bluuebunny/crossref_metadata_2025 huggingface dataset:
The TOMATO Study (Tacrolimus Metabolization in Kidney Transplantation): Impact of the Concentration–Dose Ratio on Death-censored Graft Survival
Authors: Jouve Thomas , Fonrose Xavier , Noble Johan , Janbon Benedicte , Fiard Gaelle , Malvezzi Paolo , Stanke-Labesque Françoise , Rostaing Lionel
Published: August 2019

Background.

Tacrolimus trough concentrations (mean/variability), as well as concentration-to-dose ratio (C/D ratio), affect kidney allograft outcomes. We investigated the link between the C/D ratio and death-censored kidney graft survival (DCGS).

Methods.

We performed a retrospective study on 1029 kidney transplant patients (2004–2016) with the following criteria: tacrolimus-based immunosuppression, >1-year graft survival, no initial use of everolimus, and available anti–human leukocyte antigen antibody data. We analyzed the impact of the time-varying C/D ratio on DCGS. Fast metabolizers were defined by a C/D ratio < 1.05. We also investigated the effect of an early (mo 3 to mo 6 post transplantation) C/D ratio below 1.05. Cox survival analyses were performed, adjusting for potential confounders (tacrolimus trough, variability of tacrolimus trough, de novo donor-specific antibody development, cytochrome P450 3A5 genotype, pregraft sensitization, mo 3 glomerular filtration rate).

Results.

Time-varying C/D ratio was significantly associated with DCGS (hazard ratio [HR], 2.35; P < 0.001) in a univariate model, on the full analysis set comprising 1029 patients. In the multivariate time-varying model, based on 666 patients with available cytochrome P450 3A5 genotypes, the effect of the C/D ratio remained significant (HR, 2.26; P = 0.015); even when glomerular filtration rate at month 3 < 30 mL/min/1.73 m2 (HR, 2.61; P = 0.011), de novo donor-specific antibody development (HR, 4.09; P < 0.001) and continued steroid prescription (HR=2.08, P = 0.014) were taken into account (other covariates, including tacrolimus trough concentrations, were nonsignificant). In the same multivariate model, the effect of early C/D ratio (median at mo 3 and mo 6) remained significantly associated with DCGS (HR, 2.25; P = 0.041).

Conclusions.

C/D ratio is an independent and early predictor of DCGS. Identification of fast metabolizers could be a strategy to improve graft survival, for example, by optimizing tacrolimus formulation. Mechanistic studies to understand the C/D ratio effect are required.
Anomalous water dynamics in brain: a combined diffusion magnetic resonance imaging and neutron scattering investigation
Authors: Natali F. , Dolce C. , Peters J. , Stelletta C. , Demé B. , Ollivier J. , Boehm M. , Leduc G. , Piazza I. , Cupane A. , Barbier E. L.
Published: August 2019

Water diffusion is an optimal tool for investigating the architecture of brain tissue on which modern medical diagnostic imaging techniques rely. However, intrinsic tissue heterogeneity causes systematic deviations from pure free-water diffusion behaviour. To date, numerous theoretical and empirical approaches have been proposed to explain the non-Gaussian profile of this process. The aim of this work is to shed light on the physics piloting water diffusion in brain tissue at the micrometre-to-atomic scale. Combined diffusion magnetic resonance imaging and first pioneering neutron scattering experiments on bovine brain tissue have been performed in order to probe diffusion distances up to macromolecular separation. The coexistence of free-like and confined water populations in brain tissue extracted from a bovine right hemisphere has been revealed at the micrometre and atomic scale. The results are relevant for improving the modelling of the physics driving intra- and extracellular water diffusion in brain, with evident benefit for the diffusion magnetic resonance imaging technique, nowadays widely used to diagnose, at the micrometre scale, brain diseases such as ischemia and tumours.
Mathematical modelling of the restenosis process after stent implantation
Authors: Escuer Javier , Martínez Miguel A. , McGinty Sean , Peña Estefanía
Published: August 2019

The stenting procedure has evolved to become a highly successful technique for the clinical treatment of advanced atherosclerotic lesions in arteries. However, the development of in-stent restenosis remains a key problem. In this work, a novel two-dimensional continuum mathematical model is proposed to describe the complex restenosis process following the insertion of a stent into a coronary artery. The biological species considered to play a key role in restenosis development are growth factors, matrix metalloproteinases, extracellular matrix, smooth muscle cells and endothelial cells. Diffusion–reaction equations are used for modelling the mass balance between species in the arterial wall. Experimental data from the literature have been used in order to estimate model parameters. Moreover, a sensitivity analysis has been performed to study the impact of varying the parameters of the model on the evolution of the biological species. The results demonstrate that this computational model qualitatively captures the key characteristics of the lesion growth and the healing process within an artery subjected to non-physiological mechanical forces. Our results suggest that the arterial wall response is driven by the damage area, smooth muscle cell proliferation and the collagen turnover among other factors.
The anti-parasitic agent suramin and several of its analogues are inhibitors of the DNA binding protein Mcm10
Authors: Paulson Carolyn N. , John Kristen , Baxley Ryan M. , Kurniawan Fredy , Orellana Kayo , Francis Rawle , Sobeck Alexandra , Eichman Brandt F. , Chazin Walter J. , Aihara Hideki , Georg Gunda I. , Hawkinson Jon E. , Bielinsky Anja-Katrin
Published: August 2019

