Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant species and functional group responses to changes in plant community diversity and composition

Variation in functional trait values may serve as an acclimation strategy for plants to cope with altering environmental conditions. Since plant community diversity affects the environment experienced by individual plants, the question arises how plant functional traits change in response to plant community diversity. Here, we examined the variation of morphological and physiological traits of 12 grass species in a biodiversity experiment (Jena Experiment) varying species richness (from 1 to 16 (60)) and functional group composition (1-4; grasses, legumes, tall herb, small herbs). In response to increasing log-linear species richness, grasses increased stem length and changed aboveground biomass partitioning by allocating on average more biomass into stems but less into leaves and inflorescences, and decreased their foliar δN and δC signatures. The presence of legumes in plant communities influenced almost all investigated traits, but most strongly those that reflect acquisition and use of nitrogen (massand area-based N). Growing together with legumes, grass species generally increased leaf length as well as specific leaf area or leaf area ratio. Close correlations of trait expressions with canopy height, except for traits that described nutrient acquisition, indicated strong adjustments to changing light conditions with increasing plant community diversity. Nevertheless, a large part of the trait variation was explained by species identity in all investigated morphological and physiological traits (except for the trait biomass:N ratio). Although all grass species changed trait values in response to increasing species richness, the identity of responsive traits as well as the direction and magnitude of their response greatly differed among individual grass species. We conclude that the expression of functional traits of grass species is driven by community species richness and composition in terms of legume presence, but even within the seemingly homogeneous plant functional group of grasses, species are not redundant in their functions and thus species identity matters.
Mechanisms regulating excitability of primary afferent nociceptors

Mechanisms regulating excitability of primary afferent nociceptors. Bikramjit Chopra The perception of pain burning, aching and soreness acts as a physiological warning that protects us from real or potential injury by employing both behavioural and reflex avoidance responses. Unfortunately, this sensory modality can outlive its usefulness and become chronic and debilitating. Indeed, inflammatory mediators released following tissue trauma can sensitise pain fibres (primary afferent nociceptors) to a diverse range of mechanical, chemical and thermal stimuli. The aim of the present study was to investigate the molecular mechanisms regulating the excitability of primary afferent nociceptors. The present study has demonstrated that cyclooxygenase-1 (COX-1) was constitutively expressed in a subpopulation of putatively defined nociceptors in the rat dorsal root ganglion (DRG), using immunocytochemical techniques. Consistent with these immunocytochemical findings, sharp-electrode recordings revealed that depolarisations evoked by the inflammatory mediator, bradykinin on cultured rat DRG neurons, were significantly attenuated by selective COX-1 inhibition. These findings suggest that activation of bradykinin receptors in nociceptors, may in addition to activating phospholipase C, also release arachidonic acid, which is then specifically metabolised by COX-1 to synthesise pro-inflammatory prostaglandins. There is increasing evidence to suggest that inflammatory mediators can regulate neuronal excitability by phosphorylating ion channels expressed on primary afferent nociceptors. However, the identities of the ion channels underlying these effects have not been fully elucidated. The present studies demonstrated the expression and distribution of the inwardly rectifying potassium channel, Kir2.3 and tetrodotoxinresistant (TTX-R) sodium channel Nay 1.8, in a sub-population of putatively defined nociceptors. Using the whole-cell patch clamp technique, it was demonstrated that the inflammatory mediator, bradykinin could modulate the functions of the Kir and TTX-R sodium currents in cultured rat DRG neurons. Taken together, the results from the present studies have increased our understanding of the molecular mechanisms regulating nociceptor excitability, and as such, may also contribute to the development of more efficacious analgesic therapies. Table of
The Complex Inheritance of Maize Domestication Traits and Gene Expression

