scholarly journals Quantitative proteomics reveals remodeling of protein repertoire across life phases ofDaphnia pulex

2019 ◽  
Author(s):  
Leonid Peshkin ◽  
Myriam Boukhali ◽  
Wilhelm Haas ◽  
Marc W. Kirschner ◽  
Lev Y. Yampolsky
Keyword(s):  
Life Cycle ◽  
Model Organism ◽  
Whole Body ◽  
Gene Model ◽  
Down Regulation ◽  
Protein Coding ◽  
Diapausing Eggs ◽  
Adult Females ◽  
Shock Proteins ◽  
Freshwater Plankton

AbstractThe microcrustaceanDaphniais becoming an organism of choice for genomic and proteomic studies of the effects of environmental stressors. However, the changes in protein expression across the life cycle have not been fully characterized. We analyzed the proteomes of adult females, juveniles, asexually produced embryos, and the ephippia - resting stages containing two sexually produced diapausing freezing- and desiccation-resistant embryos. Overall, we were significantly more likely to detect proteins with known molecular functions than proteins with no detectable orthology. Similarly we could detect those with stronger gene model support, as judged by mutual best BLAST hits between two independent genome assemblies than those without such support. This suggests that we could apply our proteomics pipeline to verify hypothesized proteins, even given less-than-perfect reference gene models. In particular, we observed up-regulation of vitellogenins and down-regulation of actins and myosins in embryos of both types, as compared to juveniles and adults and overrepresentation of cell-cycle related proteins in the developing embryos, as compared to both diapausing embryos and adults. We found upregulation of small heat-shock proteins and redox peroxidases, as well as overrepresentation of stress-response proteins in the ephippium relative to the asexually produced non-diapausing embryos. The ephippium also showed up-regulation of three trehalose-synthesis proteins and down-regulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.Statement of significance of the studyFreshwater plankton crustaceanDaphniais rapidly becoming a model organism of choice for ecological and developmental genomics. While there have been several advances towards establishing the protocols and reference datasets for proteomics, a detailed dataset covering several main steps of asexual and sexual phases ofDaphnialife cycle is not yet available. Moreover, different versions ofD. pulexgenome differ in the number of protein-coding genes identified; it is unclear whether these differences are caused by differences between sequenced genotypes or between gene model methodology used. In this study we report LC-MS2/MS3 proteomes of whole body adult females, juvenile females, asexually produces embryos and diapausing eggs capable of surviving freezing and desiccation.

NIR-active Nanoterminator with Mature Dendritic Cell Acitivities for Immuno-Priming Mild Photothermal Cancer Therapy

2020 ◽  
Author(s):  
zhihong sun ◽  
Guanjun Deng ◽  
Xinghua Peng ◽  
Xiuli Xu ◽  
Lanlan Liu ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Photothermal Therapy ◽  
Whole Body ◽  
Mature Dendritic Cell ◽  
Immune Microenvironment ◽  
Highly Efficient ◽  
Tumor Immune Microenvironment ◽  
Shock Proteins ◽  
Mild Temperature ◽  
Broad Interest

Recently, photothermal-immuno synergistic therapy under mild temperature (~ 45 °C) has got broad interest in cancer treatment. Inhibition the intratumorally HSPs production is the key to accomplish highly efficient and mild photothermal therapy. In this work, we developed biomimetic nanoterminators with mature DCs functions by coating the mature dendritic cell membrane on photothermal nanoagents. As-prepared nanoterminators could automatically locate on T cell in the complex tumor-immune microenvironment and promote the T cells proliferation, activation and cytokine secretion, which could not only inhibit the expression of heat shock proteins to cooperate on highly efficient mild photothermal therapy (~42°C), but also promote tumor apoptosis during the treatment. More importantly, this nanoterminator could serve as vaccine to trigger anti-tumor immune response of the whole body, which would be promising to long-life tumor inhibition and termination.

scholarly journals Metabolic reprogramming during the Trypanosoma brucei life cycle

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 683 ◽  
Author(s):  
Terry K. Smith ◽  
Frédéric Bringaud ◽  
Derek P. Nolan ◽  
Luisa M. Figueiredo
Keyword(s):  
Life Cycle ◽  
Trypanosoma Brucei ◽  
Model Organism ◽  
Protozoan Parasite ◽  
Tsetse Fly ◽  
Metabolic Reprogramming ◽  
Mammalian Host ◽  
Insect Vector ◽  
Environmental Signals ◽  
Cellular Metabolic Activity

