Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Breeding Strategies for Ornamental Dahlias II: Molecular Analyses of Genetic Distances between Dahlia Cultivars and Wild Species

Summary Genetic distances between nineteen Dahlia cultivars and three genotypes of wild Dahlia species and a hybrid were analysed with 1432 AFLP-Markers generated by 10 Hind/Mse primer combinations. Markers were transformed into a 0/1-matrix and relative distances were computed by means of the Jaccard-coefficient. From these data a dendrogram was constructed by the UPGMA-method. In the dendrogram the cultivars cluster together into one group, while the wild species and the hybrid branched off at a larger genetic distance. The level of genetic similarity of the cultivars averaged between 0.68 and 0.77. Only two varieties displayed a similarity of 0.92 to each other. This relatively large genetic distance between the cultivars indicates a vast potential for further variety development. Within the cultivars different clusters are formed which do not show any relation to phenotypic characteristics like inflorescence morphology or breeding origin. This lack of correlation indicates that a classification of dahlias into horticultural groups does not reflect genetic relationships between cultivars. Therefore, this classification should not be used to select parents for further breeding apart for the few characters it is built on. With knowledge about the genetic background additional information for the selection of genotypes as parent in breeding is available. Genotypes can be choosen for their low level of relatedness or for their genetically characteristics independent from the horticultural type.
KINETIC AND KINEMATIC ANALYSIS OF THREE DIFFERENT EXECUTION MODES OF STAG LEAP WITH AND WITHOUT THROW- CATCH BALL IN RHYTHMIC GYMNASTICS

Visual analysis of rhythmic gymnastics shows that the greatest difficulty lies in jumps. Performing jump with optimal speed, great amplitude, and better coordination and without any mistakes, does not depend only on the gymnast's capacity but also on the apparatus used, the jump made and the applied momentum. The objective was to study the qualities of strength, speed and flexibility developed during the three execution modes of stag leap with ring with and without throw-catch ball. Seven gymnasts from the national rhythmic gymnastics team aged between 15 to 21 years participated in this study. The protocol in making three stag leaps with rings consist of the following: the first without apparatus, the second with throwing ball during the chasse step, and the third with throwing ball at the time of pulse during stag leap with ring. The basic descriptive parameters and statistical significance of differences were determined by using the SPSS 20.0, statistical program for data processing. The results show a significant variation at p <0.05 in the execution factors when introducing apparatus such as, horizontal and vertical velocity, right knee angle, force, horizontal displacement of toe, the angular momentum of the centre of mass and angular velocity of right leg. This decrease differs according to the moment of throwing the ball. In conclusion, we can argue that introducing ball during the chasse step causes a change in the basic performance factors.
Functions of Argonaute Proteins in Self Versus Non-Self Recognition in the C. elegans Germline: A Dissertation

Organisms employ sophisticated mechanisms to silence foreign nucleic acid, such as viruses and transposons. Evidence exists for pathways that sense copy number, unpaired DNA, or aberrant RNA (e.g., dsRNA), but the mechanisms that distinguish “self” from “non-self” are not well understood. Our studies on transgene silencing in C. elegans have uncovered an RNA surveillance system in which the PIWI protein, PRG-1, uses a vast repertoire of piRNAs to recognize foreign transcripts and to initiate epigenetic silencing. Partial base pairing by piRNAs is sufficient to guide PRG-1 targeting. PRG-1 in turn recruits RdRP to synthesize perfectly matching antisense siRNAs (22G-RNAs) that are loaded onto worm-specific Argonaute (WAGO) proteins. WAGOs collaborate with chromatin factors to maintain epigenetic silencing (RNAe). Since mismatches are allowed during piRNA targeting, piRNAs could—in theory— target any transcript expressed in the germline, but germline genes are not subject to silencing by RNAe. Moreover, some foreign sequences are expressed and appear to be adopted as “self. ” How are “self” transcripts distinguished from foreign transcripts? We have found that another Argonaute, CSR-1, and its siRNAs—also synthesized by RdRP—protect endogenous genes from silencing by RNAe. We refer to this pathway as RNA-mediated gene activation (RNAa). Reducing CSR-1 or PRG-1 or increasing piRNA targeting can shift the balance towards expression or silencing, indicating that PRG-1 and CSR-1 compete for control over their targets. Thus worms have evolved a remarkable nucleic acids immunity mechanism in which opposing Argonaute pathways generate and maintain epigenetic memories of self and non-self nucleotide sequences.
CRISPR-Cas immunity : analysis of adaptation and interference reactions in prokaryotes

