bluuebunny/crossref_metadata_2025 huggingface dataset:
In-field detection and quantification of Septoria tritici blotch in diverse wheat germplasm using spectral-temporal features
Authors: Anderegg Jonas , Hund Andreas , Karisto Petteri , Mikaberidze Alexey
Published: June 2019

Hyperspectral remote sensing holds the potential to detect and quantify crop diseases in a rapid and non-invasive manner. Such tools could greatly benefit resistance breeding, but their adoption is hampered by i) a lack of specificity to disease-related effects and ii) insufficient robustness to variation in reflectance caused by genotypic diversity and varying environmental conditions, which are fundamental elements of resistance breeding.

We hypothesized that relying exclusively on temporal changes in canopy reflectance during pathogenesis may allow to specifically detect and quantify crop diseases whilst minimizing the confounding effects of genotype and environment. To test this hypothesis, we collected time-resolved canopy hyperspectral reflectance data for 18 diverse genotypes on infected and disease-free plots and engineered spectral-temporal features representing this hypothesis.

Our results confirm the lack of specificity and robustness of disease assessments based on reflectance spectra at individual time points. We show that changes in spectral reflectance over time are indicative of the presence and severity of septoria tritici blotch (STB) infections. Furthermore, the proposed time-integrated approach facilitated the delineation of disease from physiological senescence, which is pivotal for efficient selection of STB-resistant material under field conditions. A validation of models based on spectral-temporal features on a diverse panel of >300 wheat genotypes offered evidence for the robustness of the proposed method. This study demonstrates the potential of time-resolved canopy reflectance measurements for robust assessments of foliar diseases in the context of resistance breeding.
α-Actinin-1 promotes activity of the L-type Ca2+Channel CaV1.2
Authors: Turner Matthew , Anderson David E. , Nieves-Cintron Madeline , Bartels Peter , Coleman Andrea M. , Henderson Peter B. , Man Kwun Nok Mimi , Yarov-Yarovoy Vladimir , Bers Donald M. , Navedo Manuel F. , Horne Mary C. , Ames James B. , Hell Johannes W.
Published: June 2019

The L-type Ca2+channel CaV1.2 governs gene expression, cardiac contraction, and neuronal activity. Binding of α-actinin to the IQ motif of CaV1.2 supports its surface localization and postsynaptic targeting in neurons. We report a bi-functional mechanism that restricts CaV1.2 activity to its target sites. We solved separate NMR structures of the IQ motif (residues 1646-1664) bound to α-actinin-1 and to apo-calmodulin (apoCaM). The CaV1.2 K1647A and Y1649A mutations, which impair α-actinin-1 but not apoCaM binding, but not the F1658A and K1662E mutations, which impair apoCaM but not α-actinin-1 binding, decreased single channel open probability, gating charge movement, and its coupling to channel opening. Thus, α-actinin recruits CaV1.2 to defined surface regions and simultaneously boosts its open probability so that CaV1.2 is mostly active when appropriately localized.
Role of enhanced glucocorticoid receptor sensitivity in inflammation in PTSD: Insights from a computational model for circadian-neuroendocrine-immune interactions
Authors: Somvanshi Pramod R. , Mellon Synthia H. , Yehuda Rachel , Flory Janine D. , Bierer Linda , Makotkine Iouri , Marmar Charles , Jett Marti , Doyle Francis J.
Published: June 2019

Although glucocorticoid resistance contributes to increased inflammation, individuals with post-traumatic stress disorder (PTSD) exhibit increased glucocorticoid receptor (GR) sensitivity along with increased inflammation. It is not clear how inflammation co-exists with a hyper-responsive hypothalamic pituitary adrenal axis (HPA axis). To understand this better, we developed and analyzed an integrated mathematical model for the HPA axis and the immune system. We performed mathematical simulations for a dexamethasone suppression test and IC50-dexamethasone for cytokine suppression, by varying model parameters. The model analysis suggests that increasing the steepness of the dose response curve for GR activity may reduce anti-inflammatory effects of GRs at the ambient glucocorticoid levels thereby increasing pro-inflammatory response. The adaptive response of pro-inflammatory cytokine mediated stimulatory effects on the HPA-axis is reduced due to dominance of the GR-mediated negative feedback on the HPA-axis. To verify these hypotheses we analyzed the clinical data on neuro-endocrine variables and cytokines obtained from war-zone veterans with and without PTSD. We observed significant group differences for cortisol and ACTH suppression tests, pro-inflammatory cytokines TNFα and IL6, hs-CRP, promoter methylation of GR gene and IC50-Dex for lysozyme suppression. Causal inference modelling revealed significant associations between cortisol suppression and post-dex cortisol decline, promoter methylation of NR3C1-1F, IC50-Dex and pro-inflammatory cytokines. We noted significant mediation effects of NR3C1-1F promoter methylation on inflammatory cytokines through changes in GR sensitivity. Our findings suggest that increased GR sensitivity may contribute to increased inflammation, therefore, interventions to restore GR sensitivity may normalize inflammation in PTSD.
A Symmetric Prior for the Regularisation of Elastic Deformations: Improved Anatomical Plausibility in Nonlinear Image Registration
Authors: Lange Frederik J , Ashburner John , Smith Stephen M , Andersson Jesper L R
Published: June 2019

