bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns of ‘Analytical Irreproducibility’ in Multimodal Diseases
Authors: Basson Abigail R , Cominelli Fabio , Rodriguez-Palacios Alex
Published: March 2020

Multimodal diseases are those in which affected individuals can be divided into subtypes (or ‘data modes’); for instance, ‘mild’ vs. ‘severe’, based on (unknown) modifiers of disease severity. Studies have shown that despite the inclusion of a large number of subjects, the causal role of the microbiome in human diseases remains uncertain. The role of the microbiome in multimodal diseases has been studied in animals; however, findings are often deemed irreproducible, or unreasonably biased, with pathogenic roles in 95% of reports. As a solution to repeatability, investigators have been told to seek funds to increase the number of human-microbiome donors (N) to increase the reproducibility of animal studies (doi:10.1016/j.cell.2019.12.025). Herein, through simulations, we illustrate that increasing N will not uniformly/universally enable the identification of consistent statistical differences (patterns of analytical irreproducibility), due to random sampling from a population with ample variability in disease and the presence of ‘disease data subtypes’ (or modes). We also found that studies do not use cluster statistics when needed (97.4%, 37/38, 95%CI=86.5,99.5), and that scientists who increased N, concurrently reduced the number of mice/donor (y=-0.21x, R2=0.24; and vice versa), indicating that statistically, scientists replace the disease variance in mice by the variance of human disease. Instead of assuming that increasing N will solve reproducibility and identify clinically-predictive findings on causality, we propose the visualization of data distribution using kernel-density-violin plots (rarely used in rodent studies; 0%, 0/38, 95%CI=6.9e-18,9.1) to identify ‘disease data subtypes’ to self-correct, guide and promote the personalized investigation of disease subtype mechanisms.

Highlights

Multimodal diseases are those in which affected individuals can be divided into subtypes (or ‘data modes’); for instance, ‘mild’ vs. ‘severe’, based on (unknown) modifiers of disease severity.

The role of the microbiome in multimodal diseases has been studied in animals; however, findings are often deemed irreproducible, or unreasonably biased, with pathogenic roles in 95% of reports.

As a solution to repeatably, investigators have been told to seek funds to increase the number of human-microbiome donors (N) to increase the reproducibility of animal studies.

Herein, we illustrate that although increasing N could help identify statistical effects (patterns of analytical irreproducibility), clinically-relevant information will not always be identified.

Depending on which diseases need to be compared, ‘random sampling’ alone leads to reproducible ‘patterns of analytical irreproducibility’ in multimodal disease simulations.

Instead of solely increasing N, we illustrate how disease multimodality could be understood, visualized and used to guide the study of diseases by selecting and focusing on ‘disease modes’.
Recapitulating evolutionary divergence in a singlecis-regulatory element is sufficient to cause expression changes of the lens geneTdrd7
Authors: Roscito Juliana G. , Subramanian Kaushikaram , Naumann Ronald , Sarov Mihail , Shevchenko Anna , Bogdanova Aliona , Kurth Thomas , Foerster Leo , Kreysing Moritz , Hiller Michael
Published: March 2020

Mutations incis-regulatory elements play important roles for phenotypic changes during evolution. Eye degeneration in the blind mole rat (BMR) and other subterranean mammals is significantly associated with widespread divergence of eye regulatory elements, but the effect of these regulatory mutations on eye development and function has not been explored. Here, we investigate the effect of mutations observed in the BMR sequence of a conserved non-coding element upstream ofTdrd7, a pleiotropic gene required for lens development and spermatogenesis. We first show that this conserved element is a transcriptional repressor in lens cells and that the BMR sequence partially lost repressor activity. Next, we recapitulated the evolutionary changes by precisely replacing the endogenous regulatory element in a mouse line by the orthologous BMR sequence with CRISPR-Cas9. Strikingly, this repressor element has a large effect, causing a more than two-fold up-regulation ofTdrd7in developing lens. Interestingly, the increased mRNA level does not result in a corresponding increase in TDRD7 protein nor an obvious lens phenotype, likely explained by buffering at the posttranscriptional level. Our results are consistent with eye degeneration in subterranean mammals having a polygenic basis where many small-effect mutations in different eye-regulatory elements collectively contribute to phenotypic differences.
FcRn, but not FcγRs, drives maternal-fetal transplacental transport of human IgG antibodies
Authors: Borghi Sara , Bournazos Stylianos , Thulin Natalie K. , Li Chao , Gajewski Anna , Sherwood Robert , Zheng Sheng , Harris Eva , Jagannathan Prasanna , Wang Lai-Xi , Ravetch Jeffrey V. , Wang Taia T.
Published: March 2020

