Miracle-dz/UniFAR-FTUs huggingface dataset:
A rosette by any other name: species diversity in the Bangiales (Rhodophyta) along the South African coast

ABSTRACT The Bangiales is an order of Rhodophyta, widely distributed around the globe and best known for its economic value in the nori industry. The morphological simplicity of the group offers limited distinguishing characters for species identification. We therefore delimited species of the Bangiales along the South African coast based on two unlinked loci, the mitochondrial cox1 gene and the plastid rbcL gene, supplemented with additional sequence data from a third gene, the nuclear nSSU. Application of DNA-based species delimitation methods including the Automatic Barcode Gap Discovery (ABGD), General Mixed Yule Coalescent (GYMC) and Poisson Tree Processes (PTP), resulted in the recognition of 10 Porphyra and three Pyropia species in South Africa, only three of which had been previously described. Additional species of Bangiales previously recorded along the South African coast were added to our final species list despite not being found in the present study, resulting in an estimate of 14–16 Bangiales species occurring along this shoreline. Most of this extensive genetic diversity has been misidentified as the commonly rosette-forming species P. capensis. The name P. capensis currently refers to a species complex and cannot be attached to any one species with certainty. All species in this complex, confirmed using genetic data, are endemic to South Africa. Our results compare well with other Southern Hemisphere countries, such as Chile and New Zealand, where high genetic diversity, species richness and endemicity have also been found.
Frequent Non-random Shifts in the Temporal Sequence of Developmental Landmark Events during Fish Evolutionary Diversification

Morphology is a consequence of sequentially occurring developmental events, termed a developmental sequence, and evolutionary changes in the sequence can generate morphological diversities. In this study, we examined evolutionary dynamics of the developmental sequence at a macro-evolutionary scale using the teleost fish. From the previous literature describing development of 31 fish species, we extracted the developmental sequences of 20 landmark events involving the whole body plan, and by using them, reconstructed ancestral developmental sequences. The phylogenetic comparisons of these sequences revealed event-dependent heterogeneity in the frequency of changing the sequences. We then determined potential event shifts that can parsimoniously explain the sequence changes on each node of the fish phylogenetic tree. These “heterochronic shifts” are widely distributed on almost of all the branches across the fish phylogeny. The simulation-based analysis indicated that this distribution of heterochronic shifts is not the result of random accumulation over phylogenetic time, but exhibits a curious constant trend so that individual phylogenetic branches harbor similar numbers of heterochronic shifts regardless of length. It is of great interest to know how these findings are related to morphological divergence in animals during evolution.
Characterization of PdpC, a protein encoded by the Francisella pathogenicity island

Supervisory Committee: Dr. Francis E. Nano, (Department of Biochemistry and Microbiology) Supervisor Dr. Stephen V. Evans, (Department of Biochemistry and Microbiology) Departmental Member Dr. Terry Pearson, (Department of Biochemistry and Microbiology) Departmental Member Dr. Real Roy, (Department of Biology) Outside Member Tularemia is a zoonotic disease caused by the bacterial pathogen Francisella. A major virulence determinant of Francisella is the ability to survive and multiply within macrophages. Previous research identified a genetic element of approximately 30 kb in length, which possessed characteristics typical of a pathogenicity island. In F. novicida, the Francisella pathogenicity island (FPI) is composed of 18 genes. Initial studies revealed that several FPI-encoded genes are required for intramacrophage growth. The FPI contains several homologues of a newly described type six secretion system (T6SS). I developed a chicken embryo infection model to provide a simple, low-cost assay to evaluate the virulence of Francisella strains. The results demonstrate that this assay is able to discriminate large differences in virulence among Francisella strains. Further, this system can facilitate large-scale experiments to quickly survey mutant collections for virulence, while reducing animal suffering. Next, I adapted a genetic technique called co-transformation for use in Francisella. This technique facilitates the introduction of mutant or wild type DNA into the chromosome, without requiring the introduction of antibiotic resistance markers or negative selection markers. I also
How thalamic relays might orchestrate supervised deep training and symbolic computation in the brain

