Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of DPY-30 Proteins in Flagella

ROLE OF DPY-30 PROTEINS IN FLAGELLA RADHIKA GOPAL MARQUETTE UNIVERSITY, 2010 Cilia and flagella are similar organelles found in eukaryotic cells. A microtubulebased axonemal cytoskeleton supports these organelles that project into the extracellular environment to detect various stimuli and propel fluid. These functions enable cells to sense and respond to the changing environment. Because of their importance, the fundamental mechanisms have been conserved throughout evolution. However, it remains largely unknown how axonemes are assembled and how the motility is regulated. This thesis investigated two molecules, RSP2 and RSP23, positioned in the axonemes within a T-shaped complex, the Radial Spoke (RS). Among several axonemal complexes, flagella lacking the evolutionarily conserved RS are paralyzed suggesting that this complex is crucial for motility. It was proposed that the RS transduces mechanical and chemical signals to regulate flagellar beating. These two molecules, RSP2 and RSP23, in Chlamydomonas bind the prototype calcium sensor, calmodulin. They also share a highly conserved DPY-30 domain that resembles the RIIa domain known for dimerization and targeting of cAMP-dependent protein kinase A to specific intracellular locations. Moreover, RSP2 links the head and stalk modules in the RS while RSP23 contains a Nucleoside Diphosphate Kinase (NDK) domain presumably for maintaining the equilibrium of nucleotide species. To reveal the mechanisms mediated by these molecules, mutants defective in these domains were generated. The calmodulin-binding region in RSP2, that is absent in mammalian homologs, is not required for the assembly of RS or the oscillatory beating. However, the motile mutants cannot maintain the typical helical trajectory when cells are exposed to bright light and glass barrier simultaneously. In contrast, mutants lacking the DPY-30 domain in RSP2 are paralyzed, despite the presence of all RSPs. Mutants expressing a fraction of RSP23 with inactive NDK activity generate shorter flagella with reduced amounts of RS. Together these results suggest that DPY-30 domains targets to key locations conserved molecular modules critical for flagellar elongation and motility and the diverged calmodulin-binding regions for steering the biflagellate. Models are proposed to illustrate the various roles of these molecular domains. These discoveries provide new insight on the extraordinary mechanisms in cilia and flagella.
Proteomic and bioinformatics tools to understand virulence mechanisms in Staphylococcus aureus

Staphylococcus aureus, one of the major pathogenic bacteria, is associated with substantial morbidity and mortality. The disease burden of staphylococcal infections is significant, which is primarily attributed to its adaptability and resistance to environmental stresses. S. aureus has the ability to develop multiple resistances to antimicrobial agents. These high resistances make pathogenicity of S. aureus one of the most complex mechanisms to understand and manage. Proteomic and bioinformatics approaches show great potential in exploring microbial adaptation strategies, ability to cause disease by pathogenic bacteria and the development of diagnostic tools. A summary of the latest developments in the application of ‘omics’ technologies to understand resistance mechanisms in S. aureus and their future role in antistaphylococcal vaccine and/or drug discovery is given here.
Correlation Analysis of Mutation Severity and BTK-expression by Clinical Manifestations in Patients with X-linked Agammaglobulinemia

Backgrounds/Objectives X-linked agammaglobulinemia (XLA) is a primary immunodeficiency disorder caused by mutations in the Bruton tyrosine kinase (BTK) gene. It is characterized by severely reduced numbers of peripheral B cells and a significant deficiency in all serum immunoglobulins. In the present study, the impact of mutation severity on the clinical and immunological characteristics of XLA patients was evaluated. Methods Mutation analysis was performed in 19 XLA patients by PCR assay to identify variations in the BTK gene. Subsequently, the western blotting technique was applied for measuring BTK expression and function. A genotype-phenotype correlation was investigated regarding the impact of mutation severity on clinical and immunological parameters. Results Mutation detection in the BTK gene revealed missense mutations in 9 patients, nonsense mutations in 3 cases, splicing site defects in 5 patients, and small in-frame deletions in 2 patients; 31% of patients displayed normal BTK expression. A significant correlation was found between types of BTK mutation and BTK expression. Discussion Generally, genotype-phenotype correlation studies on XLA disease seem to be very controversial. The results of the correlation analysis in the present study could indicate that evolution of the disorder is not completely similar in all cases, even with the same mutation.
Generation and characterisation of antibodies specific for the multidrug resistance-associated protein, MRP

