Miracle-dz/UniFAR-FTUs huggingface dataset:
The Noncanonical Roles of Two Primordial Molecules in Flagella

THE NONCANONICAL ROLES OF TWO PRIMORDIAL MOLECULES IN FLAGELLA Xiaoyan Zhu, B.S. Marquette University, 2017 Motile cilia and flagella are ancient organelles that eukaryotic organisms today still rely on to thrive in their natural environment. Not surprisingly, accumulated evidence has shown that the intricate motility machinery, the microtubule-based axoneme, is evolutionarily conserved down to the molecular level. This notion is epitomized by the signature axonemal complex, the radial spoke (RS). The RS is part of a control center conferring the high frequency and tightly regulated movement. Key RS proteins discovered in biflagellate green alga, Chlamydomonas reinhardtii, are also generated by nearly all ciliated organisms, including Homo sapiens. Among them are two subunits from primordial protein families, nucleoside diphosphate kinase (NDK) and heat shock protein (HSP) 40, that are positioned at a critical juncture where two arms merge into a singular stalk in the Y-shaped complex. While it is well accepted that NDKs and HSP40s maintain nucleotide homeostasis and assist HSP70 chaperone in protein folding respectively, these actions fail to explain observations in myriads of vital cellular processes. Using the experimental approaches possible in the biflagellate green algae, genetics in particular, this dissertation discovers non-canonical applications of these two spoke proteins in the assembly and motility of the RS and entire flagellum. The versatility sheds light on the canonical mechanisms, the diverse processes adopting the non-canonical mechanisms, and their preservation since their conscription perhaps by the cell ancestral to all eukaryotes.
Telomere length, telomerase and maintenance of stem cells in the adult zebrafish brain

Neural stem cells (NSCs) are found throughout an animal’s life, but mechanisms allowing their maintenance or leading to their depletion are incompletely understood. Telomerase, avoiding telomere attrition at chromosomal ends, might be implicated in these processes. My project dealt with an involvement of telomerase in adult NSCs, using two adult neurogenic areas in zebrafish (ZF) and the dentate gyrus (DG) in mouse. Telomerase activity and expression in progenitor and stem cell areas was found in the adult ZF brain. Telomere length (TL) measurements revealed no change between proliferating and stem cells or during aging. In contrast, the DG showed distinct TL in stem cell and progenitor populations. Thus a novel correlation between constant TL, telomerase expression and adult neurogenic activity of ZF was revealed. The role of telomerase in adult NSC maintenance will be addressed in a newly identified telomerase-deficient ZF mutant.
Taxonomic Classification of Three Oyster (Ostreidae) Species from Myanmar

ABSTRACT Although oysters are important aquaculture and fishery species as well as keystone species in coastal and estuarine ecology, their global species diversity is not fully understood due to problems of oyster classification. Molecular taxonomy has contributed to oyster classification but not been applied to oysters from many regions including Myanmar. In this study, oysters from Myanmar were collected and subjected to taxonomic analysis with mitochondrial cytochrome oxidase I and 16S rRNA sequences. Sequence analysis reveals that the Myanmar oysters collected in this study belong to three species: Saccostrea malabonensis (Faustino, 1932), a distinct member of the superspecies Saccostrea cucullata (Born, 1778) group; Crassostrea belcheri (Sowerby, 1871), a common species found in Indo-Pacific; and Crassostrea gryphoides tanintharyiensis, a sister subspecies of Crassostrea gryphoides dwarkaensis from Arabian Sea that is different from the fossil species Crassostrea gryphoides (von Schlotheim, 1813). Results of this study highlight the need for molecular taxonomy of oysters from all world oceans to understand and protect the species diversity of this important species group.
Shifts in plant functional strategies over the course of wheat domestication

1. Human selection, changes in environmental conditions and management practices drove the phenotypic trajectory of crops during domestication. The characterization of the crop domestication syndrome lies mostly on reproductive characters. However, biophysical and ecophysiological constraints during vegetative growth are also at play and can strongly impact crop phenotypes. It has been argued that a broadened examination of crop phenotypes through a functional trait-based lens should improve our understanding of the domestication syndrome. 2. We used a collection of 39 genotypes representative of key steps during tetraploid wheat domestication and grew them in a common garden experiment. We quantified the vegetative phenotype of each genotype through the measurements of 13 functional traits related to root, leaf and whole-plant dimensions. 3. In modern cultivars, compared to ancestral forms, leaf longevity was shorter, while net photosynthetic rate, leaf production rate and nitrogen content were higher. Modern cultivars had a shallower root system and exhibited a larger proportion of fine roots, preferring to invest biomass above-rather than below-ground. We found ancestral forms to be integrated phenotypes characterized by coordination between above-and below-ground functioning. Conversely, in modern forms, human selection appeared to have broken this coordination and to have generated a new type of network of trait covariations. 4. Synthesis and applications. The examination of leaf, root and whole-plant traits of wheat accessions indicated a strong shift in plant functional strategies over the course of domestication. Elite genotypes tended to better optimize resource-use acquisition strategies than ancestral ones. The characterization of the crop phenotype based on vegetative traits thus suggests a much more complete domestication syndrome. Our findings highlight the benefits of using a functional trait-based characterization of crop phenotypes to document the extent of domestication syndrome and to further advance the agroecological management of cereals.
Beyond quasi-stationarity: Designing time-frequency representations for speech signals

