proliferation and other cancer-related pathways also showed intra-tumor regional differences, sometimes even within the same subclones. Neo-epitope burden negatively correlated with immune infiltration, indicating potential immune-mediated purifying selection on acquired mutations in these tumors. Taken together, our observations suggest that non-genetic heterogeneity is a major determinant of heterogeneity in histopathological characteristics and impacts evolutionary dynamics in lung cancer.
Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators
Authors: Farahmand Saman , O’Connor Corey , Macoska Jill A. , Zarringhalam Kourosh
Published: July 2019

Inference of active regulatory mechanisms underlying specific molecular and environmental perturbations is essential for understanding cellular response. The success of inference algorithms relies on the quality and coverage of the underlying network of regulator-gene interactions. Several commercial platforms provide large and manually-curated regulatory networks and functionality to perform inference on these networks. Adaptation of such platforms for open-source academic applications has been hindered by the lack of availability of accurate, high-coverage networks of regulatory interactions and integration of efficient causal inference algorithms. In this work, we present CIE, an integrated platform for causal inference of active regulatory mechanisms form differential gene expression data. Using a regularized Gaussian Graphical Model, we construct a transcriptional regulatory network by integrating publicly available ChIP-Seq experiments with gene-expression data from tissue-specific RNA-Seq experiments. Our GGM approach identifies high confidence TF-gene interactions and annotates the interactions with information on mode of regulation (activation vs. repression). Benchmarks against manually-curated databases of TF-gene interactions show that our method can accurately detect mode of regulation. We demonstrate the ability of our platform to identify active transcriptional regulators by using controlledin vitrooverexpression and stem-cell differentiation studies and utilize our method to investigate transcriptional mechanisms of fibroblast phenotypic plasticity.
Deep Learning for Alzheimer’s Disease: Mapping Large-scale Histological Tau Protein for Neuroimaging Biomarker Validation
Authors: Alegro Maryana , Chen Yuheng , Ovando Dulce , Heinser Helmut , Eser Rana , Ushizima Daniela , Tosun Duygu , Grinberg Lea T.
Published: July 2019

Deposits of abnormal tau protein inclusions in the brain are a pathological hallmark of Alzheimer’s disease (AD), and are the best predictor of neuronal loss and clinical decline, but have been limited to postmortem assessment. Imaging-based biomarkers to detect tau depositsin vivocould leverage AD diagnosis and monitoring beginning in pre-symptomatic disease stages. Several PET tau tracers are available for research studies, but validation of such tracers against direct detection of tau deposits in brain tissue remains incomplete because of methodological limitations. Confirmation of the biological basis of PET binding requires large-scale voxel-to-voxel correlation has been challenging because of the dimensionality of the whole human brain histology data, deformation caused by tissue processing that precludes registration, and the need to process terabytes of information to cover the whole human brain volume at microscopic resolution. In this study, we created a computational pipeline for segmenting tau inclusions in billion-pixel digital pathology images of whole human brains, aiming at generating quantitative, tridimensional tau density maps that can be used to decipher the distribution of tau inclusions along AD progression and validate PET tau tracers. Our pipeline comprises several pre- and post-processing steps developed to handle the high complexity of these brain digital pathology images. SlideNet, a convolutional neural network designed to process our large datasets to locate and segment tau inclusions, is at the core of the pipeline. Using our novel method, we have successfully processed over 500 slides from two whole human brains, immunostained for two phospho-tau antibodies (AT100 and AT8) spanning several Gigabytes of images. Our artificial neural network estimated strong tau inclusion from image segmentation, which performs with ROC AUC of 0.89 and 0.85 for AT100 and AT8, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. Furthermore, our pipeline successfully created 3D tau inclusion density maps that were co-registered to the histology 3D maps.
Cell Fate Clusters in ICM Organoids Arise from Cell Fate Heredity & Division – a Modelling Approach
Authors: Liebisch Tim , Drusko Armin , Mathew Biena , Stelzer Ernst H. K. , Fischer Sabine C. , Matthäus Franziska
Published: July 2019

