Biology subjects

Luo, J.

Publications and source records attributed to Luo, J..

At least 307 records · Page 17Linked to original sources

bioRxiv2019

Soil and vegetation conditions changes following the different sand dune restoration measures on the Zoige Plateau

Restoration of alpine sand dunes has been increasingly attracting the attention of ecologists due to their difficulty and importance among the mountain-river-forest-farmland-lake-grass system (referred as meta-ecosystem) restoration. Alpine sand dunes are suffered from unstable soil and lack of plants. Efficient restoration measures are vital to guide the sand dune restoration. Whether the engineering materials co-applied with seeding could achieve considerable restoration in such areas? Here, sandbag and wicker as environmental friendly materials combined with Elymus nutans seeding were implemented on the Zoige Plateau sand dune, comparing with the control treatment that only seeding. We assessed the topsoil conditions by sampled the surface soil and measured the water capacity and nutrients. We also utilized interspecific relationship and population niche to analyse the plant community structure variances among different restoration measures. Results showed that the soil conditions got clearly improved in sandbag area than that in wicker area when compared with that in control area. The community in control area was the least structured, while the species showed the closest related in sandbag area. In addition, average population niche overlap showed a control (0.26) < wicker (0.32) < sandbag (0.39) ranking. Thus, we suggested that sandbag or wicker co-applied with indigenous grass seeding is a practical and quick restoration approach in alpine sand dunes, and the sandbag may surpasses the wicker. Moreover, soil amending measures including nutrient improvement, and microbial fertilizer addition may further accelerate sand dune restoration.

ecology↗

bioRxiv2019

Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a

Accumulating evidence has shown that long noncoding RNAs (lncRNAs) are involved in several biological processes, including immune responses. However, the role of lncRNAs in antiviral innate immune responses remains largely unexplored. Here, we identify an uncharacterized human lncRNA from influenza A virus (IAV) patients, antivirus and activate neutrophil (AVAN), that is significantly up-regulated upon virus infection. Mechanistically, nuclear lncRNA-AVAN positively regulates the transcription of forkhead box O3A (FOXO3a) by associating with its promoter and inducing chromatin remodeling to promote neutrophil chemotaxis. Furthermore, we also found that cytoplasmic lncRNA-AVAN directly binds tripartite motif containing 25 (TRIM25) and enhances the association of TRIM25 and Retinoic acid inducible gene-1 proteins (RIG-I) and the ubiquitylation of RIG-I, thereby promoting TRIM25- and RIG-I-mediated antiviral innate immune signaling. More importantly, we enforced the expression of AVAN in transgenic mice and found that it significantly alleviated IAV virulence and virus production. Collectively, these findings highlight the potential clinical implications of lncRNA-AVAN as a key positive regulator of the antiviral innate immune response and a promising target for developing broad antiviral therapeutics.

immunology↗

bioRxiv2019

Human Chrysomya bezziana myiasis: A systematic review

BackgroundMyiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiases cause not only morbidity and death to animals and humans, but also economic losses in the livestock industries. Because of the aggressive and destructive nature of this disease in hosts, we initiated this study to provide a comprehensive understanding of human myiasis caused by C. bezziana.\n\nMethodsWe conducted a systematic search of the databases in English (PubMed, Embase and African Index Medicus) and Chinese (CNKI, Wanfang, and Duxiu), and international government online reports to 6th February, 2019, to identify studies concerning Chrysomya bezziana. Another ten human cases in China and Papua New Guinea that our team had recorded were also included.\n\nResultsWe retrieved 1,048 reports from which 202 studies were ultimately eligible for inclusion in the present descriptive analyses. Since the first human case due to C. bezziana was reported in 1909, we have summarized 291 cases and found that these cases often occurred in poor hygiene, low socio-economic conditions, old age, and underlying diseases including infections, age-related diseases, and noninfectious chronic diseases. But C. bezziana myiasis appears largely neglected as a serious medical or veterinary condition, with human and animal cases only reported in 16 and 24 countries respectively, despite this fly species recorded as present in 44 countries worldwide.\n\nConclusionOur findings indicate that cryptic myiasis cases due to the obligate parasite, C. bezziana, are under-recognized. Through this in-depth study to clarify the knowledge of human C. bezziana myiasis including its etiology, clinical features, diagnosis, treatment, epidemiology, prevention and control, we call for more vigilance and awareness of the disease from governments, health authorities, clinicians, veterinary workers, nursing homes, and also the general public.\n\nAuthor summaryChrysomya bezziana larvae are characterized by feeding aggressively on the living tissues and body fluids of the host. The nightmare-like feelings of patients suffering from this myiasis, severe tissues and bones destruction, even death, and enormous economic loss in the livestock industries have been described in the previous reports. But our findings indicate that C. bezziana myiases still appear to be under-recognized as a serious medical or veterinary condition throughout the world. Both in China and the world at large, it is probable that C. bezziana distribution could be greater than currently reported. For the first time, we have therefore systematically investigated human myiasis caused by C. bezziana. Our study provides an opportunity for clinicians and health authorities to gain a better understanding of this disease from its etiology, pathology, clinical features, diagnosis, treatment, epidemiology, prevention and control. In addition, our findings will hopefully engage governments, health staff, veterinary workers, the elderly homes, and also the general public in efforts to recognize, prevent and control such infestations.