Mobile genetic elements (MGEs, e.g. transposons, plasmids and phage) are an important driver of genetic diversity in microorganisms, and have diverse effects on microbe populations. Adaptation of Bacteria and Archaea to overcome negative effects of phage infection is sometimes referred to as an “arms race” that provokes the development of systems to protect against phage attack. One such defence is CRISPR-Cas, the topic of this research thesis. CRISPR (Clustered Regular Interspersed Short Palindromic Repeat) loci and Cas (CRISPR-associated) proteins are the molecular basis of this resistance mechanism. CRISPR-Cas can protect against phage and other foreign MGEs by incorporating a fragment of novel DNA into CRISPR (spacer acquisition) and using this as a template to generate a small RNA molecule, CRISPR RNA (crRNA), which targets the degradation of complementary sequences (interference). Effective interference requires formation of R-loop nucleic acid structure of crRNA base-pairing to homologous DNA, at positions flanked by PAM (Protospacer Adjacent Motif) sequence within the invader. This thesis investigates actions of CRISPR-Cas interference proteins, with focus on archaeal species Methanothermobacter thermautotrophicus (Mth) and Haloferax volcanii (Hvo). Mth and Hvo catalyse interference by utilizing a Cascade (CRISPR-associated Complex for Antiviral DEfence) protein-crRNA complex. Cas8, the large subunit protein in Cascade, was investigated to explain it’s essential role in interference. It is a PAM sensing protein that stabilizes R-loop formation to bring about interference. In addition, this analysis identified a surprising RNase activity of Cas8 that remains of unknown function. The thesis also details recent work on adaptation by Cas1 and Cas2 in Escherichia coli. Cas1 nuclease and transesterification activities upon replication fork intermediates are presented alongside a new model for spacer acquisition.
Effect of Wind on the Flight of Brown Booby Fledglings

Abstract There is increasing evidence showing that wind velocity affects the flight and foraging behavior of seabirds; however, few studies have examined these effects on seabirds inhabiting tropical oceans where lighter wind conditions usually prevail. The Brown Booby Sula leucogaster is an example of a tropical seabird with relatively low wing loading; strong wind conditions may be expected to impede the stability of their flight. We examined how different wind conditions affected the duration and flying behavior of Brown Booby fledglings during foraging trips by means of direct observation of nest attendance and by attaching video loggers to birds. The duration of foraging trips by fledglings decreased with increasing wind speed, and during flight, the body rotation of fledglings became greater with increasing wind speed. As expected, fledglings were buffeted by strong winds due to their relative inexperience in flight combined with their low wing loading. Fledglings were probably forced to flap against strong winds in order to adjust the stability of their bodies, offsetting the efficient use of wind for gliding. Furthermore, the height at which fledglings flew fluctuated more at higher wind velocities, which may have constrained their detection and capture of prey. In conclusion, our results indicate that the aerodynamic performance of Brown Booby fledglings is impaired by strong wind conditions, leading to poor flight stability and potentially reduced prey detection.
PII: S0375-9601(01)00193-1

