Miracle-dz/UniFAR-FTUs huggingface dataset:
Leaf fracture toughness and sclerophylly: their correlations and ecological implications

summary The fracture toughness of sun-leaves of 42 tropical tree species growing in Singapore was measured along a ‘least tough’ path using an instrumented cutting technique. Punch-and-die (penetrometer) tests were also conducted. Intercostal material was analyzed for crude fibre and crude protein (total nitrogen concentration × 6.25) and the ratio of the two, the index of sclerophylly, calculated for each species. Leaf anatomy was examined and specific leaf area was calculated. Thirty-seven of the species were from three definable plant communities, namely mangroves, trema belukar (secondary forest on undegraded sites) and adinandra belukar (secondary forest on highly degraded soils). There was a highly significant positive correlation between fracture toughness and index of sclerophylly for the 42 species (R2= 0.43, P < 0.001) brought about largely by a high correlation between toughness and crude fibre content. Fracture toughness was not correlated with lamina tissue dorsi-ventral thickness but high toughness was clearly associated with the presence of sclerenchyma bundle sheaths and sheath extensions. Analysis of the fracture path for 26 leaves of ten mangrove species showed a high correlation between the area fraction occupied by veins and fracture toughness if one species, Avicennia rumphiana, was excluded. The regression equation for the other nine species gave estimates of the fracture toughness of vein tissue and lamina matrix of 6053 and 327 J m−2 respectively. Punch-and-die test results only correlated well with the cutting tests when values were divided by lamina thickness. The ratio of protein to fibre in a leaf (the reciprocal of the index of sclerophylly) has been established as a good predictor of leaf palatability and digestibility to generalist chewing folivores. The high correlation between fracture toughness and the index of sclerophylly for a large sample suggests that leaf toughness could be the factor used as a proximate cue for determining food quality in herbivore foraging strategies.
Stomatal characteristics and transpiration of three species of conifer seedlings planted on a high elevation south-facing clear-cut

Douglas-fir (Pseudotsugamenziessi (Mirb.) Franco), western hemlock (Tsugaheterophylla (Raf.) Sarg. ), and Pacific silver fir (Abiesamabalis (Doug.) Forbes) seedlings were planted in the spring as 1-0 container-grown plugs on a south-facing high elevation clear-cut located on Mount Arrowsmith, Vancouver Island, British Columbia, and their stomatal responses to environmental and physiological variables were determined over two successive growing seasons. The stomatal responses of all three species to changes in environmental variables and time did not differ over the 2 years nor were there differences in response between seedlings planted a year apart. A simple multiplicative boundary-line model that related seedling stomatal conductance (gs) to measurements of hourly average solar irradiance, air temperature, vapour pressure deficit, and average root zone soil water potential accounted for over 70% of the variability in gs. When the number of hours from sunrise was included as an independent variable, over .
Sieve retention probabilities of stream benthic invertebrates

Abstract Replicate samples of cobbles and loose inorganic and organic matter collected from 3 stream-riffle sites with different periphyton communities were passed through a geometric series of 9 sieves (0.063–16 mm mesh) to quantify sieve retention probabilities of benthic invertebrates. Sieves retained all organisms with a body length >10× the mesh size. Logistic regression models were estimated to describe retention probabilities as functions of body length and mesh size. Retention probability functions differed slightly but significantly among sites, operators, and taxa. Retention probabilities were higher for samples containing filamentous algae, which entangled invertebrates. Size distributions of straight, elongate invertebrates (e.g., oligochaetes, midge larvae) retained by sieves were more variable than distributions of more spherical organisms (e.g., gastropods). On average, the 1-mm sieve retained >90% of invertebrate biomass but <33% of individuals retained by a 63-μm sieve. Size distribution of organisms retained by coarse sieves (≥1 mm), combined with logistic functions predicting retention probability, can be used to describe abundance, biomass, and size distribution of organisms retained by fine sieves. These results suggest that unbiased descriptions of benthic communities can be obtained with relatively little effort by using a minimum sieve mesh size of 1 mm.
Russian-olive (Elaeagnus angustifolia) Biology and Ecology and its Potential to Invade Northern North American Riparian Ecosystems