epidemiology↗

bioRxiv2019

Fertility intentions and influential factors in Dalian urban city ---A cross-sectional study based on Universal Two-child policy in China

BackgroundIn October, 2015, Chinese government announced that one-child policy had finally been replaced by a universal two-child policy. However, the effects of new policy may be far less than expected. So we conducted this research to explore potential influential factors of fertility intention.\n\nMethodsThis cross-sectional study was conducted and a self-administered questionnaire was designed for collecting socio-demographic information, future fertility intention and influential factors of individual reproductive behavior. The analyses were performed using the SPSS 19.0 statistical software package.\n\nResultsA total of 1370 respondents were interviewed. Our research indicated that the mean ideal number of children was only 1.73 and urban respondents sex preference was symmetrical preference. 79.1% (884) married people had the first child already, only 7.6% (71) respondents had two children. Among 1370 participants, 30.4% respondents stated that they would have a second child; while 69.6% respondents refused to have two children in future (just wanted only a child). Binary logistic regression analysis (model 1) showed that female, older age, lower education lever, birth place was Dalian, lower family income, the ideal number of children were associated with having 1 child in the future. Model 2 (only respondents with childbearing experience) showed that female, lower family income, couldnt get additional financial support from parents were more likely refused to have two children; in additional, the ideal number of children and childbearing experience were significantly influences on future fertility intention.\n\nConclusionFertility intention and reproductive behavior still below replacement in Dalian city. Our results suggest that several factors (including socioeconomic characteristics, economic factors, desired number of child, childbearing experience) have distinctive effects on fertility intention.

epidemiology↗

bioRxiv2019

Complete genome sequence of Bacillus velezensis JT3-1, a microbial germicide isolated from yak feces

Bacillus velezensis JT3-1 is a probiotic strain isolated from feces of the domestic yak (Bos grunniens) in the Gansu province of China. It has strong antagonistic activity against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella Typhimurium, Mannheimia haemolytica, Staphylococcus hominis, Clostridium perfringens, and Mycoplasma bovis. These properties have made the JT3-1 strain the focus of commercial interest. In this study, we describe the complete genome sequence of JT3-1, with a genome size of 3,929,799 bp, 3761 encoded genes and an average GC content of 46.50%. Whole genome sequencing of Bacillus velezensis JT3-1 will lay a good foundation for elucidation of the mechanisms of its antimicrobial activity, and for its future application.

genomics↗

bioRxiv2018

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

genomics↗

bioRxiv2018

DNA segment of African Swine Fever Virus first detected in hard ticks from sheep and bovine

In this study, we aimed to detect viruses in hard ticks using the small RNA sequencing based method. A 235-bp DNA segment was detected in Dermacentor nuttalli (hard ticks) and D. silvarum (hard ticks) from sheep and bovine, respectively. The detected 235-bp segment had an identity of 99% to a 235-bp DNA segment of African Swine Fever Virus (ASFV) and contained three single nucleotide mutations (C38T, C76T and A108C). C38T, resulting in an single amino acid mutation G66D, suggests the existence of a new ASFV strain, which is different from all reported ASFV strains in NCBI GenBank database. These results also suggest that ASFV could have a wide range of hosts or vectors, beyond the well known Suidae family and soft ticks. Our findings pave the way toward further studies of ASFV transmission and development of prevention and control measures.

zoology↗

bioRxiv2018

Model-Aware Deep Learning Based Strategies for Clutter Suppression in Contrast Enhanced Ultrasound

