Miracle-dz/UniFAR-FTUs huggingface dataset:
Relative effects of ambient noise and habitat openness on signal transfer for chickadee vocalizations in rural and urban green-spaces

Urbanization creates communication challenges for many species. Birds in particular rely on vocal communication for reproduction and territory defence, but in noisy or acoustically altered environments signals may be compromised. Both ambient noise and habitat openness affect signal transfer, but it is not clear how these two variables interact in urban green-spaces. Using black-capped and mountain chickadee vocalizations, we conducted transmission experiments to measure acoustic degradation and signal-to-noise ratios among a replicated set of transects spanning a range of both ambient noise levels and habitat openness. We used Akaike information criterion (AIC), an information theoretic approach, for selection and averaging of five alternative linear mixed models. We found ambient noise strongly and negatively correlated with relative signal amplitude and detection of signal features. In contrast, habitat openness appeared to have little effect on signal transfer. We also confirmed that urban green-spaces had significantly greater ambient noise levels than rural sites, which suggests that the dominant impact of anthropogenic noise on signal transfer should be an issue of concern to species conservation within these urban green-spaces.
Isolation and characterization of microsatellite loci from the Blanding’s turtle, Emydoidea blandingii

Independent microsatellite development efforts at the University of Miami and Dalhousie University resulted in seven microsatellite loci for the Blanding’s turtle (Emydoidea blandingii ). The level of polymorphism ranged from three to 15 alleles with observed heterozygosities ranging from 0.31 to 0.95. Cross species amplification suggests that these loci may have utility in other turtle species.
Factors influencing autotrophic and heterotrophic nanoflagellate abundance in five water masses surrounding New Zealand

Abstract The aim of this study was to measure nanoflagellate abundance in New Zealand waters, and identify the key factors which both influence, and are influenced by, nanoflagellate abundance. Nanoflagellate populations were sampled in winter and spring 1993 from a series of sites representing different water masses around the South Island of New Zealand. Both numbers and biomass of heterotrophic (HNF) and autotrophic nanoflagellate (ANF) populations were larger in spring by a factor of four. ANF were about three times as abundant as HNF in both seasons. The physiochemical variables, temperature, NH4‐N, and urea combined with bacteria and picophytoplankton numbers explained between 67 and 94% of the variation in nanoflagellate abundance. In addition, there was evidence that variation in abundances between seasons and water masses was influenced by food availability, predation, and changes in species composition represented by large differences in cell biovolume.
Is the exploratory behavior of Liolaemus nitidus modulated by sex

Chemoreception is an important sensory modality used by lizards to assess their environments and to communicate. However, despite growing information regarding chemoreception in this taxon, its modulation by sex has been little explored, except in researches directly focused on reproductive aspects. In this study, we compared the responses of females and males of the Iguanid lizard Liolaemus nitidus to scents from conspecifics of the same sex, themselves (own), a predator, and a control. The only stimulus that induced different responses between sexes was the scent of conspecifics; males reacted sooner than females to these scents in agreement with their lower tolerance of potential sexual competitors. The similar ecology of the sexes may explain the similarities in their responses to the other scents we tested. However, independent of the scents, we found major behavioral differences between the sexes (e.g. males always tail waved for longer), pointing intrinsic sexual variation in behaviors associated to exploration.
Canopy Photosynthesis and Time-of-day Application of Supplemental Light