The IgG Fc domain has the capacity to interact with diverse types of receptors, including FcRn and FcγRs, which confer pleiotropic biological activities. Whereas FcRn regulates IgG epithelial transport and recycling, Fc effector activities, such as ADCC and phagocytosis are mediated by FcγRs, which upon crosslinking transduce signals that modulate the function of effector leukocytes. Despite the well-defined and non-overlapping functional properties of FcRn and FcγRs, recent studies have suggested that FcγRs mediate transplacental IgG transport, as certain Fc glycoforms were reported to be enriched in fetal circulation. To determine the contribution of FcγRs and FcRn to the maternal-fetal transport of IgG, we characterized the IgG Fc glycosylation in paired maternal-fetal samples from patient cohorts from Uganda and Nicaragua. No differences in IgG1 Fc glycan profiles and minimal differences in IgG2 Fc glycans were noted, whereas the presence or absence of galactose on the Fc glycan of IgG1 did not alter FcγRIIIA or FcRn binding, half-life, or their ability to deplete target cells in FcγR/FcRn humanized mice. Modeling maternal/fetal transport in FcγR/FcRn humanized mice confirmed that only FcRn contributed to transplacental transport of IgG; IgG selectively enhanced for FcRn binding resulted in enhanced accumulation of maternal antibody in the fetus. In contrast, enhancing FcγRIIIA binding did not result in enhanced maternal/fetal transport. These results argue against a role for FcγRs in IgG transplacental transport, suggesting Fc engineering of maternally administered antibody to only enhance FcRn binding as a means to improve maternal/fetal transport of IgG.

Significance Statement

Transport of IgG antibodies from the maternal to the fetal circulation is a key process for neonatal immunity, as neonates cannot sufficiently generate IgG antibodies to reach protective levels during the first months after birth. In humans and other primates, maternal to fetal transport of IgG antibodies is largely mediated through the placental tissue. FcRn has been previously identified as the major driver of IgG transplacental transport. Here we examined whether other receptors, such as FcγRs, also contribute to the maternal-fetal IgG transfer. By characterizing the Fc domain structure of paired maternal-fetal IgG samples and modeling transplacental IgG transport in genetically engineered mouse strains, we determined that FcRn, but not FcγRs, is the major receptor that mediates transplacental IgG transport.
Click-chemistry enabled directed evolution of glycosynthases for bespoke glycans synthesis
Authors: Agrawal Ayushi , Bandi Chandra Kanth , Burgin Tucker , Woo Youngwoo , Mayes Heather B. , Chundawat Shishir P. S.
Published: March 2020

Engineering of carbohydrate-active enzymes like glycosynthases for chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable directed evolution based protein engineering methods. Currently there are no ultrahigh-throughput screening methods available for rapid and highly sensitive single cell-based screening of evolved glycosynthase enzymes employing azido sugars as substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides (versus free inorganic azides) that facilitated ultrahigh-throughputin-vivosingle cell-based assay of glycosynthase activity. This discovery has led to the development of a directed evolution methodology for screening and sorting glycosynthase mutants for synthesis of desired fucosylated oligosaccharides. Our screening technique facilitated rapid fluorescence activated cell sorting of a large library of glycosynthase variants (>106mutants) expressed inE. colito identify several novel mutants with increased activity for β-fucosyl-azide activated donor sugars towards desired acceptor sugars, demonstrating the broader applicability of this methodology.
Clonal propagation ofOsyris lanceolatathrough air layering at Bazawit Hill, Northern Ethiopia. An Endangered Medicinal and sandal wood Plant in East Africa
Authors: Admas Adugnaw , Melese Smegnew , Genetu Amare , Kidane Berhane , Yilma Zewdu , Admasu Melaku , Misga Tesaka
Published: March 2020

In the recent years medicinal and other economical important plants are getting attention due to the presence of therapeutically important active contents; however over exploitation and propagation problems are the major concern for conservation of several econmically important plant species. Among economical imprortant plants an attempt has been made to develop a propagation method for African sandalwood (Osyris lanceolata) by air layering approach aiming at providing an alternative propagation technique to the use of seeds or cuttings that germinate or root poorly. Air layers were applied root hormone to the stem branches ofOsyris lanceolata(still attached to the plant) during Novmbere 2019, at Bazawit Hill, Nothern Ethiopia at edge of Blue-Nile River from its source at Lake Tana. Root initiation were starts after 12 weeks of the experments.The factors assessed in this experiment were the effect IBA as rooting promoter at three concentrations (0,50, 100 and 150 ppm). From the data collected it was observed 88.8% rooting were achieved from air layers in the mother plants it selef those treated by IBA hormone and the controls not responding root.Making this propagation technique is a viable alternative to the use of seed or cutting propagation. Rooting response success were influenced by application of rooting hormone of IBA, soil composition and the seasons. At a rate of 150 ppm 100% all expermented plants were intiated and primarly other than other treatmeants responded root. The significance enhancing of root making onOsyris lanceolataplants stem via air layers is linked to the advantage of more rooting hormone concentartion.
Elucidating another level of epigenetic regulation in osteoarthritis by identifying functionalcis-acting long non-coding RNAs and their targets in articular cartilage
Authors: van Hoolwerff Marcella , Metselaar Paula I. , Tuerlings Margo , Suchiman H. Eka D. , Lakenberg Nico , Ramos Yolande F.M. , Cats Davy , Nelissen Rob G.H.H. , Broekhuis Demiën , Mei Hailiang , de Almeida Rodrigo Coutinho , Meulenbelt Ingrid
Published: March 2020

