Miracle-dz/UniFAR-FTUs huggingface dataset:
Dark times for dageraad Chrysoblephus cristiceps: evidence for stock collapse

The declaration of a state of emergency in the South African linefishery in 2000 has had a positive impact on a few overexploited endemic seabreams (Family Sparidae). However, the population of the reef-dwelling dageraad Chrysoblephus cristiceps has been unresponsive to progressively stricter management regulations. After decades of unsustainable fishing mortality the species is in a critical state. In this paper, a method based on standardised probability of capture is used to develop an index of relative abundance for rare species, such as dageraad, which is more robust to changes in output control regulations than conventional methods. The results show a severe decline in dageraad capture probability in the south-west region of South Africa, from 8% in 1985 to <0.1% in 2011. The east region experienced a more rapid decline, from 24% in 1999 to <0.1% in 2011. A spatial comparison of the distribution of historical and recent dageraad probability of capture along the South African coastline indicates a range contraction commonly associated with the collapse of a population. The once-widespread species is now largely limited to a few locations in the Eastern Cape province and dageraad is mostly absent across its former western distribution. Although the historical decline has commonly been attributed to commercial overexploitation, the recreational sector had an estimated 3–5 times greater impact on the dageraad population than the commercial sector in recent years. Given that previous management regulations have been unsuccessful in arresting the decline of dageraad populations, assertive management is necessary to ensure the species’ sustainability. Rehabilitation of dageraad stocks will require a further decrease in fishing mortality, in conjunction with maintaining an appropriate marine protected area (MPA) network.
ADAP1 AND ARF6 MEDIATE REGULATED SECRETORY TRAFFICKING IN NEUROSECRETORY CELLS AND NEURONS

ADP ribosylation factor 6 (Arf6) is a member of the Arf family of small GTPases known to function in vesicular membrane trafficking and cytoskeletal organization. Arf6 cycles between its GTP and GDP bound states, facilitated by GTP exchange factors (GEFs) and GTPase activating proteins (GAPs), respectively. In my dissertation studies I have investigated the neuronal functions of Arf6 and ADAP1, an Arf6 GAP and candidate PI 3kinase target required for dendritic differentiation in developing neurons. I demonstrated that in neurosecretory PC12 cells and neurons, ADAP1 and Arf6 colocalize with regulated secretory granules (SGs) that traffic chromogranin B and brain-derived neurotrophic factor (BDNF), a secreted factor important for neuronal development and synaptic plasticity. Using a pulse-chase assay in PC12 cells to monitor trafficking of chromogranin B, I demonstrated that siRNA-mediated knockdown (or expression of inactive mutants) of ADAP1 or Arf6, resulted in an inhibition of the trafficking and maturation of regulated SGs. In neurons, knock down of ADAP1 or Arf6 leads to an increase in the colocalization of BDNF-GFP with furin, a peptidase localized to immature SGs, suggesting that ADAP1 and Arf6 participate in the maturation of BDNF containing SGs. Knock down of ADAP1 or Arf6
Breeding for Cold Hardiness: Searching for Genes to Improve Fruit Quality in Cold-hardy Peach Germplasm

The generation of cold-hardy cultivars with high-quality fruit has long been a goal of peach breeding programs. While progress has been made, these traits have been difficult to combine by traditional breeding methods. Both cold hardiness and fruit quality are general terms that encompass various specific traits, many of which may be quantitatively inherited. Thus, many generations of hybridization and selection are required to combine several favorable alleles for both of these characteristics. Moreover, certain aspects of cold hardiness may be physiologically or morphologically incompatible with certain aspects of fruit quality, and/or major genes responsible for certain aspects of cold hardiness may be closely linked with particular genes influencing fruit quality. Advances in plant regeneration, molecular biology, and gene transfer (Broglie et al., 1984; DeBlock et al., 1984; Fillatti et al., 1987; McGranahan et al., 1988; Murai et al., 1983; Parsons et al.
Behaviors Related to Reproduction of the Olive Fruit Fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), in Northern California