There is increasing use of electricity for supplemental lighting in the northern European greenhouse industry. One reason for this may be to secure a high growth rate during low-light periods by an attempt to increase net photosynthesis. We wanted to clarify which period of the day resulted in the best use of a 5-h supplemental light period for photosynthesis and growth. The periods tested were supplemental light during the night, day, morning, and evening. The experiments were carried out in daylight climate chambers measuring canopy gas exchange. The air temperature was 25 8C and the CO2 level '900 ppm. Vegetative chrysanthemum was used, because this species responds quickly to change in light level. The leaf areas of the plant canopies were nondestructively measured each week during the 4-week experimental period. The fact that the quantum yield of photosynthesis is greater at low than at high light intensities favors the use of supplemental light during the dark period, but growth measured as dry weight of the treated plants at the end of the experiments was not significantly different given identical light integrals of the treatments. However, one experiment indicated that increased time with dark hours during day and night (24 h) might decrease net photosynthesis. The assimilation per unit leaf area was approximately the same during times of sunlight through a diffusing screen at 100 mmolm -2 � s -1 of photosynthetic photon flux (PPF )a s during times of supplemental (direct) light application atPPF of 200 mmolm -2 � s -1 by high- pressure sodium lamps. We conclude that during the winter and periods of low light intensities, the daily carbon gain does not depend on the time of supplemental light application, but is linked to the total light integral. However, extended time with dark hours during day and night (24 h) might be a disadvantage because of longer periods with dark respiration and subsequent loss of carbon. Our results indicate that during times of low light conditions, it is not necessary to include factors such as the timing of supplemental lighting application to achieve higher net photosynthesis in climate control strategies.
CH4 production and oxidation processes in a boreal fen ecosystem after long‐term water table drawdown

Fens, which extend over vast areas in the Northern hemisphere, are sources of the greenhouse gas CH4. Climate change scenarios predict a lowering water table (WT) in mires. To study the effect of WT drawdown on CH4 dynamics in a fen ecosystem, we took advantage of a WT drawdown gradient near a ground water extraction plant. Methane fluxes and CH4 production and oxidation potentials were related to microbial communities responsible for the processes in four mire locations (wet, semiwet, semidry, and dry). Principal component analyses performed on the vegetation, pH, CH4, and WT results clearly separated the four sampling locations in the gradient. Long‐term lowering of WT was associated with decreased coverage of Sphagnum and aerenchymatic plants, decreased CH4 field emissions and CH4 production potential. Based on mcrA terminal restriction fragment length polymorphism the methanogen community structure correlated best with the methane production and coverage of aerenchymatic plants along the gradient. Methanosarcinaceae and Methanocellales were found at the pristine wet end of the gradient, whereas the Fen cluster characterized the dry end. The methane‐oxidizing bacterial community consisted exclusively of Methylocystis bacteria, but interestingly of five different alleles (T, S, R, M, and O) of the particulate methane monooxygenase marker gene pmoA. The M allele was dominant in the wet locations, and the occurrence of alleles O, S, and T increased with drainage. The occurrence of the R allele that characterized the upper peat layer correlated with CH4 oxidation potential. These results advance our understanding of mire dynamics after long‐term WT drawdown and of the microbiological bases of methane emissions from mires.
Milk Production in Akkaraman, Sakız (Chios) x Akkaraman F1, Kıvırcık x Akkaraman F1 and Sakız (Chios) x Karayaka B1 Ewes during the First Lactation

The study was carried out to investigate milk production in Akkaraman, Sakiz (Chios) x Akkaraman F1 (SA F1), Kivircik x Akkaraman F1 (KA F1) and Sakiz (Chios) x Karayaka B1 (SKY B1) ewes during the first lactation. Daily milk yield, lactation milk yield and lactation length were 340.11 g, 50.52 kg and 144.8 days for Akkaraman; 430.66 g, 67.83 kg and 154.63 days for SA F1; 301.87 g, 44.93 kg and 145.40 days for KA F1; 210.27 g, 26.96 kg and 123.50 days for SKY B1 ewes, respectively. Differences between genotypes in terms of daily milk yield, lactation milk yield and lactation length were statistically significant (P
Winter Feeding and Changes in Somatic Energy Content of Age-0 Pacific Herring in Prince William Sound, Alaska

Abstract During the winter of 1996–1997, somatic energy content and diets of age-0 Pacific herring Clupea pallasi from Prince William Sound, Alaska, were examined. From October to March, the standard length of age-0 recruits continued to increase, indicating either growth or mortality of smaller fish. The whole-body energy content averaged 4.4 kJ/g wet weight for fish captured in October and increased to 5.0 kJ/g wet weight in November. Thereafter, somatic energy continually declined, reaching 3.9 kJ/g wet weight in March. The December–March decline in nutritional status of the recruits verified that the energy derived from feeding was not enough to meet metabolic needs. The energy density of taxa found in the diets remained steady through the winter and increased in March. Total zooplankton biomass, however, decreased as the mean water temperature decreased. Estimated assimilation rates were lower for smaller fish than larger fish and decreased as winter progressed. We concluded that juvenile herring rel.
Interspecific fish hybrids in Brazil: management of genetic resources for sustainable use