This work addresses two related questions. The first is what joint time-frequency energy representations are most appropriate for speech signals, in particular, for the analysis of formant structure. Quasi-stationarity is not assumed, since it neglects dynamic regions. A set of desired properties is proposed, and a subclass of the quadratic transforms that best meets these criteria is derived, which consists of two-dimensionally smoothed Wigner distributions with gaussian kernels. The second question addressed is how to obtain suitable symbolic descriptions of the phonetically relevant features in these time-frequency surfaces. We propose time-frequency ridges in these surfaces, the 2-D analog of spectral peaks, which can be found by examining the derivatives of the time-frequency surface produced above.
Antihepatotoxic Effect of Some Natural Antioxidants Against Liver Damage Induced By CCl4 in Rats

In recent years, the etiology of many diseases was attributed to increased oxidative stress and the role of diet or dietary constituents as natural antioxidants was magnified. The present study aims to investigate the antihepatotoxic effect of two antioxidant rich edible plants namely; Cichorium intybus (chicory) and Rhus coriaria (sumac) against carbon tetrachloride (CCl4) liver toxicity in rats as a model of increased oxidative stress. A model of chronic hepatic injury in rats was induced by carbon tetrachloride (CCl4) and then, the impact of chicory and sumac to antagonize this toxicity was evaluated. Four groups, each of eight rats were included. All animals except those in group one were administered orally with CCl4 (2 ml /Kg b.w.) in corn oil 1:1 V/V twice a week for four weeks. Group one was given only corn oil and served as a negative control group. Groups 2, 3 and 4 were pretreated with CCl4. Then the feeding experiment was started. Group one and group two were fed on standard diet so that group one was a negative control and group two was a positive control. Group three was fed on a standard diet + 150 g chicory per Kg diet while group four was given standard diet + 150 g sumac per Kg diet. After an experimental period of 8 weeks, blood was withdrawn after overnight fasting and biochemical parameters were analyzed. Activity of serum ALT and AST, serum total protein, serum albumin and serum glucose were estimated. Activity of antioxidant enzymes in liver tissue including superoxide dismutase, glutathione peroxidase and catalase were analyzed. Histopathological examination for liver tissue was done. Results obtained from this study revealed that there was an elevation in activities of s. AST, s. ALT, liver catalase and liver glutathione peroxidase as well as the concentration of s. glucose while there was a decline in the levels of s. total protein, s. albumin and the activity of liver superoxide dismutase in the positive control group. Also, the histopathological examination of liver tissue showed abnormal alterations. All these alternations in the previous parameters were more or less normalized in the groups that were fed on chicory and sumac. Thus it can be concluded that, addition of chicory and sumac to the diet can counteract the hepatotoxicity of CCl4. Consequently, chicory and sumac, those nutrients with high medicinal value, can be used for liver disorders as adjuvant therapy and for those who are exposed to increased oxidative stress that may affect their hepatic function.
Scale and organismal form : an ecological genetic perspective

Spatial variation in skull form was analyzed for white-tailed deer (Odocoileus virginianus) from eight sites within three physiographic regions [upper (UCP) and lower coastal plain (LCP) and barrier islands (BI)] of the Southeast. Components of skull form vary among the physiographic regions. Deer from BI were smaller than mainland deer, and together with LCP deer, exhibited increased fluctuating asymmetry (FA) compared to UCP deer. LCP deer exhibited decreased shape variation compared to animals from either the UCP or BI. Form components for sites within regions appeared to be influenced more by recent processes such as hunting regime, restocking effort and habitat change. Evidence for maintaining the subspecific status of O. v. hiltonensis appeared weak. Fluctuating asymmetry occurs on a smaller scale than the original character and measurement error represents a significant proportion of FA. Mixed-model ANOVA allows group-level FA to be corrected for measurement. Currently, individual-level FA estimates include measurement error. Best linear unbiased predictors (BLUP) can provide error-corrected estimates of individual FA. A simulated data set showed BLUP estimates were more efficient than arithmetic means at error reduction. An analysis of a Gambusia hybridization study showed the usefulness of individual-level FA analysis. Form is a composite character and cannot be measured. Path analysis was utilized to develop individual-level models of skull form evolution for the hispid cotton rat (Sigmodon hispidus). Path coefficients are essentially selection coefficients and translate into relative time scales. Structural size operated over the shortest time scale in six models and an intermediate scale in two models. Mass operated over the shortest time scale in four models and an intermediate scale in four models. Age operated over the shortest time scale in four models but sex operated over the shortest time scale in one model and an intermediate scale in the remaining three. Density class operated on an intermediate time scale in all models. Heterozygosity class acted over intermediate (2 models) or long (6 models) time scales. Path models allowed the identification of covariates when utilizing form as a biomarker. Structural size, mass and age together accounted for 89.8% to 95.7% of explained variation. INDEX WORDS: Form, Fluctuating Asymmetry, Size, Shape, Geometric Morphometrics, Landmarks, Mixed-Model ANOVA, Best Linear Unbiased Predictor, Path Analysis, Measurement Error, Simulation, Gambusia affinis, Gambusia heterochir, Odocoileus virginianus, Sigmodon hispidus
Effects on the Discrete Spectrum of the Finite Sequences with Different Zeros-Padding Modes

