Distribution and population structure of four Central Amazonian high-várzea timber species

Amazonian white-water (várzea) floodplains harbor many commercially important timber species which in Brazil are harvested following regulations of the Federal Environmental Agency (IBAMA). Although it is well-known that tree physiology, growth, and species distribution of Amazonian floodplain trees is linked to the heights and durations of the periodical inundations, information about timber stocks and population dynamics is lacking for most tree species. We investigated timber stocks and the population structure of four intensely logged tree species in a western Brazilian várzea forest on an area totaling 7.5 ha. Spatial distribution was investigated in all trees as a function of inundation height and duration and the distance to the river channel, and additionally for saplings (trees <10 cm diameter at breast height––DBH) as a function of the relative photosynthetically active radiation (rPAR). The diameter-class distribution in Hura crepitans and Ocotea cymbarum indicated that populations are subject to density variations that possibly are traced to small-scale flood variability. In all species, saplings concentrated at higher topographic elevations than the mature tree populations, which suggest that the physical ‘escape’ from a flooded environment is an important acclimation to flooding. While Ocotea cymbarum and Guarea guidonia were high-density wood species characterized by random dispersion and a pronounced shade-tolerance, Hura crepitans and Sterculia apetala presented lower wood density, aggregated dispersion, and were more light-demanding. All species presented exploitable stems according to the current harvest regulations, with elevated abundances in comparison to other Amazonian forest types. However, stem densities are below the harvest rates indicating that the harvest regulations are not sustainable. We recommend that the forest management in várzea forests should include specific establishment rates of timber species in dependence of the peculiar site conditions to achieve sustainability.     

Does fallen timber on floodplains influence distributions of nutrients,plants and seeds?

While much is conjectured about the ecological significance of fallen timber, there has been little work on the influence of logs on plants and nutrient distributions on periodically inundated floodplains. We compared distributions of seeds, germinated plants and a suite of soil properties around logs on (a) the floodplain proper, (b) in ‘flood runners’ (floodplain drainage channels) and (c) at randomly selected log-free locations on the floodplain. Sampling was conducted on logs oriented parallel to the river, so that we could compare the sides of logs closer to and further from the river. Numbers of exotic species germinating around flood-runner logs was much reduced compared with the other two locations. Native seeds accumulated to a greater extent on the river-side of floodplain logs compared to flood-runners logs. Densities of plants were lowest in the immediate proximity of logs, increasing up to two-fold 2 m away on both sides of logs. Gravel fraction was highest around flood-runner logs, while the fraction around floodplain logs was higher than at log-free locations. Extractable Na was higher around flood-runner logs (2.6%) than at log-free points (1.2%), but levels for floodplain logs were intermediate (2.1%). Soil samples taken near flood-runner logs were slightly more acidic than samples taken elsewhere. Our results generally were not consistent with expectations that floodplain logs would act as favourable areas for plant germination and survivorship. While certain sediment characteristics did appear to be influenced by the presence of logs (e.g., gravel fraction, pH and Na), effects were relatively small and most other measured characters were not affected by location.     

Do seasonal temperatures,species traits and nearby timber harvest predict variation in moth species richness and abundance in unlogged deciduous forests?

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Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber

Microbial biodeterioration of timber and woody material in buildings can cause costly restoration procedures. Here, we focus on Serpula lacrymans (commonly known as dry-rot) the fungus causing the most severe damages to buildings in Europe. Although its morphology, lifestyle, and dispersal have been intensively studied, research on microorganisms sharing the same habitat and interacting with the dry-rot fungus is not as comprehensive. Bacteria have long been known to inhabit dead wood, and several studies have shown their association to fungi. However, their identity, ecology, and putative interactions with co-existing fungi in dead wood remains largely underexplored. The interactions of bacterial and fungi have considerable impact on all partners involved covering the full spectrum between antagonistic and beneficial. Fungi are highly capable of manipulating the microbial community in their surroundings (e.g. via pH manipulation) and bacteria, in turn, can influence fungi by affecting the outcomes of (antagonistic) interactions or preventing fungal feedback inhibition via consumption of breakdown products. Associated bacteria on the other side could play an essential role for the fungus as bacteria can exert significant influence on fungal physiology and behaviour. This minireview summarizes the current knowledge on bacterial-fungal interactions in dead wood with a special focus on dry-rot and proposes possible bacterial-fungal interaction (BFI) mechanisms based on examples from soil or decomposing wood from forests.     