Nonlinear registration is critical to many aspects of Neuroimaging research. It facilitates averaging and comparisons across multiple subjects, as well as reporting of data in a common anatomical frame of reference. It is, however, a fundamentally ill-posed problem, with many possible solutions which minimise a given dissimilarity metric equally well. We present a novel regularisation method that aims to selectively drive solutions towards those which would be considered anatomically plausible by penalising unlikely lineal, areal and volumetric deformations. In addition, our penalty is symmetric in the sense that geometric expansions and contractions are penalised equally, which encourages inverse-consistency. We demonstrate that our method is able to significantly reduce volume and shape distortions compared to state-of-the-art elastic (FNIRT) and plastic (ANTs) registration frameworks. Crucially, this is achieved whilst matching or exceeding the registration quality of these methods, as measured by overlap scores of labelled cortical regions. Furthermore, extensive use of GPU parallelisation has allowed us to implement what is a highly computationally intensive optimisation strategy while maintaining reasonable run times of under half an hour.
Defining and predicting transdiagnostic categories of neurodegenerative disease
Authors: Cornblath Eli J. , Robinson John L. , Lee Virginia M.-Y. , Trojanowski John Q. , Bassett Danielle S.
Published: June 2019

In current models of neurodegeneration, individual diseases are defined by the presence of one or two pathogenic protein species. Yet, it is the rule rather than the exception that a patient meets criteria for more than one disease. This fact often remains hidden until autopsy, when neuropathological evaluation can assign disease labels based on gold-standard criteria. Ultimately, the prevalence of concomitant diagnoses and the inability to infer an underlying neuropathological syndrome from clinical variables hinders the identification of patients who might be good candidates for a particular intervention. Here, by applying graph-based clustering to post-mortem histopathological data from 1389 patients with degeneration in the central nervous system, we generate 4 non-overlapping, data-driven disease categories that simultaneously account for amyloid-β plaques, tau neurofibrillary tangles, α-synuclein inclusions, neuritic plaques, TDP-43 inclusions, angiopathy, neuron loss, and gliosis. The resulting disease clusters are transdiagnostic in the sense that each cluster contains patients belonging to multiple different existing disease diagnoses, who colocalize in clusters according to the pathogenic protein aggregates known to drive each disease. We show that our disease clusters, defined solely by histopathology, separate patients in terms of cognitive phenotypes, cerebrospinal fluid (CSF) protein levels, and genotype in a manner that is not trivially explained by the representation of individual diseases within each cluster. Finally, we use cross-validated multiple logistic regression to generate high accuracy predictions (AUC > 0.9) of membership to both existing disease categories and transdiagnostic clusters based on CSF protein levels and genotype, both accessible in vivo. Broadly, our approach parses phenotypic and genotypic heterogeneity in neurodegenerative disease, and represents a general framework for identifying otherwise-fuzzy disease subtypes in other areas of medicine, such as epilepsy, vascular disease, and cancer. In clinical neurology, the statistical models we generate may be useful for repurposing drugs by comparing efficacy to probabilistic estimates of disease cluster membership, as well as for future trials that could be targeted towards an algorithmically defined family of diseases.
The effect of sex and underlying disease on the genetic association of QT interval and sudden cardiac death
Authors: Mitchell Rebecca N. , Ashar Foram N. , Jarvelin Marjo-Riitta , Froguel Philippe , Sotoodehnia Nona , Brody Jennifer A. , Sebert Sylvain , Huikuri Heikki , Rioux John , Goyette Philippe , Newcomb Charles E. , Junttila M. Juhani , Arking Dan E.
Published: June 2019

Background

Sudden cardiac death (SCD) accounts for ~300,000 deaths annually in the US. Men have a higher risk of SCD and are more likely to have underlying coronary artery disease (CAD) than women. In contrast, women are more likely to have arrhythmic events in the setting of inherited or acquired QT prolongation. Moreover, there is evidence of sex differences in the underlying genetics of QT interval duration. Using sex- and CAD-stratified analyses, we assess differences in genetic association between prolonged QT interval and SCD risk.

Methods

We examined 2,282 SCD subjects with autopsy-confirmed underlying disease from the Fingesture cohort and 3,561 Finnish controls. The SCD subjects were stratified by underlying disease (ischemic vs. non-ischemic) and by sex. We used logistic regression to test for association between the top QT interval associated SNP, rs12143842 (in the NOS1AP locus), and SCD risk. We also performed Mendelian randomization to test for causal association of QT interval in the various subgroups.