Recent proposals for improved optical tests of special relativity have renewed interest in the interpretation of such tests. In this Letter we discuss the interpretation of modern realizations of the Michelson–Morley experiment in the context of a new model of electrodynamics featuring a vector-valued photon mass. This model is gauge invariant, unlike massive-photon theories based on the Proca equation, and it predicts anisotropy of both the speed of light and the electric field of a point charge. The latter leads to an orientation dependence of the length of solid bodies which must be accounted for when interpreting the results of a Michelson–Morley experiment. Using a simple model of ionic solids we show that, in principle, the effect of orientation dependent length can conspire to cancel the effect of an anisotropic speed of light in a Michelson–Morley experiment, thus, complicating the interpretation of the results.  2001 Elsevier Science B.V. All rights reserved. PACS:03.30. +p; 03.50. De
Identification in Quantile Regression Panel Data Models with Fixed Effects and Small T

This paper proposes a moments-based approach to the identification and estimation of panel data quantile regression (QR) models with fixed effects when the number of periods each individual is observed is small. When fixed effects are pure location shifts, I show that the QR model is identified and suggest an estimator based on the recovering of a distribution function from a sequence of its moments. When the covariates are continuously distributed, I show that the QR model can be identified even when fixed effects are allowed to vary across quantiles. Additionally, for a general class of random coefficients panel data models I show that those models are identified when all covariates are continuous, and show how one can identify variables with homogeneous individual responses.
The Effect of Sex of Firstborn Children on Fertility Preferences

Fertility rates around the world are falling at the same time that male-skewed sex ratios at birth are on the rise. The individual fertility choices people make contribute to this inverse relationship, exacerbating the problem of “missing women” as well as a number of other adverse social and economic effects. The decision to have a child is extremely complex. Distilling the interaction between fertility and sex compositional preferences, fertility levels, and gender norms is an important step toward understanding both the reproductive choices people make as well as the formation of fertility preferences. I use individual-level data from the Demographic and Health Survey (DHS) over the period from 1984 through 2018 to perform empirical analysis on the fertility preferences of women and men from over 75 countries. I exploit the exogenous sex of firstborn children and the timing of the DHS survey to explore the marginal effect of having a recently firstborn son or daughter on preferences for total fertility, as well as preferred numbers of sons and daughters. I then test two existing theories how on the sex of existing children influences parity progression: that the sex of existing children matters more in low fertility regimes in explaining subsequent births, and that the sex of children will matter more in places with less egalitarian gender norms. Analysis suggests that the sex of firstborn children plays a role in how fertility preferences update. The strongest preference changes are for ideal number of daughters, although total fertility also change dependent on the sex of one’s firstborn. Finally, I find evidence to support the theory that fertility regimes and gender norms play a role in determining preference updates.
Botryosphaeria rosaceae sp. nov. and B. ramosa, new botryosphaeriaceous taxa from China

A new species of Botryosphaeria (B. rosaceae) is described and illustrated from Rosaceae in China. Phylogenetic analysis based on combined ITS, LSU, tef1-α and TUB loci supported its separation from another species of Botryosphaeria. Morphologically, B. rosaceae was comparable with B. sinensia, but the smaller and slenderer ascospores and conidia as well as the broader host spectrum of B. sinensia differentiate it from B. rosaceae. In addition, Botryosphaeria ramosa was found associated with an Acacia species in this study, which is a new host and first report in the Northern Hemisphere.
Inorganic Nanomaterials; A Brief Overview of the Applications and Developments in Sensing and Drug Delivery

Recent investigations have been shown that inorganic nanomaterials including gold nanoparticles, nonporous and mesoporous silica nanoparticles, magneticnanoparticles, and quantum dots have shown great potential in bioimaging, targeted drug delivery, and cancer therapies. Biocompatibility, ease of synthesis, and ease of surface functionalization are among the significant properties of nonporous and mesoporous silica nanoparticles in various nanomedicine applications. Quantum dots due to their high brightness, long-lasting, wide and continuous absorption spectra, and high fluorescent quantum yield are being used as the new optical probes for bioassays. In addition about gold nanoparticles, the ease of preparation, stability, low cytotoxicity, and high extinction coefficient of light from visible to NIR regions are some properties that introduced them as important candidates in cancer drug and nanocarrier development. As a specific type of inorganic nanomaterials, magnetic nanoparticles that exhibit superparamagnetic are capable of being used as contrast agents in magnetic resonance imaging, site-specific gene and drug delivery, and diagnostic agents in the presence of an external magnetic field. This review will present the physicochemical properties of most popular inorganic nanoparticles and their recent applications in sensing and drug delivery.
Developing Dictyostelium discoideum as a model to study the synthesis and metabolism of inositol pyrophosphates and inorganic polyphosphate