Seasonal water chemistry and diatom changes in six boreal lakes of the Laurentian Mountains (Québec,Canada): impacts of climate and timber harvesting

The physical and chemical variabilities as well as the distribution of diatoms of six boreal lakes in the Laurentian Mountains (southern Québec, Canada) were studied. The lakes are located along an altitudinal gradient and were sampled at a biweekly resolution from May through October, 2002. In general, we found later onset and weaker lake stratification under colder climates. Lake circulation and SiO₂ are strongly correlated and together significantly explain the distribution of diatoms of the individual lakes. Diatoms that accumulated in the sediment traps were mostly composed of benthic species, suggesting resuspension. However, diatom flux and lake circulation were not significantly correlated, the diatom assemblages in the sediment traps were similar in two consecutive years, and species–environment relationships were comparable among lakes, which indicates that the effects of resuspension were minimal. In addition, we found that one lake was more productive due to forest logging. The forest in the catchment of Lake Maxi was entirely clear-cut shortly prior to our sampling. Mean total phosphorus, dissolved organic carbon, and chlorophyll a concentrations were significantly higher when compared to the other five study lakes. This study seeks to improve our understanding of how diatoms in boreal lakes respond to climate change and forest clear-cut.     

Do non-native earthworms in Southeast Alaska use streams as invasional corridors in watersheds harvested for timber?

Exotic earthworms from Europe and Asia have invaded previously earthworm-free areas of North America where they consume leaf litter, mix soil horizons, and alter nutrient cycling. Primarily, earthworm introductions occur through human activities; we hypothesized that the combination of logging (i.e., road construction and soil disturbance) and stream transport (i.e., hydrochory) allows earthworms to invade new ecosystems and spread within watersheds. On Prince of Wales Island, AK, we surveyed riparian zones in 11 watersheds with varying timber harvest intensity for terrestrial oligochaetes. Additionally, common invasive earthworms were experimentally submerged in a local stream to test for tolerance to prolonged immersion: all taxa survived immersion for at least 6 days. Using principal components analysis, watershed and harvest variables describing the watersheds upstream of our sampled riparian areas were reduced to two principal components describing harvest intensity (PC1) and harvest style (PC2). Logistic models successfully predicted earthworm abundance (r ²  = 0.70) from PC1, which indicated that watersheds with older, intense upstream timber harvest contained larger earthworm populations. Earthworm species richness was best predicted by PC2 (r ²  = 0.39), which suggested that earthworm communities in watersheds containing large clear-cut stands were more species-rich. Collectively, these results suggest that (1) invasive earthworms may use streams for dispersal and (2) upstream introductions via timber harvest can initiate downstream earthworm invasions. Hydrochory would allow invasive earthworms to spread at rates (tens of km d⁻¹) that are much greater than previously reported rates of terrestrial spread (5–10 m y⁻¹). Effective control of exotic earthworms in riparian zones will require watershed-level management and surveillance.     

Spatial, Temporal, and Economic Constraints to the Commercial Extraction of a Non–timber Forest Product: Copaíba (Copaifera spp.) Oleoresin in Amazonian Reserves

Spatial, Temporal, and Economic Constraints to the Commercial Extraction of a Non?CTimber Forest Product: Copaíba (Copaifera spp.) Oleoresin in Amazonian Reserves. The increasing prevalence of government?C and NGO?Csponsored programs to encourage commercial non?Ctimber forest product (NTFP) extractivism in the humid tropics has highlighted the need for ecological and socioeconomic appraisal of the viability of extractive industries. We adopted a novel integrative approach to examine NTFP resource potential and produced credible landscape?Cscale estimates of the projected value of an economically important Amazonian NTFP, the medicinal oleoresin of Copaifera trees, within two large contiguous extractive reserves in Brazilian Amazonia. We integrated results derived from previous spatial ecology and harvesting studies with socioeconomic and market data, and mapped the distribution of communities within the reserves. We created anisotropic accessibility models that determined the spatial and temporal access to Copaifera trees in permanently unflooded (terra firme) and seasonally flooded (várzea) forests. Just 64.9?% of the total reserve area was accessible, emphasizing the distinction between the actual resource stock and that which is available to extractors. The density of productive tree species was higher in the várzea forests, but per?Ctree productivity was greater in the terra firme forests, resulting in similar estimates of oleoresin yield per unit area (64?C67?ml?ha^?C1) in both forest types. A greater area of the várzea forests was accessible within shorter travel times of ??250 minutes; longer travel times allowed access to increasingly greater volumes of oleoresin from the terra firme forests. The estimated total volume of oleoresin accessible within the two reserves was 38,635 liters for an initial harvest, with projected offtake for a subsequent harvest falling to 8,274 liters. A household that extracted just 2 liters of oleoresin per month could generate 5?% of its mean income; market data suggested that certification could increase the value of the resource fivefold. Our approach is valuable in that it incorporates a range of methodologies and quantitatively accounts for the numerous constraints to the commercial viability of NTFP extraction.     