Multidrug resistance associated protein 1 (MRP1) is a 190kD integral membrane glycoprotein which belongs to the ATP-binding cassette (ABC) superfamily of transport proteins. The MRP1 specific MAbs, MRPrl, MRPm6 and QCRL-1 have facilitated both clinical and experimental investigations of this protein to date. In this thesis we have used various types of MRP 1-related immunogens in various species and utilising different immunisation protocols with the objective of producing additional MRP1 specific MAbs which might detect different epitopes Immunogens used included short synthetic peptides, fusion protems and MRP1 over-expressmg cells Species used for immunisation included New Zealand White rabbits, Balb\c mice and Wistar rats. A number of immunisation routes, such as mtrapentoneal, subcutaneous and the lymphatic system via footpad injections were used Variations in immunisation protocols included in-vivo and in-vitro immunisations.
The roles of transient receptor potential channels in thermostatic behavior, in thermal acclimation, and in tonic immobility in the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae)

Organisms are capable of sensing environmental conditions through diverse mechanisms. Transient receptor potential channels (TRPs) are a cation channel family that has been found to function in diverse sensing mechanisms. In this dissertation, I identified the function of several TRPs in thermosensing and mechanosensing in the red flour beetle, Tribolium castaneum. Candidate TRPs were chosen based on homology to TRPs found and studied in Drosophila melanogaster. To identify the function of candidate TRPs in T. castaneum, I suppressed the expression of target genes by RNA interference technique and investigated the phenotype of each treated beetle. Temperature is a major limiting environmental factor for organisms. I tested the function of candidate TRPs in thermotaxis (behavior) and thermal acclimation (physiology). Using bioinformatics approaches, I identified three candidate TRPs – painless, pyrexia, and trpA1 – involved in high temperature sensing. To test thermotactic behavior, I investigated beetle movement on a temperature arena with two separate temperature zones. Thermal acclimation was tested by pre-exposing beetles to either 42 °C for 10 min. When treated with double stranded RNA of TRPA1 (dstrpA1), the thermotactic response of beetles at 39 and 42 °C was reduced when compared to control groups. With pre-exposure at 42 °C, survivorship of dstrpA1treated beetles significantly increased after one minute exposure at 52 °C compared to beetles that were not pre-exposed. With dspainless treatment, beetles showed lower response to thermal acclimation and lower long-term survivorship. Beetles treated with dspyrexia showed lower recovery after heat treatment without pre-exposure at 42 °C. To identify the function of candidate TRPs in mechanosensing, I evaluated dsRNA treated beetles for survival, walking behavior, and tonic immobility. Treatment with dsnompC and dstrpA5 resulted in failure in eclosion, causing 93 % mortality in both treatments. Survivors in dsnompC showed defects in elytra sclerotization. In dsnanchung and dsinactive treatments, adults showed abnormal walking behavior and reduced walking speed that were likely caused by defects of mechanosensing in folding of the joint between the femur and tibia. For tonic immobility, beetles with dsnanchung, dsinactive, dswaterwitch and dsick2 (insect cytokine 2) treatments showed increased sensitivity to mechanical stimulation leading to tonic immobility. THE ROLES OF TRANSIENT RECEPTOR POTENTIAL CHANNELS IN THERMOSTATIC BEHAVIOR, IN THERMAL ACCLIMATION, AND IN TONIC IMMOBILITY IN THE RED FLOUR BEETLE, TRIBOLIUM CASTANEUM (COLEOPTERA: TENEBRIONIDAE)
4.1 History of Discovery of Hyperthermophiles

Introduction: My Scientific Interests Before Woese’s Discovery of the Archaea . 404 How the Discovery of the Archaea Changed My Science . 404 ‘‘Falling in Love’’ with Hot Volcanic Environments and Their Microbes . 406 Discovery of Life Above 100 C . 409 Continued Hunting for Novel Hyperthermophiles . 412 Sampling and Cultivation . 413 Energy Sources and Lifestyle . 414 Examples of Recent Hyperthermophilic Isolates . 416 Time to Quit . 422 Cross-References . 423
Digestion and metabolism in the gastrointestinal tract