Objective

To identify robustly differentially expressed long non-coding RNAs (lncRNAs) with osteoarthritis (OA) pathophysiology in cartilage. Moreover to explore potential target mRNAs by establishing co-expression networks, followed by functional validation.

Methods

RNA sequencing was performed on macroscopically lesioned and preserved OA cartilage of patients who underwent a joint replacement surgery due to OA (N=98). Differential expression (DE) analysis was performed on lncRNAs that were annotated in GENCODE and Ensembl. To identify potential interactions, correlations were calculated between the identified DE lncRNAs and previously reported DE protein-coding genes in the same samples. Modulation of chondrocyte lncRNA expression was achieved using LNA GapmeRs.

Results

By applying our in-house pipeline we identified 5,053 lncRNAs to be robustly expressed, of which 191 were FDR significant differentially expressed between lesioned and preserved OA cartilage. Upon integrating mRNA sequencing data, we showed that intergenic and antisense DE lncRNAs show high, positive correlations with their flanking, respectively, sense genes. To functionally validate this observation we selectedP3H2-AS1, which was downregulated in primary chondrocytes, resulting in downregulation ofP3H2gene expression levels. As such, we can confirm thatP3H2-AS1regulates its sense geneP3H2.

Conclusion

By applying an improved detection strategy, robustly differentially expressed lncRNAs in OA cartilage were detected. Integration of these lncRNAs with differential mRNA expression levels in the same samples showed insight into their regulatory networks. Our data signifies that intergenic, as well as antisense lncRNAs play an important role in regulating the pathophysiology of OA.
Noise ceiling on the crossvalidated performance of reweighted models of representational dissimilarity: Addendum to Khaligh-Razavi & Kriegeskorte (2014)
Authors: Storrs Katherine R. , Khaligh-Razavi Seyed-Mahdi , Kriegeskorte Nikolaus
Published: March 2020

An error was made in including noise ceilings for human data in Khaligh-Razavi and Kriegeskorte (2014). For comparability with the macaque data, human data were averaged across participants before analysis. Therefore the noise ceilings indicating variability across human participants do not accurately depict the upper bounds of possible model performance and should not have been shown. Creating noise ceilings appropriate for the fitted models is not trivial. Below we present a method for doing this, and the results obtained with this new method. The corrected results differ from the original results in that the best-performing model (weighted combination of AlexNet layers and category readouts) does not reach the lower bound of the noise ceiling. However, the best-performing model is not significantly below the lower bound of the noise ceiling. The claim that the model “fully explains” the human IT data appears overstated. All other claims of the paper are unaffected.
Social interaction influences innate color preference of zebrafish shoals
Authors: Wang Ju , Yin Lifen , Hu Bin , Zheng Lei
Published: March 2020

The color discrimination can confer survival advantages by helping animals to find nutritious food and shelter and to avoid predator. Zebrafish as a social species, data on innate color preference in shoals remain controversial and there are limited data for this organism. Here we showed that, when given a choice among two color combinations (R-Y, R-G, Y-G, B-G, B-R, B-Y), shoals of zebrafish exhibited a complex pattern of color preference and the order of RYGB preference was R>Y>G, B>G. By contrast, the individual zebrafish showed marked changes, completely losing their preference for all the tested color combinations. To investigate the role of shoaling behavior in color preference, we selected a D1-receptor antagonist (SCH23390), which could disrupt social preference and decrease social interaction in zebrafish. Interestingly, the shoals that were treated by SCH23390 showed no color preference for all color combinations. Our findings indicate that social interaction is involved in color-driven behavior in zebrafish, and reveal the possible mechanisms that the dopaminergic system may contribute to innate color preference in shoals of zebrafish.
Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems
Authors: Lamar Sarah K. , Beddows Ian , Partridge Charlyn G.
Published: March 2020

