Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Phylogeny of the Grassland Leafhopper Tribe Hecalini (Hemiptera: Cicadellidae: Deltocephalinae)

Abstract The phylogenetic status and relationships of the globally distributed grassland leafhopper tribe Hecalini were explored by analyzing a DNA sequence dataset comprising three gene regions (nuclear 28S rDNA, histone H3, 12S mtDNA) for 14 genera and 29 species plus 9 outgroups. Bayesian, maximum likelihood, and maximum parsimony analyses recovered similar trees and supported the monophyly of Hecalini and its two included subtribes, but excluded the Oriental genus Hecalusina He, Zhang & Webb, the position of which was poorly resolved among the included outgroup taxa. Within subtribe Hecalina, the analysis recovered two major lineages, one including only New World taxa and the other including a second New World clade nested within a larger lineage comprising taxa from the Afrotropical, Oriental, and Australian regions. The large, widely distributed genus Hecalus was not recovered as monophyletic. Species of this genus grouped into two separate, noncontiguous clades, one North American and the other comprising African, Australian, and Oriental species.
Chapter 8 Illegitimate Recombination

In the absence of any real understanding of ordinary recombination it may seem gratuitous to invoke an even less comprehended event to be known as illegitimate recombination. Yet there are reassociations of nucleotide sequences that apparently do not fit into the framework of classical recombination. These invite attention to yet another attribute of DNA. General recombination (Chapter 7) involves alignment of genetic homologues (DNA molecules in lower organisms, chromosomes in eukaryotes) and rejoining of material from corresponding segments of two genetically marked parents to give end products whose nucleotide sequences are the same as those in the “parent” molecules, except for the markers. Physical breakage and rejoining of DNA are involved (Taylor, 1965; Meselson, 1967). The process is relatively frequent and extremely accurate in that no losses are incurred. It depends on substantial nucleotide-sequence homology, but its frequency can be modified by the few differences in sequence introduced as genetic markers (Yanofsky et al., 1964; Norkin, 1970). Included under general recombination are examples of unequal crossing over that result from asymmetric pairing between homologues containing duplicated segments (see Hershey, 1970). Another order of genetic event is grossly perceived as rare, haphazard, and not obviously dependent upon genetic homology. In higher organisms its effects are visible as inversions, deletions, and translocations of parts of chromosomes. In bacteria and bacteriophages it is detected as new juxta-positions of genetic markers, some of which have recently been correlated with rearrangements in DNA made visible in the electron microscope (Hradecna and Szybalski, 1969; Fiandt et.
An evidence-based approach to globally assess the covariate-dependent effect of MTHFR SNP rs1801133 on plasma homocysteine: a systematic review and meta-analysis

Background The single nucleotide polymorphism (SNP) of the gene Methylenetetrahydrofolate Reductase (MTHFR) C677T (or rs1801133) is the most established genetic factor that increases plasma total homocysteine (tHcy) and consequently results in hyperhomocysteinemia. Yet given the limited penetrance of this genetic variant, it is necessary to individually predict the risk of hyperhomocysteinemia for a rs1801133 carrier. Objective We hypothesized that variability of this genetic risk is largely due to the presence of factors (covariates) that serve as effect modifiers and/or confounders, such as folic acid (FA) intake, and aimed to assess this risk in the complex context of these covariates. Design We systematically extracted from published studies the data of tHcy, rs1801133, and any previously reported rs1801133 covariates. The resulting meta-dataset was first used to analyze the covariates’ modifying effect by meta regression and other statistical means. Subsequently, we stratified tHcy data by the rs1801133 genotypes and analyzed under each genotype the variability of the risk resulted from the covariates’ confounding. Results The dataset contains data of 36 rs1801133 covariates that were collected from 114,448 subjects and 249 qualified studies, among which 6 covariates (sex, age, race, FA intake, smoking, and alcohol consumption) are the most frequently informed and therefore included for statistical analysis. The effect of rs1801133 on tHcy exhibits significant variability that can be attributed to effect modification and, to a larger degree, confounding by these covariates. Via statistical modeling, we predicted the covariate-dependent risk of tHcy elevation and hyperhomocysteinemia in a systematic manner. Conclusions we demonstrated an evidence-based approach that globally assesses the covariate-dependent effect of rs1801133 on tHcy. The results should assist clinicians in interpreting the rs1801133 data from genetic testing for their patients. Such information is also important for the public that increasingly receives genetic data from commercial services without interpretation of its clinical relevance.
Endodermal differentiation is reconstructed by coordination of two parallel signaling systems derived from the stele in roots