During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first cell fate decision, cells become either part of an outer trophectoderm or part of the inner cell mass. Subsequently, the inner cell mass (ICM) segregates into an embryonic and an extraembryonic lineage, giving rise to the epiblast and the primitive endoderm, respectively. Inner cell mass organoids represent an experimental model system for preimplantation development, mimicking the second cell fate decision taking place inin vivomouse embryos. In a previous study, the spatial pattern of the different cell lineage types was investigated. The study revealed that cells of the same fate tend to cluster stronger than expected for purely random cell fate decisions. Three major processes are hypothesised to contribute to the final cell fate arrangements at the mid and late blastocysts or 24 h old and 48 h old ICM organoids, respectively: 1) intra- and intercellular chemical signalling; 2) a cell sorting process; 3) cell proliferation. In order to quantify the influence of cell proliferation on the emergence of the observed cell lineage type clustering behaviour, we developed an agent-based model. Hereby, cells are mechanically interacting with direct neighbours, and exert adhesion and repulsion forces. The model was applied to compare several current assumptions of how inner cell mass neighbourhood structures are generated. We tested how different assumptions regarding cell fate switches affect the observed neighbourhood relationships. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. The model further shows that the observed neighbourhood structures can emerge due to cell fate heredity during cell division and allows the inference of a time point for the cell fate decision.

STATEMENT OF SIGNIFICANCE

Cell fate decisions in early embryogenesis have been considered random events, causing a random cell fate distribution. Using an agent-based mathematical model, fitted to ICM organoid data, we show that the assumed random distribution of cell fates occurs only for a short time interval, as cell fate heredity and cell division quickly lead to spatial cell fate clustering. Our results show that neighbourhood clustering can emerge without specific neighbourhood interactions affecting the cell fate decision. The approach indicates four consecutive phases of early development: 1) co-expression of cell fate markers, 2) cell fate decision, 3) division and local cell fate clustering, and 4) phase separation, whereby only the phases 1-3 occur in ICM organoids during the first 24h of growth.
Multivariate phenotypic divergence along an urbanization gradient
Authors: Santangelo James S. , Advenard Carole , Rivkin L. Ruth , Thompson Ken A.
Published: July 2019

A growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To address this gap, we generated seed families of white clover (Trifolium repens) collected from 27 populations along an urbanization gradient in Toronto, Canada, and grew them up to measure multiple phenotypic traits in a common garden. Overall, urban populations had later phenology and germination, larger flowers, thinner stolons, reduced cyanogenesis, greater biomass, and were more attractive to pollinators. Pollinator observations revealed near complete turnover between urban and nonurban sites, which may explain some of the observed divergence in floral traits and phenology. Our results suggest that adaptation to urban environments involves multiple organismal traits.
Novel tetraplex qPCR assays for simultaneous detection and identification ofXylella fastidiosasubspecies in plant tissues
Authors: Enora Dupas , Martial Briand , Marie-Agnès Jacques , Sophie Cesbron
Published: July 2019

Xylella fastidiosais an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspeciesfastidiosa,multiplexandpauca. Initially limited to the Americas,Xfhas been detected in Europe since 2013. As management ofX. fastidiosaoutbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Thus, we developed various tetraplex and triplex qPCR assays forXylella fastidiosadetection and subspecies identificationin plantain a single reaction. We designed primers and probes using SkIf, a bioinformatics tool based onk-mers, to detect specific signatures of the species and subspecies from a dataset of 58 genome sequences representative ofX. fastidiosadiversity. We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies ofX. fastidiosa, and on samples from various environmental and inoculated host plants. Sensitivity of simplex assays was equal or slightly better than the reference protocol on purified DNA. Tetraplex qPCR assays had the same sensitivity than the reference protocol and allowedX. fastidiosadetection in all spiked matrices up to 103cells.mL−1. Moreover, mix infections of two to three subspecies could be detected in the same sample with tetraplex assays. In environmental plant samples, the tetraplex qPCR assays allowed subspecies identification when the current method based on multilocus sequence typing failed. The qPCR assays described here are robust and modular tools that are efficient for differentiatingX. fastidiosasubspecies directly in plant samples.
SiZer Map to investigate significant features of body-weight profile changes in HIV infected patients in the IeDEA Collaboration
Authors: Harezlak Jaroslaw , Sarwat Samiha , Wools-Kaloustian Kara , Schomaker Michael , Balestre Eric , Law Matthew , Kiertiburanakul Sasisopin , Fox Matthew , Huis in ’t Veld Diana , Musick Beverly Sue , Yiannoutsos Constantin Theodore
Published: July 2019

Objectives

We extend the method of Significant Zero Crossings of Derivatives (SiZer) to address within-subject correlations of repeatedly collected longitudinal biomarker data and the computational aspects of the methodology when analyzing massive biomarker databases. SiZer is a powerful visualization tool for exploring structures in curves by mapping areas where the first derivative is increasing, decreasing or does not change (plateau) thus exploring changes and normalization of biomarkers in the presence of therapy.

