Miracle-dz/UniFAR-FTUs huggingface dataset:
Embracing variability: environmental dependence and plant community context in ecological restoration

In heterogeneous landscapes, one can expect a complexity of ecological restoration outcomes. The effectiveness of management often depends on environmental conditions (environmental context) and how management indirectly affects other components of the system (community context). Although managers appreciate this context dependency, it is difficult to translate it to decision‐making in restoration. We demonstrate one approach to improve this translation. We surveyed plant, soil, and landscape characteristics at 131 grassland and coastal sage sites that received herbicide treatments to remove non‐native plant species and/or propagule addition to increase native species. We used path analysis to describe how each management approach influenced target non‐native species and how interactions with environmental conditions and indirect effects of management influenced plant community composition. This approach enabled us to analyze a complex system with differing management histories to identify both direct and indirect effects of management. Management had the intended direct effects: the application of herbicide and propagule addition directly reduced non‐native species and increased native species, respectively. We found little evidence of environmental dependency: effects occurred largely independent of environmental conditions. However, management outcomes did depend on plant community context. Specifically, although herbicide reduced the cover of target, non‐native plant species, this reduction resulted in only slight increases in native species and instead led indirectly to increases in non‐targeted, non‐native species. We suggest that quantitative evaluation of variability in restoration outcomes allows management to be more adaptive and increase decision‐making efficacy in complex managed landscapes.
PATTERNS OF POSTFIRE REGENERATION IN A SOUTHERN CALIFORNIA MIXED CHAPARRAL COMMUNITY

ABSTRACT Effects of prefire stand age, fire intensity, and hillslope position on postfire vegetation recovery during the first two postfire seasons were studied in two contrasting stands of mixed chaparral at San Diego State University's Sky Oaks Field Station (San Diego County, CA). One stand was approximately 60-years old and the other 12-years old when both burned in the July 2003 Coyote Fire. The two stands showed contrasting patterns of postfire community composition among different plant groups based on their modes of postfire regeneration. Fire intensity was significantly higher in the older stand. Increased fire intensity was positively correlated with establishment of seedlings of Ceanothus greggii var. perplexans (an obligate seeder), and negatively correlated with seedling abundance of Adenostoma fasciculatum (a facultative seeder). Hillslope position was also important in determining patterns of abundance, suggesting that soil erosion and deposition following fire may have a significant effect on postfire community recovery on these steep sites. Alternatively, prefire differences in the chaparral community that were correlated with hillslope position may account for these differences. The postfire herbaceous community in the first year was dominated by Phacelia brachyloba, a fire annual. Contrary to expectations, this species was found in greater abundance in the old stand than in the young. Fire annuals were largely absent from the community in the second year, and were replaced in abundance by a variety of opportunistic native and exotic annuals.
Evidence Supporting the Hypothesis that Ambient Temperature and Dietary Composition Influence the Relative Efficacy of Methionine and Its Hydroxy Analogues for Broilers: A Review

Abstract Many comparisons have been made between DL-methionine (DLM) and various methionine hydroxy analogues (MHA) as sources of dietary methionine activity for broilers, with conflicting results between studies often reported. A review revealed that certain dietary factors may influence the outcome of such efficacy studies. Purified crystalline amino acid diets, which are generally characterized by a low Arg:Lys ratio of 1.07 or less and high levels of dietary salt (NaCl or NaHCO3), typically have shown better growth performance with DLM than with MHA supplements. When practical or when semipurified diets that contain intact proteins were fed under thermoneutral conditions, the advantages observed, when using DLM in purified crystalline amino acid diets, were greatly reduced. Indeed, in many cases the differences in biological performance between the 2 sources of methionine activity were often not significant. These latter diets generally have had Arg:Lys ratios of 1.05 and greater and much lower concentrations of NaCl than the purified crystalline amino acid diets. With practical diets under heat stress conditions, the MHA supplements appeared to perform statistically as well as, or better than, DLM supplements as long as the Arg:Lys ratio was approximately 1.20 or greater. Thus, data exist that demonstrate that particular dietary factors and ambient temperature could inadvertently influence the outcome of efficacy studies. Further, these data suggest that the selection of methionine activity source in practical conditions should be tempered by knowledge of the prevailing Arg:Lys ratio, dietary salt inclusion levels, and the thermal environment.
Nuclear localization of phosphatidylinositol 4-kinase β

