bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel protein complex that regulates active DNA demethylation inArabidopsis
Authors: Liu Pan , Nie Wen-Feng , Xiong Xiansong , Wang Yuhua , Jiang Yuwei , Huang Pei , Lin Xueqiang , Qin Guochen , Huang Huan , Niu Qingfeng , Du Jiamu , Lang Zhaobo , Lozano-Duran Rosa , Zhu Jian-Kang
Published: February 2020

Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic regions inArabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of anArabidopsisprotein complex that contains ROS1, regulatesROS1gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its functionin vivo.Loss-of-function mutations inRWD40, RMB1, orRHD1cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in theROS1promoter, plants mutated inRWD40, RMB1, orRHD1show increasedROS1expression. Importantly, ROS1 binding to theROS1promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci inArabidopsis.
Sedation modulates fronto-temporal predictive coding circuits and the double surprise acceleration effect
Authors: Witon Adrien , Shirazibehehsti Amirali , Cooke Jennifer , Aviles Alberto , Adapa Ram , Menon David K. , Chennu Srivas , Bekinschtein Tristan , Lopez Jose David , Litvak Vladimir , Li Ling , Friston Karl , Bowman Howard
Published: February 2020

Two important theories in cognitive neuroscience are predictive coding and the global workspace theory. A key research task is to understand how these two theories relate to one another, and particularly, how the brain transitions from a predictive early state to the eventual engagement of a brain-scale state (the global workspace). To address this question, we present a source-localisation of EEG responses evoked by the local-global task – an experimental paradigm that engages a predictive hierarchy, which encompasses the global workspace. The results of our source reconstruction suggest three-phases of processing. The first phase involves the sensory (here auditory) regions of the superior temporal lobe and predicts sensory regularities over a short timeframe (as per the local effect). The third phase is brain-scale, involving inferior frontal, as well as inferior and superior parietal regions; consistent with a global neuronal workspace (as per the global effect). Crucially, our analysis suggests that there is an intermediate (second) phase, involving modulatory interactions between inferior frontal and superior temporal regions. Furthermore, sedation with propofol reduces modulatory interactions in the second phase. This selective effect is consistent with a predictive coding explanation of sedation, with propofol acting on descending predictions of the precision of prediction errors; thereby constraining access to the global neuronal workspace.
Tissue-specific volatile-mediated defense regulation in maize leaves and roots
Authors: van Doan Cong , Züst Tobias , Maurer Corina , Zhang Xi , Machado Ricardo A.R. , Mateo Pierre , Ye Meng , Schimmel Bernardus C.J. , Glauser Gaétan , Robert Christelle A.M.
Published: February 2020

Plant leaves that are exposed to herbivore induced plant volatiles (HIPVs) respond by increasing their defenses. Whether this phenomenon also occurs in the roots is unknown.

Using maize (Zea mays), whose leaves respond strongly to leaf HIPVs, we measured the impact of root HIPVs, emanating from plants infested by the banded cucumber beetle (Diabrotica balteata), on constitutive and herbivore-induced levels of root soluble sugars, starch, total soluble proteins, free amino acids, volatile and non-volatile secondary metabolites, defense gene expression, growth and root herbivore resistance of neighboring plants.

HIPV exposure did not alter constitutive or induced levels of any of the measured root traits. Furthermore, HIPV exposure did not reduce the performance and survival of banded cucumber beetle larvae on maize or teosinte. Cross-exposure experiments revealed that maize roots, in contrast to maize leaves, neither emit nor respond strongly to defense-regulating HIPVs.

Together, these results demonstrate that volatile-mediated defense regulation is restricted to the leaves of maize and teosinte, a finding which is in line with the lower diffusibility of volatiles in the soil and the availability of other, potentially more efficient information conduits below ground.
Systematic functional analysis of Rab GTPases reveals limits of neuronal robustness inDrosophila
Authors: Kohrs Friederike E. , Daumann Ilsa-Maria , Pavlović Bojana , Jin Eugene Jennifer , Lin Shih-Ching , Port Fillip , Kiral F. Ridvan , Wolfenberg Heike , Mathejczyk Thomas F. , Chan Chih-Chiang , Boutros Michael , Hiesinger P. Robin
Published: February 2020