The genetic basis for morphological change in divergent species is a central question in evolutionary biology. The domestication of maize from its wild progenitor, teosinte, is an excellent system to address this question. We explore the large effect on domestication phenotypes of a poorly understood region of the maize genome using a chromosome five specific mapping population. Unlike other large effect regions of the maize genome, many traits have multiple QTL that do not stack on a single locus suggesting multiple genes on the fifth chromosome influence domestication traits. Simulation studies show clear evidence for limited power to detect QTL for highly polygenic traits that do not accurately portray the true complexity of the underlying genetic architecture. Two QTL in different locations were chosen for fine mapping studies to identify the underlying causative genes. While a single gene was not identified for either QTL, both were successfully narrowed to less than three centimorgan intervals with relatively few genes and evidence of positive selection during maize domestication. Finally, the first genome-wide effort to characterize cis and trans regulatory change between a domesticated crop and its wild progenitor found extensive regulatory variation with relatively few genes having consistent cis differences, which were determined to be under positive selection during the domestication and crop improvement of maize. Consistent with loss of diversity during the domestication bottleneck, cis expression variation explained by the maize parent is reduced in comparison to teosinte with an even greater reduction seen in cis candidate genes. A general increase in the expression of maize alleles was also observed suggesting domestication in maize may have led to a general increase in gene expression. Collectively, these experiments shed light on the evolution of divergent phenotypes and gene regulation in the domesticated maize and its wild progenitor.
Adjuvants and Growth Stage Affect Purple Nutsedge (Cyperus rotundus) Control with Chlorimuron and Imazethapyr

Chlorimuron and imazethapyr applied with nonionic surfactant, crop oil concentrate, or organosilicone-based adjuvant were evaluated for purple nutsedge control in the field. Additional experiments compared chlorimuron and imazethapyr control of purple nutsedge when applied with crop oil concentrate at two growth stages. Chlorimuron controlled purple nutsedge better than did imazethapyr in most experiments. Chlorimuron performed better when applied with crop oil concentrate than with nonionic surfactant or organosilicone-based adjuvant. Imazethapyr control with the organosilicone-based adjuvant or crop oil concentrate was similar and greater than imazethapyr with nonionic surfactant. Control was greater when herbicides were applied to 2- to 6-cm tall purple nutsedge compared with plants 8 to 10 cm tall in two of three trials.
Convex hull generation, connected component labelling, and minimum distance calculation for set-theoretically defined models

Three areas of geometric modelling have been studied in this thesis: the compu­ tation of the convex hull of a model, the labelling of the connected components of a model, and the calculation of the minimum distance between two objects in a model. The models considered for each area of research are solid models which have been defined set-theoretically, i.e. using computational solid geometry (CSG). Although the areas of research have been considered independently of the dimensionality of the models, methods developed in this work have been imple­ mented for three-dimensional models. The following new results are presented in this thesis: • Computing the convex hull of a set-theoretically defined model. A pointset that represents the model is generated by one of three m ethods (one for polyhedral models, two for non-polyhedral models). The convex hull of this point-set is then found by using an existing convex hull algorithm. • A heuristic method of computing the connectivity between two points within a given model. This works using a divide-and-conquer method to attem pt to find a series of points which are connected. • A connected-component labelling algorithm utilising a binary tree storage structure for a model by dividing a model and storing the divided model in a binary tree. Neighbouring nodes in the binary tree are examined to compute connected components. • An algorithm for the computation of the minimum distance between two models by dividing the models recursively and concentrating the division on areas within which the closest points between the models are considered more likely to be found.
Inhibition of Larval Survival and Metamorphosis of the Sea Urchin Strongylocentrotus intermedius by 2,4-dibromophenol and 2,4,6-tribromophenol

