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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of evolution & Marine Biodiversity (Ministry of Education) and institute of evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology department College of ScienceKing Saud University department of biology Bradley University Laboratory for Marine biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Effect of medicinal mushrooms on blood cells under conditions of diabetes mellitus

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World Journal of Diabetes 2017年第5期8卷 187-201页

作者： Taras Vitak Borys Yurkiv Solomon Wasser Eviatar Nevo Natalia Sybirna department of evolutionary and environmental biology Faculty of Natural ScienceUniversity of Haifa institute of evolution and department of evolutionary and environmental biology Faculty of Natural ScienceUniversity of Haifa institute of evolution Faculty of Natural ScienceUniversity of Haifa department of Biochemistry Faculty of BiologyIvan Franko National University of Lviv

Diabetes mellitus(DM) is the third most common noninfectious disease leading to early disability and high mortality. Moreover, the number of patients is growing every year. The main symptom of DM is hyperglycemia. Increased levels of blood glucose activate polyol, hexosamine, and protein kinase metabolic pathways cause the intensification of non-enzymatic glycosylation and nitration of macromolecules. This, in turn, leads to the development of oxidative and nitrative stresses and secondary complications, such as different kinds of microand macroangiopathies. Metabolic disorders caused by insulin deficiency in diabetes significantly impede the functioning of a homeostasis system, which change the physical, biochemical, morphological, and functional properties of blood cells. As a result, the oxygen-transport function of red blood cells(RBCs), rheological properties of the blood, and functions of immunocompetent cells as well as the process of apoptosis are primarily affected. Modern pharmacotherapy focuses on the search for new preparations that aim to decrease blood glucose levels. Undesirable side effects and adverse reactions caused by synthetic medicines led to the search and investigation of new preparations of natural origin. Medicinal mushrooms play an important role among such new preparations. They are a source of a large number of high-and lowmolecular compounds with pronounced biological effects. Our investigations show pronounced hypoglycemic and anti-anemic action of submerged cultivated mycelium powder of medicinal mushrooms Agaricus brasiliensis(A. brasiliensis) and Ganoderma lucidum(G. lucidum) on streptozotocin-induced DM in rats. Also, we showed that mycelium powders have membrane protective properties as evidenced by the redistribution of RBC populations towards the growth of full functional cell numbers. Normalization of parameters of leukocyte formula and suppression of apoptosis of white blood cells in diabeticrats treated with A. brasiliensis a

关键词： Diabetes mellitus Streptozotocin Agaricus brasiliensis Ganoderma lucidum Leukocytes Red blood cells

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Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans

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Science China(Life Sciences) 2019年第4期62卷 579-593页

作者： Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen institutes for Systems Genetics West China Hospital Sichuan University department of Ecology and evolution the University of Chicago department of evolutionary Genetics Max-Planck Institute for Evolutionary Biology department of evolutionary Theory Max-Planck Institute for Evolutionary Biology Committee on Genetics the University of Chicago

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

关键词： Caenorhabditis elegans,orphan genes de novo genes

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A comparison of two methods to assess audience-induced changes in male mate choice

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Current Zoology 2012年第1期58卷 84-94页

作者： Madlen ZIEGE Carmen HENNIGE-SCHULZ Frauke MUECKSCH department of Ecology & evolution J. W. Goethe University Frankfurt institute of Biochemistry & biology Unit of Evolutionary Biology & Systematic Zoology University of Potsdam

Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk： interacting more equally with different females may be advantageous because ri- vals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains un- known if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males＇ mating preferences by scoring pre-mating （nipping） and mating behavior （gonopodial thrusting）. Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male＇s behavior. A reduction in the strength of focal males＇ preferences was also seen after the rival male had an opportunity to mate with the focal male＇s preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both slimulus females not only the male＇s motivational state is reflected but also females＇ behavior such as avoidance of male sexual harassment [Current Zoology 58 （1）： 84-94, 2012].

