Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-Predator Responses of Mayfly Larvae to Conspecific and Predator Stimuli

Hydrodynamic and water-borne chemical stimuli are considered important cues that initiate anti-predator behaviours of mayfly larvae. We tested the hypotheses that chemical stimuli from conspecifics and the predacious fish Rhinichthys cataractae and hydrodynamic stimuli from a Rhinichthys model would initiate anti-predator responses by mayfly larvae of Ephemerella aurivillii, Paraleptophlebia heteronea, and Baetis tricaudatus. A second set of experiments tested the hypotheses that chemical stimuli from conspecifics and the predacious stonefly Claassenia sabulosa and hydrodynamic stimuli from a Claassenia model would initiate responses by Baetis. These hypotheses were tested in laboratory streams where mayfly larvae received either chemical stimuli, hydrodynamic stimuli, or the combination of hydrodynamic and chemical stimuli. Responses by larvae to these stimulus types, in terms of use of substratum surfaces and drift rates, were compared with those by larvae in control streams without conspecific and predator stimulus types. Responses to chemical stimuli were variable depending upon mayfly species and the chemical stimulus type. For instance, while Ephemerella and Paraleptophlebia responded to Rhinichthys odours, Baetis did not respond to either Rhinichthys or Claassenia odours. Paraleptophlebia responded to conspecific odours whereas Ephemerella and Baetis did not. In contrast, all three mayfly species responded to hydrodynamic stimuli either alone or when combined with chemical stimuli. Responses by Baetis were more complex when chemical stimuli were combined with hydrodynamic stimuli. For instance, although Baetis did not respond to conspecific odours alone, drift was significantly higher in streams receiving the three stimuli of conspecific odours, predator odours from Rhinichthys, and hydrodynamic stimuli from a Rhinichthys model when compared with streams that received only the conspecific odours combined with the fish model. Similarly, an enhanced response was observed when Baetis odours were combined with Claassenia odours and the Claassenia model. Thus, the lack of a response to a chemical stimulus did not preclude an enhanced response when combined with other stimulus types. These observations suggest that although some mayflies are capable of detecting the presence of some chemical stimuli, a response is not elicited unless the stimulus is accompanied by additional stimuli.
The outcome of shared pollination services is affected by the density and spatial pattern of an attractive neighbour

Interactions among neighbouring plants are often mediated by foraging choices of pollinators. For example, the presence of a conspicuous species may increase the number of pollinators attracted to its vicinity, indirectly increasing visitation rates also to neighbouring plants. Because pollinator choices are frequently density‐dependent, the presence of a conspicuous species at high densities may also increase competition for pollination services. Additionally, models predict that plant density will interact with spatial distribution in manipulating the pollinator behaviour, yet experimental evidence for this effect is missing. We performed a field experiment in which we introduced a highly conspicuous species in different densities and spatial configurations in a full‐factorial manner into a species‐rich meadow and studied its effect on neighbouring plants. We showed that the highly conspicuous species strongly contributed to the attractiveness of its local patch and thus benefited its neighbours. However, because of the strong density effect, the conspicuous species changed its role and became a competitor for pollinators when its density increased. We supported our theoretical assumptions and showed that when the introduced conspicuous species was regularly distributed among other plants in the patch, it increased visitation rate, and in some cases also seed set, to conspicuous neighbours relative to when it was aggregated, at least at low densities. Synthesis. We suggest that complex interactions between density and spatial distribution of plant species at the patch scale are highly relevant for the interpretation of pollinator behaviour and therefore should be treated as factors of floral attractiveness in future studies.
Light‐modulation of nitrate reductase activity in leaves and roots of maize

