A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

黑龙江嘉荫地区古新世孢粉植物群及古植被、古气候研究

植物是环境变化的重要指示物之一。晚白垩至早第三纪时期，全球生态系统发生了剧烈变化，研究这一时期植物对了解地质历史时期环境变化趋势, 认识和保护当今环境有重要意义。我国黑龙江省嘉荫县有这一时期的地层发育，其中乌云煤矿和白山头是主要的露头剖面。前人曾从地质时代、孢粉及植物化石角度对这两个剖面进行过研究，但是仍有部分问题尚存争议。在本项工作中，我们对两个剖面的孢粉样品进行了系统采样，部分孢粉类型同时在光镜和电镜下进行了拍照。我们还对存在争议的这两个剖面的地质时代进行了讨论。同时，首次用共存分析法对这两个剖面的在沉积时期的气候进行了整体及分段的定量重建。另外，我们结合中其它地点的气候重建工作对不同时期的纬度温度梯度进行了研究。 乌云煤矿和白山头两个乌云组剖面的古新世孢粉植物群的研究结果表明：乌云煤矿孢粉植物群主要是与榛属（Corylus），桤木属（Alnus），桦木属（Betula），榆属（Ulmus）及松属（Pinus）有亲缘关系的植物；白山头剖面的孢粉植物类型与乌云煤矿基本一致，但是其中针叶类植物的花粉所占比重较大。 根据乌云煤矿与白山头剖面的孢粉类型在地层中的分布，以及与其它古新世地层的对比，我们认为乌云煤矿与白山头含孢粉段的地质时代为古新世。 用共存分析法得到乌云组古新世气候参数有两组。孢粉类型的共存结果为：年均温14.8-14.9℃，年降水量816-1389mm；植物化石类型的共存结果为：年均温16.3-16.8℃, 年降水：1124-1623mm。对乌云煤矿与白山头两个剖面孢粉带中的孢粉类型的气候参数分别进行共存，结果表明，除乌云煤矿孢粉第三带到第四带外，乌云地区的年均温在整个沉积时期均呈上升趋势；年均降水量的变化趋势与年均温基本一致。 根据从古新世到现代不同地点气候定量重建的年均温参数，我们计算得到了不同时期纬度温度梯度变化的值：<0.1℃/古纬度（古新世）、 0.1℃/古纬度（始新世）、0.45℃/纬度（中新世）、0.55℃/纬度（上新世）。结合当今全球的平均温度梯度值（0.7℃/纬度），我们得出纬度温度梯度的值从古新世以来呈不断上升的趋势。这一结果显示65Ma 以来赤道与极地间的温度差异逐渐增大，同时也提示了全球温度可能呈下降趋势。

