Interacting Effects of Discharge and Channel Morphology on Transport of Semibuoyant Fish Eggs in Large,Altered River Systems

Habitat fragmentation and flow regulation are significant factors related to the decline and extinction of freshwater biota. Pelagic-broadcast spawning cyprinids require moving water and some length of unfragmented stream to complete their life cycle. However, it is unknown how discharge and habitat features interact at multiple spatial scales to alter the transport of semi-buoyant fish eggs. Our objective was to assess the relationship between downstream drift of semi-buoyant egg surrogates (gellan beads) and discharge and habitat complexity. We quantified transport time of a known quantity of beads using 2–3 sampling devices at each of seven locations on the North Canadian and Canadian rivers. Transport time was assessed based on median capture time (time at which 50% of beads were captured) and sampling period (time period when 2.5% and 97.5% of beads were captured). Habitat complexity was assessed by calculating width∶depth ratios at each site, and several habitat metrics determined using analyses of aerial photographs. Median time of egg capture was negatively correlated to site discharge. The temporal extent of the sampling period at each site was negatively correlated to both site discharge and habitat-patch dispersion. Our results highlight the role of discharge in driving transport times, but also indicate that higher dispersion of habitat patches relates to increased retention of beads within the river. These results could be used to target restoration activities or prioritize water use to create and maintain habitat complexity within large, fragmented river systems.     

Costs of jasmonate-induced responses in plants competing for limited resources

We present a design to quantify fitness consequences of jasmonate-induced responses in plants that are competing for limited resources with a conspecific. Under both high and low nitrogen supply rates, uninduced (control) Nicotiana attenuata plants growing next to a plant induced with 250 μg methyl jasmonate (MJ) yielded more seed capsules than control plants competing with another control plant. We conclude that there is a opportunity benefit for control plants growing next to an induced plant. Initially, MJ-induced plants grew more slowly, but by senescence they had produced the same number of seed capsules as control plants that had competed with another control plant. Replacement series showed that the fitness of MJ-induced plants is not influenced by the competitive status of their neighbour plant. We argue that competitive designs are useful tools for evaluating the phenotypic costs of ecologically important traits.     

Photocontrol of the hypocotyl hook opening of Sinapis alba seedlings. Involvement of phytochrome and a high irradiance response

Baumgartner, N. and Fondeville, J. C. 1989. Photocontrol of the hypocotyl hook opening of Sinapis alba seedlings. Involvement of phytochrome and a high irradiance response.
A statistical evaluation of the hypocotyl hook opening (hook opening index) was used for measurement of the hook angle in lots of etiolated Sinapis alba L. cv. Albatros seedlings. Studies of the kinetics for hook opening were carried out in continuous fluorescent white, blue and red light (6, 15 and 40 μmol m^-2s^-1) with 2-day-old dark-grown seedlings. At the beginning of the irradiation period the photoresponse in red light was the opposite to that in blue (low photon fluences). Blue rapidly induced the hook opening (in less than 20 min), while red produced hook tightening (photon fluences up to 70 mmol m^-2), which precedes the normal progressive hook opening. For low fluences, the data were consistent with the involvement of phytochrome and a specific blue light photoreceptor. A phytochrome effect was observed in the hook opening, dependent upon a high irradiance response (HIR). This HIR (like that for the inhibition of the hypocotyl elongation) was characterized by a wavelength response curve with maxima in the blue and far-red regions of the spectrum.     

Invasive species cause large-scale loss of native California oyster habitat by disrupting trophic cascades

Although invasive species often resemble their native counterparts, differences in their foraging and anti-predator strategies may disrupt native food webs. In a California estuary, we showed that regions dominated by native crabs and native whelks have low mortality of native oysters (the basal prey), while regions dominated by invasive crabs and invasive whelks have high oyster mortality and are consequently losing a biologically diverse habitat. Using field experiments, we demonstrated that the invasive whelk’s distribution is causally related to a large-scale pattern of oyster mortality. To determine whether predator–prey interactions between crabs (top predators) and whelks (intermediate consumers) indirectly control the pattern of oyster mortality, we manipulated the presence and invasion status of the intermediate and top trophic levels in laboratory mesocosms. Our results show that native crabs indirectly maintain a portion of the estuary’s oyster habitat by both consuming native whelks (density-mediated trophic cascade) and altering their foraging behavior (trait-mediated trophic cascade). In contrast, invasive whelks are naive to crab predators and fail to avoid them, thereby inhibiting trait-mediated cascades and their invasion into areas with native crabs. Similarly, when native crabs are replaced with invasive crabs, the naive foraging strategy and smaller size of invasive crabs prevents them from efficiently consuming adult whelks, thereby inhibiting strong density-mediated cascades. Thus, while trophic cascades allow native crabs, whelks, and oysters to locally co-exist, the replacement of native crabs and whelks by functionally similar invasive species results in severe depletion of native oysters. As coastal systems become increasingly invaded, the mismatch of evolutionarily based strategies among predators and prey may lead to further losses of critical habitat that support marine biodiversity and ecosystem function. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