Contrast enhanced ultrasound is a radiation-free imaging modality which uses encapsulated gas microbubbles for improved visualization of the vascular bed deep within the tissue. It has recently been used to enable imaging with unprecedented subwavelength spatial resolution by relying on super-resolution techniques. A typical preprocessing step in super-resolution ultrasound is to separate the microbubble signal from the cluttering tissue signal. This step has a crucial impact on the final image quality. Here, we propose a new approach to clutter removal based on robust principle component analysis (PCA) and deep learning. We begin by modeling the acquired contrast enhanced ultrasound signal as a combination of a low rank and sparse components. This model is used in robust PCA and was previously suggested in the context of ultrasound Doppler processing and dynamic magnetic resonance imaging. We then illustrate that an iterative algorithm based on this model exhibits improved separation of microbubble signal from the tissue signal over commonly practiced methods. Next, we apply the concept of deep unfolding to suggest a deep network architecture tailored to our clutter filtering problem which exhibits improved convergence speed and accuracy with respect to its iterative counterpart. We compare the performance of the suggested deep network on both simulations and in-vivo rat brain scans, with a commonly practiced deep-network architecture and the fast iterative shrinkage algorithm, and show that our architecture exhibits better image quality and contrast.

bioengineering↗

bioRxiv2018

Anterior insular cortex plays a critical role in interoceptive attention

Although accumulating evidence indicates that the anterior insular cortex (AIC) mediates interoceptive attention, which refers the attention towards physiological signals arising from the body, the necessity of the AIC in this process has not been demonstrated. Using a novel task that directs attention toward breathing rhythm, we assessed the involvement of the AIC in interoceptive attention in healthy participants using functional magnetic resonance imaging and examined the necessity of the AIC in interoceptive attention in patients with AIC lesions. We found that interoceptive attention was associated with greater AIC activation, as well as enhanced coupling between the AIC and somatosensory area along with reduced coupling between AIC and visual sensory areas. AIC activation and connectivity were predictive of individual differences in interoceptive accuracy. Importantly, AIC lesion patients showed disrupted interoceptive discrimination accuracy and sensitivity. Together, these results provide compelling evidence that AIC plays a critical role in interoceptive attention.

neuroscience↗

bioRxiv2018

Comparative whole-genome analysis reveals genetic adaptation of the invasive pinewood nematode

Genetic adaptation to new environments is essential for invasive species. To explore the genetic underpinnings of invasiveness of a dangerous invasive species, the pinewood nematode (PWN) Bursaphelenchus xylophilus, we analysed the genome-wide variations of a large cohort of 55 strains isolated from both the native and introduced regions. Comparative analysis showed abundant genetic diversity existing in the nematode, especially in the native populations. Phylogenetic relationships and principal component analysis indicate a dominant invasive population/group (DIG) existing in China and expansion beyond, with few genomic variations. Putative origin and migration paths at a global scale were traced by targeted analysis of rDNA sequences. A progressive loss of genetic diversity was observed along spread routes. We focused on variations with a low frequency allele (<50%) in the native USA population but fixation in DIG, and a total of 25,992 single nuclear polymorphisms (SNPs) were screened out. We found that a clear majority of these fixation alleles originated from standing variation. Functional annotation of these SNP-harboured genes showed that adaptation-related genes are abundant, such as genes that encode for chemoreceptors, proteases, detoxification enzymes, and proteins involved in signal transduction and in response to stresses and stimuli. Some genes under positive selection were predicted. Our results suggest that adaptability to new environments plays essentially roles in PWN invasiveness. Genetic drift, mutation and strong selection drive the nematode to rapidly evolve in adaptation to new environments, which including local pine hosts, vector beetles, commensal microflora and other new environmental factors, during invasion process.

genomics↗

bioRxiv2018

Synthetic Metabolic Pathway for the Production of 1-Alkenes from Lignin-derived Molecules

Integration of synthetic metabolic pathways to catabolically diverse chassis provides new opportunities for sustainable production. One attractive scenario is the use of abundant waste material to produce readily collectable product, minimizing production costs. Towards that end, we established the production of semivolatile medium-chain -olefins from lignin-derived monomers: we constructed 1-undecene synthesis pathway in Acinetobacter baylyi ADP1 using ferulate as the sole carbon source. In order to overcome the toxicity of ferulate, we first applied adaptive laboratory evolution, resulting in a highly ferulate-tolerant strain. Next, we demonstrated the 1-undecene production from glucose by heterologously expressing a fatty acid decarboxylase UndA and a thioesterase TesA in the wild type strain. Finally, we constructed the alkene synthesis pathway in the ferulate-tolerant strain. We were able to produce 1-undecene from ferulate and collect the product from the culture headspace without downstream processing. This study demonstrates the potential of bacterial lignin upgradation into value-added products.