真菌诱导子对青蒿发根生长和青蒿素生物合成的影响及开花与青蒿素生物合成的相关性研究

本论文主要包括以下两部分内容： 一、真菌诱导子对青蒿发根生长和青蒿素生物合成的影响 用3种真菌诱导子[大丽花轮枝孢（Verticillium dahliae Kleb.）、葡枝根霉(Rhizopus stolonifer (Ehrenb. ex Fr.) Vuill)和束状刺盘孢(Colleto trichumdematium (Pers.) Grove)]分别处理青蒿(Ar temisia annuaL．)的发根，这3种真菌诱导子均能促进发根中青蒿素的合成，其中以大丽花轮枝孢的诱导效果最好;对细胞生长均没有明显影响。经大丽花轮枝孢处理的发根中青蒿素含量达1. 12 mg/gDW，比对照(0. 77 mg/g DW)提高45%。诱导子的作用效果与诱导子浓度、诱导子作用时间及发根的生长状态有关。对大丽花轮枝孢来说，诱导子作用的最适浓度为每毫升培养基含糖0.4 mg;发根在指数生长末期对诱导作用最敏感：在加入诱导子4d后收获发根，发根中的青蒿素含量最高。 二、早花基因FPF1、co对青蒿开花时间的影响及开花与青蒿素生物合成的相关性 1．将来源于拟南芥的早花基因Flowering Promoting Factorl (FPFl)插入到植物表达载体pBI121中，构建CaMV 35S启动子控制下含FPFl基因的植物表达载体pBI121FPF/，用含有pBI121FPF/质粒的根癌农杆菌(Agrobacterium tumefaciens)LBA4404感染青蒿(Artemisia annua L.)叶片并诱导丛生芽，经卡那霉素筛选，获得转基因抗性植株。PCR、 PCR-Southem blot及Southern blot检测表明，外源基因FPFI已整合到青蒿基因组中：RT-PCR及RT-PCR Southern blot分析表明，外源基因在转录水平上已有表达。在短日照条件下，FPF1转基因植株的开花时间较对照提前20天左右，但提早开花的转基因植株与未开花的对照其青蒿素含量无明显差异，即提早开花并不能使开花植株的青蒿素含量有所提高，开花与青蒿素合成之间可能没有直接的关系。 2．将拟南芥的早花基因CONSTANS (CO)置于CaMV 35S启动子之下，通过根癌农杆菌(Agrobacterium tumefaciens)LBA4404介导转入青蒿(Artemisia annuaL．)，使之在青蒿中表达，并得到了抗性植株。PCR、PCR-Southem blot及Southemblot检测表明，外源基因co已整合到青蒿基因组中;RT-PCR及RT-PCR Southemblot分析表明，外源基因在转录水平上已有表达。在短日照条件下，co转基因植株的开花时间较对照提前2周左右，但提早开花的转基因植株的青蒿素含量与未丌花的对照无明显差异，即植株开花前青蒿素含量的提高并不是由于开花本身引起的，再次证明，开花与青蒿素合成之间可能没有直接的关系。

Use of homeo drug for curing ulcerative syndrome in fishes

Fungal infection was observed in Catla catla and Labeo rohita cultured in two private fish farms. The later stage of the infection resulted in ulcerations followed by haemorrhage on the dorsal surface of the body. Initially, usual treatments of copper sulphate, potassium permanganate and common salt solution were tried, but no improvement was observed. Then repeated intramuscular injections of homeopathic drug Heaper Sulpher and Arnica spray were given with encouraging results. Infection reported in another farm was also successfully controlled using a similar treatment.

中国都江堰地区两种林龄森林中外生菌根真菌的多样性

外生菌根是重要的菌根类群，在自然界中分布广泛。外生菌根真菌参与了生物地球化学循环，是森林生态系统中的重要组分。由于外生菌根真菌的宿主植物通常是一些生态系统的优势种和建群种，并且这些真菌还参与了许多森林生态系统的有机和无机元素循环、物种的竞争和共存、生物多样性的维持、生态系统的演替等过程，因而对外生菌根真菌的研究有助于对这些生态系统维持和演替机制的深入理解。作者在中国四川都江堰地区选择了两个不同林龄的森林，应用分子生物学方法，研究了它们的外生菌根真菌群落组成。比较分析了两种年龄亚热带森林下真菌群落的物种组成、密度和多样性的差异，并分析了外生菌根真菌群落与宿主植物群落之间的相互关系，主要研究结果如下： (1) 用分子方法(巢式PCR, RFLP和DNA测序)鉴定了87个土样中的ECM真菌。共检测到70种真菌，属于13目21科30属，其中,子囊菌门5目6科6属8种,担子菌门8目15科24属62种。在担子菌门中，革菌目、红菇目和伞菌目三个目的真菌为常见种。 (2) 成熟林的ECM真菌物种数、密度和物种多样性都显著高于幼林。 (3) 少数几种ECM真菌在群落中占绝对优势，而大多数种类的相对多度和相对频度都较低。重要值（IV）至少在一个样地中大于4.0％的真菌共有12种。成熟林中，IV大于4.0％的ECM真菌有8种，分别是：Russula sp.01，Tomentella sp.01，Tomentella sp.04，Tomentella sp.05，Boletales-01，Lactarius sp.01，Tricholomataceae-01，Leptodontidium sp.01；幼林中IV大于4.0％的真菌有6种，分别是：Lactarius quietus，Russula sp.01，Tomentella sp.01，Tomentella sp.02，Tomentella sp.03， Trechisporales-01。 (4) 成熟林与幼林中的优势属有所不同，成熟林以绵菌属和红菇属最丰富，幼林以乳菇属最丰富，其次是绵菌属和红菇属； (5) ECM真菌群落与乔木群落关系密切，ECM真菌群落物种多样性随着菌根乔木群落物种多样性的增加而增加；ECM群落密度随着非菌根乔木群落密度的增加而降低；ECM群落物种数随着非菌根乔木群落物种数的增加而降低。 (6) ECM真菌群落间的相似性与菌根乔木群落间相似性之间呈显著正相关，即，菌根乔木群落之间越相似，则菌根群落之间也越相似；ECM群落间的相似性与非菌根乔木群落间的相似性之间无相关性。

