Miracle-dz/UniFAR-FTUs huggingface dataset:
Are you what you eat? A geometric morphometric analysis of gekkotan skull shape

The morphological variation of the gekkotan skull, as visualized through dorsal and lateral views of a large sample of skulls (164 species; 68% of all gekkotan genera), was analysed using geometric morphometrics. We describe skull changes using variables associated with the contour variations (uniform components), as well as localized changes (partial warps). We defined dietary categories based on the available information for 105 species. These categories, together with phylogenetic affinities, were used as descriptors of the skull shape variables in subsequent statistical analyses. Changes based on the morphological variables are described and discussed in an ecological and phylogenetic context. We consider that this new information relating gekkotan phylogeny and diet will be useful in future phylogenetic analyses of this group. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 677–707.
Frequency of photoperiod‐insensitive Ppd‐A1a alleles in tetraploid, hexaploid and synthetic hexaploid wheat germplasm

With 2 tables Abstract Differences in photoperiod sensitivity are widely used in wheat breeding to provide adaptation to diverse agronomic environments. Two photoperiod insensitive (PI) mutations in the A genome (Ppd-A1a alleles) were previously identified using near-isogenic lines of tetraploid durum wheat. We show that these Ppd-A1a alleles predominate in modern durum wheat but are absent from wild tetraploid wheat and from conventional hexaploid wheat, suggesting they were selected for improved adaptation during durum cultivation. To increase genetic diversity in hexaploid wheat, synthetic hexaploid wheat lines were developed at CIMMYT by hybridizing elite durum lines with Aegilops tauschii accessions. Ppd-A1a alleles from durum wheat were found in 71.4% of 447 synthetic hexaploids and 9.6% of 115 advanced selections. Backcrosses to hexaploid wheat showed that the durum Ppd-A1a alleles conferred a PI phenotype and that one allele was intermediate between known B and D genome mutations, providing a new source of flowering time variation in hexaploid wheat and the potential for novel combinations of PI alleles.
Centriolar and ciliary responses to DNA damage

xiv Abstract Centrosome duplication is tightly controlled and takes place only once every cell cycle. In recent years more light has been shed on the mechanism of centrosome duplication, with key players being identified and characterised. We sought to characterise Stil, a gene mutated in autosomal recessive microcephaly and which encodes a centrosomal protein. We found that Stil localises to the centrosome in chicken DT40 and that it is evolutionarily conserved between chicken and mammals. We were unable to generate a Stil knockout cell line in DT40 and concluded that Stil is essential for viability and that precise expression levels are critical for viability. Various centrosome abnormalities are observed in cancer cells and in cells with defective DNA damage responses. Moreover, centrosome abnormalities can arise following DNA damage. In this study, we aimed to characterise the impact of irradiation-induced DNA damage on the structure of the centrosome. We found that irradiation leads to the isolation of single centrioles, termed centriole splitting, and that this precedes DNA damage-induced centrosome amplification. We observed that DNA damage causes centriole splitting in non-transformed human cells, with the isolated centrioles carrying the mother markers Ninein and CEP170 but not Cenexin or Kizuna. Loss of centrosome cohesion through siRNA depletion of C-NAP1 or Rootletin increased radiation-induced centriole splitting, with C-NAP1-depleted isolated centrioles losing all maturation markers. Primary cilia are sensory organelles which receive chemical and mechanical signals from the extracellular environment. Defects in primary cilia structure and signalling cause human diseases termed ciliopathies and cancer. As the mother centriole forms the primary cilium, we tested whether DNA damage or centriole splitting affected ciliogenesis. We found that irradiated cells formed apparently normal primary cilia, which arose primarily from centriole clusters and not isolated centrioles. Additionally, multiple primary cilia can form in irradiated cells. Furthermore, C-NAP1 or Rootletin knockdown reduced primary cilium formation. Therefore, the centrosome cohesion apparatus at the proximal end of centrioles may provide a target that can affect primary cilium formation as part of the DNA damage response.
Fungicide management of maize head smut (Sphacelotheca reiliana) by seed treatment.