bioengineering↗

bioRxiv2018

Microbial Cells Harboring a Mitochondrial Gene Are Capable of CO2 Capture

Global warming is escalating with increased temperatures reported worldwide. Given the enormous land mass on the planet, biological capture of CO2 remains a viable approach to mitigate the crisis as it is economical and easy to implement. In this study, a gene capable of CO2 capture was identified via selection in minimal media. This mitochondrial gene named as OG1 encodes the OK/SW-CL.16 protein and shares homology with cytochrome oxidase subunit III of various species and PII uridylyl-transferase from Loktanella vestfoldensis SKA53. CO2 capture experiments indicate that {delta}13C was substantially higher in the cells harboring the gene OG1 than the control in the nutrition-poor media. This study suggests that CO2 capture using engineered microorganisms in barren land can be exploited to address the soaring CO2 level in the atmosphere, opening up vast land resources to cope with global warming.\n\nIMPORTANCEGlobal warming crisis is deteriorating with increased CO2 levels in the atmosphere each year. Action must be taken before catastrophic consequences occur in the not-so-distant future. Biological capture of CO2 is a feasible approach to alleviate the current crisis. We have identified a mitochondrial gene which demonstrated CO2 utilization capability. Data presented in this study suggest that CO2 capture using engineered microorganisms can be harnessed to address the ever-rising CO2 level in the atmosphere.

bioengineering↗

bioRxiv2018

Synthetic chromosome fusion: effects on genome structure and function

As part of the Synthetic Yeast 2.0 (Sc2.0) project, we designed and synthesized synthetic chromosome I. The total length of synI is [~]21.4% shorter than wild-type chromosome I, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns of potential instability and karyotype imbalance. We used a variation of a previously developed, robust CRISPR-Cas9 method to fuse chromosome I to other chromosome arms of varying length: chrIXR (84kb), chrIIIR (202kb) and chrIVR (1Mb). All fusion chromosome strains grew like wild-type so we decided to attach synI to synIII. Through the investigation of three-dimensional structures of fusion chromosome strains, unexpected loops and twisted structures were formed in chrIII-I and chrIX-III-I fusion chromosomes, which depend on silencing protein Sir3. These results suggest a previously unappreciated 3D interaction between HMR and the adjacent telomere. We used these fusion chromosomes to show that axial element Red1 binding in meiosis is not strictly chromosome size dependent even though Red1 binding is enriched on the three smallest chromosomes in wild-type yeast, and we discovered an unexpected role for centromeres in Red1 binding patterns.

synthetic biology↗

bioRxiv2018

TCR/ITK signaling via mTOR tunes CD8+ T cell homeostatic proliferation, metabolism, and anti-tumor effector function

T cell homeostatic proliferation (HP) is regulated by T cell receptor (TCR) signals and homeostatic cytokines, and suggested to be proportional to TCR signal strength. However, we show here that ITK, a positive regulator of TCR signaling, negatively tunes CD8+ T cell HP, metabolism, and effector function. Under lymphopenic environments, Itk-/- CD8+ T cells exhibit significant increase in T cell-intrinsic HP, which requires mTOR activity and can be driven by T cell-T cell interaction. TCR signals through ITK tune IL-7-mediated CD8+ T cell metabolism and HP in a mTOR-dependent manner. The lack of ITK also resulted in enhanced effector cell fate programming, antigen sensitivity and anti-tumor immunity by HP cells. Thus, TCR signaling via ITK, is a negative tuner of CD8+ T cell homeostasis, metabolism and effector function, and may be a target for clinical benefit in cancer therapy.\n\nOne Sentence SummaryTCR signal strength had been long-thought to be proportional to T cell proliferation and effector function, here we demonstrate a counterintuitive role of the TCR signaling through ITK in negatively tuning proliferation under lymphopenic conditions via regulating mTOR activity, T cell metabolism, proliferation, and effector function.

