Biology subjects

Zhao, Y.

Publications and source records attributed to Zhao, Y..

At least 19 recordsLinked to original sources

bioRxiv2018

Differential Metabolic and Multi-tissue Transcriptomic Responses to Fructose Consumption among Genetically Diverse Mice

High fructose intake is a major risk for metabolic syndrome; however, its effects seem to vary across individuals. To determine main factors involved in the inter-individual responses to fructose, we fed inbred mouse strains C57BL/6J (B6), DBA/2J (DBA) and FVB/NJ (FVB) with fructose. DBA mice showed the highest susceptibility to gain adiposity and glucose intolerance. Elevated insulin was found in DBA and FVB mice, and cholesterol levels were uniquely elevated in B6 mice. The transcriptional profiles of liver, hypothalamus, and adipose tissues showed strain- and tissue-specific pathways altered by fructose, such as fatty acid and cholesterol pathways for B6 and PPAR signaling for DBA in liver, and oxidative phosphorylation for B6 and protein processing for DBA in hypothalamus. Using network modeling, we predicted potential strain-specific key regulators of fructose response such as Fgf21 (DBA) and Lss (B6) in liver, and validated strain-biased responses as well as the regulatory actions of Fgf21 and Lss in primary hepatocytes. Our findings support that fructose perturbs individualized tissue networks and pathways and associates with distinct features of metabolic dysfunctions across genetically diverse mice. Our results elucidate the molecular pathways and gene regulatory mechanisms underlying inter-individual variability in response to high fructose diet.

systems biology↗

bioRxiv2018

Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice

BackgroundIt is unclear how high fructose consumption induces disparate metabolic responses in genetically diverse mouse strains. ObjectiveWe aim to investigate whether the gut microbiota contributes to differential metabolic responses to fructose. MethodsEight-week-old male C57BL/6J (B6), DBA/2J (DBA), and FVB/NJ (FVB) mice were given 8% fructose solution or regular water (control) for 12 weeks. The gut microbiota composition in cecum and feces was analyzed using 16S rDNA sequencing, and PERMANOVA was used to compare community across mouse strains, treatments, and time points. Microbiota abundance was correlated with metabolic phenotypes and host gene expression in hypothalamus, liver and adipose tissues using Biweight midcorrelation. To test the causal role of the gut microbiota in determining fructose response, we conducted fecal transplants from B6 to DBA mice and vice versa for 4 weeks, as well as gavaged antibiotic-treated DBA mice with Akkermansia for 9 weeks, accompanied with or without fructose treatment. ResultsCompared to B6 and FVB, DBA mice had significantly higher Firmicutes/Bacteroidetes ratio and lower baseline levels of Akkermansia and S24-7 (P < 0.05), accompanied by metabolic dysregulation after fructose consumption. Fructose altered specific microbial taxa in individual mouse strains, such as a 7.27-fold increase in Akkermansia in B6 and 0.374-fold change in Rikenellaceae in DBA (FDR < 5%), which demonstrated strain-specific correlations with host metabolic and transcriptomic phenotypes. Fecal transplant experiments indicated that B6 microbes conferred resistance to fructose-induced weight gain in DBA mice (F = 43.1, P < 0.001), and Akkermansia colonization abrogated the fructose-induced weight gain (F = 17.8, P <0.001) and glycemic dysfunctions (F = 11.8, P = 0.004) in DBA mice. ConclusionsOur findings support that differential microbiota composition between mouse strains is partially responsible for host metabolic sensitivity to fructose, and that Akkermansia is a key bacterium that confers resistance to fructose-induced metabolic dysregulation.

systems biology↗

bioRxiv2018

Atypically larger variability of resource allocation accounts for visual working memory deficits in schizophrenia

