Taxonomic aggregation does not alleviate the lack of consistency in analysing diversity in long‐term phytoplankton monitoring data: a rejoinder to Pomati et al. (2015)

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Progesterone analogs influence germination of Clostridium sordellii and Clostridium difficile spores in vitro

Clostridium sordellii and Clostridium difficile are closely related anaerobic Gram-positive, spore-forming human pathogens. C. sordellii and C. difficile form spores that are believed to be the infectious form of these bacteria. These spores return to toxin-producing vegetative cells upon binding to small molecule germinants. The endogenous compounds that regulate clostridial spore germination are not fully understood. While C. sordellii spores require three structurally distinct amino acids to germinate, the occurrence of postpregnancy C. sordellii infections suggests that steroidal sex hormones might regulate its capacity to germinate. On the other hand, C. difficile spores require taurocholate (a bile salt) and glycine (an amino acid) to germinate. Bile salts and steroid hormones are biosynthesized from cholesterol, suggesting that the common sterane structure can affect the germination of both C. sordellii and C. difficile spores. Therefore, we tested the effect of sterane compounds on C. sordellii and C. difficile spore germination. Our results show that both steroid hormones and bile salts are able to increase C. sordellii spore germination rates. In contrast, a subset of steroid hormones acted as competitive inhibitors of C. difficile spore germination. Thus, even though C. sordellii and C. difficile are phylogenetically related, the two species' spores respond differently to steroidal compounds.     

Recent climate changes interact with stand structure and management to determine changes in tree carbon stocks in Spanish forests

Most temperate forests are accumulating carbon (C) and may continue to do so in the near future. However, the situation may be different in water‐limited ecosystems, where the potentially positive effects of C and N fertilization and rising temperatures interact with water availability. In this study, we use the extensive network of plots of two consecutive Spanish national forest inventories to identify the factors that determine the spatial variation of the C stock change, growth, and mortality rate of forests in Peninsular Spain (below‐ and aboveground). We fitted general linear models to assess the response of C stock change and its components to the spatial variability of climate (in terms of water availability), forest structure (tree density and C stock), previous forest management, and the recent warming trend. Our results show that undisturbed forests in Peninsular Spain are accumulating C at a rate of ~1.4 Mg C ha^?1 yr^?1, and that forest structural variables are the main determinants of forest growth and C stock change. Water availability was positively related to growth and C accumulation. On the other hand, recent warming has reduced growth rate and C accumulation, especially in wet areas. Spatial variation in mortality (in terms of C loss) was mostly driven by differences in growth rate across plots, and was consistent with ‘natural’, self‐thinning dynamics related to the recent abandonment of forest management over large areas of Spain, with the consequent increase in tree density and competition. Interestingly, the negative effect of warming on forest C accumulation disappears if only managed stands are considered, emphasizing the potential of forest management to mitigate the effects of climate change. However, the effect of forest management was weak and, in some cases, not significant, implying the need of further research on its impact.     

Quantitative evaluation of siRNA delivery in vivo

Effective small interfering RNA (siRNA)-mediated therapeutics require the siRNA to be delivered into the cellular RNA-induced silencing complex (RISC). Quantitative information of this essential delivery step is currently inferred from the efficacy of gene silencing and siRNA uptake in the tissue. Here we report an approach to directly quantify siRNA in the RISC in rodents and monkey. This is achieved by specific immunoprecipitation of the RISC from tissue lysates and quantification of small RNAs in the immunoprecipitates by stem-loop PCR. The method, expected to be independent of delivery vehicle and target, is label-free, and the throughput is acceptable for preclinical animal studies. We characterized a lipid-formulated siRNA by integrating these approaches and obtained a quantitative perspective on siRNA tissue accumulation, RISC loading, and gene silencing. The described methodologies have utility for the study of silencing mechanism, the development of siRNA therapeutics, and clinical trial design.     