关键词： Communication networks Male mate choice Non-independent mate choice Sexual selection Sperm competition risk Audience effect

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LEAF COLOR SEGMENTATION AND POT VOLUME INFLUENCE ON THE CO_(2) ABSORPTION EFFICIENCY IN TWO COMMON GREEN-WALL PLANTS

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Journal of Green Building 2021年第3期16卷 3-12页

作者： Har’el Agra Daphna Uni Rael Horwitz Tamir Klein Leon Blaustein The Kadas Green Roofs Ecology Center University of HaifaMt Carmel3498838Israel department of Plant&environmental Sciences Weizmann Institute of ScienceRehovot 76100Israel institute of evolution and department of evolutionary&environmental biology University of HaifaMt Carmel3498838Israel

Green walls can improve indoor air-quality by reducing concentrations of carbon dioxide(CO_(2))and other air *** study focused on the spider plant,Chlorophytum comosum,and devil’s ivy,Epipremnum aureum,both common green-wall plants that have been found to be efficient CO_(2) *** species have multiple variants with varying degrees of leaf green-white *** pho-tosynthesis depends on the concentration of leaf chlorophylls,we hypothesized that green variants are more efficient carbon absorbers than green-white *** addi-tion,we tested the hypothesis that the photosynthetic rate of plants is affected by pot volume,as suggested by previous *** used a portable gas exchange system to determine the rate of photosynthesis of the study *** evidence was found for better photosynthetic performance in the green ***-white variants of each *** fact,our results suggest the *** was observed that a spider plants assimilated carbon more efficiently when grown in a larger pot *** conclusion,our study shows that in terms of carbon assimilation,green-white variants of spider plants are the better choice for indoor green *** efficiency can be improved dramatically by increasing pot volume.

关键词： air quality carbon dioxide Chlorophytum comosum Epipremnum aureum indoor green wall photosynthesis

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The birth hour of mammals:insights from intra-specific variation in wild blue monkeys

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Current Zoology 2022年第5期68卷 499-506页

作者： Marina Cords Emma Gometz department of Ecology Evolution and Environmental BiologyColumbia UniversityNew YorkNY 10027USA New York Consortium in evolutionary Primatology 695 Park AvenueNew YorkNY 10065USA

While most mammals show birth hour peaks at times of the 24-h cycle when they are less active,there are exceptions to this general *** exceptions have been little explored,but may clarify evolutionary reasons for the diel timing of *** investigated intraspecific variation in birth hour in wild blue monkeys Cercopithecus mitis stuhlmanni,a diurnal primate,to identify factors that differentiated daytime versus nighttime *** and life history data from 14 groups over 14 years revealed that 4%of 484 births occurred during the *** of daytime birth varied with mother’s age,peaking at 15.7 *** whose annual timing deviated most from the population’s peak birth months were 5 times more likely to occur during daytime than those that deviated *** was no evidence that mother’s rank or infant sex influenced birth hour,and mixed evidence that daytime births were more probable in larger *** did not differ significantly for infants born during the day versus ***-aged mothers may be able to handle the consequences of an unusual birth hour more successfully than mothers with less experience or those weakened by *** birth may be more advantageous in the off-season because nights are colder at that time of *** findings are consistent with hypotheses relating birth hour to the risk of losing social protection in group-living animals,but are not consistent with those emphasizing risk of conspecific *** of within-species variation can help in evaluating evolutionary hypotheses for non-random birth hour.

关键词： birth timing Cercopithecus mitis circadian pattern diel cycle guenon parturition

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Preliminary attempt to distinguish the domesticated pigs from wild boars by the methods of carbon and nitrogen stable isotope analysis

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Science China Earth Sciences 2009年第1期52卷 85-92页

作者： Michael P.RICHARDS department of Human evolution Max-Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D-04103LeipzigGermany

Despite great achievements in the origins of domestic pigs made by the methods of zooarchaeology and molecular biology,how to scientifically distinguish the domesticated pigs from wild boars during the early stage of pig domestication is still poorly *** to wild boar's diets which come from the natural environment,the diets of domestic pigs are more easily influenced by human feeding ***,in principle,exploration of the dietary differences among pigs and understanding the impact on pig diets fed by humans can have great potential to differentiate between wild boars and domesticated *** reveal dietary differences among pigs and distinguish the domesticated pigs from wild boars based on comparison with the diets of humans and other animals,we analyzed the carbon and nitrogen stable isotopes of human bones from Xiaojingshan Site and animal bones from Yuezhuang Site,both of which belong to Houli Culture in Shandong Province and date to about 8500―7500 years *** mean δ 13C value((-17.8 ± 0.3)‰) and δ 15N value((9.0±0.6)‰) in human collagen indicate that although millet agriculture began it was not the main subsistence strategy as millets are typical of C4 plants and that humans made a living mainly by gathering,hunting or raising some domesticated *** δ 13C value(-16.1‰) and δ 15N value(6.9‰) in the bovine suggest that C3 plants were dominant in its diet with some C4 plants *** fish has lower δ 13C value(-24.9‰) and higher δ 15N value(8.8‰) than the bovine,which is the characteristic of the isotopic values from Eurasian freshwater *** on the differences in carbon and nitrogen isotope values,the pigs can be divided into three groups.A group,composed of two pigs,has low δ 13C values(-18.1‰,-20.0‰) and low δ 15N values(4.7‰,6.0‰).B group,only one pig,has the highest δ 13C value(-10.6‰) and mediate δ 15N value(6.4‰).As for the C group,also only one pig,low δ 13C value(-19.0‰) and the highest δ 15N value(9.1‰