Methods

We propose a penalized spline SiZer (PS-SiZer) which can be expressed as a linear mixed model of the longitudinal biomarker process to account for irregularly collected data and within-subject correlations. Through simulations we show how sensitive PS-SiZer is in detecting existing features in longitudinal data versus existing versions of SiZer. In a real-world data analysis PS-SiZer maps are used to map areas where the first derivative of weight change after antiretroviral therapy (ART) start is significantly increasing, decreasing or does not change, thus exploring the durability of weight increase after the start of therapy. We use weight data repeatedly collected from persons living with HIV initiating ART in five regions in the International Epidemiologic Databases to Evaluate AIDS (IeDEA) worldwide collaboration and compare the durability of weight gain between ART regimens containing and not containing the drug stavudine (d4T), which has been associated with shorter durability of weight gain.

Results

Through simulations we show that the PS-SiZer is more accurate in detecting relevant features in longitudinal data than existing SiZer variants such as the local linear smoother (LL) SiZer and the SiZer with smoothing splines (SS-SiZer). In the illustration we include data from 185,010 persons living with HIV who started ART with a d4T (53.1%) versus non-d4T (46.9%) containing regimen. The largest difference in durability of weight gain identified by the SiZer maps was observed in Southern Africa where weight gain in patients treated with d4T-containing regimens lasted 52.4 weeks compared to 94.4 weeks for those with non-d4T-containing regimens. In the other regions, persons receiving d4T-containing regimens experienced weight gains lasting 51-61 weeks versus 59-77 weeks in those receiving non-d4T-based regimens.

Discussion

PS-SiZer, a SiZer variant, can handle irregularly collected longitudinal data and within-subject correlations and is sensitive in detecting even subtle features in biomarker curves.
Modeling Uncertainty-Seeking Behavior Mediated by Cholinergic Influence on Dopamine
Authors: Belkaid Marwen , Krichmar Jeffrey L.
Published: July 2019

Recent findings suggest that acetylcholine mediates uncertainty-seeking behaviors through its projection to dopamine neurons – another neuromodulatory system known for its major implication in reinforcement learning and decision-making. In this paper, we propose a leaky-integrate-and-fire model of this mechanism. It implements a softmax-like selection with an uncertainty bonus by a cholinergic drive to dopaminergic neurons, which in turn influence synaptic currents of downstream neurons. The model is able to reproduce experimental data in two decision-making tasks. It also predicts that i) in the absence of cholinergic input, dopaminergic activity would not correlate with uncertainty, and that ii) the adaptive advantage brought by the implemented uncertainty-seeking mechanism is most useful when sources of reward are not highly uncertain. Moreover, this modeling work allows us to propose novel experiments which might shed new light on the role of acetylcholine in both random and directed exploration. Overall, this study thus contributes to a more comprehensive understanding of the roles of the cholinergic system and its involvement in decision-making in particular.
Contributions of spatial and temporal control of step length symmetry in the transfer of locomotor adaptation from a motorized to a non-motorized split-belt treadmill
Authors: Gregory Daniel L. , Sup Frank C. , Choi Julia T.
Published: July 2019

Background

Locomotor adaptation during motorized split-belt walking depends on independent processes for spatial and temporal control of step length symmetry. The unique mechanics of motorized split-belt walking that constrains two limbs to move at different speeds during double support may limit transfer of step length adaptations to new walking contexts.

Research question

How do spatial and temporal locomotor outputs contribute to transfer of step length adaptation from constrained motorized split-belt walking to unconstrained non-motorized split-belt walking?

Methods

We built a non-motorized split-belt treadmill that allows the user to walk at their own pace while simultaneously allowing the two belts to be self-propelled at different speeds. 10 healthy young participants walked on the non-motorized split-belt treadmill after an initial 10-minute adaptation on the motorized split-belt with a 2:1 speed ratio. Foot placement relative to the body and timing between heel strikes were calculated to determine spatial and temporal motor outputs, respectively. Separate repeated measures ANOVAs were used for step length difference and its spatial and temporal components to assess for transfer to the non-motorized treadmill.

Results

We found robust after-effects in step length difference during transfer to non-motorized split-belt treadmill walking that were primarily driven by changes in temporal motor outputs. Conversely, residual after-effects observed during motorized tied-belt treadmill walking (post-transfer) were driven by changes in spatial motor outputs.

Significance

Our data showed decoupling of adapted spatial and temporal locomotor outputs during the transfer to non-motorized split-belt walking, raising the new possibility of using a non-motorized split-belt treadmill to target specific spatial or temporal gait deficits.