Flood avoidance behaviour in Brown Dippers Cinclus pallasii

Extreme weather events such as tropical cyclones are becoming more frequent, but efforts to understand their impact on wildlife have focused on population-level change rather than the behavioural responses of individuals. In this study, we monitored individually marked Brown Dippers Cinclus pallasii in upland Taiwanese streams in order to investigate the movements of these birds following typhoons in 2004, 2012 and 2013. Individuals moved significantly longer distances immediately after floods compared with before, and in typhoon years compared with other years. Most of these movements involved temporary displacement from a major stream to one of its tributaries, where population size and food abundance are typically lower. These results suggest that movements after flooding were not driven by food abundance but that relatively poor quality streams may provide an important refuge for birds following typhoons

Introduction of a strong temperature-sensitive phenotype into enterovirus 71 by altering an amino acid of virus 3D polymerase

AbstractIn 1998, an enterovirus 71 (EV71) epidemic in Taiwan resulted in 78 deaths; however, the molecular basis of EV71 pathogenicity remains poorly understood. Comparison of the deduced amino acid sequences in 3D polymerases of EV71clinical isolates showed the T251V or T251I substitution from 1986 and 1998 outbreaks. An EV71 replicon system showed that introducing an I251T mutation did not affect luciferase activities at 35 °C when compared with wild type; however, lower luciferase activities were observed when they were incubated at 39.5 °C. In addition, the I251T mutation in the EV71 infectious clone not only reduced viral replication at 39.5 °C in vitro but also decreased the virulence of the mouse adaptive strain MP4 in neonatal mice in an i.p. infection model. Therefore, these results suggested that the threonine at position 251 results in a temperature sensitivity phenotype of EV71 which may contribute to the attenuation of circulating strains

Statistical identification of gene association by CID in application of constructing ER regulatory network

<p>Abstract</p> <p>Background</p> <p>A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating <it>in silico </it>inference of regulatory network structure. The new measure of association, coefficient of intrinsic dependence (CID), is model-free and can be applied to both continuous and categorical distributions. When given two variables X and Y, CID answers whether Y is dependent on X by examining the conditional distribution of Y given X. In this paper, we apply CID to analyze the regulatory relationships between transcription factors (TFs) (X) and their downstream genes (Y) based on clinical data. More specifically, we use estrogen receptor α (ERα) as the variable X, and the analyses are based on 48 clinical breast cancer gene expression arrays (48A).</p> <p>Results</p> <p>The analytical utility of CID was evaluated in comparison with four commonly used statistical methods, Galton-Pearson's correlation coefficient (GPCC), Student's <it>t</it>-test (STT), coefficient of determination (CoD), and mutual information (MI). When being compared to GPCC, CoD, and MI, CID reveals its preferential ability to discover the regulatory association where distribution of the mRNA expression levels on X and Y does not fit linear models. On the other hand, when CID is used to measure the association of a continuous variable (Y) against a discrete variable (X), it shows similar performance as compared to STT, and appears to outperform CoD and MI. In addition, this study established a two-layer transcriptional regulatory network to exemplify the usage of CID, in combination with GPCC, in deciphering gene networks based on gene expression profiles from patient arrays.</p> <p>Conclusion</p> <p>CID is shown to provide useful information for identifying associations between genes and transcription factors of interest in patient arrays. When coupled with the relationships detected by GPCC, the association predicted by CID are applicable to the construction of transcriptional regulatory networks. This study shows how information from different data sources and learning algorithms can be integrated to investigate whether relevant regulatory mechanisms identified in cell models can also be partially re-identified in clinical samples of breast cancers.</p> <p>Availability</p> <p>the implementation of CID in R codes can be freely downloaded from <url>http://homepage.ntu.edu.tw/~lyliu/BC/</url>.</p

