bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing root measurements in rhizotrons
Authors: Ytting NK , Kirkegaard JA , Thorup-Kristensen K
Published: March 2019

Background and Aims

The line intersect method is widely used in rhizotron and minirhizotron studies to quantify roots and study cultivar and treatment differences in root growth. We investigated ways to optimize the line intersect method and root depth measurements with respect to data variability and the time spent on counting roots.

Methods

Root intensity was measured with three different grid patterns and different lengths of counting line on 2 m long transparent tube rhizotrons. Rooting depth was recorded by measuring the depth of the deepest root and by measuring the depth below which 5, 10 and 25 roots were observed.

Results

For root intensity the coefficient of variation (CV) was reduced 10-50 percentage points for grids that distributed counting lines equally across the measured area compared to using a restricted centralized area. In addition, the CV approached an asymptote of around 40 % when more than 50 root intersections per grid were observed. Further we show that recordings of the deepest root gave the most variance and least difference between means with a p-value of 0.65 for difference between cultivars. In contrast, a significant difference between cultivar rooting depths (p = 0.01) was found when using the depth below which 25 roots were observed.

Conclusion

We propose the use of grid designs adapted to different root densities to decrease time spent on counting roots at high root intensities, and minimize data variability at low root intensities. Further on rooting depth measurements including more roots may be a more useful parameter statistically to reveal variety or treatment differences in rooting depth.
CD16-158-Valine Chimeric Receptor T Cells Overcome the Resistance of KRAS-mutated Colorectal Carcinoma Cells to Cetuximab
Authors: Arriga Roberto , Caratelli Sara , Lanzilli Giulia , Ottaviani Alessio , Cenciarelli Carlo , Sconocchia Tommaso , Spagnoli Giulio Cesare , Iezzi Giandomenica , Roselli Mario , Lauro Davide , Dotti Gianpietro , Ferrone Soldano , Sconocchia Giuseppe
Published: March 2019

KRAS mutation hinders the therapeutic efficacy of epidermal-growth-factor-receptor (EGFR) mAb (cetuximab and panitumumab)-based immunotherapy of EGFR+ cancers. Although, cetuximab controls KRAS-mutated cancer cell growthin vitroutilizing a NK cell-mediated antibody-dependent-cellular-cytotoxicity-(ADCC) mechanism, KRAS-mutated colorectal carcinoma (CRC) cells can still escape NK cell immunosurveillance. To overcome this limitation, we used cetuximab and panitumumab to redirect Fcγ chimeric receptor (CR) T cells against KRAS-mutated HCT116 CRC cells. We compared 4 polymorphic Fcγ-CR constructs including CD16158F-CR, CD16158V-CR, CD32131H-CR, and CD32131R-CR which were transduced into T cells utilizing retroviral transduction. Percentages of transduced T cells expressing CD32131H-CR (83.5±9.5) and CD32131R–CR (77.7.±13.2) were significantly higher than those expressing with CD16158F-CR (30.3±10.2) and CD16158V-CR (51.7±13.7) (p<0.003). CD32131R-CR T cells specifically bound soluble cetuximab and panitumumab. However, only CD16158V-CR T cells released significantly higher levels of interferon gamma (IFNγ=1145.5 pg/ml ±16.5 pg/ml, p<0.001) and tumor necrosis factor alpha (TNFα=614 pg/ml ± 21 pg/ml, p<0.001) than non-transduced T cells when incubated with KRAS-mutated HCT116 cells opsonized with cetuximab. Only CD16158V-CR T cells combined with cetuximab controlled the growth of HCT116 cells subcutaneously engrafted in CB17-SCID mice. These results suggest that CD16158V-CR T cells combined with cetuximab represent useful reagents to develop an effective immunotherapy of EGFR+KRAS-mutated cancer.
Depletion of resident muscle stem cells inhibits muscle fiber hypertrophy induced by lifelong physical activity
Authors: Englund Davis A. , Murach Kevin A. , Dungan Cory M. , Figueiredo Vandré C. , Vechetti Ivan J. , Dupont-Versteegden Esther E. , McCarthy John J. , Peterson Charlotte A.
Published: March 2019

Background

A reduction in skeletal muscle stem cell (satellite cell) content with advancing age is thought to directly contribute to the progressive loss of skeletal muscle mass and function with aging (sarcopenia). However, we reported that the depletion of satellite cells throughout adulthood did not affect the onset or degree of sarcopenia observed in sedentary old mice. The current study was designed to determine if lifelong physical activity would alter the requirements for satellite cells during aging.