Whereas most phosphatidylinositol 4-kinase (PtdIns 4-kinase) activity is localized in the cytoplasm, PtdIns 4-kinase activity has also been detected in membranedepleted nuclei of rat liver and mouse NIH 3T3 cells. Here we have characterized the PtdIns 4-kinase that is present in nuclei from NIH 3T3 cells. Both type II and type III PtdIns 4-kinase activity were observed in the detergent-insoluble fraction of NIH 3T3 cells. Dissection of this fraction into cytoplasmic actin filaments and nuclear lamina-pore complexes revealed that the actin filament fraction contains solely type II PtdIns 4-kinase, whereas lamina-pore complexes contain type III PtdIns 4-kinase activity. Using specific antibodies, the nuclear PtdIns 4-kinase was identified as PtdIns 4-kinase β. Inhibition of nuclear export by leptomycin B resulted in an accumulation of PtdIns 4-kinase β in the nucleus. These data demonstrate that PtdIns 4-kinase β is present in the nuclei of NIH 3T3 fibroblasts, suggesting a specific function for this kinase in nuclear processes.
Assessment of mitochondrial function in vivo with a breath test utilizing α—ketoisocaproic acid

A breath test to assess hepatic mitochondrial function in vivo was evaluated in rats. Following the i.p. administration of [1‐14C]‐α‐ketoisocaproic acid, 14CO2 exhalation reached a peak within 10 to 20 min and then declined exponentially, with a half‐life of 14.3 min. Control animals exhaled 38.6% of the administered radioactivity within 1 hr. In functionally anhepatic animals, 14CO2 in breath amounted to 23% of that in control animals, indicating that α‐ketoisocaproic acid decarboxylation reflects mainly hepatic mitochondrial function in vivo. Ethanol (3 gm per kg) significantly decreased α‐ketoisocaproic acid decarboxylation (21.8% of the dose appearing in breath in 1 hr), probably due to the ethanol‐induced shift in the NAD+:NADH ratio. In contrast, an uncoupler of mitochondrial respiration, sodium salicylate (375 mg per kg), increased the decarboxylation of α—ketoisocaproic acid (56.3% of the dose recovered as 14CO2 in 1 hr). Mitochondrial damage induced by 4‐pentenoic acid decreased the decarboxylation of α‐ketoisocaproic acid but did not affect the microsomal metabolism of antipyrine. The present data indicate that the α‐ketoisocaproic acid breath test provides a noninvasive estimate of hepatic mitochondrial function in vivo which, when applied to man, might yield clinically useful information.
Molecular cloning, polymorphism and association of porcine WARS2 gene with litter size

Mitochondrial tryptophanyl tRNA synthetase 2 (WARS2) is an important reproduction-related gene. In this study, the full-length coding sequence of porcine WARS2 gene was cloned through reverse transcription-polymerase chain reaction. Sequence analysis revealed that the pig WARS2 gene encoded a protein of 360 amino acids and has 6 exons and 5 introns. Phylogenetic analysis demonstrated that the pig WARS2 gene had a close genetic relationship with the WARS2 gene of cattle. Polymerase chain reaction-Pst I-restriction fragment length polymorphism (PCR-Pst I-RFLP) was established to detect the EU650788:c.291 G > A substitution of the porcine WARS2 gene coding sequence and eight pig breeds displayed obvious allele frequency differences at this mutation locus. Association of this single nucleotide polymorphism with litter size was assessed in Large White (n = 200) and Landrace (n = 200) populations, and the results indicated that this polymorphic locus was significantly associated with the total number of piglets born of all parities in Large White and Landrace sows (P < 0.05). Therefore, the WARS2 gene could be a useful candidate gene for increasing the litter size in pigs.
Estimators of Tree Species Richness: An Assessment for Central and Eastern Canada