The plant roots represent the exquisitely controlled cell fate map in which different cell types undergo a complete status transition from stem cell division and initial fate specification, to the terminal differentiation. The endodermis is initially specified in meristem but further differentiates to form Casparian strips (CSs), the apoplastic barrier in the mature zone for the selective transport between stele and outer tissues, and thus is regarded as plant inner skin. In the Arabidopsis thaliana root the transcription factors SHORTROOT (SHR) regulate asymmetric cell division in cortical initials to separate endodermal and cortex cell layer. In this paper, we utilized synthetic approach to examine the reconstruction of fully functional Casparian strips in plant roots. Our results revealed that SHR serves as a master regulator of a hierarchical signaling cascade that, combined with stele-derived small peptides, is sufficient to rebuild the functional CS in non-endodermal cells. This is a demonstration of the deployment of two parallel signaling systems, in which both apoplastic and symplastic communication were employed, for coordinately specifying the endodermal cell fate.
The plastid-nucleus located DNA/RNA binding protein WHIRLY1 regulates microRNA-levels during stress

In this article a novel mechanism of retrograde signaling by chloroplasts during stress is described. This mechanism involves the DNA/RNA binding protein WHIRLY1 as a regulator of microRNA levels. By virtue of its dual localization in chloroplasts and the nucleus of the same cell, WHIRLY1 was proposed as an excellent candidate coordinator of chloroplast function and nuclear gene expression (Grabowski et al., 2008; Foyer et al., 2014). In this study the putative involvement of WHIRLY1 in stress dependent retrograde signaling was investigated by comparison of barley (Hordeum vulgare L., cv. Golden Promise) wild-type and transgenic plants with an RNAi-mediated knockdown of WHIRLY1. In contrast to the wild type, the transgenic plants were unable to cope with continuous high light conditions. They were impaired in production of several microRNAs mediating post-transcriptional responses during stress (Kruszka et al., 2012, Sunkar et al., 2012). The results support a central role of WHIRLY1 in retrograde signaling and underpin a so far underestimated role of microRNAs in this process.
Evaluation of two MiniSTR loci mutation events in five Father-Mother-Child trios of Yoruba origin

The robustness of short tandem repeats for use in forensic and paternity depends on their high polymorphism and mutation rate. This study tried to determine the event of mutation of two miniSTR loci in the Yoruba population. Blood samples were collected from five father-motherchild trios of Yoruba origin. Two DNA extraction methods, an homemade method and Zymogen gDNA kit were tested for yield and purity for use in the STR assay. The DNA were amplified and resolved on 4% Agarose gel. The first DNA extraction method yielded an average DNA concentration of 1399 ng/μl and while the Kit yielded 984.1 ng/μl; absorbence quotient at 260/280 of 1.78 and 1.55 respectively. Locus D1GATA113 was detected in the father and mother of two families; A and C. D5S2500 was detected only in the male parent (father) in family D. DNA extracted using any of the two methods in this study is appriopriate for use in STR mutation assay but the PCR condition for mutation miniSTR loci among the yoruba still requires extensive optimization. Keywords : DNA extraction Methods, miniSTRs, mutation, Yoruba
Excitatory Inputs to Starburst Amacrine Cells: Adaptation, Computations, Development