Methods

We administered vehicle or tamoxifen to adult (5 months old) female Pax7-DTA mice for 5 consecutive days to effectively deplete satellite cells. Following a 2-month washout period, mice were assigned to physically active (free access to a running wheel) or sedentary (locked running wheel) conditions. Thirteen months later, at a mean age of 20 months, mice were sacrificed for subsequent analysis.

Results

Satellite cell depletion throughout adulthood negatively impacted physical function and limited muscle fiber hypertrophy in response to lifelong physical activity. To further interrogate these findings, we performed transcriptome-wide analyses on the hind limb muscles that experienced hypertrophic growth (plantaris and soleus) in response to lifelong physical activity. Our findings demonstrate that satellite cell function is muscle type-specific; fusion with fibers is apparent in oxidative muscles, while initiation of Gαi2 signaling appears to require satellite cells in glycolytic muscles to induce muscle growth..

Conclusions

These findings suggest that satellite cells, or their secretory products, are viable therapeutic targets to preserve physical function with aging and promote muscle growth in older adults who regularly engage in physical activity.
Time-resolved NMR monitoring of tRNA maturation
Authors: Barraud Pierre , Gato Alexandre , Heiss Matthias , Catala Marjorie , Kellner Stefanie , Tisné Carine
Published: March 2019

Although the biological importance of post-transcriptional RNA modifications in gene expression is widely appreciated, methods to directly detect the introduction of these modifications during RNA biosynthesis are rare and do not easily provide information on the temporal nature of events. Here we introduce the application of NMR spectroscopy to observe the maturation of tRNAs in cell extracts. By following the maturation of yeast tRNAPhewith time-resolved NMR measurements, we found that modifications are introduced in a defined sequential order, and that the chronology is controlled by cross-talk between modification events. In particular, we uncovered a strong hierarchy in the introduction of the T54, Ψ55 and m1A58 modifications in the T-arm, and demonstrate that the modification circuits identified in yeast extract with NMR also impact the tRNA modification process in living cells. The NMR-based methodology presented here could be adapted to investigate different aspects of tRNA maturation and RNA modifications in general.
Development and Application of a Tri-allelic PCR Assay for ScreeningVgsc-L1014FKdrMutations Associated with Pyrethroid and Organochlorine Resistance in the MosquitoCulex quinquefasciatus
Authors: Silva Martins Walter Fabricio , Silva Pereira Bárbara Natieli , Vieira Alves Ana Thayse , Murphy Annabel , Silva Martins Paulo Geovani , Weetman David , Wilding Craig Stephen , Donnelly Martin James
Published: March 2019

Background

Culex quinquefasciatus,has a widespread distribution across tropical and sub-tropical regions, and plays an important role in the transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF) and multiple arboviruses. Increased resistance to insecticides threatens the efficacy and sustainability of insecticide-based anti-vector interventions which mitigate the burden of mosquito transmitted diseases in endemic regions. InC. quinquefasciatustwo non-synonymous voltage gated sodium channel (Vgsc) variants, both resulting in a leucine to phenylalanine change at codon 1014, are associated with resistance to pyrethroids and DDT. This tri-allelic variation has compromised the ability to perform high-throughput single-assay screening. To facilitate the detection and monitoring of theVgsc-1014 locus in field-caught mosquitoes, an Engineered-Tail Allele-Specific-PCR (ETAS-PCR) diagnostic assay was developed and applied to wild mosquitoes from Brazil, Tanzania and Uganda.

Results

This new cost-effective, single-tube assay was compared to two, well-established, genotyping approaches – pyrosequencing and TaqMan. The ETAS-PCR assay showed high specificity for discriminating the three alleles atVgsc-L1014F, with genotyping results strongly correlated with 98.64% and 100% against pyrosequencing and TaqMan, respectively.

Conclusions

Our results support the utility of the ETAS-PCR/Vgsc-1014 diagnostic assay, which stands as an effective alternative for genotyping tri-allelic variants.
Splicing conservation signals in plant long non-coding RNAs
Authors: Corona-Gomez Jose Antonio , Garcia-Lopez Irving Jair , Stadler Peter F. , Fernandez-Valverde Selene L.
Published: March 2019

Long non-coding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis. Despite their prominent functions only over a dozen lncRNAs have been experimentally and functionally characterized.