Abstract Russian-olive is a small tree or large multistemmed shrub that was introduced to Canada and the United States from Eurasia in the early 1900s. It was provisioned in large numbers during the last century to prairie farmers as a shelterbelt plant and remains a popular and widely available ornamental. Now invasive within some riparian ecosystems in the western United States, Russian-olive has been declared noxious in the states of Colorado and New Mexico. With traits including high shade tolerance and a symbiotic association with nitrogen-fixing bacteria, Russian-olive has the potential to dominate riparian vegetation and thus radically transform riparian ecosystems. Especially alarming is its capacity to influence nutrient dynamics within aquatic food webs. Our objective is to draw attention to Russian-olive as a potential threat to riparian ecosystems within Canada, especially in the southwest, where invasion is becoming commonplace. We review what is known about its biology and about the threats it poses to native organisms and ecosystems, and we summarize management and control efforts that are currently underway. We conclude by proposing a research agenda aimed at clarifying whether and how Russian-olive poses a threat to riparian ecosystems within western Canada. Nomenclature: Russian-olive; Elaeagnus angustifolia L. ELGAN.
A Double Gas‐Hydrate Related Bottom Simulating Reflector at the Norwegian Continental Margin

Abstract: An unusual pattern of two bottom simulating reflections (BSRs) has been observed on seismic profiles from the continental margin offshore Western Norway. One of these reflections (BSR1) extends over large areas and has the characteristics of the classical BSR, that is a phase‐reversed reflection from the base of the gas‐hydrate stability zone. The second BSR (BSR0) occurs at approximately 70 ms two‐way travel time beneath BSR1 and is here called a double BSR. The distribution of BSR0 is more local than that of BSR1 and it does not show the phase‐reversal relative to the sea floor reflection that is characteristic for a BSR at the gas hydrate‐free gas boundary. Results from an industrial borehole, from full waveform inversion of multichannel seismic data, from high‐frequency ocean bottom hydrophones, and interpretation of seismic profiles, clearly indicate that BSR1 is reflected from the base of the methane hydrate equilibrium field. Results from full waveform inversion indicate that BSR0 corresponds to a 16–20 m zone where the velocity drops from about 1.8 km/s to a minimum of 1.4 km/s and then increases again. The low velocity of 1.4 km/s suggests the presence of free gas. The results support the hypothesis that BSR0 is a reflection from the base of gas hydrates containing hydrocarbons with a heavier molecular weight in addition to methane gas. Interference of reflections from the top and base of the low‐velocity zone associated with BSR0 explain why BSR0 is not phase‐reversed.
Terrestrial Herpetofauna of Île des Pins, New Caledonia, with an Emphasis on its Surrounding Islands1

Abstract: New Caledonia is recognized globally as a biodiversity hot spot due, in part, to the high levels of endemism seen among the region–s unique fauna and flora. Although substantial research efforts have been dedicated to the remarkable reptile diversity of the main island, the Grande Terre, comparably few studies have focused on the Île des Pins that lies off its southern tip. The last review of the herpetofauna of the Île des Pins was 18 yr ago; since then increased effort has been directed toward investigating the reptiles of the Île des Pins and its satellite islands. In this update we provide an overview of this region's lizard fauna, including new reptile records and the results of surveys of previously herpetologically unexplored islands in the vicinity of the Île des Pins, all in the context of a revised taxonomy. Results presented expand known ranges of 18 species and identify eight species not previously known from the area. Satellite islands surrounding the Île des Pins, despite their small size, contribute substantially to the biodiversity of the region and support several reptile species of conservation concern not recorded for the Île des Pins proper, nor the New Caledonian mainland.
Epistasis-Driven Bias in the Estimates of Additive and Dominance Genetic Variance in Dolichos Bean (Lablab Purpureus L.) Var. Lignosus