Cellular metabolic activity is a highly complex, dynamic, regulated process that is influenced by numerous factors, including extracellular environmental signals, nutrient availability and the physiological and developmental status of the cell. The causative agent of sleeping sickness, Trypanosoma brucei, is an exclusively extracellular protozoan parasite that encounters very different extracellular environments during its life cycle within the mammalian host and tsetse fly insect vector. In order to meet these challenges, there are significant alterations in the major energetic and metabolic pathways of these highly adaptable parasites. This review highlights some of these metabolic changes in this early divergent eukaryotic model organism.

scholarly journals Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic

2011 ◽  
Vol 78 (2) ◽  
pp. 549-559 ◽  
Author(s):  
Thibault Varin ◽  
Connie Lovejoy ◽  
Anne D. Jungblut ◽  
Warwick F. Vincent ◽  
Jacques Corbeil
Keyword(s):  
High Arctic ◽  
Environmental Stresses ◽  
The Arctic ◽  
Functional Responses ◽  
Protein Coding ◽  
Content Type ◽  
Stress Genes ◽  
Cyanobacterial Genes ◽  
Shock Proteins ◽  
The Antarctic

ABSTRACTPolar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived fromProteobacteriaandCyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation ofActinobacteriaandAlphaproteobacteriain the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.

New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

2021 ◽  
Author(s):  
Fangfang Huang ◽  
Yingru Jiang ◽  
Tiantian Chen ◽  
Haoran Li ◽  
Mengjia Fu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Rice Genome ◽  
Model Organism ◽  
Gene Families ◽  
Food Crop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

scholarly journals Differential expression of heat-shock proteins and spontaneous synthesis of HSP70 during the life cycle of Blastocladiella emersonii

1987 ◽  
Vol 163 (1) ◽  
pp. 211-220 ◽  
Author(s):  
M. Christina M. BONATO ◽  
Aline M. SILVA ◽  
Suely L. GOMES ◽  
Jose Carlos C. MAIA ◽  
Maria Helena JULIANI
Keyword(s):  
Life Cycle ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Differential Expression ◽  
Blastocladiella Emersonii ◽  
Shock Proteins

Transcriptomics throughout the life cycle of Leishmania infantum: High down-regulation rate in the amastigote stage

2010 ◽  
Vol 40 (13) ◽  
pp. 1497-1516 ◽  
Author(s):  
Pedro J. Alcolea ◽  
Ana Alonso ◽  
Manuel J. Gómez ◽  
Inmaculada Moreno ◽  
Mercedes Domínguez ◽  
...  
Keyword(s):  
Life Cycle ◽  
Leishmania Infantum ◽  
Down Regulation ◽  
Amastigote Stage

scholarly journals Reproductive diapause in Nysius huttoni White (Heteroptera Lygaeidae)

2002 ◽  
Vol 55 ◽  
pp. 308-311
Author(s):  
X.Z. He ◽  
Q. Wang ◽  
A. Carpenter
Keyword(s):  
Life Cycle ◽  
Immature Stages ◽  
Life Stages ◽  
Reproductive Diapause ◽  
Entire Life ◽  
Entire Life Cycle ◽  
Adult Females ◽  
Critical Photoperiod

The induction of reproductive diapause of Nysius huttoni was studied in the laboratory at 20 1C and 60 10 RH under a series of photoperiod regimes 168 h 1410 h 1212 h and 1014 h lightdark Reproductive diapause was considered to have occurred if females failed to lay eggs for 50 days after emergence The sensitivity of different life stages to diapauseinducing photoperiods varied When newly emerged females whose immature stages had been reared at 168 h were transferred to 1014 h and 1212 h 467 and 793 of them entered reproductive diapause respectively However when fifth instar nymphs were transferred from 168 h to 1014 h and 1212 h 100 of adult females entered reproductive diapause If the entire life cycle was maintained at 1014 h and 1212 h 667 and 400 of females entered reproductive diapause respectively The critical photoperiod for reproductive diapause was estimated to lie between 1311 h and 135105 h

scholarly journals A reference translatome map reveals two modes of protein evolution

2021 ◽  
Author(s):  
Aaron Wacholder ◽  
Omer Acar ◽  
Anne-Ruxandra Carvunis
Keyword(s):  
Model Organism ◽  
Great Majority ◽  
High Sensitivity ◽  
Ribosome Profiling ◽  
Computational Framework ◽  
Protein Coding ◽  
Biologically Relevant ◽  
Protein Coding Genes ◽  
Representative Subset ◽  
Evolutionarily Conserved