Rab GTPases are molecular switches that regulate membrane trafficking in all cells. Neurons have particular demands on membrane trafficking and express numerous Rab GTPases of unknown function. Here we report the generation and characterization of molecularly defined null mutants for all 26rabgenes inDrosophila. In addition, we created a transgenic fly collection for the acute, synchronous release system RUSH for all 26 Rabs. In flies, allrabgenes are expressed in the nervous system where at least half exhibit particularly high levels compared to other tissues. Surprisingly, loss of any of these 13 nervous-system enriched Rabs yields viable and fertile flies without obvious morphological defects. However, 9 of these 13 affect either developmental timing when challenged with different temperatures, or neuronal function when challenged with continuous stimulation. These defects are non-lethal under laboratory conditions, but represent sensitized genetic backgrounds that reveal limits of developmental and functional robustness to environmental challenges. Interestingly, the neuronalrab26was previously proposed to function in synaptic maintenance by linking autophagy and synaptic vesicle recycling and we identifiedrab26as one of sixrabmutants with reduced synaptic function under continuous stimulation conditions. However, we found no changes to autophagy or synaptic vesicle markers in therab26mutant, but instead a cell-specific role in membrane receptor turnover associated with cholinergic synapses in the fly visual system. Our systematic functional analyses suggest that several Rabs ensure robust development and function under varying environmental conditions. The mutant and transgenic fly collections generated in this study provide a basis for further studies of Rabs during development and homeostasisin vivo.
Gene expression has more power for predictingin vitrocancer cell vulnerabilities than genomics
Authors: Dempster Joshua M. , Krill-Burger John M. , McFarland James M. , Warren Allison , Boehm Jesse S. , Vazquez Francisca , Hahn William C. , Golub Todd R. , Tsherniak Aviad
Published: February 2020

Achieving precision oncology requires accurate identification of targetable cancer vulnerabilities in patients. Generally, genomic features are regarded as the state-of-the-art method for stratifying patients for targeted therapies. In this work, we conduct the first rigorous comparison of DNA- and expression-based predictive models for viability across five datasets encompassing chemical and genetic perturbations. We find that expression consistently outperforms DNA for predicting vulnerabilities, including many currently stratified by canonical DNA markers. Contrary to their perception in the literature, the most accurate expression-based models depend on few features and are amenable to biological interpretation. This work points to the importance of exploring more comprehensive expression profiling in clinical settings.
Medium spiny neurons activity reveals the discrete segregation of mouse dorsal striatum
Authors: Alegre-Cortés J. , Sáez M. , Montanari R. , Reig R.
Published: February 2020

Behavioural studies differentiate the rodent dorsal striatum (DS) into lateral and medial regions; however, anatomical evidence suggests that it is a unified structure. To understand striatal dynamics and basal ganglia functions, it is essential to clarify the circuitry that supports this behavioural-based segregation. Here, we show that the mouse DS is made of two non-overlapping functional circuits divided by a boundary. Combiningin vivooptopatch-clamp and extracellular recordings of spontaneous and evoked sensory activity, we demonstrate different coupling of lateral and medial striatum to the cortex together with an independent integration of the spontaneous activity, due to particular corticostriatal connectivity and local attributes of each region. Additionally, we show differences in slow and fast oscillations and in the electrophysiological properties between striatonigral and striatopallidal neurons. In summary, these results demonstrate that the rodent DS is segregated in two neuronal circuits, in homology with the caudate and putamen nuclei of primates.
Genetic factors outside the metabolic cluster for plastid-derived sesquiterpenes are required to pursue arthropod-resistant tomatoes
Authors: Therezan Rodrigo , Kortbeek Ruy , Vendemiatti Eloisa , Legarrea Saioa , de Alencar Severino M. , Schuurink Robert , Bleeker Petra , Peres Lázaro E. P.
Published: February 2020

To deal with arthropod pests the tomato wild relatives produce a variety of defense compounds in their glandular trichomes. InSolanum habrochaitesLA1777, a functional cluster of genes on chromosome 8 controls plastid-derived sesquiterpene synthesis not found in cultivated tomatoes. The main genes at the cluster areZ-prenyltransferase (zFPS)that producesZ-Z-farnesyl diphosphate (Z,Z-FPP), andSantalene and Bergamotene Synthase(SBS) that usesZ,Z-FPP to produce α-santalene, β-bergamotene, and α-bergamotene in type-VI glandular trichomes. Both LA1777 and cultivated tomatoes have type-VI trichomes, but the gland in cultivated tomato is much smaller containing low levels of monoterpenes and cytosolic-derived sesquiterpenes, which do not provide tomato with the same pest resistance as in LA1777. We successfully transferred the plastid-derived sesquiterpene pathway from LA1777 to type-VI trichomes of a cultivated tomato (cv. Micro-Tom, MT) by a back-crossing approach. The trichomes of the introgressed line named MT-Sesquiterpene synthase 2(MT-Sst2) produced even higher levels of α-santalene, β-bergamotene, and α-bergamotene than the type-VI glandular trichomes of LA1777. We also noticed that the type-VI trichome internal storage-cavity size increases in MT-Sst2, probably as an “inflated balloon” effect of the increased amount of sesquiterpenes. Surprisingly, the presence of high amounts of plastid-derived sesquiterpenes was not sufficient to confer resistance to various tomato pests in MT-Sst2. Since MT-Sst2made the same sesquiterpenes as LA1777, this points to additional factors, outside the genomic region thought to be the metabolic cluster, necessary to obtain arthropod-resistant tomatoes. Our results also provide a better understanding of the morphology ofS. habrochaitestype-VI trichomes.

