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PubMed2000

Forest Canopy Stratification-Is It Useful?

It has long been recognized that the forest canopy has a complex structure that is significant for environmental interactions, regeneration, growth, and biotic habitat. Not only is the structure variously complex, but also there are many ways to conceptualize that complexity. Yet the persistent theme when considering the structure of canopies continues to be that of stratification: whether structural units are arranged in layers above the ground. We examined the use of the terms "stratification," "layering," and others in connection with canopy structure and found they had various meanings (often only implied) that were difficult to reconcile and to measure. We applied the definitions to the structure of a single, well-studied canopy located in Virginia, U.S.A., and found they failed to define consistently and clearly the presence, number, or location of strata. Additionally, we found the concept had limitations related to scale dependence, point of reference, and spatial averaging. Thus, asserting that a forest is stratified or naming the number of layers generally provided no guide to its structure. We propose alternative ways of conceptualizing and studying the forest canopy that avoid most of the problems associated with stratification. Among these are direct measurement and mapping of structural and environmental variables that have clear potential connections with canopy functions and viewing the distribution of structures or environmental conditions within the canopy as ecological gradients.

canopy↗
PubMed1986

Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus.

The nucleotide sequence coding for the nonstructural proteins of Semliki Forest virus has been determined from cDNA clones. The total length of this region is 7381 nucleotides, it contains an open reading frame starting at position 86 and ending at an UAA stop codon at position 7379-7381. This open reading frame codes for a 2431 amino acids long polyprotein, from which the individual nonstructural proteins are formed by proteolytic processing steps, so that nsPl is 537, nsP2 798, nsP3 482 and nsP4 614 amino acids. In the closely related Sindbis and Middelburg viruses there is an opal stop codon (UGA) between the genes for nsP3 and nsP4. Interestingly, no stop codon is found in frame in this region of the Semliki Forest virus 42S RNA. In other aspects the amino acid sequence homology between Sindbis, Middelburg and Semliki Forest virus nonstructural proteins is highly significant.

Amino Acid Sequence↗
PubMed1979

Functional defects of RNA-negative temperature-sensitive mutants of Sindbis and Semliki Forest viruses.

Defects in RNA and protein synthesis of seven Sindbis virus and seven Semliki Forest virus RNA-negative, temperature-sensitive mutants were studied after shift to the restrictive temperature (39 degrees C) in the middle of the growth cycle. Only one of the mutants, Ts-6 of Sindbis virus, a representative of complementation group F, was clearly unable to continue RNA synthesis at 39 degrees C, apparently due to temperature-sensitive polymerase. The defect was reversible and affected the synthesis of both 42S and 26S RNA equally, suggesting that the same polymerase component(s) is required for the synthesis of both RNA species. One of the three Sindbis virus mutants of complementation group A, Ts-4, and one RNA +/- mutant of Semliki Forest virus, ts-10, showed a polymerase defect even at the permissive temperature. Seven of the 14 RNA-negative mutants showed a preferential reduction in 26S RNA synthesis. The 26S RNA-defective mutants of Sindbis virus were from two different complementation groups, A and G, indicating that functions of two viral nonstructural proteins ("A" and "G") are required in the regulation of the synthesis of 26S RNA. Since the synthesis of 42S RNA continued, these functions of proteins A and G are not needed for the polymerization of RNA late in infection. The RNA-negative phenotype of 26S RNA-deficient mutants implies that proteins regulating the synthesis of this subgenomic RNA must have another function vital for RNA synthesis early in infection or in the assembly of functional polymerase. Several of the mutants having a specific defect in the synthesis of 26S RNA showed an accumulation of a large nonstructural precursor protein with a molecular weight of about 200,000. One even larger protein was demonstrated in both Semliki Forest virus- and Sindbis virus-infected cells which probably represents the entire nonstructural polyprotein.

DNA-Directed RNA Polymerases↗
PubMed1990

Nuclear localization of Semliki Forest virus-specific nonstructural protein nsP2.