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

<p>Abstract</p> <p>Background</p> <p><it>Neocallimastix patriciarum</it> is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (<it>GHs</it>) produced by this anaerobic fungus.</p> <p>Results</p> <p>We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to <it>N. patriciarum </it>to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative <it>GH </it>contigs and classified them into 25 <it>GH</it> families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the <it>GH1</it>, <it>GH3</it>, <it>GH5</it>, <it>GH6</it>, <it>GH9</it>, <it>GH18</it>, <it>GH43 </it>and <it>GH48 </it>gene families, which were highly expressed in <it>N. patriciarum </it>cultures grown on different feedstocks.</p> <p>Conclusions</p> <p>These <it>GH </it>genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.</p

Population ecology of green peach aphid, Myzus persicae (Sulzer) n radish and cabbage

桃蚜有翅蚜出現之時間及比例受溫度及起始密度所影響，營養品質高、 30℃高溫及5℃低溫皆會抑制有翅蚜之形成，以15℃時有翅蚜出現之比例 最多。有翅蚜之發育臨界低溫皆較無翅蚜為低，而總積溫則較之為高。各 定溫下以起始密度高者，族群發展較快，種內競爭較明顯，族群之存活亦 較短。15℃以上之定溫，密度依變死亡率(K值)之波動皆比低溫5℃及10℃ 者為大，且族群生長至末期死亡率直線上升，25℃以上則隨溫度、起始密 度升高，種內競爭愈趨嚴重，其爭奪性競爭 (scramble competition)亦 愈明顯。密度愈高，出現有翅蚜之比例亦愈大，而植物品質愈差，桃蚜愈 擁擠時，隨溫度自低溫升高至15℃時，有翅蚜出現之時間愈提前，出現比 例亦愈大。15℃時為出現有翅蚜之主要溫度。桃蚜體內蛋白質量經定量後 在4∼8%之間，受溫度及蚜蟲年齡所影響，隨溫度升高，蛋白質量明顯上 升，隨蚜蟲年齡增加，蛋白質量則明顯下降。種內競爭及溫度之影響，使 蚜蟲體重下降，隨溫度升高，體重下降愈明顯。桃蚜及偽菜蚜在甘藍及蘿 蔔田之空間分布皆為聚集型。11月為族群發生高峰，有翅四齡若蚜於11月 下旬始出現， 12月時為田間族群受寄生蜂寄生之盛期。顯示11月時兩種 蚜蟲族群密度皆過於擁擠，族群本身除產生有翅蚜以調節並擴散族群外， 天敵亦為族群調節因子之一。甘藍田中之桃蚜及偽菜蚜共存，其族群密度 依變死亡率之作用皆為補償不足之作用(b=0.305及0.430)，族群密度維持 平穩發展。寄生於桃蚜之天敵煙蚜繭蜂整個未成熟期發育所需時間以30℃ 時之8.5天為最短，隨溫度降低而直線增加，至15℃時需 23.1天為最長。 化蛹率及羽化率以20℃時為最高。田間族群羽化率達57∼65%，雌性比高 達77.2∼78.1%，重複寄生蜂蚜金小蜂於 30℃發育僅需7.20天、壽命僅 為2.90天，皆隨溫度降低而延長，15℃時發育需時22.67天、壽命為13.93 天。低溫5及10℃無此蜂出現。重複寄生蜂蚜金小蜂之發育臨界低溫較寄 生蜂煙蚜繭蜂為高，煙蚜繭蜂又較寄主桃蚜為高，但其總積溫，三者間無 此明顯關係。Occurrence and emergence rate of alate of the green peach aphid, Myzus persicae (Sulzer), were influenced by temperature and initial apterous female density. Nutrition, high and low temperatures might suppress occurrence of alate individuals. The emergence rate of alate aphids was highest at 15℃.The population growth time was always shortest at high initial density of 16 aphids/leaf when tested with various temperatures. Usually the highest peak occurred at about 20 days after starting the population growth, however, peaks took longer time at low temperatures and reached earlier