One-sentence summary

Cultivated tomatoes harboring the plastid-derived sesquiterpenes fromS. habrochaitesneed additional genetic components necessary to convert them into effective insecticides.
Leading-edge VASP clusters assemble at sites containing lamellipodin and exhibit size-dependent instability
Authors: Cheng Karen W. , Mullins R. Dyche
Published: February 2020

The shape of many eukaryotic cells depends on the actin cytoskeleton; and localized changes in actin assembly dynamics underlie many changes in cell shape. Polymerases of the Ena/VASP family modulate cell shape by locally accelerating actin filament assembly and slowing filament capping. When concentrated into discrete foci at the leading edge, VASP promotes formation of filopodia, but the mechanisms that drive VASP clustering are poorly understood. Here we show that, in migrating B16F1 cells, VASP molecules assemble on pre-existing foci of the adaptor protein, lamellipodin, and that dimerization of lamellipodin is essential for cluster formation. VASP/lamellipodin clusters grow by accumulating monomers and by fusing, but their growth is limited by a previously undescribed, size-dependent instability. Our results demonstrate that assembly and disassembly dynamics of filopodia tip complexes are determined, in part, by a network of multivalent interactions between VASP, lamellipodin, and actin.
Perturbation of GABA Biosynthesis Links Cell Cycle to ControlArabidopsis thalianaLeaf Development
Authors: Gong Yaxin , Yue Han , Xiang Yu , Yu Guanghui
Published: February 2020

To investigate the molecular mechanism underlying increasing leaf area in γ-Aminobutyric acid (GABA) biosynthetic mutants, the first pair of true leaves of GABA biosynthetic mutants was measured. The results showed that the leaf blade area in GABA biosynthetic mutants was larger than that of the wild type to different extents, and the area of the leaf epidermal cells in mutants was larger than that of the wild type. DNA polyploid analysis showed that polyploid cells in GABA biosynthetic mutants were appearing earlier and more abundant than in the wild type. To check the correlation between cell size and endoreplication, the expression of factors involving endocycles, including D-type cyclin gene (CYCD3;1, CYCD3;2, CYCD3;3, andCYCD4;1) and kinaseCKDA;1, were analysed by qRT-PCR. The results showed thatCKDA;1in GABA biosynthetic mutants was downregulated, and four types ofCYCDsshowed different expression patterns in different GABA biosynthetic mutants. Inconsistent with this result, forCCS52A(CELL CYCLE SWITCH 52A) (controlling the endocycle entry) ingad2andgad1/gad2mutants, the expression ofCCS52A2was significantly higher than that in the wild type. The expression ofSIM(SIAMESE) andSMR(SIAMESE-RELATED), which inhibit kinase activity, were also upregulated compared with the control. To further study the possible potential relationship between GABA metabolism and endoreplication, we analysed the reactive oxygen species (ROS) levels in guard cells using ROS fluorescent probes. ROS levels were significantly higher in GABA biosynthetic mutants than the control. All results indicated that cyclin, the cyclin-dependent kinase, and its inhibitory protein were coordinated to participate in endoreplication control at the transcription level in the leaves of GABA biosynthetic mutantArabidopsis.

Contribution to the field statement

γ-Aminobutyric acid (GABA) metabolic pathway plays a dual role in plant development. This research investigated the perturbation of GABA biosynthesis onArabidopsisleave endoreplication for the first time. In the GABA biosynthetic mutants, many genes, participating in cell division regulation, are coordinately transcriptionally expressed to trigger the onset and maintenance of endoreplication, and this led to the cell expansion and the increase leaf blade area. However, this initiation of endoreplication links with the decrease of endogenous GABA level and the increase Reactive oxygen species (ROS). This may be a compensation mechanism to adapt to abnormal GABA level in plant leaf development. Present evidence provided hypothesized that the normal GABA level in plant leaf development plays a brake to inhibit the immature cell expansion and differentiation, and this negative regulation functions a guarantee mechanism to watchdog the normal leaf development. In all, this contribution provides an updated perspective on the role of GABA in plant development.
Integrated decoding hematopoiesis and leukemogenesis at single-cell resolution and its clinical implication
Authors: Qin Pengfei , Pang Yakun , Hou Wenhong , Fu Ruiqing , Zhang Yingchi , Wang Xuefei , Meng Guofeng , Liu Qifa , Zhu Xiaofan , Hong Ni , Cheng Tao , Jin Wenfei
Published: February 2020