The thalamus appears to be involved in the flexible routing of information among cortical areas, yet the computational implications of such routing are only beginning to be explored. Here we create a connectionist model of how selectively gated cortico-thalamo-cortical relays could underpin both symbolic and sub-symbolic computations. We first show how gateable relays can be used to create a Dynamically Partitionable Auto-Associative Network (DPAAN) (Hayworth, 2012) consisting of a set of cross-connected cortical memory buffers. All buffers and relays in a DPAAN are trained simultaneously to have a common set of stable attractor states that become the symbol vocabulary of the DPAAN. We show via simulations that such a DPAAN can support operations necessary for syntactic rule-based computation, namely buffer-to-buffer copying and equality detection. We then provide each DPAAN module with a multilayer input network trained to map sensory inputs to the DPAAN’s symbol vocabulary, and demonstrate how gateable thalamic relays can provide recall and clamping operations to train this input network by Contrastive Hebbian Learning (CHL) (Xie and Seung, 2003). We suggest that many such DPAAN modules may exist at the highest levels of the brain’s sensory hierarchies and show how a joint snapshot of the contents of multiple DPAAN modules can be stored as a declarative memory in a simple model of the hippocampus. We speculate that such an architecture might first have been ‘discovered’ by evolution as a means to bootstrap learning of more meaningful cortical representations feeding the striatum, eventually leading to a system that could support symbolic computation. Our model serves as a bridging hypothesis for linking controllable thalamo-cortical information routing with computations that could underlie aspects of both learning and symbolic reasoning in the brain.
Interspecific Hybridization of Prunus persica with P.armeniaca and P.salicina Using Embryo Rescue

Some interspecific hybrids were obtained after hybridization of Prunus persica with treated pollens from P.armeniaca and P.salicina,then the hybrid embryos were successfully rescued,and a molecular identification was made in part of the hybrids.The results showed that the hybrid embryo abortion started from the 7th or 8th week after pollination in cross when used the Yuhualu or Zhonghua Shoutao as the female parent.The cultivars with different durations for fruit development and the ages of hybrid embryos have great effects on the rate of embryo germination and growth.At the same age(when the PF value was around 0.5),the late peach cultivar Zhonghua Shoutao acquired more than 50% of embryo germination rate,but the early peach cultivar Yuhualu gave only 6.7% of it.Treatment of male parent pollen in the electrostatic field at an appropriate dosage improved the efficiency of bud inducement and multiplication,but treatment with 60Co γ-ray reduced the efficiency and produced weak buds.For rescuing! the hybrid embryos,it is concluded that the medium 1/2MS + 6-BA 4 mg·L-1 + IBA 0.5 mg·L-1 can increase the embryo germination rate up to 90%,the MS + 6-BA 1.0 mg·L-1 + IBA 1.0 mg·L-1 is the best medium for bud induction and multiplication,and the MS + IAA 0.5 mg·L-1 + NAA 0.2 mg·L-1 is the best rooting medium.SSR identification proves that the hybrids obtained by the embryo rescuing system are true ones.
Advances in the understanding of the Cryptococcus neoformans and C. gattii species complexes and cryptococcosis

The rising incidence of cryptococcosis, a potentially fatal fungal infection affecting both immunocompromised and immunocompetent humans and animals, and the emergenceofdiseaseoutbreaks, has increased theneed formore in-depth studies andconstant vigilanceof its twoetiological agents, the cosmopolitan and well known Cryptococcus neoformans and its sibling species C. gattii. As a result, a global scientific network has established formal links between institutions to gain better insights into Cryptococcus and cryptococcosis, enabling collaborations amongst researchers with different backgrounds, perspectives and skills. Interdisciplinaryprojects include: (1) thestudyof the ecology and geographical distribution of the agents of cryptococcosis; (2) the application of newalternativemethodologies for the rapid and accurate identification of the two sibling species and major molecular types/possible cryptic species (VNI-VNIV and VGI-VGIV); (3) the use of different animal models of infection to assess cryptococcal pathogenesis and virulence factors; and (4) population genetics studies directed towards the discovery of virulence/tissue tropism associated genetic signatures. These studies enrich the knowledge and understanding of the epidemiology of this mycosis and help to better comprehend fungal virulence, genetics, pathogenesis, antifungal susceptibility, aswell as investigating the regional and global spread, to improve treatment options of the disease caused by these important emerging pathogenic yeasts.
Transverse Velocity Field Measurements in High-resolution Solar Images Based on Deep Learning