Minichromosome maintenance protein 10 (Mcm10) is essential for DNA unwinding by the replisome during S phase. It is emerging as a promising anti-cancer target as
MCM10
expression correlates with tumour progression and poor clinical outcomes. Here we used a competition-based fluorescence polarization (FP) high-throughput screening (HTS) strategy to identify compounds that inhibit Mcm10 from binding to DNA. Of the five active compounds identified, only the anti-parasitic agent suramin exhibited a dose-dependent decrease in replication products in an
in vitro
replication assay. Structure–activity relationship evaluation identified several suramin analogues that inhibited ssDNA binding by the human Mcm10 internal domain and full-length
Xenopus
Mcm10, including analogues that are selective for Mcm10 over human RPA. Binding of suramin analogues to Mcm10 was confirmed by surface plasmon resonance (SPR). SPR and FP affinity determinations were highly correlated, with a similar rank between affinity and potency for killing colon cancer cells. Suramin analogue NF157 had the highest human Mcm10 binding affinity (FP

K
i

170 nM, SPR
K
D
460 nM) and cell activity (IC
50
38 µM). Suramin and its analogues are the first identified inhibitors of Mcm10 and probably block DNA binding by mimicking the DNA sugar phosphate backbone due to their extended, polysulfated anionic structures.
Catalytic synthesis of
n
-butyl carboxylate with immobilized ionic liquid based on response surface methodology optimization
Authors: Liu Ran , Zhang Ke , Liu Chen , Hu Yanhui , Zhou Lilong , Zhang Juan
Published: August 2019

Four kinds of functional ionic liquids (ILs) ([C
3
SO
3
Hnmp]HSO
4
), 1-(3-sulfopropyl)-1-methylpyrrolidone phosphate ([C
3
SO
3
Hnmp]H
2
PO
4
), 1-(3-sulfopropyl)-1-methylpyrrolidone p-toluene sulfonate ([C
3
SO
3
Hnmp]CH
3
SO
3
H) and 1-(3-sulfopropyl)-1-methylpyrrolidone methyl sulfonate ([C
3
SO
3
Hnmp]C
6
H
6
SO
3
H)) were prepared and the catalytic activity of these ILs during esterification of carboxylic acids (formic acid, acetic acid, propionic acid, butyric acid) with alcohols was investigated. The results indicated that the IL ([C
3
SO
3
Hnmp]HSO
4
) exhibited an optimal catalytic performance. And then the IL ([C
3
SO
3
Hnmp]HSO
4
) was immobilized to the silica gel. The immobilized IL performed more excellent catalytic activity than the unsupported [C
3
SO
3
Hnmp]HSO
4
. The effects of reaction temperature, reaction time, molar ratio of acid to alcohol and catalyst dosage were investigated. The response surface methodology based on the Box–Behnken design (BBD) was used to explore the best reaction condition of different experimental variables. Accordingly, a high
n
-butyl butyrate yield of 97.10% under the deduced optimal reaction conditions was obtained, in good agreement with experimental results and that predicted by the BBD model. The immobilized IL [C
3
SO
3
Hnmp]HSO
4
maintained high catalytic activity after five cycles.
Antimicrobial activities of Korean mugwort (Artemisia iwayomogi and Artemisia princeps) extracts against Staphylococcus aureus and Cutibacterium acnes
Authors: Park Eun Jeong , Oh Jun-Hyun
Published: August 2019