Serrasalmid and pimelodid fish hybrids represent important advances for aqua- culture in Brazil, but they also constitute serious genetic risks to cultivated and natural populations. Serrasalmid hybrids ('tambacu', 'tambatinga' and 'patinga') result from crosses between Colossoma macropomum, Piaractus meso- potamicus and Piaractus brachypomus. Pimelodid hybrids ('ponto e virgula', 'cachandia´' and 'cachapira') arise from crosses between Pseudoplatystoma corruscans, Pseudoplatystoma reticulatum, Phractocephalus hemioliopterus and Leiarius marmoratus. The problems associated with hybrids mainly result from inappropriate use because these animals are reproductively compatible with their parental species. This review shows that monitoring of fish hybrids using genetic techniques is necessary for their sustainable development in aquacul- ture. The genetic technologies used to identify fish hybrids include cytogenetic methods, which are considered to be low cost, and polymerase chain reaction- based molecular markers, which are associated with high throughput. Therefore, both types of genetic methodologies should be applied in monitor- ing programs aimed at brood stock management, wild stocks, the trade of hybrid juveniles and processed fish products in markets. Moreover, physical and genetic confinement of hybrids in aquaculture operations will be necessary to avoid the problems posed by these animals. The expected result of these measures will be the production of genetically improved animals by fish farms, allowing the sector to develop further and offering high-quality animal protein.
Risk Assessment of Herbicide-Resistant Crops: A Latin American Perspective Using Rice (Oryza sativa) as a Model1

Herbicide-resistant crops (HRCs), particularly glyphosate-resistant soybean, are increasingly important in Latin America. Prior to commercial release of these crops, their short- and long-term risks should be thoroughly assessed. A risk assessment should include the identification and characterization of potential hazards and an estimation of the likelihood of these hazards occurring. For HRCs the agro-ecological hazards are mostly related to the occurrence of herbicide-resistant (HR) weeds and crop volunteers and the adverse effects from the use of pesticides within the agricultural area. Herbicide-resistant rice is used as a case study to visualize the key components of such a risk assessment. For this purpose, a model that simulates a typical rain-fed rice production system in Central America was developed. The model was used to investigate the selection of HR weedy rice populations under various scenarios. Scenarios included contrasting weed management practices, hybridization levels between the commercial HR cultivated and weedy rice, and seed predation rates. Because risks may become apparent only after long-term cultivation of HR rice, simulations were run for a 10-yr period. In a cropping system relying on glufosinate-resistant rice for weed control, the model predicted that resistance to glufosinate would occur after 3 to 8 yr of monoculture. Increasing the hybridization level from 1 to 5% decreased the time for resistance to occur by 1 to 3 yr. Increasing annual rate of weedy rice seed predation at the soil surface delayed the development of resistance. Tillage as a weed control tactic also delayed the occurrence of resistance when compared with a no-till situation. Nomenclature: Glufosinate; glyphosate; red or weedy rice, Oryza sativa L. #3 ORYSA; rice (crop), Oryza sativa L; soybean, Glycine max (L.) Merr. Additional index words: Brassica napus, Brassica rapa, ECHCE, ECHCO, Echinochloa colona, Echinochloa crus-galli, Echinochloa crus-pavonis, ecological hazard assessment, herbicide-resistant crops, herbicide-resistant rice, Latin America, ORUSA, Oryza latifolia, red rice, Sagittaria montevidensis, weedy rice. Abbreviations: ALS, acetolactate synthase; DAS, days after sowing; FAO, Food and Agriculture Organization; GMO, genetically modified organism; HR, herbicide resistant; HRC, herbicide-resistant crop; WHO, World Health Organization.
INTER- AND INTRASPECIFIC LARVAL COMPETITION IN APHIDIUS SMITHI AND PRAON PEQUODORUM (HYMENOPTERA: APHIDIIDAE)

