bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome analysis reveals the difference between “healthy” and “common” aging and their connection with age-related diseases
Authors: Zeng Lu , Yang Jialiang , Peng Shouneng , Zhu Jun , Zhang Bin , Suh Yousin , Tu Zhidong
Published: August 2019

A key goal of aging research is to understand mechanisms underlying healthy aging and use them to develop methods to promote the human healthspan. One approach is to identify gene regulations differentiating healthy aging from aging in the general population (i.e., “common” aging). In this study, we leveraged GTEx (Genotype-Tissue Expression) project data to investigate “healthy” and “common” aging in humans and their interconnection with diseases.

We selected GTEx donors who were not annotated with diseases to approximate a “healthy” aging cohort. We then compared the age-associated genes derived from this cohort with age-associated genes from our “common” aging cohort which included all GTEx donors; we also compared the “healthy” and “common” aging gene expressions with various disease-associated gene expression to elucidate the relationships among “healthy”, “common” aging and disease. Our analyses showed that 1. “healthy” and “common” aging shared a large number of gene regulations; 2. Despite the substantial commonality, “healthy” and “common” aging genes also showed distinct function enrichment, and “common” aging genes had a higher enrichment for disease genes; 3. Disease-associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with the “healthy” aging gene regulations.

In summary, our work highlights several unique features of human “healthy” aging program. This new knowledge can be used for the development of therapeutics to promote human healthspan.
Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes
Authors: Li Liguan , Dechesne Arnaud , Madsen Jonas Stenløkke , Nesme Joseph , Sørensen Søren J. , Smets Barth F.
Published: August 2019

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes ofAeromonas,PseudomonasandEnterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in a high-throughput way without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognized potential to maintain plasmids for long-term community-wide access.
Transition from background selection to associative overdominance promotes diversity in regions of low recombination
Authors: Gilbert Kimberly J. , Pouyet Fanny , Excoffier Laurent , Peischl Stephan
Published: August 2019

Linked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworthet al.1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyetet al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.
The tooth on-a-chip: a microphysiologic model system mimicking the pulp-dentin interface and its interaction with biomaterials
Authors: França Cristiane Miranda , Tahayeri Anthony , Rodrigues Nara Sousa , Ferdosian Shirin , Puppin-Rontani Regina , Ferracane Jack L. , Bertassoni Luiz E.
Published: August 2019

The tooth has a unique configuration with respect to biomaterials that are used for its treatment. Cells inside of the dental pulp interface indirectly with biomaterials via a calcified permeable membrane, formed by a dentin barrier which is composed of several thousands of dentinal tubules (~2 µm in diameter) connecting the dental pulp tissue to the outer surface of the tooth. Although the cytotoxic response of the dental pulp to biomaterials has been extensively studied, there is a shortage of in vitro model systems that mimic the dentin-pulp interface, enabling an improved understanding of the morphologic, metabolic and functional influence of biomaterials on live dental pulp cells. To address this shortage, here we developed an organ-on-a-chip model system which integrates cells cultured directly on a dentin wall within a microdevice which replicates some of the architecture and dynamics of the dentin-pulp interface. The tooth-on-a-chip is made out of molded polydimethylsiloxane (PDMS) with a design consisting of two chambers separated by a dentin fragment. To characterize pulp cell responses to dental materials on-chip, stem cell-derived odontoblasts were seeded onto the dentin surface, and observed using live-cell microscopy. Standard dental materials used clinically (2-hydroxyethylmethacrylate - HEMA, Phosphoric Acid - PA, and Adper-Scotchbond - SB) were tested for cytotoxicity, cell morphology and metabolic activity on-chip, and compared against standardized off-chip controls. All dental materials had cytotoxic effects in both on-chip and off-chip systems in the following order: HEMA>SB>PA (p<0.05), and cells presented consistently higher metabolic activity on-chip than off-chip (p<0.05). Furthermore, the tooth-on-a-chip enabled real-time tracking of odontoblast monolayer formation, remodeling, and death in response to biomaterial treatments, and gelatinolytic activity in a model hybrid layer (HL) formed in the microdevice. In conclusion, the tooth-on-a-chip is a novel platform that replicates near-physiologic conditions of the pulp-dentin interface, and enables live-cell imaging to study dental pulp cell response to biomaterials.
Low frequency of pathogenic allelic variants in the 46,XY differences of sex development (DSD)-related genes in small for gestational age children with hypospadias
Authors: Braga Barbara L. , Gomes Nathalia L. , Nishi Mirian Yumie , Freire Bruna Lucheze , Batista Rafael Loch , Lerario Antonio Marcondes , de Assis Funari Mariana Ferreira , Frade Costa Elaine Maria , Domenice Sorahia , Faria Junior José Antonio D. , Lima Jorge Alexander Augusto , Mendonca Berenice Bilharinho
Published: August 2019

