Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding confidence limits on population growth rates : Monte Carlo test of a simple analytic method

Estimates of population growth rates are subject to uncertainties because of errors incurred in estimating the individual rates of fecundity, survival and growth. However, the non-linear relationship between the population growth rate and the vital rates makes this a difficult task, and confidence limits are rarely assigned to growth rate estimates. The mean and standard error of the population growth rate may be approximated using a Taylor's series expansion. Assuming a particular type of sampling distribution for the population rate, one may use this analytic estimate to assign confidence limits. Available simulations do not enable generalizations concerning the performance of this analytic approach, especially for estimates obtained for age or stage-structured populations
Variability in 20th century climate change reconstructions and its consequences for predicting geographic responses of California mammals

Empirical species distribution models are widely used to predict the effects of climate change on biodiversity distribution but rely on multiple assumptions about the certainty of the locality and climate data. Here, we assess the effect of historical climate data variability when forecasting geographic responses of California mammals to 20th century climate change. We first used two methods to derive gridded climate surfaces from weather station data (ANUSPLIN and PRISM) representing two sampling eras: historic (1900–1940) and current (1980–2005). We then used the two sources of climate data in conjunction with a maximum entropy algorithm (MAXENT) to predict both the historic and current distributions of all major mammal species vouchered historically in California. Results indicate that levels of disagreement between the two climate datasets are considerably greater in the historical era than in the current era. For the bioclimatic variables used in modeling historical mammal distributions, precipitation variables were less concordant than temperature variables. These discrepancies are reflected in the low agreement between historic mammal range predictions and further propagated when the historic models are projected to present day. Nonetheless, some common patterns exist across mammal species and climate estimates. Range stability is the most common prediction between the two eras, followed by expansion and contraction. Jepson ecoregions with relatively high levels of range stability include parts of the Great Central Valley and Sierra Nevada, while other parts of the Central Valley, the Sonoran desert, and Central‐ and Southwestern California yield predictions of range shifts. Historical species distribution modeling can greatly inform studies attempting to describe how species will continue to move geographically in response to future changes in climate. We suggest that alternative estimates of historical climate and their uncertainties are ultimately required in order to provide a quantitative measure of the confidence in predicted changes in distribution.
Pectate lyase in transgenic potatoes confers pre-activation of defence againstErwinia carotovora

Abstract Erwinia carotovora bacteria cause blackleg and soft-rot of potatoes by enzymic maceration of host tissue. Pectate lyases (PLs), the main E. carotovora enzymes, depolymerize pectic substances of plant cell walls. The degradation products, unsaturated oligogalacturonates, have been proposed to induce plant defence reactions. The expression of the isoenzyme PL3 in planta and its effect on the soft-rot resistance of transgenic potatoes was investigated. The DNA sequence encoding the mature enzyme was fused to the promoter of the potato patatin B33 gene and to the 35S promoter of the cauliflower mosaic virus. The expression cassettes were inserted into the binary vector pBin19. The plasmids pB33-PL3 and p35S-PL3 were used for Agrobacterium -mediated transformation of potato, cv. Desiree. Enzyme production in plant lines transformed with plasmid pB33-PL3 was confined to tuber tissue, yielding a maximum of 340 mU ml −1 extract. Plants harbouring the 35S-PL3 chimeric gene exhibited constitutive expression of PL in various tissues, with activities up to 280 mU ml −1 in leaf extracts and 50 mU ml −1 in tuber tissue. After wounding the tuber tissue, the liberated PL3 caused a decrease of cell viability. Compared with non-transformed plants, the transgenic lines which synthesized PL3 were more resistant to tissue maceration by E. carotovora or its enzymes. Wounding induced the transcription of the plant defence related gene encoding phenylalanine ammonia-lyase to a high level in tubers of a PL3-expressing transgenic line. The possible implications of PLs and their enzymatic products for protection against invading microbes are discussed.
Population dynamics of brushtail possums subject to fertility control