We examined the inhibitory effects of 2,4-dibromophenol (DBP) and 2,4,6-tribromophenol (TBP), which are released by the kelps Eisenia bicyclis and Ecklonia kurome, on survival and metamorphosis of larvae of the sea urchin Strongylocentrotus intermedius. Almost all larvae were fallen in the presence of 5 and 10 ppm, and died in the presence of 20 and 50 ppm DBP and TBP after 24 h, indicating that DBP and TBP have strong toxicity for the larvae of S. intermedius. The percentage of larvae that underwent metamorphosis in filtered seawater after 1 h of exposure to a one-half dilution of saturated dibromomethane solution (~60 ppm) as a chemical inducer reached 43% after 1 h and rose to 75% after 24 h. However, the percentage of metamorphosed larvae in filtered seawater containing 10 ppm DBP was reduced markedly to 25-34% within 24 h, and that in filtered seawater containing 10 ppm and 20 ppm TBP was reduced markedly to 24-34% and 4-10%, respectively, within 24 h. All larvae exposed to 20 ppm and 50 ppm DBP and to 50 ppm TBP died after 1 h. These findings suggest that DBP and TBP have a strong inhibitory effect on larval survival and metamorphosis for S. intermedius. These bromophenols may play a important role in the chemical defense of kelps against sea urchin recruitment in the field.
Morphological variability of the marine planktonic diatom Chaetoceros similis (Bacillariophyceae)

Chaetoceros similis est une diatomee planctonique marine decrite par Cleve en 1896. L'espece est relativement bien connue dans le phytoplancton de l'Ocean Atlantique du Nord, des mers interieures et semi-closes de l'hemisphere du Nord et de l'Ocean Pacifique du Nord. Ce travail etudie sur sa variabilite morphologique, a partir d'echantillons recoltes pendant l'ete de 2003 a Roscoff (Bretagne). Generalement Chaetoceros similis est present comme une forme solitaire mais parfois il forme de courtes chaines (6 cellules au maximum). Dans les chaines, les valves-soeurs des cellules intercalaires sont connectees par les faces valvaires qui sont gonflees au centre. Les valves montrent un dessin de costae a partir des annuli legerement excentriques et une rimoportula centrale dans les valves terminales seulement. Toutes les soies ont leur origine aux apex des valves. Elles sont droites et forment un angle de 30-35° avec les axes apicaux ; dans les chaines les soies-soeurs ne sont pas fusionnees. Quelques specimens presentent des formes teratologiques, surtout dans les chaines. Quelques valves intercalaires ont une seule soie plus grosse sans soie correspondante a l'autre apex. Quelques valves a trois soies sont aussi presentes, et quelques cellules dans les chaines courtes ont une seule soie terminale par valve. Ce dernier morphotype ressemble a une autre espece de ce genre, Chaetoceros throndsenii. Dans les chaines, la nature des cellules reliees par les faces valvaires gonflees et l'absence de fusionnement des soies-sœurs peuvent contribuer a expliquer la variabilite du numero et de la structure des soies-soeurs.
Sea surface height variability of the intra-Americas sea from Topex/Poseidon satellite altimetry : 1992-1995

This study analyzes sea surface height (SSH) variability over the Intra-Americas Sea for the period of September 1992 through December 1995. The TOPEX/Poseidon data set used herein is the SSH anomaly after subtracting the marine geoid and the 1993-1995 3-yr mean sea level for the region. The study of the time-series from SSH anomaly deviations involved 526 points located along the satellite tracks. Points that were in close proximity to land masses showed aliasing of the M 2 tide. In the vicinity of the Gulf Loop Current, results had similarity to prior studies, i.e., SSH variability of ±20-25 cm, and substantial eddy energy in the western Gulf of Mexico. The Caribbean Sea had less variability than the Gulf of Mexico with values of ±10-12 cm, also consistent with prior results. Employing Hovmoller (space-time) analysis, variances in the SSH time-series were identified and tracked from east of the Lesser Antilles, along the path of the Caribbean Current and in the Gulf Loop Current, in an attempt to quantify the frequency and magnitude of eddy events. The region of highest SSH activity was in the vicinity of the Gulf Loop Current with an eddy-shedding frequency of more than one per year.
Turbulent mixing in a stratified estuarine tidal channel: Hikapu Reach, Pelorus Sound, New Zealand