Abstract Superparasitism and multiple parasitism of the pea aphid, Acyrthosiphon pisum (Harris), by the solitary hymenopterous parasites Aphidius smithi Sharma & Subba Rao and Praon pequodorum Viereck were studied in the laboratory. In intraspecific competition, an older larva usually eliminated a younger one; exceptions to this rule depended on the relative age difference and developmental stage of the competitors. In interspecific competition, P. pequodorum was intrinsically superior to A. smithi, regardless of the latter's age. The stage of host parasitized and the number of competing larvae had no significant effect on the outcome of the contest. A. smithi females discriminated against aphids previously parasitized by a conspecific female or by P. pequodorum, the degree of oviposition restraint increasing with the time between ovipositions. P. pequodorum females attacked aphids already parasitized by A. smithi, regardless of the age of the Aphidius larva, but avoided oviposition when the aphid contained a Praon larva or embryo. The rate of embryonic development is shown as a major factor in contest-type competition between first-stage larvae. Résumé Le superparasitisme et le parasitisme multiple du puceron du pois, Acyrthosiphon pisum (Harris) par les parasites hyménoptères solitaires Aphidius smithi Sharma & Subba Rao et Praon pequodorum Viereck, ont été étudiés au laboratoire. Dans les cas de compétition intra-spécifique, une larve plus agée a généralement éliminé une larve plus jeune; les exceptions à cette règle dépendaient de la différence relative d'âge et du stade de développement des compétiteurs. Dans les cas de compétition interspécifique, P. pequodorum s'est révélé intrinsèquement supérieur à A. smithi, peu importe l'âge de ce dernier. Le stade de l'hôte parasité et le nombre de larves concurrentes n'ont pas eu d'effet significatif sur le résultat de la compétition. Les femelles d'A. smithi ont discriminé les hôtes déjà parasités par une femelle conspécifique ou par P. pequodorum, le degré restriction de l'oviposition augmentant avec le temps écoulé entre les ovipositions. Les femelles de P. pequodorum ont attaqué les pucerons déjà parasités par A. smithi peu importe l'âge de la larve d'Aphidius, mais ont évité la ponte dans un puceron contenant une larve ou un embryon de Praon. La vitesse de développement embryonnaire apparait comme facteur d'importance majeure dans la compétition de type concurrence entre larves de premier stade.
‘Universal’ PCR assays detecting mutations in acetyl-coenzyme A carboxylase or acetolactate synthase that endow herbicide resistance in grass weeds

Delye C, Pernin F & Michel S (2011). ‘Universal’ PCR assays detecting mutations in acetyl-coenzyme A carboxylase or acetolactate synthase that endow herbicide resistance in grass weeds. Weed Research51, 353–362. Summary Herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) or acetolactate synthase (ALS) are key for grass weed control. Yet, numerous cases of resistance have evolved. Using the derived cleaved amplified polymorphic sequence method, we developed molecular assays to detect amino acid replacements at the seven ACCase codons (1781, 1999, 2027, 2041, 2078, 2088 and 2096) and at two ALS codons (197 and 574) known to play a role in herbicide resistance in grass weeds. For each codon, one assay detecting all known amino acid replacements endowing herbicide resistance was developed. The nine assays were successfully used to genotype ACCase and ALS in 39 grass species. Their flexible design enables easy detection of new mutations at the targeted codons. Because they can be implemented with basic molecular biology facilities and no previous knowledge of the ACCase or ALS sequence of the grass weed of interest, these assays are tools of choice to easily detect resistance caused by alteration(s) of ACCase or ALS in such species.
Expression of genes from the lignin synthesis pathway in guineagrass genotypes differing in cell-wall digestibility