About 50% of Semliki Forest virus-specific nonstructural protein nsP2 is associated with the nuclear fraction in virus-infected BHK cells. Transport into the nucleus must be specific, since only trace amounts of nsP3 and nsP4 and about 13% of nsP1, all derived from the same polyprotein, were found in the nucleus. Subfractionation of [35S]methionine-labeled Semliki Forest virus-infected cells showed that 80 to 90% of the nuclear nsP2 was associated with the nuclear matrix. Indirect immunofluorescence, with anti-nsP2 antiserum, showed the most intensive staining of structures which by Nomarski optics appeared to be nucleoli. In the presence of 1 to 5 micrograms of dactinomycin per ml the nuclei were stained evenly and no nucleoli could be found. Transport of nsP2 into the nucleus occurred early in infection and was fairly rapid. A cDNA encoding the complete nsP2 was isolated by the polymerase chain reaction technique and ligated into a simian virus 40 expression vector derivative. When BHK cells were transfected with this pSV-NS2 vector by the lipofection procedure, nsP2 was expressed in about 1 to 5% of the cells, as shown by indirect immunofluorescence. In positively transfected cells the immunofluorescence stain was most intensive in the nucleoli. Thus, Semliki Forest virus-specific nsP2 must have information which directs it into the nuclear matrix and, more specifically, into the nucleoli.

Animals↗
PubMed2026

Dynamics of Antibiotic Resistance Gene Profiles in Captive Forest Musk Deer (Moschus berezovskii) Along a Breeding Duration Gradient.

BACKGROUND: To conserve wild populations and ensure a sustainable supply of musk, China initiated the captive breeding of forest musk deer. The temporal dynamics of gut antibiotic resistance gene (ARG) profiles in captive forest musk deer along a breeding duration gradient remain poorly characterized. METHODS: In this study, we employed metagenomic sequencing to systematically characterize the profiles and potential mobility of ARGs. Samples were divided into short-term, medium-term and long-term groups according to breeding durations. RESULTS: A total of 331 ARG subtypes and 71 mobile genetic element (MGE) subtypes were annotated across all samples. ARG Shannon diversity differed overall across groups (Kruskal-Wallis, p = 0.03); Bonferroni-adjusted Dunn's test showed no significant pairwise differences. PCoA (Bray-Curtis) demonstrated distinct separation of the ST group (p = 0.002), and shared core ARG subtypes gradually increased with extended breeding years. A strong positive correlation between ARG and MGE abundances was identified (r = 0.85, p = 0.0001). In total, 63 contigs carrying co-localized ARG-MGE complexes were recovered. The ST group contained the highest proportion of such contigs. The ST group displayed tight physical ARG-MGE linkage within 1-3 kb genomic intervals. CONCLUSIONS: Our results reveal that breeding duration is associated with the gut ARG characteristics of captive forest musk deer. Short-term captivity has higher ARG-MGE co-localization, suggesting a higher possibility of mobilization.

One Health↗
PubMed1990

The effect of gold sodium thiomalate and its constituent part, thiomalate, on the virus titres and the lysosomal enzyme activity in peritoneal macrophages of Swiss/A2G mice infected with the avirulent strain of Semliki Forest virus.

Treatment of adult mice with gold sodium thiomalate made the normally non-lethal Semliki Forest virus infection lethal. Associated with this was a significant increase in brain virus titre and a depression of peritoneal macrophage lysosomal enzyme activity. In contrast, treatment of adult mice with the constituent part, thiomalate, did not make the non-lethal Semliki Forest virus infection lethal. Brain virus titre and peritoneal macrophage lysosomal enzyme activity were comparable to the controls. The mechanism by which gold sodium thiomalate increases the virulence of Semliki Forest virus is discussed.

Acid Phosphatase↗
PubMed1985

Effects of monovalent cations on Semliki Forest virus entry into BHK-21 cells.

