Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of transpiration from the upper canopy of a tropical forest: the role of stomatal, boundary layer and hydraulic architecture components

Concurrent, independent measurements of stomatal conductance (gs), transpiration (E) and microenvironmental variables were used to characterize control of crown transpiration in four tree species growing in a moist, lowland tropical forest. Access to the upper forest canopy was provided by a construction crane equipped with a gondola. Estimates of boundary layer conductance (gb) obtained with two independent methods permitted control of E to be partitioned quantitatively between gs and gb using a dimensionless decoupling coefficient (Ω) ranging from zero to 1. A combination of high gs (c. 300–600 mmol m−2 s−1) and low wind speed, and therefore relatively low gb (c. 100–800 mmol m−2 s−1), strongly decoupled E from control by stomata in all four species (Ω= 0.7–0.9). Photosynthetic water-use efficiency was predicted to increase rather than decrease with increasing gs because gb was relatively low and internal conductance to CO2 transfer was relatively high. Responses of gs to humidity were apparent only when the leaf surface, and not the bulk air, was used as the reference point for determination of external vapour pressure. However, independent measurements of crown conductance (gc), a total vapour phase conductance that included stomatal and boundary layer components, revealed a clear decline in gc with increasing leaf-to-bulk air vapour pressure difference (Va because the external reference points for determination of gc and Va were compatible. The relationships between gc and Vc and between gs and Vs appeared to be distinct for each species. However, when gs and gc were normalized by the branch-specific ratio of leaf area to sapwood area (LA/SA), a morphological index of potential transpirational demand relative to water transport capacity, a common relationship between conductance and evaporative demand for all four species emerged. Taken together, these results implied that, at a given combination of LA/SA and evaporative demand scaled to the appropriate reference point, the vapour phase conductance and therefore transpiration rates on a leaf area basis were identical in all four contrasting species studied.
Using egg IgY antibodies for health, diagnostic and other industrial applications

Abstract: Immunoglobulin Y (IgY) is the major antibody in chickens, and is transferred in large quantities to the egg yolk to confer passive immunity to the developing embryo. IgY can easily be harvested from the yolk, and is an ideal alternative to using mammalian IgG antibodies. The following chapter discusses the production and purification of IgY, as well as its many advantages and applications, including the use of IgY as a diagnostic and analytical tool and for passive immunotherapy to treat numerous health conditions.
Production and transformation of conidia of Venturia inaequalis

High yields of conidia of Venturia inaequalis were produced from either mycelial fragments or conidia on cellophane-covered surfaces of agar media incubated under continuous near-ultraviolet light. Optimal conditions required a cellophane-covered surface of potato-dextrose agar in combination with light and incubation for 1 wk. The procedure represents a convenient techique for the mass-production of clonal and sterile V. inaequalis conidia. Conidia were biolistically transformed to hygromycin B resistance with a plasmid (pOHT) containing a bacterial phosphotransferase gene spliced between regulatory elements from Aspergillus nidulans. Southern hybridization analysis showed that the plasmid was incorporated into heterologous regions of the genome. Hygromycin B-resistant transformants were mitotically stable during nonselective propagation. The heterologous gene conferring hygromycin B resistance was expressed during early stages of conidia germination and during vegetative growth of mycelium
Morfología craneana en tigres dientes de sable: alometría, función y filogenia

Abstract. Cranial Morphology in Sabertooth cats: allometry, function and phylogeny. Cranial morphology of felids and other sabre-toothed mammals has been studied using different approaches and methodologies. Recent studies used geometric morphometry analyses of the lateral view of the mandible and skull, and showed that “derived” sabretooth cats differ from recent felids by having a set of characters (e.g., small coronoid process, large chin and mastoid processes) associated with the presence of hypertrophied upper canines. In this study, we used geometric morphometrics to analyze the shape of the skull (dorsal and ventral views) and mandible (lateral view) in a large sample of extant felids (Felinae), extinct sabretooth felids (machairodontines), nimravids, creodonts, and the marsupial sabretooth Thylacosmilus Riggs. Results were congruent with those obtained using a lateral view of the skull: “primitive” sabretooth fell next to recent Felinae, but “derived” ones fell outside the range of Felinae, because they possessed larger mastoid process, larger and more procumbent upper incisors, and smaller temporal fossa, among other characters. However, sabretooth shared some features (e.g., large palate and canines) with larger Felinae (e.g., Panthera spp.), suggesting that they were able to hunt large mammals. The pattern of cranial variability of these groups is explained by ecological factors but also by phylogenetic constraints. The shape of the skull was correlated with the size and the length of the upper canines, two features that presented a clear correlation along the phylogeny of the group.
Factors influencing the timing of spring migration in common toads (Bufo bufo)