Results

Female SCD victims with underlying non-ischemic disease had the strongest association between rs12143842 and SCD risk (OR=1.37; 95% CI, 1.07-1.75) and the strongest causal association, established using Mendelian randomization, between prolonged QT interval and SCD (OR in SCD risk per SD increase in QT, 3.60; 95% CI, 1.22-10.49). Ischemic SCD victims, irrespective of sex, did not show an association between rs12143842 and SCD risk or a causal association for QT interval.

Conclusions

This study provides evidence that the causal effect of QT prolongation on SCD risk differs by sex and underlying disease.
Artificial selection on male size depletes genetic variance but not covariance of life history traits in the yellow dung fly
Authors: Blanckenhorn WU , Llaurens V , Reim C , Teuschl Y , Postma E
Published: June 2019

The evolutionary potential of organisms depends on the presence of sufficient genetic variation for traits subject to selection, as well as on the genetic covariances among them. While genetic variation ultimately derives from mutation, theory predicts the depletion of genetic (co)variation under consistent directional or stabilizing selection in natural populations. We estimated and compared additive genetic (co)variances for several standard life history traits, including some for which this has never been assessed, before and after 24 generations of artificial selection on male size in the yellow dung flyScathophaga stercoraria(Diptera: Scathophagidae) using a series of standard half-sib breeding experiments. As predicted, genetic variances (VA), heritabilities (h2) and evolvabilities (IA) of body size, development time, first clutch size, and female age at first clutch were lower after selection. As independent selection lines were crossed prior to testing, we can rule out that this reduction is due to genetic drift. In contrast to the variances, and against expectation, the additive genetic correlations between the sexes for development time and body size remained strong and positive (rA =0.8–0.9), while the genetic correlation between these traits within the sexes tended to strengthen (but not significantly so). Our study documents that the effect of selection on genetic variance is predictable, whereas that on genetic correlations is not.
Rapid response to the Alpha-1 Adrenergic Agent Phenylephrine in the Perioperative Period is Impacted by Genomics and Ancestry
Authors: Wenric Stephane , Jeff Janina M. , Joseph Thomas , Yee Muh-Ching , Belbin Gillian M. ,   Regeneron Genetics Center,   CBIPM Genomics Group, Obeng Aniwaa Owusu , Ellis Stephen B. , Bottinger Erwin P. , Gottesman Omri , Levin Matthew A. , Kenny Eimear E.
Published: June 2019

Background

The emergence of genomic data in biobanks and health systems offers new ways to derive medically important phenotypes, including acute phenotypes that occur during in-patient clinical care. We hypothesized that there is a genetic underpinning to the magnitude of the response to phenylephrine, an α1-adrenergic receptor agonist commonly used to treat hypotension during anesthesia and surgery.

Methods

We quantified the response to phenylephrine by determining the delta between the minimum blood pressure (BP) within five minutes before and the maximum BP within five minutes after bolus administration. We then performed a genome-wide association study (GWAS) adjusted for genetic ancestry, demographics, and relevant clinical covariates to investigate genetic factors underlying individual differences systolic BP response to phenylephrine (ΔSBP), as well as mean arterial pressure (ΔMAP) and diastolic BP (ΔDBP), for both the entire study cohort as well as for each of 3 ancestry sub-cohorts; European American(EA), African American(AA), and Hispanic American(HA).

Results

4,317 patients met inclusion criteria, of which 3,699 were genotyped. Average ΔBP values over the entire cohort were ΔSBP=17(+-25) mmHg, ΔMAP=14(+-18) mmHg, ΔDBP=11(+-14) mmHg. The largest difference between populations was observed for ΔSBP (ΔSBPEA=20(+-24) mmHg; ΔSBPHA=16(+-25) mmHg; ΔSBPAA=15(+-25) mmHg). The differences remained after adjusting for clinical covariates and ancestry (EA vs. HA: ΔSBP, p<0.032;ΔMAP, p<0.021;ΔDBP,p<0.008);(EA vs. AA:ΔSBP,p<5.13×10-5;ΔMAP,p<2.1×10-4;ΔDBP,p<3.3×10-4). GWAS revealed significant associations between loci and BP response in 5 different genome regions (p<5×10-8) in the entire cohort, and suggestive associations in 2 different regions in EAs (p<6×10-8,p<7×10-8). We observed non-random enrichment in association with SBP drug response in 165 loci previously reported to be associated with systolic blood pressure. Finally, we discovered rare variants, rs188427942 and rs147664194 present at ∼1% in EAs and rs146535276 present at ∼1% in AAs respectively, where patients carrying one copy of these variants show no response to phenylephrine.