Zeros-padding can be operated in different ways. The zeros-block can be inserted to the head, the tail or any in-between position of the finite sequences. Zeros-paddingcan also be operated in the interpolation mode. The effects of these different zeros-padding ways on the discrete spectrum of the finite sequences are investigated in this paper. The corresponding verification procedure and results with MATLAB are detailed addressed.
Comparative Performance of Three Tropical Turfgrasses Digitaria longiflora, Axonopus compressus and St. Augustinegrass under Simulated Shade Conditions

Shade affects turf quality by reducing light for photosynthesis. The shade tolerance of the tropical grasses, Digitaria longiflora and Axonopus compressus were evaluated against Stenotaphrum secundatum (St. Augustinegrass). The grasses were established under shade structures that provide 0%, 50%, 75% or 90% shade level for 30 days. A suite of leaf traits, recorded from similar leaf developmental stage, displayed distinct responses to shade conditions. Leaf length, relative to control, increased in all three species as shade level increased. The mean leaf extension rate was lowest in St. Augustinegrass (80.42%) followed by A. compressus (84.62%) and D. longiflora (90.78%). The higher leaf extension rate in D. longiflora implied its poor shade tolerance. Specific leaf area (SLA) increased in all species with highest mean SLA increase in D. longiflora (348.55 cm2 mg−1) followed by A. compressus (286.88 cm2 mg−1) and St. Augustinegrass (276.28 cm2 mg−1). The highest SLA increase in D. longiflora suggested its lowest performance under shade. The percent green cover, as estimated by digital image analysis, was lowest in D. longiflora (53%) under 90% shade level compared to both species. The relative shade tolerance of the three turfgrasses could be ranked as St. Augustinegrass > A. compressus > D. longiflora.
Understanding Poor Storage Potential of Recalcitrant Seeds

Trees producing recalcitrant seeds are dominant among Asian (89%) and neo-tropical species (44%), but are rare among African tree species (9%). Among the families, Dipterocarpaceae is the most populous with 98% of recalcitrant species, followed by Meliaceae (17%), Moraceae (14%), Malvaceae (8%), Rubiaceae (7%) and Bignoniaceae (3%). Since desiccationsensitive recalcitrant seeds are shed from the tree after maturation, with high moisture content, high metabolic activity and poor storage potential, it leads to significant challenge for ex situ conservation through seed-gene bank. A general understanding of the mechanisms underlying the poor viability potential of recalcitrant seeds is important to redefine our research programmes on these desiccation-intolerant seeds. There are three general categories of damage that may take place in recalcitrant seeds, eventually causing loss of viability: (i) mechanical damage, (ii) metabolism-induced damage, and (iii) macromolecular denaturation. This article discusses the occurrence of these three categories of damage, in the light of the various biochemical and structural changes reported in the different recalcitrant seeds, relative to (i) storage temperature, (ii) seed moisture content and (iii) rate of seed drying. Among these factors, maintenance of appropriate storage temperature is viewed as the most appropriate way to contain all the three types of damage. Storage of seeds in lowest suitable temperature is known to restrain the rate of moisture loss from seeds, thereby reducing mechanical damage and macromolecular denaturation; further, it can also minimize aberrant metabolism, eventually reducing metabolism- induced damage. Thus, the most practical way to extend the storage life of intact recalcitrant seeds is by storing them at lower temperatures, wherein the above damages can be reduced and at the same time chilling or freezing injury may not occur. Nevertheless, the 'lowest temperature' which is most suitable for seeds of a particular recalcitrant species should be standardized through dedicated research.
Site‐directed mutagenesis and footprinting analysis of the interaction of the sunflower KNOX protein HAKN1 with DNA