Cutibacterium acnes and Staphylococcus aureus are recognized as pus-forming bacteria that trigger skin inflammation in acne. The goal of this research was to determine the antimicrobial activity of Korean mugworts including In-jin-ssuk (Artemisia iwayomogi) and Yak-ssuk (Artemisia princeps). Dried mugwort powders were extracted using water, ethanol and methanol. The antimicrobial activities of the extracts were evaluated by determining minimum inhibitory concentrations (MICs) and squares of inhibition zone widths. The chemical compositions of the chloroform fractions were analyzed by GC/MS. The inhibitory effects of the ethanol and methanol extracts of In-jin-ssuk (A. iwayomogi) (20 mg/mL) against C. acnes were significantly greater than the inhibitory effect of the water extract (p<0.05). Among various extracts, the ethanol extract of A. iwayomogi exhibited the greatest antimicrobial activity against S. aureus. The MICs of the chloroform fractions of ethanol- and methanol-extracted A. iwayomogi were determined to be 15 and 10 mg/mL, respectively, against both C. acnes and S. aureus. The chloroform fraction of the methanol extract exhibited squares of zone widths of 44 and 41 mm2 against C. acnes and S. aureus, respectively, which were the highest among the tested fractions. Scopoletin (484 mg/100 g) was found to be a major phenolic compound in the chloroform extract, while 2-furanmethanol (61 mg/100 g) and isofraxidin (55 mg/100 g) were minor phenolic compounds.
Physicochemical properties and immunomodulatory effects of polysaccharides isolated from Styela plicata
Authors: Lee Dae-Hoon , Hong Joo-Heon
Published: August 2019

The physicochemical properties and immunomodulatory effects of polysaccharides isolated from the sea squirt Styela plicata were investigated. The crude polysaccharide (SP) was further fractionated into an unabsorbed fraction (SF-1) and absorbed fractions (SF-2 and SF3) to isolate polysaccharides with different molecular weights. The major constituents in the crude and fractionated polysaccharides were total carbohydrate (28.03-42.65%), uronic acid (9.88-23.76%), sulfate (18.03-29.25%), and protein (1.48-26.47%). The average molecular weights of the fractionated polysaccharides ranged from 28 to 1,187 kDa. The significant monosaccharide components of the polysaccharides were galactose (27.91-62.21%), glucose (14.79-37.63%), and glucosamine (10.74-28.31%). FT-IR analysis indicates that SP, SF-1, SF-2, and SF-3 were sulfated polysaccharides. SF-1 increased the production of nitric oxide and cytokines, such as tumor necrosis factor alpha and interleukin 6, in a dose-dependent manner in RAW 264.7 cells. Further, polymerase chain reaction analysis revealed that the mRNA expression of inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) was markedly increased. These results indicate that SF-1 can enhance the activation of macrophages and that increasing the molecular weight and the uronic acid and sulfate content of fractionated polysaccharides can enhance their immunomodulatory function.
Effect of steaming on the functional compounds and antioxidant activity of Fijian taro (Colocasia esculenta L. Schott) corms
Authors: Kim Yeon Soo , Adeyemi Damilare , Korovulavula Ponijese , Jang Dong Wook , Park Mi-Kyung
Published: August 2019

We investigated the effects of steaming Fijian taro (Colocasia esculenta L. Schott) corms on their functional compound contents and antioxidant activities by comparison with those of un-steamed Fijian taro corms. Taro corms from Fiji were washed, peeled, cut, then either steamed or left un-steamed, and freeze-dried. Ten gram of each freeze-dried taro corm sample was extracted with water, methanol, and ethanol. The total phenolic content (TPC) and total flavonoid content (TFC) of the taro corms were determined using the Folin-Ciocalteu’s colorimetric and the aluminum chloride colorimetric methods, respectively. The antioxidant activity was determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, ferric reducing antioxidant power (FRAP), and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activity. The water-extracted steamed Fijian taro corm showed the greatest extraction yield of 11.58±1.20%, whereas the ethanol-extracted un-steamed Fijian taro corm exhibited the lowest extraction yield of 4.24±0.77%. The TPC (42.77±3.39 mg gallic acid equivalents/g dry weight) and TFC (12.68±4.85 mg catechin equivalents/g dry weight) of the methanol-extracted steamed Fijian taro corms were significantly larger than those of the other extracts (p<0.05). The steamed Fijian taro corms extracted with methanol significantly demonstrated greatest activities in DPPH radical scavenging activity (34.82±2.91%), FRAP (339.08±20.50 mM Trolox equivalents), and ABTS radical scavenging activity (56.34±3.54%) (p<0.05). This study provides the basis for developing a healthy snack food based on steamed Fijian taro.
IgEvolution: clonal analysis of antibody repertoires
Authors: Safonova Yana , Pevzner Pavel A.
Published: August 2019