The retina in our eyes is full of tiny neuronal computers, cells with diversely elaborate dendritic arbors that transform, sort, and integrate information about light bouncing off of objects in the world. The focus of this dissertation was to understand how dendrites of one type of cell in the retina, called the starburst amacrine cell, perform computations on visual information. The starburst amacrine cell is a part of the retina’s “direction selective circuit”, a model system for studying the cellular and synaptic implementation of a neural computation. Within this circuit, the starburst amacrine cells are responsible for detecting the direction of motion in the environment—right, left, up, or down—and cueing downstream cells, which pass on this information about motion direction to the brain. To begin, Chapter I presents the recent advances in our understanding of how the direction selective circuit works. Then, the experimental investigations presented in this dissertation attempt to clarify three issues about starburst amacrine cells. First, I examined the precise role of starburst amacrine cells in the direction selective circuit by altering their response properties and investigating how the performance of the circuit changes (Chapter II). I found that perturbations to the excitatory inputs to starburst amacrine cells using either visual adaptation of the retina or a chemo-genetic manipulation substantially altered the computational output of the entire circuit. Second, I described how the cells’ excitatory synaptic inputs are organized and contribute to the cells’ computations (Chapter III). I discovered that the precise distribution of excitatory inputs to the starburst amacrine cells shapes the cells’ ability to detect motion direction. Because of the elaborate structure of the dendrites, this precise arrangement is necessary for the electrical signals coming at different times and onto different dendritic locations to be integrated together in a direction-dependent fashion. Third, I investigated the development of the excitatory inputs to starburst amacrine cells and starburst amacrine cells’ velocity tuning (Chapter IV). These preliminary experiments provide a framework for further inquiry in these areas. Together, these experiments reveal how anatomical wiring and electrical properties of neurons in the retina produce exquisite computational abilities.
The effect of conformational transition of gelatin-polysaccharide polyelectrolyte complex on its functional properties

The blends of gelatin and shear-thinning hydrocolloids (guar gum, kappa-carrageenan and xanthan gum) were examined to determine the effect of the conformational change on the functional properties of the solutions. The polyelectrolyte complexes of 0.5% gelatin/0.5% polysaccharide in 70 mM KCl or 70 mM NaCl were investigated by the laboratory rheometer and conductivity meter in the temperature range 25 - 45 °C. The rheological data were fitted by the power-law and Herschel-Bulkley model to obtain the flow parameters. The functional properties of the samples were substantially affected by the conformational change of the polysaccharide, as well as by the type of the hydrocolloid and salt solution. There was an evident change of viscosity and conductivity of the solutions upon heating, corresponding to the helix-coil transition of the polysaccharide at temperature about 35 °C. The type of the salt solvent had an effect on the gelation properties of the samples. Gelatin/kappa-carrageenan blend in NaCl provided a gel of high consistency at ambient temperature (20 - 25 °C), whereas the blend in KCl did not gel in the studied temperature range. The potential stability of the blends was determined by zeta-potential analysis. The low values of ζ-potential indicate that the gelatin/polysaccharide blends are electrically unstable systems which tend to coagulate. The mixtures of gelatin/polysaccharide electrostatic complexes may have a great potential in many food applications.
Community structure and distribution of culturable bacteria in soil along an altitudinal gradient of Tianshan Mountains, China