Background

Hypospadias is a congenital disorder of male genital formation where the urinary opening is not on the head of the penis and genetic factors play an important role in the incidence of this early developmental defect in 46,XY individuals, in both isolated and syndromic forms. Children born small for gestational age (SGA) present a high frequency of hypospadias of undetermined etiology, ranging from 15 to 30%, but the detection of hypospadias’ etiology remains low.

Patients and methods

from a cohort of 46,XY DSD patients, we identified 25 SGA children with medium or proximal hypospadias; four of them with associated syndromic characteristics. DNA samples from subjects were studied by massively parallel targeted sequencing (MPTS) using a targeted panel. MLPA was used for molecular diagnosis in two children with clinical phenotype of Silver Russel syndrome.

Results

Loss of DNA methylation (11p15 LOM) at ICR1 was identified in two out of four syndromic children. The other syndromic patient had 3M syndrome phenotype and two novel likely-pathogenic variants in compound heterozygous state were found in CUL7 gene. The last syndromic subject had Mulibrey nanism and, a homozygous variant in TRIM37 was identified in the patient and confirmed in heterozygous state in the mother. Among non-syndromic children seven rare heterozygous variants with uncertain significance in six DSD-related genes were identified: two children had DHX37 variants associated with GATA4 and WWOX variants, respectively; three children had heterozygous variants, in WT1, IGF1R, and BMP8B genes.

Conclusion

Pathogenic or likely-pathogenic variants in DSD-related genes were not identified in non-syndromic SGA children with hypospadias, suggesting that multi-factorial causes, unknown genes or unidentified environmental factors (epigenetic defects), may be involved in the etiology of this condition.
The fasciola cinereum subregion of the hippocampus is important for the acquisition of visual contextual memory
Authors: Park Seong-Beom , Lee Eun-Young , Lim Heung-Yeol , Yoo Seung-Woo , Lee Eunsoo , Jung Hyun-Suk , Sun Woong , Lee Inah
Published: August 2019

The fasciola cinereum (FC) is a subregion of the hippocampus that has received relatively little research attention compared with other hippocampal subregions with respect to anatomical characteristics and functional significance. Here, we show that the FC exhibits clear anatomical borders with CA1. The FC consists of granule cells, but adult neurogenesis was not found. The FC receives inputs from the lateral entorhinal cortex and perirhinal cortex while projecting to the crest of the dentate gyrus (DG). Neurotoxic lesioning of the FC using colchicine impaired the acquisition, but not retrieval, of visual contextual memory in rats. FC lesions also impaired place recognition and object-in-place memory. Place cells in the FC showed robust place fields but fired only transiently in their fields compared with those in CA1. Our findings suggest that the FC may play critical roles in learning a novel environment by facilitating pattern separation in the DG of the hippocampus.
Evolution in interacting species alters predator life history traits, behavior and morphology in experimental microbial communities
Authors: Cairns Johannes , Moerman Felix , Fronhofer Emanuel A. , Altermatt Florian , Hiltunen Teppo
Published: August 2019

Predator-prey interactions are key for the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and co-evolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defense and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co-)evolving systems remain poorly understood. Here we investigated changes in predator traits after ~600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator’s evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behavior. Consistent with previous studies, we found that prey evolution impaired growth of the predator. In contrast, predator evolution did not cause a clear increase in fitness when feeding on ancestral prey. However, predator evolution affected morphology and behavior, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co-)evolving systems, predator adaptation can occur in traits relevant to offense level without translating into an increased ability of the predator to grow on the ancestral prey type.
Female resource limitation does not make the opportunity for selection more female biased
Authors: Martinossi-Allibert Ivain , Rönn Johanna Liljestrand , Immonen Elina
Published: August 2019