Integrated analyses of hematopoiesis and leukemogenesis could provide new biological and clinical insights1,2. Here we constructed a comprehensive cell atlas using ∼100,000 single cell transcriptomes of bone marrow mononuclear cells and its subsets from 5 healthy samples and 13 leukemia samples. Trajectory analysis showed hematopoietic stem cells continuously differentiated through tree-like structure into 7 lineages. Although our single cell analyses showed the major cellular heterogeneity were inter-patients, there were distinct leukemia cell subpopulations within patient. We developed counterpart composite index (CCI) for projecting leukemia cell subpopulation into reference hematopoietic cells, to identify their healthy counterparts that could predict leukemia subtype and clinical outcome. Interestingly, we found the trajectories of leukemogenesis were similar to that of their healthy counterparts, indicating lineage relationship of leukemia cell subpopulations. Single cell analyses of leukemia patient at diagnosis, refractory, remission and relapse vividly presented dynamics of cell population and the underlying genes. Single cell transcriptomic variants analyses showed the relapsed leukemia cells, whose healthy counterparts were closer to the root of hematopoietic tree, were derived from an early minor leukemia cell population. This study not only increased our understanding of hematopoiesis and leukemogenesis, but also provided an approach for leukemia classification and clinical outcome prediction.
Evolutionarily conserved regulation of embryonic fast-twitch skeletal muscle differentiation by Pbx factors
Authors: Farr Gist H. , Li Bingsi , Risolino Maurizio , Johnson Nathan M. , Yao Zizhen , Kao Robert M. , Majesky Mark W. , Tapscott Stephen J. , Selleri Licia , Maves Lisa
Published: February 2020

Vertebrate skeletal muscles are composed of both slow-twitch and fast-twitch fiber types. How the differentiation of distinct fiber types is activated during embryogenesis is not well characterized. Skeletal muscle differentiation is initiated by the activity of the myogenic basic helix-loop-helix (bHLH) transcription factors Myf5, Myod1, Myf6, and Myog. Myod1 functions as a muscle master regulatory factor and directly activates muscle differentiation genes, including those specific to both slow and fast muscle fibers. Our previous studies showed that Pbx TALE-class homeodomain proteins bind with Myod1 on the promoter of the zebrafish fast muscle genemylpfaand are required for proper activation ofmylpfaexpression and the fast-twitch muscle-specific differentiation program in zebrafish embryos. Pbx proteins have also been shown to bind regulatory regions of muscle differentiation genes in mammalian muscle cells in culture. Here, we use new zebrafish mutant strains to confirm the essential roles of zebrafish Pbx factors in embryonic fast muscle differentiation. Furthermore, we examine the requirements forPbxgenes in mouse embryonic skeletal muscle differentiation, an area that has not been investigated in the mammalian embryo. RemovingPbx1function from skeletal muscle inMyf5Cre/+;Pbx1fl/flmouse embryos has minor effects on embryonic muscle development. However, concomitantly deletingPbx2function inMyf5Cre/+;Pbx1fl/fl;Pbx2-/-mouse embryos causes delayed activation and reduced expression of fast muscle differentiation genes. In the mouse,Pbx1/Pbx2-dependent fast muscle genes closely match those that have been previously shown to be dependent on murineSix1andSix4. This work establishes evolutionarily conserved requirements for Pbx factors in embryonic fast muscle differentiation. Our studies are revealing how Pbx homeodomain proteins help direct specific cellular differentiation pathways.
Molecular Survey for Selected Viral Pathogens in Wild Leopard Cats (Prionailurus bengalensis) in Taiwan with an Emphasis on the Spatial and Temporal Dynamics of Carnivore Protoparvovirus 1
Authors: Chen Chen-Chih , Chang Ai-Mei , Chen Wan-Jhen , Chang Po-Jen , Lai Yu-Ching , Lee Hsu-Hsun
Published: February 2020

The leopard cat (Prionailurus bengalensis) has been listed as an endangered species under the Wildlife Conservation Act in Taiwan since 2009. In this study, we targeted viral pathogens, included carnivore protoparvovirus 1 (CPPV-1), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), coronavirus (CoV), and canine morbillivirus (CMV), using molecular screening. The spatial and temporal dynamics of the target pathogens were evaluated. Through sequencing and phylogenetic analysis, we aimed to clarify the phylogenetic relationship of isolated viral pathogens between leopard cats and domestic carnivores. Samples from 23 and 29 leopard cats that were live-trapped and found dead, respectively, were collected from Miaoli County from 2015 to 2019 in northwestern Taiwan. CPPV-1 and coronavirus were detected in leopard cats. The prevalence (95% confidence interval) of CPPV-1, and CoV was 63.5% (50.4%–76.6%) and 8.8% (0%–18.4%), respectively. The majority of sequences of each CPPV-1 strain amplified from Taiwanese leopard cats and domestic carnivores were identical. All the amplified CoV sequences from leopard cats were identified as feline coronavirus. The spatial and temporal aggregation of CPPV-1 infection in leopard cats was not determined in the sampling area, which indicated a wide distribution of CPPV-1 in the leopard cat habitat. We consider sympatric domestic carnivores to be the probable primary reservoir for the pathogens identified. We strongly recommend establishing efforts to manage CPPV-1 and FCoV in the leopard cat habitat, with an emphasis on vaccination programs and population control measures for free-roaming dogs and cats.