Invasive species provide an opportune system to investigate how populations respond to new environments. Baby’s breath (Gypsophila paniculata) was introduced to North America in the 1800’s and has since spread throughout the United States and western Canada. We used an RNA-seq approach to explore how molecular processes contribute to the success of invasive populations with similar genetic backgrounds across distinct habitats. Transcription profiles were constructed from seedlings collected from a sand dune ecosystem in Petoskey, MI (PSMI) and a sagebrush ecosystem in Chelan, WA (CHWA). We assessed differential gene expression and identified SNPs within differentially expressed genes. We identified 1,146 differentially expressed transcripts across all sampled tissues between the two populations. GO processes enriched in PSMI were associated with nutrient starvation, while enriched processes in CHWA were associated with abiotic stress. Only 7.4% of the differentially expressed transcripts contained SNPs differing in allele frequencies of at least 0.5 between populations. Common garden studies found the two populations differed in germination rate and seedling emergence success. Our results suggest the success ofG. paniculatain these two environments is likely due to plasticity in specific molecular processes responding to different environmental conditions, although some genetic divergence may be contributing to these differences.
FPfilter: A false-positive-specific filter for whole-genome sequencing variant calling from GATK
Authors: Tan Yuxiang , Zhang Yu , Yang Hengwen , Yin Zhinan
Published: March 2020

1.

Motivation

As whole genome sequencing (WGS) is becoming cost-effective progressivelly, it has been applied increasingly in medical and scientific fields. Although the traditional variant-calling pipeline (BWA+GATK) has very high accuracy, false positives (FPs) are still an unavoidable problem that might lead to unfavorable outcomes, especially in clinical applications. As a result, filtering out FPs is recommended after variant calling. However, loss of true positives (TPs) is inevitable in FP-filtering methods, such as GATK hard filtering (GATK-HF). Therefore, to minimize the loss of TPs and maximize the filtration of FPs, a comprehensive understanding of the features of TPs and FPs, and building an improved model of classification are necessary. To obtain information about TPs and FPs, we used Platinum Genome (PT) as the mutation reference and its 300× deep sequenced dataset NA12878 as the simulation template. Then random sampling across depth gradients from NA12878 was performed to study the depth effect.

Results

FPs among heterozygous mutations were found to have pattern distinct from that of FPs among homozygous mutations. FPfilter makes use of this model to filter out FPs specifically. We evaluated FPfilter on a training dataset with depth gradients from NA12878 and a test dataset from NA12877 and NA24385. Compared with GATK-HF, FPfilter showed a significantly higher FP/TP filtration ratio and F-measure score. Our results indicate that FPfilter provides an improved model for distinguishing FPs from TPs and filters FPs with high specificity.

Availability

FPfilter is freely available for download on GitHub (https://github.com/yuxiangtan/FPfilter). Users can easily install it from anaconda.
The evolution of suppressed recombination between sex chromosomes by chromosomal inversions
Authors: Olito Colin , Abbott Jessica K.
Published: March 2020

The idea that sex-differences in selection drive the evolution of suppressed recombination between sex chromosomes is well-developed in population genetics. Yet, despite a now classic body of theory, empirical evidence that sexual antagonism drives the evolution of recombination suppression remains meagre and alternative hypotheses underdeveloped. We investigate whether the length of ‘evolutionary strata’ formed by chromosomal inversions that expand the non-recombining sex determining region (SDR) on recombining sex chromosomes can offer an informative signature of whether, and how, selection influenced their fixation. We develop population genetic models that determine how the length of a chromosomal inversion that expands the SDR affects its fixation probability for three categories of inversions: (i) neutral, (ii) directly beneficial (i.e., due to breakpoint or position effects), and (iii) indirectly beneficial (especially those capturing sexually antagonistic loci). Our models predict that neutral inversions should leave behind a unique signature of large evolutionary strata, and that it will often be difficult or impossible to distinguish between smaller strata created by directly or indirectly beneficial inversions. An interesting and unexpected prediction of our models is that the physical location of the ancestral SDR on the sex chromosomes is the most important factor influencing the relation between inversion size and the probability of expanding the SDR. Our findings raise a suite of new questions about how physical as well as selective processes influence the evolution of recombination suppression between sex chromosomes.
WOX9 functions antagonistic to STF and LAM1 to regulate leaf blade expansion inMedicago truncatulaandNicotiana sylvestris
Authors: Wolabu Tezera W. , Wang Hui , Tadesse Dimiru , Zhang Fei , Behzadirad Marjan , Tvorogova Varvara E. , Abdelmageed Haggagi , Liu Ye , Chen Naichong , Chen Jianghua , Allen Randy D. , Tadege Million
Published: March 2020