Start codon targeted (SCoT) polymorphism-based genetic relationships and diversity among populations of <Emphasis Type="Italic">Tecomella undulata</Emphasis> (Sm.) Seem—an endangered timber tree of hot arid regions

Tecomella undulata (Sm.) Seem commonly called Rohida or Desert teak (family bignoniaceae) is an important agroforestry tree having an important pharmacological and therapeutic uses. Its distribution is restricted to hot arid regions of India and Pakistan having <150 to 500 mm annual rainfall. Genetic diversity status of this important endangered timber tree species designated state flower of Rajasthan remains unrevealed. Genetic diversity of 21 populations (108 accessions) encompassing yellow, red and orange coloured flower bearing morphotypes collected from all 12 districts of western Rajasthan, India, has been examined using start codon targeted (SCoT) polymorphism for the first time. Fingerprinting with 22 SCoT primers (out of 36 screened) generated 294 amplicons of 100 to 3000 bp size, of which 212 (71.6%) were polymorphic. Amplicon number varied from 4 (SCoT-9) to 24 (SCoT-15) with an average of 13.4 amplicons per primer. Average polymorphism information content (PIC), Nei’s diversity index (H) and Shannon index (I) were 0.54, 0.22 and 0.36, respectively. Dendrogram generated using unweighted pair-group method with arithmetic mean (UPGMA) delineated the 108 accessions into 5 clusters while 2 accessions out grouped. Principal coordinate analysis (PCoA) also revealed similar clustering. High level of genetic differentiation among accessions/populations was attributed to cross pollination and continuous evolution under harsh agro-climatic conditions.     

Syntheses and spectroscopic properties of α- and β-phosphatidylcholines and phosphatidylethanolamines

The widely used partial synthesis of phospholipids via deacylation of naturally occurring phospholipids, followed by reacylation with fatty acid anhydrides, is accompanied by phosphoryl migration. The resulting mixture of α- and β-phospholipids was separated by short-column chromatography. Milder acylation procedures in which no phosphoryl migration occurs, were developed. 1,2-Dilinoleoyl-sn-glycero-3-phosphocholine was prepared in 50% yield by acylation of sn-glycero-3-phosphocholine (GPC) with N-linoleoylimidazole. Detailed NMR and infrared spectra of α- and β-phosphatidylcholines (PCs) and -ethanolamines (PEs) are reported and the differences between isomers discussed.     

Phenotypic plasticity and longevity in plants and animals: cause and effect?

Immobile plants and immobile modular animals outlive unitary animals. This paper discusses competing but not necessarily mutually exclusive theories to explain this extreme longevity, especially from the perspective of phenotypic plasticity. Stem cell immortality, vascular autonomy, and epicormic branching are some important features of the phenotypic plasticity of plants that contribute to their longevity. Monocarpy versus polycarpy can also influence the kind of senescent processes experienced by plants. How density-dependent phenomena affecting the establishment of juveniles in these immobile organisms can influence the evolution of senescence, and consequently longevity, is reviewed and discussed. Whether climate change scenarios will favour long-lived or short-lived organisms, with their attendant levels of plasticity, is also presented.     

Dogmatisms and Catechisms — Ethics and Companion Animals

Abstract

The current reconsideration of the place in nature of human beings unfortunately continues to be an acrimonious one. All too often the debate is more akin to a warlike encounter where each side attempts to gain control or the upper hand than a search for points of agreement. Given this context, it is important to entertain views that emanate from different cultural traditions as a way to infuse the debate with new life. Students of Native American culture have consistently pointed out that the essential concepts of life balance and reciprocity represented there may serve as useful points of consideration as we struggle with the appropriate relationships with animals and nature. This article presents a representative Zuni story, told by Governor Robert E. Lewis, that illustrates these notions.     

DCCP and DICP： Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins

Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases （DCCP and DICP） containing the known copper- and iron-chelating proteins~ which are freely available from the website http：//sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.     