IMPORTANCE

The leopard cat (Prionailurus bengalensis) is an endangered species in Taiwan. The effects of infectious diseases on the wildlife population have increasingly been recognized. In this study, we targeted highly pathogenic viral pathogens in wild cat species, included carnivore protoparvovirus 1 (CPPV-1), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), coronavirus (CoV), and canine morbillivirus (CMV), using molecular screening. Furthermore, we collected the epidemiological and phylogenetic data to understand the spatial and temporal dynamics of the target pathogens in the wild leopard cat population and identified the possible origin of target pathogens. Based on our study, we consider sympatric domestic carnivores to be the probable primary reservoir for the pathogens identified. Our study provides a deeper understanding related to the distribution of target viral pathogens in the wild leopard cats. The information is essential for leopard cat conservation and pathogen management.
SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango,Mangifera indica
Authors: Li Wei , Zhu Xun-Ge , Zhang Qun-Jie , Li Kui , Zhang Dan , Shi Cong , Gao Li-Zhi
Published: February 2020

Mango (Mangifera indica), a member of the family Anacardiaceae, is one of the world’s most popular tropical fruits. Here we sequenced the variety, “Hong Xiang Ya”, and generated a 371.6-Mb mango genome assembly with 34,529 predicted protein-coding genes. Aided with the published genetic map, for the first time, we assembled theM. indicagenome to the chromosomes, and finally about 98.77% of the genome assembly was anchored to 20 pseudo-chromosomes. The availability of the chromosome-length genome assembly ofM. indicawill provide novel insights into genome evolution, understand the genetic basis of specialized phytochemical composites relevant to fruit quality, and enhance allele mining in genomics-assisted breeding for mango genetic improvement.
Environmental and geographic data optimizeex situcollections and the preservation of adaptive evolutionary potential
Authors: Di Santo Lionel N. , Hamilton Jill A.
Published: February 2020

Maintenance of biodiversity, through seed banks and botanical gardens where the wealth of species’ genetic variation may be preservedex situ, is a major goal of conservation. However, challenges can persist in optimizingex situcollections where trade-offs exist between expense, effort, and conserving species evolutionary potential, particularly when genetic data is not available. Within this context, we evaluate the genetic consequences of guiding population preservation using geographic (isolation-by-distance, IBD) and environmental (isolation-by-environment, IBE) data forex situcollections where provenance data is available. We use 19 genetic and genomic datasets from 15 plant species to (i) assess the proportion of population genetic differentiation explained by geographic and environmental factors, and (ii) simulateex situcollections prioritizing source populations based on pairwise geographic or environmental distances. Specifically, we test the impact prioritizing sampling based on environmental and geographic distances may have on capturing neutral, functional or putatively adaptive genetic diversity and differentiation. We find that collectively IBD and IBE explain a substantial proportion of genetic differences among functional (median 45%) and adaptive (median 71%) loci, but not for neutral loci (median 21.5%). Simulatedex situcollections reveal that inclusion of IBD and IBE increases both allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections using environmental and geographic distance data can impact genetic variation capturedex situ. This provides value for the vast majority of plant species for which we have no genetic data, informing conservation of genetic variation needed to maintain evolutionary potential within collections.
Biochar effect - mediated ammonium transporter genes and GDH may be the core of improvement nitrogen assimilation in cotton seedling
Authors: Feng Lei , Tang Guangmu , Xu Wanli , Gu Meiying , Geng Zengchao
Published: February 2020

Biochar enhancement of nitrogen efficiency in crops is highly essential not only to reduce costs of agricultural production but also to conserve resources, lower energy consumption for products of these fertilizers, strengthen soil health, and eventually helps in slowing climate change; however nitrogen efficiency physiology by biochar effects is not clear. Here, we reported on the morphological, nitrogen metabolism and cytokinin, at seedling stage, under different layers of biochar and limited urea conditions grown in soil culture. Expression profile of miRNAs and AOB was further studied in fine and medium roots. It showed active root absorption area, fresh weight, and nitrogen agronomic efficiency responded significantly under biochar and reduction by 20% urea condition in the surface soil layer. Also, NR and GPT activity in fine roots remarkably increased with cytokinin, but decreased significantly in medium roots, meanwhile both NR and GDH activity did so. GOGAT activity was to be dependent with biochar and urea locations. In addition, AMT1;1, gdh3 and gdh2 in fine roots showed their up-regulation with reduction 20% urea and biochar. It revealed that co-expression of gdh3 and gdh2 in fine roots significantly affected nitrogen assimilation under reduction 20% urea with biochar on surface soil at seedling stage.

Highlights

The co-expression of ammonium transporter gene and GDH induced by biochar effect improves nitrogen efficiency and seedling growth.

These data emphasizes the importance of effects of cytokinin on nitrate reductase activity closely related to the position under biochar condition, which is a key element of enhancement nitrogen assimilation efficiency in cotton seedling.

