FragAnchor： A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring

A glycosylphosphatidylinositol （GPI） anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed a computational system, called FragAnchor, based on the tandem use of a neural network （NN） and a hidden Markov model （HMM）. Firstly, NN selects potential GPI-anchored proteins in a dataset, then HMM parses these potential GPI signals and refines the prediction by qualitative scoring. FragAnchor correctly predicted 91% of all the GPI-anchored proteins annotated in the Swiss-Prot database. In a large-scale analysis of 29 eukaryote proteomes, FragAnchor predicted that the percentage of highly probable GPI-anchored proteins is between 0.21% and 2.01%. The distinctive feature of FragAnchor, compared with other systems, is that it targets only the C-terminus of a protein, making it less sensitive to the background noise found in databases and possible incomplete protein sequences. Moreover, FragAnchor can be used to predict GPI-anchored proteins in all eukaryotes. Finally, by using qualitative scoring, the predictions combine both sensitivity and information content. The predictor is publicly available at http：//navet .ics.hawaii.edu/- fraganchor/NNHMM/NNHMM.ht ml.     

Ethanol in the stems of trees

Acetaldehyde and ethanol are usually thought to be produced in plant tissues as a mechanism to tolerate hypoxic conditions. We have found acetaldehyde and ethanol to be common in the vascular cambium and in the transpiration stream of trees. In nonflooded trees, acetaldehyde and ethanol concentrations averaged 130 and 40 μ M in the cambium and 130 and 50 μ M in the xylem sap, respectively. Ethanol concentrations in the transpiration stream and the cambium increased to as much as 5 m M upon flooding. Ethanol concentrations in the vascular cambium of Populus deltoides could not be eliminated by placing logs from nonflooded trees in a pure oxygen environment for as long as 96 h, but increased by almost 3 orders of magnitude when logs were exposed to low external partial pressures of O₂. These results suggest that the vascular cambium was not hypoxic, despite the presence of acetaldehyde, ethanol and the enzymes for their synthesis.     

Deficits of olfactory interneurons in polysialyltransferase‐ and NCAM‐deficient mice

The neurogenic niche of the anterior subventricular zone (SVZ) persistently generates neuroblasts, which migrate along the rostral migratory stream (RMS) into the olfactory bulb (OB), where they differentiate into granule and periglomerular cells. Loss of the neural cell adhesion molecule NCAM or its post‐translational modification polysialic acid (polySia) impairs migration causing accumulations of cells in the proximal RMS and decreased OB volume. Polysialylation of NCAM is implemented by two polysialyltransferases, ST8SIA2 and ST8SIA4, with overlapping functions. Here, we used mice with Ncam1 and polysialyltransferase deletions to analyze how partial or complete loss of polySia synthesis or a combined loss of polySia and NCAM affects the RMS and the interneuron composition in the OB. Numerous calretinin (CR)‐positive cells were detected dispersed around the RMS in Ncam1 knockout, St8sia2, St8sia4 double‐knockout, and St8sia2, St8sia4, Ncam1 triple‐knockout mice, as well as in St8sia2 ^?/? but not in St8sia4 ^?/? mice. These changes were not reflected by reductions of CR‐positive cells in the granule or glomerular layer of the OB. Instead, calbindin‐positive periglomerular interneurons were strongly reduced in all polySia‐NCAM negative mice and slightly attenuated in St8sia2 ^?/? as well as in the St8sia4 ^?/? mice, which were devoid of ectopic CR‐positive cells along the RMS. Consistent with the early developmental generation of calbindin‐ as compared with CR‐positive OB interneurons, this phenotype was fully developed at postnatal day 5. Together, these results demonstrate that the early development of calbindin‐positive periglomerular interneurons depends on the presentation of polySia on NCAM and requires the activity of both polysialyltransferases. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 421–433, 2016     

Anthropogenic noise reduces bird species richness and diversity in urban parks

Anthropogenic noise is becoming more prevalent in the world and has been shown to affect many animal species, including birds. The impact of such noise was measured in Neotropical urban parks to assess how the noise affects avifauna diversity and species richness. We sampled bird species, and concurrently measured sound pressure (noise) levels (L_eq, equivalent noise levels) in eight urban green areas or parks located in a large city (Belo Horizonte) in south‐eastern Brazil over a 1‐year period. The diversity of sampled points was measured by means of total species richness, Fisher's alpha and Shannon–Wiener diversity indices. Noise levels within all parks were greater than those in natural areas. We found that an increase in noise levels and the area of open habitats surrounding sampling points were negatively related to species richness. Social factors reflecting increased urbanization, such as higher incomes, were also negatively correlated with bird species richness. However, noise was the factor that explained most of the variance. These results suggest that anthropogenic noise can have a significant negative impact on the conservation value of urban parks for bird species.     