Local expression of the ipt gene in transgenic tobacco (Nicotiana tabacum L. cv. SR1) axillary buds establishes a role for cytokinins in tuberization and sink formation

The developmental characteristics of a transgenic tobacco line (BIK62) expressing the ipt cytokinin-biosynthetic gene under the control of a tagged promoter were analysed. In situ hybridization and cytokinin immunocytochemistry revealed that the ipt gene was mainly expressed in the axillary buds after the floral transition. The ipt-expressing axillary buds presented morphological alterations such as short and narrow scale-leaflets, and swollen internodes filled with starch grains, giving rise to short and tuberized lateral branches. In addition, the modification of the endogenous cytokinin balance in the axillary meristems resulted in a fast rate of leaf initiation and cytokinins accumulated mostly in the lateral zones of the reactivated axillary meristems, suggesting a role in leaf organogenesis. Cell cycle analysis revealed that the reactivated axillary meristems were characterized by predominant S+G2 nuclei. Terminal internodes displayed low levels of hexose and sucrose concomitant with starch accumulation. Extracellular invertases (EC 3.1.26) were also present in higher amounts in the tuberizing internodes compared to the axillary buds of wild-type tobacco. These results underline the role of cytokinins in cell cycle regulation and in the creation of a sink--source effect. They also provide new information about cytokinin involvement in the process of tuberization and their overproduction in axillary buds giving rise to tuberized lateral branches in a naturally non-tuberizing species.     

Viability Testing of Orchid Seed and the Promotion of Colouration and Germination

This study reports the ability of Fusarium to induce orchidseed colouration and germination. The in vitro bioassay germinationtest, using a Fusarium isolate from the protocorm of Cypripediumreginae, was compared with standard chemical procedures of triphenyltetrazolium chloride (TTC) and acid fuchsin (AC) for testingseed viability. With Cypripedium reginae, Cypripedium parviflorumand Platanthera grandiflora, the efficiency of the bioassaywas similar to that of the TTC and AC procedures. However, thebioassay was more appropriate for estimating embryo viabilityafter a prolonged seed pretreatment (more than 2 h) in 10% sodiumhypochlorite, a surface sterilant often used to enhance germinationof terrestrial species. We also obtained in vitro Cypripediumreginae seed germination induction and protocorm formation bythe same Fusarium isolate. This is the first confirmation ofBernard's early reports that orchid fusaria could stimulateseed germination (Bernard N. 1990.Révue Généralede Botanique12 : 108–120). However, the importance ofthe non-mycorrhizal Fusarium fungus in promoting germinationseems to be relatively minor compared to that of specificRhizoctoniaorchid mycorrhizas. Our results are discussed in light of thecurrent North American strategy on orchid conservation methodswhich proposes the use of symbiotic germination.Copyright 2000Annals of Botany Company Orchid, Cypripedium, Platanthera, seed, Fusarium, bioassay, staining, viability, germination, protocorm, mycorrhiza     

The Effects of Periphyton, Fish and Fertilizer Dose on Biological Processes Affecting Water Quality in Earthen Fish Ponds

The potential of periphyton-based aquaculture in South Asia is under investigation in an extensive research program. This paper is a further analysis of data from four experiments carried out in that framework, to explore periphyton, fish and fertilizer dose effects on water quality. Factor analysis and ANOVA models applied to a data matrix of water quality parameters in ponds with and without artificial substrates (bamboo poles and kanchi sticks), with and without fish (filter feeders catla and rohu, with and without bottom feeder kalbaush), and with a standard or 50% increased fertilizer dose, allowed us to identify the underlying ecological processes governing this novel periphyton-based pond system, and construct conceptual graphic models of the periphyton–environment relationships observed. We clearly established that the phosphorus flow is mainly linked to phytoplankton activity in the water column and decomposition on the pond bottom, while nitrogen flow is mainly linked to autotrophic (photosynthesis) and heterotrophic (decomposition and nitrification) processes that take place in the periphyton in addition to the water column and pond bottom. Consequently, disruption of the pond bottom by bottom feeding fish primarily promoted phosphate cycling and phytoplankton, while periphyton development on the supplied substrates and fertilization mainly improved oxygen balance and nitrogen related processes developing in the water column. The use of bamboo poles led to better results than kanchi sticks, related to the greater autotrophic periphyton development on bamboo and to the larger surface of bamboo poles that facilitate fish grazing and periphyton dislodgment that in turn have a renewal effect on periphyton. Stocking bottom feeding fish produces a fertilizing effect through the food web that benefits the filter-feeding fish and that makes it unnecessary to increase the dose of inorganic and organic fertilizers applied to the ponds. Thus, the output of this analysis will help the fish farmers in resource constrained countries to improve their production in periphyton-based ponds just by choosing bamboo substrates, stocking a bottom feeder fish together with the filter feeders, and saving money on fertilizers.