In order to examine the light-modulation of nitrate reductase (NR ; EC 1.6.6.1) activity in tissues of maize (Zea mays L. cv. Plauto), the enzyme was assayed under both selective (5 mM Mg 2+ ) and unselective conditions (2 mM EDTA ; V max ), in leaf and root extracts from seedlings transferred from high irradiance (HI ; 450 μmol m- 2 s-' PAR) to shade (200 μmol m- 2 s -1 ) or to darkness. The corresponding changes in tissue nitrate were also evaluated. The results show that maize leaf NR activity (NRA) is subjected to reversible light-modulation involving rapid changes in the sensitivity of the enzyme to inhibition by Mg 2+ . In fact, NR assayed in the presence of Mg 2+ lost about 60% and 20% of its activity after 30 min in the dark and in the shade, respectively. V max started to decrease only after 1-3 h, depending on the extent of light reduction. Deactivation in the shade was reversed in vivo by returning the plants to HI, the kinetics of reactivation being similar to those of deactivation. Following dark-deactivation in vivo, spontaneous reactivation of leaf NR occurred during in vitro incubation at 25°C, and the process was accelerated by AMP. The NR from HI-leaves was deactivated (half-time 2 min) by incubation with MgATP, but the extent of the in vitro deactivation was small. Maize root NR was more sensitive to Mg 2+ than leaf NR, with 5 mM Mg 2+ causing a 50% inhibition of the activity in HI-roots. In contrast to leaves, marked changes in the Mg 2+ -sensitivity of maize root NRA became apparent only after 3 h in the dark or in the shade, when V max had also declined significantly.
Secondary Succession and Natural Habitat Restoration in Abandoned Rice Fields of Central Korea

Floristic composition and soil characteristics (moisture, pH, nutrient contents) in abandoned upland rice paddies of different ages were analyzed to clarify the regenerative aspects of succession as a tool for habitat restoration. The study sites represented five seral stages: newly abandoned paddy fields; successional paddy fields abandoned for 3, 7, and 10 years; and a 50‐year‐old Alnus japonica forest. A vegetation sere was apparent in changes of dominant plant species in the order Alopecurus aequalis var. amurensis (annual grass), Aneilema keisak (annual forb), Juncus effusus var. decipiens (rush), Salix koriyanagi (willow), and Alnus japonica (alder) communities. These temporal stages resemble the spatial zonation of vegetation in local riparian floodplain ecosystems, indicating a hydrosere, with soil moisture decreasing over time. Age distributions and life forms of the dominant plant species support a “tolerance” model of secondary succession, in which the established species persist into later successional stages. Persistence of earlier colonizers led to a net cumulative increase in species richness and a more even distribution of species cover with increasing field age. Between 10 and 50 years, vegetation stabilizes as an alder community. Soil moisture content decreased steadily with paddy field age after an initial rise immediately after their abandonment, whereas pools of organic matter, N, P, K, Ca, and Mg, increased with field age. The pace and direction of recovery of native vegetation and natural soil properties in these abandoned rice paddies resembled classic old field succession, a form of secondary succession that often serves as a template for guiding restoration efforts. Active intervention, in particular dismantling artificial levees, could accelerate the recovery process, but natural habitat recovery generally appears sufficiently robust to achieve “passive” restoration of this rare community without intervention.
Individual and Temporal Variation in Outcrossing Rates and Pollen Flow Patterns in Ceiba pentandra (Malvaceae: Bombacoidea)

Ceiba pentandra is a tropical tree with high rates of selfing in some populations. In mixed‐mating species, variation in selfing is due to changes in adult density or variability of incompatibility systems. The effect of spatial isolation and phenology on selfing rates and pollen flow distances was analyzed using microsatellites in a fragmented population of Ceiba pentandra, in southern Costa Rica. Adult trees within a heterogeneous landscape were classified as grouped or isolated. We compared selfing rates at the individual level, between isolation conditions and 2 yr (2007, 2009), which differed in the number of flowering individuals. Mixed mating was estimated in both years (tm = 0.624–0.759). Trees mated predominantly by outcrossing, while only a few trees reproduced through selfing. Spatial isolation did not significantly affect outcrossing rates. The progeny of grouped trees was mostly sired by near‐neighbors (<1 km) and by long‐distance pollen flow events in isolated trees. A reduction in the number of flowering individuals in 2009 reduced near‐neighbor matings, increased selfing in grouped trees, and decreased the number of unsampled sires in the progeny. Comparing selfing rates on individuals that flowered in both reproductive periods suggests a flexible mating system. Variation in self‐fertilization rates in this population appears to depend on variation of individual traits, such as genetic variability in self‐incompatibility genes, but it is independent of landscape heterogeneity. In contrast, pollen flow distances depend on local tree density as bats concentrate their foraging between near individuals to maximize energy efficiency.
Characterization of L-Arabinose Isomerase in Bacillus subtilis, a GRAS Host, for the Production of Edible Tagatose