Biochar addition applied into 0 to 10cm soil had a more positive effect on seedling growth than that into 10 to 20cm soil layers.
Endosidin20 is a broad-spectrum cellulose synthesis inhibitor with an herbicidal function
Authors: Huang Lei , Zhang Chunhua
Published: February 2020

Cellulose is an important component of plant cell wall that controls anisotropic cell growth. Disruption of cellulose biosynthesis often leads to inhibited cell growth. Endosidin20 (ES20) was recently identified as a cellulose biosynthesis inhibitor (CBI) that targets the catalytic domain of Arabidopsis cellulose synthase 6 (CESA6) to inhibit plant growth. Here, we characterized the effects of ES20 on the growth of some other plant species and found that ES20 is a broad-spectrum plant growth inhibitor. We compared the inhibitory effects of ES20 and other CBIs on the growth ofcesa6plants that have reduced sensitivity to ES20. We found that most of thecesa6with reduced sensitivity to ES20 show normal inhibited growth by other CBIs. ES20 also shows synergistic inhibitory effect on plant growth when applied together with other CBIs. We show ES20 has a different mode of action than tested CBIs isoxaben, indaziflam and C17. ES20 not only inhibits Arabidopsis growth under tissue culture condition, it inhibits plant growth under soil condition after direct spraying. We demonstrate that plants carrying two missense mutations can tolerate dual inhibition by ES20 and isoxaben.

One sentence summary

Cellulose biosynthesis inhibitor Endosidin20 has synergistic effect with other cellulose synthesis inhibitors and has the potential to be used as a spray herbicide.
Using changes in host demographic rates to reveal the effects of infection with hidden variable models
Authors: Ferguson Jake M. , González-González Andrea , Kaiser Johnathan A. , Winzer Sara M. , Anast Justin M. , Ridenhour Ben , Miura Tanya A. , Parent Christine E.
Published: February 2020

The impacts of disease on host vital rates can be clearly demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of disease, caused by infection, from population-level measurements of survival and fecundity when longitudinal studies are not possible. Our approach seeks to explain temporal changes in population-level vital rates by coupling observed changes in the infection status of individuals to an epidemiological model. We tested the approach using both single and coinfection viral challenge experiments on populations of fruit flies (Drosophila melanogaster).Specifically, we determined whether our approach yielded reliable estimates of disease prevalence and of the effects of disease on survival and fecundity rates for treatments of single infections and coinfection. We found two conditions are necessary for reliable estimation. First, diseases must drive detectable changes in vital rates, and second, there must be substantial variation in the degree of prevalence over time. This approach could prove useful for detecting epidemics from public health data in regions where standard surveillance techniques are not available, and in the study of epidemics in wildlife populations, where longitudinal studies can be especially difficult to implement.
Estimation of COVID-2019 burden and potential for international dissemination of infection from Iran
Authors: Tuite Ashleigh R. , Bogoch Isaac I. , Sherbo Ryan , Watts Alexander , Fisman David , Khan Kamran
Published: February 2020

The Coronavirus Disease 2019 (COVID-19) epidemic began in Wuhan, China in late 2019 and continues to spread globally, with exported cases confirmed in 28 countries at the time of writing. During the interval between February 19 and 23, 2020, Iran reported its first 43 cases with eight deaths. Three exported cases originating in Iran were identified, suggesting a underlying burden of disease in that country than is indicated by reported cases. A large epidemic in Iran could further fuel global dissemination of COVID-19. We sought to estimate COVID-19 outbreak size in Iran based on known exported case counts and air travel links between Iran and other countries, and to anticipate where infections originating in Iran may spread to next. We assessed interconnectivity between Iran and other countries using using International Air Transport Association (IATA) data. We used the methods of Fraser et al. to estimate the size of the underlying epidemic that would result in cases being observed in the United Arab Emirates (UAE), Lebanon, and Canada. Time at risk estimates were based on a presumed 6 week epidemic age, and length of stay data for visitors to Iran derived from the United Nations World Tourism Organization (UNWTO). We evaluated the relationship between the strength of travel links with Iran, and destination country rankings on the Infectious Disease Vulnerability Index (IDVI), a validated metric that estimates the capacity of a country to respond to an infectious disease outbreak. Scores range between 0-1, with higher scores reflecting greater capacity to manage infectious outbreaks. UAE, Lebanon, and Canada ranked 3rd, 21st, and 31st, respectively, for outbound air travel volume from Iran in February 2019. We estimated that 18,300 (95% confidence interval: 3770 to 53,470) COVID-19 cases would have had to occur in Iran, assuming an outbreak duration of 1.5 months in the country, in order to observe these three internationally exported cases reported at the time of writing. Results were robust under varying assumptions about undiagnosed case numbers in Syria, Azerbaijan and Iraq. Even if it were assumed that all cases were identified in all countries with certainty, the "best case" outbreak size was substantial (1820, 95% CI: 380-5320 cases), and far higher than reported case counts. Given the low volumes of air travel to countries with identified cases of COVID-19 with origin in Iran (such as Canada), it is likely that Iran is currently experiencing a COVID-19 epidemic of significant size for such exportations to be occurring. This is concerning, both for public health in Iran itself, and because of the high likelihood for outward dissemination of the epidemic to neighbouring countries with lower capacity to respond to infectious diseases epidemics.
A genetically encoded GRAB sensor for measuring serotonin dynamicsin vivo
Authors: Wan Jinxia , Peng Wanling , Li Xuelin , Qian Tongrui , Song Kun , Zeng Jianzhi , Deng Fei , Hao Suyu , Feng Jiesi , Zhang Peng , Zhang Yajun , Zou Jing , Pan Sunlei , Zhu J. Julius , Jing Miao , Xu Min , Li Yulong
Published: February 2020