Plant specific WOX family transcription factors are known to regulate embryogenesis, meristem maintenance and lateral organ development. Modern clade WOX genes function through a transcriptional repression mechanism, and the intermediate clade transcriptional activator WOX9 functions with the repressor WOX genes in embryogenesis and meristems maintenance, but the mechanism of this interaction is unclear.WOX1homologuesSTFandLAM1are required for leaf blade outgrowth inMedicago truncatulaandNicotiana Sylvestris, respectively. Here we show thatWOX9negatively regulates leaf blade outgrowth and functions antagonistically toSTFandLAM1. WhileNsWOX9ectopic expression enhances thelam1mutant phenotype, and antisense expression partially rescues thelam1mutant, both overexpression ofNsWOX9and knockout by CRISPR/Cas9 genome editing inN. sylvestrisresulted in a range of severe leaf blade distortions, indicating that controlled negative regulation by NsWOX9 is required for proper blade development. Our results indicate that direct repression of WOX9 transcriptional activation activity by the transcriptional repressor STF/LAM1 is required for correct blade architecture and patterning inM. truncatulaandN. sylvestris. These findings suggest that a balance between transcriptional activation and repression mechanisms by direct interaction of activator and repressor WOX genes may be required for cell proliferation and differentiation homeostasis, and could be an evolutionarily conserved mechanism for the development of complex and diverse morphology in higher plants.

One sentence summary

WOX9 negatively regulates blade outgrowth antagonizing STF function but directly repressed by STF indicating WOX-mediated homeostasis in cell proliferation and differentiation during leaf morphogenesis.
Systemic characterization of pppGpp, ppGpp and pGpp targets inBacillusreveals NahA converts (p)ppGpp to pGpp to regulate alarmone composition and signaling
Authors: Yang Jin , Anderson Brent W. , Turdiev Asan , Turdiev Husan , Stevenson David M. , Amador-Noguez Daniel , Lee Vincent T. , Wang Jue D.
Published: March 2020

The alarmones pppGpp and ppGpp (collectively (p)ppGpp) protect bacterial cells from nutritional and other stresses. Here we demonstrate the physiological presence of pGpp as a third closely related alarmone in bacterial cells and also characterize and compare the proteomic targets of pGpp, ppGpp and pppGpp in Gram-positiveBacillusspecies. We revealed two regulatory pathways for ppGpp and pppGpp that are highly conserved across bacterial species: inhibition of purine nucleotide biosynthesis and control of ribosome assembly/activity through GTPases. Strikingly, pGpp potently regulates the purine biosynthesis pathway but does not interact with the GTPases. Importantly, we identified a key enzyme NahA that efficiently produces pGpp by hydrolyzing (p)ppGpp, thus tuning alarmone composition to uncouple the regulatory modules of the alarmones. Correspondingly, anahAmutant displays significantly reduced pGpp levels and elevated (p)ppGpp levels, slower growth recovery from nutrient downshift, and loss of competitive fitness. These cellular consequences for regulating alarmone composition strongly implicate an expanded repertoire of alarmones in a new strategy of stress response inBacillusand its relatives.
Cytokinin response induces immunity and fungal pathogen resistance in tomato by modulating cellular trafficking of PRRs
Authors: Gupta Rupali , Pizarro Lorena , Leibman-Markus Meirav , Marash Iftah , Bar Maya
Published: March 2020

Plant immunity is often defined by the “immunity hormones”: salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). These hormones are well known for differentially regulating defense responses against pathogens. In recent years, the involvement of other plant growth hormones such as auxin, gibberellic acid, abscisic acid, and cytokinins (CKs) in biotic stresses has been recognized. Previous reports have indicated that endogenous and exogenous CK treatment can result in pathogen resistance. We show here that CK induces systemic tomato immunity, modulating cellular trafficking of the PRR LeEIX2 and promoting biotrophic and necrotrophic pathogen resistance in an SA and ET dependent mechanism. CK perception within the host underlies its protective effect. Our results support the notion that CK acts as a priming agent, promoting pathogen resistance by inducing immunity in the host.
Accelerating Maximal-Exact-Match Seeding with Enumerated Radix Trees
Authors: Subramaniyan Arun , Wadden Jack , Goliya Kush , Ozog Nathan , Wu Xiao , Narayanasamy Satish , Blaauw David , Das Reetuparna
Published: March 2020

Motivation

Read alignment is a time-consuming step in genome sequence analysis. In the read alignment software BWA-MEM and the recently published faster version BWA-MEM2, the seeding step is a major bottleneck, for instance, contributing 38% to the overall execution time in BWA-MEM2 when aligning single-end whole human genome reads from the Platinum Genomes dataset. This is because both BWA-MEM and BWA-MEM2 use a compressed index structure called the FMD-Index, which results in high memory bandwidth requirements for seeding, primarily due to its character-by-character processing of reads.