L-Arabinose isomerase (AI; E.C. 5.3.1.4), a commercial enzyme for the production of edible tagatose in vitro and ribulose production in vivo, has been studied using enzymes expressed in an Escherichia coli system, which might cause noxious by-products in food. To ensure food safety in the tagatose manufacturing process, we studied an AI expression system in Bacillus subtilis. The AI gene from Geobacillus stearothermophilus (GSAI) was expressed in Bacillus subtilis, a GRAS host used in the production of fermented soybean in Korea, after subcloning into a Bacillus subtilis - E. coli shuttle vector, and was characterized after purification. The activities of the crude enzyme extract and a purified sample were 0.15 U/mg protein and 2.7 U/mg protein, respectively. The optimal pH and the optimal temperature for arabinose and galactose as substrates were pH 8.0 and 60°C, respectively, the same as those for GSAI in an E. coli expression system. Substrate affinities (Km) for arabinose and galactose were 77 mM and 279 mM, respectively, whereas in the E. coli expression system, they were 100 mM and 578 mM, respectively. Catalytic efficiencies (kcat/Km) for arabinose and galactose were 58.3 and 11.4 mM−1 min−1, respectively. The potential use of GSAI expressed in a GRAS host for the production of edible tagatose is discussed in light of these results.
Fine-grained and accurate source code differencing

At the heart of software evolution is a sequence of edit actions, called an edit script, made to a source code file. Since software systems are stored version by version, the edit script has to be computed from these versions, which is known as a complex task. Existing approaches usually compute edit scripts at the text granularity with only add line and delete line actions. However, inferring syntactic changes from such an edit script is hard. Since moving code is a frequent action performed when editing code, it should also be taken into account. In this paper, we tackle these issues by introducing an algorithm computing edit scripts at the abstract syntax tree granularity including move actions. Our objective is to compute edit scripts that are short and close to the original developer intent. Our algorithm is implemented in a freely-available and extensible tool that has been intensively validated.
Apolipoprotein A‐I structure in high‐density lipoproteins

High‐density lipoproteins (HDL) have attracted significant attention in recent years due to their apparent role in reducing the risk of coronary heart disease (CHD). There is convincing evidence that apolipoprotein (apo) A‐I, the main protein component in HDL, is a major mediator of HDL function that interacts with a host of plasma enzymes and cell surface proteins. ApoA‐I is highly adaptable and may associate with, and modulate the function of, different HDL subspecies. To better understand HDL function, studies have focused on apoA‐I structure in reconstituted HDL species that model different native subclasses of HDL. Powerful experimental strategies, such as X‐ray crystallography and mass spectrometry, combined with chemical cross‐linking and spectroscopy, have dramatically improved our understanding of apoA‐I structure in reconstituted HDL. In this review, we present an overview of the current understanding of apoA‐I structure and look forward to methodological developments in the near future that will allow the study of apoA‐I in native subspecies of HDL found in human plasma.
A new locality, range extension and record of Batrachochytrium dendrobatidis in the endangered terrestrial breeding frog Pristimantis katoptroides Flores, 1988 (Anura: Craugastoridae) in Peru

We provide a new record of the poorly known and endangered Pristimantis katoptroides from the Cordillera Central in Peru, based on a specimen collected in the Alto Mayo Protected Forest, San Martin Department. We provide notes on the morphology and coloration of the species and two other specimens previously collected in Peru, as well as photographs and an updated map indicating the known localities of P. katoptroides . This record represents an extension of 210 km in the southern limit of the geographic range. Additionally, we report the presence of the chytrid fungus in this species.
Phenotypic and Genomic Characterization of Enterococcus Species from Some Nigerian Fermented Foods