Abstract A total of 11 sample-based estimators of tree species richness (S) are evaluated in terms of accuracy and precision in a Monte Carlo simulated simple random sampling from 39,779 forest inventory plots with 7.8 million trees belonging to 85 species. The plots represent a 108 million hectare forested region in central and eastern Canada. Sample sizes varied from 50 to 800. A weighted index combining estimates of accuracy and precision identified Chao's first estimator (CHAO1) as overall best with an estimator based on the assumption of a gamma mixed Poisson distribution of species occurrence as a close runner-up. The observed sample species richness was almost always the most negatively biased estimate. A sample size of 400-700 conventional fixed area forest inventory plots are needed to produce results with bias <20%.
Home range and shelter site selection in the greater hedgehog tenrec in the dry deciduous forest of Western Madagascar

Information on the spatial distribution and habitat use of the Tenrecidae (Supraorder: Afrotheria) of Madagascar are severely lacking. Here, we present the first data available on home range size, as well as further data on population distribution and rest site selection of a large tenrec, the greater hedgehog tenrec (Setifer setosus). Data were collected over two rainy seasons in the dry deciduous woodland of Western Madagascar, in Ankarafantsika National Park. Home ranges were surprisingly large for a 200–300-g animal: males had an average home range (95% minimum convex polygon) of 13.7 ± 4.9 ha (n = 5), and females of 6.7 ± 2.0 ha (n = 5). A high overlap between multiple individuals of the opposite sex supports a promiscuous mating system for this species. Daytime shelter sites proved to be highly variable and differed between sex and reproductive status.
Considerations on the Advantages of Small Tracers for Optical Molecular Imaging

Molecular imaging is nowadays gaining a complementary role in cancer therapy, specifically in diagnosis, selection of therapy, monitoring of therapeutic efficacy, and also in the surgical setting. Many tumor-targeted tracers have been developed for these applications. Optical molecular imaging has been gaining more importance, particularly due to the absence of ionizing radiation, rendering its use friendlier and safer for patients and medical personnel. Recently, clinical trials have been initiated for tumor optical imaging with monoclonal antibodies conjugated to the near-infrared fluorophore IRDye 800CW. Yet, preclinical studies clearly indicate several aspects that favor smaller tracer formats over antibodies, namely, their rapid distribution, efficient penetration, and the rapid clearance of unbound tracers. Altogether, these small tracers lead to adequate contrast within minutes or hours after administration, instead of days. Here, the discussion will be centered on the properties of the different formats of tracers, in particular the small formats. Although, the conventional antibody format has already reached clinical trials, optical imaging trials with smaller formats are eagerly awaited to clarify whether their advantages over antibodies are also evident in patients.
Selective impact of filter‐feeding gizzard shad on zooplankton community structure1

Comparison of ponds containing gizzard shad with control ponds without fish showed that gizzard shad predation suppressed populations of Keratella sp. , Diaphanosoma brachyurum, copepod nauplii, Chaoborus sp. , and cyclopoid copepodids and adults, but enhanced populations of Diaptomus pallidus copepodids and adults. These results confirm previous laboratory studies which showed that filter-feeding gizzard shad are not size-selective predators, as is typically assumed of planktivorous fish, but instead feed on those animals which have little ability to escape, so that their predation results in a community shift toward the more evasive prey.
More than propagule pressure: Successful invading algae have physiological adaptations suitable to anthropogenically changing nutrient environments