Serotonin (5-HT) is a phylogenetically conserved monoamine neurotransmitter modulating a variety of processes in the brain. To directly visualize the dynamics of 5-HT, we developed a genetically encodedGPCR-Activation-Based 5-HT (GRAB5-HT) sensor with high sensitivity, selectivity, and spatiotemporal resolution. GRAB5-HT, detected 5-HT release in multiple physiological and pathological conditions in both flies and mice, and thus provides new insights into the dynamics and mechanisms of 5-HT signaling.
Kinetics characterization of ASXL1/2-mediated allosteric regulation of BAP1 deubiquitinase
Authors: Peng Hongzhuang , Cassel Joel , McCracken Daniel S. , Prokop Jeremy W. , Collop Paul R. , Polo Alexander , Joshi Surbhi , Mandell Jacob P. , Ayyanathan Kasirajan , Hinds David , Malkowicz S. Bruce , Harbour J. William , Bowcock Anne M. , Salvino Joseph , Kennedy Eileen J. , Testa Joseph R. , Rauscher Frank J.
Published: February 2020

BAP1 is a ubiquitin hydrolase whose deubiquitinase activity is mediated by polycomb group-like protein ASXL2. Cancer-related mutations/deletions ofBAP1lead to loss-of-function either by directly targeting the catalytic (UCH) or ULD domains of BAP1, the latter disrupts binding to ASXL2, an obligate partner for BAP1 enzymatic activity. However, the biochemical and biophysical properties of the domains involved in forming the enzymatically active complex are unknown. Here we investigate the molecular dynamics, kinetics and stoichiometry of these interactions. We demonstrate that the BAP1 and ASXL2 domain/proteins or protein complexes produced in either bacteria or baculovirus are structurally and functionally active. The interaction between BAP1 and ASXL2 is direct, specific, and stable toin vitrobiochemical and biophysical manipulations as detected by isothermal titration calorimetry, GST association, and optical biosensor assays. Association of the ASXL2-AB box greatly stimulates BAP1 deubiquitinase activity. A stable ternary complex can be formed comprised of the BAP1-UCH, BAP1-ULD, and ASXL2-AB domains. Binding of the BAP1-ULD domain to the ASXL2-AB box is rapid, with fast association and slow dissociation rates. Stoichiometric analysis revealed that one molecule of the ULD domain directly interacts with one molecule of the AB Box. Real-time kinetics analysis of ULD/AB protein complex to the UCH domain of BAP1, based on SPR, indicated that formation of the ULD/AB complex with the UCH domain is a single-step event with fast association and slow dissociation rates. These structural and dynamic parameters implicate the possibility for future small-molecule approaches to reactivate latent wild-type UCH activity in BAP-mutant malignancies.
ANME-1 archaea drive methane accumulation and removal in estuarine sediments
Authors: Kevorkian Richard , Callahan Sean , Winstead Rachel , Lloyd Karen G.
Published: February 2020

Uncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteriaDesulfatiglans sp.and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide.

Abstract Importance

Life may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.
Antinociceptive modulation by the adhesion-GPCR CIRL promotes mechanosensory signal discrimination
Authors: Dannhäuser Sven , Lux Thomas J. , Hu Chun , Selcho Mareike , Chen Jeremy Tsung-Chieh , Ehmann Nadine , Sachidanandan Divya , Pawlak Matthias , Langenhan Tobias , Soba Peter , Rittner Heike , Kittel Robert J.
Published: February 2020

Adhesion-type G protein-coupled receptors (aGPCRs) participate in a vast range of physiological processes. Correspondingly, these receptors are associated with diverse human diseases, such as developmental disorders, defects of the nervous system, allergies and cancer. Several aGPCRs have recently been linked to mechanosensitive functions suggesting that processing of mechanical stimuli may be a common feature of this receptor family. CIRL (ADGRL/Latrophilin, LPHN), one of the oldest members of the aGPCR family, sensitizes sensory responses of larvalDrosophilato gentle touch and sound by amplifying mechanosensory signal transduction in low-threshold mechanoreceptors (Scholz et al., 2015; 2017). In the present study, we show thatCirlis also expressed in high-threshold mechanical nociceptors where it adjusts nocifensive behaviour under physiological and pathophysiological conditions. Optogeneticin vivoexperiments indicate that CIRL quenches cAMP levels in both mechanosensory submodalities. However, contrasting its effect in touch sensitive neurons, CIRL dampens the response of nociceptors to mechanical stimulation. Consistent with this finding, rat nociceptors display a drop inCirl1expression during allodynia. Taken together, these results demonstrate that CIRL exerts opposing modulatory functions in low-threshold mechanosensors and high-threshold nociceptors. This intriguing bipolar action likely facilitates the separation of mechanosensory signals carrying different physiological information.
Quantitative LCMS for ceramides/dihydroceramides: pregnancy baseline biomarkers and potential metabolic messengers
Authors: Huang Qianyang , Hao Shiying , Yao Xiaoming , You Jin , Li Xiao , Lai Donghai , Han Chunle , Schilling James , Hwa Kuo Yuan , Thyparambil Sheeno , Whitin John , Cohen Harvey J. , Chubb Henry J. , Ceresnak Scott R. , McElhinney Doff B. , Shaw Gary M. , Stevenson David K. , Sylvester Karl G. , Ling Xuefeng B.
Published: February 2020