Environmental and physiological conditions affect how individual variation is expressed and translated into variance in fitness, the opportunity for natural selection. Competition for limiting resources can magnify variance in fitness and therefore selection, while abundance of resources should reduce it. But even in a common environment the strength of selection can be expected to differ across the sexes, as their fitness is often limited by different resources. Indeed most taxa show a greater opportunity for selection in males than in females, a bias often ascribed to intense competition among males for access to mating partners. This sex-bias could reverberate on many aspects of evolution, from speed of adaptation to genome evolution. It is unclear however, whether the sex-bias in opportunity for selection is robust to variations in environment or physiological condition that limit sex-specific resources. Here we test this in the model speciesC. maculatusby comparing female and male variance in relative fitness (opportunity for selection) under mate competition (i) with and without limitation of quality oviposition sites, and (ii) under delayed age at oviposition. Decreasing the abundance of the resource key to females or increasing their reproductive age was indeed challenging as shown by a reduction in mean fitness, however variance in fitness remained male-biased across the three treatments, with even an increased male-bias when females were limited by oviposition sites. This suggests that males remain the more variable sex independent of context, and that the opportunity for selection through males is indirectly affected by female-specific resource limitation.
Dissecting adaptive traits with nested association mapping: Genetic architecture of inflorescence morphology in sorghum
Authors: Olatoye Marcus O. , Marla Sandeep R. , Hu Zhenbin , Bouchet Sophie , Perumal Ramasamy , Morris Geoffrey P.
Published: August 2019

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. Here we characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under largely independent genetic control, while lower branch length and rachis diameter are pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1%–5.0% of variation across the entire NAM population. Overall, there is a significant enrichment (2.4-fold) of QTL colocalizing with homologs of grass inflorescence genes, notably with orthologs of maize (Ramosa2) and rice (Aberrant Panicle Organization1, TAWAWA1) inflorescence regulators. In global georeferenced germplasm, allelic variation at the major inflorescence morphology QTL is significantly associated with precipitation gradients, consistent with a role for these QTL in adaptation to agroclimatic zones. The findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. This genotype-phenotype trait dissection in global germplasm provides a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.
The choreography of human attraction: physiological synchrony in a blind date setting
Authors: Prochazkova E. , Sjak-Shie E. E. , Behrens F. , Lindh D. , Kret M. E.
Published: August 2019

Humans are social animals whose mental wellbeing is shaped by the ability to attract and connect with each other. In a dating world, in which success can be determined by brief interactions, apart from physical features, there is a whole choreography of movements, physical reactions and subtle expressions that drive humans’ sexual attraction. To determine what drives attraction, we measured nonverbal dynamics between people during real-life interactions outside the laboratory, where dating is most relevant. Participants wore eye-tracking glasses with embedded cameras, and devices to measure physiological signals including heart rate and skin conductance. Crucially, visible signals that can be controlled, such as facial expressions or gaze, did not predict attraction. Instead, attraction was predicted by synchrony in heart rate and skin conductance between partners, which are unconscious and difficult to regulate. Our findings suggest that shared emotionality is vital for mutual attraction. Moreover, physiological synchrony may provide a medium for translating visible expressions into embodied emotions, which can turn into intentions via somatosensory simulation.

Significance Statement

In our modern world where millions of people meet online without interacting face-to-face, the question “what defines attraction” has become very relevant. In this study, we used modern technologies to lay down a foundation for the processes that drive human attraction during real-life interactions. Contrary to common belief, we found that attraction is not predicted by a frequency of expression or eye fixation duration, nor is linearly related to the participant’s autonomic nervous system activity. Importantly, we found that the more a participant synchronized their heart rate and skin conductance with their partner, the more they felt attracted toward that person. This study reveals a fundamental physiological process that plays a role in the formation of romantic relations.
Face Selective Neural Activity: Comparison Between Fixed and Free Viewing
Authors: Auerbach-Asch Carmel R. , Bein Oded , Deouell Leon Y.
Published: August 2019

Event Related Potentials (ERPs) are widely used to study category-selective EEG responses to visual stimuli, such as the face-selective N170 component. Typically, this is done by flashing stimuli abruptly at the point of static gaze fixation. While allowing for good experimental control, these paradigms ignore the dynamic role of eye-movements in natural vision. Fixation-related potentials (FRPs) obtained using simultaneous EEG and eye-tracking, overcome this limitation. Various studies have used FRPs to study processes such as lexical processing, target detection and attention allocation. The goal of this study was to compare face-sensitive activity evoked by stimulus abrupt appearance with that evoked by self-controlled gaze fixations on a stimulus. Twelve participants were studied in three experimental conditions: Free-viewing (FRPs), Cued-viewing (FRPs) and Control (ERPs). We used a multiple regression approach to disentangle overlapping activity components. Our results show that the N170 face effect (face vs. non-face) is evident for the first fixation on a stimulus, whether it follows a self-generated saccade or stimulus appearance at fixation point. Furthermore, the N170 exhibits category-specific adaptation in free viewing. The N170 face effect had similar topography across viewing conditions, but there were major differences within each stimulus category. We ascribe these differences to an overlap of the fixation-related Lambda response and the N170. We tested the plausibility of this account using dipole simulations. This study establishes the use of the N170 face effect as a signature of face detection in free-viewing experiments while highlighting the importance of accounting for eye-movement related effects.
Identification of RNA 3’ ends and termination sites in Haloferax volcanii
Authors: Berkemer Sarah J. , Maier Lisa-Katharina , Amman Fabian , Bernhart Stephan H. , Wörtz Julia , Märkle Pascal , Pfeiffer Friedhelm , Stadler Peter F. , Marchfelder Anita
Published: August 2019

