scholarly journals Dynamically expressed genes provide candidate viability biomarkers in a model coccidian

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258157
Author(s):  
Matthew S. Tucker ◽  
Celia N. O’Brien ◽  
Mark C. Jenkins ◽  
Benjamin M. Rosenthal
Keyword(s):  
Carbon Fixation ◽  
Protein A ◽  
Energy Utilization ◽  
Hypothetical Proteins ◽  
Oocyst Wall ◽  
Kegg Pathways ◽  
Coccidian Parasites ◽  
Study Interval ◽  
Go Terms

Eimeria parasites cause enteric disease in livestock and the closely related Cyclospora cayetanensis causes human disease. Oocysts of these coccidian parasites undergo maturation (sporulation) before becoming infectious. Here, we assessed transcription in maturing oocysts of Eimeria acervulina, a widespread chicken parasite, predicted gene functions, and determined which of these genes also occur in C. cayetanensis. RNA-Sequencing yielded ~2 billion paired-end reads, 92% of which mapped to the E. acervulina genome. The ~6,900 annotated genes underwent temporally-coordinated patterns of gene expression. Fifty-three genes each contributed >1,000 transcripts per million (TPM) throughout the study interval, including cation-transporting ATPases, an oocyst wall protein, a palmitoyltransferase, membrane proteins, and hypothetical proteins. These genes were enriched for 285 gene ontology (GO) terms and 13 genes were ascribed to 17 KEGG pathways, defining housekeeping processes and functions important throughout sporulation. Expression differed in mature and immature oocysts for 40% (2,928) of all genes; of these, nearly two-thirds (1,843) increased their expression over time. Eight genes expressed most in immature oocysts, encoding proteins promoting oocyst maturation and development, were assigned to 37 GO terms and 5 KEGG pathways. Fifty-six genes underwent significant upregulation in mature oocysts, each contributing at least 1,000 TPM. Of these, 40 were annotated by 215 GO assignments and 9 were associated with 18 KEGG pathways, encoding products involved in respiration, carbon fixation, energy utilization, invasion, motility, and stress and detoxification responses. Sporulation orchestrates coordinated changes in the expression of many genes, most especially those governing metabolic activity. Establishing the long-term fate of these transcripts in sporulated oocysts and in senescent and deceased oocysts will further elucidate the biology of coccidian development, and may provide tools to assay infectiousness of parasite cohorts. Moreover, because many of these genes have homologues in C. cayetanensis, they may prove useful as biomarkers for risk.

scholarly journals RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 656
Author(s):  
Jing Jin ◽  
Rui Shi ◽  
Ramsey Steven Lewis ◽  
Howard David Shew
Keyword(s):  
Partial Resistance ◽  
Molecular Mechanisms ◽  
Biological Activities ◽  
Effective Means ◽  
Phytophthora Nicotianae ◽  
Economic Losses ◽  
Black Shank ◽  
Differential Gene ◽  
Go Terms

Phytophthora nicotianae is a devastating oomycete plant pathogen with a wide host range. On tobacco, it causes black shank, a disease that can result in severe economic losses. Deployment of host resistance is one of the most effective means of controlling tobacco black shank, but adaptation to complete and partial resistance by P. nicotianae can limit the long-term effectiveness of the resistance. The molecular basis of adaptation to partial resistance is largely unknown. RNAseq was performed on two isolates of P. nicotianae (adapted to either the susceptible tobacco genotype Hicks or the partially resistant genotype K 326 Wz/Wz) to identify differentially expressed genes (DEGs) during their pathogenic interactions with K 326 Wz/Wz and Hicks. Approximately 69% of the up-regulated DEGs were associated with pathogenicity in the K 326 Wz/Wz-adapted isolate when sampled following infection of its adapted host K 326 Wz/Wz. Thirty-one percent of the up-regulated DEGs were associated with pathogenicity in the Hicks-adapted isolate on K 326 Wz/Wz. A broad spectrum of over-represented gene ontology (GO) terms were assigned to down-regulated genes in the Hicks-adapted isolate. In the host, a series of GO terms involved in nuclear biosynthesis processes were assigned to the down-regulated genes in K 326 Wz/Wz inoculated with K 326 Wz/Wz-adapted isolate. This study enhances our understanding of the molecular mechanisms of P. nicotianae adaptation to partial resistance in tobacco by elucidating how the pathogen recruits pathogenicity-associated genes that impact host biological activities.

scholarly journals Acinetobacter baylyi Starvation-Induced Genes Identified through Incubation in Long-Term Stationary Phase