We analysed 12 years of data on the spring migration of the common toad Bufo bufo L. to breeding ponds across 25 locations in Derbyshire, UK, to determine factors influencing the number of toads active per night. We also tested whether the timing of spring migration is predicted by annual variation in temperature or precipitation. More toads migrate in warmer temperatures and as the moon waxes, whereas precipitation did not have a significant effect on toad activity. Across years, spring migration begins earlier in warmer years, but the main migration of toads was not predicted by air temperatures before the onset of the breeding season. Contrary to the majority of studies of amphibian breeding phenology, there has been a temporal shift towards later timing of breeding over the past 12 years. Overall, comparison of our results with that of previous studies suggests that it can be difficult to generalize about the factors that influence breeding phenology, even within species. However, as more studies accumulate, it should be possible to address whether variation in breeding phenology is consistently linked to geographic variation in abiotic conditions or species biology, which will help to evaluate its consequences under climate change.
Genotypical Variability for the Tasks of Water Collecting and Scenting in a Honey Bee Colony

The polyandrous mating behaviour of the honey bee queen increases the genotypical variability amongst her worker offspring. Microsatellite DNA analyses revealed a total of 16 subfamilies in one colony of honey bees. The subfamilies were represented in significantly different proportions in two subgroups of bees, water collecting bees and scenting bees, indicating a genetic component in task choice.
Isolation, Serologic Identification and Antibiotic Sensitivity Testing of Salmonella spp. in Chickens

The present study aimed to isolate Salmonella from chickens and identify the serotypes and determine the antibiotic sensitivity patterns of the isolates. Meats and eggs were obtained from two local public markets whereas cloacal swabs were collected from two broiler and two layer farms. Isolation and serotyping of Salmonella were done by using conventional method and specific typing sera, respectively. Antibiotic sensitivity test was carried out by the Kirby- Bauer method. Of the 325 samples, 16 (4.9%) contained Salmonella. These consisted of 9.3% out of 150 meat and 2.0% out of 100 cloacal swab samples. Salmonella was not detected in 75 pooled egg samples. There was no significant difference in the recovery rates of Salmonella based on the type of meat sampled. Seven serotypes were found with S. weltevreden predominating, followed by S. derby, S. enteritidis PT1, S. enteritidis phage type untypable, S. newport and S. lexington. S. albany was isolated locally for the first time. All isolates were sensitive to norfloxacin, gentamicin, cephalothin but were resistant to nitrofurantoin. All serotypes were also resistant to at least one antibiotic while 9.7% showed multi-drug resistance to nitrofurantoin, tetracycline and trimethoprim-sulfamethoxazole. This study reveals that Salmonella continues to contaminate our food with new serotypes present including S. enteritidis PT1 and S. albany. The antibiotic sensitivity patterns of Salmonella serotypes have changed and showed particular resistance to nitrofurantoin. Therefore, it is recommended that proper food handling practices be emphasized repeatedly and that antibiotics be prudently used in food animals. Keywords: antibiotic sensitivity, chicken, resistance, Salmonella
Remodeling of Human Sperm Chromatin Mediated by Nucleoplasmin from Amphibian Eggs

