Miracle-dz/UniFAR-FTUs huggingface dataset:
Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

An important goal of the angiosperm systematics community has been to develop a shared approach to molecular data collection, such that phylogenomic data sets from different focal clades can be combined for meta-studies across the entire group. Although significant progress has been made through efforts such as DNA barcoding, transcriptome sequencing, and whole-plastid sequencing, the community current lacks a cost efficient methodology for collecting nuclear phylogenomic data across all angiosperms. Here, we leverage genomic resources from 43 angiosperm species to develop enrichment probes useful for collecting ~500 loci from non-model taxa across the diversity of angiosperms. By taking an anchored phylogenomics approach, in which probes are designed to represent sequence diversity across the group, we are able to efficiently target loci with sufficient phylogenetic signal to resolve deep, intermediate, and shallow angiosperm relationships. After demonstrating the utility of this resource, we present a method that generates a heat map for each node on a phylogeny that reveals the sensitivity of support for the node across analysis conditions, as well as different locus, site, and taxon schemes. Focusing on the effect of locus and site sampling, we use this approach to statistically evaluate relative support for the alternative relationships among eudicots, monocots, and magnoliids. Although the results from supermatrix and coalescent analyses are largely consistent across the tree, we find support for this deep relationship to be more sensitive to the particular choice of sites and loci when a supermatrix approach as employed. Averaged across analysis approaches and data subsampling schemes, our data support a eudicot-monocot sister relationship, which is supported by a number of recent angiosperm studies.
SEXUAL DIMORPHISM IN THE GENITAL MORPHOLOGY OF YOUNG AMERICAN ALLIGATORS, ALLIGATOR MISSISSIPPIENSIS

Egg temperature during incubation determines sex in the American alligator (Al- ligator mississippiensis). Although juveniles and adults (>0.6 m) may be sexed effectively, smaller alligators are reportedly difficult to sex. We developed a method for sexing young alligators by inspection of the genitalia and quantified effects of incubation temperature on genital morphology. We predicted the sex of a hatchling by examining its genitalia within the cloaca. Our predictions were verified by inspecting the gonads macroscopically and histologically. The male clitero-penis typically is red, round, and large (mean length = 4.1 mm) in comparison with the female organ (mean length = 2.8 mm), which is white and smaller. Sex identification by cloacal examination was highly reliable (accuracy 296%). Clitero-penis dimensions of hatchlings incubated at 29, 31, 32, 33, and 34 C increased significantly with increasing incubation temperature, both within and between sexes. Based on differences apparent in hatchlings, incubation temperature seems to affect genital differentiation during development in a graded fashion. During posthatching growth, size increased rapidly in males versus females; based on previous studies, we think that these changes can be attributed to ontogenetic changes in the levels of circulating sex steriods. Observable size differences in the genitalia of males versus females permit an accurate, noninvasive diagnosis of sex in young alligators. Sex identification by this method will facilitate experimental study, as well as the management of wild and captive alligators.
Evolution of offspring desertion in a stickleback fish

Abstract:Parental care is expected to evolve when its principal benefit, increased survival of offspring, outweighs the cost of diminished future reproduction of the care giver(s). All sticklebacks (Gasterosteidae) show male parental care, but the males of a newly described form with iridescent white sexual colors (“white” stickleback) are here shown to be emancipated; they actively remove embryos from the nest after fertilization and disperse them over plumes of filamentous algae. Experiments show that the emancipation behaviors are heritable and that desertion apparently imposes little cost in environments with abundant filamentous algae. This evolutionary reversal from paternal care to desertion is the first reported for fishes. It is consistent with models of the adaptive evolution of parental care, and it illustrates that traits which exhibit a long phylogenetic stasis may nevertheless retain sufficient underlying variance to permit adaptive evolution under appropriate ecological conditions.
The effects of temperature on hatching and survival of northern rock sole larvae (Lepidopsetta polyxystra)