immunology↗

bioRxiv2018

Seasonal changes of metabolites in phloem sap from Broussonetia papyrifera

Gas chromatography-Mass spectrometry (GC-MS) were employed to analyze the whole metabolites in phloem sap of Broussonetia papyrifera and the seasonal changes of content of these metabolites were also investigated. Thirty-eight metabolites were detected in BP phloem exudates. The highest content (44.59mg g-1) of total metabolites was presented in March. High contents of organic acids and sugars were detected in BP phloem exudates from all growing months. Smaller amounts of fatty acids and alcohols were also detected in BP phloem exudates. Interestingly, some metabolites, such as PI3 kinase inhibitor, Chlorogenic acid, Chelerythrine and palmitic acid, which have properties of bioactivity to anticancer and anti-inflammation, were also detected. Quininic acid was the most abundant organic acid, representing up to 86.3% (average value) of all organic acids. D-fructose, D-glucose, and sucrose were the major soluble sugars in phloem saps and the maximum of sugars content was 19.76mg g-1 (average value) in November. Seasonal changes of contents of metabolites were different among individuals. The metabolites analysis double confirmed that the BP phloem sap can be serviced as an important resource for synthesis of pharmaceutical and human health products.

plant biology↗

bioRxiv2018

Type-2 CD8+ T lymphocytes responsive to PGD2 and LTE4 in severe eosinophilic asthma

The functions and in vivo roles of type-2 CD8+ T cells in humans have not been well defined and this cell type has been largely overlooked in models of disease. We investigated this in the context of severe asthma with persistent airway eosinophilia - a phenotype associated with high exacerbation risk and responsiveness to type-2 cytokine-targeted therapies. In two independent cohorts we show that, in contrast to Th2 cells, type-2 cytokine-secreting CD8+CRTH2+ (Tc2) cells are enriched in blood and airways in severe eosinophilic asthma. Concentrations of prostaglandin D2 (PGD2) and cysteinyl leukotriene E4 (LTE4) are also increased in the airways of the same group of patients. In vitro PGD2 and LTE4 function synergistically to trigger Tc2 cell recruitment and activation in a TCR-independent manner. These lipids regulate diverse genes in Tc2 cells inducing type-2 cytokines and many other pro-inflammatory cytokines and chemokines which could contribute to eosinophilia. These findings are consistent with an important innate-like role for human Tc2 cells in severe eosinophilic asthma and suggest a potential target for therapeutic intervention in this and other diseases.

immunology↗

bioRxiv2017

The prognostic effects of somatic mutations in ER-positive breast cancer

More than 50 genes are recurrently affected by somatic mutation in estrogen receptor positive (ER+) breast cancer but prognostic effects have not been definitively established. Primary tumor DNA was therefore subjected to targeted sequencing from 625 postmenopausal (UBC-TAM series) and 328 premenopausal (MA12 trial) hormone receptor-positive (HR+) patients. Independent validation of prognostic interactions was achieved using independent data from the METABRIC study. Associations between MAP3K1 and PIK3CA with luminal A status and TP53 mutations with Luminal B/non-luminal tumors were observed, validating the methodological approach. In UBC-TAM, NF1 frame-shift nonsense (FS/NS) mutation was validated as a poor outcome driver. For MA12, poor outcome associated with PIK3R1 mutation was similarly validated. DDR1 mutations were strongly associated with poor prognosis in UBC-TAM despite stringent false-discovery correction (q=0.0003). In conclusion, uncommon recurrent somatic mutations should be further explored to create a more complete explanation of the highly variable outcomes that typify ER+ breast cancer.

genomics↗

bioRxiv2017

Clinically Important sex differences in GBM biology revealed by analysis of male and female imaging, transcriptome and survival data

Sex differences in the incidence and outcome of human disease are broadly recognized but in most cases not adequately understood to enable sex-specific approaches to treatment. Glioblastoma (GBM), the most common malignant brain tumor, provides a case in point. Despite well-established differences in incidence, and emerging indications of differences in outcome, there are few insights that distinguish male and female GBM at the molecular level, or allow specific targeting of these biological differences. Here, using a quantitative imaging-based measure of response, we found that temozolomide chemotherapy is more effective in female compared to male GBM patients. We then applied a novel computational algorithm to linked GBM transcriptome and outcome data, and identified novel sex-specific molecular subtypes of GBM in which cell cycle and integrin signaling were identified as the critical determinants of survival for male and female patients, respectively. The clinical utility of cell cycle and integrin signaling pathway signatures was further established through correlations between gene expression and in vitro chemotherapy sensitivity in a panel of male and female patient-derived GBM cell lines. Together these results suggest that greater precision in GBM molecular subtyping can be achieved through sex-specific analyses, and that improved outcome for all patients might be accomplished via tailoring treatment to sex differences in molecular mechanisms.\n\nOne Sentence SummaryMale and female glioblastoma are biologically distinct and maximal chances for cure may require sex-specific approaches to treatment.

cancer biology↗