Constructing antibody repertoires is an important error-correcting step in analyzing immunosequencing datasets that is important for reconstructing evolutionary (clonal) development of antibodies. However, the state-of-the-art repertoire construction tools typically miss low-abundance antibodies that often represent internal nodes in clonal trees and are crucially important for clonal tree reconstruction. Thus, although repertoire construction is a prerequisite for follow up clonal tree reconstruction, the existing repertoire reconstruction algorithms are not well suited for this task. Since clonal analysis has the potential to reveal errors in the constructed repertoires and contribute to constructing more accurate repertoires, we advocate a tree-guided construction of antibody repertoires that combines error correction and clonal reconstruction as interconnected (rather than independent) tasks. We developed the IgEvolution algorithm for simultaneous repertoire and clonal tree reconstruction and applied it for analyzing multiple immunosequencing datasets representing antigen-specific immune responses. We demonstrate that analysis of clonal trees reveals highly mutable positions that correlate with antigen-binding sites and light-chain contacts in crystallized antibody-antigen complexes. We further demonstrate that this analysis leads to a new approach for identifying complementarity determining regions (CDRs) in antibodies.
A report on the detection and management of a finding of PSTVd (Potato Spindle Tuber Viroid) in potato breeding material in Northern Ireland, UK
Authors: O’Hanlon Richard , Watts Paul , Martin Rodney , Young Gillian , Fleming Colin
Published: August 2019

Potato Spindle Tuber Viroid (PSTVd) is an infectious unencapsidated, small, circular, single-stranded RNA, that causes serious losses in infected potato plants. The pathogen has been detected in several European countries, including in England in the UK. In August 2016, the National Plant Protection Organisation of the Netherlands reported a finding of PSTVd in breeding material that originated in Northern Ireland, UK. A scheme of testing was carried out in Northern Ireland to identify the source of the infected breeding material. Trace-forward and trace-back tests identified 21 infected samples, of which 16 were from true seed samples, out of a total of 591 tested up to November 2016. The number of positive findings in true seed was further reduced to 4 after the samples were surface sterilized. Tests indicated that the infection probably entered the breeding station in Northern Ireland in the mid 1980’s, with limited spread in the collection via contaminated breeding equipment. The instance of spread in the field could not be ruled out. Eradication efforts included removal and destruction of infected field stocks and neighbouring stocks, destruction of stored museum material by deep burial, and destruction of other field material by ploughing and exposing tubers to frost. The risk of potato genitor material for spreading PSTVd is discussed. The situation of PSTVd in Northern Ireland, UK is Transient, actionable, under eradication.
Identifying and removing haplotypic duplication in primary genome assemblies
Authors: Guan Dengfeng , McCarthy Shane A. , Wood Jonathan , Howe Kerstin , Wang Yadong , Durbin Richard
Published: August 2019

Motivation

Rapid development in long read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either only focus on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors.

Results

Here we present a novel tool “purge_dups” that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with the current standard, purge_haplotigs, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can be easy integrated into assembly pipelines.

Availability

The source code is written in C and is available at https://github.com/dfguan/purge_dups.

Contact

ydwang@hit.edu.cn, rd109@cam.ac.uk
Reply: Evidence that APP gene copy number changes reflect recombinant vector contamination
Authors: Lee Ming-Hsiang , Liu Christine S. , Zhu Yunjiao , Kaeser Gwendolyn E. , Rivera Richard , Romanow William J. , Kihara Yasuyuki , Chun Jerold
Published: August 2019

In the accompanying comment1, Kim et al. concluded that somatic gene recombination (SGR) and amyloid precursor protein (APP) genomic complementary DNAs (gencDNAs) in brain are contamination artifacts and do not naturally exist. We disagree. Here we address the three types of analyses used by Kim et al. to reach their conclusions: informatic contaminant identification, plasmid PCR, and single-cell sequencing. Additionally, Kim et al. requested “reads supporting novel APP insertion breakpoints,” and we now provide 10 different examples that support APP gencDNA insertion within eight chromosomes beyond wildtype APP on chromosome 21 from Alzheimer’s disease (AD) samples. If SGR exists as experimentally supported here and previously2,3, contamination scenarios become moot. Our informatic analyses of data generated by an independent laboratory (Park et al.)4, complement and are entirely consistent with what Lee et al.2 presented via nine distinct lines of evidence, in addition to three from a prior publication3. Plasmid contamination was identified in a single pull-down dataset after publication of Lee et al.2; however subsequent analyses did not alter any of our conclusions including those of our prior publications3,5 and plasmid contamination-free replication of this approach by ourselves and others supported the original conclusions. Novel retro-insertion sites, alterations of APP gencDNA number and form with cell type from the same brain and pathogenic SNVs occurring only in AD, all support the existence of APP gencDNAs produced by SGR.
Properties of decision-making tasks govern the tradeoff between model-based and model-free learning
Authors: Abzug Zachary M , Sommer Marc A , Beck Jeffrey M
Published: August 2019