Northern rock sole (Lepidopsetta polyxystra) is a commercially important flatfish in Alaska and was recently classified as a distinct species from southern rock sole (L. bilineata). Taxonomic and vital rate data for northern rock sole are still not fully described, notably at early egg and larval stages. In this study, we provide new taxonomic descriptions of late-stage eggs and newly hatched larvae, as well as temperature-response models of hatching (timing, duration, success), and larval size-at-hatch and posthatch survival at four temperatures (2°, 5°, 9°, and 12°C). Time-to-first-hatch, hatch cycle duration, and overall hatching success showed a negative relationship with temperature. Early hatching larvae within each temperature treatment were smaller and had larger yolk sacs, but larvae incubated at higher temperatures (9° and 12°C) had the largest yolk reserves overall. Despite having smaller yolks, size-at-hatch and the maximum size achieved during the hatching cycle was highest for larvae reared at cold temperatures (2° and 5°C), indicating that endogenous reserves are more efficiently used for growth at these temperatures. In addition, larvae reared at high temperatures died more rapidly in the absence of food despite having more yolk reserves than cold-incubated larvae. Overall, northern rock sole eggs and larvae display early life history traits consistent with coldwater adaptation for winter spawning in the North Pacific.
Tidying up the genus Letharia: introducing L. lupina sp. nov. and a new circumscription for L. columbiana

Abstract Western North America is the global centre of diversity for Letharia, a distinctive and cryptically diverse genus of lichenized fungi belonging to the Parmeliaceae. The genus is characterized by a shrubby, fruticose habit and presence of vulpinic acid. Previous studies using multiple fungal nuclear loci revealed the existence of two distinct species-level lineages within the traditional concept of L. vulpina and four such lineages within L. columbiana. Here we use molecular sequence data in an attempt to settle long-standing taxonomic issues in the genus. Our results confirm the widespread existence within L. vulpina s. lat. of two distinct species-level groups, each forming a mutually exclusive partnership with a separate algal clade within Trebouxia jamesii s. lat. Accordingly, we formally describe the segregate species L. lupina sp. nov. Our results also support the evolutionary independence of four candidate species previously circumscribed from L. columbiana s. lat. One of these lineages, L. ‘gracilis’, has already received species recognition as L. gracilis, while a second, L. ‘lucida’, is epitypified here against L. columbiana s. str. Based on results from species delimitation analyses under the multispecies coalescent model, the two remaining lineages, L. ‘barbata’ and L. ‘rugosa’, also warrant formal taxonomic recognition; however, we refrain from describing these species pending additional studies of diagnostic characters, ecological preference, and distributions.
Autophagy in Ocular Pathophysiology

Autophagy is an evolutionarily conserved intracellular recycling pathway that is indispensable for cellular quality control. Dysfunctional autophagy has been associated with several neurodegenerative, myodegenerative, infectious, and cancerous disorders. Autophagic processes are not only important for cellular maintenance in the retina but also intimately involved with phagocytosis and the very core of retinal visual process. Additionally, excessively upregulated autophagy may culminate into a cell death modality, which may be detrimental to the non-dividing cells of various eye segments. Major advances have been made in understanding the role and fate of autophagy in different ocular tissue layers. In this chapter, we summarize the current understanding of autophagy in the eye in the context of development, aging, and disease. We also speculate on the putative therapeutic strategies where autophagy may be incorporated to treat oculopathies. function. Furthermore, melanoregulin (MREG) facilitates LC3 recruitment to the phagosomes. Phagocytosis is essential for renewal of all-trans retinol to 11-cis retinal visually active chromophore that is sent to the photoreceptors for ena-bling the visual cycle. Hence, while basal canonical autophagy is essential for basic housekeeping of the RPE, non-can- onical autophagy supports at least in part the visual cycle and photoreceptor disk processing.
Suitable stocking density of tilapia in an aquaponic system