Schizophrenia patients are known to have profound deficits in visual working memory (VWM), and almost all previous studies attribute the deficits to decreased memory capacity. This account, however, ignores the potential contributions of other VWM components (e.g., memory precision). Here, we measure the VWM performance of schizophrenia patients and healthy control subjects on two classical delay-estimation tasks. Moreover, we thoroughly evaluate several established computational models of VWM to compare the performance of the two groups. We find that the model assuming variable precision across items and trials is the best model to explain the performance of both groups. According to the variable-precision model, schizophrenia subjects exhibit abnormally larger variability of allocating memory resources rather than resources per se. These results invite a rethink of the widely accepted decreased-capacity theory and propose a new perspective on the diagnosis and rehabilitation of schizophrenia.

neuroscience↗

bioRxiv2018

Covariate Assisted Principal Regression for Covariance Matrix Outcomes

Modeling variances in data has been an important topic in many fields, including in financial and neuroimaging analysis. We consider the problem of regressing covariance matrices on a vector covariates, collected from each observational unit. The main aim is to uncover the variation in the covariance matrices across units that are explained by the covariates. This paper introduces Covariate Assisted Principal (CAP) regression, an optimization-based method for identifying the components predicted by (generalized) linear models of the covariates. We develop computationally efficient algorithms to jointly search the projection directions and regression coefficients, and we establish the asymptotic properties. Using extensive simulation studies, our method shows higher accuracy and robustness in coefficient estimation than competing methods. Applied to a resting-state functional magnetic resonance imaging study, our approach identifies the human brain network changes associated with age and sex.

neuroscience↗

bioRxiv2018

The Population Genetic Variation Analysis of Bitter Gourd Wilt Caused by Fusarium oxysporum f. sp. momordicae in China by Inter Simple Sequence Repeats (ISSR) Molecular Marker

The bitter gourd fusarium wilt caused by Fusarium oxysporum f.sp. momordicae (FOM) was a devastating disease in China and leading to great economic losses every year. A total of 152 isolates, which have the typical Fusarium oxysporum characteristics with abundant microconidia and macroconidia on the white or ruby colonies, were obtained from diseased plant tissues with typical fusarium wilt symptoms. The BLASTn analysis of rDNA-ITS showed 99% identity with F.oxysporum species. Among the tested isolates, three isolates infected tower gourd, and five isolates were pathogenic to bottle gourd. However, they were all pathogenic to bitter gourd. Based on the molecular and morphologic results, the isolates were identified as FOM. For genetic variation analysis, forty ISSR primers were screened and eleven primers were used in PCR amplification. Totally, 121 loci were detected, of which 52 loci were polymorphic at rate of 42.98%. The POPGENE analysis showed that Neis gene diversity index (H) and Shannons information index (I) were 0.0902 and 0.1478, respectively, which indicated that the genetic diversity for the tested 152 isolates was relatively low. It also means that each geographical population was a relatively independent unit. While the value of coefficient of gene differentiation (Gst=0.4929 > 0.15) pointed to the genetic differentiation was mainly among populations. The strength of gene flow (Nm=0.5143<1.0) was weaker, indicating that gene exchanges were blocked to some degree. The dendrogram based on ISSR markers showed that the eight geographical populations were clustered into four groups at the threshold of genetic similar coefficient 0.96. Fujian, Jiangxi and Guangdong populations were clustered into Group I. Group II contained Hunan and Guangxi populations. Group III only had Hainan population. Group IV consisted Shandong and Henan populations. The geographical populations closer to each other grouped together, suggesting a correlationship between geographical origin and genetic differentiation. Two hybridization events were observed between Hainan and Hunan populations and between Guangdong and Guangxi by Structure analysis. Our findings enrich the knowledge on genetic variation characteristics of the FOM populations with helpful of development of effective disease management programs and disease resistance breeding.

microbiology↗

bioRxiv2018

Adopting Literature-based Discovery on Rehabilitation Therapy Repositioning for Stroke