To address the problem of the low accuracy of transverse velocity field measurements for small targets in high-resolution solar images, we proposed a novel velocity field measurement method for high-resolution solar images based on PWCNet. This method transforms the transverse velocity field measurements into an optical flow field prediction problem. We evaluated the performance of the proposed method using the Hα and TiO data sets obtained from New Vacuum Solar Telescope observations. The experimental results show that our method effectively predicts the optical flow of small targets in images compared with several typical machine- and deep-learning methods. On the Hα data set, the proposed method improves the image structure similarity from 0.9182 to 0.9587 and reduces the mean of residuals from 24.9931 to 15.2818; on the TiO data set, the proposed method improves the image structure similarity from 0.9289 to 0.9628 and reduces the mean of residuals from 25.9908 to 17.0194. The optical flow predicted using the proposed method can provide accurate data for the atmospheric motion information of solar images. The code implementing the proposed method is available on https://github.com/lygmsy123/transverse-velocity-field-measurement.
Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

Oncogenic fusion events have been identified in a broad range of tumors. Among them, RET rearrangements represent distinct and potentially druggable targets that are recurrently found in lung adenocarcinomas. Here, we provide further evidence that current anti-RET drugs may not be potent enough to induce durable responses in such tumors. We report that potent inhibitors such as AD80 or ponatinib that stably bind in the DFG-out conformation of RET may overcome these limitations and selectively kill RET-rearranged tumors. Using chemical genomics in conjunction with phosphoproteomic analyses in RET-rearranged cells we identify the CCDC6-RETI788N mutation and drug-induced MAPK pathway reactivation as possible mechanisms, by which tumors may escape the activity of RET inhibitors. Our data provide mechanistic insight into the druggability of RET kinase fusions that may be of help for the development of effective therapies targeting such tumors.
The roles of dispersal and mass extinction in shaping palm diversity across the Caribbean

The rich flora of the Caribbean islands and surrounding mainland evolved in a context of isolation alternated with phases of terrestrial connectivity between landmasses, climatic fluctuations and episodes of mass extinctions during the Cenozoic. We explored how these events affected the evolution of the sister palm tribes Cryosophileae and Sabaleae, and how continent‐island exchanges, endemic radiations and mass extinction shaped their extant diversity.
Character Association Analysis for Yield, Yield Attributes in Swarna X Type 3 Ril Population of Rice

The present study was undertaken with the objective to determine the degree of association between grain yield and yield attributing traits in Swarna x Type 3 RIL population of rice. 100 RIL populations were evaluated for identifying their efficiency with respect to eight characters. The correlation studies revealed that grain yield per plant showed strong positive significant association with plant height and 1000-seed weight. Positive nonsignificant association of grain yield per plant was observed with days to 50 per cent flowering, panicle length, number of filled grains per panicle.
Fish oil substitution by soybean oil in Sharpsnout seabream Diplodus puntazzo: Performance, fatty acid profile, and liver histology

ABSTRACT The present study was conducted to determine the effect of soybean oil on the performance and liver histology in Sharpsnout seabream (Diplodus puntazzo) (initial body mass 35 g). Four experimental diets were formulated containing 0%, 25%, 50%, and 75% of soybean oil substituting fish oil. Fish were fed for 84 days. Increasing the level of soybean oil had no significant effects on growth and feed efficiency parameters. Biometrics, body composition, protein efficiency, and energy efficiency were not affected by the fish oil replacement. Muscle and liver fatty acids reflected fish oil substitution. Moreover, histology did not show statistical differences among treatments. Sharpsnout seabream juveniles can be fed with diets in which fish oil has been replaced with soybean oil at up to 75% of total lipid in the diet for a period of 84 days without affecting growth, feed efficiency, biometric parameters, and body composition.
Evaluation of essential oils against Sitophilus zeamais (Motshulsdy) (Coleoptera: Curculionidae)