An aquaponic system was studied through the integrated culture of mono-sex GIFT and two types of vegetables viz. morning glory, Ipomoea reptans and taro, Colocasia esculenta in a recirculating system for 15 weeks. Tilapia fry of uniform size of 0.76 g were released in three treatments (stocking densities): 106 fish/m³ (T1), 142 fish/m³ (T2) and 177 fish/m³ (T3) to assess the effect of stocking density on the growth performance of fish. Fish were fed with a commercial feed containing 25% protein. Weight gain (g) of tilapia ranged from 19.41 to 32.67 g and was inversely related with stocking density. Percent weight gain varied between 2553.99 and 4298.68% and was significantly different among the treatments. SGR ranged from 3.09 to 3.59% per day and varied significantly. FCR varied from 2.19 to 2.69 and had a positive correlation with stocking density. The highest survival rate (%) was achieved in T1 (99%) followed by T2 (98%) and T3 (96%). Production of fish ranged from 3.43 to 3.52 kg/m³ and was inversely related with stocking density. The present study demonstrated that 106 fish/m³ was the best stocking density in terms of growth, food conversion ratio, survival and production for tilapia culture in the aquaponic system.
Modelagem do rendimento no desdobro de toras de Manilkara spp. (Sapotaceae) em serraria do estado de Roraima, Brasil

The aim of this study was to estimate the yield of sawing Manilkara spp. logs, to quantify the wood by products generated, to evaluate differences in the yield between the diameter classes and to adjust models to estimate the yield in lumber and to estimate the volume of the hollow part of the logs. Seventy-one logs were sampled and grouped into diameter classes. Log volumes were determined by the Smalian method and the volume of lumber was calculated to determine the yield. Twelve models were tested to estimate the sawn lumber and twelve models to estimate the volume of the hollow logs. The choice of the best models was made based on the highest adjusted coefficient of determination (Rajust), lowest standard error of estimate (Syx%) and homogeneous distribution of the residues. The average yield was 30.1% and showed no statistical differences in yield between the diameter classes and between hollow logs and nonhollow logs. Class 5 (70<79,9 cm) was the one that presented the best yield. To estimate the yield, the best equation was the number seven. To estimate the volume of the hollow part of the logs, the best equations were number two, three and ten.
Stability study in aromatic rice (Oryza sativa l.)

The present study was undertaken with 30 aromatic rice genotypes grown in four environments (24 June and 14 July sown for two years; kharif 2008 and 2009) in randomized block design following standard package of practices for aromatic rice at Rice research Field, RAU, Pusa, Bihar. Observations were recorded on quantitative and quality traits. It was observed that among the different dates of sowing, E3 (24 June, kharif 2009) gave the highest grain yield followed by E1 (24 June, kharif 2008). Genotype × environment interaction was observed to be significant for most of the characters except for panicle length, effective tillers per plant, spikelets per panicle, filled grain per panicle, leaf area index, specific leaf weight and gelatinization temperature under study. For grain yield, Sanwal Basmati was observed as above average stable, whereas Pusa Sugandh-3 was the average stable and Jasmine and NDR 9542 were below average stable genotypes. These stable genotypes, namely, Sanwal Basmati, Pusa Sugandh-3, Jasmine and NDR 9542 have reflected stability for component traits.
Nearest-neighbor contingency table analysis of spatial segregation for several species

Abstract Spatial segregation of species occurs when a species is more likely to be located in the vicinity of conspecifics. This can be investigated by mapping and identifying all locations in a study area, then analyzing the nearest-neighbor contingency table, where each location is classified by its species and the species of its nearest neighbor. Nearest-neighbor contingency tables for two species can be analyzed using the methods in Dixon (1994). Here, I present methods to analyze contingency tables for any number of species. Calculation and interpretation of the multispecies contingency table are illustrated by two examples: spatial segregation of species in a swamp forest, with five types of points (Fraxinus caroliniana, Nyssa sylvatica, Nyssa aquatica, Taxodium disticum, and “other species”), and spatial segregation in the gamodioecious tree Nyssa aquatica, with three types of points (male, female, and juvenile). Two issues that affect the results and their interpretation are the choice of randomization (random labelling or toroidal rotation) and the choice of test (pairwise or multispecies).
Seed shatter of six economically important weed species in producer fields in Saskatchewan