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3’ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea. In this study, only part of the genome had been investigated. Here, we developed a novel algorithm that allows an unbiased, genome-wide identification of RNA 3’ termini independent of annotation. In an RNA fraction enriched for primary transcripts by terminator exonuclease (TEX) treatment we identified 1,543 RNA 3’ termini. A strong sequence signature consistent with known termination events at intergenic loci indicates a clear enrichment for native TTS among them. Using these data we determined distinct putative termination motifs for intergenic (a T stretch) and coding regions (AGATC). In vivo reporter gene tests of selected TTS confirmed termination at these sites, which exemplify the different motifs. For several genes, more than one termination site was detected, resulting in transcripts with different lengths of the 3’ untranslated region.
An assessment of LRRK2 serine 935 phosphorylation in human peripheral blood mononuclear cells in idiopathic Parkinson’s disease and G2019S LRRK2 cohorts
Authors: Padmanabhan Shalini , Lanz Thomas A. , Gorman Donal , Wolfe Michele , Levers Najah , Joshi Neal , Liong Christopher , Narayan Sushma , Alcalay Roy N. , Hutten Samantha J. , Baptista Marco A. S. , Merchant Kalpana
Published: August 2019

The phosphorylated form of LRRK2, pS935 LRRK2, has been proposed as a target modulation biomarker for LRRK2 inhibitors. To qualify the biomarker for therapeutic trials, we assessed pS935 LRRK2 levels in Peripheral Blood Mononuclear Cells (PBMCs). Analyses of PBMCs from healthy controls, idiopathic Parkinson’s disease (iPD), and G2019S carriers with and without PD showed significant reductions in pS935 LRRK2 levels normalized to total LRRK2 levels in G2019S carriers with PD compared to those without PD or iPD. Neither analyte correlated with age, gender, or disease severity. Thus, pS935 LRRK2 in PBMCs may reflect a state marker for G2019S LRRK2-driven PD.
Efficient whole genome sequencing of influenza A viruses
Authors: Escalera-Zamudio Marina , Cobián-Güemes Ana Georgina , Taboada Blanca , López-Martínez Irma , Vázquez-Pérez Joel Armando , Montalvo-Corral Maricela , Hernandez Jesus , Díaz-Quiñonez José Alberto , Badillo Gisela Barrera , López Susana , Arias Carlos F. , Iša Pavel
Published: August 2019

The constant threat of emergence for novel pathogenic influenza A viruses with pandemic potential, makes full-genome characterization of circulating influenza viral strains a high priority, allowing detection of novel and re-assorting variants. Sequencing the full-length genome of influenza A virus traditionally required multiple amplification rounds, followed by the subsequent sequencing of individual PCR products. The introduction of high-throughput sequencing technologies has made whole genome sequencing easier and faster. We present a simple protocol to obtain whole genome sequences of hypothetically any influenza A virus, even with low quantities of starting genetic material. The complete genomes of influenza A viruses of different subtypes and from distinct sources (clinical samples of pdmH1N1, tissue culture-adapted H3N2 viruses, or avian influenza viruses from cloacal swabs) were amplified with a single multisegment reverse transcription-PCR reaction and sequenced using Illumina sequencing platform. Samples with low quantity of genetic material after initial PCR amplification were re-amplified by an additional PCR using random primers. Whole genome sequencing was successful for 66% of the samples, whilst the most relevant genome segments for epidemiological surveillance (corresponding to the hemagglutinin and neuraminidase) were sequenced with at least 93% coverage (and a minimum 10x) for 98% of the samples. Low coverage for some samples is likely due to an initial low viral RNA concentration in the original sample. The proposed methodology is especially suitable for sequencing a large number of samples, when genetic data is urgently required for strains characterization, and may also be useful for variant analysis.
Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids
Authors: Sun Miao , Folk Ryan A. , Gitzendanner Matthew A. , Guralnick Robert P. , Soltis Pamela S. , Chen Zhiduan , Soltis Douglas E.
Published: August 2019

Premise of the Study

Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. Here we use an empirical example to examine effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionists based on those results.

