State-dependent modulation of neuronal circuits in C. elegans sleep

C. elegans is a compact system of 302 neurons with identifiable and mapped connections that makes it ideal for systems analysis. This work is a demonstration of what I have been able to learn about the nature of state-specific modulation and reversibility during a state called lethargus, a sleep-like state in the worm. I begin with description about the nervous system of the worm, the nature of sleep in the worm, the questions about behavior and its apparent circuit properties, the tools available and used to manipulate the nervous system, and what I have been able to learn from these studies. I end with clues that the physiology helps to teach us about the dynamics of state specific modulation, what makes sleep so different from other states, and how we can use these measurements to understand which modulators, neurotransmitters, and channels can be used to create different dynamics in a simple model system.

Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c

A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.

Signal transduction, regulation, and developmental logic of EGFR signalling in C. elegans

RTKs-mediated signaling systems and the pathways with which they interact (e.g., those initiated by G protein-mediated signaling) involve a highly cooperative network that sense a large number of cellular inputs and then integrate, amplify, and process this information to orchestrate an appropriate set of cellular responses. The responses include virtually all aspects of cell function, from the most fundamental (proliferation, differentiation) to the most specialized (movement, metabolism, chemosensation). The basic tenets of RTK signaling system seem rather well established. Yet, new pathways and even new molecular players continue to be discovered. Although we believe that many of the essential modules of RTK signaling system are rather well understood, we have relatively little knowledge of the extent of interaction among these modules and their overall quantitative importance.

My research has encompassed the study of both positive and negative signaling by RTKs in C. elegans. I identified the C. elegans S0S-1 gene and showed that it is necessary for multiple RAS-mediated developmental signals. In addition, I demonstrated that there is a SOS-1-independent signaling during RAS-mediated vulval differentiation. By assessing signal outputs from various triple mutants, I have concluded that this SOS-1-independent signaling is not mediated by PTP-2/SHP-2 or the removal of inhibition by GAP-1/ RasGAP and it is not under regulation by SLI-1/Cb1. I speculate that there is either another exchange factor for RASor an as yet unidentified signaling pathway operating during RAS-mediated vulval induction in C. elegans.

In an attempt to uncover the molecular mechanisms of negative regulation of EGFR signaling by SLI-1/Cb1, I and two other colleagues codiscovered that RING finger domain of SLI-1 is partially dispensable for activity. This structure-function analysis shows that there is an ubiquitin protein ligase-independent activity for SLI-1 in regulating EGFR signaling. Further, we identified an inhibitory tyrosine of LET-23/ EGFR requiring sli-1(+)for its effects: removal of this tyrosine closely mimics loss of sli-1 but not loss of other negative regulator function.

By comparative analysis of two RTK pathways with similar signaling mechanisms, I have found that clr-1, a previously identified negative regulator of egl-15 mediated FGFR signaling, is also involved in let-23 EGFR signaling. The success of this approach promises a similar reciprocal test and could potentially extend to the study of other signaling pathways with similar signaling logic.

Finally, by correlating the developmental expression of lin-3 EGF to let-23 EGFR signaling activity, I demonstrated the existence of reciprocal EGF signaling in coordinating the morphogenesis of epithelia. This developmental logic of EGF signaling could provide a basis to understand a universal mechanism for organogenesis.

Chemical composition of Iraq water resources (abbreviated translation) [Translation from: Vodnye Resursy 1975(4,) 173-185]

This abbreviated translation summarises the chemical composition of Iraq water resources. Among the described water bodies are the River Euphrates, Shatt al Arab River and a number of standing waters.

I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

Progressive Decrease in the Potential Usefulness of Meningococcal Serogroup B Vaccine (4CMenB, Bexsero (R)) in Gipuzkoa, Northern Spain

The effectiveness of a vaccine is determined not only by the immunogenicity of its components, but especially by how widely it covers the disease-causing strains circulating in a given region. Because vaccine coverage varies over time, this study aimed to detect possible changes that could affect vaccine protection during a specific period in a southern European region. The 4CMenB vaccine is licensed for use in Europe, Canada, and Australia and is mainly directed against Neisseria meningitidis serogroup B. This vaccine contains four main immunogenic components: three recombinant proteins, FHbp, Nhba and NadA, and an outer membrane vesicle [PorA P1.4]. The allelic distribution of FHbp, Nhba, NadA, and PorA antigens in 82 invasive isolates (B and non-B serogroups) isolated from January 2008 to December 2013 were analyzed. 4CMenB was likely protective against 61.8% and 50% of serogroup B and non-B meningococci, respectively, in the entire period, but between 2012 and 2013, the predicted protection fell below 45% (42.1% for serogroup B isolates). The observed decreasing trend in the predicted protection during the 6 years of the study (X-2 for trend = 4.68, p=0.03) coincided with a progressive decrease of several clonal complexes (e. g., cc11, cc32 and cc41/44), which had one or more antigens against which the vaccine would offer protection.

Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal 'Out-of-Africa' route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started similar to 40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia similar to 15 KYA and finally made its way to the Americas. Journal of Human Genetics (2010) 55, 428-435; doi:10.1038/jhg.2010.40; published online 7 May 2010

Merging effects of vitamin E and C on biological factors, blood characteristics and resistance against thermal stress in rainbow trout (Onchorhyncus mykiss)

This study was conducted to assay the effects of different levels of dietary vitamins C and E on growth indices and survival and resistance against thermal stress of rainbow trout (Oncorhynchus mykiss) in pond culture of Marzan abad from December 2011 to February 2011. Seven diets were supplemented. 300 fish with the average weight of 17 g were introduced to ponds for 60 days. The results showed that the highest and the lowest weight gain were in fish fed with diet containing 50 mg/kg vitamin C and E and 0 mg/kg vitamin C and E(control) , respectively. The highest and the lowest Feed Conversion Ratio (FCR) were measured in control and diet 50 mg/kg vitamin C and E. There is a significant difference in their treatments (P<0.05). Also, the lowest and highest amount of Weight Gain (WG) were observed in (E) treatment with 165.04% and 117.5% in control, the highest and lowest Specific Growth Rate (SGR), Protein Efficiency Ratio (PER), Condition Factor (CF) was found in control and treatment 50 mg/kg vitamin C and E, respectively(P<0.05). In conclusion vitamin C and E have an important role in enhancement of growth performance and feed efficiency of rainbow trout.The highest red blood cells were found in combined treatments and which the vitamin C was added.The highest RBC were found in E treatment(1.1×104 /mm3) and the lowest one in control (P˂0.05). Counting white blood cells also confirmed highest quantity in combined treatments with (69.83×104/mm3) and the lowest one (28.83×104 /mm3) in control. In conclusion these vitamins have a significant role in blood characteristics. Meantime, the resistance against termal stress was measured at the end of 60 days by facing fishes into 5 centigrade warmer water so consentration of Cortisol and Glucose measured for this reason.The lowest cortisol amount was measured in E treatment with 188.74 ng/ml and the highest was found in control(P<0.05). There was a significant difference in blood glucose consentration of fishes in F treatment with (78.66 mg/dl) and control with 136 mg/dl as a highest one(P<0.05).

On-going generation of multiple forms of HIV-1 intersubtype recombinants in the Yunnan Province of China

Objectives: To investigate the molecular epidemiology of HIV in China's Yunnan Province, where the initial HIV-1 outbreak among injecting drug users (IDU) occurred in 1989, and to analyse the genesis and interrelationship of the epidemic with that in surrounding areas. Design: A molecular epidemiological investigation was conducted among IDU in three prefectures in Yunnan Province, including Wenshan (east), Honghe (southeast) and Dehong (west). Methods: Thirty-nine specimens were collected from consenting IDU in 2000-2001. The nucleotide sequences of 2.6 kb gag-RT and 340 base pair (bp) env (C2/V3) regions were determined. Phylogenetic tree and recombination breakpoint analyses were performed. Results: The circulating recombinant form (CRF), CRF08_BC, predominated in east Yunnan near Guangxi Province (89% in Wenshan and 81% in Honghe), whereas it was not detected in Dehong(0/14) in the west. In contrast, 71% (10/14) of the Dehong isolates were unique recombinant forms (URF), mostly between subtypes B' (Thailand variant of subtype B) and C, with distinct profiles of recombination breakpoints. The subtype B' accounts for the remaining 29% (4/14) of Dehong isolates. Interestingly, two Honghe isolates (2/16) shared some of the precise B'/C recombination breakpoints with CRF07_BC. Conclusion: New recombinant strains are arising continually in west Yunnan near the Myanmar border. Some appeared to be secondary recombinants derived from CRF07_BC that had further recombined with other strains. The uneven distribution of subtypes, CRF and URF, suggests the presence of independent transmission networks and clusters among IDU in Yunnan. (C) 2002 Lippincott Williams Wilkins.

A subdivision-based implementation of the hierarchical b-spline finite element method

A novel technique is presented to facilitate the implementation of hierarchical b-splines and their interfacing with conventional finite element implementations. The discrete interpretation of the two-scale relation, as common in subdivision schemes, is used to establish algebraic relations between the basis functions and their coefficients on different levels of the hierarchical b-spline basis. The subdivision projection technique introduced allows us first to compute all element matrices and vectors using a fixed number of same-level basis functions. Their subsequent multiplication with subdivision matrices projects them, during the assembly stage, to the correct levels of the hierarchical b-spline basis. The proposed technique is applied to convergence studies of linear and geometrically nonlinear problems in one, two and three space dimensions. © 2012 Elsevier B.V.