iv Acknowledgements . v Chapter 1: Seasonal Trap Catches of the olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae) in Northern California: asynchrony with host (olive tree) phenology? 1 Abstract . 2 Introduction . 3 Materials and Methods . 6 Results . 9 Discussion . 11 Acknowledgements . 13 References . 14 Tables . 20 Figures . 22 Chapter 2: Diurnal activity of the olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), implications for mating. 24. 2 Introduction . 3 Materials and Methods . 6 Results . 9 Discussion . 11 Acknowledgements . 13 References . 14 Tables . 20 Figures . 22 Chapter 2: Diurnal activity of the olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), implications for mating. 24 Abstract . 25 Introduction . 26 Materials and Methods . 27 Results . 29 Discussion . 30 Acknowledgements . 33 References . 33 Tables . 37 Figures . 40 Chapter 3: Courtship and mating behaviors of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae). 41. 25 Introduction . 26 Materials and Methods . 27 Results . 29 Discussion . 30 Acknowledgements . 33 References . 33 Tables . 37 Figures . 40 Chapter 3: Courtship and mating behaviors of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae). 41 Abstract . 42. 42
Molecular Probing and Phylogenetic Analysis of Glutamate synthase of Arthrobacter nicotianae.

Introduction: Glutamate synthase is an oxidoreduactase transaminating enzyme that catalyzes the conversion of L-glutamate to L-glutamine with the aid of cofactors like NADP, NAD, FMN, Fe and sulfur. Its activities are in part to regulate the levels of glutamate and glutamine in a manner dependent on energy (ATP) and metabolite, ammonia. Methods and results: In this study we were able to demonstrate the presence of glutamate synthase by employing PCR utilizing genomic DNA isolated from soil bacteria Arthrobacter nicotianae PR. Cloning, sequencing and alignment revealed glutamate synthase with conserved amino acid residues specific to this group of functional proteins. 3D analysis of the GltS using Cn3D 4.1 software revealed well conserved alpha and beta sheets that in part form the TIM barrel and cofactor bonding site. Amino acids that bind the phosphate group of the cofactor were revealed. Un-rooted phylogenetic tree revealed unique distant metabolic relationship, potential development and adaptation of Artherobacter nicotianae PR compared to other bacteria including strains in the Athrobacter group. Conclusion: The phylogenetic divergence of GltS in the matching bacteria suggests possible evolutionary pressure being exerted by the local environment among other factors
Mechanism of HPV8-E7 mediated keratinocyte invasion

High-risk patient groups, such as immunosuppressed organ-transplant recipients and patients with the inherited skin disease Epidermodysplasia verruciformis, exhibit cancerisation of the skin, which are positive for human papillomaviruses (HPV) of the genus beta (e.g. HPV8). Transgenic mouse models, expressing either all HPV8 early proteins (E1, E2/E4, E6, E7) or E2 and E6 individually, develop skin papillomas with varying degrees of dysplasia and squamous cell carcinoma. The specific contribution of the viral E7 protein to tumour formation and the molecular mechanism for HPV8 induced keratinocyte invasion was not known. During this study, a transgenic mouse model expressing the HPV8-E7 oncoprotein in the murine epidermis under the control of the keratin-14 promoter was generated and proved a carcinogenic potential of HPV8-E7 in vivo. It could previously be shown that HPV8-E7 induces keratinocyte invasion in organotypic skin cultures (OSCs), which were based on de-epidermalised dermis, whereby invasion could not be triggered in OSCs based on collagen type I. Therefore, it was hypothesised that the composition of the extracellular matrix (ECM) enables HPV8-E7 mediated keratinocyte invasion. We now could show, that the adherens and tight junction proteins β-catenin and zona occludens-1 are strongly upregulated in E7 positive keratinocytes in OSC, in the skin of HPV8-E7 transgenic mice and in betaHPV positive human skin lesions. When cells were grown on a fibronectin matrix, E7-positive keratinocytes acquired an invasive cell phenotype which was accompanied by an epithelial-mesenchymal-transition mediated cadherin switch leading to E-cadherin down-, and N-cadherin up-regulation. In addition, E7-positive keratinocytes displayed enhanced fibronectin expression and secretion and stimulated dermal fibroblasts to express fibronectin. When grown on fibronectin, E7-positive keratinocytes exhibited increased cell surface levels of the integrin α3 chain. Functional blocking of α3 using siRNA confirmed α3 as a critical molecule sufficient to induce E7-mediated invasion. This mechanistic link was further supported by the fact that the invasion-deficient E7-mutant L23A did not target cell surface levels of α3. Furthermore, high α3 levels were coupled with an upregulation of the fibronectin-associated ECM protein Fibulin-2, known to mediate a transformed cell phenotype. Using E7wt and E7-L23A positive cell extracts and Co-IP/mass spectrometric analysis the cellular factors ATP5B, PTRF/cavin-1 and phosphatidylserine could be identified as possibly important for keratinocyte invasion. These findings highlight the importance of cell-cell and epithelial-ECM interactions required for keratinocyte invasion and provide mechanistic evidence for the role of betaHPV in skin carcinogenesis.
Bayesian multi-species modelling of non-negative continuous ecological data with a discrete mass at zero