The choice of suitable selection strategy for genetic improvement of any crop species hinges on the relative contribution of additive and non-additive components of genotypic variation of economic traits. Simplified triple test cross (STTC) design was used to detect epistasis and assess epistasis-driven bias in the estimates of additive (σ2A) and dominance (σ2D) components of genotypic variation of economic traits in Dolichos bean. The material for the study consisted of 12 genetically diverse inbred lines and two pairs of testers contrasting for economic traits. The 12 inbred lines were crossed to two pairs of testers in 2012 rainy season to generate two sets of STTC progenies, which were evaluated in 2013 and 2014 rainy season at the University of Agricultural Sciences, Bengaluru, India. The results indicated an important role of epistasis in inheritance of all the traits in Dolichos bean. While σ2A predominated in the inheritance of racemes/ plant, σ2D predominated in the inheritance of pod weight/plant. Only σ2A was important in the inheritance of days to flowering and seed weight/plant. The 12 inbred lines used in the study contributed significantly to varying extent to epistasis governing different traits in both sets of STTC progenies in both years. The bias in the estimates of σ2A was greater than that in the estimates of σ2D. Therefore, it is not advisable to ignore epistasis in studies designed for determining the relative magnitude of σ2A and σ2D controlling target traits in Dolichos bean.
Effects of environmental variation on the composition and dynamics of an arid-adapted Australian bird community

Environmental variables influence the dynamics of bird communities. Australian arid-adapted bird communities must cope with particularly high levels of spatial and temporal variability, including inevitable but unpredictable periods of drought. Over four years, which included a severe drought and a period of above-average rainfall, I quantified the responses of a bird community in arid north-western New South Wales to regular seasonal and irregular climatic variation, especially rainfall, as well as spatial variation. I found pronounced changes in the abundance and composition of the avifauna that related to drought and, to a lesser extent, seasonal variability. Overall bird abundance and species richness declined during the drought but the magnitude and direction of population fluctuations of resident, nomadic and migratory species, different feeding groups, and individual species were not consistent. Avian densities and species richness in the study area were higher in mesic habitats associated with drainage lines than in run-off areas. The study demonstrated the importance of local habitat heterogeneity. The asynchronous species responses to a fluctuating environment indicated that drought is likely to have a differential effect on resources and that individual species respond differently to environmental variability. Effective land management and conservation of Australian arid-adapted bird communities requires an understanding of their spatial and temporal variability and dynamics at both local and regional level. A proper understanding of the variability and dynamics of the avifauna is especially important as climate change is predicted to exacerbate the climatic variability and unpredictability of the arid zone in future years.
Different habitat selection by two sympatric Maculinea butterflies at small spatial scale

Abstract. 1. Worldwide extinction of species due to habitat loss and habitat degradation can be recognised among butterflies pronouncedly. Therefore, conservation biologists devote special attention to identify the most important ecological factors affecting distribution and survival of butterflies. These efforts have been dominated by landscape‐scale studies, although variation in habitat quality at smaller spatial scales may be of crucial importance. This applies for the highly specialised Maculinea species, which usually do not form classic metapopulations.
Seasonal controls on interannual variability in carbon dioxide exchange of a near‐end‐of rotation Douglas‐fir stand in the Pacific Northwest, 1997–2006

This study analyzes 9 years of eddy‐covariance (EC) data carried out in a Pacific Northwest Douglas‐fir (Pseudotsuga menzesii) forest (58‐year old in 2007) on the east coast of Vancouver Island, Canada, and characterizes the seasonal and interannual variability in net ecosystem productivity (NEP), gross primary productivity (GPP), and ecosystem respiration (Re) and primary climatic controls on these fluxes. The annual values (± SD) of NEP, GPP and Re were 357 ± 51, 2124 ± 125, and 1767 ± 146 g C m−2 yr−1, respectively, with ranges of 267–410, 1592–2338, and 1642–2071 g C m−2 yr−1, respectively. Spring to early summer (March–June) accounted for more than 80% of annual NEP while late spring to early autumn (May–August) was mainly responsible for its interannual variability (∼80%). The major drivers of interannual variability in annual carbon (C) fluxes were annual and spring mean air temperatures (Ta) and water deficiency during late summer and autumn (July–October) when this Douglas‐fir forest growth was often water‐limited. Photosynthetically active radiation (Q), and the combination of Q and soil water content (θ) explained 85% and 91% of the variance of monthly GPP, respectively; and 91% and 96% of the variance of monthly Re was explained by Ta and the combination of Ta and θ, respectively. Annual net C sequestration was high during optimally warm and normal precipitation years, but low in unusually warm or severely dry years. Excluding 1998 and 1999, the 2 years strongly affected by an El Niño/La Niña cycle, annual NEP significantly decreased with increasing annual mean Ta. Annual NEP will likely decrease whereas both annual GPP and Re will likely increase if the future climate at the site follows a trend similar to that of the past 40 years.
Chlorophyll fluorescence in rice: probing of senescence driven changes of PSII activity on rice varieties differing in grain yield capacity