Methods

We used a supermatrix for rosids, a large clade of angiosperms, and its well-sampled subclade Cucurbitaceae, as empirical case studies. We compared results using this large phylogeny with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA, BAMM) and semiparametric (DR).

Key Results

We find the impact of sampling on diversification estimates is idiosyncratic and often strong. As compared to full empirical sampling, representative and random sampling schemes either depress or exaggerate speciation rates depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.

Conclusions

We (1) urge caution in use of summary backbone trees containing only higher-level taxa, (2) caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees, and (3) stress the importance of explicit sampling methodologies in macroevolutionary studies.
Insight into the genomic history of the Near East from whole-genome sequences and genotypes of Yemenis
Authors: Haber Marc , Saif-Ali Riyadh , Al-Habori Molham , Chen Yuan , Platt Daniel E. , Tyler-Smith Chris , Xue Yali
Published: August 2019

We report high-coverage whole-genome sequencing data from 46 Yemeni individuals as well as genome-wide genotyping data from 169 Yemenis from diverse locations. We use this dataset to define the genetic diversity in Yemen and how it relates to people elsewhere in the Near East. Yemen is a vast region with substantial cultural and geographic diversity, but we found little genetic structure correlating with geography among the Yemenis – probably reflecting continuous movement of people between the regions. African ancestry from admixture in the past 800 years is widespread in Yemen and is the main contributor to the country’s limited genetic structure, with some individuals in Hudayda and Hadramout having up to 20% of their genetic ancestry from Africa. In contrast, individuals from Maarib appear to have been genetically isolated from the African gene flow and thus have genomes likely to reflect Yemen’s ancestry before the admixture. This ancestry was comparable to the ancestry present during the Bronze Age in the distant Northern regions of the Near East. After the Bronze Age, the South and North of the Near East therefore followed different genetic trajectories: in the North the Levantines admixed with a Eurasian population carrying steppe ancestry whose impact never reached as far south as the Yemen, where people instead admixed with Africans leading to the genetic structure observed in the Near East today.
Structure-guided design of a synthetic mimic of an EPCR-binding PfEMP1 protein
Authors: Barber Natalie M. , Lau Clinton K. Y. , Turner Louise , Watson Gareth , Thrane Susan , Lusingu John P.A. , Lavstsen Thomas , Higgins Matthew K.
Published: August 2019

Structure-guided vaccine design provides a route to elicit a focused immune response against the most functionally important regions of a pathogen surface. This can be achieved by identifying epitopes for neutralizing antibodies through structural methods and recapitulating these epitopes by grafting their core structural features onto smaller scaffolds. In this study, we have conducted a modified version of this protocol. We focused on the PfEMP1 protein family found on the surfaces of erythrocytes infected withPlasmodium falciparum. A subset of PfEMP1 proteins bind to endothelial protein C receptor (EPCR), and their expression correlates with development of the symptoms of severe malaria. Structural studies revealed the PfEMP1 to present a helix-kinked-helix motif which forms the core of the EPCR binding site. Using Rosetta-based design we successfully grafted this motif onto a three-helical bundle scaffold. We show that this synthetic binder interacts with EPCR with nanomolar affinity and adopts the expected structure. We also assessed its ability to bind to antibodies found in immunized animals and in humans from malaria endemic regions. Finally, we tested its capacity to effectively elicit antibodies that prevent EPCR binding and analysed the degree of cross-reactivity of these antibodies across a diverse repertoire of EPCR-binding PfEMP1. This provides a case study of immunogen design, assessing the effect of designing a focused immunogen that contains the core features of a ligand binding site, rather than those of a neutralizing antibody epitope.
Functional genetic validation of key genes conferring insecticide resistance in the major African malaria vector, Anopheles gambiae
Authors: Adolfi Adriana , Poulton Beth , Anthousi Amalia , Macilwee Stephanie , Ranson Hilary , Lycett Gareth J
Published: August 2019