ABSTRACT The Tianshan Mountains hold important and complex ecosystems. They host some unique biological resources, especially some microbes that have very crucial application values. In this study, the composition and distribution of bacterial communities from soil at different elevations of the Tianshan Mountains, China, were investigated using culture-based and molecular-based methods. The relationship between the abundance of culturable bacteria and environmental factors was also analysed. A total of 121 isolates showing different phenotypic characteristics were obtained from soil and identified by 16S rRNA gene sequencing analysis. All strains were assigned to four phyla: Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Actinobacteria and Proteobacteria were the dominating bacterial phyla; Arthrobacter, Pseudomonas and Sphingomonas were the most prevalent genera. The community structures of culturable bacteria were significantly different at different elevations, there being some common bacterial communities and some unique groups at each altitude. The principal component analysis (PCA) showed that the abundance of culturable bacterial communities has a significant positive correlation with the NO3− content in the soil. It indicated that NO3− was a better predictor of soil culturable bacterial abundance in this region. The strains isolated from alpine soil in this study are not only an invaluable part of microbial diversity, but also good candidates for further elucidating the interaction relationship between plants and microorganisms.
Characterization of physicochemical composition, microbiology, sensory evaluation and microscopical attributes of sweetened condensed milk

According to Brazilian legislation, SCM is manufactured by removing part of water from a mixture of milk and sucrose or glucose by evaporation. During subsequent cooling of the product after sugar addition and evaporation, lactose crystallization is induced. Today, there are considerable variations in the methods and equipment used to manufacture SCM. The stages of the process include heat treatment, homogenization, addition of sugar (liquid or dry, before or during concentration), concentration (or hydration if powder is used), seeding and cooling (Tan, 2009).
How to fight multiple enemies: target-specific chemical defences in an aposematic moth

Animals have evolved different defensive strategies to survive predation, among which chemical defences are particularly widespread and diverse. Here we investigate the function of chemical defence diversity, hypothesizing that such diversity has evolved as a response to multiple enemies. The aposematic wood tiger moth (Arctia plantaginis) displays conspicuous hindwing coloration and secretes distinct defensive fluids from its thoracic glands and abdomen. We presented the two defensive fluids from laboratory-reared moths to two biologically relevant predators, birds and ants, and measured their reaction in controlled bioassays (no information on colour was provided). We found that defensive fluids are target-specific: thoracic fluids, and particularly 2-sec-butyl-3-methoxypyrazine, which they contain, deterred birds, but caused no aversive response in ants. By contrast, abdominal fluids were particularly deterrent to ants, while birds did not find them repellent. Our study, to our knowledge, is the first to show evidence of a single species producing separate chemical defences targeted to different predator types, highlighting the importance of taking into account complex predator communities in studies on the evolution of prey defence diversity.
Plant recolonization of reclamation areas from patches of salvaged forest floor material

Question Understory development is a great challenge in the restoration of many forest sites, particularly when sources of vegetation propagules are scarce. Can placement of propagule-rich soil patches within reclaimed landscapes otherwise covered with propagule-poor material promote the dispersal of vegetation from the patches into the surrounding areas? Location A large reclamation site located in the Canadian (Alberta) boreal forest. Method Patches of propagule-rich forest floor material were placed within a matrix of propagule-poor peat material. Vegetation assessments (cover estimates, seed rain) were done surrounding these patches in the third and fourth growing seasons. Results There was significant egress of species from the patches into the peat after four growing seasons and overall species associated with the patches had higher cover in the peat than the species that were associated with the peat itself. While wind-dispersed herbaceous species from the patches were found at the leading edge of the egressing community, most species used vegetative propagation resulting in short egress distances. Several patch associated species were found in seed rain collected on the peat areas but were not observed in this material, suggesting seedbed limitations. Conclusion Despite the relatively short distance of egress, this experiment suggests that placement of propagule-rich soil material within reclaimed landscapes will promote egress into adjacent propagule-poor soil material. This article is protected by copyright. All rights reserved.
The role of Culex pipiens mosquitoes in transmission of West Nile virus in Europe