The gram-positive Enterococci bacteria are generally used as a starter and probiotic cultures in foods. However, they have emerged as one of the leading causes of nosocomial infections worldwide, and this feature is aggravated by the development of antibiotic resistance. Accurate identification of Enterococci at the species level is an important task in food microbiology. In this study, 144 strains of Enterococcus species were isolated from traditional fermented vegetable condiment and West African soft cheese (wara) with the most predominant species being E. gallinarum (75%) followed by E. faecium (14.5%), E. faecalis (7.6%), and E. casselliflavus (2.8%). The strains isolated were characterized and identified using the polyphasic taxonomy approach. Phenotypically, 108 strains were characterized and identified to be E. gallinarum, 21 strains as E. faecium, 11 strains as E. faecalis, and 4 strains as E. casselliflavus. Thirty representative strains were also subjected to genomic characterization, and the result obtained with the phenotypic approach was confirmed. Therefore, the polyphasic taxonomy approach was successful in the accurate identification of the Enterococcus species isolated.
How did invertebrates respond to eradication of rats from Kapiti Island, New Zealand?

Abstract Kapiti Island is an important wildlife sanctuary off the west coast of the North Island, New Zealand. Restoration of the island after human occupation has included a 60‐year programme of eradication of 10 pest mammals, ending with the removal of Norway and Pacific rats in 1996 using brodifacoum rodenticide bait. We monitored the impact of rat removal on invertebrate communities using pitfall traps. Three years after rat eradication we detected a significant decrease in invertebrate catch frequency and diversity, most obvious in the Carabidae and Amphipoda. Site and season accounted for most of the variation in the data. A four‐fold increase in the conspicuousness and condition of some insectivorous birds, and fluctuations between El Niño and La Niña weather patterns may have affected the “recovery” of the island invertebrates.
Inducible defence against a ciliate grazer Pseudomicrothorax dubius, in two strains of Phormidium (cyanobacteria)

Experiments were done with two strain of filamentous, mat–forming Phormidiumand their ciliate grazer Pseudomicrothorax dubius, to explain why the ciliates remain hungry in an apparent surplus of food, except for the first 24 hours after feeding. Under grazing pressure, both strains of cyanobacteria showed statistically significant increases in the number of filaments terminating in an empty sheath, compared to the control. Direct observations revealed that the mechanism behind this effect was active withdrawal of the trichomes inside the sheaths when disturbed by grazers. As P. dubius is unable to ingest trichomes with such endings, we conclude that cyanobacteria are not limited to chemical means of defence against grazers but can also defend themselves by means of movement and changes in filament morphology. This is apparently the first report on behavioural defence observed in cyanobacteria.
Establishment of Aster sedifolius and Aster caucasicus callus cultures as a potential source of antioxidants

Abstract Callus cultures were established for Aster sedifolius and Aster caucasicus, two Aster species used in natural medicine for their anticancer, antibacterial and antiviral activities attributed to the high content of antioxidant compounds such as polyphenols and ascorbate. The effects of growth medium and light condition on the induction and growth rate of callus from leaf, petiole and root explants are reported. Callus induction and proliferation depended on the genotype and the experimental conditions. In particular, a profuse callus culture was obtained from leaf explants grown in the light on medium supplemented with 2,4-D (0.1 mg l−1) for A. caucasicus and on medium supplemented with 2,4-D (0.44 mg l−1) plus 6-benzil-ammino-purine (BAP) (0.22 mg l−1) for A. sedifolius. The content of total polyphenol and ascorbic acid was estimated in leaf and petiole explants of in vivo plants and in the relative derived calli. In calli, polyphenol content was lower than in the corresponding in vivo organs. Furthermore, the total ascorbic acid content decreased in calli while the reduced ascorbic acid pool increased. These findings demonstrate that Aster callus cultures produce antioxidant compounds and as such might be a model system to investigate the regulation and production of these important metabolites.
Detection of Single Nucleotide Mismatches via Fluorescent Polymer Superquenching