In NorFor the digestion and metabolism are simulated in three compartments: (1) the rumen, (2) the small intestine and (3) the large intestine. This chapter describes the modelling of the digestion processes in the three compartments and the microbial OM synthesis in the rumen and large intestine. Most of the equations in this chapter could have been presented in a simpler form, but we present them here in the format they are implemented in the computer program since we believe this makes it easier to follow their biological rationale.
Phylogeography and taxonomy of the Indo-Pacific reef cave dwelling coralline demosponge Astrosclera 'willeyana': new data from nuclear internal transcribed spacer sequences

Astrosclera `willeyana' is a common `living fossil' coralline demosponge, living in cryptic areas of Indo-Pacific coral reefs with an alleged widespread distribution from the Red Sea to Tahiti. Spicule morphology (geometry, size, ornamentation) the main taxonomic character for sponge classification is highly variable between regional populations supporting the hypothesis that there may be more than one species of Astrosclera. An initial genetic (PCR-RFLP) survey of the internal transcribed spacer (ITS) regions of rDNA of several populations by Worheide (1998, Facies 38: 1-88) did not detect any genetic differences that would support species distinction based solely on phenotypic criteria. We have now sequenced the ITS regions of 12 specimens from the Red Sea, the Great Barrier Reef, Fiji, and Vanuatu and found small, but consistent differences in sequences from allopatric populations. These consistent morphological and genetic differences between populations are now regarded as clear evidence for the presence of at least two distinct cryptic species in addition to Astrosclera willeyana sensu stricto, originally described from the Loyalty Islands. Our Fiji/Vanuatu population most likely represents Astrosclera willeyana s.s. , the two new cryptic species are Astrosclera sp. 1 (Red Sea), Astrosclera sp. 2 (GBR, Osprey Reef). Taxa will be formally described elsewhere. 1 Queensland Centre for Biodiversity, Queensland Museum, P.O. Box 3300, South Brisbane, Qld 4101, Australia. E-mail: GertW@qm.qld. gov.au 2 Department of Zoology and Entomology, The University of Queensland, St. Lucia, Qld 4072, Australia 3 Abt. Geobiologie, Gottinger Zentrum Geowissenschaften, Goldschmidtstr. 3, 33077 Gottingen, Germany
Characterization of Vitronectin and Plasminogen Activator Inhibitor Type 1: Insights into Metal Binding, and Production of Reagents to Facilitate Structural Studies

Vitronectin is a multifunctional glycoprotein involved in regulation of such processes as hemostasis, cell migration, immunity, and tumor metastasis. Many of its functions require interaction with various binding partners. One such partner, plasminogen activator inhibitor-type 1 (PAI-1), belongs to the serine protease inhibitor (serpin) superfamily of proteins. PAI-1 helps regulate hemostasis by affecting blood clot breakdown, and helps regulate cell migration and tissue remodeling by affecting extracellular matrix digestion. Our laboratory is pursuing structural information on vitronectin and the complex formed between vitronectin and PAI-1. To this end, the work presented in this thesis focuses on two aims: characterizing the interaction of vitronectin and PAI-1 with metal ions, and developing reagents to be used in structural studies of vitronectin. We have used electron paramagnetic resonance (EPR) spectroscopy to study metal binding by vitronectin and PAI-1. We have tested vitronectin and PAI-1 for binding of Mn and Cu, and also established the feasibility of studying protein-Cu interaction in solution by EPR, using bovine serum albumin (BSA) and Cu. In another set of experiments, we have used activity assays to assess the effect of metal ions on PAI-1 activity and on stabilization of PAI-1 by vitronectin. Regarding reagents, we have expressed and purified active, perdeuterated PAI-1, which can be used in complex with vitronectin in neutron scattering and NMR experiments. We characterized several monoclonal antibodies to vitronectin, and identified one suitable for use in cocrystallization screens. These accomplishments will aid in development of a more detailed picture of the interaction between vitronectin and PAI-1. iv
Do the gluteal muscles influence dynamic knee valgus when single-leg landing?