Infection of mammalian cells with Semliki Forest virus requires the endocytosis of the virus, its delivery to prelysosomal endosomes, and fusion of the viral envelope with the endosome membrane. Previous studies have indicated that the low endosomal pH triggers a conformational change in the viral spike glycoproteins rendering them fusogenic. In this paper, we demonstrate an additional factor(s) which regulates virus fusion in endosomes. We found that Semliki Forest virus is unable to penetrate or infect baby hamster kidney (BHK-21) cells grown in medium containing reduced Na+ concentrations. Virus endocytosis and degradation are nearly normal, the virus is transported to endosomes where a characteristic low pH-induced loss of trypsin-sensitivity of the E1 spike glycoprotein occurs. Nevertheless, the viral envelope fails to fuse with the endosomal membrane and the viral RNA is not released into the cytosol. As judged by the uptake of the voltage-sensitive probe [3H]triphenylmethyl phosphonium we observed a close correlation between conditions which inhibit virus infection and which cause depolarization of the cells. We propose that in intact cells, the fusion of Semliki Forest virus with the endosome membrane depends not only on acidic endosomal pH, but also on the maintenance of the potential.

Animals↗
PubMed1964

PARTIAL SUPPRESSION OF MALARIA PARASITES, AND OF THE TRANSMISSION OF MALARIA, IN AEDES AEGYPTI (L.) DOUBLY-INFECTED WITH SEMLIKI FOREST VIRUS AND PLASMODIUM GALLINACEUM BRUMPT.

Laboratory experiments were undertaken with Aedes aegypti infected with both Semliki Forest virus (SFV) from infant mice and Plasmodium gallinaceum from fowls to determine if such double infection of mosquitos suppressed their ability to transmit the malaria parasite, a possibility suggested to explain reduction in malaria transmission in Uganda in 1960 when Anopheles funestus and Anopheles gambiae were transmitting both malaria and o'nyongnyong virus to the African population. In general, transmission of fowl malaria was not prevented by SFV infection in Aedes, although some malariometric indices, and consistently the mean oocyst count, were slightly lower in doubly-infected mosquitos than in controls. In one experiment, however, 60% of the Aedes infected 8 days previously with SFV died within 48 hours of ingesting a malarious meal. Mortality was selectively in favour of the survival of SFV-infected mosquitos negative for, or least heavily infected with, malaria; depression in the presence of the virus of the intensity of malaria infection in the individual Aedes also occurred. Some physiological factor-a stress in adult life or, possibly more important, suboptimal larval nutrition-appears to have been crucial to eliciting the adverse effect on the mosquitos themselves and on their malaria infections. Suppression of the development of a malaria parasite in a mosquito, and of malaria transmission, by concurrent infection of the vector with an arbovirus can happen, but is by no means inevitable.It is shown that a doubly-infected Aedes can transmit both Semliki Forest virus and P. gallinaceum simultaneously.

Aedes↗
PubMed1997

Pulmonary function and respiratory symptoms in forest firefighters.

This study evaluated effects on respiratory health of forest firefighters exposed to high concentrations of smoke during their work shift. This is the first study of cross-shift respiratory effects in forest firefighters conducted on the job. Spirometric measurements and self-administered questionnaire data were collected before and after the 1992 firefighting season. Seventy-six (76) subjects were studied for cross-shift and 53 for cross-season analysis. On average, the cross-season data were collected 77.7 days after the last occupational smoke exposure. The cross-shift analysis identified significant mean individual declines in FVC. FEV1, and FEF25 75. The preshift to midshift decreases were 0.089 L, 0.190 L, and 0.439 I/sec. respectively, with preshift to postshift declines of 0.065 L, 0.150 L, and 0.496 L/sec. Mean individual declines for FVC, FEV1 and FEF25 75 of 0.033 L, 0.104 L, and 0.275 I/sec. respectively, also were noted in the cross-season analysis. The FEV1 changed significantly (p < 0.05). The use of wood for indoor heat also was associated with the declines in FEV1. Although annual lung function changes for a small subset (n = 10) indicated reversibility of effect, this study suggests a concern for potential adverse respiratory effects in forest firefighters.

Adult↗
PubMed2000

Primary seed shadow generated by gibbons in the rain forests of Barito Ulu, central Borneo.

Gibbons are one of the main frugivores in the forests of Southeast Asia, and consequently have long been considered to be good seed dispersers. This is the first study in which the primary seed shadow they create by their ranging and foraging activities is evaluated in detail. I studied two gibbon groups over 12 months in lowland dipterocarp forest in central Borneo. The gibbons dispersed up to 81% of the species they consumed and destroyed the seeds of only 12%. Fruit with elongated seeds (up to 20 mm wide) were more likely to be dispersed than round seeds. Considering that the survival rate of seeds in the forest to one year was 8%, the gibbons effectively dispersed 13 seedlings ha(-1) group(-1) year(-1). Their effect on germination was very variable, although most species did eventually germinate. Most seeds were deposited along their major ranging routes and close to or under feeding trees.