Stroke is a common disabling disease severely affecting the daily life of the patients. There is evidence that rehabilitation therapy can improve the movement function. However, there are no clear guidelines that identify specific, effective rehabilitation therapy schemes, and the development of new rehabilitation techniques has been fairly slow. One informatics translational approach, called ABC model in Literature-based Discovery, was used to mine an existing rehabilitation candidate which is most likely to be repositioned for stroke. As in the classic ABC model originated from Don Swanson, we built the internal links of stroke (A), assessment scales (B), rehabilitation therapies (C) in PubMed relating to upper limb function measurements for stroke patients. In the first step, with E-utility we retrieved both stroke related assessment scales and rehabilitation therapies records, and complied two datasets called Stroke_Scales and Stroke_Therapies, respectively. In the next step, we crawled all rehabilitation therapies co-occurred with the Stroke_Theapies, named as All_Therapies. Therapies that were already included in Stroke_Therapies were deleted from All_Therapies, so that the remaining therapies were the potential rehabilitation therapies, which could be repositioned for stroke after subsequent filtration by manual check. We identified the top ranked repositioning rehabilitation therapy following by subsequent clinical validation. Hand-arm bimanual intensive training (HABIT) ranked the first in our repositioning rehabilitation therapies list, with the most interaction links with Stroke_Scales. HABIT showed a significant improvement in clinical scores on assessment scales of Fugl-Meyer Assessment and Action Research Arm Test in the clinical validation on upper limb function for acute stroke patients. Based on the ABC model and clinical validation of the results, we put forward that HABIT as a promising rehabilitation therapy for stroke, which shows that the ABC model is an effective text mining approach for rehabilitation therapy repositioning. The results seem to be promoted in clinical knowledge discovery.\n\nAuthor SummaryIn the present study, we proposed a text mining approach to mining terms related to disease, rehabilitation therapy, and assessment scale from literature, with a subsequent ABC inference analysis to identify relationships of these terms across publications. The clinical validation demonstrated that our approach can be used to identify potential repositioning rehabilitation therapy strategies for stroke. Specifically, we identified a promising rehabilitation method called HABIT previously used in pediatric congenital hemiplegia. A subsequent clinical trial confirmed this as a highly promising rehabilitation therapy for stroke.

bioinformatics↗

bioRxiv2018

MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions centered on cohesin, CTCF and H3K4me3 associated regions in multiple cell types. MAPS is freely available at https://github.com/ijuric/MAPS.

bioinformatics↗

bioRxiv2018

Pelagiphages in the Podoviridiae family integrate into host genomes

The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here we report 11 new pelagiphages in the Podoviridae family. Comparative genomic analysis revealed that they are all closely related to previously reported pelagiphages HTVC011P and HTVC019P, in the HTVC019Pvirus genus. HTVC019Pvirus pelagiphages share a core genome of 15 genes, with a pan-genome of 234 genes. Phylogenomic analysis clustered these pelagiphages into three subgroups. Integrases were identified in all but one pelagiphage genomes. Evidence of site-specific integration was obtained by high-throughput sequencing and sequencing PCR amplicons containing predicted integration sites, demonstrating the capacity of these pelagiphages to propagate by both lytic and lysogenic infection. HTVC019P, HTVC021P, HTVC022P, HTVC201P and HTVC121P integrate into tRNA-Cys genes. HTVC011P, HTVC025P, HTVC105P, HTVC109P, HTVC119P and HTVC200P target tRNA-Leu genes, while HTVC120P integrates into the tRNA-Arg. Evidence of pelagiphage integration was also retrieved from Global Ocean Survey (GOS) database, suggesting the occurrence of pelagiphage integration in situ. The capacity of HTVC019Pvirus pelagiphages to integrate into host genomes suggests they could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction, and prophage-induced viral immunity. HTVC019Pvirus pelagiphages are a rare example of a lysogenic phage that can be implicated in ecological processes on broad scales, and thus have potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.\n\nIMPORTANCEPelagiphages are ecologically important because of their extraordinarily high census numbers, which makes them potentially significant agents in the viral shunt, a concept that links viral predation to the recycling of dissolved organic matter released from lysing plankton cells. Lysogenic Pelagiphages, such as the HTVC019Pvirus pelagiphages we investigate here, are also important because of their potential to contribute to the hypothesized processes such as the \"Piggy-Back-the-Winner\" and \"King-of-the-Mountain\". The former explains nonlinearities in virus to host ratios by postulating increased lysogenization of successful host cells, while the latter postulates host-density dependent propagation of defensive alleles. Here we report multiple Pelagiphage isolates, and provided detailed evidence of their integration into SAR11 genomes. The development of this ecologically significant experimental system for studying phage-dependent processes is progress towards the validation of broad hypotheses about phage ecology with specific examples based on knowledge of mechanisms.