Similar to its animal counterparts, the rates of sequence divergence are much higher in plant lncRNAs than in protein coding mRNAs, making it difficult to identify lncRNA conservation using traditional sequence comparison methods. Beyond this, little is known about the evolutionary patterns of lncRNAs in plants. Here, we characterized the splicing conservation of lncRNAs in Brassicaceae. We generated a whole-genome alignment of 16 Brassica species and used it to identify synthenic lncRNA orthologues. Using a scoring system trained on transcriptomes from A. thaliana and B. oleracea, we identified splice sites across the whole alignment and measured their conservation. Our analysis revealed that 17.9% (112/627) of all intergenic lncRNAs display splicing conservation in at least one exon, an estimate that is substantially higher to previous estimates of lncRNA conservation in this group. Our findings agree with similar studies in vertebrates, demonstrating that splicing conservation can be evidence of stabilizing selection. We provide conclusive evidence for the existence of evolutionary deeply conserved lncRNAs in plants and describe a generally applicable computational workflow to identify functional lncRNAs in plants.
Familiar neighbours, but not relatives, enhance fitness in a territorial mammal
Authors: Siracusa Erin R. , Boutin Stan , Dantzer Ben , Lane Jeffrey E. , Coltman David W. , McAdam Andrew G.
Published: March 2019

One of the outstanding questions in evolutionary biology is the extent to which mutually beneficial interactions and kin-selection can facilitate the evolution of cooperation by mitigating conflict between interacting organisms. The indirect fitness benefits gained from associating with kin are an important pathway to conflict resolution [1], but conflict can also be resolved if individuals gain direct benefits from cooperating with one another (e.g. mutualism or reciprocity) [2]. Owing to the kin-structured nature of many animal societies, it has been difficult for previous research to assess the relative importance of these mechanisms [3–5]. However, one area that might allow for the relative roles of kin-selection and mutualistic benefits to be disentangled is in the resolution of conflict over territorial space [6]. While much research has focused on group-living species, the question of how cooperation can first be favoured in solitary, territorial species remains a key question. Using 22 years of data from a population of North American red squirrels, we assessed how kinship and familiarity with neighbours affected fitness in a territorial mammal. While living near kin did not enhance fitness, familiarity with neighbours increased survival and annual reproductive success. These fitness benefits were strong enough to compensate for the effects of aging later in life, with potential consequences for the evolution of senescence. We suggest that such substantial fitness benefits provide the opportunity for the evolution of cooperation between adversarial neighbours, offering insight into the role that mutually beneficial behaviours might play in facilitating and stabilizing social systems.

Graphical Abstract
Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vectorCulex quinquefasciatus
Authors: Martins Walter Fabricio Silva , Wilding Craig Stephen , Isaacs Alison Taylor , Rippon Emily Joy , Megy Karine , Donnelly Martin James
Published: March 2019

Culex quinquefasciatusplays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackleC. quinquefasciatusvectored diseases are based on either mass drug administration (MDA) for LF, or insecticide-based interventions. Widespread and intensive insecticide usage has resulted in increased resistance in mosquito vectors, includingC. quinquefasciatus. Herein, the transcriptome profile of Ugandan bendiocarb-resistantC. quinquefasciatuswas explored to identify candidate genes associated with insecticide resistance. Resistance to bendiocarb in exposed mosquitoes was marked, with 2.04% mortality following 1h exposure and 58.02% after 4h. Genotyping of the G119SAce-1target site mutation detected a highly significant association (p<0.0001; OR=25) between resistance andAce1-119S. However, synergist assays using the P450 inhibitor PBO or the esterase inhibitor TPP resulted in markedly increased mortality (to ≈80%), suggesting a role of metabolic resistance in the resistance phenotype. Using a novel, custom 60K whole-transcriptome microarray 16 genes significantly overexpressed in resistant mosquitoes were detected, with the P450Cyp6z18showing the highest differential gene expression (>8-fold increase vs unexposed controls). These results provide evidence that bendiocarb-resistance in UgandanC. quinquefasciatusis mediated by both target-site mechanisms and over-expression of detoxification enzymes.
Epigenomic Landscape ofArabidopsis thalianaMetabolism Reveals Bivalent Chromatin on Specialized Metabolic Genes
Authors: Zhao Kangmei , Rhee Seung Y.
Published: March 2019

Metabolism underpins development and physiology, but little is known about how metabolic genes and pathways are regulated, especially in multicellular organisms. Here, we identified regulatory patterns of 16 epigenetic modifications across metabolism inArabidopsis thaliana. Surprisingly, specialized metabolic genes, often involved in defense, were predominantly regulated by two modifications that have opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation). Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. Mutants defective in H3K27m3 and H3K18ac modifications showed that both modifications are required to determine the normal transcriptional kinetics of these genes upon stress stimuli. Our study suggests that this type of bivalent chromatin, which we name a kairostat, controls the precise timing of gene expression upon stimuli.