With Japonica rice BRS Firmeza and indica rice BRS Pelota (low and high grain yield, respectively) as materials, Chl content and Chl a fluorescence parameters in flag leaves from the heading to mature grain stage were investigated. The Chl content and the Chl a fluorescence were measured using a portable chlorophyll meter CL-01 and portables fluorometer Handy-PEA and FMS-2 (Hansatech, Kings Lynn, UK), respectively. All measurements were taken on middle part of the flag leaves (n = 10). The results showed that the Chl content and Chl a fluorescence parameters declined after full expansion of flag leaves in both rice cultivars. However, these biochemical and photochemical parameters did not show similar changing pattern and the behavior of flag leaves senescence showed some differences between BRS Pelota and BRS Firmeza rice cultivars. During the senescence of flag leaves, BRS Pelota, the rice cultivar with higher grain yield capacity, was characterized by significant reductions in Chl content, PIABS,Total, TR0/ABS, ET0/ABS, ET0/TR0, RC/ABS compared to BRS Firmeza. On the other hand, DI0/RC, TR0/RC and ET0/RC were significantly higher in BRS Pelota. These results show that the decreased photosystem II activity, evaluated through chlorophyll fluorescence analysis, was resultant of leaves senescence process, which was much more expressive in BRS Pelota rice variety. We suggest that the higher productivity of BRS Pelota rice cultivar results from its higher assimilate mobilization ability or energy usage efficiency, in despite of its lower light absorption capacity.
Effect of lactic acid bacteria on properties of gluten-free sourdoughs, batters, and quality and ultrastructure of gluten-free bread

ABSTRACT The objective of this study was to test whether sourdough could improve quality and delay staling of gluten-free (GF) bread. Three strains of lactic acid bacteria used were Lactobacillus plantarum 2115KW, L. plantarum FST 1.11, and L. sanfranciscensis TMW 1.52, and these were subsequently compared with nonacidified control and chemically acidified sourdoughs, batters, and GF breads. Bread characteristics such as pH, total titratable acidity, and crumb hardness (five-day storage) were evaluated. Extrusion (texture analyzer) measurements showed that the sourdoughs became significantly softer during 24 hr of fermentation (P < 0.001). Both LP 2115KW and LP FST 1.11 strains grew better and produced more acid than LS 1.52. Confocal laser-scanning microscopy also revealed a breakdown in the structure of the sourdoughs over time. Crumb hardness increased significantly for all breads (P < 0.05). After five days of storage, two strains yielded significantly softer bread than the nonacidified control (P < 0.
ESTIMATES OF GENE ACTION IN CUCUMBER (CUCUMIS SATIVUS L.)

A study of fifteen F1 hybrids of cucumber (Cucumis sativus L.) in a diallel set involving six parents showed over-dominance and low narrow-sense heritability for earliness, number of fruits per plant and total yield per plant. Components of additive gene actions were significant for fruit weight, fruit length and fruit diameter. The breeding methods like pure line selection for the above characters which have additive gene effects at significant levels and heterosis breeding which having predominant role of non-additive gene action, may be exploited for improvement of these traits.
DIFFERENCES IN THE MIDGUT PROTEOLYTIC ACTIVITY OF TWO HELIOTHIS VIRESCENS STRAINS, ONE SUSCEPTIBLE AND ONE RESISTANT TO BACILLUS THURINGIENSIS TOXINS