While increased propagule pressure may increase the possibility of success of an invading species, success is also a function of the environment to which the organisms have been introduced and the physiological strategies of the invading organisms and how those strategies relate to those of the native fauna or flora. Using examples of altered nutrients in aquatic environments, the effects of environment on the success of harmful algae are herein considered. Many harmful algae are introduced species, especially via ballast water. While increasing numbers and frequency of harmful algal blooms in eutrophic waters may be comparatively easy to understand—more nutrients, more biomass, more opportunities for species to proliferate—one of the more perplexing issues is why some harmful algal bloom species seem to become more prevalent under conditions of disproportionate nutrient supply. Focusing here specifically on the case of excess nitrogen loading relative to that of phosphorus, there are a number of key adaptive strategies that may allow certain types of harmful algal blooms to thrive. Successful invaders may be smaller in cell size, thereby reducing phosphorus cellular demands, and they may have nutrient substitution or acquisition strategies allowing them to use a source of nutrient not otherwise available to competitors. They may also create local environmental changes, such as increases in pH that detrimentally affect competitors while altering sediment biogeochemical processes increasing efflux of the otherwise limiting nutrient. Finally, their growth and cellular elemental stoichiometry also affect food quality for grazers, including toxin production, which has been shown in numerous species to increase when the cells are not grown under nutrient-balanced conditions. Through their detrimental effects on grazers, they may further destabilize ecosystem environments increasing susceptibility for additional ecosystem changes, including creating environmental conditions suitable for additional invasions to occur.
Controlling the proportion of false positive (PFP) in a multiple test genome scan for marker-QTL linkage.

INTRODUCTION When heritability analysis shows that QTL are segregating in the population, the large number of markers employed ensures that an appreciable proportion is in linkage to segregating QTL. The challenge is to identify the markers in linkage, while controlling Type I error in this “multiple test” situation. Previous attempts have been based on controlling the overall genomewise Type I error (GWER) (Lander and Kruglyak, 1995), or the False Discovery Rate (FDR) (Weller et al., 1998). The GWER approach results in a drastic reduction in experimental power, while the FDR approach is theoretically inappropriate (Zaykin et al., 2000). Combining previous studies (Southey and Fernando, 1998 ; Mosig et al., 2001) we here present an approach based on controlling the proportion of false positives (PFP), which avoids the limitations of both GWER and FDR. The PFP is derived from the posterior Type I error rate (PER) long used in human linkage studies (Morton, 1955 ; Ott, 1991).
Numerical Changes and Population Regulation in Brook Trout Salvelinus fontinalis

A brook trout population in a stable stream environment was studied for 14 years. Population estimates were made each September, the catch of fish by anglers was recorded, and collections of fish were made to determine sex ratio, age at sexual maturity, and fecundity.The sex ratio was close to 1:1 for all age-groups. Some male trout were sexually mature at the end of the 1st year of life, most were mature at the end of the 2nd year, and all were mature at the end of the 3rd. No females were mature at the end of their 1st year, most were mature at the end of the 2nd, and all were mature at the end of the 3rd year of life. The regression of egg content on total length of female trout was determined.On the average 132,000 eggs were produced annually by the population in the study area, from which 4813 fish survived to the end of the 1st year; 1966 to the end of the 2nd; 356 to the 3rd; 29 to the 4th; and 0.6 to the end of the 5th year.The growth rate of the fish varied little during the period of study. Annu.
Courtship Songs of Chrysoperla nipponensis (Neuroptera: Chrysopidae) Delineate Two Distinct Biological Species in Eastern Asia

ABSTRACT The substrate-borne vibrational courtship songs of type A and type B Chrysoperla nipponensis (Okamoto) (Neuroptera: Chrysopidae) are described in detail, from populations sampled throughout Japan and near Beijing, China. The song of type A is long (≈ 5–6 s) and is made up of numerous (four to 12) volleys of four distinct forms that differ in their carrier frequencies. The song of type B is shorter (≈2 s) and functions as a repeated single-volley song, but each volley is shown here to consist of four to six distinct subsections. During heterosexual duets, partners of type A exchange their long multi-volley songs, whereas partners of type B repeatedly exchange short single-volley songs. Geographical variation within each song type is low and largely insignificant. In addition, previously recognized mitochondrial (cytochrome oxidase subunit I) haplotypes Al and A2 of type A C. nipponensis do not have different songs. These results support the hypothesis that types A and B C. nipponensis are distinct species, with type A corresponding to the nominate species (i.e., C. nipponensis s. str.) and type B as yet unnamed. Their songs are among the most complex yet found in the Chrysoperla carnea swarm of cryptic species.
Selective mapping of QTL conditioning disease resistance in common bean.