One Sentence Summary

This study identified a novel regulatory mechanism controlling specialized metabolism inArabidopsis thaliana.
Discovery of ongoing selective sweeps withinAnophelesmosquito populations using deep learning
Authors: Xue Alexander T. , Schrider Daniel R. , Kern Andrew D. ,   Ag1000G Consortium
Published: March 2019

Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introducepartialS/HIC, a deep learning method to discover selective sweeps from population genomic data.partialS/HICuses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstratepartialS/HIC’s performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by theAnopheles gambiae1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms,partialS/HICaddresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics.
Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging
Authors: Mikhaylova A. G. , Mikhailova A. A. , Ushakova K. , Tretiakov E.O. , Shamansky V. , Yurchenko A. , Zazhytska M. , Zdobnov E. , Makeev V. , Yurov V. , Tanaka M. , Gostimskaya I. , Fleischmann Z. , Annis S. , Franco M. , Wasko K. , Kunz W.S , Knorre D.A. , Mazunin I. , Nikolaev S. , Fellay J. , Reymond A. , Khrapko K. , Gunbin K. , Popadin K.
Published: March 2019

Mutational spectrum of the mitochondrial genome (mtDNA) does not resemble signatures of any known mutagens and variation in mtDNA mutational spectra between different tissues and organisms is still incomprehensible. Since mitochondria is tightly involved in aerobic energy production, it is expected that mtDNA mutational spectra may be affected by the oxidative damage which is increasing with cellular and organismal aging. However, the well-documented mutational signature of the oxidative damage, G>T substitutions, is typical only for the nuclear genome while it is extremely rare and age-independent in mtDNA. Thus it is still unclear if there is a mitochondria - specific mutational signature of the oxidative damage. Here, reconstructing mtDNA mutational spectra for human cancers originated from 21 tissues with various cell turnover rate, human oocytes fertilized at different ages, and 424 mammalian species with variable generation length which is a proxy for oocyte age, we observed that the frequency of AH>GHsubstitutions (H- heavy chain notation) is positively correlated with cellular and organismal longevity. Moreover, this mutational bias from AHto GHaffects nucleotide content at the fourfold degenerative synonymous positions leading to a deficit of AHand excess of GH, which is especially pronounced in long-lived mammals. Taking into account additionally, that AH>GHis sensitive to time being single stranded during mtDNA asynchronous replication and A>G is associated with oxidative damage of single-stranded DNA in recent bacterial experiments we propose that AH>GHis a mutational signature of oxidative damage in mtDNA.
Identification of PKCα-dependent phosphoproteins in mouse retina
Authors: Wakeham Colin M. , Wilmarth Phillip A. , Cunliffe Jennifer M. , Klimek John E. , Ren Gaoying , David Larry L. , Morgans Catherine W.
Published: March 2019

Adjusting to a wide range of light intensities is an essential feature of retinal rod bipolar cell (RBC) function. While persuasive evidence suggests this modulation involves phosphorylation by protein kinase C-alpha (PKCα), the targets of PKCα phosphorylation in the retina have not been identified. PKCα activity and phosphorylation in RBCs was examined by immunofluorescence confocal microscopy using a conformation-specific PKCα antibody and antibodies to phosphorylated PKC motifs. PKCα activity was dependent on light and expression of TRPM1, and RBC dendrites were the primary sites of light-dependent phosphorylation. PKCα-dependent retinal phosphoproteins were identified using a phosphoproteomics approach to compare total protein and phosphopeptide abundance between phorbol ester-treated wild type and PKCα knockout (PKCα-KO) mouse retinas. Phosphopeptide mass spectrometry identified over 1100 phosphopeptides in mouse retina, with 12 displaying significantly greater phosphorylation in WT compared to PKCα-KO samples. The differentially phosphorylated proteins fall into the following functional groups: cytoskeleton/trafficking (4 proteins), ECM/adhesion (2 proteins), signaling (2 proteins), transcriptional regulation (3 proteins), and homeostasis/metabolism (1 protein). Two strongly differentially expressed phosphoproteins, BORG4 and TPBG, were localized to the synaptic layers of the retina, and may play a role in PKCα-dependent modulation of RBC physiology. Data are available via ProteomeXchange with identifier PXD012906.

Significance

Retinal rod bipolar cells (RBCs), the second-order neurons of the mammalian rod visual pathway, are able to modulate their sensitivity to remain functional across a wide range of light intensities, from starlight to daylight. Evidence suggests that this modulation requires the serine/threonine kinase, PKCα, though the specific mechanism by which PKCα modulates RBC physiology is unknown. This study examined PKCα phosophorylation patterns in mouse rod bipolar cells and then used a phosphoproteomics approach to identify PKCα-dependent phosphoproteins in the mouse retina. A small number of retinal proteins showed significant PKCα-dependent phosphorylation, including BORG4 and TPBG, suggesting a potential contribution to PKCα-dependent modulation of RBC physiology.