at high temperatures. The intraspecific competition was a scramble one. The protein content in the body of the green peach aphid was measured to be 4%∼8%, and raised with increase of temperature and declined with aphid age. The protein content was affected by temperature and population growth of aphid. The aphid population growth was hampered by high temperature at 30℃, the body weight of adult reduced to the lightest. Both M. persicae and the turnip aphid, Lipaphis erysimi (Kalt.), were found coexisted and clumped distribution in the fields. The peaks of population of both species appeared in November. Following the high population density, the field populations of aphids were heavily parasitized by parasitoids in December. The developmental time of immature stage of Aphidius gifuensis Ashmead decreased with rise of temperature. The rates of pupation and adult emergence were highest at 20℃. In field population, the emergence rate was 57∼65%. The female sex ratio was 77.2∼78.1%. The developmental duration of the immature stage of Pachyneuron aphidis (Bouche) required as long as 22.67 days at 15℃ and as shortest as 7.20 days at 30℃. The Tb of the hyperparasite was significantly higher than the parasitoid, whereas the parasitoid Tb value was higher than that of its host aphid.封面 目錄 頁次 誌謝 中文摘要 英文摘要 緒言 文獻摘述 一、蚜蟲生活史 二、溫度、光週期、擁擠及植物品質對蚜蟲有翅型發生之影響 三、溫度、擁擠及植物品質對蚜蟲生長發育之影響 四、發育臨界低溫度及總積溫 五、空間分布 六、田間族群變動 七、蚜蟲與植物間之關係 八、種內競爭及密度依變死亡率 九、蚜蟲與植物間之關係 十、植物含氮量對昆蟲之關係 十一、共生物與蚜蟲之關係 十二、蚜繭蜂之基本生態學 十三、煙蚜繭蜂及重複寄生蜂蚜金小蜂之特性 材料與方法 一、不同溫度與密度下有翅挑蚜在蘿蔔及甘藍上之出現及其發育總積溫 二、不同溫度及起始密度下桃蚜於蘿蔔葉上之族群增長與密度依變死亡率 三、溫度及桃蚜密度與作物含氮量及有翅蚜出現之關係 四、溫度、族群生長、密度及作物含氮量對桃蚜體內蛋白質量及體重之影響 五、桃蚜及偽菜蚜在甘藍及蘿蔔田之空間分布與族群增長 六、桃蚜及偽菜在甘藍田之生存及與寄主含氮量之關係 七、寄生桃蚜之煙蚜繭蜂及重複寄生蜂呀金小蜂於不定溫下之發育 結果與討論 一、不同溫度與密度下有翅桃蚜在蘿蔔及甘藍上之出現及其發育總積溫 1.蘿蔔及甘藍葉上有翅蚜之出現與發育 2.蘿蔔及甘藍苗上有翅蚜之出現與發育 3.發育臨界低溫及總積溫 二、不同溫度與密度下有翅桃蚜在蘿蔔葉上之族群增長與密度依變死亡率 1.不同溫度及起始密度下桃蚜之族群密度 2.不同溫度及起始密度下桃蚜之族群增長率 3.不同溫度及起始密度下桃蚜之密度依變死亡率 三、溫度及桃蚜密度與作物含氮量及有翅蚜出現之關係 1.不同溫度及起始密度下蘿蔔葉含氮量與有翅蚜出現之關係 2.不同溫度及起始密度下甘藷葉含氮量與有翅蚜出現之關係 3.甘藍之含氮量與有翅蚜出現之關係 4.不同定溫下蘿蔔苗及甘藍苗含氮量與桃蚜之關係 四、溫度、族群生長、密度及作物含氮量對桃蚜體內蛋白質量及體重之影響 1.不同定溫下成蚜及若蚜體內蛋白質量 2.桃蚜體內蛋白質與族群生長之關係 3.桃蚜體重、體內蛋白質量與溫度、族群生長、密度及植物含氮量之關係 五、桃蚜及偽菜蚜在甘藍及蘿蔔田之空間分布與族群增長 1.空間分布 2.族群增長 六、桃蚜及偽菜蚜在甘藍及蘿蔔田之生存及與寄主含氮量之關係 七、寄生桃蚜之煙蚜繭蜂及重複寄生蜂蚜金小蜂於不同溫下之發育 1.煙蚜繭蜂於不同溫度處理下之羽化、性比及壽命 2.不同定溫下煙蚜繭蜂之化蛹率、發育時間、發育臨界低溫及總積溫 3.蚜金小蜂之發育及壽命 引用文獻 表

Factors Controlling Changes in Epilithic Algal Biomass in the Mountain Streams of Subtropical Taiwan.