Results

We propose a memory bandwidth-aware data structure for maximal-exact-match seeding called Enumerated Radix Tree (ERT). ERT trades off memory capacity to improve seeding performance (∼60 GB index for human genome). Together with optimizations to the seeding algorithm and mate-rescue step, ERT when integrated into BWA-MEM2 speeds up overall read alignment by 1.28× and provides up to 2.1× higher seeding performance while guaranteeing identical output to the original software. Furthermore, we prototype an FPGA implementation of ERT on Amazon EC2 F1 cloud and observe 1.6× higher seeding throughput over a 48-thread optimized CPU-ERT implementation.

Availability and implementation

https://github.com/arun-sub/bwa-mem2

Contact

arunsub@umich.edu,reetudas@umich.edu
Conspicuous candidate alleles point tocis-regulatory divergence underlying rapidly evolving craniofacial phenotypes
Authors: McGirr Joseph A. , Martin Christopher H.
Published: March 2020

Developing a mechanistic understanding of genetic variation contributing to variation in complex craniofacial traits is a major goal of both basic and translational research. Investigating closely related species that evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidatecis-acting genetic variation influencing rapidly evolving craniofacial phenotypes within an adaptive radiation ofCyprinodonpupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists – a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species – only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kb of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found strong evidence for twocis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1andpycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador pupfish system as an evolutionary model for craniofacial development.
WalkingDrosophilanavigate complex plumes using stochastic decisions biased by the timing of odor encounters
Authors: Demir Mahmut , Kadakia Nirag , Anderson Hope D. , Clark Damon A. , Emonet Thierry
Published: March 2020

Insects find food, mates, and egg-laying sites by tracking odor plumes swept by complex wind patterns. Previous studies have shown that moths and flies localize plumes by surging upwind at odor onset and turning cross- or downwind at odor offset. Less clear is how, once within the expanding cone of the odor plume, insects use their brief encounters with individual odor packets, whose location and timing are random, to progress towards the source. Experiments and theory have suggested that the timing of odor encounters might assist navigation, but connecting behaviors to individual encounters has been challenging. Here, we imaged complex odor plumes simultaneous with freely-walking flies, allowing us to quantify how behavior is shaped by individual odor encounters. Combining measurements, dynamical models, and statistical inference, we found that within the plume cone, individual encounters did not trigger reflexive surging, casting, or counterturning. Instead, flies turned stochastically with stereotyped saccades, whose direction was biased upwind by the timing of prior odor encounters, while the magnitude and rate of saccades remained constant. Odor encounters did not strongly affect walking speed. Instead, flies used encounter timing to modulate the rate of transitions between walks and stops. When stopped, flies initiated walks using information from multiple odor encounters, suggesting that integrating evidence without losing position was part of the strategy. These results indicate that once within the complex odor plume, where odor location and timing are unpredictable, animals navigate with biased random walks shaped by the entire sequence of encounters.
Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy
Authors: Hong Senlian , Yu Chenhua , Wang Peng , Shi Yujie , Cheng Bo , Chen Mingkuan , Chapla Digantkumar G. , Reigh Natalie , Narimatsu Yoshiki , Chen Xing , Clausen Henrik , Moremen Kelly W. , Macauley Matthew Scott , Paulson James C. , Wu Peng
Published: March 2020

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 (Rituxan™) on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced killer (CIK) cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killingin vitrowithout harming healthy B cells. For effective lymphoma cell killing in vivo we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The cells containing the ligands of both CD22 and selectins resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that NK cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.
Characterization of amyloid β fibril formation under microgravity conditions
Authors: Yagi-Utsumi Maho , Yanaka Saeko , Song Chihong , Satoh Tadashi , Yamazaki Chiaki , Kasahara Haruo , Shimazu Toru , Murata Kazuyoshi , Kato Koichi
Published: March 2020

Amyloid fibrils are self-assembled and ordered proteinaceous supramolecules structurally characterized by the cross-β spine. Amyloid formation is known to be related to various diseases typified by neurogenerative disorders and involved in a variety of functional roles. Whereas common mechanisms for amyloid formation have been postulated across diverse systems, the mesoscopic morphology of the fibrils is significantly affected by the type of solution condition in which it grows. Amyloid formation is also thought to share a phenomenological similarity with protein crystallization. While many studies have demonstrated the effect of gravity on protein crystallization, its effect on amyloid formation has not been reported. In this study, we conducted an experiment at the International Space Station (ISS) to characterize fibril formation of 40-residue amyloid β (Aβ(1-40)) under microgravity conditions. Our comparative analyses revealed that the Aβ(1-40) fibrilization progresses much more slowly on the ISS than on the ground, similarly to protein crystallization. Furthermore, microgravity promoted the formation of distinct morphologies of Aβ(1-40) fibrils. Our findings demonstrate that the ISS provides an ideal experimental environment for detailed investigations of amyloid formation mechanisms by eliminating the conventionally uncontrollable factors derived from gravity.
HELLO: A hybrid variant calling approach
Authors: Ramachandran Anand , Lumetta Steven S. , Klee Eric , Chen Deming
Published: March 2020