ABSTRACT Channel constrictions within an estuary can influence overall estuary-sea exchange of salt or suspended/dissolved material. The exchange is modulated by turbulent mixing through its effect on density stratification. Here we quantify turbulent mixing in Hikapu Reach, an estuarine channel in the Marlborough Sounds, New Zealand. The focus is on a period of relatively low freshwater input but where density stratification still persists throughout the tidal cycle, although the strength of stratification and its vertical structure vary substantially. The density stratification increases through the ebb tide, and decreases through the flood tide. During the spring tides observed here, ebb tidal flow speeds reached 0.7 m s−1 and the buoyancy frequency squared was in the range 10−5 to 10−3 s−2. Turbulence parameters were estimated using both shear microstructure and velocimeter-derived inertial dissipation which compared favourably. The rate of dissipation of turbulent kinetic energy reached 1 × 10−6 m2 s−3 late in the ebb tide, and estimates of the gradient Richardson number (the ratio of stability to shear) fell as low as 0.1 (i.e. unstable) although the results show that bottom-boundary driven turbulence can dominate for periods. The implication, based on scaling, is that the mixing within the channel does not homogenise the water column within a tidal cycle. Scaling, developed to characterise the tidal advection relative to the channel length, shows how riverine-driven buoyancy fluxes can pass through the tidal channel section and the stratification can remain partially intact.
Structural and biochemical characterization of yeast alkylpurine DNA glycosylases

DNA glycosylases specialized for alkylation damage must identify, with exquisite specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of S. pombe Mag1 in complex with DNA and performed a mutational analysis of spMag1 and the close homolog from S. cerevisiae Mag. Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N-ethenoadenine (εA) is influenced by a minor groove interrogating residue more than the composition of the nucleobase binding pocket. Exchanging this residue between Mag proteins swapped their εA activities, providing evidence that residues outside of the extrahelical base binding pocket play a role in identification of a particular modification in addition to sensing damage. *The work presented in this chapter was published in Adhikary, S. and B. F. Eichman (2011). "Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase. " EMBO Rep 12(12): 1286-1292.
Colchicine-induced somatic polyploids from in vitro-germinated seeds of South African Watsonia species

Polyploidy represents a useful tool for increasing marketability of floriculture crops. The efficacy of 250 μM colchicine [0.01% (w/v)] as a means of inducing polyploidy in six South African Watsonia species (W. borbonica subsp. ardernei, W. humilis, W. laccata, W. lepida, W. pulchra, and W. vanderspuyiae), as determined through high-resolution flow cytometry, is reported. Exposure to colchicine during imbibition and as 24-, 48-, or 72-h pulse treatments for in vitro-germinated seeds resulted in seedlings with increased ploidy, reaching a maximum of 60% induction after the 72-h pulse treatment. The greatest proportions of induced individuals from both the pre- and post-germination exposure treatments were of mixed ploidy. These mixoploids were induced in five species. Non-chimeric tetra- and octaploids were produced in low frequencies only for W. vanderspuyiae during radicle-pulse exposure of 24 and 48 h. Increasing colchicine exposure at radicle emergence manifested as aberrant phenotypic expression and was typified by a reduction in leaf length and rooting capacity in vitro coupled with overall slowed growth. In vitro regeneration and multiplication is easily achievable for the genus and should allow for the capture and refinement of desirable polyploid tissues.
Testing Acute Toxicity in the Embryo of Zebrafish, Brachydanio rerio, as an Alternative to the Acute Fish Test: Preliminary Results