The three dimensional distribution of the fauna in a single riffle in a stream in Ontario

The surface and hyporheic fauna of a riffle area in Salem Creek near Elmira, Ontario, was investigated with a Surber and a corer sampler. A stratified random sampling design estimated the number of invertebrates at 154 561 (109 805–224 155) m^–2 in June and at 64 407 (40 905–97 996) m^–2 in October with more than 70% of the animals occurring below 5 cm. There was a great spatial variation of the hyporheos density in the three dimensions of the riffle, which seemed to be related mostly to hydrogeological characteristics (superficial groundwater flow and grain size). Upward water movement in the centre of the stream occurred in the upper two transects, especially from the upper right bank, while the lower transect showed little water transmission. Hyporheos composition is discussed in regard to life history and the input of organic materials. Only two of nine pairs of Surber samples showed a high degree of similarity (0.68, 0.81). The surficial spatial density and diversity were examined in relation to the available surface and to substrate heterogeneity. It is concluded that the great variations between samples caused by many factors present severe problems in the collection of reliable quantitative samples.

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Résumé La faune de surface et celle de l'hyporhélique d'un radier de Salem Creek près d'Elmira, Ontario, ont été étudiées à l'aide de l'échantillonneur de Surber et d'un carottier. Un échantillonnage aléatoire stratifié a permis d'estimer le nombre d'invertébrés a 154 561 (109 805–224 155) m^–2 en juin et à 64 407 (40 905–97 996) m^–2 en octobre. Environ 70% de la faune benthique a été retrouvée entre 5 et 65 cm. La densité de l'hyporhéos présente de grandes variations spatiales, et celles-ci semblent etre reliées aux caractéristiques hydrogéologiques (mouvement des eaux souterraines superficielles et taille des particules). Un net mouvement ascendant dirigé vers le centre du radier a été détecté dans les deux transects situés en amont; aucun mouvement n'a été mesuré dans un troisième transect situé an aval. La composition de l'hyporhéos est mise en relation avec les cycles vitaux et avec l'apport des matières organiques. Des 9 paires d'échantillons recueillis au Surber, deux seulement présentent un certain degré de similarité (0.68, 0.81). Les variations spatiales de la densité et de la diversité de la faune de surface furent mises en corrélation avec la surface disponible et l'hétérogénéité du substrat. On en conclu que la grande variabilité entre les échantillons dans les deux habitats est due à plusieurs facteurs et qu'elle pose de sérieux problèms pour l'estimation de paramètres quantitatifs.

     

Ectopic expression of ROR1 prevents cochlear hair cell loss in guinea pigs with noise‐induced hearing loss

Noise‐induced hearing loss (NIHL) is one of the most frequent disabilities in industrialized countries. Evidence shows that hair cell loss in the auditory end organ is responsible for the majority of various ear pathological conditions. The functional roles of the receptor tyrosine kinase ROR1 have been underscored in various tumours. In this study, we evaluated the ability of ROR1 to influence cochlear hair cell loss of guinea pigs with NIHL. The NIHL model was developed in guinea pigs, with subsequent measurement of the auditory brainstem response (ABR). Gain‐of‐function experiments were employed to explore the role of ROR1 in NIHL. The interaction between ROR1 and Wnt5a and their functions in the cochlear hair cell loss were further analysed in response to alteration of ROR1 and Wnt5a. Guinea pigs with NIHL demonstrated elevated ABR threshold and down‐regulated ROR1, Wnt5a and NF‐κB p65. The up‐regulation of ROR1 was shown to decrease the cochlear hair cell loss and the expression of pro‐apoptotic gene (Bax, p53) in guinea pig cochlea, but promoted the expression of anti‐apoptotic gene (Bcl‐2) and the fluorescence intensity of cleaved‐caspase‐3. ROR1 interacted with Wnt5a to activate the NF‐κB signalling pathway through inducing phosphorylation and translocation of p65. Furthermore, Wnt5a overexpression decreased the cochlear hair cell loss. Collectively, this study suggested the protection of overexpression of ROR1 against cochlear hair cell loss in guinea pigs with NIHL via the Wnt5a‐dependent NF‐κB signalling pathway.     

TEMPORARY THRESHOLD SHIFTS AFTER NOISE EXPOSURE IN THE BOTTLENOSE DOLPHIN (TURSIOPS TRUNCATUS) MEASURED USING EVOKED AUDITORY POTENTIALS

The time course of recovery from temporary threshold shift (TTS) was measured in a bottlenose dolphin, Tursiops truncatus , using an evoked-potential procedure. The envelope-following response (EFR), which is a rhythmic train of auditory brainstem responses (ABR) to sinusoidally amplitude-modulated tones, was used as an indicator of the sound reception by the animal. Variation of the intensity of the stimulus allowed us to measure the animal's hearing via EFR thresholds. During each session, following an initial measure of threshold, the trained animal voluntary positioned itself within a hoop 1 m underwater while a 160 dB re 1 μPa noise of a 4–11 kHz bandwidth was presented for 30 min. After the noise exposure, thresholds were measured again at delays of 5, 10, 15, 25, 45, and 105 min. Measurements were made at test frequencies of 8, 11.2, 16, 22.5, and 32 kHz. The maximum TTS occurred 5 min after exposure and rapidly recovered with a rate of around 1.5 dB per doubling of time. TTS occurred at test frequencies from 8 to 16 kHz, with the maximum at 16 kHz. TTS was negligible at 22.5 kHz and absent at 32 kHz.     