When decisions must be made between uncertain options, optimal behavior depends on accurate estimations of the likelihoods of different outcomes. The contextual factors that govern whether these estimations depend on model-free learning (tracking outcomes) vs. model-based learning (learning generative stimulus distributions) are poorly understood. We studied model-free and model-based learning using serial decision-making tasks in which subjects selected a rule and then used it to flexibly act on visual stimuli. A factorial approach defined a family of behavioral models that could integrate model-free and model-based strategies to predict rule selection trial-by-trial. Bayesian model selection demonstrated that the subjects strategies varied depending on lower-level task characteristics such as the identities of the rule options. In certain conditions, subjects integrated learned stimulus distributions and tracked reward rates to guide their behavior. The results thus identify tradeoffs between model-based and model-free decision strategies, and in some cases parallel utilization, depending on task context.
Rough substrates constrain walking speed in ants through modulation of stride frequency and not stride length
Authors: Clifton G.T. , Holway D. , Gravish N.
Published: August 2019

Natural terrain is rarely flat. Substrate irregularities challenge walking animals to maintain stability, yet we lack quantitative assessments of walking performance and limb kinematics on naturally rough ground. We measured how continually rough 3D-printed substrates influence walking performance of Argentine ants by measuring walking speeds of workers from lab colonies and by testing colony-wide substrate preference in field experiments. Tracking limb motion in over 8,000 videos, we used statistical models that associate walking speed with limb kinematic parameters to compare movement over flat versus rough ground. We found that rough substrates reduced preferred and peak walking speeds by up to 42% and that ants actively avoided rough terrain in the field. Observed speed reductions were modulated primarily by shifts in stride frequency and not stride length, a pattern consistent across flat and rough substrates. Modeling revealed that walking speeds on rough substrates were accurately predicted based on flat walking data for over 89% of strides. Those strides that were not well modeled primarily involved limb perturbations, including missteps, active foot repositioning, and slipping. Together these findings relate kinematic mechanisms underlying walking performance on rough terrain to ecologically-relevant measures under field conditions.
Th22 cells are a major contributor to the mycobacterial CD4+ T cell response and are depleted during HIV infection
Authors: Bunjun Rubina , Omondi Fidilia M.A. , Makatsa Mohau S. , Müller Tracey L. , Prentice Caryn S.L. , Wilkinson Robert J. , Riou Catherine , Burgers Wendy A.
Published: August 2019

HIV-1 infection substantially increases the risk of developing tuberculosis (TB). Some mechanisms, such as defects in the Th1 response to Mycobacterium tuberculosis (M.tb) in HIV-infected individuals have been widely reported. However, Th1-independent mechanisms also contribute to protection against TB. To identify a broader spectrum of defects in TB immunity during HIV infection, we examined IL-17 and IL-22 production in response to mycobacterial antigens in individuals with latent TB infection (LTBI) and HIV co-infection. Upon stimulating with mycobacterial antigens, we observed a distinct CD4+ T helper lineage producing IL-22 in the absence of IL-17 and IFN-γ. Th22 cells were present at high frequencies in response to mycobacterial antigens in blood and contributed up to 50% to the CD4+ T cell response to mycobacteria, comparable in magnitude to the IFN-γ Th1 response (median 0.91% and 0.55%, respectively). Phenotypic characterization of Th22 cells revealed that their memory differentiation was similar to M.tb-specific Th1 cells (i.e. predominantly early-differentiated CD45RO+CD27+ phenotype). Moreover, CCR6 and CXCR3 expression profiles of Th22 cells were similar to Th17 cells, while their CCR4 and CCR10 expression patterns displayed an intermediate phenotype between Th1 and Th17 cells. Strikingly, mycobacterial IL-22 responses were three-fold lower in HIV-infected individuals compared to uninfected individuals, and the magnitude of responses correlated inversely with HIV viral load. These data provide important insights into mycobacteria-specific T helper subsets and suggest a potential role for IL-22 in protection against TB during HIV infection. Further studies are needed to fully elucidate the role of IL-22 in protective TB immunity.
Unfolding and identification of membrane proteins in situ
Authors: Galvanetto Nicola , Ye Zhongjie. , Marchesi Arin , Mortal Simone , Maity Sourav , Laio Alessandro , Torre Vincent
Published: August 2019

Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.
Parallel genomic architecture underlies repeated sexual signal divergence in HawaiianLaupalacrickets
Authors: Blankers Thomas , Oh Kevin P. , Shaw Kerry L.
Published: August 2019

When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favored over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricketLaupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and the likelihood that sharing QTL is related to phenotypic effect sizes. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
Parallel Distributed Networks Dissociate Episodic and Social Functions Within the Individual
Authors: DiNicola Lauren M. , Braga Rodrigo M. , Buckner Randy L.
Published: August 2019