The interaction of the homeodomain of the sunflower KNOX protein HAKN1 with DNA was studied by site‐directed mutagenesis, hydroxyl radical footprinting and missing nucleoside experiments. Binding of HAKN1 to different oligonucleotides indicated that HAKN1 prefers the sequence TGACA (TGTCA), with changes within the GAC core more profoundly affecting the interaction. Footprinting and missing nucleoside experiments using hydroxyl radical cleavage of DNA showed that HAKN1 interacts with a 6‐bp region of the strand carrying the GAC core, covering the core and nucleotides towards the 3′ end. On the other strand, protection was observed along an 8‐bp region, comprising two additional nucleotides complementary to those preceding the core. Changes in the residue present at position 50 produced proteins with different specificities. An I50S mutant showed a preference for TGACT, while the presence of lysine shifted the preference to TGACC, suggesting that residue 50 interacts with nucleotide(s) 3′ to GAC. Mutation of Lys54→Val produced a protein with reduced affinity and relaxed specificity, able to recognize the sequence TGAAA, while the conservative change of Arg55→Lys completely abolished binding to DNA. Based on these results, we propose a model for the interaction of HAKN1 with DNA in which helix III of the homeodomain accommodates along the major groove with Arg55, Asn51, Lys54 and Ile50, establishing specific contacts with bases of the GACA sequence or their complements. This model can be extended to other KNOX proteins given the conservation of these amino acids in all members of the family.
Evaluation of machine learning methods to predict peptide binding to MHC Class I proteins

Binding of peptides to Major Histocompatibility Complex (MHC) proteins is a critical step in immune response. Peptides bound to MHCs are recognized by CD8+ (MHC Class I) and CD4+ (MHC Class II) T-cells. Successful prediction of which peptides will bind to specific MHC alleles would benefit many cancer immunotherapy appications. Currently, supervised machine learning is the leading computational approach to predict peptide-MHC binding, and a number of methods, trained using results of binding assays, have been published. Many clinical researchers are dissatisfied with the sensitivity and specificity of currently available methods and the limited number of alleles for which they can be applied. We evaluated several recent methods to predict peptide-MHC Class I binding affinities and a new method of our own design (MHCnuggets). We used a high-quality benchmark set of 51 alleles, which has been applied previously. The neural network methods NetMHC, NetMHCpan, MHCflurry, and MHCnuggets achieved similar best-in-class prediction performance in our testing, and of these methods MHCnuggets was significantly faster. MHCnuggets is a gated recurrent neural network, and the only method to our knowledge which can handle peptides of any length, without artificial lengthening and shortening. Seventeen alleles were problematic for all tested methods. Prediction difficulties could be explained by deficiencies in the training and testing examples in the benchmark, suggesting that biological differences in allele-specific binding properties are not as important as previously claimed. Advances in accuracy and speed of computational methods to predict peptide-MHC affinity are urgently needed. These methods will be at the core of pipelines to identify patients who will benefit from immunotherapy, based on tumor-derived somatic mutations. Machine learning methods, such as MHCnuggets, which efficiently handle peptides of any length will be increasingly important for the challenges of predicting immunogenic response for MHC Class II alleles. Author Summary Machine learning methods are a popular approach for predicting whether a peptide will bind to Major Histocompatibility Complex (MHC) proteins, a critical step in activation of cytotoxic T-cells. The input to these methods is a peptide sequence and an MHC allele of interest, and the output is the predicted binding affinity. MHC Class I and II proteins bind peptides of 8-11 amino acids and 16-26 amino acids respectively. This has been an obstacle for machine learning, because the methods used to date can only handle fixed-length inputs. We show that a recently developed technique known as gated recurrent neural networks can handle peptides of variable length and predict peptide-MHC binding as well or better than existing methods, at substantially faster speeds. Our results have implications for the hundreds of MHC alleles that cannot be predicted with current methods.
CDC Horizon forage pea

Warkentin, T. , Kostuik, J., Klassen, E. , Barlow, B. , Ife, S. , Tar'an, B. and Vandenberg, A. 2012. CDC Horizon forage pea. Can. J. Plant Sci. 92: 207-209. CDC Horizon is a forage pea (Pisum sativum L.) cultivar released in 2010 by the Crop Development Centre, University of Saskatchewan, for distribution to Select seed growers in Saskatchewan and Alberta through the Variety Release Program of the Saskatchewan Pulse Growers. CDC Horizon has a semileafless leaf type, high biomass production, good biomass quality, good seed yield, and resistance to powdery mildew (caused by Erysiphe pisi Syd.). It has superior lodging resistance to the check cultivars Trapper, 40-10 and CDC Sonata, but with slightly greater seed weight than Trapper and 40-10. CDC Horizon had similar lodging resistance and grain yield compared with the field pea check cultivar CDC Minuet. CDC Horizon had similar overall performance to CDC Leroy and CDC Tucker, but with 8-9% greater forage dry matter production, respectively.