Severe declines in the number of some songbirds over the last 40 years have caused heated debate amongst interested parties. Many factors have been suggested as possible causes for these declines, including an increase in the abundance and distribution of an avian predator, the Eurasian sparrowhawk Accipiter nisus. To test for evidence for a predator effect on the abundance of its prey, we analyse data on 10 species visiting garden bird feeding stations monitored by the British Trust for Ornithology in relation to the abundance of sparrowhawks. We apply Bayesian hierarchical models to data relating to averaged maximum weekly counts from a garden bird monitoring survey. These data are essentially continuous, bounded below by zero, but for many species show a marked spike at zero that many standard distributions would not be able to account for. We use the Tweedie distributions, which for certain areas of parameter space relate to continuous nonnegative distributions with a discrete probability mass at zero, and are hence able to deal with the shape of the empirical distributions of the data. The methods developed in this thesis begin by modelling single prey species independently with an avian predator as a covariate, using MCMC methods to explore parameter and model spaces. This model is then extended to a multiple-prey species model, testing for interactions between species as well as synchrony in their response to environmental factors and unobserved variation. Finally we use a relatively new methodological framework, namely the SPDE approach in the INLA framework, to fit a multi-species spatio-temporal model to the ecological data. The results from the analyses are consistent with the hypothesis that sparrowhawks are suppressing the numbers of some species of birds visiting garden feeding stations. Only the species most susceptible to sparrowhawk predation seem to be affected.
A contingent valuation study of buriti ( Mauritia flexuosa L.f.) in the main region of production in Brazil: is environmental conservation a collective responsibility?

The immature leaves of the buriti palm (Mauritia flexuosa) are widely harvested in the municipality of Barreirinhas, Maranhao, for the production of handicrafts, which are sold to locals and tourists. The increasing demand for these artisanal goods is stimulating the emergence of an informal market for immature buriti leaves, leading to an intensification of their extraction and resulting in negative effects on local buriti palm populations and the ecosystem. Thus, the objective of the present study was to assess the environmental value of the buriti palm tree based on the maximum willingness to pay (WTP) for its conservation, using the contingent valuation method. Among the respondents, 99.74% reported that the palm species should be protected and the majority of them (65.75%) agreed to pay for its conservation (annual WTP R$ 179.49 ± 222.05). Multivariate analysis revealed that the WTP was not influenced by the socio-economic profile of the respondents. The main reasons for non-WTP are related to dissatisfaction with the government and the belief that financial contributions would not solve problems of environmental damage. Overall, the evaluated population believes that environmental conservation is not an obligation of the government or that of the population, but is a collective responsibility.
CO2 laser enhances the chilling tolerance of wheat seedlings by stimulating NO synthesis