Highlights

PKCα is a major source of phosphorylation in retinal RBC dendrites and its activity in RBCs is light dependent.

Proteins showing differential phosphorylation between phorbol ester-treated wild type and PKCα-KO retinas belong to the following major functional groups: cytoskeleton/trafficking (4 proteins), ECM/adhesion (2 proteins), signaling (2 proteins), transcriptional regulation (3 proteins), and homeostasis/metabolism (1 protein).

The PKCα-dependent phosphoproteins, BORG4 and TPBG, are present in the synaptic layers of the retina and may be involved in PKCα-dependent modulation of RBC physiology.
A chemical counterpunch:Chromobacterium violaceumATCC31532 produces violacein in response to translation-inhibiting antibiotics
Authors: Lozano Gabriel L. , Guan Changhui , Cao Yanzhuan , Borlee Bradley R. , Broderick Nichole A. , Stabb Eric V. , Handelsman Jo
Published: March 2019

Bacterially produced antibiotics play important roles in microbial interactions and competition. Antibiosis can induce resistance mechanisms in target organisms and may induce other countermeasures as well. Here, we show that hygromycin A fromStreptomycessp. 2AW inducesChromobacterium violaceumATCC31532 to produce the purple antibiotic violacein. Sublethal doses of other antibiotics that similarly target the polypeptide elongation step of translation likewise induced violacein production, unlike antibiotics with different targets.C. violaceumbiofilm formation and virulence againstDrosophila melanogasterwere also induced by translation-inhibiting antibiotics, and we identified anantibiotic-inducedresponse (air) two-component regulatory system that is required for these responses. Genetic analyses indicated a connection between the Air system, quorum-dependent signaling, and the negative regulator VioS, leading us to propose a model for induction of violacein production. This work suggests a novel mechanism of interspecies interaction in which a bacterium produces an antibiotic in response to inhibition by another bacterium.
Ray tracing 3D spectral scenes through human optics models
Authors: Lian Trisha , MacKenzie Kevin J. , Brainard David H. , Cottaris Nicolas P. , Wandell Brian A.
Published: March 2019

Scientists and engineers have created computations and made measurements that characterize the first steps of seeing. ISETBio software integrates such computations and data into an open-source software package. The initial ISETBio implementations modeled image formation (physiological optics) for planar or distant scenes. The ISET3d software described here extends that implementation, simulating image formation for three-dimensional scenes. The software system relies on a quantitative computer graphics program that ray traces the scene radiance through the physiological optics to the retinal irradiance. We describe and validate the implementation for several model eyes. Then, we use the software to quantify the impact of several physiological optics parameters on three-dimensional image formation. ISET3d is integrated with ISETBio, making it straightforward to convert the retinal irradiance into cone excitations. These methods help the user compute the predictions of optics models for a wide range of spatially-rich three-dimensional scenes. They can also be used to evaluate the impact of nearby visual occlusion, the information available to binocular vision, or the retinal images expected from near-field and augmented reality displays.
Cortical changes associated with parenthood are present in late life
Authors: Orchard Edwina R , Ward Phillip GD , Sforazzini Francesco , Storey Elsdon , Egan Gary F , Jamadar Sharna D
Published: March 2019

Early parenthood results in changes in cortical thickness in regions related to parental care. However, the enduring effects of this period on the structure of the human brain, and cognition in late-life, is unknown. In an elderly sample, we examined the relationship between the number of children parented (here, 1-6 children) and cortical thickness in 267 males (74.0 ±3.5 years) and 231 females (73.8±3.5 years). We also compared cognition and cortical thickness between parents of one child and non-parents, in n=36 males (73.4±3.7 years), and n=46 females (72.8±3.3 years). We obtained a positive relationship between number of children parented and verbal memory performance, showing increasing memory performance with number of children. For mothers, number of children positively correlated with cortical thickness in the parahippocampal gyrus and negatively correlated with regions of the visual cortex. Mothers of one child showed thinner cortical thickness in the dorsolateral prefrontal cortex and visual cortex compared with childless women. Fathers of one child showed thinner cortical thickness in the anterior cingulate cortex and thicker cortical thickness in the temporal pole compared with childless men. Our results are the first to reveal distributed differences in cortical thickness related to parenthood that are evident beyond the postpartum period. Our findings overlap substantially with the areas found to be altered across pregnancy and the postpartum period, suggesting that neural changes associated with early parenthood persist into older age, and are potentially cognitively beneficial.
Brodifacoum does not modulate human cannabinoid receptor-mediated hyperpolarization of AtT20 cells or inhibition of adenylyl cyclase in HEK 293 cells
Authors: Sachdev Shivani , Boyd Rochelle , Grimsey Natasha L , Connor Mark
Published: March 2019