microbiology↗

bioRxiv2018

Wheat avenin-like protein and its significant Fusarium Head Blight resistant functions

Wheat Avenin-like proteins (TaALP) are atypical storage proteins belonging to the Prolamin superfamily. Previous studies on ALPs have focused on the proteins positive effects on dough strength, whilst no correlation has been made between TaALPs and the plant immune system. Here, we performed genome-wide characterization of ALP encoding genes in bread wheat. In silico analyses indicated the presence of critical peptides in TaALPs that are active in the plant immune system. Pathogenesis-related nucleotide motifs were also identified in the putative promoter regions of TaALP encoding genes. RT-PCR was performed on TaALP and previously characterised pathogenesis resistance genes in developing wheat caryopses under control and Fusarium graminearum infection conditions. The results showed that TaALP and NMT genes were upregulated upon F. graminearum inoculation. mRNA insitu hybridization showed that TaALP genes were expressed in the embryo, aleurone and sub-aleurone layer cells. Seven TaALP genes were cloned for the expression of recombinant proteins in Escherichia coli, which displayed significant inhibitory function on F. graminearum under anti-fungal tests. In addition, FHB index association analyses showed that allelic variations of two ALP genes on chromosome 7A were significantly correlated with FHB symptoms. Over-expression of an ALP gene on chromosome 7A showed an enhanced resistance to FHB. Yeast two Hybridization results revealed that ALPs have potential proteases inhibiting effect on metacaspases and beta-glucosidases. A vital infection process related pathogen protein, F. graminearum Beta-glucosidase was found to interact with ALPs. Our study is the first to report a class of wheat storage protein or gluten protein with biochemical functions. Due to its abundance in the grain and the important multi-functions, the results obtained in the current study are expected to have a significant impact on wheat research and industry.

molecular biology↗

bioRxiv2018

Inferring the molecular mechanisms of noncoding Alzheimer’s disease-associated genetic variants

Structured AbstractO_ST_ABSINTRODUCTIONC_ST_ABSWe set out to characterize the causal variants, regulatory mechanisms, tissue contexts, and target genes underlying noncoding late-onset Alzheimers Disease (LOAD)-associated genetic signals.\n\nMETHODSWe applied our INFERNO method to the IGAP genome-wide association study (GWAS) data, annotating all potentially causal variants with tissue-specific regulatory activity. Bayesian co-localization analysis of GWAS summary statistics and eQTL data was performed to identify tissue-specific target genes.\n\nRESULTSINFERNO identified enhancer dysregulation in all 19 tag regions analyzed, significant enrichments of enhancer overlaps in the immune-related blood category, and co-localized eQTL signals overlapping enhancers from the matching tissue class in ten regions (ABCA7, BIN1, CASS4, CD2AP, CD33, CELF1, CLU, EPHA1, FERMT2, ZCWPW1). We validated the allele-specific effects of several variants on enhancer function using luciferase expression assays.\n\nDISCUSSIONIntegrating functional genomics with GWAS signals yielded insights into the regulatory mechanisms, tissue contexts, and genes affected by noncoding genetic variation associated with LOAD risk.

bioinformatics↗

bioRxiv2018

Dimethylarsenic acid (DMA) accumulation positively correlates with realgar-induced subchronic toxicity in rats