河流水质的景观组分阈值研究进展

土地利用/覆被变化产生的区域生态环境负面效应已引起国内外研究者的广泛关注,其中,河流水质对景观组分变化的响应已在区域及更大尺度的研究中,成为热点。探讨河流水质的景观组分阈值,可以弥补非点源污染研究在区域尺度上的景观变化影响水质问题研究中的不足,而这是当前流域水环境管理及土地利用规划与管理的主要依据之一。从景观组分指数与水质指标出发,分析了当前研究的常用指标,认为:具有明确物理意义的景观组分指数,如不透水表面指数、植被指数等,受到水质的景观组分阈值研究的青睐;在水质指标中,水化学指标应用最为广泛,同时,表征水生生态系统条件的如生物类指标、综合生物类与非生物类指标,也逐渐受到重视,方兴未艾。尽管河流水质的景观组分阈值是当前的研究重点,但在区域以及更大尺度上,阈值的差异较大。在今后的研究中,水质退化的景观组分阈值还需在研究尺度、水质指标及阈值标准等问题上进一步深化,而景观格局指数的应用将会促进对水质退化受景观组分空间配置影响的研究。对水质的景观组分阈值研究进行综述,可以为区域尺度上开展水质保护、流域水环境管理及土地利用规划提供前沿信息。     

高寒森林不同生境对凋落叶分解灰分动态的影响

灰分是凋落叶的重要组成部分,其浓度直接关系到凋落叶的分解过程及有机组分的动态特征,且可能受生境和分解时期的影响,然而有关凋落叶分解过程中灰分动态的研究鲜有报道。采用凋落袋法,以岷江上游高寒森林4种代表性植物康定柳(Salix paraplesia)、高山杜鹃(Rhododendron lapponicum)、方枝柏(Sabina saltuaria)和四川红杉(Larix mastersiana)凋落叶为研究对象,研究了高寒森林凋落叶在3种不同环境条件下(林下、溪流、河岸带)分解过程中灰分的动态特征。结果表明,灰分量随凋落叶的分解整体呈现降低的趋势,且不同环境条件和不同物种之间存在明显的差异。与之相反,经过两年的分解,除溪流中康定柳凋落叶灰分浓度略有下降外(-0.99%),林下和河岸带中康定柳凋落叶及其它物种凋落叶中灰分浓度在所有环境条件下均表现出了增加的趋势(5.86%—72.15%)。凋落叶分解过程中灰分浓度变异量在不同分解时期存在明显或显著的差异,且受物种和环境因子的调控。这些结果表明,传统上认为凋落叶分解过程中灰分浓度比较稳定的观点是不准确的,且以凋落叶分解过程中灰分浓度不变的前提下采用无灰分质量损失(ash free mass loss)而计算凋落叶质量损失的方法存在一定的不准确性。研究为认识凋落叶分解过程中灰分的动态特征及凋落叶质量损失的测定方法提供了一定的参考。     

Scaling up: how do exogenous fluctuations in individual-based resource competition models re-emerge in aggregated stochastic population models?

In applied population dynamics the choice of stochastic per capita growth function has implications for population viability analyses, management recommendations, and pest control. This model choice is often based on statistical criteria, mathematical tractability or personal preferences, and general ecological guidelines are either too vague or entirely missing. To identify such guidelines, it is important to understand how exogenous and endogenous factors interact at the individual level and re-emerge at the aggregated population level. We therefore study different types of resource competition (contest vs. scramble competition) and different types of exogenous fluctuations (food and weather fluctuations) at the individual level in a simple individual-based simulation model. We statistically fit the resulting time series to find out (1) which functional form of the growth function (‘hyperbolic’ or ‘exponential’) better describes contest and scramble competition and (2) whether the pattern of population fluctuations resulting from the simulations can be assigned to vertical, lateral or nonlinear perturbations in the stochastic growth function (a classification scheme suggested by Royama 1992, Analytical Population Dynamics, Chapman and Hall, London). We found that the same type of competition can result in ‘hyperbolic’ or ‘exponential’ functional forms, depending on the type of exogenous fluctuations. So it is the interplay between exogenous variability and endogenous resource competition that affects model performance. In contrast to the widespread assumption of vertical (additive) perturbations, our findings highlight the importance of (non-additive) lateral and nonlinear perturbations and their combinations with vertical perturbations. The choice of the stochastic growth function should therefore consider not only statistical criteria but also ecological guidelines. We derive such ecological guidelines from our analysis.