Association cortex is organized into large-scale distributed networks. One such network, the default network (DN), is linked to diverse forms of internal mentation, opening debate about whether shared anatomy supports multiple forms of cognition. Alternatively, subtle distinctions in cortical organization could remain to be resolved. Using within-individual analysis procedures that preserve idiosyncratic details of cortical anatomy, we probed whether multiple tasks from two domains - Episodic Projection and Theory of Mind (ToM) - rely upon the same or distinct networks. In an initial experiment (n=6, subjects scanned 4 times each), we found evidence that Episodic Projection and ToM tasks activate distinct functional regions distributed throughout cortex, with adjacent regions in parietal, temporal, prefrontal and midline zones. These distinctions were predicted by the hypothesis that the DN comprises two parallel, interdigitated networks. One network, linked to parahippocampal cortex (PHC), is preferentially recruited during Episodic Projection, including both remembering the past and imagining the future. A second juxtaposed network, which includes the temporoparietal junction (TPJ), is differentially engaged during multiple forms of ToM tasks. The TPJ-linked network is interwoven with the PHC-linked network in multiple zones, including the posterior and anterior midline, making clear why it is difficult to fully resolve the two networks in group-averaged or lower-resolution data. We replicated all aspects of this network dissociation in a second, prospectively acquired dataset (n=6). These results refine our understanding of the functional-anatomical organization of association cortex as well as raise questions about how functional specialization might arise in parallel, juxtaposed association networks.
Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage
Authors: Cheung Kathleen , Burgers Marjolein J. , Young David A. , Cockell Simon , Reynard Louise N.
Published: August 2019

Background

DNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying 865859 CpG sites, almost double the number of sites present on the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms.

Methods

DNA methylation was measured in 21 human cartilage samples using the Illumina Infinium Methylation450K BeadChip and the Infinium methylationEPIC array. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833 respectively. Data were processed using the Bioconductor package Minfi. Additionally, DNA methylation of six CpG sites was validated for the same 21 cartilage samples by use of pyrosequencing.

Results

In cartilage samples, overall sample correlations between methylation values generated by the two arrays were high (Pearson correlation coefficient r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulfite pyrosequencing did not highlight one array as generating more accurate methylation values that the other. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour and whole blood, reflecting the difference in methylation variance between cell types. These patterns can be observed across different tissues with different CpG site variances. When performing differential methylation analysis, the mean probe correlation co-efficient increased with increasing Δβ threshold used.

Conclusion

CpG sites with low variability within a tissue showed poor reproducibility between arrays. However, variance and thus reproducibility differs across different tissue types. Therefore, researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of platform or method used to assay methylation.
Cellular contractile forces are non-mechanosensitive
Authors: Feld Lea , Kellerman Lior , Mukherjee Abhishek , Livne Ariel , Bouchbinder Eran , Wolfenson Haguy
Published: August 2019

Cells’ ability to apply contractile forces to their environment and to sense its mechanical properties (e.g. rigidity) are among their most fundamental features. Yet, the interrelations between contractility and mechanosensing, in particular whether contractile force generation depends on mechanosensing, are not understood. We use theory and extensive experiments to study the time evolution of cellular contractile forces and show that they are generated by time-dependent actomyosin contractile displacements that are independent of the environment’s rigidity. Consequently, contractile forces are non-mechanosensitive. We further show that the force-generating displacements are directly related to the evolution of the actomyosin network, most notably to the time-dependent concentration of F-actin. The emerging picture of force generation and mechanosensitivity offers a unified framework for understanding contractility.

One Sentence Summary

Cellular contractile forces are generated by rigidity-independent displacements that are determined by the time evolution of F-actin assembly.
Cellular memory enhances bacterial chemotactic navigation in rugged environments
Authors: Gosztolai Adam , Barahona Mauricio
Published: August 2019

The response of microbes to external signals is mediated by biochemical networks with intrinsic time scales. These time scales give rise to a memory that impacts cellular behaviour. Here we study theoretically the role of cellular memory in Escherichia coli chemotaxis. Using an agent-based model, we show that cells with memory navigating rugged chemoattractant landscapes can enhance their drift speed by extracting information from environmental correlations. Maximal advantage is achieved when the memory is comparable to the time scale of fluctuations as perceived during swimming. We derive an analytical approximation for the drift velocity in rugged landscapes that explains the enhanced velocity, and recovers standard Keller-Segel gradient-sensing results in the limits when memory and fluctuation time scales are well separated. Our numerics also show that cellular memory can induce bet-hedging at the population level resulting in long-lived multi-modal distributions in heterogeneous landscapes.
The potentials and pitfalls of a human cervical organoid model including Langerhans cells
Authors: Jackson Robert , Lukacs Jordan D , Zehbe Ingeborg
Published: August 2019