Two pot experiments were conducted at Lumle Centre in the 1991 and 1992 seasons to evaluate the effectiveness of maize (Zea mays L.) seed treatment with triadimenol (Baytan), Sumi-8 (diniconazole), and tebuconazole (Raxil-50) in the prevention of head smut (Sphacelotheca reiliana). In both years these fungicides effectively controlled the disease since the plants from treated seeds suffered less than 3% smut. These fungicides were tested next under conditions of artificial exposure at three mid-hill sites in farmers' fields in the 1994 season except that propiconazole (Tilt-250) replaced Sumi-8. Propiconazole, tebuconazole, and triadimenol were applied at the rate of 4 mL or 4 g kg -1 of maize seeds. The lowest number of smutted plants was produced by propiconazole (0.7%), and followed by tebuconazole (6.1%) and triadimenol (13.2%) treatments while the untreated control suffered 35.9%. The per cent head smut control by the three fungicides was highly significant (P<0.001) compared with the untreated control. Propiconazole treatment of seed produced a stunting effect at the seedling stage from which the plants recovered later in the growth phase. However, 2-3 mL propiconazole kg -1 seed treatment produced relatively less detrimental effect on germination or seedling growth.
Maize AUXIN-BINDING PROTEIN 1 and AUXIN-BINDING PROTEIN 4 impact on leaf growth, elongation, and seedling responsiveness to auxin and light

In maize, at least five auxin-binding proteins (ABPs) have been identified, yet their functions remain unclear. The present study reports the use of maize abp1, abp4, and abp1abp4 mutants to investigate the role of ABPs during maize growth and development. Single and double abp mutant plants grown in a greenhouse differ from the wild type (WT) in their leaf declination and leaf blade growth. The effect of the dark (D), blue light (BL), red light (RL), and exogenous auxin on the development of mutant seedlings was also studied. Relative to WT, etiolated mutant seedlings were shorter and showed a reduced responsiveness to exogenous auxin. In BL or RL, the responsiveness of maize seedlings to auxin was distinctly less than in D. The reducing effect of light on seedling responsiveness to auxin is mediated at least by phytochromes. The suppression of ABP1 and (or) ABP4 led to a distinct accumulation of free indole-3-acetic acid (IAA) in etiolated and light-grown seedling organs. We concluded that ABP1 and ABP4.
Classification of Transmembrane Protein Families Based on Topological Similarity

The issue at hand is whether investors should be required to arbitrate claims before panels which must include an arbitrator who is affiliated with the very industry they are suing. The premise behind FINRA's argument for delay is that FINRA will conduct a study that might show that industry arbitrators are, in some maimer, "better" for investors. FINRA does not begin to suggest how this could be proven on the basis of data fi'om a voluntary pilot program in which members were not required to participate. Thus, firms which had the most to fear from all public panels may not have participated in the pilot. Neither does FINRA indicate what metrics could be used to assess "success," palticularly when most cases settle for undisclosed sums.
Studies of technology systems for tissue culture and rapid propagation of Asparagus officinalis.

The technological systems of tissue culture for Asparagus' rapid propagation was established through the study about its bud initation and rapid propagation and transplantation.MS mediume supplemented with 0.1 mg/L NAA +0.1 mg/L BA was the initiative medium,with a survival rate of 53.7 % for green shoots.MS supplemented with 0.1 mg/L NAA + 0.1mg/L KT + 0.3-0.4 mg/L BA,the multiplication coefficient being 5.40-6.41 and 3.41-5.19 for stem-base and middle stem.1/2MS supplemented with 0.1 mg/L KT +0.5 mg/L IAA + 0.1 mg/L NAA +2.0mg/L IBA was the rooting medium of shoot tips for 15 days,and the average root length of 4.63-5.05 cm,root number of 10.9-12.1 after 20 days'culture with MS medium without any plant hormones.The transplantation survival rate was 95.20 % with medium of coir dust.
Characterisation of pneumococcal peptidoglycan cross-linking enzymology

Despite the introduction of penicillin, infections caused by Streptococcus pneumoniae are associated with significant morbidity and mortality. As a result, there is an urgent need for successful identification of new drug targets within the organism. This thesis focuses on characterisation of MurM, which initiates the synthesis of branched muropeptides within pneumococcal peptidoglycan. MurM and MurN generate either alanyl-alanine or seryl-alanine appendages on the stem peptide lysine of Lipid II, ultimately resulting in indirect cross-linkage of the cell wall. Inactivation of murMN causes a reversion to penicillin sensitivity in penicillinresistant strains. However, elucidation of the relationship between MurM activity and penicillin-resistance is complicated by some penicillin-sensitive strains, including R6, having an unusually high proportion of indirect cross-linkage in their cell wall. Therefore, MurMR6 has been kinetically characterised with Lipid II, AlatRNAAla and Ser-tRNASer for comparison to MurMPn16 (penicillin-sensitive) and MurM159 (penicillin-resistant). These results confirmed that MurM159 is more catalytically active than MurMPn16. However, in the presence of Ser-tRNASer, the catalytic activity of MurMR6 approaches that of MurM159. Stimulation of MurM by cardiolipin indicates the potential role of pneumococcal membrane phospholipid composition in the regulation of this enzyme. Assessment of MurM substrate specificity was made using misaminoacylated SertRNAAla. Results indicate that Ser-tRNAAla is used more efficiently by MurM providing a link between peptidoglycan biosynthesis and the fidelity of protein synthesis in S. pneumoniae. A 2’-amino minihelix analogue of Ala-tRNAAla inhibits MurM with an IC50 of 0.5 μM demonstrating specific acceptance of the amino acid from the 2’ hydroxyl of the terminal adenine of the tRNA substrate. Crystallisation of MurM in the presence of zinc and subsequent characterisation of its metal-ion binding properties by kinetic analysis, isothermal titration calorimetry and bioinformatics-informed site-directed mutagenesis have identified that this enzyme is zinc-dependent. In combination, these findings have far-reaching implications for future drug design.
CPT-sondering. Utrustning - utförande - utvärdering. En in-situ metod för bestämning av jordlagerföljd och egenskaper i jord