The objective of the current study was to determine the fumigant toxicity of essential oils for control stored product insects pest. Essential oils from ten plant species currently found in Thailand: pine (Pinus Palustris), lemon grass (Cymbopogon citratus Stapf), peppermint (Mentha Piperita), citronella grass (Cymbopogon nardus Linn), sweet acacia (Acacia farnesiana), cinnamon (Cinnamomum verum J.S. Presl), sweet orange (Citrus sinensis Pers), basil (Ocimum basilicum L.), clove (Syzygium aromaticum L.), and star anise (Illicium verum Hook) were extracted by steam distillation and tested for their insecticidal activities against maize weevil (Sitophilus zeamais Motshulsdy). Fumigant toxicity test was evaluated on adult of the maize weevil under laboratory conditions. Mortality of the maize weevil was observed and recorded every 12 h until 72 h. Responses varied with the test applied 100 and 10 μl of essential oils from the ten plants species on the tested insects. Three of the essential oils (sweet acacia, basil and star anise) showed high toxicity and were selected for the residuality test to mortality by contact with a surface of treated petri dish and glass jar. The results revealed that diluted 7.5 μl and 205.0 μl of essential oils from three plants (star anise, basil and sweet acacia) achieved a high mortality of the tested insects at 100% within 36 h after exposure to surface of treated petri dish and glass jar respectively.
Mutations causing hemophilia B in Algeria: Identification of two novel mutations of the factor 9 gene

Abla Z, Mouloud Y, Hejer El, Emna G, Abdi Meriem A, Ouarhlent Yamina O, Naouel S. 2018. Mutations causing hemophilia B in Algeria: Identification of two novel mutations of the factor 9 gene. Biodiversitas 19: 52-58. Hemophilia B (HB) (also known as Christmas disease; Christmas is the family name of the first patient.) is an X linked recessive hemorrhagic disorder caused by mutations in factor 9 (F9: is used for the gene) gene that leads to deficient or defective coagulation factor IX (FIX: is used for the protein). The variable phenotype of HB results from wide range of mutations affecting the F9 gene. Our study was aimed at molecular analysis of HB to identify the causative mutation in known patients with HB in a part of Algeria. For genotyping, polymerase chain reaction (PCR) and direct sequencing have been applied to all the essential regions of the F9 gene from 39 Algerian HB patients belonging to 13 unrelated families. We identified 10 different mutations. The identified mutations included 1 duplication and 9 substitutions. In total 9 point mutations were identified, of which 5 are located in exon 8, the hotspot region in the F9 gene. Among the 10 mutations, 2 are novel and not deposited in database sites nor described in recently published articles. The results of this study emphasize the heterogeneity of HB. In summary, our preliminary results will be used to build an Algerian mutation database which would facilitate genetic counseling.
Socio-economic factors and management practices followed in eastern Uttar Pradesh for rearing of Jaunpuri goat

The present investigation was undertaken to study the management practices and socio-economic factors affecting the farming of Jaunpuri goat in two districts of its native tracts in eastern Uttar Pradesh. viz., Allahabad and Jaunpur. Ten villages from Jaunpur and fifteen villages from Allahabad district were randomly selected for the present investigation. The findings revealed that most of the goat farmers in Jaunpur and Allahabad district were of marginal type in their land holding capacity with 47.61 and 68.18% respectively and they earned more than Rs.5000 per annum from goatery. Besides the goatery, the other professions of goat rearers are 60% farming, 33.33% labor, 6.67% small business in Jaunpur and 58.82% labour, 41.18% farming in Allahabad district. The literacy of the head of the Jaunpuri goat rearing family was 66.67 and 68.18 % respectively in the Jaunpur and Allahabad district and most of farmers have 6-8 members per family. The farmers of both districts used to house their goats mostly during night time. The result indicated that 70.48 and 80.91% farmers from Jaunpur and Allahabad districts keep their animal in the house during night. However, 29.52 and 19.09% of the farmers used to keep their animals in the goat shed both day and night. The overall percentages of close and open type house were 27.91 and 72.09%, respectively in Jaunpur and Allahabad district. Most goat sheds were Kuccha type, because of the poor economic status of goat farmer in these districts. The Jaunpuri goat is dual type of goat which produces milk and meat both. Thus the present findings indicated that in both the districts the farmers reared this breed for dual purpose.
The Effects of Discoidin Domain Receptor 1 on Macrophage Phenotype in Vascular Inflammatory Disease