Inositol pyrophosphates and inorganic polyphosphate (polyP) represent two of the most phosphate-rich molecules in the cell. However, the synthesis, metabolism and function of these “high-energy” molecules are not well understood. This work develops the amoeba, Dictyostelium discoideum, as a genetic model to study both classes of molecule. By applying improved polyacrylamide gel electrophoresis (PAGE) techniques, unlabelled inositol pyrophosphates and polyP extracted from D. discoideum have been visualised for the first time. Deletion of a range of inositol phosphate kinases reveals a complex synthetic pathway of the inositol pyrophosphates in the amoeba. Surprisingly, strains lacking the majority of inositol pyrophosphates do not display a dramatic phenotype. However, these cells retain low levels of inositol pyrophosphates. In fact, this work identified at least four enzymes capable of synthesising inositol pyrophosphates in the amoeba, including the novel inositol phosphate kinases IPKA and IPKB. In vitro, both IPKA and IPKB act as specific IP 7 kinases. However, in vivo both enzymes are catalytically flexible and are able to phosphorylate other substrates. In addition, PAGE technology allows the detection of polyP extracted from D. discoideum, revealing the unprecedented increase of polyP during development. Deletion of the Polyphosphate kinase (PPK)1 gene confirms this to be the only PPK in the amoeba. Deletion of PPK has a negative effect on the fitness of the amoeba, a phenotype underpinned by the ability of polyP to regulate primary metabolism. The ppk1-null strain fails to accumulate polyP during development and is defective in spore germination. Loss of polyP during the development of ppk1 is partially compensated by an increase in inositol pyrophosphates. These observations support a model in which there is a functional interplay between inositol pyrophosphates, polyP and primary metabolism.
Pollination ecology of two Dieffenbachia in French Guiana

The reproductive ecology of two species of Dieffenbachia (D. seguine [Jacq.] Schott and D. paludicola N.E. Br. ex Gleason) was studied at the Nouragues field station research in French Guiana. As in other known Dieffenbachia, the two studied species presented the classical cyclocephaline (dynastine scarab beetle) pollination system: Nocturnal anthesis with a strong odor, protogynous and short anthesis over 2 (3) days, female flowers being receptive on the first night and pollen being released on the second night. Inflorescences of D. seguine were visited by two species of scarab beetles (Cyclocephalini, Dynastinae): the dark brown Cyclocephala rustica and the black Erioscelis proba; while Inflorescences of D. paludicola were only visited by Erioscelis proba. Scarab beetles were efficient pollinators resulting in a high reproductive success even if some self-pollination can occur. Original data were gathered on flower and fruit predation leading to pollen and seed loss but their effect of the reproductive success still needs to be quantified.
The Relative Recoverability Of Dna And Rna Profiles From Forensically Relevant Body Fluid Stains