West Nile virus (WNV) is maintained in a natural transmission cycle between mosquito vectors and bird hosts. However, mosquitoes can also transmit WNV to mammals, such as humans and horses, which may result in disease. In Europe, such cases of WNV disease are yearly recurring in southern and central Europe, but have not been detected in northern Europe. The absence of WNV outbreaks in northern Europe may be explained by lowered vector competence of the main vector for WNV: the northern house mosquito, Culex (Cx.) pipiens. The aim of this thesis was, therefore, to investigate the role of Cx. pipiens mosquitoes in transmission of WNV in Europe, in order to understand differences in WNV circulation between northern and southern Europe. The species Cx. pipiens consists of two biotypes, pipiens and molestus, which can form hybrids. Both biotypes and their hybrids are morphologically identical but differ in their behaviour, which may have consequences for WNV transmission. In this thesis, the Cx. pipiens biotype composition was investigated in The Netherlands, and more broadly at the European scale. These studies revealed that both biotypes and their hybrids are present throughout The Netherlands, and that there is a shift towards relatively more biotype pipiens mosquitoes at northern latitudes in Europe. The next step was to assess vector competence of these northern European biotypes and their hybrids, and to make a direct comparison with vector competence of a southern European population. Both biotypes and their hybrids originating from The Netherlands are competent vectors for WNV. Interestingly, no differences in vector competence were found between a Dutch and Italian biotype pipiens population. However, both studies revealed that low temperatures of 18 °C are an important limiting factor for WNV transmission. A more in-depth study on the effects of WNV on the host-seeking behaviour of biotype pipiens mosquitoes revealed that WNV infection reduces the host-seeking response towards host odour, but that other fitness parameters (e.g. flight activity, blood-feeding, and survival) are not affected. When results from the biotype composition and vector competence studies were included in a newly developed R0 model, it becomes clear that biotype pipiens is the main contributor to WNV transmission. The results presented in this thesis show that the Cx. pipiens biotypes and their hybrids are present throughout The Netherlands, and that they can transmit WNV under favourable climatic conditions. The absence of WNV outbreaks in northern Europe can most likely be explained by low temperature which has a negative effect on mosquito abundance, vector competence, and the duration of the infectious period. When considering the outcomes of this thesis in the light of climate change, northern European countries such as The Netherlands should be prepared for future WNV transmission.
Optimization and toxocologic effects of cancer immuno-electrogene therapy using a tumor-targeted interleukin-12 gene construct

This dissertation includes a comprehensive current review of reversible electroporation (EP) and other related physical gene transfection techniques; an overview of results of electrochemogene therapy (ECGT) used to treat naturally occurring spontaneous neoplasms in dogs; and the results of comprehensive, pre-clinical toxicology testing of electrogene therapy (EGT) of a tumor-targeted version of interleukin-12 (IL-12) in mice. Intralesional bleomycin (BLM) and feline interleukin-12 (fIL-12) DNA injection combined with trans-lesional EP resulted in complete cure of two recurrent oral squamous cell carcinomas and an acanthomatous ameloblastoma in a series of six cases of spontaneous neoplasia in pet dogs. The three remaining dogs, which had no other treatment options, had partial responses to ECGT. One of these dogs had mandibular melanoma with pulmonary and lymph node metastases; one dog had cubital histiocytic sarcoma with spleen metastases; and one had soft palate fibrosarcoma. Treatment of all six dogs was associated with minimal side effects, was easy to perform, was associated with repair of bone lysis in cured dogs; improved the quality of life for dogs with partial responses; and extended overall survival time. For the purpose of meeting pre-clinical safety requirements for an Investigational New Drug filing, we assessed the safety of tumor-targeted interleukin-12 (ttIL-12) when administered by EGT in C3H/HeJ mice by identifying an initial safe dose for human dose escalation schemes, toxicity target organs, markers of toxicity, and toxicity reversibility. Dystrophic cardiac calcification in older, 5 μg ttIL-12-treated mice was the only serious toxicity. Based on these results and the lack of any effect on wound healing when combined with surgery, low-intensity EGT with ttIL-12 appears to be safe and well tolerated as both a single treatment modality and when combined with surgical tumor resection.