Summary 1 Reducing the fertility of pest species using immunocontraceptive vaccines holds promise for the humane and effective control of vertebrate pest populations. However, despite much research into the development of contraceptive vaccines, there are few data illustrating the effectiveness of fertility control for managing wild populations of vertebrate pests. 2 In New Zealand, introduced brushtail possums Trichosurus vulpecula have been the focus for the development of contraceptive vaccines to provide a possible alternative to lethal control techniques. 3 The effect of fertility control on the population dynamics of brushtail possums was investigated experimentally using surgical sterilization to suppress breeding on six 12-ha study sites between January 1996 and October 2000. Sterilization treatments, consisting of 0%, 50% and 80% of resident females sterilized, were applied at a particular site, with adjustments made annually on recruits to maintain levels of sterility. Mark–recapture trapping was used to estimate age-specific demographic rates and their relative contribution to age-specific population growth rates (λ). 4 Sterility treatments resulted in reductions to per capita rates of local recruitment (surviving young per adult female) of 60% and 74% on average for 50% and 80% levels of sterility, respectively. However, immigration by yearling-aged possums compensated for reductions in local recruitment because of sterility treatments, leading to the stable (λ = 1) population trajectories on sterility treatment sites. 5 There was some evidence that sterilized females had higher annual survival rates than fertile females, but otherwise there was no evidence of any other compensatory responses to imposed sterility. However, additional studies are needed to clarify possible density-dependent responses that could compensate for the effects of fertility control. 6 Synthesis and applications. Demographic compensation by pest populations can negate the effects of fertility control. Results from this study suggest that immigration can easily compensate for fertility control in pest species where adult survival is high and fecundity is low. This suggests that fertility control will need to be applied at large spatial scales to reduce this effect. Where adult survival makes a relatively high contribution to the population growth rate, the benefits of fertility control would be enhanced if integrated with conventional control to provide rapid initial population reduction.
Does survey effort influence sightability of mountain goats Oreamnos americanus during aerial surveys?

Abstract Practical techniques to estimate the sightability of mountain goats Oreamnos americanus during aerial surveys have not been developed or have been poorly tested. I evaluated sightability of 28 radio-collared goats in two study areas in southeastern British Columbia to assess whether sightability increased with increased helicopter survey effort, and to explore which factors might affect sightability. Three surveys at different survey efforts were conducted in each study area, during which attempts were made to locate collared goats 64 times. I detected no relationship between survey effort in the range tested (1.3-6.1 minutes/km2) and sightability (38-83%). Sightability averaged 63%. Only animal activity and larger group size influenced goat sightability. Sightability tended to decrease with increased vegetation cover. Survey efforts of > 2.0 minutes/km2 do not appear to result in higher sightability. For surveys of large areas not well-known to surveyors, a 60-65% sightability correction may be realistic, with a target of approximately 1.5 minutes/km2 effort.
Comparing and modifying penaeid beam and otter trawls to improve ecological efficiencies

In an attempt to improve the selectivity and engineering performances of generic penaeid trawls, three established and one novel spreading-mechanism configurations were assessed: otter boards attached (1) with and (2) without 3.15-m sweeps to a 7.35-m headline trawl, and a beam rigged directly to a 9.19-m trawl (3) with and (4) without a horizontal wire and plastic streamers. Despite more surface area (7.5 vs 6.0 m), both beam-trawl configurations had significantly lower drag than the otter trawls (≤30%). When catches were standardised to per ha, the otter trawl with sweeps retained significantly more (1.3-2.4 times) school prawns, Metapenaeus macleayi (Haswell), than the other three configurations. Within systems, removing sweeps or adding a horizontal wire significantly reduced the unwanted catches of a key teleost (southern herring, Herklotsichthys castelnaui Ogilby) by 41 and 48%. The results illustrate the utility of simple anterior modifications for independently addressing penaeid-trawling environmental issues.
Managing aquatic non-native species: the role of biosecurity