Background

Synthetic cannabinoids are a commonly used class of recreational drugs that can have significant adverse effects. There have been sporadic reports of co-consumption of illicit drugs with rodenticides such as warfarin and brodifacoum (BFC) over the past 20 years but recently, hundreds of people have been reported to have been poisoned with a mixture of synthetic cannabinoids and BFC. We have sought to establish whether BFC directly affects cannabinoid receptors, or their activation by the synthetic cannabinoid CP55940 or the phytocannabinoid Δ9-tetrahydrocannabinol (Δ9-THC).

Methods

The effects of BFC on the hyperpolarization of wild type AtT20 cells, or AtT20 cells stably expressing human CB1- and CB2-mediated receptors, were studied using a fluorescent assay of membrane potential. The effects of BFC on CB1and CB2mediated inhibition of forskolin-stimulated adenylyl cyclase (AC) activation was measured using a BRET assay of cAMP levels in HEK 293 cells stably expressing human CB1and CB2.

Results

BFC did not activate CB1or CB2receptors, or affect the hyperpolarization of wild type AtT20 cells produced by somatostatin. BFC (10µM) did not affect the hyperpolarization of AtT20-CB1or AtT20-CB2cells produced by CP55940 or Δ9-THC. BFC (1µM) did not affect the inhibition of forskolin-stimulated AC activity by CP55940 in HEK 293 cells expressing CB1or CB2. BFC (1µM) also failed to affect the desensitization of CB1and CB2signalling produced by prolonged (30 min) application of CP55940 or Δ9-THC to AtT20 cells.

Discussion

BFC is not a cannabinoid receptor agonist, and appeared not to affect cannabinoid receptor activation. Our data suggests there is no pharmacodynamic rationale for mixing BFC with synthetic cannabinoids, however, it does not speak to whether BFC may affect synthetic cannabinoid metabolism or biodistribution. The reasons underlying the mixing of BFC with synthetic cannabinoids are unknown, and it remains to be established whether the “contamination” was deliberate or accidental. However, the consequences for people who ingested the mixture were often serious, and sometimes fatal, but this seems unlikely to be due to BFC action at cannabinoid receptors.
VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure
Authors: Xu Kui , Liu Nan , Xu Jingle , Guo Chunlong , Zhao Lingyun , Wang Hong-Wei , Zhang Qiangfeng Cliff
Published: March 2019

Past decades have seen much effort devoted to the tool development for biomacromolecule structural visualization and analysis. In recent years, we have witnessed tremendous advancement in computational technologies, especially in graphics and internet. Here we present an integrative cloud-based, virtual reality (VR) system -- VRmol that exploits these technology advances to visualize and study macromolecule structures in various forms. The immersive environment can improve user experiences in visualization, calculation, and editing of complex structures with more intuitive perception. VRmol is also a system with cloud-based capability to directly access disease-related databases, and couples the structure with genomic variation as well corresponding drugs information in a visual interface, thus serving as an integrative platform to aid structure-based translational research and drug design. VRmol is freely available athttps://VRmol.net.
Phospho-tuning immunity through Denisovan, modern human and mouse TNFAIP3 gene variants
Authors: Zammit Nathan W. , Siggs Owen M. , Gray Paul , Horikawa Keisuke , Daley Stephen R. , Langley David B. , Cultrone Daniele , Malle Elisabeth K. , Walters Stacey N. , Villanueva Jeanette E. , Warren Joanna , Russell Amanda , Cowley Mark J. , Gayevskiy Velimir , Dinger Marcel E. , Loetsch Claudia , King Cecile , Brink Robert , Zahra David , Chaudhri Geeta , Karupiah Gunasegaran , Whittle Belinda , Roots Carla , Bertram Edward , Yamada Michiko , Jeelall Yogesh , Enders Anselm , Clifton Benjamin E. , Mabbitt Peter D. , Jackson Colin J. , Watson Susan R. , Jenne Craig N. , Lanier Lewis L. , Wiltshire Tim , Spitzer Matthew H. , Nolan Garry P. , Schmitz Frank , Aderem Alan , Porebski Benjamin T. , Buckle Ashley M. , Abbott Derek W. , Ziegler John B. , Craig Maria E. , Benitez-Aguirre Paul , Teo Juliana , Wong Melanie , Cox Murray P. , Phung Wilson , Wertz Ingrid E. , Christ Daniel , Goodnow Christopher C. , Grey Shane T.
Published: March 2019