Abstract: Seed shatter of wild oat (Avena fatua L.), green foxtail [Setaria viridis (L.) P. Beauv. ], wild mustard (Sinapis arvensis L.), cleavers (Galium spurium L. and G. aparine L.), wild buckwheat (Polygonum convolvulus L.), and kochia [Kochia scoparia (L.) Schrad. ] was evaluated in field pea, spring wheat, and canola fields in Saskatchewan in 2014 and 2015. Seed shatter was assessed using shatter trays collected once a week during the crop ripening stage, as well as at swathing or direct-harvest (direct-combining). Seed shatter differed among weed species in field pea and wheat at maturity: 22%–30% for wild oat, and generally ≤10% for the other species. Seed shatter of investigated weeds in canola at swathing, including that of wild oat, was uniformly low (<5%). The relatively low level of seed shatter for cleavers, wild mustard, green foxtail, and wild buckwheat suggests that these species may be suitable candidates for harvest weed seed control (HWSC). Because of the amount and timing of wild oat seed shatter, HWSC may not reduce population abundance of this grassy weed, except in canola when swathed.
Confirmation and mechanism of resistance to glyphosate in giant ragweed (Ambrosia trifida) in Ontario

Preliminary Investigation of the Mechanism of Resistance to Glyphosate in Giant Ragweed (Ambrosia trifida) in Ontario Amanda Catherine Green Advisors: University of Guelph, 2014 Dr. François J. Tardif Dr. Peter H. Sikkema The basis of resistance to glyphosate in two giant ragweed populations exhibiting different phenotypic responses to glyphosate is unknown. Population R1 exhibits a rapid necrosis of mature leaves followed by eventual regrowth of young tissue while population R2 shows general chlorosis and cessation of growth followed by growth in 21 to 28 days. The objectives were to determine the resistance index of the two populations and investigate mechanisms of resistance. The resistance index, based on LD50 values, was 16 and 19 for R1 and R2, respectively. Accumulation of shikimate in leaf discs (an indicator of glyphosate target site sensitivity) occurred at lower glyphosate doses for S populations than in R1 and R2 suggesting differential target site inhibition. [ 14 C]glyphosate was used to measure absorption and translocation. Absorption levels of R1 and susceptible populations were similar. Less [ 14 C]-glyphosate was translocated to the roots and above the treated leaf in the R1 population.
Gene Discovery in Mendelian and Complex Diseases

Through the Finding of Rare Disease Genes in Canada (FORGE Canada) initiative, individuals affected with rare Mendelian diseases were clinically ascertained with a goal of identifying the genetic origin of their disease. Herein, I describe the methods for identifying the genetic basis of four Mendelian diseases. The application of next generation sequencing led to the discovery of non-synonymous variation in the DNA of individuals affected by rare diseases. The effects of the candidate variants were assessed using a series of functional experiments to complement the human genetics data. The variants observed in patients’ cells are extremely rare, were consistently predicted to be pathogenic by multiple in silico predictive programs, segregated with disease status in the family, and affected the biological properties of their respective gene products, as measured by functional assays. Having successfully identified genetic variants underlying the Mendelian diseases, we sought to use the same approach to extract the genetic variation that may predispose individuals to complex diseases, primarily neurodegenerative disorders. We designed a neurodegeneration specific gene panel that utilizes next generation sequencing chemistry. We sequenced patients diagnosed with one of five neurodegenerative diseases: 1) Alzheimer’s disease; 2) amyotrophic lateral sclerosis (ALS); 3) frontotemporal dementia (FTD); 4) Parkinson’s disease; or 5) vascular cognitive impairment, as part of the Ontario Neurodegenerative Disease Research Initiative (ONDRI). We were successful in detecting rare variants in a large fraction of cases that may be related to the neurodegenerative phenotypes. We also independently ascertained three large, unique families affected with familial ALS and FTD across multiple generations. The three families are diagnosed with ALS and/or FTD and in which the same hexanucleotide repeat expansion in the C9orf72 gene has been observed in all three pedigrees, but their phenotypes vary significantly. We sequenced affected individuals and observed several, distinct variants in these families that may explain the additional neurodegenerative phenotypes observed. In summary, the application of next generation sequencing has successfully identified novel genetic loci in both Mendelian and complex diseases.
Development of efficient and optimized protocol for rapid micropropagation of Physalis ixocarpa, a medicinal herb.