海南省及云南西双版纳州HIV-1的分子流行病学比较研究

目的调查比较HIV-1在海南省及云南西双版纳州的流行情况及分子流行病学分析高危因素传播的情况以及传播链的鉴定。方法我们与海南省CDC及西双版纳州CDC合作在其境内开展了HIV血清学调查,筛查了海南省（1991～2006）及西双版纳州（1996～2005）高危人群志愿者血清样本。在本次两地调查中,我们通过系统进化分析方法,对已诊断的HIV感染者进行分子流行病学的追踪,来分析其中的主要流行亚群以及结合个案追踪进行传播链的鉴定。结果我们共筛查了海南省499725人,共检出HIV阳性感染者523例（0.1%）,以注射器吸毒感染为主要传播途径（经共用注射器吸毒感染占69．2％、经性接触传播占19．3％、供血和使用血液／血液制品感染占3．3％、母婴传播占0．8％、不详占7．7％）。然而,在西双版纳州筛查中发现了较海南省高20倍的检出率：在25390受检人中,共检出HIV阳性感染者501例（2％）并以异性性传播为主（经异性性接触传播占77．3％、经共用注射器吸毒感染占21．1％、经同性性接触传播占0．4％、母婴传播占1．2％）。在海南省抽样的83人中,以CRF01_-AE重组亚型（70人,84．3％）为主要病毒亚型,其他病毒亚型包括B’亚型（8人）、C亚型（2人）、CRF08_BC重组亚型（1人）、B亚型（1人）和1个未报道过的CRF01～AE／B’重组亚型。同样,在版纳抽样的44人中,也以CRF01_AE重组亚型（27人,61．3％）为主要病毒亚型,其他病毒亚型包括CRF08_BC重组亚型（15人）、G亚型（1人）、和1个未报道过的B／C重组亚型。在海南省抽样中有66人（79．5％）分布于4个大小不同的传播群,传播群1（59人）较大（奠基效应）,属于CRF01_AE重组亚型,传播群2、3、4则较小,分别为3、2、2人,分别属于CRF01_AE重组亚型、C亚型和B’亚型。相反,在版纳抽样中有18人（40．9％）分布于8个较小的传播群（每群平均含2．25感染个体）。在海南省抽样中怀疑的6对异性性接触的传播链中,经系统进化分析方法确认了其中的4对,2对被拒绝。在版纳抽样中怀疑的8对异性性接触的传播链中,经系统进化分析方法确认了其中的5对,2对被拒绝,1对无法分析,此外还新发现了3对异性性接触传播群。结论HIV-1感染者的分子流行病学的追踪和分析对于追溯艾滋病流行的源头和地区性预防策略的制定有着重大的意义。     

Limiting the Persistence of a Chromosome Break Diminishes Its Mutagenic Potential

To characterize the repair pathways of chromosome double-strand breaks (DSBs), one approach involves monitoring the repair of site-specific DSBs generated by rare-cutting endonucleases, such as I-SceI. Using this method, we first describe the roles of Ercc1, Msh2, Nbs1, Xrcc4, and Brca1 in a set of distinct repair events. Subsequently, we considered that the outcome of such assays could be influenced by the persistent nature of I-SceI-induced DSBs, in that end-joining (EJ) products that restore the I-SceI site are prone to repeated cutting. To address this aspect of repair, we modified I-SceI-induced DSBs by co-expressing I-SceI with a non-processive 3′ exonuclease, Trex2, which we predicted would cause partial degradation of I-SceI 3′ overhangs. We find that Trex2 expression facilitates the formation of I-SceI-resistant EJ products, which reduces the potential for repeated cutting by I-SceI and, hence, limits the persistence of I-SceI-induced DSBs. Using this approach, we find that Trex2 expression causes a significant reduction in the frequency of repair pathways that result in substantial deletion mutations: EJ between distal ends of two tandem DSBs, single-strand annealing, and alternative-NHEJ. In contrast, Trex2 expression does not inhibit homology-directed repair. These results indicate that limiting the persistence of a DSB causes a reduction in the frequency of repair pathways that lead to significant genetic loss. Furthermore, we find that individual genetic factors play distinct roles during repair of non-cohesive DSB ends that are generated via co-expression of I-SceI with Trex2.     