Ribosome profiling experiments demonstrate widespread translation of eukaryotic genomes outside of annotated protein-coding genes. However, it is unclear how much of this "noncanonical" translation contributes biologically relevant microproteins rather than insignificant translational noise. Here, we developed an integrative computational framework (iRibo) that leverages hundreds of ribosome profiling experiments to detect signatures of translation with high sensitivity and specificity. We deployed iRibo to construct a reference translatome in the model organism S. cerevisiae. We identified ~19,000 noncanonical translated elements outside of the ~5,400 canonical yeast protein-coding genes. Most (65%) of these non-canonical translated elements were located on transcripts annotated as non-coding, or entirely unannotated, while the remainder were located on the 5' and 3' ends of mRNA transcripts. Only 14 non-canonical translated elements were evolutionarily conserved. In stark contrast with canonical protein-coding genes, the great majority of the yeast noncanonical translatome appeared evolutionarily transient and showed no signatures of selection. Yet, we uncovered phenotypes for 53% of a representative subset of evolutionarily transient translated elements. The iRibo framework and reference translatome described here provide a foundation for further investigation of a largely unexplored, but biologically significant, evolutionarily transient translatome.

Diverse patterns of expression of the cytochrome c oxidase subunit I gene and unassigned reading frames 4 and 5 during the life cycle of Trypanosoma brucei

1985 ◽  
Vol 5 (11) ◽  
pp. 3041-3047
Author(s):  
D P Jasmer ◽  
J E Feagin ◽  
K Stuart
Keyword(s):  
Life Cycle ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Trypanosoma Brucei ◽  
Protein Coding ◽  
Oxidase Subunit ◽  
Life Cycle Stages ◽  
Multiple Processes ◽  
Mitochondrial Transcripts ◽  
Reading Frames

Transcription of a maxicircle segment from Trypanosoma brucei 164 that contains nucleotide (nt) sequences corresponding to cytochrome c oxidase subunit I (COI) and unassigned reading frames (URFs) 4 and 5 of other mitochondrial systems was investigated. Two major transcripts that differ in size by ca. 200 nt map to each of the COI and URF4 genes, while a single major transcript maps to URF5. In total RNA, the larger COI transcript is more abundant in procyclic forms (PFs) than in bloodstream forms (BFs), the smaller COI and both URF4 transcripts have similar abundances in both forms, and the single URF5 transcript is more abundant in BF than PF. These patterns of expression differ in poly(A)+ RNA as a result of a higher proportion of poly(A)+ mitochondrial transcripts in PFs than in BFs. In addition, small (300- to 500-nt) RNAs that are transcribed from C-rich sequences located between putative protein-coding genes also exhibit diverse patterns of expression between life cycle stages and differences in polyadenylation in PFs compared with BFs. These observations suggest that multiple processes regulate the differential expression of mitochondrial genes in T. brucei.

A taxonomic review of the Margarodoid genus Stigmacoccus Hempel  (Hemiptera: Sternorrhyncha: Coccoidea: Stigmacoccidae), with some details on their biology

Zootaxa ◽  
2007 ◽  
Vol 1507 (1) ◽  
pp. 1-55 ◽  
Author(s):  
CHRIS HODGSON ◽  
HEATHER GAMPER ◽  
AMAURI BOGO ◽  
GILLIAN WATSON
Keyword(s):  
Life Cycle ◽  
Scale Insect ◽  
Present Knowledge ◽  
Passerine Birds ◽  
Adult Males ◽  
Undescribed Species ◽  
Annual Life Cycle ◽  
Honey Production ◽  
Adult Females ◽  
The Family

Stigmacoccus is an unusual scale insect genus from Central and South America that has been little studied. It belongs to the family Stigmacoccidae within the archaeococcoid group of genera which used to comprise the family Margarodidae (Morrison, 1927) but which are now considered to represent at least 9 families. The present paper describes or redescribes the adult females, adult males, cyst stages and crawlers of the three known species (S. asper, S. garmilleri, and S. paranaensis), plus the prepupa of S. garmilleri and S. paranaensis, and (briefly), the pupa of S. paranaensis. It is considered that the female has two cyst stage instars; the number in the male is uncertain. Adult female S. asper and S. paranaensis appear to have groups of loculate pores on the walls of the vagina. A lectotype for S. asper is designated. In addition, cyst stages of three further undescribed species are described (but not formally named) and illustrated. Some observations on the biology and life cycle are also included. The honeydew of Stigmacoccus species has been shown to be an important energy source for overwintering passerine birds which defend this resource. A summary of our present knowledge is presented, including how the honedew is eliminated (through a long anal tube) and details are given with regard to rates of honeydew flow, sugar concentration, cyst densities and annual timing of peak flows. The annual life cycle, as far as it is known, is discussed. It is concluded that this honeydew could be economically important as a source of sugar for honey production but this would need to be carefully managed to maintain an ecological balance.

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