Ceramides and dihydroceramides are sphingolipids that present in abundance at the cellular membrane of eukaryotes. Although their metabolic dysregulation has been implicated in many diseases, our knowledge about circulating ceramide changes during the pregnancy remains limited. In this study, we present the development and validation of a high-throughput liquid chromatography-tandem mass spectrometric (LC/MS/MS) method for simultaneous quantification of 16 ceramides and 10 dihydroceramides in human serum within 5 mins by using stable isotope-labeled ceramides as internal standards (ISs). This method employs a protein precipitation method for high throughput sample preparation, reverse phase isocratic elusion for chromatographic separation, and Multiple Reaction Monitoring (MRM) for mass spectrometric detection. To qualify for clinical applications, our assay was validated against the FDA guidelines: the Lower Limit of Quantitation (LLOQ as low as 1 nM), linearity (R2>0.99), precision (Coefficient of Variation<15%), accuracy (Percent Error<15%), extraction recovery (>90%), stability (>85%), and carryover (<0.1%). With enhanced sensitivity and specificity from this method, we have, for the first time, determined the serological levels of ceramides and dihydroceramides to reveal unique temporal gestational patterns. Our approach could have value in providing insights into disorders of pregnancy.
Structural and luminescent properties of co-crystals of tetraiodoethylene with two azaphenanthrenes
Authors: Cui Yu-Jin , Su Feng , Jin Wei-Jun
Published: February 2020

Two new co-crystals, tetraiodoethylene–phenanthridine (1/2), 0.5C2I4·C13H9N (1) and tetraiodoethylene–benzo[f]quinoline (1/2), 0.5C2I4·C13H9N (2), were obtained from tetraiodoethylene and azaphenanthrenes, and characterized by IR and fluorescence spectroscopy, elemental analysis and X-ray crystallography. In the crystal structures, C—I...π and C—I...N halogen bonds link the independent molecules into one-dimensional chains and two-dimensional networks with subloops. In addition, the planar azaphenanthrenes lend themselves to π–π stacking and C—H...π interactions, leading to a diversity of supramolecular three-dimensional structural motifs being formed by these interactions. Luminescence studies show that co-crystals 1 and 2 exhibit distinctly different luminescence properties in the solid state at room temperature.
Financial constraints and marketing investment: evidence from text analysis
Authors: Mishra Sagarika , Ewing Mike T.
Published: February 2020

Purpose

The purpose of this study to examine the effect of financial constraint on intangible investment because intangible investment provides an overall picture of marketing investment and activity. Intangible investment also plays a significant role in facilitating future sales. Using a new measure of intangible investment (Peters and Taylor, 2017), the authors first establish that intangible investment is positively related with future sales. Then, using a new text-based measure of financial constraint, the authors show that financial constraint has a significant negative effect on future intangible investments after controlling for other factors. Intangible investment has three components. The first is R&D, the second is 30 per cent of selling and general administrative expense (SGA) and the third is other intangibles. The authors find that the negative and significant effect of financial constraint on 30 per cent SGA is stronger. This indicates that financially constrained firms reduce marketing related investments. The authors then considered firm size and found that smaller firms facing financial constraint continue to increase their intangible investments, whereas larger firms reduce their intangible investment. As a robustness test, the authors use advertising expenditure as a measure of promotion related investment and find that financial constraint has a negative effect on advertising spending. The authors then use two traditional measures of financial constraint in their analysis to compare with the new text-based measure.

Design/methodology/approach

The authors use ordinary least squares with cluster robust standard error to conduct their empirical analysis.

Findings

First the authors establish that intangible investment positively affects future sales. Further the authors find that financial constraint negatively affects intangible investment. Moreover, financial constraint negatively affects the brand capital of intangible investment.

Research limitations/implications

The authors did not conduct any industry specific analysis to see how financial constraints affect intangible investment across different industries. Industry specific analysis is important because in some industries/sectors intangibles are clearly more important than in others, so this is an important avenue for future research. It will also be interesting to explore if and how financial constraint has a mediating effect on sales growth via intangible investment and different components of intangibles.

Practical implications

This study identifies another important factor that can negatively affect brand capital investment.

Originality/value

The authors have used a measure of financial constraint and text mined all the annual reports of US firms for the period of 1994-2016 to compute this measure.