Three-dimensional cell culturing to capture a life-like experimental environment has become a versatile tool for basic and clinical research. Mucosal and skin tissues can be grown as “organoids” in a petri dish and serve a wide variety of research questions. Here, we report our experience with human cervical organoids which could also include an immune component, e.g. Langerhans cells. We employ commercially available human cervical keratinocytes and fibroblasts as well as a myeloid cell line matured and purified into langerin-positive Langerhans cells. These are then seeded on a layer of keratinocytes with underlying dermal equivalent. Using about 10-fold more than the reported number in healthy cervical tissue (1–3%), we obtain differentiated cervical epithelium after 14 days with ~ 1% being Langerhans cells. We provide a detailed protocol for interested researchers to apply the described “aseptic” organoid model for all sorts of investigations—with or without Langerhans cells.
Defects in the assembly of ribosomes selected for β-amino acid incorporation
Authors: Ward Fred R. , Watson Zoe L. , Ad Omer , Schepartz Alanna , Cate Jamie H. D.
Published: August 2019

Ribosome engineering has emerged as a promising field in synthetic biology, particularly concerning the production of new sequence-defined polymers. Mutant ribosomes have been developed that improve the incorporation of several non-standard monomers including D-amino acids, dipeptides, and β-amino acids into polypeptide chains. However, there remains little mechanistic understanding of how these ribosomes catalyze incorporation of these new substrates. Here we probed the properties of a mutant ribosome–P7A7–evolved for betterin vivoβ-amino acid incorporation throughin vitrobiochemistry and cryo-electron microscopy. Although P7A7 is a functional ribosomein vivo, it is inactivein vitro, and assembles poorly into 70S complexes. Structural characterization revealed large regions of disorder in the peptidyltransferase center and nearby features, suggesting a defect in assembly. Comparison of RNA helix and ribosomal protein occupancy with other assembly intermediates revealed that P7A7 is stalled at a late stage in ribosome assembly, explaining its weak activity. These results highlight the importance of ensuring efficient ribosome assembly during ribosome engineering towards new catalytic abilities.
Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model
Authors: Sethuraman Arun , Lynch Melissa
Published: August 2019

Unsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics likeFSTare under-estimated, andπis over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.
A molecular switch for Cdc48 activity and localization during oxidative stress and aging
Authors: Radzinski Meytal , Yogev Ohad , Yesharim Yarden , Brielle Esther S. , Israeli Ran , Fassler Rosi , Melamed-Book Naomi , Shai Nadav , Arkin Isaiah T. , Pick Elah , Ravid Tommer , Schuldiner Maya , Reichmann Dana
Published: August 2019

Control over a healthy proteome begins with the birth of the polypeptide chain and ends with coordinated protein degradation. One of the major players in eukaryotic protein degradation is the essential and highly conserved ATPase, Cdc48 (p97/VCP in mammals). Cdc48 mediates clearance of misfolded proteins from the nucleus, cytosol, ER, mitochondria, and more. Here we dissect the crosstalk between cellular oxidation and Cdc48 activity by identification of a redox-sensitive site, Cys115. By integrating proteomics, biochemistry, microscopy, and bioinformatics, we show that removal of Cys115’s redox-sensitive thiol group leads to accumulation of Cdc48 in the nucleus and consequently, results in severe defects in the oxidative stress response, mitochondrial fragmentation, and a decrease in ERAD and sterol biogenesis. We have thus identified a unique redox switch in Cdc48, which may provide a clearer picture of the importance of Cdc48’s localization in maintaining a “healthy” proteome during oxidative stress and chronological aging in yeast.
Estimation of Global and Local Complexities of Brain Networks: A Random Walks Approach
Authors: Sotero Roberto C. , Sanchez-Rodriguez Lazaro M. , Moradi Narges
Published: August 2019

The complexity of brain activity has been observed at many spatial scales and there exists increasing evidence supporting its use in differentiating between mental states and disorders. Here we proposed a new measure of network (global) complexity that is constructed as the sum of the complexities of its nodes (i.e, local complexity). The local complexity of each node is regarded as an index that compares the sample entropy of the time series generated by the movement of a random walker on the network resulting from removing the node and its connections, with the sample entropy of the time series obtained from a regular lattice (the ordered state) and an Erdös-Renyi network (disordered state). We studied the complexity of fMRI-based resting-state functional networks. We found that positively correlated, or “pos”, network comprising only the positive functional connections has higher complexity than the anticorrelation (“neg”) network (comprising the negative functional connections) and the network consisting of the absolute value of all connections (“abs”). We also found a significant correlation between complexity and the strength of functional connectivity. For the pos network this correlation is significantly weaker at the local scale compared to the global scale, whereas for the neg network the link is stronger at the local scale than at the global scale, but still weaker than for the pos network. Our results suggest that the pos network is related to the information processing in the brain and should be used for functional connectivity analysis instead of the abs network as is usually done.
Differences in Early and Late Pattern-Onset Visual-Evoked Potentials between Self-Reported Migraineurs and Controls
Authors: Fong Chun Yuen , Crystal Law Wai Him , Braithwaite Jason , Mazaheri Ali
Published: August 2019