Background: The presence of dynamic knee valgus on landing has been found to be a significant risk factor in the development non-contact anterior cruciate ligament ACL injury. Gluteal muscles especially gluteus maximus and medius are believed to have a role in controlling hip motion that is associated with dynamic knee valgus. Landing onto one leg is a common scenario of ACL injury mechanism and would appear to require considerable Gluteal muscle activity to control the forces if the relationship were true. Aim: the aim of the study was to investigate the relationship between the Gluteal muscles (strength and EMG activity) and the degree of dynamic knee valgus during Single Leg Squat (SLS) and multi-directional single leg landing. Methods: Thirty-four active, healthy participants comprising of 17 males and 17 females participated in this study. Hip extension and abduction isokinetic (concentric / eccentric) strength was assessed, gluteus maximus and gluteus medius muscles Electromyography (EMG) activity was also assessed along with 3D motion lower limb biomechanics during SLS and multi-directional single leg landing tasks. Findings: Moderate correlations were found between gluteus medius EMG activity and hip adduction angles during all landing tasks with R2 ranging from 0.13 to 0.22. Gluteus medius EMG activity moderately correlated with knee abduction angle during right SLS and with internal hip rotation angle during left SLS. Significant moderate to strong correlations between hip abductors’ and extensors’ strength and knee abduction angle, hip adduction angle, knee abduction moment, hip adduction moment and internal hip rotation moment were found during landing tasks with R2 ranging from 0.11 to 0.26. Conclusion: There appears to be limited to moderate relationships existing between Gluteal muscles strength and EMG activity and lower limb biomechanical variables during SLS and multi-directional single leg landing tasks. Furthermore, the relationship appears also to be task, limb and gender dependent. Keywords: ACL, Landing, gluteal muscles, Hip, Strength, EMG, Biomechanics.
Influence of Anti-Mullerian Hormone on ART Outcomes in Infertility Patients of Different Ages

Changes in life patterns in most developed countries have resulted in marriage at a later age. The mean age of couples has increased gradually, which may expose them to an age-related fertility disorder. Such social and clinical cases are considered a serious problem that leads to population decline. Aging accompanies diminished ovarian reserves and further understanding of reproductive physiology at middle age is critical for mobilizing developmentally competent oocytes during infertility treatment in aging women. Thus, establishing new parameters to precisely predict fecundity of a patient contributes to developing an efficient applied reproductive technology (ART) program for couples that marry late. Aging induces a gradual decrease in the level of endogenous antiMullerian hormone (AMH), which directly influences the number of primordial follicles [1-3] and the sensitivity of the ovarian follicles to the follicle stimulating hormone (FSH)-dependent follicular wave [4] and folliculogenesis [5, 6]. Due to its relationship with endogenous FSH levels, AMH has been used as a parameter to evaluate the status of the controlled ovarian hyperstimulation cycle [7-13]. Based on previous reports, we evaluated whether measuring blood AMH levels would be useful to predict ART outcomes in middle-aged, infertile patients. Two major factors, the AMH level and patient age, were used to categorize the patients, and various patient profiles and ART outcomes including
Raffinose family oligosaccharides (RFO) biosynthesis in chickpea (Cicer arietinum L.) seeds