The development of resistance to Bacillus thuringiensis toxic proteins is a growing concern because it could threaten both conventional and gene transfer use of this environmentally safe biological insecticide. The most common mechanism of resistance involves changes in binding affinity of toxin receptors in the insect midgut membrane. This has not been the case in Heliothis virescens. We have investigated changes in midgut proteolytic activity as a possibility to explain the resistance observed in this insect species. We have developed an improvement of known methods to demonstrate proteolytic activity in crude extracts. Using this method we have found differences in the proteolytic activity profile of midgut extracts of a susceptible and a resistant H. virescens strain. We also have studied the in vitro processing of CrylA(b) toxin and protoxin by midgut contents of both strains. SDS-PAGE of the in vitro degradation products showed differences between the strains. The resistant strain degrades protoxin more slowly and processes the active toxin more quickly than the susceptible strain. © 1996 Wiley-Liss, Inc.
Diet of young‐of‐the‐year bluefin tuna, Thunnus thynnus (Linnaeus, 1758), in the southern Tyrrhenian (Mediterranean) Sea

Summary The diet of juvenile bluefin tuna (Thunnus thynnus) caught 2 to 8 miles off NE Sicily was investigated in order to improve knowledge of the species’ early life history. From 1998 to 2000, 107 specimens ranging from 63 to 495 mm (total length) were fished between July and November. Fishes were caught by trolling line or purse seine in a Fish Aggregating Devices (FADs) area 2 to 8 miles offshore and as by-catch of the purse-seine sardine fishery 2 to 4 miles offshore. Most frequently found items in the T. thynnus stomachs were fishes (84.5%), crustaceans (54.6%) and cephalopods (50.5%). The largest contribution in weight was provided by cephalopods (47.3%) and fishes (46.5%), while the most abundant items were fishes (51%), cephalopods (27.2%) and crustaceans (21.1%). These results suggest that young-of-the-year tuna have an essentially piscivorous diet, although invertebrate prey provide a substantial contribution to the food array. Prey show little relationship with FADs, although one prey species (blue runner, Caranx crysos) is associated with FADs in the Mediterranean.
Transcriptional Regulation of the Nickel and Iron Metabolism in Helicobacter pylori

textabstractUp to 50 % of the world's population is infected with Helicobacter pylori. Colonization of the mucus layer of the human stomach by H. pylori, is lifelong unless treated with antibiotics (26). H. pylori, which is a neutralophilic bacterium, survives in the mucus layer of the human stomach with the help of the enzyme urease. Urease is an enzyme that converts urea into ammonium and carbon dioxide, thereby keeping the intracellular and periplasmic pH at neutral. It is estimated that up to 10% of the whole cell protein consists of this nickelcofactored enzyme (19). The nickel necessary to activate the urease is thought to come from foodsources, such as nuts, tea and cereals, which are rich in nickel (1). Metal ions like nickel or iron can be dangerous for bacteria, as they can react with oxygen in order to create reactive oxygen species that in turn can destroy macromolecules like nucleic acids, proteins and cell wall components (27). Therefore, the bacterial metal metabolism has to be tightly regulated. In H. pylori, regulatory proteins are scarce. Only two metal-regulatory proteins are known, the ferric uptake regulator Fur (4), and the nickel responsive regulator NikR (31). Fur is a regulatory protein that can sense and bind intracellular ferrous ions, and subsequently displays iron-dependent binding to conserved promoter sequences (Fur boxes) of its target genes (17). The classical regulation is repression of iron uptake genes in iron-replete conditions (15, 17, 33). Unlike all other Fur homologs known so far, H. pylori Fur can also bind to Fur-boxes in an iron free form (apo-Fur), as was shown for pfr (16) and sodB (Chapter 3). The second metal-dependent regulatory protein is NikR, the nickel responsive regulator, which belongs to the family of Ribbon-Helix-Helix regulatory proteins (9). NikR is directly involved in the regulation of acid resistance via urease and nickel-uptake (Chapter 4), and was previously demonstrated to mediate regulation of the ferric uptake regulator Fur (7, 12, 29). The aim of this thesis was to gain further insight into the transcriptional regulation the ferric uptake regulator Fur and the nickel responsive regulator NikR.