Abstract: To investigate the mechanism by which laser irradiation enhances the chilling tolerance of wheat seedlings, seeds were exposed to different treatments, and biochemical parameters were measured. Compared with the control group, chilling stress (CS) led to an increase in the concentrations of malondialdehyde (MDA) and H2O2, and decreases in the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), peroxidase (POD), and nitric oxide synthase (NOS), and the concentrations of nitric oxide (NO) and protein. Treatment with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (PTIO), sodium tungstate (ST), and NG-nitro-L-arginine methyl ester (L-NAME) followed by CS resulted in further increases in the concentrations of MDA and H2O2 and further decreases in the other parameters. However, treatment with PTIO, ST, and L-NAME followed by laser irradiation had the opposite effects on these parameters. When the seeds were treated with PTIO, ST, and L-NAME followed by laser and CS, the concentrations of MDA and H2O2 were significantly lower and the other parameters were higher than in the PTIO, ST, and L-NAME plus CS groups. These results suggest that CO2 laser irradiation enhances the chilling tolerance of wheat seedlings by stimulating endogenous NO synthesis.
Polyhydroxyalkanoate (PHA) production by Lynisibacillus sp. strain UEA-20.171

PHA is a biodegradable and biocompatible natural thermoplastic produced from renewable bioresources and is hence attracting attention as a plastic material for use in the environment and medical fields. In the present study, the Lynisibacillus sp. strain UEA-20.171 was selected for production of polyhydroxyalkanoate (PHA) in bioreactor. The accumulation of polymer in the bacterium occurs when there is an imbalance in the concentration of nitrogen in relation to carbon (glucose). After the period of adaptation in mineral medium from 12 to 24 h, the cell division occurred from 12 to 24 h, and the formation of biopolymers from 36 to 48 h. It was observed that the polymer produced by the isolated UEA-20.171, was P(3HB). Keywords: Polyhydroxyalkanoates, polyhydroxybutyrate, bioplastics, Lysinibacillus
Host records of Grammia ursina Schmidt, 2009 (Lepidoptera: Noctuidae: Arctiinae) on San Clemente Island and its potential effect on rare plant restoration

Abstract. Using molecular tools, we identify Grammia ursina Schmidt, 2009 to be present at high densities on San Clemente Island, California. As a generalist herbivore, G. ursina has many hosts and is a potential pest of rare and endemic plants. We present a list of host records of G. ursina, including rare plants on San Clemente Island. Conservation efforts to support rare plants on the island include outplantings, which have been negatively affected in G. ursina outbreaks. We suggest continual monitoring of G. ursina populations to predict future outbreaks and population peaks and to monitor its effects on endemic plant species and restoration efforts.
ROLE OF COQ10 SUPPLEMENTED TO THAWING SOLUTION IN IMPROVEMENT HUMAN SPERM PARAMETERS POST- CRYOPRESERVATION

Background: Cryopreservation techniques are highly developed field of Assisted Reproductive Technologies (ARTs) to help infertile couples to overcome infertility. Coenzyme Q10 (CoQ10) is a vitamin – like substance is present in most eukaryotic cell, and produced in the mitochondria primarily. Objective: To study the effects of CoQ10 supplemented to thawing solution on sperm parameters postcryopreservation technique. Materials and Methods: One hundred and eight males were participated in this study. The mean age for all males included in this study was (29.94 ± 0.65) years and duration of infertility was 2-14 years. Semen samples were collected and seminal fluid analysis was done according to WHO (2010] All groups contain 1mL from semen sample mixed with 0.7 mL of cryopreservation solution. All groups after thawing were divided into 3 subgroups (GA: control group; without honey bee), (GB: contain 5 µm from CoQ10) and (GC: contain 10 µm] Results: There was significant increase (P<0.05) in the progressive sperm motility (%), progressive sperm motility (%) grade (A), progressive sperm motility (%) grade (B) and normal sperm morphology when compared among groups (GA: control group), (GB:5 µm CoQ10 ),(GC:10 µm CoQ10] Significant reduction (P<0.05) in the percentages of sperm immobility (%) when compared to control group with GB and GC. In the present study appeared that the direct swim-up technique resulted in significantly (P<0.05) better results for sperm parameters than the swim-up technique from all types of ejaculates classified according to male infertility factors. The study proved that there was significant (P<0.05) improvement in sperm
The Potential Use of a Three Dimensional Cell Culture of Spheroids in the Study of Various Therapeutic Approaches