To increase the global acceptability of chickpea by improving its nutritional quality, seed RFO (Raffinose Family Oligosaccharides) concentration needs to be reduced without affecting their role during seed development and positive impact on human health. To achieve this objective, the key regulating step(s) of RFO biosynthesis needs to be identified. The three main objectives of the thesis were: (1) to optimize an analytical method to determine soluble sugars concentration in chickpea seeds including RFO, (2) to determine chickpea genotypes with contrasting seed RFO concentration, and (3) to optimize and validate RFO biosynthetic enzyme activity assays. These three objectives of the thesis provided basis of the fourth objective. For the first objective, a modified HPAEC-PAD (High performance anion exchange chromatography with pulsed amperometric detector) based gradient approach was optimized to study the concentration and composition of soluble sugars in chickpea seeds. The optimized method separated all the soluble sugars within 20 min of run time with higher accuracy, sensitivity and precision compared to previously reported methods. Therefore, the optimized method was utilized to study the natural variation in RFO concentration of 171 chickpea genotypes. Sucrose (0.60 - 3.59 g/100 g) and stachyose (0.18 − 2.38 g/100 g) were predominant among soluble sugars and RFO, respectively. Analysis of variance revealed a significant impact (P ≤ 0.001) of genotype (G), environment (E), and their interaction (G×E) on seed RFO concentration in chickpea. A significant positive correlation was observed between substrate and product concentration in RFO biosynthesis. Raffinose, stachyose and verbascose showed moderate broad sense heritability (0.25 − 0.56) suggesting the quantitative nature of the RFO trait in chickpea seeds. Desi (ICC 1163, ICC 1471, ICC 9562, ICCV 07115, ICCV 07116 and ICCV 07117) and kabuli (ICC 5270, ICC 10674, ICC 16216, ICC 16528, ICCV 3 and ICCV 91302) chickpea genotypes with high and low RFO concentrations (high RFO genotypes are underlined) were identified. RFO biosynthetic enzymes activities were optimized for substrate and protein concentration, temperature (25 °C), time (10 min for galactinol synthase and 60 min for other biosynthetic enzymes) and pH (7.0). These assays were validated at different seed developmental stages of two released varieties: CDC Vanguard and CDC Frontier. Simultaneously, RFO accumulation at different seed developmental stages was also studied. During 18 - 38 DAF (days after flowering), about a 75 % decrease in seed moisture was observed coinciding with the accumulation of RFO providing desiccation tolerance to maturing seeds. The initial substrates viz. myo-inositol and sucrose were observed throughout seed development process having maximum accumulation at 18 - 20 (0.50 – 0.57 g/100 g) and 20 - 22 (9.94 - 11.17 g/100 g) DAF that decreased afterwards supporting the biosynthesis of galactinol and raffinose, respectively. Galactinol is considered as the universal galactosyl…
Selection of folate-producing lactic acid bacteria for improving fermented goat milk

Goat milk is a complete food but its low level of folic acid diminisches its nutritional efficacy. In this study, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lb. delbrueckii subsp. lactis and Lb. helveticus strains were selected for folate production in goat milk to improve its quality. A suitable HPLC method was developed to directly determine both total folate and its biologically active derivatives such as 5-methyl-tetrahydrofolate (5- CH 3 -H 4 -PteGlu), tetrahydrofolate (H 4 -PteGlu) and 5 formyl-tetrahydrofolate (5-CHO-H 4 -PteGlu). Results showed that S. thermophilus, Lb. delbrueckii subsp. lactis and Lb. helveticus strains produced higher amounts of total folate than Lb. delbrueckii subsp. bulgaricus , especially 5-CH 3 -H 4 -PteGlu and H 4 -PteGlu. Moreover the use of selected S. thermophilus strains in association with Lb. delbrueckii subsp. bulgaricus resulted in yoghurt with a significant quantity of folate and good organoleptic features.
Shortleaf pine reproduction abundance and growth in pine-oak stands in the Missouri Ozarks

We conducted an operational study to evaluate effect of site preparation treatments on pine reproduction density and the impact of overstory basal area and understory density on pine reproduction height and basal diameter in pine-oak stands in the Missouri Ozarks. Stands were harvested to or below B-level stocking, but patchiness of the oak decline lead to some plots having no overstory and some having over 200 ft2/ac basal area at the end of the study. In all stands, the midstory and understory were chainsaw felled. If stands were inadequately stocked with pine reproduction, then mechanical scarifying or prescribed burning treatments were applied to increase the density of shortleaf pine reproduction. Pine reproduction basal diameter, height, and crown class within the understory were measured three to eight growing seasons later. We found no long-term difference in pine reproduction density by treatment. Overstory density and reproduction competition both affected the growth of shortleaf pine seedlings. The basal diameter and height of pine reproduction were greatest when overstory basal area was low, reproduction density was low, and pine seedlings were dominant or codominant to competitors within the understory. Pines had an 80 percent chance of being dominant/codominant with 2,000 TPA of mixed-species reproduction with no overstory, but only a 50 percent probability with 6,000 TPA of reproduction and 70 ft2/ac of overstory basal area.