Animals↗
PubMed2000

The occurrence of yeasts in the forest soils.

One hundred and eighty one yeast strains were isolated from 180 soil samples collected in three types of forest. The samples were taken during one year. The yeast species found were similar in spite of distinct forest types. Cryptococcus laurentii, Cystofilobasidium capitatum, Leucosporidium scottii, Rhodotorula aurantiaca, and Trichosporon cutaneum were the predominant species in both deciduous and coniferous forests. The number of yeasts ranged from 1.5 x 10(3) to 1.1 x 10(4) CFU/g soil. We found that yeasts occurred unevenly in soils during the year. The lowest number of yeasts was ascertained in December and the highest one in May.

Ecosystem↗
PubMed2002

Mineral content as a basis for food selection by western lowland gorillas in a forest clearing.

The forests in northwest Republic of Congo contain a number of herbaceous swamp clearings that provide foraging sites for lowland gorillas (G.g. gorilla). A 10-month study at the Maya Nord clearing (Parc National d'Odzala) showed that feeding activities occupied 72% of the time visiting gorillas spent on the clearing. They fed on four plant species: Enydra fluctuans (Asteraceae), Cyperus sp., Pycreus mundtii, and Rhynchospora corymbosa (Cyperaceae) among the 45 species recorded on the clearing. These clearing food species have higher mineral contents (especially Na and Ca) than the dominant Marantaceae species (Haumania liebrechtsiana) that constituted a staple food plant for gorillas in this forest. They also have higher potassium contents and contain less lignin than non-eaten clearing items/species. Finally, the most actively searched for clearing food (Enydra fluctuans) was characterized by the highest amount of Na and Ca. These results suggest that the mineral content (especially in Na, Ca, and/or K) could determine the feeding selectivity of gorillas at the clearing. They also tend to confirm that the amount of fiber plays a deterrent role in food selectivity, as has been found by many authors. The high density of gorillas in that region could result from the combination of the large areas of Marantaceae forests that provide abundant though monotonous food, and the number of clearings that provide sufficient mineral supplies. Clearings should thus be considered as key habitats for the conservation of gorillas.

Animal Nutritional Physiological Phenomena↗
PubMed2007

Living in forest fragments reduces group cohesion in diademed sifakas (Propithecus diadema) in eastern Madagascar by reducing food patch size.

Forest fragmentation is thought to threaten primate populations, yet the mechanisms by which this occurs remain largely unknown. However, fragmentation is known to cause dietary shifts in several primate species, and links between food resource distribution and within-group spatial dynamics are well documented. Thus, fragmentation has the potential to indirectly affect spatial dynamics, and these changes may present additional stresses to fragmented populations. I present the results from a 12-month study of Propithecus diadema at Tsinjoarivo, eastern Madagascar, including two groups in fragments and two in continuous forest. Instantaneous data on activity and spatial position were collected during all-day focal animal follows. Fragment groups had much lower cohesion, being more likely to have no neighbor within 5 and 10 m. For continuous forest groups, cohesion was highest in the rainy season (when food patches are large) and lowest in winter (when the animals rely on small-crowned mistletoes), and the chance of having no neighbor within 5 m was positively correlated with mistletoe consumption. Thus their decreased cohesion in fragment groups is inferred to result from their increased reliance on mistletoes and other small resources, which causes them to spread out among multiple patches. This scenario is consistent with the reduced body mass of subordinate individuals (males and immatures) in fragments, and suggests the occurrence of steeper within-group fitness gradients. Further research is necessary to determine whether these patterns apply to other primates; however, since fragmentation tends to cause the loss of the largest trees, many primates in fragments may lose their largest food resources and undergo similar behavioral shifts.

Analysis of Variance↗
PubMed2004

Seasonal change in terrestriality of chimpanzees in relation to microclimate in the tropical forest.