Conclusions

It is possible to derive a quantitative phenotype suited for comparative statistics and genome-wide association studies from routinely collected perioperative data. There are population differences in rapid response to phenylephrine, large effect alleles and novel genes affecting pharmaceutical response, and phenylephrine non-responders, with implications for personalized treatment during surgery.
Anatomical meniscus construct with zone specific biochemical composition and structural organization
Authors: Bahcecioglu G. , Bilgen B. , Hasirci N. , Hasirci V.
Published: June 2019

A PCL/hydrogel construct that would mimic the structural organization, biochemistry and anatomy of meniscus was engineered. The compressive (380 ± 40 kPa) and tensile modulus (18.2 ± 0.9 MPa) of the PCL scaffolds were increased significantly when constructs were printed with a shifted design and circumferential strands mimicking the collagen organization in native tissue (p<0.05). Presence of circumferentially aligned PCL strands also led to elongation and alignment of the human fibrochondrocytes. Gene expression of the cells in agarose (Ag), gelatin methacrylate (GelMA), and GelMA-Ag hydrogels was significantly higher than that of cells on the PCL scaffolds after a 21-day culture. GelMA exhibited the highest level of collagen type I (COL1A2)mRNA expression, while GelMA-Ag exhibited the highest level of aggrecan (AGG)expression (p<0.001, compared to PCL). GelMA and GelMA-Ag exhibited a high level of collagen type II (COL2A1) expression (p<0.05, compared to PCL). Anatomical scaffolds with circumferential PCL strands were impregnated with cell-loaded GelMA in the periphery and GelMA-Ag in the inner region. GelMA and GelMA-Ag hydrogels enhanced the production of COL 1 and COL 2 proteins after a 6-week culture (p<0.05). COL 1 expression increased gradually towards the outer periphery, while COL 2 expression decreased. We were thus able to engineer an anatomical meniscus with a cartilage-like inner region and fibrocartilage-like outer region.
An ultra high-densityArabidopsis thalianacrossover map that refines the influences of structural variation and epigenetic features
Authors: Rowan Beth A. , Heavens Darren , Feuerborn Tatiana R. , Tock Andrew J. , Henderson Ian R. , Weigel Detlef
Published: June 2019

Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions ofArabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
Type-2-diabetes Alters CSF but not Plasma Metabolomic and AD Risk Profiles in Vervet Monkeys
Authors: Kavanagh Kylie , Day Stephen M. , Pait Morgan C. , Mortiz William R. , Newgard Christopher B. , Ilkayeva Olga , Mcclain Donald A. , Macauley Shannon L.
Published: June 2019

Epidemiological studies suggest that individuals with type 2 diabetes (T2D) have a 2-4 fold increased risk for developing Alzheimer’s disease (AD), however the exact mechanisms linking the two disease is unknown. In both conditions, the majority of pathophysiological changes (including glucose and insulin dysregulation, insulin resistance, and AD-related changes in Aβ and tau) occur decades before the onset of clinical symptoms and diagnosis. In this study, we investigated the relationship between metabolic biomarkers associated with T2D and AD-related pathology, including Aβ levels, from cerebrospinal fluid (CSF) and fasting plasma of healthy, prediabetic (PreD), and T2D vervet monkeys (Chlorocebus aethiops sabeus). Consistent with the human disease, T2D monkeys have increased plasma and CSF glucose levels as they transition from normoglycemia to pre-diabetic and diabetic states. Although plasma levels of acylcarnitines and amino acids remained largely unchanged, peripheral hyperglycemia correlated with decreased CSF acylcarnitines and CSF amino acids, including branched chain amino acid (BCAA) concentrations, suggesting profound changes in cerebral metabolism coincident with systemic glucose dysregulation. Moreover, CSF Aβ40 and CSF Aβ42 levels decreased in T2D monkeys, a phenomenon observed in the human course of AD which coincides with increased amyloid deposition within the brain. In agreement with our previous studies in mice, CSF Aβ40 and CSF Aβ42 were highly correlated with CSF glucose levels, suggesting that glucose levels in the brain are associated with changes in Aβ metabolism. Interestingly, CSF Aβ40 and CSF Aβ42 levels were also highly correlated with plasma but not CSF lactate levels, suggesting that plasma lactate might serve as a potential biomarker of disease progression in AD. Moreover, CSF glucose and plasma lactate levels were correlated with CSF amino acid and acylcarnitine levels, demonstrating alterations in cerebral metabolism occurring with the onset of T2D. Together, these data suggest that peripheral metabolic changes associated with the development of T2D produce alterations in brain metabolism that lead to early changes in the amyloid cascade, similar to those observed in pre-symptomatic AD.
Why evolve reliance on the microbiome for timing of ontogeny?
Authors: Metcalf C. Jessica E. , Henry Lucas P. , Rebolleda-Gómez María , Koskella Britt
Published: June 2019