Next Generation Sequencing (NGS) technologies that cost-effectively characterize genomic regions and identify sequence variations using short reads are the current standard for genome sequencing. However, calling small indels in low-complexity regions of the genome using NGS is challenging. Recent advances in Third Generation Sequencing (TGS) provide long reads, which call large-structural variants accurately. However, these reads have context-dependent indel errors in low-complexity regions, resulting in lower accuracy of small indel calls compared to NGS reads. When both small and large-structural variants need to be called, both NGS and TGS reads may be available. Integration of the two data types with unique error profiles could improve robustness of small variant calling in challenging cases. However, there isn’t currently such a method integrating both types of data. We present a novel method that integrates NGS and TGS reads to call small variants. We leverage the Mixture of Experts paradigm which uses an ensemble of Deep Neural Networks (DNN), each processing a different data type to make predictions. We present improvements in our DNN design compared to previous work such as sequence processing using one-dimensional convolutions instead of image processing using two-dimensional convolutions and an algorithm to efficiently process sites with many variant candidates, which help us reduce computations. Using our method to integrate Illumina and PacBio reads, we find a reduction in the number of erroneous small variant calls of up to ~30%, compared to the state-of-the-art using only Illumina data. We also find improvements in calling small indels in low-complexity regions.
Multiband entropy-based feature-extraction method for automatic identification of epileptic focus based on high-frequency components in interictal iEEG
Authors: Akter Most. Sheuli , Islam Md. Rabiul , Iimura Yasushi , Sugano Hidenori , Fukumori Kosuke , Wang Duo , Tanaka Toshihisa , Cichocki Andrzej
Published: March 2020

Presurgical investigations for categorizing focal patterns are crucial, leading to localization and surgical removal of the epileptic focus. This paper presents a machine learning approach using information theoretic features extracted from high-frequency subbands to detect the epileptic focus from interictal intracranial electroencephalogram (iEEG). It is known that high-frequency subbands (>80 Hz) include important biomarkers such as high-frequency oscillations (HFOs) for identifying epileptic focus commonly referred to as the seizure on-set zone (SOZ). In this analysis, the multi-channel interictal iEEG signals were splitted into segments and each segment was decomposed into multiple high-frequency subbands. The different types of entropy were calculated for each of the subbands and the sparse linear discriminant analysis (sLDA) was applied to select the prominent entropy features. Due to the imbalance of SOZ and non-SOZ channels in iEEG data, the use of machine learning techniques is always tricky. To deal with the imbalanced learning problem, an adaptive synthetic oversampling approach (ADASYN) with radial basis function kernel-based SVM was used to detect the focal segments. Finally, the epileptic focus was identified based on detection of focal segments on SOZ and non-SOZ channels. Eight patients were examined to observe the efficiency of the automatic detector. The experimental results and statistical tests indicate that the proposed automatic detector can identify the epileptic focus accurately and efficiently.
Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago
Authors: Taki Yuto , Vincenot Christian E. , Sato Yu , Inoue-Murayama Miho
Published: March 2020

The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. AlthoughP. dasymallusis listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.

mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.

Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.

We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.
Occurrence cubes: a new paradigm for aggregating species occurrence data
Authors: Oldoni Damiano , Groom Quentin , Adriaens Tim , Davis Amy J.S. , Reyserhove Lien , Strubbe Diederik , Vanderhoeven Sonia , Desmet Peter
Published: March 2020

In this paper we describe a method of aggregating species occurrence data into what we coined “occurrence cubes”. The aggregated data can be perceived as a cube with three dimensions - taxonomic, temporal and geographic - and takes into account the spatial uncertainty of each occurrence. The aggregation level of each of the three dimensions can be adapted to the scope. Built on Open Science principles, the method is easily automated and reproducible, and can be used for species trend indicators, maps and distribution models. We are using the method to aggregate species occurrence data for Europe per taxon, year and 1km2European reference grid, to feed indicators and risk mapping/modelling for the Tracking Invasive Alien Species (TrIAS) project.
Reusable and Sensitive Detection Method for Exonuclease III Activity by DNB Nanoarrays Based on cPAS Sequencing Technology
Authors: Chen Ying , Wang Hui , Yang Jin , Yang Huanming , Drmanac Radoje , Xu Chongjun , Zhang Wenwei
Published: March 2020