In upstream reaches, epilithic algae are one of the major primary producers and their biomass may alter the energy flow of food webs in stream ecosystems. However, the overgrowth of epilithic algae may deteriorate water quality. In this study, the effects of environmental variables on epilithic algal biomass were examined at 5 monitoring sites in mountain streams of the Wuling basin of subtropical Taiwan over a 5-year period (2006-2011) by using a generalized additive model (GAM). Epilithic algal biomass and some variables observed at pristine sites obviously differed from those at the channelized stream with intensive agricultural activity. The results of the optimal GAM showed that water temperature, turbidity, current velocity, dissolved oxygen (DO), pH, and ammonium-N (NH4-N) were the main factors explaining seasonal variations of epilithic algal biomass in the streams. The change points of smoothing curves for velocity, DO, NH4-N, pH, turbidity, and water temperature were approximately 0.40 m s-1, 8.0 mg L-1, 0.01 mg L-1, 8.5, 0.60 NTU, and 15°C, respectively. When aforementioned variables were greater than relevant change points, epilithic algal biomass was increased with pH and water temperature, and decreased with water velocity, DO, turbidity, and NH4-N. These change points may serve as a framework for managing the growth of epilithic algae. Understanding the relationship between environmental variables and epilithic algal biomass can provide a useful approach for maintaining the functioning in stream ecosystems

Effect of warming with temperatureoscillations on a low-latitude aphid,Aphis craccivora

To estimate the net effect of climate change on natural populations, we must take into account the positive and negative effects of temperature oscillations and climate variability. Warming because of climate change will likely exceed the physiological optima of tropical insects, which currently live very close to their thermal optima. Tropical insects will be negatively affected if their optima are exceeded otherwise warming may affect them positively. We evaluate the demographic responses of the cowpea aphid, Aphis craccivora, to summer warming in subtropical and tropical Taiwan, and examine the effects of diel temperature oscillation on these responses. Aphids were reared at four temperatures (current summer mean, +1.4, +3.9 and +6.4 °C), the latter three simulating different levels of warming. At each average temperature, aphids experienced constant or oscillating (from −2.9 to +3.6 °C of each mean temperature) regimes. As the simulated summer temperatures increased, so did the negative effects on life-history traits and demographic parameters. Compared with aphids reared in constant temperatures, aphids reared in oscillating temperatures developed more slowly and had a longer mean generation time, but their net reproductive rate was higher. These findings demonstrate that climate warming will affect demographic parameters and life-history traits differentially. Studies that use constant temperatures are unlikely to accurately predict biotic responses to climate change

A Mini-Review of Strategies for Quantifying Anthropogenic Activities in Microplastic Studies in Aquatic Environments

Microplastic pollution is no longer neglected worldwide, as recent studies have unveiled its potential harm to ecosystems and, even worse, to human health. Numerous studies have documented the ubiquity of microplastics, reflecting the necessity of formulating corresponding policies to mitigate the accumulation of microplastics in natural environments. Although anthropogenic activities are generally acknowledged as the primary source of microplastics, a robust approach to identify sources of microplastics is needed to provide scientific suggestions for practical policymaking. This review elucidates recent microplastic studies on various approaches for quantifying or reflecting the degree to which anthropogenic activities contribute to microplastic pollution. Population density (i.e., often used to quantify anthropogenic activities) was not always significantly correlated with microplastic abundance. Furthermore, this review argues that considering potential sources near sample sites as characteristics that may serve to predict the spatial distribution of microplastics in aquatic environments is equivocal. In this vein, a watershed-scale measure that uses land-cover datasets to calculate different percentages of land use in the watershed margins delineated by using Geographic Information System (GIS) software is discussed and suggested. Progress in strategies for quantifying anthropogenic activities is important for guiding future microplastic research and developing effective management policies to prevent microplastic contamination in aquatic ecosystems