(1) Sonderingsprincip; (2) CPT-utrustning; (3) Utforande av CPT-sondering; (4) Redovisning och databehandling av sonderingsresultat; (5) Utvardering av jordlagerfoljd och klassificering av jord; (6 .
Impact of climate and land use type on the distribution of Finnish casual arable weeds in Europe

Hyvonen T, Glemnitz M, Radics L & Hoffmann J (2011). Impact of climate and land use type on the distribution of Finnish casual arable weeds in Europe. Weed Research51, 201–208. Summary The aim of the study was to explore the impact of climate and land use type on species richness and abundance of arable weeds found as casual aliens in Finland. We used an empirical data set collected along a European climate gradient, from which 163 plants were selected for the analyses. Using generalised linear modelling (GLMM) and redundancy analysis (RDA), we compared species richness and abundance of all species and three functional groups (dicotyledons and grasses, C3 and C4 species, alien and native species to Europe), as well as occurrence of the 13 most common individual species between three land use types (fallow, low-input and conventionally cultivated) and six regions. In general, fallowing and low-input cultivation, as well as warmer climate, supported greater weed species richness and abundance. Temperature was found to be a more important factor for weed abundance than land use. The only exception was C4 species richness, which did not respond to either factor. The impact of land use was independent of climate for all variables, except C4 species abundance. Non-cultivated fallows had more weeds than cultivated fields, in most cases. No difference was found in the species richness and abundance of grasses or in the occurrence of individual species between low-input and conventionally cultivated fields. It was evident that climate and land use affect the distribution of arable weed species currently found as casual aliens in Finland. This suggests that climate warming will increase the risk of the population establishment of new weed species in northern regions.
Biomass recalcitrance. Part II: Fundamentals of different pre‐treatments to increase the enzymatic digestibility of lignocellulose

A number of pre‐treatment methods have been developed during the last few decades to overcome biomass recalcitrance. Although the mechanisms of these pre‐treatments are different, the final objective is the same – increasing cellulose accessibility to cellulase enzymes. Generally, pre‐treatment is the process to disrupt the compact structure of lignocellulosic biomass and expose cellulose fibers, which can be achieved by mechanical comminution, chemical modifications of biomass compositions, biological degradation, or a combination of these methods. After pre‐treatment, the accessible surface area is increased resulting in the enhancement of cellulose digestibility. In this paper, we review the recent progress of the fundamental researches of various biomass pre‐treatment processes, especially on how these pre‐treatments alter chemical composition and physically change cell wall structure. Understanding these changes would be helpful to further optimize existing pre‐treatments, and would aid in developing novel pre‐treatment methods. © 2012 Society of Chemical Industry and John Wiley & Sons, Ltd
Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% .
The effect of food and water on development, longevity, and fecundity in the Rutherglen bug, Nysius vinitor (Hemiptera : Lygaeidae)

N. vinitor subsists primarily upon the seeds of various plants. A wide range of seeds was found to be suitable for nymphal development, but some seeds were more suitable than others. Seeds suited for nymphal growth were not necessarily adequate for egg production. Some seeds promoted higher fecundity than others when used as food for adults. Nutritional requirements for fecundity appeared to be more specific than for development. Egg production was dependent mainly on the food consumed by the adult and was little affected by nymphal diet which, however, influenced potential egg production if obviously inadequate for nymphal development. Survival of females with access to water was uninfluenced by availability of food, but food was essential for egg production. Starvation decreased potential reproduction of females. Lack of water, even for a short period, stopped egg production and increased mortality.
Genetic inhibition of the ubiquitin-proteasome pathway : insights into proteasomal targeting