The current study describes optimized protocol for in vitro micropropagation of medicinally important accession of Physalis ixocarpa. Plant extract from P. ixocarpa is used for stomach disorder, for purifying blood, as an antidote against local poison and in folk medicine to treat sore throat. Shoots were induced from nodal shoot explants using Murashige and Skoog (MS) media supplemented with different concentrations of benzyalminopurine (BAP). The effect of different concentrations of benzyalminopurine on shoot length, shoot number and per cent shoot induction of explant was observed. Sprouting of shoot explants started within 7-8 days of inoculation. Application of benzylaminopurine @1.5 mg L induced maximum shoot length (3.45 cm) with an average of 3.5 shoots explant -1 and 96% shoot induction. The healthy cultured shoots were transferred into new culture tubes having rooting media with different concentrations of indole-3-butyric acid (0.25 mg L, 0.5 mg L, 1 mg LIBA). Indole-3-butyric acid at the rate of 1 mg L was best for both primary and secondary roots production. In vitro grown plantlets having strong roots were successfully transferred to soil through successive acclimatization which yielded 90% survival rate.
Optimization of the performance of microbial fuel cells containing alkalophilic Bacillus sp.

A systematic study of microbial fuel cells comprised of alkalophilic Bacillus sp. B-31 has been carried out under various operating conditions. A significant amount of electricity was generated when redox mediators were used. Among the phenothiazine-type redox dyes tested, azure A was found to be the most effective both in maintaining a high cell voltage and for the long-term operation. The maximum efficiency was and for the long-term operation. The maximum efficiency was obtained at ca. giving an open circuit voltage of 0.7V. A small change in temperature did not significantly affect the cell performance, but a rapid decrease in performance was observed below and above . It was noticeable that fuel cell efficiency and discharge pattern depended strongly on the carbon source used in the initial culture medium. Regardless of the initial carbon sources, only glucose and trehalose were utilized as substrates. Galactose, however, was not substantially utilized except when galactose was used in the initial medium. Glucose, in particular, showed coulombic efficiency, which was the highest value ever reported, when Bacillus sp. was cultured in a maltose-containing medium. This study demonstrates that highly efficient microbial fuel cells can be constructed with alkalophilic microorganisms by fine-tuning the operating conditions and by carefully selecting carbon sources in the initial culture medium.
Protein and energy evaluation of detoxified Canavalia seeds as a feedstuff for poultry in the tropics.

Legumes are a very important protein resource in tropical areas both for human and animal consumption. Among them, Canavalia ensiformis is used widely in many parts of the world. The most important inconvenience of the use of Canavalia is the content of anti-nutritional factors such as phytates, cyanogenic glycosides and tannins among others. Various treatments using heat are available to eliminate toxicity, but high temperature reduces protein digestibility and energy concentration. Treatments using low heat in combination with salting or the separation of the protein fraction from the rest of the constituents of the grain, may be alternative methods to eliminate toxic elements. The objective of these trials was to reduce the antinutritional factors and to determine the possible change in protein digestibility and TME content of Canavalia ensiformis after detoxification using low heat combined with salting-in or obtaining a protein concentrate, in order to incorporate it into poultry diets. Beans were grinded and submitted to two different experimental treatments and control: Detoxification using an acidified saline solution with low heat (ASOL-H); and an extraction of its protein concentrate (PC); raw Canavalia was used as Control. The following toxic compounds were analyzed: phytates, cyanogenic glycosides, tannins, trypsin inhibitors, lectins and canavanine, as well as protein digestibility and true metabolic energy. Means and standard deviation were calculated and data was also analyzed using the General Lineal Model (GLM) procedure to detect effects of treatments. Results showed a sharp reduction of antinutritional factors due to treatments (P>0.05). PC reduced more efficiently all toxic substances. Protein digestibility and TME were not affected by the use of either method of detoxification. Therefore the use of both treatments, but specially PC, may be advantageous to eliminate toxicity preserving the protein and energy value of Canavalia to be used in poultry diets.