Biological material (fluids or tissues) whether from the victim or suspect is often collected as forensic evidence, and methods to obtain and analyze the DNA found in that material have been well established. The type of body fluid (i.e. blood, saliva, semen, vaginal secretions, and menstrual blood) from which the DNA originated is also of interest, and messenger RNA typing provides a specific and sensitive means of body fluid identification. In order for mRNA profiling to be utilized in routine forensic casework, RNA of sufficient quantity and quality must be obtained from biological fluid stains and the methods used for RNA analysis must be fully compatible with current DNA analysis methodologies. Several DNA/RNA co-extraction methods were evaluated based on the quantity and quality of DNA and RNA recovered and were also compared to standard non-co-extraction methods. The two most promising methods, the in-house developed NCFS co-extraction and the commercially available AllPrep DNA/RNA Mini kit, were then optimized by improving nucleic acid recovery and consistency of CE (capillary electrophoresis) detection results. The sensitivity of the two methods was also evaluated, and DNA and RNA profiles could be obtained for the lowest amount of blood (0.2 µL) and saliva and semen (1 µL) tested. Both extraction methods were found to be acceptable for use with forensic samples, and the ability to obtain full DNA profiles was not hindered by the co-extraction of RNA. It is generally believed that RNA is less stable than DNA which may prevent its use in forensic casework. However, the degradation rates of DNA and RNA in the same biological fluid stain have not been directly compared. To determine the relative stability of DNA and RNA, the optimized NCFS co-extraction protocol was used to isolate DNA and RNA from iv environmentally compromised stains. Dried blood, saliva, and semen stains and vaginal secretions swabs were incubated at set temperatures and outside for up to 1 year. Even at 56°C, DNA and RNA were both stable out to 1 year in the blood and semen stains, out to 3 months (DNA) and 1 year (RNA) in the saliva stains, and out to 6 months (DNA) and 3 months (RNA) in the vaginal secretions swabs. The recoverability of both nucleic acids was reduced when the samples were exposed to increased humidity, sunlight, and rain. In general, DNA and RNA stability was found to be similar with a loss in ability to obtain a DNA or RNA profile occurring at the same time point; however, there were instances where RNA body fluid markers were detected when a poor/no DNA profile was obtained, indicating that RNA in dried stains is sufficiently stable for mRNA body fluid typing to be used in forensic casework.
A quick introduction to Markov chains and Markov chain Monte Carlo (revised version)

These notes are intended to provide the reader with knowledge of basic concepts of Markov chain Monte Carlo (MCMC) and hopefully also some intuition about how MCMC works. For more thorough accounts of MCMC the reader is referred to e.g. Gilks et al. (1996), Gamerman (1997), or Robert and Casella (1999). Suppose that we are interested in generating samples from a target probability distribution π on R and that π is so complex that we can not use direct methods for simulation. Using Markov chain Monte Carlo methods it is, however, often feasible to generate an ergodic Markov chain X1, X2, . which has π as equilibrium distribution, i.e. after a suitable burn-in period m, Xm+1, Xm+2, . provides a (correlated) sample from π which can be used e.g. for Monte Carlo computations. Before we turn to MCMC methods we briefly consider in the next section the concepts of Markov chains and equilibrium distributions.
Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa

Abstract We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9 kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
Rothamsted Repository Download

: Mineral deﬁciencies in livestock are often prevented by using prophylactic supplementation, which is imprecise and ine ﬃ cient. Instead, the trend for increased species diversity in swards is an opportunity to improve mineral concentrations in the basal diet. Currently, there are limited data on the mineral concentrations of di ﬀ erent species and botanical groups, particularly for I and Se, which are among the most deﬁcient minerals in livestock diets. We grew 21 pasture species, including some cultivar / wild type comparisons, of grasses, legumes and forbs, as single species stands in a pot study in a standard growth medium. Herbage concentrations of Co, Cu, I, Mn, Se, Zn, S, Mo and Fe showed no consistent di ﬀ erences between the wild and cultivated types. There were signiﬁcant di ﬀ erences between botanical groups for many minerals tested. Forbs were highest in I and Se, grasses in Mn and legumes in Cu, Co, Zn and Fe. Comparing species concentrations to recommended livestock intakes, the forbs Achillea millefolium , Cichorium intybus and Plantago lanceolata , and the legumes Medicago lupulina , Trifolium hybridum and Lotus corniculatus , appear to be good sources of Co, Cu, I, Se and Zn. Further work is required to ensure these results are consistent in multispecies mixtures, in di ﬀ erent soil types and in ﬁeld trials.