The molecular events associated with decondensation of human sperm nuclei were analyzed by incubating sperm with egg extracts from an amphibian, Bufo japonicus. Acid‐urea‐Triton polyacrylamide gel electrophoresis (AUT‐PAGE) showed that the nuclear basic proteins of human sperm consist mainly of protamines (HPI, HPII) with minor amounts of nucleosomal histones. On incubation of lysolecithin (LC)‐ and dithiothreitol (DTT)‐treated human sperm with the egg extract, the nuclei lost HPI and HPII within 15 min in association with extensive nuclear decondensation, and the acquirement of a whole set of nucleosomal histones. Incubation of LC‐DTT‐sperm with nucleoplasmin purified from Bufo eggs also induced nuclear decondensation and loss of protamines within 30 min. Native‐PAGE and Western blot analyses of incubation medium indicated tight association of the released protamines to nucleoplasmin, strongly suggesting that protamines are removed from sperm nuclei not enzymatically but by their specific binding to nucleoplasmin. On incubation of LC‐DTT‐sperm with nucleoplasmin and exogenous nucleosomal core histones, micrococcal nuclease‐protected DNA fragments were released, although their unit repeat length was slightly less than that of somatic nucleosomes. Thus remodeling of human sperm during fertilization can be mimicked under defined conditions with nucleoplasmin and exogenous histones.
Butea frondosa as a gastro protective against induced gastric lesions

The study was undertaken to evaluate the potential of alcoholic extract of Butea frondosa Koen. ex Roxb against gastric lesions induced in rats using acetic acid plus pyloric ligation. The impact of alcoholic extract of Butea frondosa in doses of 100, 200 and 400 mg/kg as single dose schedules and 200 mg/kg for 7, 14, 21 and 28 days was determined. Parameters assessed were ulcer index, total acidity, acid volume, total protein and pH, non protein sulfhydryls and gastric wall mucus. Extract in dose of 400 mg/kg as a single schedule signifi cantly reduced ulcer severity, total protein and pH as against the control (p<0.05). Concurrent fi ndings were also observed with 200 mg/kg administered for 21 and 28 days. Treatment with 400 mg/kg of the extract as a single dose and 200 mg/kg for 28 days produced an elevation in the content on non protein sulfhydryls. Gastric wall mucus was enhanced with 200 mg/kg of the extract administered for 28 days with a value of 186±2.74 ig Alcian blue/g wet weight compared with the control (p<0.05). A palpable decline in incidence of ulcers was observed with the extract which might be largely due to the presence of fl avonoids.
κ-Opioid Receptor Model in a Phospholipid Bilayer: Molecular Dynamics Simulation

A three-dimensional molecular model of the transmembrane domain of the κ-opioid receptor in a phospholipid bilayer is presented. The endogenous ligand, dynorphin A (1), and synthetic ligands, benzomorphan-based compounds (2a, 2b) (Figure 1), are docked into the model. We report the results of a 500 ps molecular dynamics simulation of these protein−ligand complexes in a simplified bilayer of 97 molecules of the lipid dipalmitoylphosphatidylcholine and 26 water molecules per lipid. The simulations explore the stability and conformational dynamics of the model in a phospholipid bilayer; we also investigate the interactions of the protein with its ligands. Molecular simulation of the receptor−ligand complexes, endogenous and synthetic, has confirmed the existence of different binding domains for peptide and non-peptide ligands. Similarities are found in the dynamics and binding mode of all conformations of the synthetic ligands studied. The protonated hydrogen of the benzomorphan is always involved in an H-bo.
Milk oligosaccharides: A review

Milk oligosaccharides (OSs) confer unique health benefits to the neonate. Although human digestive enzymes cannot degrade these sugars, they support specific commensal microbes and act as decoys to prevent the adhesion of pathogenic micro-organisms to gastrointestinal cells. The limited availability of human milk oligosaccharides (HMOs) impedes research into these molecules and their potential applications in functional food formulations. Recent studies show that complex OSs with fucose and N-acetyl neuraminic acid (key structural elements of HMO bioactivity) also exist in caprine milk, suggesting a potential source of bioactive milk OSs suitable as a functional food ingredient.
Unravelling population structure of black musselcracker Cymatoceps nasutus: evidence for multiple populations in South African coastal waters