Resistance in Anopheles gambiae to members of all four major classes (pyrethroids, carbamates, organochlorines and organophosphates) of public health insecticides limits effective control of malaria transmission in Africa. Increased expression of detoxifying enzymes has been associated with resistance, but direct functional validation in An. gambiae has been lacking. Here we perform transgenic analysis using the GAL4/UAS system to examine insecticide resistance phenotypes conferred by increased expression of the three genes - Cyp6m2, Cyp6p3 and Gste2 - most often found upregulated in resistant An. gambiae. We report the first evidence in An. gambiae that organophosphate and organochlorine resistance is conferred by overexpression of GSTE2 in a broad tissue profile. Pyrethroid and carbamate resistance is bestowed by similar Cyp6p3 overexpression, and Cyp6m2 confers only pyrethroid resistance when overexpressed in the same tissues. Conversely, such Cyp6m2 overexpression increases susceptibility to the organophosphate malathion, presumably due to conversion to a more toxic metabolite. No resistant phenotypes are conferred when either Cyp6 gene overexpression is restricted to the midgut or oenocytes, answering long standing questions related to the importance of these tissues in resistance to contact insecticides. Validation of genes conferring resistance provides markers to guide control strategies, and the observed negative cross-resistance due to Cyp6m2 gives credence to proposed dual insecticide strategies to overcome pyrethroid resistance. These trasnsgenic An. gambiae resistant lines are being used to test potential liabilities in new active compounds early in development.

SIGNIFICANCE STATEMENT

Insecticide resistance in Anopheles gambiae mosquitoes can derail malaria control programs, and to overcome it we need to discover the underlying molecular basis. Here, for the first time, we characterise three genes most often associated with insecticide resistance directly by their overproduction in genetically modified An. gambiae. We show that overexpression of each gene confers resistance to representatives of at least one insecticide class and, taken together, the three genes provide cross-resistance to all four major insecticide classes currently used in public health. These data validate the candidate genes as markers to monitor the spread of resistance in mosquito populations. The modified mosquitoes produced are also valuable tools to pre-screen new insecticides for potential liabilities to existing resistance mechanisms.
Population-specific sequence and expression differentiation in Europeans
Authors: Jiang Xueyuan , Assis Raquel
Published: August 2019

Much of the enormous phenotypic variation observed across human populations is thought to have arisen from events experienced as our ancestors peopled different regions of the world. However, little is known about the genes involved in these population-specific adaptations. Here we explore this problem by simultaneously examining population-specific sequence and expression differentiation in four human populations. In particular, we design a branch-based statistic to estimate population-specific differentiation in four populations, and apply this statistic to single nucleotide polymorphism (SNP) and RNA-seq data from Italian, British, Finish, and Yoruban populations. As expected, genome-wide estimates of sequence and expression differentiation each independently recapitulate the known demographic history of these four human populations, highlighting the utility of our statistic for identifying genic targets of population-specific adaptations. Application of our statistic reveals that genes containing large copy number variations (CNVs) have elevated levels of population-specific sequence and expression differentiation, consistent with the hypothesis that gene turnover is a key reservoir of adaptive variation. Further, European genes displaying population-specific sequence and expression differentiation are enriched for functions related to epigenetic regulation, immunity, and reproduction. Together, our findings illustrate that population-specific sequence and expression differentiation in humans may preferentially target genes with CNVs and play important roles in a diversity of adaptive and disease-related phenotypes.
Microbial Community Dissimilarity for Source Tracking with Application in Forensic Studies
Authors: Carter Kyle M. , Lu Meng , Jiang Hongmei , An Lingling
Published: August 2019

Microbial source-tracking is a useful tool for trace evidence analysis in Forensics. Community-wide massively parallel sequencing profiles can bypass the need for satellite microbes or marker sets which are unreliable when handling unstable samples. We propose a method utilizing Aitchison distance to select important suspects/sources and then propose several methods to estimate the proportions of microbial communities/samples coming from important suspects/sources. A series of comprehensive simulation studies show that these methods are capable of accurate selection and improve the performance of current methods Bayesian SourceTracker and FEAST in the presence of noise microbial sources.
Functional effects of chimeric antigen receptor co-receptor signaling domains in human Tregs
Authors: Dawson Nicholas A.J. , Rosado-Sánchez Isaac , Novakovsky German E. , Fung Vivian C.W. , Huang Qing , McIver Emma , Sun Grace , Gillies Jana , Speck Madeleine , Orban Paul C. , Mojibian Majid , Levings Megan K
Published: August 2019