Striped patterns have been shown to induce strong visual illusions and discomforts to migraineurs in the literature. Previous research has suggested that those unusual visual symptoms be linked with the hyperactivity on the visual cortex of migraine sufferers. The present study searched for evidence supporting this hypothesis by comparing the visual evoked potentials (VEPs) elicited by striped patterns of specific spatial frequencies (0.5, 3, and 13 cycles) between a group of 29 migraineurs (17 with aura/12 without) and 31 non-migraineurs. In addition, VEPs to the same stripped patterns were compared between non-migraineurs who were classified as hyperexcitable versus non-hyperexcitable using a previously established behavioural pattern glare task. We found that the migraineurs had a significantly increased N2 amplitude for stimuli with 13 cpd gratings but an attenuated late negativity (LN: 400 – 500 ms after the stimuli onset) for all the spatial frequencies. Interestingly, non-migraineurs who scored as hyperexcitable appeared to have similar response patterns. We proposed that the enhanced N2 could reflect disruption of the balance between parvocellular and magnocellular pathway, which is in support of a grating-induced cortical hyperexcitation mechanism on migraineurs. On the other hand, the attenuation of the late negativity could reflect a top-down feedback mechanism to suppress visual processing of an aversive stimulus.
Homeoprotein ENGRAILED-1 promotes motoneuron survival and motor functions
Authors: Vargas Abonce Stephanie E. , Lebœuf Mélanie , Moya Kenneth L. , Prochiantz Alain
Published: August 2019

Motoneuron degeneration leads to skeletal muscle denervation and impaired motor functions, yet the signals involved remain poorly understood. We find that extracellular ENGRAILED-1, a homeoprotein expressed in spinal cord V1 interneurons that synapse on α-motoneurons, has non-cell autonomous activity. Mice heterozygote for Engrailed-1 develop muscle weakness, abnormal spinal reflex and partial neuromuscular junction denervation. A single intrathecal injection of ENGRAILED-1 restores innervation, limb strength, extensor reflex and prevents lumbar α-motoneuron death for several months. The autophagy gene p62, which was found to network with Engrailed-1 and amyotrophic lateral sclerosis genes, is misregulated in Engrailed-1 heterozygote mice α-motoneurons and is rescued following ENGRAILED-1 injection. These results identify ENGRAILED-1 as an α-motoneuron trophic factor with long-lasting protective activity.
Identification ofEscherichia coliClpAP in regulating susceptibility to type VI secretion system-mediated attack byAgrobacterium tumefaciens
Authors: Lin (林筱涵) Hsiao-Han , Yu (余文廸) Manda , Sriramoju Manoj Kumar , Hsu (徐尚德) Shang-Te Danny , Liu (劉啟德) Chi-Te , Lai (賴爾珉) Erh-Min
Published: August 2019

Type VI secretion system (T6SS) is an effector delivery system used by gram-negative bacteria to kill other bacteria or eukaryotic host to gain fitness. InAgrobacterium tumefaciens, T6SS has been shown to kill other bacteria such asEscherichia coli. Interestingly, theA. tumefaciensT6SS killing efficiency differs when using differentE. colistrains as recipient cells. Thus, we hypothesize that a successful T6SS killing not only relies on attacker T6SS activity but also depends on recipient factors. A high-throughput interbacterial competition assay was employed to test the hypothesis by screening for mutants with reduced killing outcomes caused byA. tumefaciensstrain C58. From the 3909E. coliKeio mutants screened, 16 candidate mutants were filtered out. One strain, ΔclpP::Kan, showed ten times more resistant to T6SS-mediating killing but restored its susceptibility when complemented withclpP in trans. ClpP is a universal and highly conserved protease that exists in both prokaryotes and eukaryotic organelles. InE. coli, ClpP uses either ClpA or ClpX as an adaptor for substrate specificity. Therefore, the susceptibility of the ΔclpA::Kan and ΔclpX::Kan was also tested. The T6SS attack susceptibility of ΔclpA::Kan is at the same level as ΔclpP::Kan, while ΔclpX::Kan showed no difference as compared to that of wild-typeE. coliBW25113. The data also suggest that ClpA-ClpP interaction, rather than its protease activity, is responsible for enhancing susceptibility to T6SS killing. This study highlights the importance of recipient factors in determining the outcome of T6SS killing.