In atherosclerosis, the expression of discoidin domain receptor 1 (DDR1) promotes macrophage accumulation in the arterial vessel wall in hyper-­‐cholesterolemic mice; however, the mechanism involved remains elusive. DDR1 has been hypothesized to enhance macrophage accumulation by mediating the phenotypic polarization of these leukocytes. We report here that DDR1-expressing and DDR1-null macrophages displayed incongruent cytokine profiles in the in vivo plaque. In vitro, DDR1 blunted the up-regulation of anti-inflammatory genes in peritoneal macrophages following IL-4 stimulation. Moreover, DDR1 correlated with a relative decrease in the mRNA expression of select MMPs and TIMP-2, suggestive of a reduced matrix remodeling efficiency that may contribute to accelerated plaque expansion. Our findings preliminarily demonstrate that DDR1 effects an overall pro-inflammatory status in macrophages by dampening their adaptability to anti-inflammatory stimuli. Further effort to determine how DDR1 fine-tunes macrophage polarization will be relevant to the engineering of effective treatment for atherosclerosis and other inflammatory diseases.
Rungia flaviflora (Acanthaceae), a New Species from Yunnan, China

Abstract Rungia flaviflora (Acanthaceae), a new species from Southeast Yunnan, China, is described and illustrated. The new species resembles R. burmanica in shape and texture of leaf, as well as bract and corolla shape, but differs in its growth habit, plant size, cystolith shape, spike length, bract margin, and corolla colour. Among known taxa in the genus, this species is also distinctive in having tricolporate pollen grains and a chromosome number of 22. Information on pollen morphology, chromosome number, and karyotype is given, and a line drawing, color plate, and distribution map of the new species are also provided. This new species was previously misidentified as R. monetaria, which is restricted to Vietnam and does not occur in China.
Evolution of Specialization in Heterogeneous Environments: Equilibrium Between Selection, Mutation and Migration

Adaptation in spatially heterogeneous environments results from the balance between local selection, mutation, and migration. We study the interplay among these different evolutionary forces and demography in a classical two-habitat scenario with asexual reproduction. We develop a new theoretical approach that goes beyond the Adaptive Dynamics framework, and allows us to explore the effect of high mutation rates on the stationary phenotypic distribution. We show that this approach improves the classical Gaussian approximation, and captures accurately the shape of this equilibrium phenotypic distribution in one- and two-population scenarios. We examine the evolutionary equilibrium under general conditions where demography and selection may be nonsymmetric between the two habitats. In particular, we show how migration may increase differentiation in a source–sink scenario. We discuss the implications of these analytic results for the adaptation of organisms with large mutation rates, such as RNA viruses.
Modelling the G51D alpha-synuclein Parkinson’s mutation in the rat

vi List of figures . xiii List of tables . xviii Introduction . 1 1.1 Thesis introduction . 1 1.2 Parkinson’s disease . 2 Clinical presentation. 2 Neuropathological findings . 3 Neuroimaging . 9 Structural neuroimaging . 9 Molecular neuroimaging . 11 Overview of PET/CT imaging . 13 Analysis of the non-dopaminergic systems . 15 Analysis of the dopaminergic system . 17 Underlying causes . 24 Idiopathic Parkinson’s disease . 24 Lifestyle and environmental factors, or chemical exposure . 24 Genetic mutations linked to the development of Parkinson’s disease or parkinsonism . 24 Mutations in SNCA . 26 1.3 Alpha-synuclein . 31 Normal structure and function . 31 Effect of the G51D mutation. 34 1.4 Rodent models of Parkinson’s disease . 35 Pharmacological, toxin and chemical models . 35 Genetic models . 36 Models with mutations in parkin, PINK1, DJ-1 and LRRK2 . 42 Models with mutations in SNCA . 45 Mouse models . 45 Rat models . 46 1.5 CRISPR/Cas9 genetic engineering . 47 1.6 Aims of the thesis and hypotheses . 50 Material and methods . 52 2.1 The overall experimental plan . 52 2.2 Establishment of the G51D rat colony . 53