2010 ◽  
Vol 76 (14) ◽  
pp. 4905-4908 ◽  
Author(s):  
C. Phoebe Lostroh ◽  
Bruce A. Voyles
Keyword(s):  
Gene Expression ◽  
Stationary Phase ◽  
Batch Culture ◽  
Exponential Growth ◽  
Hypothetical Proteins ◽  
Acinetobacter Baylyi ◽  
Metabolic Gene Expression ◽  
Induced Genes ◽  
Dna Maintenance

ABSTRACT Acinetobacter species encounter cycles of feast and famine in nature. We show that populations of A cinetobacter baylyi strain ADP1 remain dynamic for 6 weeks in batch culture. We created a library of lacZ reporters inserted into SalI sites in the genome and then isolated 30 genes with lacZ insertions whose expression was induced by starvation during long-term stationary phase compared with their expression during exponential growth. The genes encode metabolic, gene expression, DNA maintenance, envelope, and conserved hypothetical proteins.

An Empirical Analysis of the Relationship between Economic Growth and Energy Utilization in China

2013 ◽  
Vol 734-737 ◽  
pp. 1666-1670
Author(s):  
Fei Hu Yang ◽  
Peng Zhang ◽  
Xiao Wei Wang
Keyword(s):  
Economic Growth ◽  
Empirical Analysis ◽  
Energy Utilization ◽  
Correction Model ◽  
Vector Autoregressive ◽  
Integration Test ◽  
Recycling Economy ◽  
The Relationship ◽  
The Empirical Analysis

Based on the co-integration test, error correction model and vector autoregressive model, the empirical analysis results show a long-term co-integration relationship between economic growth and energy utilization in China, energy consumption increased by 1%, GDP will increase by 1.342%. In order to raise the efficiency of energy utilization during China's economic development, suggestions like saving energy conservation, reducing emission and recycling economy have been proposed.

Macrophages primed by overnight culture demonstrate a marked stimulation of surfactant protein A degradation

1997 ◽  
Vol 273 (4) ◽  
pp. L831-L839 ◽  
Author(s):  
Sandra R. Bates ◽  
Jin Xu ◽  
Chandra Dodia ◽  
Aron B. Fisher
Keyword(s):  
Protein A ◽  
Surfactant Protein ◽  
Surfactant Protein A ◽  
Prolonged Culture ◽  
Primed State ◽  
Elevated Rate ◽  
Hand Length ◽  
Macrophage Uptake ◽  
Overnight Culture

The current study examined whether long-term culture of macrophages affects their metabolism of surfactant components. Compared with freshly isolated resting macrophages in culture for 1 h, macrophages attached to plastic dishes for 24 h showed evidence of conversion to a “primed” state with 1) an altered morphology characterized by a larger size, ruffled membranes, lamellipodia, and a “foamy” appearance after attachment to glass and 2) a fivefold greater respiratory burst in response to phorbol 12-myristate 13-acetate stimulation. On incubation with iodinated surfactant protein A (SP-A), the 24-h alveolar or tissue macrophages showed a 5- or a 23-fold greater increase in SP-A degradation, respectively, than macrophages cultured for 1 h. Conditioned media experiments demonstrated that the elevated rate of SP-A degradation after prolonged culture was not a result of proteases secreted by the macrophages. Incubation of cells with NH4Cl reduced the degradation of SP-A to a similar extent (to 33% of control values) in resting and primed tissue macrophages. On the other hand, length of time of cell culture did not affect macrophage uptake and degradation of [3H]dipalmitoylphosphatidylcholine in mixed unilamellar liposomes. Thus freshly isolated resting tissue and alveolar macrophages can be primed to specifically increase their rate of SP-A degradation. Activation of macrophages associated with lung disease may be important for SP-A metabolism and surfactant function.

scholarly journals Transcriptomic and proteomic responses to herbivory in cultivated, Bt-transgenic and wild rice

2020 ◽  
Author(s):  
Yongbo Liu ◽  
Weiqing Wang ◽  
Yonghua Li ◽  
Fang Liu ◽  
Weijuan Han ◽  
...  
Keyword(s):  
Transgenic Rice ◽  
Wild Rice ◽  
Crop Production ◽  
Brown Planthopper ◽  
Hierarchical Cluster ◽  
Nilaparvata Lugens ◽  
Cultivated Rice ◽  
Kegg Pathways ◽  
Itraq Analysis ◽  
Go Terms