Pathology of mixed infections of saprolegniasis-myxosporidiosis in Indian major carp (Catla catla Ham.)

An outbreak of saprolegniasis in Catla catla in composite carp culture ponds were recorded during winter season. The typical cotton wool growths were observed on whole body surfaces of catla along with sporadic mortality. The fungal invasion was only restricted to skin and no fungal elements were visible in any internal organs after periodic acid schiff staining. On histology, periportal accumulation of mononuclear cells in liver, presence of myxosporidean cysts in antieror kidney, eosinophilic granular cells reaction in submucosa of stomach and intestine, dilated and engorged blood vessels of brain along with sloughing of epidermis and hyperplasia at gill lamellar base were pronounced changes. The possible role of release of Saprolegnia toxin in producing internal organs pathology has been discussed.

Microbiological quality of some iced fishes of Imphal market, Manipur

Imphal is the main marketing centre of fish in Manipur. As fish production of the state is not sufficient to meet the demands, about 120 metric tons of iced fishes are annually brought from other states and sold in this market. Microbiological quality of iced Wallago attu, Labeo rohita, L. gonius and Aorichthy aor in respect of total fungal count (TFC), total plate count of bacteria (TPC), Most Probable Number (MPN) of coliforms, Streptococci, Staphylococcus, Salmonella and Escherichia coli in four tissues (skin, muscle, gill and intestine) were analysed. In all cases, the counts were highest in the gills and lowest in the muscles. The values of TFC, TPC, coliforms, Streptococci and Staphylococci were 0-10³/g 10(sup)6-10⁸/g, 2-α/g, 10-10⁵/g, 10-10⁵/g respectively. E. coli and Salmonella were not detected in any of the samples while the ice used in the preservation contained 10⁵-10⁷ of TPC per gram. The microbiological qualities of the iced fishes of Imphal market were adjudged poor. The extremely high counts of bacteria might be due to (1) poor quality and left over fishes being packed, (2) contact with contaminated ice and (3) repeated thawing and freezing during the process of marketing and transportation.

Toxigenic molds on fish feeds-1: impact of climatic change

The present communication is a survey report carried out to assess the incidence of toxic mycoflora on seven types of agriculture products/by products incorporated during fish culture as supplementary dietary items. Samples were obtained from various sources at Darbhanga, Madhubani and Samashtipur districts during summer, winter and monsoon months. Out of the total 1774 samples, only 894 appeared to be fresh visually reflecting average incidence of contamination around 46.6%. However, the apparently fresh samples, when subjected to culture, 26.9% of them were found to be contaminated. Thus, degree of fungal spoilage in feed ingredients in parts of north Bihar appears to be significantly high (73.5%). The present study illustrates the facts with special reference to Aspergillus flavus, A. parasiticus (elaborating aflatoxins) A. ochraceous, Penicilium viradicatuin (elaborating ochratoxins) and A. versicolor (elaborating sterigmatocystin). The other strains already known for their toxigenic potentials that appeared on the present substrates included A. niger, A. fumigatus, A. candidus, P. islandicum, Rhizopus spp. and Mucur spp. Studies indicate that the prevalent climatic factors like temperature and relative humidity facilitate a congenial condition almost all through the year and in particular during summer and monsoon months. But water content of the substrates is a vital factor that further accelerates the pace of mycobial spoilage. A thorough sun-drying of the agricultural commodities before prolonged storage to bring water content below the "low risk limit" may significantly reduce the incidence of molds.