Biosynthesis of geraniol and nerol and their β-d-glucosides in Perlargonium graveolens and Rosa dilecta

1. 3R-[2-(14)C]Mevalonate was incorporated into geranyl and neryl beta-d-glucosides in petals of Rosa dilecta in up to 10.6% yield, and the terpenoid part was specifically and equivalently labelled in the moieties derived from isopentenyl pyrophosphate and 3,3-dimethylallyl pyrophosphate. A similar labelling pattern, with incorporations of 0.06-0.1% was found for geraniol or nerol formed in leaves of Pelargonium graveolens The former results provide the best available evidence for the mevalonoid route to regular monoterpenes in higher plants. 2. Incorporation studies with 3RS-[2-(14)C,(4R)-4-(3)H(1)]-mevalonate and its (4S)-isomer showed that the pro-4R hydrogen atom of the precursor was retained and the pro-4S hydrogen atom was eliminated in both alcohols and both glucosides. These results suggest that the correlation of retention of the pro-4S hydrogen atom of mevalonate with formation of a cis-substituted double bond, such as has been found in certain higher terpenoids, does not apply to the biosynthesis of monoterpenes. It is proposed that either nerol is derived from isomerization of geraniol or the two alcohols are directly formed by different prenyltransferases. Possible mechanisms for these processes are discussed. 3. The experiments with [(14)C,(3)H]mevalonate also show that in these higher plants, as has been previously found in animal tissue and yeast, the pro-4S hydrogen atom of mevalonate was lost in the conversion of isopentenyl pyrophosphate into 3,3-dimethylallyl pyrophosphate.     

Zinc and diabetes — clinical links and molecular mechanisms

Zinc is an essential trace element crucial for the function of more than 300 enzymes and it is important for cellular processes like cell division and apoptosis. Hence, the concentration of zinc in the human body is tightly regulated and disturbances of zinc homeostasis have been associated with several diseases including diabetes mellitus, a disease characterized by high blood glucose concentrations as a consequence of decreased secretion or action of insulin. Zinc supplementation of animals and humans has been shown to ameliorate glycemic control in type 1 and 2 diabetes, the two major forms of diabetes mellitus, but the underlying molecular mechanisms have only slowly been elucidated. Zinc seems to exert insulin-like effects by supporting the signal transduction of insulin and by reducing the production of cytokines, which lead to beta-cell death during the inflammatory process in the pancreas in the course of the disease. Furthermore, zinc might play a role in the development of diabetes, since genetic polymorphisms in the gene of zinc transporter 8 and in metallothionein (MT)-encoding genes could be demonstrated to be associated with type 2 diabetes mellitus. The fact that antibodies against this zinc transporter have been detected in type 1 diabetic patients offers new diagnostic possibilities. This article reviews the influence of zinc on the diabetic state including the molecular mechanisms, the role of the zinc transporter 8 and MT for diabetes development and the resulting diagnostic and therapeutic options.     

siRNA, miRNA and HIV： promises and challenges

Small interfering RNA （siRNA） and microRNA （miRNA） are small RNAs of 18-25 nucleotides （nt） in length that play important roles in regulating gene expression. They are incorporated into an RNA-induced silencing complex （RISC） and serve as guides for silencing their corresponding target mRNAs based on complementary base-pairing. The promise of gene silencing has led many researchers to consider siRNA as an anti-viral tool. However, in long-term settings, many viruses appear to escape from this therapeutical strategy. An example of this may be seen in the case of human immunodeficiency virus type-1 （HIV-1） which is able to evade RNA silencing by either mutating the siRNA-targeted sequence or by encoding for a partial suppressor of RNAi （RNA interference）. On the other hand, because miRNA targeting does not require absolute complementarity of base-pairing, mutational escape by viruses from miRNA-specified silencing may be more difficult to achieve. In this review, we discuss stratagems used by various viruses to avoid the cells＇ antiviral si/mi-RNA defenses and notions of how viruses might control and regulate host cell genes by encoding viral miRNAs （vmiRNAs）.     

Toxoplasmosis and Epilepsy — Systematic Review and Meta Analysis

Background

Toxoplasmosis is an important, widespread, parasitic infection caused by Toxoplasma gondii. The chronic infection in immunocompetent patients, usually considered as asymptomatic, is now suspected to be a risk factor for various neurological disorders, including epilepsy. We aimed to conduct a systematic review and meta-analysis of the available literature to estimate the risk of epilepsy due to toxoplasmosis.

Methods

A systematic literature search was conducted of several databases and journals to identify studies published in English or French, without date restriction, which looked at toxoplasmosis (as exposure) and epilepsy (as disease) and met certain other inclusion criteria. The search was based on keywords and suitable combinations in English and French. Fixed and random effects models were used to determine odds ratios, and statistical significance was set at 5.0%.

Principal findings

Six studies were identified, with an estimated total of 2888 subjects, of whom 1280 had epilepsy (477 positive for toxoplasmosis) and 1608 did not (503 positive for toxoplasmosis). The common odds ratio (calculated) by random effects model was 2.25 (95% CI 1.27–3.9), p = 0.005.

Conclusions

Despite the limited number of studies, and a lack of high-quality data, toxoplasmosis should continue to be regarded as an epilepsy risk factor. More and better studies are needed to determine the real impact of this parasite on the occurrence of epilepsy.