Rapid decline in cell-wall digestibility hinders efficient use of warm-season grasses. The objective of this study was to identify genes whose expressions are related to the slope of decline in cell-wall digestibility. Eleven guineagrass genotypes were harvested at three ages and classified according to fibre digestibility. Extreme genotypes were separated into groups with either FAST or SLOW decline in fibre digestibility. Expression of transcripts from six genes from the lignin synthesis pathway was quantified by real-time PCR. Fast decline in fibre digestibility was associated with higher DM yield after 90d of regrowth. Apart from lower fibre digestibility and higher lignin content for the FAST group, there were no other differences between the two groups for the chemical composition of stems and leaves. Maturity affected differently the expression of two of the six genes, cinnamate 4-hydroxylase and caffeoyl-CoA O-methyltransferase (C4H and CCoAOMT). Genotypes with fast decline in fibre digestibility had greater increase in the expression of C4H and CCoAOMT from 30 to 60d of regrowth, than genotypes with slower decline. Expression of C4H and CCoAOMT appears to be related to the decline in cell-wall digestibility with advance in maturity of guineagrass.
Characterization of the early stages in biofilm development

Complex biofilm communities have extensively been studied in the past. Less work has been done on the early stages of biofilm formation. This study aimed to assess initial colonization patterns of biofilms on different surfaces and under different environmental conditions with application of novel methods describing biofilm surface profiles. Biofilms were cultivated on glass, polyvinylchloride (PVC) and polished stainless steel. Results from microscopy, followed by mathematical analysis and contact angle measurements proved that glass was the most appropriate substrate for this study. More extensive extracellular polymeric substances (EPS) production and apparently less cell attachment were observed on PVC and polished stainless steel surfaces. Two different series of experiments were conducted where biofilms were cultivated on the glass. Biofilm morphology was analysed under various conditions of temperature and nutrient concentration. Different temperature conditions were 8°C, 22°C and 37°C and different nutrient concentrations were 0.1%, 1% and 10% Tryptic Soy Broth (TSB). After obtaining samples after 1, 2, 3 and 4 days respectively, the biofilm surfaces were visualised using atomic force microscopy (AFM) and epifluorescence microscopy. Less cell attachment was displayed at lower temperatures and nutrient limitations. The roughness profile of the early stages of biofilm development was explored by the novel application of various existing statistical methods. Benoit software was applied for the statistical analysis of various data sets obtained from AFM imaging, using power spectrum, variogram and wavelet methods to determine the Hurst exponent. The variogram method proved to be the most suitable to describe biofilm surface profiles with consistent values of ± 0.9, indicating that biofilm growth behaviour will continue in a similar pattern. Fractal dimension values of images obtained from epifluorescence microscopy was determined by the box dimension method. The values described the self-affine patterns displayed by biofilms. Using the results of these investigations, a series of models concerning the initial stages of biofilm formation was compared to describe the development of colony patterns. This study showed that the AFM and epifluorescence microscopy can be used as analytical tools for raw data assembly. It also demonstrated a novel application of existing statistical methods in order to describe the early stages of biofilm formation. Using this approach it was shown that the early stages of biofilm formation display certain colony patterns that can be Stellenbosch University http://scholar.sun.ac.za
Spider web guilds in cacao agroforestry – comparing tree, plot and landscape‐scale management

Aim Owing to their role as insect predators, web‐building spiders can be important biological control agents within agricultural systems. In complex tropical agroecosystems such as agroforests, management determines plant architecture, vegetation composition and associated ant density, but little is known on how these attributes, together with landscape context, determine spider web density. We hypothesized that all three spatial scales and the presence of Philidris ants significantly contribute to the explanation of spider web density with web types being differently affected.
Isolation of both fast and slow growing rhizobia effectively nodulating a medicinal legume, Mucuna pruriens.

Strains of root nodulating bacteria were isolated from the root nodules of a medicinal legume plant, Mucuna pruriens (Kaunch), growing wildly in the foothills of Himalayas. The strains were morphologically, physiologically and biochemically characterised according to the Bergey's Manual of Determinative Bacteriology (Holt et al., 1994). According to their generation time the strains were both fast and slow growers. Both fast and slow growing strains showed marked differences in morphology, physiology and biochemical characteristics. Morphological, cultural, biochemical characters, G+C mole percent and in vivo infectivity on their original host and other plants confirmed that the fast growing isolates were Rhizobium meliloti while the slow growers belong to the Bradyrhizobium sp. (Mucuna). The fast growing strains were highly salt tolerant being able to tolerate 850 mM NaCl concentration in vitro. Slow growing strains showed growth at wide temperature range, being tolerant up to 45°C.