The toxicity of realgar depends largely on different arsenic species accumulation and distribution in the body. Here, after continuous oral administration of different doses of realgar for 90 days and subsequent 60-day withdrawal period, clinical observations, food consumption, body weights, blood biochemistry, hematology, and histomorphological examination of rats were performed. Realgar 40mg{middle dot}kg-1{middle dot}d-1 and 170 mg{middle dot}kg-1{middle dot}d-1 of realgar (which is equivalent to 40-fold and 100-fold the maximum clinical dose, respectively) can cause toxicity in rats, including degreased body weight, peripheral blood neutrality abnormal ratio of granulocytes and lymphocytes, hypercoagulability of the blood, liver and kidney tissue damage, liver and kidney may be the main toxic target organs of realgar. The no observed adverse effect level (NOAEL) dose is 10 mg{middle dot}kg-1. At the same time, the content and distribution of arsenic species in tissues were determined. The content of total arsenic (tAs) and Dimethylarsenic acid (DMA) in the tissues of the realgar group was significantly higher than those of the control group. After 60 days of discontinuation, the DMA content in the realgar group decreased, but it was still higher than that in the control group, and liver and kidney damage occurred during the administration period basically returned to normal. Therefore, the authors speculated that when the DMA content in the tissue exceeds a certain range, liver and kidney toxicity will be induced. However, when the DMA content is lower than the above threshold after drug withdrawal, the liver and kidney lesions can return to normal.

pharmacology and toxicology↗

bioRxiv2018

Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products

Marine phytoplankton contributes to about one half of global primary production, and a significant proportion of their photosynthetically fixed organic carbon is released after viral infection as dissolved organic matter (DOM). This DOM pool is known to be consumed by heterotrophic microorganisms; however, its impact on the uninfected co-occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of viral lysis products on the unicellular cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. While Prochlorococcus growth was not affected by viral lysis products, many tRNAs increased in abundance, which was also seen after amino acid addition, suggesting that amino acids are one of the compounds in viral lysis products that affected the expression of tRNA genes. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds, consistent with abundant amino acids in viral lysis products. The addition of viral lysis products to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO2 fixation while increased its respiration rate, consistent with differentially expressed genes related to photosynthesis and respiration. One of the highest positive fold-changes was observed for the 6S RNA, a non-coding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds.\n\nImportancePhotosynthetic microorganisms called phytoplankton are abundant in the oceans and contribute to about one half of global CO2 fixation. Phytoplankton are frequently infected by viruses and after infection their organic carbon is released into the ocean as dissolved organic matter (DOM). Marine DOM is important for the marine food web because it supports the growth of heterotrophic microorganisms. However, the impact of viral DOM on the uninfected phytoplankton is largely unknown. In this study, we conducted transcriptomic analyses and identified many differentially expressed genes when viral DOM was added to the marine cyanobacterium Prochlorococcus. One effect of viral DOM is that the carbon fixation of Prochlorococcus was reduced by ~16%, which might affect carbon cycling in the worlds oceans since Prochlorococcus is the most abundant photosynthetic organism on Earth.

microbiology↗

bioRxiv2018

Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution

Optical and electron microscopy have made tremendous inroads in understanding the complexity of the brain, but the former offers insufficient resolution to reveal subcellular details and the latter lacks the throughput and molecular contrast to visualize specific molecular constituents over mm-scale or larger dimensions. We combined expansion microscopy and lattice light sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain, including synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly neuropil domain. The technology should enable statistically rich, large scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.\n\nOne Sentence SummaryCombined expansion and lattice light sheet microscopy enables high speed, nanoscale molecular imaging of neural circuits over large volumes.