The timing of life history events has important fitness consequences. Since the 1950s, researchers have combined first principles and data to predict the optimal timing of life history transitions. Recently, a striking mystery has emerged. Such transitions can be shaped by a completely different branch of the tree of life: bacterial species in the microbiome. Probing these interactions using testable predictions from evolutionary theory could illuminate whether and how host-microbiome integrated life histories can evolve and be maintained. Beyond advancing fundamental science, this research program could yield important applications. In an age of microbiome engineering, understanding the contexts that lead to microbiota signaling shaping ontogeny could offer novel mechanisms for manipulations to increase yield in agriculture, or reduce pathogen transmission by affecting vector efficiency. We combine theory and evidence to illuminate the essential questions underlying the existence ofMicrobiomeDependentOntogeneticTiming (MiDOT) to fuel research on this emerging topic.
Neuronal TORC1 modulates longevity via AMPK and cell nonautonomous regulation of mitochondrial dynamics inC. elegans
Authors: Zhang Yue , Lanjuin Anne , Chowdhury Suvagata Roy , Mistry Meeta , Silva Garcia Carlos G. , Weir Heather J. , Lee Chia-Lin , Escoubas Caroline C. , Tabakovic Emina , Mair William B.
Published: June 2019

Target of rapamycin complex 1 (TORC1) and AMP-activated protein kinase (AMPK) antagonistically modulate metabolism and aging. However, how they coordinate to determine longevity and if they act via separable mechanisms is unclear. Here, we show that neuronal AMPK is essential for lifespan extension from TORC1 inhibition, and that TORC1 suppression increases lifespan cell non autonomously via distinct mechanisms from global AMPK activation. Lifespan extension by null mutations in genes encodingraga-1(RagA) orrsks-1(S6K) is fully suppressed by neuronal-specific rescues. Loss of RAGA-1 increases lifespan via maintaining mitochondrial fusion. Neuronal RAGA-1 abrogation ofraga-1mutant longevity requires UNC-64/syntaxin, and promotes mitochondrial fission cell nonautonomously. Finally, deleting the mitochondrial fission factor DRP-1 renders the animal refractory to the pro-aging effects of neuronal RAGA-1. Our results highlight a new role for neuronal TORC1 in cell nonautonomous regulation of longevity, and suggest TORC1 in the central nervous system might be targeted to promote healthy aging.
Multiplex chromatin interaction analysis by signal processing and statistical algorithms
Authors: Kim Minji , Zheng Meizhen , Tian Simon Zhongyuan , Capurso Daniel , Lee Byoungkoo , Chuang Jeffrey H. , Ruan Yijun
Published: June 2019

The single-molecule multiplex chromatin interaction data generated by emerging non-ligation-based 3D genome mapping technologies provide novel insights into high dimensional chromatin organization, yet introduce new computational challenges. We developed MIA-Sig (https://github.com/TheJacksonLaboratory/mia-sig.git), an algorithmic framework to de-noise the data, assess the statistical significance of chromatin complexes, and identify topological domains and inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains.
A burst of genetic innovation in actin-related proteins (Arps) for testis-specific function in aDrosophilalineage
Authors: Schroeder Courtney M. , Valenzuela John , Hocky Glen M. , Malik Harmit S.
Published: June 2019

Many cytoskeletal proteins form the core of fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification inDrosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that originated in the common ancestor of theobscuragroup ofDrosophilaspecies and have been mostly preserved in this lineage. All four Arp paralogs have evolved under positive selection and are predominantly expressed in the male germline. We focus our analyses on the divergentArp2Dparalog, which arose via a retroduplication event fromArp2, a component of the 7-membered Arp2/3 complex that polymerizes branched actin networks. Computational modeling analyses suggest that Arp2D should be able to replace Arp2 in the Arp2/3 complex and bind daughter actin monomers, suggesting that Arp2D may augment Arp2’s functions in the male germline. We find that Arp2D is expressed during and following meiosis in the male germline, where it localizes to distinct locations such as actin cones–pecialized cytoskeletal structures that separate bundled spermatids into individual mature sperm. We hypothesize that this unprecedented burst of genetic innovation in cytoskeletal proteins may have been driven by the evolution of sperm heteromorphism in theobscuragroup ofDrosophila.
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity
Authors: Specht Harrison , Emmott Edward , Petelski Aleksandra A. , Huffman R. Gray , Perlman David H. , Serra Marco , Kharchenko Peter , Koller Antonius , Slavov Nikolai
Published: June 2019

Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of limitations of quantitative single-cell protein analysis. To overcome this limitation, we developed SCoPE2, which substantially increases quantitative accuracy and throughput while lowering cost and hands-on time by introducing automated and miniaturized sample preparation. These advances enable us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiate into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 3,042 proteins in 1,490 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allow us to discern single cells by cell type. Furthermore, the data uncover a continuous gradient of proteome states for the macrophages, suggesting that macrophage heterogeneity may emerge in the absence of polarizing cytokines. This gradient correlates to the inflammatory axis of classically and alternatively activated macrophages. Parallel measurements of transcripts by 10x Genomics suggest that our measurements sample 20-fold more protein copies than RNA copies per gene, and thus SCoPE2 supports quantification with improved count statistics. The joint distributions of proteins and transcripts allowed exploring regulatory interactions, such as between the tumor suppressor p53, its transcript, and the transcripts of genes regulated by p53. Our methodology lays the foundation for quantitative single-cell analysis of proteins by mass-spectrometry and demonstrates the potential for inferring transcriptional and post-transcriptional regulation from variability across single cells.