Regulated proteolysis plays a major role in diverse cellular processes, including cell-cycle progression, endocytosis, apoptosis, transcription, and signal transduction. Proteins destined for proteolysis undergo two key steps in the ubiquitin-proteasome pathway. First, a complex enzymatic cascade controls conjugation of a multiubiquitin chain onto a protein. Once ubiquitinated, protein substrates must be recognized and targeted to the proteasome complex, where they are unfolded and degraded. Receptor proteins, such as Rad23, recognize ubiquitinated proteins and deliver them to the proteasome. While the list of enzymes involved in ubiquitination is steadily growing, the first enzymatic reaction required for all ubiquitin-dependent processes is catalyzed by one protein, the ubiquitin-activating enzyme, E1. In this work, we describe a genetic screen that targets the Saccharomyces cerevisiae E1 gene, UBA1. We report the isolation of uba1-204, a temperature-sensitive allele UBA1 that exhibits dramatic inhibition of the ubiquitin-proteasome pathway. Shifting mutant cells to the restrictive temperature results in the depletion of cellular ubiquitin conjugates within minutes, accompanied by stabilization of multiple protein substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play the recognition and delivery of substrates to the proteasome. It is possible to purify intact and active proteasomes complexes from uba1-204 cells. In the absence of ubiquitin activation, these proteasome complexes are depleted of ubiquitin conjugates and the ubiquitin-binding receptor proteins Rad23 and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo. As an additional example of the value of this novel genetic mutant in the study of the ubiquitin-proteasome system, we present preliminary results from a quantitative mass spectrometric analysis of the proteins associated with proteasome complexes isolated from uba1-204 cells. In summary, we have created a genetic method of rapidly inhibiting the ubiquitin-proteasome system. This will enable future exploration of the ubiquitin-proteasome system and potentially many other ubiquitin-dependent cellular processes.
Cold-adapted enzymes

In the last few years, increased attention has been focused on a class of organisms called psychrophiles. These organisms, hosts of permanently cold habitats, display metabolic fluxes more or less comparable to those exhibited by mesophilic organisms at moderate temperatures. Psychrophiles have evolved by producing, among others, “cold-evolved” enzymes which have to cope with the reduction of chemical reaction rates induced by low temperatures. Thermal compensation in these enzymes is reached, in most cases, through a high catalytic efficiency as compared to their mesophilic counterparts at temperatures ranging from 0 to 30°C. Optimisation of the catalytic parameters can originate from an increased flexibility of either a selected area of the molecular edifice or of the overall protein structure. The increased resilience probably enhances abilities to undergo conformational changes during catalysis at low temperatures. In return, this flexibility would be responsible for the weak thermal stability of the psychrophilic enzymes. Structure modelling and recent crystallographic data have allowed the identification of the structural parameters that could be involved in a higher plasticity. The current consensus is that only subtle modifications of the conformation of cold-adapted enzymes can be related to the structural flexibility and that each enzyme adopts its own strategy. Moreover, it appears that there is a continuum in the strategy of protein adaptation to temperature, since known structural factors involved in protein stability of thermophiles are either reduced in number or modified, in order to increase flexibility in psychrophilic enzymes. The possible biotechnological purposes of cold-adapted enzymes are numerous. Due to their attractive properties, i.e. high specific activity and low thermal stability, they are very promising in various fields such as the detergent and food industries, molecular biology, bioremediation, etc.
Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana

Recombinant inbred (RI) lines of Arabidopsis thaliana (Arabidopsis) have been generated from a cross between the ecotypes Landsberg erecta and Columbia. Progeny of 300 individual F2 seedlings were taken by single seed descent to the F8 generation. Sixty-seven loci, scored using 64 RFLP probes and one phenotypic marker, chosen at approximately 20 cM intervals from the two previously published RFLP maps, were mapped using 100 of these RI lines. More than 500 other new loci are currently being mapped using these RI lines by several other groups. These 100 RI lines thus provide the material to map new probes or phenotypic traits polymorphic between Landsberg erecta and Columbia, relative to an increasing number of molecular markers. Higher resolution mapping of distinct chromosomal regions can be achieved by analysing the segregation of particular markers on the additional 200 RI lines.
A re-evaluation of evolutionary stasis between the bivalve species Chione erosa and Chione cancellata (Bivalvia: Veneridae)

Demonstrating stasis in the fossil record has proven to be problematic with respect to both data collection and analysis. A previous approach is morphometric analysis of lineages sampled temporally and geographically. A hypothesis of stasis is apparently supported if morphological distances between descendent species and ancestral species are no greater than those between geographically distant samples of the descendent species. Evidence presented in this paper conflicts with such interpretations for at least one bivalve lineage, Chione erosa–Chione cancellata, of the late Neogene of tropical America. The direction and magnitude of morphological variance were quantified between two geographically distant groups of C. cancellata from the Recent, and compared to Pleistocene samples of C. cancellata and Pliocene samples of C. erosa. The results indicate that, although the magnitude of intraspecific geographic variation is as great as interspecific temporal variation, the species are morphologically discrete groups. The direction of morphological variance is as important as its magnitude, and interpretations overlooking this point are at best equivocal.