neuroscience↗

bioRxiv2018

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles

Benzimidazoles (BZ) are essential components of the limited chemotherapeutic arsenal available to control the global burden of parasitic nematodes. The emerging threat of BZ resistance among nearly all nematode species necessitates the development of novel strategies to identify genetic and molecular mechanisms underlying this resistance. All detection of parasitic helminth resistance to BZ is focused on the genotyping of three variant sites in the orthologs of the {beta}-tubulin gene found to confer resistance in the free-living nematode Caenorhabditis elegans. Because of the limitations of laboratory and field experiments in parasitic nematodes, it is difficult to look beyond these three sites, and additional BZ resistance is observed in the field. Here, we took an unbiased genome-wide mapping approach in the free-living nematode species C. elegans to identify the genetic underpinnings of natural resistance to the commonly used BZ, albendazole (ABZ). We found a wide range of natural variation in ABZ resistance in natural C. elegans populations. In agreement with known mechanisms of BZ resistance in parasites, we find that a majority of the variation in ABZ resistance among wild C. elegans strains is caused by variation in the {beta}-tubulin gene ben-1. This result shows empirically that resistance to ABZ naturally exists and segregates within the C. elegans population, suggesting that selection in natural niches could enrich for resistant alleles. We identified 25 distinct ben-1 alleles that are segregating at low frequencies within the C. elegans population, including many novel molecular variants. Population genetic analyses indicate that ben-1 variation arose multiple times during the evolutionary history of C. elegans and provide evidence that these alleles likely occurred recently because of local selective pressures. Additionally, we find purifying selection at all five {beta}-tubulin genes, despite predicted loss-of-function resistants variants in ben-1, indicating that BZ resistance in natural niches is a stronger selective pressure than loss of one {beta}-tubulin gene. Furthermore, we use genome-editing to show that the most common parasitic nematode {beta}-tubulin allele that confers BZ resistance, F200Y, confers resistance in C. elegans. Importantly, we identified a novel genomic region that is correlated with ABZ resistance in the C. elegans population but independent of ben-1 and the other {beta}-tubulin loci, suggesting that there are multiple mechanisms underlying BZ resistance. Taken together, our results establish a population-level resource of nematode natural diversity as an important model for the study of mechanisms that give rise to BZ resistance.\n\nAuthor summaryNematode parasites have a tremendous impact on human health with almost two billion people infected worldwide. The control of nematode infections relies mainly on the efficacy of a limited repertoire of anthelmintic compounds, including the benzimidazoles (BZ). Already a significant problem in veterinary medicine, increasing evidence exists for the development of BZ resistance in nematodes that infect humans. Laboratory screens and field surveys identified {beta}-tubulin genes as major determinants of BZ resistance in nematodes but detailed population-wide genetic analyses of resistance mechanisms are only just beginning. Therefore, we took advantage of the free-living model organism Caenorhabditis elegans to study the genetic basis of resistance to the commonly used BZ, albendazole (ABZ) in a natural nematode population. Performing genome-wide association mappings, we were able to identify extreme heterogeneity in the {beta}-tubulin gene ben-1 as a major determinant of ABZ resistance. Moreover, our study provided new insights into the effects of missense and loss-of-function alleles at this locus, and how anthelmintic resistance could have developed within a natural nematode population.

genetics↗

bioRxiv2018

Dynamic plant height QTL revealed in maize through remote sensing phenotyping using a high-throughput unmanned aerial vehicle (UAV)

Plant height is the key factor for plant architecture, biomass and yield in maize (Zea mays). In this study, plant height was investigated using unmanned aerial vehicle high-throughput phenotypic platforms (UAV-HTPPs) for maize diversity inbred lines at four important growth stages. Using an automated pipeline, we extracted accurate plant heights. We found that in temperate regions, from sowing to the jointing period, the growth rate for temperate maize was faster than tropical maize. However, from jointing to flowering stage, tropical maize maintained a vigorous growth state, and finally resulted in a taller plant than temperate lines. Genome-wide association study for temperate, tropical and both groups identified a total of 238 quantitative trait locus (QTLs) for the 16 plant height related traits over four growth periods. And, we found that plant height at different stages were controlled by different genes, for example, PIN1 controlled plant height at the early stage and PIN11 at the flowering stages. In this study, the plant height data collected by the UAV-HTTPs were credible and the genetic mapping power is high, indicating that the application of this UAV-HTTPs into the study of plant height will have great prospects.\n\nHighlightWe used UAV-based sensing platform to investigate plant height over 4 growth stages for different maize populations, and detected numbers of reliable QTLs using GWAS.

genetics↗

bioRxiv2018

How do wind speed, release height, seed morphology interact to determine seed dispersal trajectory of Calligonum (Polygonaceae) species