Resisting or tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here, genomic analyses of anatomically modern humans, extinct Denisovan hominins, and mice revealed a series of missense variants in the immune response inhibitor A20 (encoded byTNFAIP3), substituting non-catalytic residues of the ubiquitin protease domain to diminish IκB-dependent phosphorylation and activation of A20. Two A20 variants with partial phosphorylation deficits appeared beneficial: one originating in Denisovans and introgressed in modern humans throughout Oceania, and another in a mouse strain resistant to Coxsackievirus. By contrast, a variant with 95% loss of phosphorylation caused spontaneous inflammatory disease in humans and mice. Analysis of the partial phosphorylation variant in mice revealed diminished tolerance of bacterial lipopolysaccharide or to poxvirus inoculation as trade-offs for enhanced immunity.

One Sentence Summary

Modern and ancient variants reveal a genetically tunable element for balancing immunity and microbial tolerance.
A model of collective behavior based purely on vision
Authors: Bastien Renaud , Romanczuk Pawel
Published: March 2019

Classical models of collective behavior often take a “birds-eye perspective,” assuming that individuals have access to social information that is not directly available (e.g., the behavior of individuals outside of their field of view). Despite the explanatory success of those models, it is now thought that a better understanding needs to incorporate of the perception of the individual, i.e. how internal and external information are acquired and processed. In particular, vision has appeared to be a central feature to gather external information and influence the collective organization of the group. Here we show that a vision based model of collective behavior is sufficient to generate organized collective behavior in the absence of spatial representation and collision. Our work suggests a novel approach for development of purely vision-based autonomous swarm robotic systems, and formulates a mathematical framework for exploration of perception-based interactions and how they differ from physical ones. Thus, it is of broader relevance for self-organization in complex systems, neuroscience, behavioral sciences and engineering.
Observing an antisense drug complex in intact human cells by in-cell NMR
Authors: Schlagnitweit Judith , Sandoz Sarah Friebe , Jaworski Aleksander , Guzzetti Ileana , Aussenac Fabien , Carbajo Rodrigo J. , Chiarparin Elisabetta , Pell Andrew J. , Petzold Katja
Published: March 2019

Gaining insight into the uptake of drugs into cells, trafficking and their target engagement enhances understanding of the drug’s function and efficiency. Here we study an antisense oligonucleotide drug (ASO) delivered into HEK293T and HeLa cells, by Nuclear Magnetic Resonance (NMR). Using a combination of transfection, cryoprotection and dynamic nuclear polarization (DNP), we were able to detect the drug directly in intact frozen cells. Activity of the drug was confirmed by qRT-PCR, measuring downregulation of its target mSTAT3. Applying DNP NMR to frozen cells, we overcome limitations of traditional solution-state in-cell NMR (e.g. size, stability and sensitivity) as well as of visualization techniques, where (e.g. fluorescent) tagging of the ASO decreases its activity. The possibility to study an untagged, active drug, interacting in its natural environment, will increase insights into molecular mechanisms of delivery, intracellular trafficking and target engagement in intact cells.
Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments
Authors: Tariel Juliette , Plénet Sandrine , Luquet Émilien
Published: March 2019

While an increasing number of studies highlights that parental environment shapes offspring phenotype (transgenerational plasticity TGP), TGP beyond the parental generation has received less attention. Studies suggest that TGP impacts population dynamics and evolution of phenotype, but these impacts will depend on how long an environmental effect can persist across generations and whether multigenerational effects are cumulative. Here we tested the impact of both grand-parental and parental environments on offspring reaction norm in a prey-predator system. We exposed three generations ofPhysa acutasnails without and with predator-cues according to a full factorial design and measured offspring inducible defenses. We found that both grand-parental and parental exposure to predator cues impacted offspring anti-predator defenses, but their effects were not cumulative and depended on the defenses considered. We also highlighted that grand-parental environment could alter reaction norm of offspring shell thickness, demonstrating an interaction between the grand-parental TGP and the within-generational WGP plasticity. We called for more studies covering the combine effects of multigenerational environments.
The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris
Authors: Bebane P.S.A , Hunt B.J. , Pegoraro M. , Jones A.R.C , Marshall H. , Rosato E. , Mallon E.B.
Published: March 2019

Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff tailed bumblebee Bombus terrestris workers exposed to field realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
Macro-to-nano scale investigation of wall-plate joints in the acorn barnacle Semibalanus balanoides: correlative imaging, biological form and function, and bioinspiration
Authors: Mitchell R.L , Coleman M. , Davies P. , North L. , Pope E.C. , Pleydell-Pearce C. , Harris W. , Johnston R.
Published: March 2019

1.