MOJ Immunol 2016, 3(4): 00096 human stem cell technology has allowed for the development of three dimensional cell cultures that may more accurately reflect the pathophysiology of human diseases. Three dimensional cell cultures allow for increased cell-to-cell and extracellular matrix interactions and are closer in structure and architecture to in vivo organs and tissues. The use of spheroids, a three dimensional cell culture method, has allowed for greater understanding and advances in cancer cell interactions and testing toxicity, drugs, and therapeutic methods. Spheroid use in the study of gastrointestinal tract diseases, cystic fibrosis research, and cancer research and therapy will be discussed in this mini-review.
The Influence of Parental Status on Courtship Effort in a Paternal Caring Fish

It is widely assumed that caring for young limits the motivation of parents to seek additional mating opportunities. However, in situations where parental care does not involve direct provisioning of the offspring, but rather activities directed at the brood as a whole (e.g. guarding), it may be more efficient for parents to care for large numbers of young at once. This may be especially true for species with exclusive paternal care, with fathers that have recently acquired a brood of young potentially benefitting from vigorously courting prospective mates, so as to maximise their chances of attaining a large number of young to rear together. We experimentally tested this hypothesis in the three-spined stickleback (Gasterosteus aculeatus), a fish with male only care. Contrary to our predictions, we found no evidence of any differences in courtship between recently spawned egg-tending fathers and males that had not spawned. However, males that were permitted to spawn, but then had their eggs taken from them, courted less vigorously. Together, the results of our study suggest that the potential benefits of vigorous courtship in terms of acquiring additional young may be offset by additional costs faced by parental males.
Population genetic processes of a Populus nigra/P. x canadensis hybrid complex-spatially explicit studies on gene flow as abasis for conservation measures

A correct identification of members of the poplar h ybrid complex Populus x canadensis essential in breeding programmes and studies in int rogressive gene flow. Molecular marker protocols have been developed for this purpose. How ever, due to missing standards, these techniques have so far not been suited to the trans fer of results between different laboratories. We present here a powerful system of nuclear micros atellite DNA (nSSR) fingerprints, standardised by allelic ladders and reference genot ypes. Seven nSSR loci provided fingerprints of 65 commercial poplar clones. Their alleles were used to construct allelic ladders. Thus, a first standardised register of pop lar clones is now available. All procedures were optimised according to simplified DNA extracti on protocols, multiplexed PCR and electrophoresis procedures. Corresponding data orig inat ng from two different electrophoretic platforms in different laboratories were congruent when the allelic ladder was used. Unambiguous differentiation of the clones was based on a very low probability of identity (PI) of 1.95 × 10. Our results revealed discrepancies between clone de otations and genetic fingerprints. This suggests that, potentially, memb rs of the clone collection could have been
Delineating the Molecular Mechanisms of KIF7 in Vertebrate Hedgehog Signal Transduction

The Hedgehog (Hh) signalling pathway plays important roles in embryonic development and for adult tissue homeostasis and regeneration of multi-cellular organisms. Mutations in components of this pathway often result in human developmental disorders and cancer. The primary cilium, a microtubule based extension from the cell surface is required for Hh signalling in vertebrates. Hh ligand binding to the Patched (Ptch1) receptor leads to the ciliary accumulation and activation of the seven transmembrane protein Smoothened (Smo) and changes the localization of several pathway components within primary cilia subdomains. How Smo activation affects the localization of effector proteins in cilia and how this relates to the activation of target genes is unclear. Genetic and biochemical analysis revealed that the kinesin family protein 7 (Kif7) trafficks to the primary cilia upon pathway activation and fulfills dual positive and negative roles during mouse Hh signalling. Through proteomic and biochemical analysis, we aim to better understand the molecular mechanisms underlying the functions of Kif7 in vertebrate Hedgehog signalling. Using a mass spectrometry-based proteomic approach, we identified Liprin-α1 (PPFIA1) and the PP2A phosphatase as Kif7-interacting proteins, and showed that these proteins regulate Kif7 phosphorylation and its activity. We further identified DYRK2 as a iii protein kinase that phosphorylates Kif7. Overall, our study identified phosphorylation as a posttranslational modification that dictates Kif7 localization within primary cilia and its control of Gli transcriptional activity. Lastly, through biochemical assays we examined the relationship between SuFu and Kif7, two key regulators of the Hh pathway. Collectively, these studies highlight the importance of Kif7 in vertebrate Hh signalling.