An improved assay for the detection of a 20-mer DNA sequence coding for the Anthrax Lethal Factor sequence that utilizes fluorescence superquenching and peptide nucleic acids (PNAs) is reported. The basis for this assay is a microsphere sensor that is coated with both Neutravidin (a biotin-binding protein) and biotinylated poly(phenylene)ethynylene (a fluorescent conjugated polymer). A 15-mer PNA tethered through its N-terminus to a biotin serves as a capture ligand for DNA oligonucleotides. When mixed, the PNAs and microspheres form a strong complex through the biotin−avidin interaction, creating a sensor for DNA detection. The 20-mer DNA target strand and a 17-mer DNA-QTL (QTL = quencher tether ligand, where the quencher is a QSY-7 label at the 3‘-terminus of the DNA strand) of a similar sequence to the target strand are then used to develop an assay for DNA detection. A sequential addition of target, followed by DNA-QTL, yields a sensitive and selective assay for DNA detection. This study compares PNA .
Distribution of Cereal Luteoviruses and molecular diversity of BYDV-PAV isolates in central and southern Iran: proposal of a new species in the genus Luteovirus.

During a survey, 148 wheat, 70 barley and 24 wild grass samples of plants showing symptoms of yellowing or reddening of leaves and general stunting were collected in central and southern provinces of Iran and tested for Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV) infection by enzyme-linked immunosorbent assay (ELISA) and tissue print immunoassay (TPIA). The results showed the presence of the viruses in most regions. Positive reactions to BYDV-PAV, BYDV-MAV, CYDV-RPV and BYDV-SGV antisera were recorded. BYDV-PAV was the most prevalent virus. The genetic diversity of BYDV-PAV isolates in central and southern provinces was studied by analysing ORF1 (903 nt) and read through domain (RTD) (575 nt) of 13 and nine isolates respectively. Sequence analysis of RTD at nucleotide and amino acid levels revealed a high identity (91.8–97.2% and 91.4–100% respectively) between Iranian and other available isolates in the GenBank. However, in regards to ORF1, a high genetic diversity among Iranian and other known PAV isolates at both amino acid (2–16.9%) and nucleotide (4.1–16.5%) levels were detected. Based on phylogenetic analysis of ORF1, two major groups of BYDV-PAV isolates were distinguished. The Iranian isolates were divided between the two clusters. Our results suggest that the occurrence of two genetically distinct groups of PAV isolates in central and southern Iran, from which according to the ICTV criteria for species demarcation in the family Luteoviridae, four isolates from central parts of the country, qualify for designation as new species.
An approach to describing ecosystem performance "through the eyes of salmon"

The intent of this paper is to show that discussion of watershed health and salmon (Oncorhynchus sp.) performance can incorporate a much greater degree of complexity without loss of clarity. We can and should include more temporal-spatial detail, more life history complexity, and more watershed-specific information. The framework and performance measures used in watershed management generally, and salmon management specifically, are inadequate. The bottleneck metaphor is cited all too frequently as a basis for discussion. The bottleneck analogy is useful in understanding capacity, but capacity alone cannot explain observed responses of salmon populations to environmental change. An argument can be made that where protection and enhancement of weak stocks is the priority, productivity is a more critical variable. However, a framework built only around productivity and capacity is also not sufficient. It neglects the need for connectivity of habitats that salmon must pass through to complete their life hist.
New plant disease record in New Zealand: tomato pith necrosis caused by Pseudomonas corrugata

Abstract Pseudomonas corrugata Scarlett et al. 1978 is identified as the cause of tomato pith necrosis of glasshouse and field-grown tomato (Lycopersicon lycopersicum (L.) Karst ex Farw. ). This is the first record of the pathogen in New Zealand.
Chironomids: From Genes to Ecosystems

The Chironomidae popularly are called "non-biting midges" to distinguish them from their biting relatives. Although the impact of these flies excludes human-feeding and disease transmission, chironomids are still the subject of much study. This book presents current research on topics such as the use of chironomid larvae in pollution monitoring; austral chironomid patterns; biology and control; chironomid communities and auto-ecology; morphology and systematics of chironomids. The value of chironomids and other aquatic biota in the monitoring of waterway health is emphasised with reviews from both the northern and southern hemispheres.