Abstract Figure
Dynamics of Meiotic Sex Chromosome Inactivation and Pachytene Activation in Mice Spermatogenesis
Authors: Vértesy Ábel , Frias-Aldeguer Javier , Sahin Zeliha , Rivron Nicolas , van Oudenaarden Alexander , Geijsen Niels
Published: June 2019

During germ cell development, cells undergo a drastic switch from mitosis to meiosis to form haploid germ cells. Sequencing and computational technologies now allow studying development at the single-cell level. Here we developed a multiplexed trajectory reconstruction to create a high-resolution developmental map of spermatogonia and prophase-I spermatocytes from testes of a Dazl-GFP reporter mouse. We identified three main transitions in the meiotic prophase-I: meiotic entry, the meiotic sex chromosome inactivation (MSCI), and concomitant pachytene activation. We validated the key features of these transitionsin vivousing single molecule FISH. Focusing on MSCI, we found that 34% of sex chromosomal genes are induced shortly before MSCI, that silencing time is diverse and correlates with specific gene functions. These highlight a previously underappreciated level of regulation of MSCI. Finally, we found that spermatozoal genes in pachytene are activated in a temporal pattern reflecting the future anatomic and functional order of the sperm cell. Altogether we highlighted how precise and sequential changes in gene expression regulate cellular states in meiotic prophase-I.
Circadian diversity in SwedishArabidopsisaccessions is associated with naturally occurring genetic variation inCOR28
Authors: Rees Hannah , Joynson Ryan , Brown James K.M. , Hall Anthony
Published: June 2019

Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this, we used a Delayed Fluorescence (DF) imaging assay to screen 191 naturally occurring SwedishArabidopsisaccessions for their circadian phenotypes. We demonstrate period variation with both latitude and sub-population. Several candidate loci linked to period, phase and Relative Amplitude Error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution withinCOR28is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants.COR28is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. Finally, we tested circadian variation under reduced temperatures and show that fast and slow period phenotypic tails remain diverged and follow a distinctive ‘arrow-shaped’ trend indicative of selection for a cold-biased temperature compensation response.
Auto-regressive modeling and diagnostics for qPCR amplification
Authors: Hsu Benjamin , Sherina Valeriia , McCall Matthew N.
Published: June 2019

Current methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or in early amplifications are likely responsible for these deviations. Commonly-used 4- and 5-parameter sigmoidal models appear to be particularly susceptible to this issue, often displaying patterns of autocorrelation in the residuals. The presence of this phenomenon, even for technical replicates, suggests that these parametric models may be misspecified. Specifically, they do not account for the sequential dependent nature of qPCR fluorescence measurements. We demonstrate that a Smooth Transition Autoregressive (STAR) model addresses this limitation by explicitly modeling the dependence between cycles and the gradual transition between amplification regimes. In summary, application of a STAR model to qPCR amplification data improves model fit and reduces autocorrelation in the residuals.
Beyond redistribution: In-stream habitat restoration increases capacity for young-of-the-year Chinook salmon and steelhead in the Entiat River, WA
Authors: Polivka Carlos M. , Claeson Shannon M.
Published: June 2019

We conducted snorkel surveys for juvenile salmonids in reaches of the Entiat River (Washington, USA) treated with engineered log jams (ELJs), and in reaches without treatments, to determine if habitat-unit-scale observations can identify whether restoration has increased the habitat capacity of a reach. The conceptual basis and field methodology emphasize fish density data (fish/habitat area in m2) from unrestored habitat within a reach treated with ELJs compared to surveys in 1) unrestored habitat in untreated reaches and 2) restored habitat in treated reaches. A Bayesian generalized linear model enabled us to quantify density differences among habitat types using advanced computational statistics. Modal density of young-of-the-year Chinook salmon (Oncorhynchus tschawytscha) and steelhead (O. mykiss) was at least 3.1-fold and 2.7-fold greater, respectively, in restored habitat compared with unrestored habitat for all treated reaches examined. To distinguish the density differences in those reaches as capacity increases rather than redistribution from poor habitat to good habitat, we compared density in unrestored habitat in both treated and untreated reaches. Here we found no differences for either species, confirming that the increased density in restored habitat units did not come from depletion of unrestored habitat in the same reach. We thus concluded that restoration increased the habitat capacity of the reach at the scale of pools created by ELJs.
A blueprint of seed desiccation sensitivity in the genome ofCastanospermum australe
Authors: Marques Alexandre , Costa Maria-Cecília D. , Chathuri Udisha , Jonkheer Eef , Zhao Tao , Schijlen Elio , Derks Martijn , Nijveen Harm , Marcet-Houben Marina , Julca Irene , Delahaie Julien , Schranz M. Eric , Gabaldon Toni , Pelletier Sandra , Leprince Olivier , Ligterink Wilco , Buitink Julia , Hilhorst Henk W.M. , Farrant Jill M.
Published: June 2019