Across the globe, invasive non-native species (INNS) are a major ecological and economic problem with freshwater environments particularly susceptible to their impacts. Preventing their introduction and spread is considered the most environmentally desirable and cost-effective form of management by the Convention on Biological Diversity, and is advocated in new EU INNS legislation which comes into force in 2015. Biosecurity – a term describing actions taken to prevent the introduction and spread of unwanted organisms – is central to this preventative approach. This PhD combines ecological and social research to identify human-mediated pathways for the spread of INNS in freshwater environments; to examine the effectiveness of biosecurity measures; and to identify how biosecurity awareness and compliance could be improved. Initial questionnaire research revealed that recreational water users in the UK are potential vectors for INNS due to their movement patterns and low biosecurity compliance. A survival experiment showed that many aquatic INNS threatening the UK can survive in damp conditions for 16 days but demonstrated that hot water (45˚C, 15 mins) is an effective biosecurity control measure, causing 99% mortality in many high risk INNS within 1 hour. As a result of a long-term biosecurity campaign, New Zealand water users had high biosecurity awareness and compliance compared to the UK. The development of regional partnerships and the support of national legislation were key components of the country’s streamlined approach to biosecurity. Invasive non-native crayfish had a significantly lower diversity and prevalence of parasites than native crayfish in the UK, supporting the concept of enemy release. Finally, a global meta-analysis revealed that recreational activities also act as vectors for the introduction of INNS in terrestrial and marine environments and require biosecurity measures of a similar magnitude. The results provide an evidence base from which to develop freshwater biosecurity strategies in the UK and wider Europe.
Dispersal characteristics and management of a rare damselfly

Summary 1 Coenagrion mercuriale is a rare damselfly in Britain and mainland Europe and has been declining in the last 30 years. It has specialized habitat requirements and has been viewed, traditionally, as a poor disperser. Knowledge of its dispersal ability was considered in its Biodiversity Species Action Plan as essential for the formulation of appropriate conservation management strategies. 2 Mark–release–recapture (MRR) studies of C. mercuriale in two large UK heathland populations were undertaken. Mature adults had a low rate of movement within continuous areas of habitat (average < 25 m movement), low emigration rates (1·3–11·4%) and low colonization distances (maximum 1 km), all comparable to similarly sized coenagrionids. 3 Movements were more likely within than between patches of suitable habitat over short to medium distances (50–300 m). Between-patch movements were more likely between patches that were close together. Scrub barriers reduced dispersal. 4 The probability of dispersal between two recaptures depended on the length of the time interval between them. Coenagrion mercuriale performed considerable between-patch movements within a small fraction (1–2 days) of its mean mature adult life span (7–8 days). 5 Qualitative comparison of field colonization distances measured here and distances between UK sites occupied by C. mercuriale revealed that empty sites within large clusters of sites would probably be recolonized rapidly and dispersal events would be frequent. However, such events would occur rarely within small isolated sites or clusters of sites, leaving local populations prone to extinction. 6 Synthesis and applications. These data show that management effort should be directed towards maximizing the likelihood of C. mercuriale recolonizing sites naturally within 1–3 km of other populations (particularly within large clusters). Scrub boundaries should be removed between existing populations and empty, but suitable, sites to facilitate stepping-stone dispersal movements.
Selective control of grass weeds in soyabeans with some recently developed post‐emergence herbicides

Abstract Four trials in soyabeans were conducted in Parana, Brazil, to evaluate the activity and selectivity of the post‐emergence herbicides fluazifop‐butyl, sethoxydim, diclofop‐methyl, CGA 82725, Ro 13–8895, and the mixed formulation mefluidide + bentazone. Diclofop‐methyl and, to a greater extent, mefluidide + bentazone, caused necrotic spots and stains on the trifoliated leaves of soyabeans; the mixture had a dwarfing effect on the crop. The remaining herbicides caused a slight delay in crop growth, but the plants recovered rapidly. CGA 82725, Ro 13–8895 and fluazifop‐butyl, all at 0.25 kg a.i./ha, and sethoxydim at 0.18 kg a.i./ha, gave good control of Brachiaria plantaginea (Link) Hitchc, Digitaria sanguinalis (L.) Scop, and Cenchrus echinatus L. , when applied up to the 3–4 tiller stage. At later stages, efficacy was lower but acceptable. These herbicides acted slowly and took 20 days to take complete effect. CGA 82725, Ro 13–8895 and fluazifop‐butyl left some residual effect, preventing later rein.
Characterization of U2AF6, a Splicing Factor Related to U2AF35