Genetic studies on South African marine fishes have shown that many species exist as single, well-mixed stocks throughout their core distribution. The black musselcracker or poenskop Cymatoceps nasutus is a slow-growing, late-maturing and long-lived sparid (Perciformes: Sparidae) that is endemic to South African coastal waters. Conventional tagging studies suggest that it is resident, with limited connectivity between different regions along the coast. Mitochondrial and nuclear DNA were used to investigate the genetic structure of C. nasutus along the South African coastline and showed evidence of at least two populations. Samples collected from the Tsitsikamma Marine Protected Area on the South Coast to KwaZulu-Natal on the East Coast showed no significant population structure over much of the distribution. Gene flow for C. nasutus within this region is not limited by geographic distance and appears to be unaffected by various oceanographic barriers and biogeographical boundaries. Samples from the Western Cape to the west of Tsitsikamma, however, showed moderate to substantial differentiation for both markers, which may be influenced by a temperature barrier – a coldwater ridge – along the South Coast. These data provide the first genetic assessment of this South African sparid, and suggest that a two-stock management strategy would be appropriate for the species.
Generation of cDNA libraries : methods and protocols

Complementary DNA Libraries: An Overview Shao-Yao Ying Rapid Amplification of cDNA Ends Yue Zhang cDNA Generation on Paramagnetic Beads Zhaohui Wang and Michael G. K. Jones Construction of a Normalized cDNA Library by mRNA-cDNA Hybridization and Subtraction Ye-Guang Chen Amplification of cDNA Ends Using PCR Suppression Effect and Step-Out PCR Mikhail V. Matz, Naila O. Alieva, Alex Chenchik, and Sergey Lukyanov Use of Inverse PCR to Clone cDNA Ends Sheng-He Huang, Steven H. M. Chen, and Ambrose Y. Jong Construction of Size-Fractionated cDNA Library Assisted by an In Vitro Recombination Reaction Osamu Ohara Construction of a Full-Length Enriched and 5'-End Enriched cDNA Library Using the Oligo-Capping Method Yutaka Suzuki and Sumio Sugano cDNA Library Construction Using In Vitro Transcriptional Amplification Shi-Lung Lin and Henry Ji Amplification of Representative cDNA Pools from Microscopic Amounts of Animal Tissue Mikhail V. Matz Single-Cell cDNA Library Construction Using Cycling aRNA Amplification Shi-Lung Lin mRNA/cDNA Library Construction Using RNA-Polymerase Cycling Reaction Shi-Lung Lin and Shao-Yao Ying Quality Assessment of cDNA Libraries Hans-Jurgen Fulle Assessment of the Quality of mRNA Libraries by Agarose Gel Electrophoresis Tsen-Yin Lin and Shao-Yao Ying PACS RT-PCR: A Method for the Generation and Measurement of any Poly(A)-Containing mRNA Not Affected by Contaminating Genomic DNA Igor Nepluev and Rodney J. Folz Single-Cell mRNA Library Analysis by Northern Blot Hybridization Shi-Lung Lin Generation of cDNA Libraries for Profiling Gene Expression of Given Tissues or Cells Xin Zhang, Qiu-Hua Huang, and Ze-Guang Han Screening Poly [dA/dT(-)] cDNA for Gene Identification San MingWang, Scott C. Fears, Lin Zhang, Jian-Jun Chen, and Janet D. Rowley Generation of Longer cDNA Fragments from SAGE Tags for Gene Identification Jian-Jun Chen, Sanggyu Lee, Guolin Zhou, Janet D. Rowley, and San Ming Wang Generation of Full-Length cDNA Libraries Enriched for Differentially Expressed Genes Bakhyt Zhumabayeva, Cynthia Chang, Joseph McKinley, Luda Diatchenko, and Paul D. Siebert Subtractive Hybridization for the Identification of Differentially Expressed Genes Using Uracil-DNA Glycosylase and Mung-Bean Nuclease Tsen-Yin Lin and Shao-Yao Ying Subtractive Cloning of Differential Genes Using RNA-PCR Shao-Yao Ying and Shi-Lung Lin Strategy for Construction of a cDNA Encoding a Repetitive Amino Acid Sequence Masahiro Asada and Toru Imamura Preparing Lambda Libraries for Expression of Proteins in Prokaryotes or Eukaryotes Rebecca L. Mullinax and Joseph A. Sorge Peptide Library Construction from RNA-PCR-Derived RNAs Shi-Lung Lin Identifying Interacting Proteins in an Escherichia coli-Based Two-Hybrid System Bonnie Wu, Rebecca L. Mullinax, and Joseph A. Sorge Future Perspectives, Shao-Yao Ying Index
Recovery of Methanogenesis Following Summer Drought in Soils from Two Cool Temperate Peatlands, New York State, USA