Seasonal change in time spent for terrestrial behavior of chimpanzees was investigated from the viewpoint of the distribution of food and microclimate in the forest at Bossou, Guinea, West Africa. Daily and monthly data for activity budgets of three focal animals, climatic variables in the forest, and indices of fruit availability and distribution of fruit-bearing trees were estimated and analyzed. Mean activity budgets calculated by monthly means were 23.4% for terrestrial behavior (range, 2.9% in August to 42.1% in November) and 76.6% for arboreal behavior. Chimpanzees spent more time on the ground in warm or dry months. Chimpanzees also spent less time in trees in months with high fruit production (trees of diameter at breast height >/=10 cm). The daily percentage of terrestrial behavior showed a positive correlation with maximum temperature and a negative correlation with the minimum humidity of the day. Only maximum temperature of the observation day influenced time spent on the ground significantly, as analyzed by generalized linear models (GLZ), which included all variables (fruit production, distribution of fruit-bearing trees, and climatic variables). It was concluded that the reason why arboreal behavior increased in the rainy season was not owing to the vertical distribution of food, but rather in order to reduce thermoregulation costs by resting in trees during cool periods and taking advantage of the vertical structure of the microclimate in the tropical forest (i.e., higher temperatures in higher positions).

Animals↗
PubMed2006

Do food availability, parasitism, and stress have synergistic effects on red colobus populations living in forest fragments?

Identifying factors that influence animal density is a fundamental goal in ecology that has taken on new importance with the need to develop informed management plans. This is particularly the case for primates as the tropical forest that supports many species is being rapidly converted. We use a system of forest fragments adjacent to Kibale National Park, Uganda, to examine if food availability and parasite infections have synergistic affects on red colobus (Piliocolobus tephrosceles) abundance. Given that the size of primate populations can often respond slowly to environmental changes, we also examined how these factors influenced cortisol levels. To meet these objectives, we monitored gastrointestinal parasites, evaluated fecal cortisol levels, and determined changes in food availability by conducting complete tree inventories in eight fragments in 2000 and 2003. Red colobus populations declined by an average of 21% among the fragments; however, population change ranged from a 25% increase to a 57% decline. The cumulative basal area of food trees declined by an average of 29.5%; however, forest change was highly variable (a 2% gain to a 71% decline). We found that nematode prevalence averaged 58% among fragments (range 29-83%). The change in colobus population size was correlated both with food availability and a number of indices of parasite infections. A path analysis suggests that change in food availability has a strong direct effect on population size, but it also has an indirect effect via parasite infections.

Animals↗
PubMed2005

Identifying SNPs predictive of phenotype using random forests.

There has been a great interest and a few successes in the identification of complex disease susceptibility genes in recent years. Association studies, where a large number of single-nucleotide polymorphisms (SNPs) are typed in a sample of cases and controls to determine which genes are associated with a specific disease, provide a powerful approach for complex disease gene mapping. Genes of interest in those studies may contain large numbers of SNPs that classical statistical methods cannot handle simultaneously without requiring prohibitively large sample sizes. By contrast, high-dimensional nonparametric methods thrive on large numbers of predictors. This work explores the application of one such method, random forests, to the problem of identifying SNPs predictive of the phenotype in the case-control study design. A random forest is a collection of classification trees grown on bootstrap samples of observations, using a random subset of predictors to define the best split at each node. The observations left out of the bootstrap samples are used to estimate prediction error. The importance of a predictor is quantified by the increase in misclassification occurring when the values of the predictor are randomly permuted. We extend the concept of importance to pairs of predictors, to capture joint effects, and we explore the behavior of importance measures over a range of two-locus disease models in the presence of a varying number of SNPs unassociated with the phenotype. We illustrate the application of random forests with a data set of asthma cases and unaffected controls genotyped at 42 SNPs in ADAM33, a previously identified asthma susceptibility gene. SNPs and SNP pairs highly associated with asthma tend to have the highest importance index value, but predictive importance and association do not always coincide.

Case-Control Studies↗
PubMed2004

Assessing the use of delta(13)C natural abundance in separation of root and microbial respiration in a Danish beech (Fagus sylvatica L.) forest.