Reversible photobleaching of enhanced green fluorescent proteins

Color variants of green fluorescent protein (GFP) are increasingly used for multicolor imaging, fluorescence resonance energy transfer (FRET), and fluorescence recovery after photobleaching (FRAP). Here we show that experimental settings commonly used in these imaging experiments may induce an as yet uncharacterized reversible photobleaching of fluorescent proteins, which is more pronounced at acidic pH. Whereas the reversible photobleaching spectrum of eCFP corresponds to its absorption spectrum, reversible photobleaching spectra of yellow variants resemble absorption spectra of their protonated states. Fluorescence intensities recover spontaneously with time constants of 25-58 s. The recovery of eCFP can be further accelerated by illumination. The resulting steady-state fluorescence reflects a variable equilibrium between reversible photobleaching, spontaneous recovery, and light-induced recovery. These processes can cause significant artifacts in commonly applied imaging techniques, photobleach-based FRET determinations, and FRAP assays.     

Production and purification of human indoleamine 2,3-dioxygenase (HuIDO) protein in a baculovirus expression system and production and characterization of egg yolk antibody against the purified HuIDO

The human indoleamine 2,3-dioxygenase (HuIDO) baculoviral construct, for expression of HuIDO protein with a hexa-histidine and FLAG (DYKDDDDK) tag, was produced using the BacPAK Baculovirus Expression System. HuIDO baculovirus was used to infect Sf21 insect cells to produce functionally active protein in large amounts. Conditions for protein purification by metal affinity chromatography were determined and optimized. Addition of haemin ensured optimal activity of the purified heme-containing oxygenase. The soluble purified protein was used to immunize a chicken to produce large quantities of polyclonal IgY against HuIDO. The anti-HuIDO IgY antibody specifically detected HuIDO produced by a range of cell types including transfectants and native HuIDO expression induced in IFN-gamma-stimulated cells. The antibody detected HuIDO in cell lysates by western blotting and in the cytoplasm of cells by microscopy. The antibody was unable to block the function of the enzyme, indicating that this antibody binds outside the active site of HuIDO.     

Decomposition of old organic matter as a result of deeper active layers in a snow depth manipulation experiment

A snow addition experiment in moist acidic tussock tundra at Toolik Lake, Alaska, increased winter snow depths 2–3 m, and resulted in a doubling of the summer active layer depth. We used radiocarbon (?¹⁴C) to (1) determine the age of C respired in the deep soils under control and deepened active layer conditions (deep snow drifts), and (2) to determine the impact of increased snow and permafrost thawing on surface CO₂ efflux by partitioning respiration into autotrophic and heterotrophic components. ?¹⁴C signatures of surface respiration were higher in the deep snow areas, reflecting a decrease in the proportion of autotrophic respiration. The radiocarbon age of soil pore CO₂ sampled near the maximum mid-July thaw depth was approximately 1,000 years in deep snow treatment plots (45–55 cm thaw depth), while CO₂ from the ambient snow areas was ~100 years old (30-cm thaw depth). Heterotrophic respiration ?¹⁴C signatures from incubations were similar between the two snow depths for the organic horizon and were extremely variable in the mineral horizon, resulting in no significant differences between treatments in either month. Radiocarbon ages of heterotrophically respired C ranged from <50 to 235 years BP in July mineral soil samples and from 1,525 to 8,300 years BP in August samples, suggesting that old soil C in permafrost soils may be metabolized upon thawing. In the surface fluxes, this old C signal is obscured by the organic horizon fluxes, which are significantly higher. Our results indicate that, as permafrost in tussock tundra ecosystems of arctic Alaska thaws, carbon buried up to several thousands of years ago will become an active component of the carbon cycle, potentially accelerating the rise of CO₂ in the atmosphere.