ABSTRACT The essential splicing factor U2AF (U2 auxiliary factor) is a heterodimer composed of 65-kDa (U2AF65) and 35-kDa (U2AF35) subunits. U2AF35 has multiple functions in pre-mRNA splicing. First, U2AF35 has been shown to function by directly interacting with the AG at the 3′ splice site. Second, U2AF35 is thought to play a role in the recruitment of U2AF65 by serine-arginine-rich (SR) proteins in enhancer-dependent splicing. It has been proposed that the physical interaction between the arginine-serine-rich (RS) domain of U2AF35 and SR proteins is important for this activity. However, other data suggest that this may not be the case. Here, we report the identification of a mammalian gene that encodes a 26-kDa protein bearing strong sequence similarity to U2AF35, designated U2AF26. The N-terminal 187 amino acids of U2AF35 and U2AF26 are nearly identical. However, the C-terminal domain of U2AF26 lacks many characteristics of the U2AF35 RS domain and, therefore, might be incapable of interacting with SR proteins. We show that U2AF26 can associate with U2AF65 and can functionally substitute for U2AF35 in both constitutive and enhancer-dependent splicing, demonstrating that the RS domain of the small U2AF subunit is not required for splicing enhancer function. Finally, we show that U2AF26 functions by enhancing the binding of U2AF65 to weak 3′ splice sites. These studies identify U2AF26 as a mammalian splicing factor and demonstrate that distinct U2AF complexes can participate in pre-mRNA splicing. Based on its sequence and functional similarity to U2AF35, U2AF26 may play a role in regulating alternative splicing.
Expression pattern of CYC‐like genes relating to a dorsalized actinomorphic flower in Tengia (Gesneriaceae)

Abstract Tengia has been called a “natural peloria” in the family Gesneriaceae because it exhibits an almost perfect actinomorphic flower from whorl one to whorl three. It would be especially interesting to know whether or how CYC‐like gene activities are related to this type of perfect actinomorphic flower. To address this, we have isolated four CYC‐like TCP genes and carried out an investigation on their expression patterns in Tengia. TsCYC1C and TsCYC1D have similar expression patterns with strong signals being detected in all five petals and stamens, whereas TsCYC2A and TsCYC2B are only transiently expressed in the very early floral meristem. Our results suggest that the expansion of the expressions of TsCYC1C and TsCYC1D from the dorsal to the ventral petals is likely responsible for the evolutionary formation of the fully dorsalized actinomorphic corolla, that is, an expanded functional domain of CYC‐like gene dorsal identity in Tengia corolla. However, the expressions of TsCYC1C and TsCYC1D are not correlated with stamen abortion; therefore, TsCYC genes do not functionally repress the stamen development in Tengia flowers. This is probably due to changed cis‐activities that result in the cell cycle‐related genes uncoupling from the TsCYC regulatory pathway in Tengia.
Seasonal Variations in Essential Oil from Brazilian Propolis

Abstract Seasonal variations in the chemical composition of essential oil from Brazilian propolis were investigated using GC and GC/MS. Seasonal differences were not very significant and were predominantly quantitative. The main components of the oil were spathulenol (3.0–13.9%), (2Z,6E)-farnesol (1.6–14.9%), benzyl benzoate (0.3–18.3%) and prenylated acetophenones (3.4–17.1%). On the basis of the results obtained some suggestions are made concerning the plant origin of the oils.
Oviposição dos curculionídeos-das-raízes dos citros (Coleoptera: Curculionidae)