Correlative imaging combines information from multiple modalities (physical-chemical-mechanical properties) at various length-scales (cm to nm) to understand complex biological materials across dimensions (2D-3D). Here, we have used numerous coupled systems: X-ray microscopy (XRM), scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), optical light microscopy (LM), and focused-ion beam (FIB-SEM) microscopy to ascertain the microstructural and crystallographic properties of the wall-plate joints in the barnacle Semibalanus balanoides. The exoskeleton is composed of six interlocking wall-plates, and the interlocks between neighbouring plates (alae) allow barnacles to expand and grow whilst remaining sealed and structurally strong. Our results indicate that the ala contain functionally-graded orientations and microstructures in their crystallography, which has implications for naturally functioning microstructures, potential natural strengthening, and preferred oriented biomineralisation. Elongated grains at the outer edge of the ala are oriented perpendicularly to the contact surface, and the c-axis rotates with the radius of the ala. Additionally, we identify for the first time three-dimensional nano-scale ala pore networks revealing that the pores are only visible at the tip of the ala, and that pore thickening occurs on the inside (soft-bodied) edge of the plates. The pore networks appear to have the same orientation as the oriented crystallography, and we deduce that the pore networks are probably organic channels and pockets which are involved with the biomineralisation process. Understanding these multi-scale features contributes towards an understanding of the structural architecture in barnacles, but also their consideration for bioinspiration of human-made materials. The work demonstrates that correlative methods spanning different length-scales, dimensions and modes enable the extension of structure-property relationships in materials to form and function of organisms.
Denoising of Aligned Genomic Data
Authors: Fischer-Hwang Irena , Ochoa Idoia , Weissman Tsachy , Hernaez Mikel
Published: March 2019

Noise in genomic sequencing data is known to have effects on various stages of genomic data analysis pipelines. Variant identification is an important step of many of these pipelines, and is increasingly being used in clinical settings to aid medical practices. We propose a denoising method, dubbed SAMDUDE, which operates on aligned genomic data in order to improve variant calling performance. Denoising human data with SAMDUDE resulted in improved variant identification in both individual chromosome as well as whole genome sequencing (WGS) data sets. In the WGS data set, denoising led to identification of almost 2,000 additional true variants, and elimination of over 1,500 erroneously identified variants. In contrast, we found that denoising with other state-of-the-art denoisers significantly worsens variant calling performance. SAMDUDE is written in Python and is freely available athttps://github.com/ihwang/SAMDUDE.
A Membrane-Bound Cytochrome EnablesMethanosarcina acetivoransto Conserve Energy to Support Growth from Extracellular Electron Transfer
Authors: Holmes Dawn E , Ueki Toshiyuki , Tang Hai-Yan , Zhou Jinjie , Smith Jessica A , Chaput Gina , Lovley Derek R
Published: March 2019

Conservation of energy to support growth solely from extracellular electron transfer was demonstrated for the first time in a methanogen.Methanosarcina acetivoransgrew with methanol as the sole electron donor and the extracellular electron acceptor anthraquione-2,6-disulfonate (AQDS) as the sole electron acceptor when methane production was inhibited with bromoethanesulfonate. Transcriptomics revealed that transcripts for the gene for the transmembrane, multi-heme,c-type cytochrome MmcA were 4-fold higher in AQDS-respiring cells versus methanogenic cells. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction whereas strains in which other cytochrome genes were deleted grew as well as the wild-type strain. The MmcA-deficient strain grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and components of the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenezyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation ofM. acetivoransmakes it an excellent model microbe for evaluatingc-type cytochrome-dependent extracellular electron transfer in Archaea.

Importance

Extracellular electron exchange inMethanosarcinaspecies and closely related Archaea plays an important role in the global carbon cycle and can enhance the speed and stability of anaerobic digestion, an important bioenergy strategy. The potential importance ofc-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea has been suspected for some time, but the studies withMethanosarcina acetivoransreported here provide the first genetic evidence supporting this hypothesis. The results suggest parallels with Gram-negative bacteria, such asShewanellaandGeobacterspecies, in which outer-surfacec-type cytochromes are an essential component for electrical communication with the extracellular environment.M. acetivoransoffers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens, but possibly also for anaerobic methane oxidation.
DEEPCON: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout
Authors: Adhikari Badri
Published: March 2019

Background

Exciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural network methods (ConvNets) may be best designed and developed to solve this long-standing problem.

Method

With publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts, and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods.

Results

The proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3,456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1,426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. DEEPCON will be made publicly available athttps://github.com/badriadhikari/DEEPCON/.