How seed dispersal trajectory shifts with abiotic and biotic factors and what is the relationship between seed dispersal distance and dispersal trajectory are remain unclear. We used wind tunnel and video camera to track the seed dispersal trajectory of 7 Calligonum species with different appendages under the different wind speeds and the release heights. Dispersal trajectories and distances were determined by video analysis and spatial coordinate transformation. Based on perspective principle, 4 modes of trajectories were determined. Wind speed, seed mass and release height were the key factors determining seed dispersal trajectory modes. Release height and wind speed tended to have the strongest explanatory power on seeds with bristles and wings, respectively. Different trajectory modes lead to different dispersal distance, while the same dispersal distance can be the result of different trajectory modes. The proportion of species trajectory modes formed its trajectory spectrum. Wind speed tends to have strong influence on light and low-wind-loading seeds, release height tends to have that on heavy and high-wind-loading seeds. Species with high proportion of horizontal projectile and projectile have high dispersal capacity, vice versa. Therefore, trajectory spectrum of a species reveals its primary dispersal strategies and evolutionary consequences.

ecology↗

bioRxiv2018

Duplications and functional specialization force distinct evolution of isoflavonoid biosynthetic genes in legumes

Isoflavonoids are specialized plant metabolites, almost exclusive to legumes, and synthesized by the phenylpropanoid pathway. Leguminous plants produce 5-deoxyflavonoids and 5-deoxyisoflavonoids that act in symbiosis with nitrogen-fixing bacteria and involved in plant pathogen and stress response. However, little is known about evolutional origin of legume-specific isoflavonoid biosynthesis pathway. Here, we explored the genome-wide analysis of key genes: chalcone synthase (CHS), chalcone reductase (CHR), isoflavone synthase (IFS) and isoflavone reductase (IFR), encoding enzymes involved in the biosynthesis of (iso) flavonoids in legumes and nonlegumes. Among them, CHS, CHR and IFR comprise multigene families, underling the significant role of gene duplication in the evolutionary. Most duplications of CHS were highly the conventional leguminous type, whereas some were grouped with nonleguminous CHS genes. We also found that CHR homologs in soybean and Sesbania rostrata previously reported were ambiguous and should be re-identified. Phylogenetic analysis and protein sequences alignment indicated that IFSs in legumes are highly conserved. Intriguingly, unlike other IFRs in legumes, IFR-like homologs in Sophora flavescens and Lupinus angustifolius shared high sequence similarity and protein structures with homologs in nonlegumes. Overall, these results offer reasonable gene annotations and comparative analysis and also provided a glimpse into evolutional route of legume-specific isoflavonoid biosynthesis.\n\nHighlightIsoflavonoids are specialized plant metabolites, almost exclusive to legumes. We firstly provide evidence that evolutional origin of legume-specific isoflavonoid biosynthesis may be driven by gene duplications and functional specialization.

genomics↗

bioRxiv2018

Tetrahymena RIB72A and RIB72B are Microtubule Inner Proteins in the ciliary doublet microtubules

Doublet and triplet microtubules are essential and highly stable core structures of centrioles, basal bodies, cilia and flagella. In contrast to dynamic cytoplasmic microtubules, their luminal surface is coated with regularly arranged Microtubule Inner Proteins (MIPs). However, the protein composition and biological function(s) of MIPs remain poorly understood. Using genetic, biochemical and imaging techniques we identified Tetrahymena RIB72A and RIB72B proteins as ciliary MIPs. Fluorescence imaging of tagged RIB72A and RIB72B showed that both proteins co-localize to Tetrahymena cilia and basal bodies, but assemble independently. Cryo-electron tomography of RIB72A and/or RIB72B knockout strains revealed major structural defects in the ciliary A-tubule involving MIP1, MIP4 and MIP6 structures. The defects of individual mutants were complementary in the double mutant. All mutants had reduced swimming speed and ciliary beat frequencies, and high-speed video imaging revealed abnormal highly curved cilia during power stroke. Our results show that RIB72A and RIB72B are crucial for the structural assembly of ciliary A-tubule MIPs and are important for proper ciliary motility.\n\nSUMMARYMicrotubule Inner Proteins (MIPs) bind to the luminal surface of highly stable microtubules. Combining cell biology and cryo-electron tomography, Stoddard et al. show that RIB72A and RIB72B are conserved MIPs in ciliary doublet microtubules and that they are important for proper ciliary motility.

cell biology↗