Abstract Background: Strategies are still employed to decrease insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with the insertion of foreign genes, while the insect-resistant mechanism of these strategies remains unclear. Results: Under the feeding of brown planthopper (Nilaparvata lugens), cultivated rice (WT) showed less DEGs (568) and DAPs (4) than transgenic rice (2098 and 11) and wild rice CL (1990 and 39) and DX (1932 and 25). Hierarchical cluster of DEGs showed gene expression of CL and DX were similar, slightly distinct to GT, and clearly different from WT. DEGs assigned to the GO terms were less in WT rice than GT, CL and DX, and “Metabolic process”, “cellular process”, “response to stimulus” were dominant. Wild rice CL significantly enriched in KEGG pathways of “Metabolic pathways”, “biosynthesis of secondary metabolites”, “plant-pathogen interaction” and “plant hormone signal transduction”. The iTRAQ analysis confirmed the results of RNA-seq, which showing the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. Synthesize conclusions: This study demonstrated that similarity in the transcriptomic and proteomic response to herbivory for the wild rice and Bt-transgenic rice, while cultivated rice lack of enough pathways in response to herbivory. Our results highlighted the importance of conservation of crop wild species.

scholarly journals Oocyst wall formation and composition in coccidian parasites

2009 ◽  
Vol 104 (2) ◽  
pp. 281-289 ◽  
Author(s):  
Kelly Mai ◽  
Philippa A Sharman ◽  
Robert A Walker ◽  
Marilyn Katrib ◽  
David De Souza ◽  
...  
Keyword(s):  
Oocyst Wall ◽  
Wall Formation ◽  
Coccidian Parasites

A 1 Ma record of climate-induced vegetation changes using sed aDNA and pollen in a biodiversity hotspot: Lake Towuti, Sulawesi, Indonesia

2021 ◽  
Author(s):  
Akhtar-E Ekram ◽  
Rebecca Hamilton ◽  
Matthew Campbell ◽  
Chloe Plett ◽  
Sureyya Kose ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Carbon Fixation ◽  
Biodiversity Hotspot ◽  
Fossil Pollen ◽  
Vegetation Changes ◽  
Pollen Record ◽  
River Channels ◽  
Sedimentary Record ◽  
Lake Towuti

<p>Several studies have shown that ancient plant-derived DNA can be extracted and sequenced from lake sediments and complement the analysis of fossil pollen in reconstructing past vegetation responses to climate variability and anthropogenic perturbations. The majority of such studies have been performed on Holocene lakes located in cooler higher latitude regions whereas similar studies from tropical lakes are limited. Here, we report a ~1 Ma record of vegetation changes in tropical Lake Towuti (Sulawesi, Indonesia) through parallel pollen and sedimentary ancient DNA (sed aDNA) analysis. Lake Towuti is located in a vegetation biodiversity hotspot and in the centre of the Indo Pacific Warm Pool (IPWP), which comprises the world’s warmest oceanic waters and influences globally important climate systems. In the context of global change, the surface area of the IPWP is rapidly expanding. Lake Towuti is of particular interest since it provides a unique opportunity to obtain a long-term record of IPWP-controlled climate-ecosystem interactions and ecosystem resilience. Stratigraphic analysis of fossil pollen vs. sequencing of preserved chloroplast DNA (cpDNA) signatures (i.e., trnL-P6) both revealed that Lake Towuti experienced significant vegetation changes during the transition from a landscape initially characterized by active river channels, shallow lakes and swamps into a permanent lake ~1 Ma ago. Both proxies marked a predominance of trees or shrubs during most of Lake Towuti’s history, but the trnL-P6 barcoding approach revealed a much higher relative abundance of remote montane conifers, which likely have produced large amounts of chloroplast-rich airborne pollen that were subsequently buried in the sedimentary record. The pollen record showed a higher relative abundance of evergreen tropical forest vegetation, whereas the trnL-P6 record revealed a higher relative abundance of predominantly wetland herbs that must have entered the lake from the local catchment in the form of chloroplast-rich litter. Furthermore, the sedimentary record was rich in presumably wind-derived chloroplast-lacking fern spores, while fern trnL-P6 was only sporadically detected. Only through trnL-P6 barcoding, fern-derived biomass in the sedimentary record could be identified as Schizaeaceae, which is a primitive tropical grass-like fern family often associated with swampy or moist soils. Unlike pollen, trnL-P6 could identify grasses at clade and subfamily levels and confirmed that the majority of grasses in the area represented wet climate C3 grasses or those that can switch between C3 and C4 carbon fixation pathways, whereas grasses that can only perform C4 carbon fixation, indicative of dry climate conditions, were not detected. At least for sediments deposited prior to the Last Glacial Maximum, neither pollen nor trnL-P6 revealed significant vegetation changes between alternating layers of lacustrine green and red sideritic clays thought to have been deposited during orbitally controlled wetter vs. drier periods. These preliminary results suggest that vegetation in this tropical biodiversity hotspot may be relatively resilient to long-term variations in IPWP hydrology.</p>

scholarly journals Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy by bioinformatics