Survey on the quality of Jaadi available [in] Sri Lankan market

A quality of survey was conducted at the fish curing yards in a northwest coast and the southern coast in Sri Lanka. A total of 40 samples different varieties of fishes were collected from the market and jaadi curing yards and all were evaluated for the quality, fungal and insect infestation. Samples were analyzed for proximate composition chemical, microbiological and sensory quality. Thirty percent of the total analyzed samples of fish were found to be unfit for consumption. Samples collected from Negombo were found to the infected with maggots. Only 42% samples had dry matter above 50%. All the samples showed a protein content above 20%. The highest protein content was 27.92% in hurulla. Over 90% of the samples had TVN at acceptable quality limits (>40). The TBC for 33% of the samples were in the range 104-105/g range, while 48% were in the range of 107-108/g due to contamination of maggots and fungi. The Survey showed jaadi had a high level of protein in its composition. But defects of curing process such on imperfect cleaning inadequate salting resulted in low (Chemical and microbiological) quality of the product.

Histopathological studies of EUS affected shing, Heteropneustes fossilis (Bloch) from a fish farm of Mymensingh, Bangladesh

An investigation was carried out to observe histopathological changes in liver and kidney of suspected epizootic ulcerative syndrome (EUS)-affected shing fish, Heteropneustes fossilis (Bloch) collected from the "Agro-3 fish farm" situated at Boilor, Trishal, Mymensingh. Focal necrosis, haemorrhages and atrophy of the sinusoidal region were observed in the liver tissue. Fungal granulomas were found both in liver and kidney. In some cases fatty depositions were observed in all over the hepatic tissue. Degeneration and necrosis of renal tubular epithelial cells were also occurred. Missing of glomerulus and necrosis surrounding the Bowman's capsule in the kidney tissue were found.

An anionic antimicrobial peptide from toad Bombina maxima

Amphibian skin is a rich resource of antimicrobial peptides like maximins and maximins H from toad Bombina maxima. A novel cDNA clone encoding a precursor protein that comprises maximin 3 and a novel peptide. named maximin H5. was isolated from a skin cDNA library of B. maxima. The predicted primary structure of maximin H5 is ILGPVLGLVSDTLDDVLGIL-NH2,. Containing three aspartate residues and no basic amino acid residues. maximin H5 is characterized by an anionic property. Different from cationic maximin H peptides. only Gram-positive strain Staphylococcus aureus was sensitive to maximin H5. while the other bacteria] and fungal strains tested ere resistant to it. The presence of metal ions. like Zn2+ and Mg2+, did not increase its antimicrobial potency. Maximin H5 represents the first example of potential anionic antimicrobial peptides from amphibians, The results provide the first evidence that. together kith cationic antimicrobial peptides. anionic antimicrobial peptides may also exist naturally as part of the innate defense system. (C), 2002 Elsevier Science (USA). All rights reserved.

Maximin 9, a novel free thiol containing antimicrobial peptide with antimycoplasma activity from frog Bombina maxima

Amphibian skin is a rich resource of antimicrobial peptides, like maximins and maximin Hs from frog Bombina maxima. Novel cDNA clones encoding a precursor protein, which comprises a novel maximin peptide (maximin 9) and reported maximin H3, were isolated from two constructed skin cDNA libraries of B. maxima. The predicted primary structure of maximin 9 is GIGRKFLGGVKTTFRCGVKDFASKHLY-NH2. A surprising substitution is at position 16, with a free cysteine in maximin 9 rather than usual conserved glycine in other reported maximins. Maximin 9, the homodimer form and its Cys(16) to Gly(16) mutant were synthesized and their antimicrobial activities were evaluated. Unlike previously reported maximin 3, the tested bacterial and fungal strains were resistant to maximin 9, its homodimer and the Cys(16) to Gly(16) mutant (with MICs > 100 mu M). On the other hand, interestingly, while eight clinical Mollicutes strains were generally resistant to maximin 9 homodimer and its Cys(16) to Gly(16) mutant, most of them are sensitive to maximin 9 at a peptide concentration of 30 mu M, especially in the presence of dithiothreitol. These results indicate that the presence of a reactive Cys residue in maximin 9 is important for its antimycoplasma activity. The diversity of antimicrobial peptide cDNA structures encountered in B. maxima skin cDNA libraries and the antimicrobial specificity differences of the peptides may reflect well the species' adaptation to the unique microbial environments. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Tolerance of Penaeus monodon larvae to cupric sulfate added in bath