Antigen-specific regulatory T cells (Tregs) engineered with chimeric antigen receptor (CARs) are a potent immunosuppressive cellular therapy in multiple disease models. To date the majority of CAR Treg studies employed second generation CARs, encoding a CD28 or 4-1BB co-receptor signaling domain and CD3ζ, but it was not known if this CAR design was optimal for Tregs. Using an HLA-A2-specific CAR platform and human Tregs, we compared ten CARs with different co-receptor signaling domains and systematically tested their function. Tregs expressing a CAR encoding wild-type CD28 were markedly superior to all other CARs tested in anin vivomodel of graft-versus-host disease. In vitro assays revealed stable expression of Helios and ability to suppress CD80 expression on DCs as keyin vitropredictors ofin vivofunction. This comprehensive study of CAR signaling-domain variants in Tregs can be leveraged to optimize CAR design for use in antigen-specific Treg therapy.
Pitching single-focus confocal data analysis one photon at a time with Bayesian nonparametrics
Authors: Tavakoli Meysam , Jazani Sina , Sgouralis Ioannis , Shafraz Omer M. , Sivasankar Sanjeevi , Donaphon Bryan , Levitus Marcia , Pressé Steve
Published: August 2019

Fluorescence time traces are used to report on dynamical properties of molecules. The basic unit of information in these traces is the arrival time of individual photons, which carry instantaneous information from the molecule, from which they are emitted, to the detector on timescales as fast as microseconds. Thus, it is theoretically possible to monitor molecular dynamics at such timescales from traces containing only a sufficient number of photon arrivals. In practice, however, traces are stochastic and in order to deduce dynamical information through traditional means–such as fluorescence correlation spectroscopy (FCS) and related techniques–they are collected and temporally autocorrelated over several minutes. So far, it has been impossible to analyze dynamical properties of molecules on timescales approaching data acquisition without collecting long traces under the strong assumption of stationarity of the process under observation or assumptions required for the analytic derivation of a correlation function. To avoid these assumptions, we would otherwise need to estimate the instantaneous number of molecules emitting photons and their positions within the confocal volume. As the number of molecules in a typical experiment is unknown, this problem demands that we abandon the conventional analysis paradigm. Here, we exploit Bayesian nonparametrics that allow us to obtain, in a principled fashion, estimates of the same quantities as FCS but from the direct analysis of traces of photon arrivals that are significantly smaller in size, or total duration, than those required by FCS.
Acute effects of Adaptive Deep Brain Stimulation in Parkinson’s disease
Authors: Piña-Fuentes Dan , van Dijk J. Marc C. , van Zijl Jonathan C. , Moes Harmen R. , Oterdoom D. L. Marinus , Little Simon , Brown Peter , Beudel Martijn
Published: August 2019

Background

Beta-based adaptive Deep Brain Stimulation (aDBS) is effective in Parkinson’s disease (PD), when assessed in the immediate post-implantation phase. However, the potential benefits of aDBS in patients with electrodes chronically implanted, in whom the benefits of the microlesion effect have disappeared, are yet to be assessed.

Methods

To determine the acute effectiveness and side-effect profile of aDBS in PD compared to conventional continuous DBS (cDBS) and no stimulation (NoStim), years after DBS implantation. 13 PD patients undergoing battery replacement were pseudo-randomised in a crossover fashion, in- to three conditions (NoStim, aDBS or cDBS). Patient videos were blindly evaluated using a short version of the Unified Parkinson’s Disease Rating Scale (subUPDRS) and the Speech Intelligibility Test (SIT).

Results

Patients had a mean disease duration of 16 years, and the mean time since DBS implantation was 6.9 years. subUPDRS scores (11 patients tested) were significantly lower both in aDBS (p=<.001), and cDBS (p=.001), when compared to NoStim. Bradykinesia subscores were significantly lower in aDBS (p=.002), but not in cDBS (p=.08), when compared to NoStim. Two patients presented re-emerging tremor during NoStim. SIT scores of patients with stimulation-induced dysarthria (11 patients tested) significantly worsened in cDBS (p=.009), but not in aDBS (p=.407), when compared to NoStim. Overall, stimulation was applied 48.8% of the time during aDBS.