2020 ◽  
Vol 38 (6) ◽  
pp. 1717-1729
Author(s):  
Ying Zhang ◽  
Francesca Garofano ◽  
Xiaolong Wu ◽  
Matthias Schmid ◽  
Peter Krawitz ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Candidate Genes ◽  
Thyroid Dysfunction ◽  
Functional Enrichment ◽  
Ppi Network ◽  
Effective Treatment Option ◽  
Autoimmune Thyroid ◽  
Go Annotation ◽  
Kegg Pathways ◽  
Go Terms

Summary Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), the first immune checkpoint to be targeted clinically, has provided an effective treatment option for various malignancies. However, the clinical advantages associated with CTLA-4 inhibitors can be offset by the potentially severe immune-related adverse events (IRAEs), including autoimmune thyroid dysfunction. To investigate the candidate genes and signaling pathways involving in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy, integrated differentially expressed genes (DEGs) were extracted from the intersection of genes from Gene Expression Omnibus (GEO) datasets and text mining. The functional enrichment was performed by gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Protein-protein interaction (PPI) network, module enrichment, and hub gene identification were constructed and visualized by the online Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. A total of 22 and 17 integrated human DEGs in hypothyroidism and hyperthyroidism group related to anti-CTLA-4 therapy were identified, respectively. Functional enrichment analysis revealed 24 GO terms and 1 KEGG pathways in the hypothyroid group and 21 GO terms and 2 KEGG pathways in the hyperthyroid group. After PPI network construction, the top five hub genes associated with hypothyroidism were extracted, including ALB, MAPK1, SPP1, PPARG, and MIF, whereas those associated with hyperthyroidism were ALB, FCGR2B, CD44, LCN2, and CD74. The identification of the candidate key genes and enriched signaling pathways provides potential biomarkers for autoimmune thyroid dysfunction related to anti-CTLA-4 therapy and might contribute to the future diagnosis and management of IRAEs for cancer patients.

scholarly journals Design of an Integrated Remote and Ground Sensing Monitor System for Assessing Farmland Quality

Sensors ◽  
2020 ◽  
Vol 20 (2) ◽  
pp. 336
Author(s):  
Feiyang Zhang ◽  
Guangxing Wang ◽  
Yueming Hu ◽  
Liancheng Chen ◽  
A-xing Zhu
Keyword(s):  
High Resolution ◽  
Monitoring System ◽  
Data Transmission ◽  
Remote Sensing Data ◽  
Energy Utilization ◽  
Utilization Efficiency ◽  
Quality Data ◽  
Conventional System ◽  
Sensing Data

Quality monitoring is important for farmland protection. Here, high-resolution remote sensing data obtained by unmanned aerial vehicles (UAVs) and long-term ground sensing data, obtained by wireless sensor networks (WSNs), are uniquely suited for assessing spatial and temporal changes in farmland quality. However, existing UAV-WSN systems are unable to fully integrate the data obtained from these two monitoring systems. This work addresses this problem by designing an improved UAV-WSN monitoring system that can collect both high-resolution UAV images and long-term WSN data during a single-flight mission. This is facilitated by a newly proposed data transmission optimization routing protocol (DTORP) that selects the communication node within a cluster of the WSN to maximize the quantity of data that can be efficiently transmitted, additionally combining individual scheduling algorithms and routing algorithms appropriate for three different distance scales to reduce the energy consumption incurred during data transmission between the nodes in a cluster. The performance of the proposed system is evaluated based on Monte Carlo simulations by comparisons with that obtained by a conventional system using the low-energy adaptive clustering hierarchy (LEACH) protocol. The results demonstrate that the proposed system provides a greater total volume of transmitted data, greater energy utilization efficiency, and a larger maximum revisit period than the conventional system. This implies that the proposed UAV-WSN monitoring system offers better overall performance and enhanced potential for conducting long-term farmland quality data collection over large areas in comparison to existing systems.

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