Our understanding of forest biosphere-atmosphere interactions is fundamental for predicting forest ecosystem responses to climatic changes. Currently, however, our knowledge is incomplete partly due to inability to separate the major components of soil CO(2) effluxes, viz. root respiration, microbial decomposition of soil organic matter and microbial decomposition of litter material. In this study we examined whether the delta(13)C characteristics of solid organic matter and respired CO(2) from different soil-C components and root respiration in a Danish beech forest were useful to provide information on the root respiration contribution to total CO(2) effluxes. The delta(13)C isotopic analyses of CO(2) were performed using a FinniganMAT Delta(PLUS) isotope-ratio mass spectrometer coupled in continuous flow mode to a trace gas preparation-concentration unit (PreCon). Gas samples in 2-mL crimp seal vials were analysed in a fully automatic mode with an experimental standard error +/-0.11 per thousand. We observed that the CO(2) derived from root-free mineral soil horizons (A, B(W)) was more enriched in (13)C (delta(13)C range -21.6 to -21.2 per thousand ) compared with CO(2) derived from root-free humus layers (delta(13)C range -23.6 to -23.4 per thousand ). The CO(2) evolved from root respiration in isolated young beech plants revealed a value intermediate between those for the soil humus and mineral horizons, delta(13)C(root) = -22.2 per thousand, but was associated with great variability (SE +/- 1.0 per thousand ) due to plant-specific differences. delta(13)C of CO(2) from in situ below-ground respiration averaged -22.8 per thousand, intermediate between the values for the humus layer and root respiration, but variability was great (SE +/- 0.4 per thousand ) due to pronounced spatial patterns. Overall, we were unable to statistically separate the CO(2) of root respiration vs. soil organic matter decomposition based solely on delta(13)C signatures, yet the trend in the data suggests that root respiration contributed approximately 43% to total respiration. The vertical gradient in delta(13)C, however, might be a useful tool in partitioning respiration in different soil layers. The experiment also showed an unexpected (13)C-enrichment of CO(2) (>3.5 per thousand ) compared with the total-C signatures in the individual soil-C components. This may suggest that analyses of bulk samples are not representative for the C-pools actively undergoing decomposition.

Biomass↗
PubMed2005

13C-isotopic fingerprint of Pinus pinaster Ait. and Pinus sylvestris L. wood related to the quality of standing tree mass in forests from NW Spain.

Pine forest plantations of Pinus pinaster Ait. and P. sylvestris L. located in Galicia, NW Spain, were selected to study the 13C/12C-isotopic fingerprint in wood core samples in order to find possible relationships between the delta(13)C at natural abundance levels and the quality of the standing tree mass. For each pine species, 24 forests growing on acidic soils were studied: half developed over granite and half over schists. Two dominant trees from each plot, corresponding to all possible combinations of forest stands with high or low site index and with adults or young trees, were drilled at the basal part of trunks using a Pressler drill to obtain tree ring samples. The C-isotopic compositions of the litter and the soil organic matter from different soil depths were also determined and statistically significant correlations between these values and the 13C content of the wood were observed. Despite internal variations due to the influence of site index, tree age and parent material, the isotopic fingerprint of P. pinaster wood (mean value delta13C=-26.2+/-0.8 per thousand) significantly differed (P<0.001) from that of P. sylvestris (mean value delta13C=-24.6+/-0.7 per thousand). Relationships between the quality of the stand and the C-isotopic composition of the wood were observed, high quality stands having trees more 13C-depleted than low quality ones. A high correlation between wood delta13C and site index values for P. pinaster stands (r=-0.667, P<0.001) was found, this correlation being even clearer when only P. pinaster growing over schists (r=-0.833, P<0.001) are considered. Again, the correlation between the site index and the wood delta13C of young P. pinaster trees is higher when plots over granite or schists are separately considered. A similar fact occurs for adult P. sylvestris trees from schists stands, high quality specimens being 13C-depleted compared with low quality ones. On the other hand, 13C natural abundance of wood from P. sylvestris trees seems to be also strongly influenced by the underlying parent material, young trees from granite stands having a statistically higher 13C-isotopic composition (P<0.05) than young trees from schists stands.

Biomass↗