Acute toxicity testing in fish is a standard method used in estimating the influences of chemicals on aquatic vertebrates. The ecotoxicological data obtained from acute toxicity tests in fish are, however, not sufficiently reliable to justify the continued use of this test. Fertilised eggs of zebrafish (Brachydanio rerio) were used to test the acute toxicity of chemicals. They were chosen because the development of B. rerio has been studied extensively and information already exists concerning the normal development of this species. The following parameters of the development of B. rerio were observed: coagulation of the egg, gastrulation, number of somites, movement, development of organs, pigmentation, heartbeat and circulation. Some of these toxicological endpoints indicate lethality. In addition, various interactions between the test chemical and the embryos can be measured by investigating these parameters. Six chemicals (2,4-dinitrophenol, 4,6-dinitro-o-cresol, malathion, carbaryl, phenol and 4-nitrophenol) were selected for testing in the embryos of zebrafish within the first 48 hours of their development. The toxicities of the test chemicals to zebrafish embryos were compared with their acute toxicities to adult fish. Further investigations with more chemicals are in progress. The effective concentrations (EC50) and the lowest effect concentrations (LOEC) investigated in this preliminary study were comparable to the LC50 values for adult fish. The use of this test system as an alternative method to testing toxicity in adult fish is discussed.
The extent of colicin B resistance among IncH plasmids

Vingt et un sur vingt-deux plasmides appartenant au sous-groupe HI2 du groupe d'incompatibilite HI(IncHI) diminuent la sensibilite de Escherichia coli K-12 contre l'action bactericide de la colicine B. Cette propriete est aussi mediee par les plasmides representatifs du sousgroupe IncHI3 et du groupe IncHII, mais ne l'est pas par deux representants du sous-groupe IncHI1. Parmi onze autres plasmides, appartenant chacun a un groupe d'incompatibilite different, seul le plasmide IncT diminue la sensibilite de E. coli a l'activite de la colicine B
Use of cortical terpenes to discriminate Pinus brutia (Ten.), Pinus halepensis (Mill.) and their hybrids

Terpene composition of cortical oleoresin was analyzed by gas chromatography in 283 individuals from F1 and F2 Pinus brutia x Pinus halepensis hybrids, back - crosses and parental species. The objective was to explore the utility of terpenes in hybrid identification between the 2 species. Fifteen compounds were detected in the cortical oleoresin of all trees, 14 of which were identified. No qualitative differences were found among species and hybrids. Aleppo pine oleoresin composition differs significantly in the amounts of several major terpenes from that of Pinus brutia whereas the composition of hybrids was more or less intermediate between the 2 species. A cluster analysis of the data revealed the classification of all trees into 7 major chemotypes. Occurrence of various chemotypes within parental species and hybrids in different rates has the result to separate the taxa and distinguish the hybrids.
Molecular cloning, sequence characterization, and tissue expression analysisof three water buffalo ( Bubalus bubalis ) genes – ST6GAL1 , ST8SIA4 , and SLC35C1

Abstract. Recent studies have shown that ST6 beta-galactosamide alpha-2,6-sialyltransferase 1 (ST6GAL1), ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 (ST8SIA4), and solute carrier family 35, member C1 (SLC35C1) play essential roles in the metabolism of milk glycoconjugates in mammals. However, studies on their coding genes in water buffalo have not been reported. In the present study, cloning and sequencing showed that the coding sequences (CDSs) of buffalo ST6GAL1, ST8SIA4, and SLC35C1 were 1218, 1080, and 1095 bp in length, which encoded a precursor protein composed of 405, 359, and 364 amino acids, respectively. The deduced sequences of these three proteins in turn showed 97.6–98.5, 98.6–99.7, and 97.8–99.2 % similarities with other bovine species. Both buffalo ST6GAL1 and ST8SIA4 were predicted to be a member of glycosyltransferase family 29 and were all hydrophilicity proteins functioning in the Golgi apparatus. Buffalo SLC35C1 was a hydrophobic membrane protein located in the Golgi membrane, containing a TPT domain that is found in a number of sugar phosphate transporters. In addition, semi-quantitative RT-PCR analysis in 13 lactating buffalo tissues revealed that the ST6GAL1 and ST8SIA4 were expressed in 9 tissues, while SLC35C1 was expressed in 11 tissues. The expression levels of these three genes in the mammary gland were significantly higher in lactating than in non-lactating stage. Collectively, our data indicate that ST6GAL1, ST8SIA4, and SLC35C1 are potentially involved in the process of buffalo lactation.