Conclusion

Beta oscillations is effective in PD patients with bradykinetic phenotypes, delivers less stimulation than cDBS, and potentially has a more favourable speech side-effect profile. Patients with prominent tremor may require a modified adaptive control strategy.
Multi-shanks SiNAPS Active Pixel Sensor CMOS probe: 1024 simultaneously recording channels for high-density intracortical brain mapping
Authors: Boi Fabio , Perentos Nikolas , Lecomte Aziliz , Schwesig Gerrit , Zordan Stefano , Sirota Anton , Berdondini Luca , Angotzi Gian Nicola
Published: August 2019

The advent of implantable active dense CMOS neural probes opened a new era for electrophysiology in neuroscience. These single shank electrode arrays, and the emerging tailored analysis tools, provide for the first time to neuroscientists the neurotechnology means to spatiotemporally resolve the activity of hundreds of different single-neurons in multiple vertically aligned brain structures. However, while these unprecedented experimental capabilities to study columnar brain properties are a big leap forward in neuroscience, there is the need to spatially distribute electrodes also horizontally. Closely spacing and consistently placing in well-defined geometrical arrangement multiple isolated single-shank probes is methodologically and economically impractical. Here, we present the first high-density CMOS neural probe with multiple shanks integrating thousand’s of closely spaced and simultaneously recording microelectrodes to map neural activity across 2D lattice. Taking advantage from the high-modularity of our electrode-pixels-based SiNAPS technology, we realized a four shanks active dense probe with 256 electrode-pixels/shank and a pitch of 28 µm, for a total of 1024 simultaneously recording channels. The achieved performances allow for full-band, whole-array read-outs at 25 kHz/channel, show a measured input referred noise in the action potential band (300-7000 Hz) of 6.5 ± 2.1µVRMS, and a power consumption <6 µW/electrode-pixel. Preliminary recordings in awake behaving mice demonstrated the capability of multi-shanks SiNAPS probes to simultaneously record neural activity (both LFPs and spikes) from a brain area >6 mm2, spanning cortical, hippocampal and thalamic regions. High-density 2D array enables combining large population unit recording across distributed networks with precise intra- and interlaminar/nuclear mapping of the oscillatory dynamics. These results pave the way to a new generation of high-density and extremely compact multi-shanks CMOS-probes with tunable layouts for electrophysiological mapping of brain activity at the single-neurons resolution.
Natural killer cell activation by respiratory syncytial virus-specific antibodies is decreased in infants with severe respiratory infections and correlates with Fc-glycosylation
Authors: van Erp Elisabeth A. , Lakerveld Anke J. , de Graaf Erik , Larsen Mads D. , Schepp Rutger M. , Hipgrave Ederveen Agnes L. , Ahout Inge M. L. , de Haan Cornelis A. M. , Wuhrer Manfred , Luytjes Willem , Ferwerda Gerben , Vidarsson Gestur , van Kasteren Puck B.
Published: August 2019

Background

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and there is no vaccine available. In early life, the most important contributors to protection against infectious diseases are the innate immune system and maternal antibodies. However, the mechanisms by which antibodies can protect against RSV disease are incompletely understood, as both antibody levels and neutralization capacity correlate poorly with protection. We therefore asked whether antibody-mediated natural killer (NK) cell activation correlates with RSV disease.

Methods

We performed an observational case-control study including infants hospitalized for RSV infection (n=43, cases), hernia surgery (n=16, controls), or RSV-negative viral respiratory tract infections (n=18, controls). First, we determined RSV antigen-specific antibody levels in infant plasma using a multiplex immunoassay. Subsequently, we measured the capacity of these antibodies to activate NK cells. Finally, we assessed Fc-glycosylation of the RSV-specific antibodies by mass spectrometry.

Results

We found that RSV-specific maternal antibodies potently activate NK cellsin vitro. While the concentrations of RSV-specific antibodies did not differ between cases and controls, antibodies from infants hospitalized for severe lower respiratory tract infections (RSV and/or other) induced significantly less NK cell interferon gamma production than those from uninfected controls. Furthermore, NK cell activation correlated with Fc-fucosylation of RSV-specific antibodies, but their glycosylation status did not significantly differ between cases and controls.

Conclusions

Our results suggest that Fc-dependent antibody function and quality, exemplified by NK cell activation and glycosylation, contribute to protection against severe RSV disease and warrant further studies to evaluate the potential of harnessing these activities to develop an effective vaccine.
Multi-modal communication: Song sparrows increase signal redundancy in noise
Authors: Akçay Çağlar , Beecher Michael D.
Published: August 2019

Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multimodal communication is affected by anthropogenic noise is relatively poorly understood. Here we ask whether song sparrows (Melospiza melodia) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (1) that song sparrows will shift signaling effort to the visual modality (the multi-modal shift hypothesis), and (2) that they will increase redundancy of their multi-modal signaling (the back-up hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signaling effort to visual modality (i.e., wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase redundancy of their multi-modal signals, which may aid in robustness of the communication system.