Most angiosperms produce seeds that are desiccated on dispersal with the ability to retain viability in storage facilities for prolonged periods. However, some species produce desiccation sensitive seeds which rapidly lose viability in storage, precludingex situconservation. Current consensus is that desiccation sensitive seeds either lack or do not express mechanisms necessary for the acquisition of desiccation tolerance.

We sequenced the genome ofCastanospermum australe, a legume species producing desiccation sensitive seeds, and characterized its seed developmental physiology and - transcriptomes.

C. australehas a low rate of evolution, likely due to its perennial life-cycle and long generation times. The genome is syntenic with itself, with several orthologs of genes from desiccation tolerant legume seeds, from gamma whole-genome duplication events being retained. Changes in gene expression during development ofC. australeseeds, as compared to desiccation tolerantMedicago truncatulaseeds, suggest they remain metabolically active, prepared for immediate germination.

Our data indicates that the phenotype ofC. australeseeds arose through few changes in specific signalling pathways, precluding or bypassing activation of mechanisms necessary for acquisition of desiccation tolerance. Such changes have been perpetuated as the habitat in which dispersal occurs is favourable for prompt germination.
Thalamic-medial temporal lobe connectivity underpins familiarity memory
Authors: Kafkas Alex , Mayes Andrew R. , Montaldi Daniela
Published: June 2019

The neural basis of memory is highly distributed, but the thalamus is known to play a particularly critical role. However, exactly how the different thalamic nuclei contribute to different kinds of memory is unclear. Moreover, whether thalamic connectivity with the medial temporal lobe (MTL), arguably the most fundamental memory structure, is critical for memory, remains unknown. We explore these questions using an fMRI recognition memory paradigm that taps familiarity and recollection (i.e., the two types of memory that support recognition) for objects, faces and scenes. We show that the mediodorsal thalamus (MDt) plays a material-general role in familiarity, while the anterior thalamus plays a material-general role in recollection. Material-specific regions were found for scene familiarity (ventral posteromedial and pulvinar thalamic nuclei) and face familiarity (left ventrolateral thalamus). Critically, increased functional connectivity between the MDt and the parahippocampal (PHC) and perirhinal cortices (PRC) of the MTL underpinned increases in reported familiarity confidence. These findings suggest that familiarity signals are generated through the dynamic interaction of functionally connected MTL-thalamic structures.
Using low-cost alcohol sensors to monitor real-time olfactory information during odor-guided navigation
Authors: Tariq Mohammad F. , Lewis Suzanne M. , Lowell Aliena , Perkel David J. , Gire David H.
Published: June 2019

Olfaction — an evolutionarily conserved chemosensory modality — guides navigation and decision-making in organisms from multiple phyla within the animal kingdom. However, using olfactory cues to guide navigation is a complicated problem. This is because the spread of odor molecules from the source is governed by turbulent and chaotic air currents, resulting in intermittent and spatiotemporally varying sensory cues as odor plumes. Precisely correlating olfactory information with behavior and neurophysiology from freely behaving animals has thus been a challenging avenue due to the dynamic nature of the odor plumes. Current technologies for chemical quantification are cumbersome and not feasible for monitoring the olfactory information at the temporal and spatial scales relevant for plume and odor tracking in animals. Here we present an alternate method for real-time monitoring of olfactory information using low-cost, lightweight sensors that robustly detect common solvent molecules, like alcohols. Paired recordings were made from these ethanol sensors with a Photoionization detector (PID) to precisely controlled ethanol stimuli. The ethanol sensor recordings were then deconvolved using a double exponential kernel, showing robust correlations with the PID recordings at behaviorally relevant time, frequency and spatial scales. Furthermore, the light weight of these sensors allows us to mount them on the heads of freely behaving rodents engaged in odor-guided navigation. Our preliminary experiments in mice show robust behavioral and neurophysiological responses correlated with ethanol plume contacts detected by these sensors.
Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships1
Authors: Zhou Julian Q. , Kleinstein Steven H.
Published: June 2019