The aim of this work was to study some characteristics of oviposition of citrus root weevils. The insects and vegetal substrats (fruits, leaves, branches and debris) were colected in citrus groves, in Itapetininga, SP, Brazil, and conducted to Laboratorio de Biologia de Insetos ESALQ/USP, in Piracicaba-SP, Brazil. The species Naupactus cervinus Boheman, Naupactus versatilis Hustache, Naupactus tarsalis Boheman, Parapantomorus fluctuosus (Boheman) and Teratopactus nodicollis (Boheman) were reared, and the oviposition was observed. Six assays were conducted, all in plastic boxes (10.0 x 20.0 x 30.0cm), at a 25 ± 1oC, 60 ± 10% RU. The preference was evaluated by leaves, fruits and vax paper, with free choice Assay A and without chance Assay B; preference for three fruit color (green, yellow-green and yellow), at Assay C; three distances from husk to chalice (adhered, intermediate (=1,5mm) and far (=1,5mm) Assay D, and by leaf, fruit and wet soil and vegetal debris Assay D. The species showed differences in oviposition characteristics. They oviposit in fruits with no preference by color and in vax paper. The latter is an alternative for eggs collect at laboratory. Some species oviposit in the soil or in debris at soil surface.
Role of Oxidants in NF-κB Activation and TNF-α Gene Transcription Induced by Hypoxia and Endotoxin1

The transcription factor NF-κB stimulates the transcription of proinflammatory cytokines including TNF-α. LPS (endotoxin) and hypoxia both induce NF-κB activation and TNF-α gene transcription. Furthermore, hypoxia augments LPS induction of TNF-α mRNA. Previous reports have indicated that antioxidants abolish NF-κB activation in response to LPS or hypoxia, which suggests that reactive oxygen species (ROS) are involved in NF-κB activation. This study tested whether mitochondrial ROS are required for both NF-κB activation and the increase in TNF-α mRNA levels during hypoxia and LPS. Our results indicate that hypoxia (1.5% O2) stimulates NF-κB and TNF-α gene transcription and increases ROS generation as measured by the oxidant sensitive dye 2′,7′-dichlorofluorescein diacetate in murine macrophage J774.1 cells. The antioxidants N-acetylcysteine and pyrrolidinedithiocarbamic acid abolished the hypoxic activation of NF-κB, TNF-α gene transcription, and increases in ROS levels. Rotenone, an inhibitor of mitochondrial complex I, abolished the increase in ROS signal, the activation of NF-κB, and TNF-α gene transcription during hypoxia. LPS stimulated NF-κB and TNF-α gene transcription but not ROS generation in J774.1 cells. Rotenone, pyrrolidinedithiocarbamic acid, and N-acetylcysteine had no effect on the LPS stimulation of NF-κB and TNF-α gene transcription, indicating that LPS activates NF-κB and TNF-α gene transcription through a ROS-independent mechanism. These results indicate that mitochondrial ROS are required for the hypoxic activation of NF-κB and TNF-α gene transcription, but not for the LPS activation of NF-κB.
Proteins from Thermophiles for the Design of Advanced Fluorescence Biosensors. Glucose sensing as Model

Glucose sensing is used as a model to explore the advantages deriving from the use of sugar binding proteins isolated from thermophilic organisms to develop stable fluorescence biosensors. The gene of a putative thermostable sugar-binding protein was cloned and expressed in E. coli. The recombinant protein was purified to homogeneity and used as a probe for the development of a fluorescence biosensor for the detection of glucose. Fluorescence spectroscopy experiments demonstrated that the recombinant protein binds glucose with a dissociation constant of about 10 mM, a concentration of sugar close to the concentration of glucose present in the human blood. A docking simulation on the modeled structure of the protein confirmed its ability to bind glucose and proposed possible modifications to improve the affinity for glucose and/or its detection. The obtained results suggest the use of this thermostable protein as a probe for a stable glucose biosensor.
SOME THOUGHTS ON NUTRIENT LIMITATION IN ALGAE 1

An empirical relation relating specific growth, rate in steady state systems to nutrient status with respect to more than one nutrient simultaneously is proposed, based on 3 experimentally verifiable postulates: (1) that uptake depends on the external substrate concentration; (2) that growth depends on the interval substrate concentration; and (3) in a steady state system specific rate of uptake (in the absence of significant, excretion) is necessarily the product of the specific growth rate and internal substrate concentration. The implications of this model are discussed in particular in respect to the concept of luxury consumption and Liebig's law of minimum. Some aspects of uptake in transient situations are also discussed.