Following a summer drought, intact cores of peat soil from two cool temperate peatlands (a rain-fed bog and a groundwater-fed swamp) were exposed experimentally to three different water table levels. The goal was to examine recovery of anaerobic methanogenesis and to evaluate peat soil decomposition to methane (CH4), carbon dioxide (CO2), and dissolved organic carbon (DOC) upon rewetting. Methane emission from soils to the atmosphere was greatest (mean = 80 μmol m−2 s−1) when the entire peat core was rewetted quickly; emission was negligible at low water level and when peat cores were rewetted gradually. Rates of CO2 emission (mean = 1.0 μmol m−2 s−1) were relatively insensitive to water level. Concentrations of CH4 in soil air spaces suggest that onset of methanogenesis induces, but later represses, aerobic oxidation of CH4 above the water table. Concentrations of CO2 suggest production at the soil surface of swamp peat versus at greater depths in bog peat. Portions of peat soil incubated in vitro without oxygen (O2) exhibited a lag before the onset of methanogenesis, and the lag time was less in peat from the cores rewetted quickly. The inhibition of methanogenesis by the selective inhibitor 2-bromoethanesulfonic acid (BES) decreased CO2 production by 20 to 30% but resulted in an increase in concentrations of DOC by 2 to 5 times. The results show that methanogens in peat soils tolerate moderate drought, and recovery varies among different peat types. In peat soils, the inhibition of methanogenesis might enhance DOC availability.
Feeding behaviour of Merino wethers under conditions similar to lot-feeding before live export.

Sheep from different farms (lines) in Western Australia were mixed in 3 experiments and lot-fed for 6-7 days as if for export. A marking method to identify sheep which eat from troughs was tested and used to examine the effects of feeding treatments on the proportion of sheep which eat during lot-feeding. Paint soaked sponges attached to troughs were used to monitor whether sheep ate. Positive linear relationships between liveweight change and paint marking score (R = 0.93, 0.93 and 0.94, in the 3 experiments) suggested that the technique was a reliable indicator of feed intake. Feeding treatments imposed were period of fasting before lot feeding (experiments 2 and 3); and diet type (hay pellets, hay/pellet mix) and trough location in the feedlot (experiment 3). There were large differences between lines in the percentage of sheep not marked. Values ¦ s.e. ranged from 1 ¦ 1 to 79 ¦ 3% for the 8 lines used in 3 experiments. In experiment 2, fasting for 48 h before lot-feeding resulted in more sheep (P<0.05) not marked (18 ¦ 7 3%) than did fasting for <12 h (9 ¦ 3%) and <24 h (8 ¦ 2%). In experiment 3, fasting for 96 h compared with 48 h resulted in fewer sheep marked daily when fed a hay-pellet mixture (75 ¦ 2 v. 93 ¦ 1%; P<0.001). When fed only pellets in experiment 3, the percentages of marked sheep increased with time (days). Feeding pellets only compared with a hay-pellet mixture resulted in fewer sheep marked daily (60 ¦ 2 v. 79 ¦ 2%; P<0.001) and more sheep not marked (11 ¦ 3 v. 3 ¦ 2%; P<0.05). If troughs were located in the centre of yards instead of on the fenceline, it took 2 rather than 7 days for the daily percentage of animals marked on the pellets only diet to exceed 80%. The central location also resulted in a mean of 78 ¦ 2% of sheep marked daily compared with 67 ¦ 2% for fenceline troughs (P<0.001) and a mean intake higher (P<0.01) by 0.13 ¦ 0.04 kg/wether.day. It was concluded that line of sheep, fasting, diet and trough location all had significant effects on feeding behaviour during lot feeding. Of these treatments, the greatest variation in feeding behaviour was associated with the line of sheep.