Abstraction

In this article, we have designed a sensitive and recycled DNB (DNA nanoball) nanoarrays sequencing complex structures based on BGISEQ-500RS sequencer for the monitoring performance of Exo III activity. In the shortage of Exo III, the effective number ratio of DNB would be captured by an optical system due to one fluorescent. In contrast, in the presence of Exo III, some DNB would disappear or discard from the fields of the optical system by fluorescence extinction and uncleaned fluorescent, respectively. As a result, the effective number of DNB of this strategy was relative to the concentration of Exo III. For Exo III, our strategy showed a highly sensitive linear response in the low detection range of 0.01 U/mL to 0.5 U/mL, with detection limits below 0.01 U/mL. With the comparison between DNB nanoarrays and other fluorescent sensors, this study possessed superior sensitivity, selectivity, and reusability, accompanying with the low cost and simple setup.
IL8 Drives an Elaborate Signal Transduction Process for CD38 to Produce NAADP from NAAD and NADP+in Endolysosomes to Effect Cell Migration
Authors: Nam Tae-Sik , Park Dae-Ryoung , Rah So-Young , Woo Tae-Gyu , Chung Hun Taeg , Brenner Charles , Kim Uh-Hyun
Published: March 2020

Nicotinic acid adenine dinucleotide phosphate (NAADP) is an obligate driver of calcium signaling whose formation from other metabolites of nicotinamide adenine dinucleotide (NAD+) has remained elusive.In vitro, CD38-mediated NAADP synthesis requires an acidic pH and a nonphysiological concentration of nicotinic acid (NA). We discovered that the type II membrane form of CD38 catalyzes synthesis of NAADP by exchanging the nicotinamide moiety of nicotinamide adenine dinucleotide phosphate (NADP+) for the NA group of nicotinic acid adenine dinucleotide (NAAD) inside endolysosomes of interleukin 8 (IL8)-treated lymphokine-activated killer cells. Upon IL8 stimulation, cytosolic NADP+is transported to acidified endolysosomes via connexin 43 via cAMP-EPAC-RAP1-PP2A signaling. Luminal CD38 then performs a base exchange reaction with the donor NA group deriving from NAAD, produced by newly described endolysosomal activities of NA phosphoribosyltransferase and NMN adenyltransferase 3. Thus, the membrane organization of endolysosomal CD38, a signal-mediated transport system for NADP+and luminal NAD+biosynthetic enzymes integrate signals from a chemokine and cAMP to specify the spatiotemporal mobilization of calcium to drive cell migration.
An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase
Authors: Anselmi Massimiliano , Hub Jochen S.
Published: March 2020

SHP2 is a protein tyrosine phosphatase (PTP) involved in multiple signaling pathways. Mutations of SHP2 can result in Noonan syndrome or pediatric malignancies. Inhibition of wild-type SHP2 represents a novel strategy against several cancers. SHP2 is activated by binding of a phosphopeptide to the N-SH2 domain of SHP2, thereby favoring dissociation of the N-SH2 domain and exposing the active site on the PTP domain. The conformational transitions controlling ligand affinity and PTP dissociation remain poorly understood. Using molecular simulations, we revealed an allosteric interaction restraining the N-SH2 domain into a SHP2-activating and a stabilizing state. Only ligands selecting for the activating N-SH2 conformation, depending on ligand sequence and binding mode, are effective activators. We validate the model of SHP2 activation by rationalizing modified basal activity and responsiveness to ligand stimulation of several N-SH2 variants. This study provides mechanistic insight into SHP2 activation and may open routes for SHP2 regulation.
Protective effect of agmatine against cisplatin-induced apoptosis in an auditory cell line
Authors: Park Euyhyun , Lee Se Hee , Lee Hoyoung , Kim Young-Chan , Jung Hak Hyun , Im Gi Jung
Published: March 2020

Objectives

Agmatine, an endogenous metabolite of arginine, is known to have antioxidant activity, protect mitochondrial function, and confer resistance to cellular apoptosis. The aim of this study was to evaluate the protective effects of agmatine against cisplatin-induced cellular apoptosis in an auditory cell line.

Methods

HEI-OC1 cells were co-treated with agmatine at different concentrations and 15 µM cisplatin for 48 h. Cell viability was measured and annexin V-FITC/propidium iodide (PI) staining was performed to analyze apoptosis. The levels of intracellular reactive oxygen species (ROS) were measured using flow cytometry. The expression of BAX (Bcl2-associated X protein) and the enzymatic activity of caspase-3 were measured to examine the pathway of apoptosis induction.

Results

Co-treatment with 8 mM agmatine protected HEI-OC1 cells against cisplatin-induced cell apoptosis. Agmatine exerted a significant protective effect against 15 µM cisplatin when applied for 48 h and reduced the proportion of necrotic and late apoptotic cells. Agmatine did not reduce the cisplatin-induced increase in ROS but decreased the expression of BAX and the activity of caspase-3.

Conclusions

Agmatine protected against cisplatin-induced cellular apoptosis in an auditory cell line. These effects were mediated by the protection of mitochondrial function and inhibition of apoptosis.