B cell clonal expansion is vital for adaptive immunity. High-throughput B cell receptor (BCR) sequencing enables investigating this process, but requires computational inference to identify clonal relationships. This inference usually relies on only the BCR heavy chain, as most current protocols do not preserve heavy:light chain pairing. The extent to which paired light chains aids inference is unknown. Using human single-cell paired BCR datasets, we assessed the ability of heavy chain-based clonal clustering to identify clones. Of the expanded clones identified, <20% grouped cells expressing inconsistent light chains. Heavy chains from these misclustered clones contained more distant junction sequences and shared fewer V segment mutations than the accurate clones. This suggests that additional heavy chain information could be leveraged to refine clonal relationships. Conversely, light chains were insufficient to refine heavy chain-based clonal clusters. Overall, the BCR heavy chain alone is sufficient to identify clonal relationships with confidence.
An assessment of land use land cover change in Central Highland of Deccan Peninsula and Semi-Arid tracts of India
Authors: Mondal Tamali , Basu Parabita , Qureshi Qamar , Jhala Yadvendradev
Published: June 2019

Human consumption and management of land, i.e., how people transmit to a landscape as a source of livelihood, shelter, recreation, or industry, are powerful forces shaping patterns and dynamics in human-occupied landscapes. Understanding and managing landscape change, therefore, requires a thorough knowledge of the developmental processes the area is undergoing, causing the change in the land use pattern over time. In this study land use/cover dynamics of the Central Highland of Deccan Peninsula and Semi-Arid zone of Gujarat Rajputana bio-geographic regions of India was assessed using a combination of hybrid classification, markov analysis approach within the time frame of 2000-2013. In this time frame, major changes have been identified in dense forest, open forest, cropland, fallow land and in the barren landforms. The landscape has witnessed a substantial increase in built-up areas from 31317 sq. km. in 2000 to 52338 sq. km in 2013. The scrubland has largely declined from 35713.06 sq. km in 2000 to 23003.88 sq.km in 2013; it might have resulted from the transition of scrubland to the fallow land which was predicted as more than 70% in the first phase and more than 30% in the later phase. The area under dense forest constantly decreased in the studied time (84027 sq. km to 71225.37 sq. km). The Markov analysis estimated a probability of changing of open forest types to fallow land (36% in 2000-2006 and 20% in 2006-2013). As the environmental damage is irreversible due to industrialization, therefore a sound strategy needs to be implemented for sustainable use of natural resources that can go hand in hand.
The Arabidopsis Diacylglycerol Kinase 4 is involved in nitric oxide-dependent pollen tube guidance and fertilization
Authors: Wong Aloysius , Donaldson Lara , Portes Maria Teresa , Eppinger Jörg , Feijó José , Gehring Christoph
Published: June 2019

Nitric oxide (NO) is a key signaling molecule that regulates diverse biological processes in both animals and plants. In animals, NO regulates vascular wall tone, neurotransmission and immune response while in plants, NO is essential for development and responses to biotic and abiotic stresses [1–3]. Interestingly, NO is involved in the sexual reproduction of both animals and plants mediating physiological events related to the male gamete [2, 4]. In animals, NO stimulates sperm motility [4] and binding to the plasma membrane of oocytes [5] while in plants, NO mediates pollen-stigma interactions and pollen tube guidance [6, 7]. NO generation in pollen tubes (PTs) has been demonstrated [8] and intracellular responses to NO include cytosolic Ca2+ elevation, actin organization, vesicle trafficking and cell wall deposition [7, 9]. However, the NO-responsive proteins that mediate these responses are still elusive. Here we show that PTs of Arabidopsis lacking the pollen-specific Diacylglycerol Kinase 4 (DGK4) grow slower and become insensitive to NO-dependent growth inhibition and re-orientation responses. Recombinant DGK4 protein yields NO-responsive spectral and catalytic changes in vitro which are compatible with a role in NO perception and signaling in PTs. NO is a fast, diffusible gas and, based on our results, we hypothesize it could serve in long range signaling and/or rapid cell-cell communication functions mediated by DGK4 downstream signaling during the progamic phase of angiosperm reproduction.
A systematic comparison of chloroplast genome assembly tools
Authors: Freudenthal Jan A , Pfaff Simon , Terhoeven Niklas , Korte Arthur , Ankenbrand Markus J , Förster Frank
Published: June 2019

Background

Chloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information. Plastid genomes accommodate essential genes and are regularly utilized in biotechnology or phylogenetics. Different assemblers that are able to assess the plastid genome have been developed. These assemblers often use data of whole genome sequencing experiments, which usually contain reads from the complete chloroplast genome.

Results

The performance of different assembly tools has never been systematically compared. Here we present a benchmark of seven chloroplast assembly tools, capable of succeeding in more than 60% of known real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements. The examination of 105 data sets from species with unknown plastid genomes leads to the assembly of 20 novel chloroplast genomes.

Conclusions

We create docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow the analysis and screening of data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts within genomic sequencing data is feasible.