Genetic markers linked with quantitative trait loci (QTL) may enable indirect selection of complex disease resistance. Construction of separate linkage maps to identify QTL for each complex disease resistance trait of common bean (Phaseolus vulgaris L.) is unfeasible, however. We investigated whether selective mapping could be used to hasten identification of random amplified polymorphic DNA (RAPD) associated with QTL conditioning bean golden mosaic virus (BGMV) or common bacterial blight (CBB) resistance. The mapping population ('Dorado' x XAN 176) consisted of 79 F 5:7 recombinant inbred lines. A bulked segregant analysis (BSA) of as few as three individuals and selective genotyping was used. The 101 RAPDs identified between the parents were tested across resistant vs. susceptible bulks for BGMV reaction, combined greenhouse (leaf) and field reactions to CBB, and pod (greenhouse) reaction to CBB. Fourteen of 22 RAPDs selectively mapped because they cosegregated among lines within bulks, were linked with seven of the nine QTL conditioning resistance as identified by QTL mapping using all 101 RAPDs. The two QTL not identified by this approach had minor effects. BSA and selective genotyping required only about one-third the cost and labor of completely classifying the whole population with each marker and was similarly effective for identifying RAPD markers associated with major-effect QTL that condition disease resistance in common bean. Two-locus models (R 2 ), for select environments, explained 60% of the phenotypic variation in BGMV reaction, and 65, 58, and 46% of the phenotypic variation in greenhouse-leaf, -pod, and field reactions to CBB. Repulsion linkages between QTL for BGMV and CBB may complicate the combination of resistance alleles for these two traits.
Effect of Temperature on Larval Sunshine Bass Growth and Survival to the Fingerling Stage

Abstract Determining the optimum conditions for tank culture of sunshine bass (female white bass Morone chrysops × male striped bass M. saxatilis) fingerlings will facilitate a year-round supply of seed for the production cycle of this increasingly popular food fish. This study determined the relationship between temperature and larval sunshine bass growth and survival to the time when fish were trained to accept commercial feeds. At 4 d posthatch (dph), larvae were stocked at five temperatures from 20°C to 32°C at 3°C increments. There were two replicates for each temperature. The larvae were fed rotifers through 8 dph. Conversion to a diet of brine shrimp Artemia spp. nauplii began at 6 dph, and training for acceptance of dry starter feed began at 20 dph. At harvest, average total length and average weight of the fish increased in a linear relationship with temperature, while relative survival and number of fish harvested decreased linearly with temperature. Tank yield had a curvilinear relationship wit.
Time-scale dependency of plant biomass- and trait-mediated indirect effects of large herbivores on phytophagous insects

報告番号: 甲28109 ; 学位授与年月日: 2012-03-22 ; 学位の種別: 課程博士 ; 学位の種類: 博士(農学) ; 学位記番号: 博農第3825号 ; 研究科・専攻: 農学生命科学研究科生圏システム学専攻
Atividade inseticida in vitro do óleo de sementes de nim sobre Lutzomyia longipalpis (Diptera: Psychodidae)

Lutzomyia longipalpis is the main vector of visceral leishmaniasis in Brazil. The objective was to evaluate the effect of oil from (Azadirachta indica) neem seeds on eggs, larvae and adults of the vector. The insects were captured in the field and kept in the laboratory at ± 27 °C and 80% relative humidity. Five treatments with different concentrations were performed using two negative controls (distilled water and Tween 80) and a positive control. The eggs were sprayed with the oil at different concentrations and the number of hatched larvae evaluated for 10 days. Mortality of larvae was observed to pupation and adult mortality was observed after 24, 48, and 72 hours. Statistical analysis was performed by Tukey test at 5% probability. The highest oil concentration of eggs obtained 65.16 ± 3.24% efficacy for reducing egg hatching. The test with larvae showed 67.75 ± 2.21% efficacy at a concentration of 100 mg.mL-1. In adults, the efficacy of the 100 mg.mL-1 concentration was 96.64 ± 4.11% after 24 hours. The phytochemical analysis revealed the presence of triterpenes. These results demonstrate the potential use of this oil in the control of this vector.