关键词： origins of domestic pigs early stage of domestication differentiation of domesticated pigs from wild boars carbon and nitrogen stable isotope analysis millet agriculture

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Distribution of fatty acids in the alpine grassland soils of the Qinghai-Tibetan Plateau

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Science China Earth Sciences 2016年第7期59卷 1329-1338页

作者： DAI Guo Hua ZHU Shan Shan LIU Zong Guang CHEN Li Tong HE Jin Sheng FENG Xiao Juan State Key Laboratory of Vegetation and environmental Change Institute of Botany Chinese Academy of Sciences Key Laboratory of Adaptation and evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences department of Ecology College of Urban and Environmental Sciences Peking University

As an important biomarker, fatty acids(FAs) have been extensively used to trace the origin of organic matter in sediments and soils. However, studies of the distribution and abundance of FAs in alpine grassland soils are still rare, especially on the Qinghai-Tibetan Plateau(QTP), the highest plateau in the world, which contributes sediments to many large rivers in Asia. This study investigates the composition, distribution and source of FAs with increasing soil depths from 17 typical alpine grassland sites in the QTP. The most abundant FAs included the ubiquitous C16 FA and even-numbered long-chain FAs(C20–C30), indicating mixed inputs from microbial and higher plant sources. Source apportionment showed that higher plants were the dominant contributor of FAs(approximately 40%) in QTP soils. The abundance of FAs decreased with soil depth, with the highest value(1.08±0.09 mg/g C) at a 0–10 cm depth and the lowest value(0.46±0.12 mg/g C) at a 50–70 cm depth, due to much lower plant inputs into the deeper horizons. The total concentration of FAs was negatively correlated to the mean annual temperature(MAT; Penvironmental parameters, such as the soil mineral content(aluminum and iron oxide), microbial community composition as well as litter quality and quantity, may also exert a strong control on the preservation of FAs in QTP soils and warrant further research to better understand the mechanisms responsible for the preservation of FAs in QTP soils.

关键词： Qinghai-Tibetan Plateau Soil organic matter Biomarker Fatty acids Distribution sources

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New calculations indicate that 90% of flowering plant species are animal-pollinated

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National Science Review 2023年第10期10卷 17-19页

作者： Ze-Yu Tong Ling-Yun Wu Hui-Hui Feng Meng Zhang W.Scott Armbruster Susanne S.Renner Shuang-Quan Huang institute of evolution and Ecology School of Life Sciences Central China Normal University Faculty of Resources and environmental Science Hubei University School of Biological Sciences University of Portsmouth institute of Arctic biology University of Alaska Fairbanks department of biology Washington University

The services of animal pollinators that deliver compatible pollen to receptive stigmas are essential for the reproduction of many flowering plants [1,2].The maintenance of plant-pollinator interactions,therefore,is the basis for the function and sustainability of healthy *** this reason, there has been widespread concern over the past two decades about the global decline in pollinators and the effects of this loss on pollination services for both wild plants and crops [3,4].

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The evolutionary consequences of selfish genetic elements

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Current Zoology 2016年第6期62卷 655-658页

作者： Anna K. LINDHOLM Tom A.R. PRICE department of evolutionary biology and environmental Studies University of Zurich Winterthurerstrasse 190 Zurich Switzerland institute of Integrative biology University of Liverpool Crown Street Liverpool UK

The traditional view of the genome was once that it is broadly cooperative, with all genes working together amicably to improve the success of the individual as a whole. Benefits to the individual, after all, benefit all the component genes, as fair Mendelian inheritance ensures that all the genes and alleles a parent carries are equally likely to be inherited by an offspring. However, more detailed studies of inheritance have shown that this rosy view of cooperation within the genome is untrue. Instead, many genes act selfishly, manipulating gametogenesis to bias transmission in their favor （Butt and Trivers 2006）. This increases their representation in offspring at a cost to the fitness of the individual and the cooperative genes.

关键词：遗传因素进化基因组孟德尔遗传等位基因合作多基因后代

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