Copper is used to deter the growth of bacterial, fungal and protozoan disease organism in fishes. Zoeae (Z SUB-1 ), myses (M SUB-1 ) and postlarvae (P SUB-1 ) were exposed to copper sulfate at concentrations of 0 . 025, 0 . 05, 0 . 75, 0 . 1 and 0 . 2 ppm from 24 to 96 hours. The number of surviving larvae were counted at the end of each 24-hour period and the percentage of survival is determined for each dose level. The LC SUB-50 for each of the larval stages was interpolated from the data whenever possible. Three trials with 2 replicates per trial were conducted. The physico-chemical characteristics of the bath taken before and at the end of the experimental period show insignificant differences between initial and final values in each trial. Results indicate that mortality rates of all larval stages increased with exposure time and that mortality rates of the experimental group is higher than the control. Interpolation of the LC SUB-50 is possible only for the 48-h and 72-h exposure times for both zoeae and myses and for the 48-h exposure time for the postlarvae. This is due to the high survival percentage of the 24-h group and the low survival percentage (below 50%) of the larvae exposed for 96 hours. The 48-hour LC SUB-50 for Z SUB-1 , M SUB-1 and P SUB-1 are 0 . 225, 0 . 350 and 0 . 125 ppm respectively. Postlarvae seem to be more sensitive than either of the 2 larval stages having a lower 48-h LC SUB-50 and a low survival rate after 72 hours. The larvae were observed to lose their balance and were lethargic, producing few swimming movements so that they were mostly confined to the bottom of the aquaria. Moribund larvae observed under the microscope had a faster but weak heartbeat compared to healthy larvae. Slight or complete loss of feeding ability indicated by empty guts and delayed molting of Z SUB-1 to Z SUB-2 were also noted.

Notes on the induced maturation and spawning in four-month-old Penaeus monodon Fabricius by eyestalk ablation

The ablation technique consisted of making an incision across the eyeball to allow free flow of fluids while holding the prawn under water, squeezing the eyeball contents outwards, and pinching hard the eyestalk tissue. The cut area heals completely in about a week; no application of antibiotics is necessary. Spent spawners were tagged with thin brass rings (Rodriguez, 1976) around the unablated eyestalk for a separate experiment on rematuration. Two spawning yielding approximately 277,000 eggs were obtained three weeks after ablation, followed four days later by two more spawnings with 160,000 eggs; all four spawners weighed more than 100 g. With a hatching rate of 98% and 78% for the first and second batch, respectively, the spawnings produced viable nauplii. Water temperatures as low as 23 degree C due to a delayed cold spell in March depressed molting; weakened larvae had to be discharged at the mysis stage. Although ovarian development continued, no further spawnings were obtained due mainly to the onset of bacterial and fungal disease. Infection is initiated in injured portions of the exoskeleton, sometimes penetrating right through the muscles to the ovarian tissues. The non-flowthrough conditions and mussel meat feeding led to fouling of the culture water resulting in consecutive mortalities caused by disease. Female P.monodon held in maturation pens were ablated at the age of 15 months (Santiago, et al., 1976); they averaged only 16 g body weight after four months growth in ponds. In another experiment, pond-reared P.monodon females ranging from 50 to 80 g were ablated at approximately seven months (Aquacop, 1977). The present results show a minimum age of four months from postlarve that P.monodon is capable of ovarian development and spawning upon ablation. However, maturation is probably affected by size as well as age - the four-month old females weighed an average of 100 g in contrast to the smaller animals in the earlier experiments.

Studies on dried/smoked barracuda

Physical, chemical and organoleptic characteristics of dried and smoked barracuda (Sphyraena spp.) during storage at ambient temperature are reported. Initial increase in total volatile basic nitrogen (TVBN) content after drying as well as smoking did not have any significant effect on the organoleptic qualities of the products. Smoking was found effective in delaying the onset of fungal attack and also in improving the organoleptic qualities.