Alteration of the C-terminal ligand specificity of the Erbin PDZ domain by allosteric mutational effects

Modulation of protein binding specificity is important for basic biology and for applied science. Here we explore how binding specificity is conveyed in PDZ (postsynaptic density protein-95/discs large/zonula occludens-1) domains, small interaction modules that recognize various proteins by binding to an extended C terminus. Our goal was to engineer variants of the Erbin PDZ domain with altered specificity for the most C-terminal position (position 0) where a Val is strongly preferred by the wild-type domain. We constructed a library of PDZ domains by randomizing residues in direct contact with position 0 and in a loop that is close to but does not contact position 0. We used phage display to select for PDZ variants that bind to 19 peptide ligands differing only at position 0. To verify that each obtained PDZ domain exhibited the correct binding specificity, we selected peptide ligands for each domain. Despite intensive efforts, we were only able to evolve Erbin PDZ domain variants with selectivity for the aliphatic C-terminal side chains Val, Ile and Leu. Interestingly, many PDZ domains with these three distinct specificities contained identical amino acids at positions that directly contact position 0 but differed in the loop that does not contact position 0. Computational modeling of the selected PDZ domains shows how slight conformational changes in the loop region propagate to the binding site and result in different binding specificities. Our results demonstrate that second-sphere residues could be crucial in determining protein binding specificity.

Using genome-Wwide complex trait analysis to quantify 'missing heritability' in Parkinson's disease

Genome-wide association studies (GWASs) have been successful at identifying single-nucleotide polymorphisms (SNPs) highly associated with common traits; however, a great deal of the heritable variation associated with common traits remains unaccounted for within the genome. Genome-wide complex trait analysis (GCTA) is a statistical method that applies a linear mixed model to estimate phenotypic variance of complex traits explained by genome-wide SNPs, including those not associated with the trait in a GWAS. We applied GCTA to 8 cohorts containing 7096 case and 19 455 control individuals of European ancestry in order to examine the missing heritability present in Parkinson's disease (PD). We meta-analyzed our initial results to produce robust heritability estimates for PD types across cohorts. Our results identify 27% (95% CI 17-38, P = 8.08E - 08) phenotypic variance associated with all types of PD, 15% (95% CI -0.2 to 33, P = 0.09) phenotypic variance associated with early-onset PD and 31% (95% CI 17-44, P = 1.34E - 05) phenotypic variance associated with late-onset PD. This is a substantial increase from the genetic variance identified by top GWAS hits alone (between 3 and 5%) and indicates there are substantially more risk loci to be identified. Our results suggest that although GWASs are a useful tool in identifying the most common variants associated with complex disease, a great deal of common variants of small effect remain to be discovered. © Published by Oxford University Press 2012.

Rockmelon Processing Quality

Considerable export opportunities exist in countries such as Japan, Canada, and Europe (Germany) for peeled rockmelon frozen in quarters or as diced product. Processing of these products is limited because the cost of hand labour for peeling is prohibitive. Consequently, development of mechnanical peeling equipment is essential for Australian industry to compete. In this project, appropriate machinery for the production of a high quality product is being developed, and basic studies in food technology, marketing, and production are being carried out. There are no Australian publications on rockmelon freezing, although fresh fruit quality of various cultivars has been investigated (Mutton, 1978). Very little overseas information on freezing rockmelons has been published (del Rio and Miller, 1979 and Martinez-Javega et al., 1975). In this project, the freezing quality of new rockmnelon and honeydew melon cultivars was evaluated.

Fundamental Principles and Rights At Work: Value, Viability, Incidence and Importance as Elements For Economic Progress and Social Justice

Working Paper prepared for the ILO by Maria Luz Vega Ruiz and Daniel Martinez, focusing on the rights at work in Latin America and the Caribbean.

Impact of working conditions on the quality of working life: Case manufacturing sector colombian Caribbean Region [Impacto de las Condiciones de Trabajo en Calidad de Vida Laboral: Caso del Sector Manufacturero de la Región Caribe Colombiana]

La presenta investigación centra su atención en evaluar el impacto de las Condiciones de Trabajo en la Calidad de Vida Laboral del talento humano de sector manufacturero de la región Caribe colombiana. Para analizar este proceso se entrevistaron a 518 empleados del sector. El diseño utilizado fue no experimental de tipo transversal descriptivo, puesto que a cada participante se le aplicó una entrevista con el instrumento de Condiciones de Trabajo y la Herramienta de Calidad de Vida Laboral (Condiciones Salariales y Subjetivas). Los datos fueron analizados mediante análisis de correlación y modelos de regresión logística. Los resultados mostraron que el ambiente térmico y las normas de seguridad en el trabajo afectan de forma positiva la Calidad de Vida Laboral de los empleados del sector. Estos resultados ponen de manifiesto que la relación entre las condiciones de trabajo y la CVL se basa en la competencia y distan de ser una relación lineal y simple relacionada con la consideración de la presencia o la ausencia de las condiciones de trabajo. Ello tiene implicaciones a la hora de formular políticas, programas e intervenciones para prevenir, erradicar y amortiguar los efectos negativos de las condiciones de trabajo y mejorar la seguridad industrial dentro de las empresas.

Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive dugongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

Implications of high level pseudogene transcription in Mycobacterium leprae

Background: The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and translational potentials of this genome should increase our understanding of their impact on M. leprae physiology. Results: Gene expression analysis identified transcripts from 49% of all M. leprae genes including 57% of all ORFs and 43% of all pseudogenes in the genome. Transcribed pseudogenes were randomly distributed throughout the chromosome. Factors resulting in pseudogene transcription included: 1) co-orientation of transcribed pseudogenes with transcribed ORFs within or exclusive of operon-like structures; 2) the paucity of intrinsic stem-loop transcriptional terminators between transcribed ORFs and downstream pseudogenes; and 3) predicted pseudogene promoters. Mechanisms for translational ``silencing'' of pseudogene transcripts included the lack of both translational start codons and strong Shine-Dalgarno (SD) sequences. Transcribed pseudogenes also contained multiple ``in-frame'' stop codons and high Ka/Ks ratios, compared to that of homologs in M. tuberculosis and ORFs in M. leprae. A pseudogene transcript containing an active promoter, strong SD site, a start codon, but containing two in frame stop codons yielded a protein product when expressed in E. coli. Conclusion: Approximately half of M. leprae's transcriptome consists of inactive gene products consuming energy and resources without potential benefit to M. leprae. Presently it is unclear what additional detrimental affect(s) this large number of inactive mRNAs has on the functional capability of this organism. Translation of these pseudogenes may play an important role in overall energy consumption and resultant pathophysiological characteristics of M. leprae. However, this study also demonstrated that multiple translational ``silencing'' mechanisms are present, reducing additional energy and resource expenditure required for protein production from the vast majority of these transcripts.

X-ray scattering and diffraction enhanced imaging studies of in vitro breast tissues

This thesis is a study of the x-ray scattering properties of tissues and tumours of the breast. Clinical radiography is based on the absorption of the x-rays when passing right through the human body and gives information about the densities of the tissues. Besides being absorbed, x-rays may change their direction within the tissues due to elastic scattering or even to refraction. The phenomenon of scattering is a nuisance to radiography in general, and to mammography in particular, because it reduces the quality of the images. However, scattered x-rays bear very useful information about the structure of the tissues at the supra-molecular level. Some pathologies, like breast cancer, produce alterations to the structures of the tissues, being especially evident in collagen-rich tissues. On the other hand, the change of direction due to refraction of the x-rays on the tissue boundaries can be mapped. The diffraction enhanced imaging (DEI) technique uses a perfect crystal to convert the angular deviations of the x-rays into intensity variations, which can be recorded as images. This technique is of especial interest in the cases were the densities of the tissues are very similar (like in mammography) and the absorption images do not offer enough contrast. This thesis explores the structural differences existing in healthy and pathological collagen in breast tissue samples by the small-angle x-ray scattering (SAXS) technique and compares these differences with the morphological information found in the DEI images and the histo-pathology of the same samples. Several breast tissue samples were studied by SAXS technique in the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Scattering patterns of the different tissues of the breast were acquired and compared with the histology of the samples. The scattering signals from adipose tissue (fat), connective tissue (collagen) and necrotic tissue were identified. Moreover, a clear distinction could be done between the scattering signals from healthy collagen and from collagen from an invasive tumour. Scattering from collagen is very characteristic. It includes several scattering peaks and scattering features that carry information about the size and the spacing of the collagen fibrils in the tissues. It was found that the collagen fibrils in invaded tumours were thinner and had a d-spacing length 0,7% longer that fibrils from healthy tumours. The scattering signals from the breast tissues were compared with the histology by building colour-coded maps across the samples. They were also imaged with the DEI technique. There was a total agreement between the scattering maps, the morphological features seen in the images and the information of the histo- pathological examination. The thesis demonstrates that the x-ray scattering signal can be used to characterize tissues and that it carries important information about the pathological state of the breast tissues, thus showing the potential of the SAXS technique as a possible diagnostic tool for breast cancer.

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN.

Fabrication of Yy‐Pr1‐y ‐Ba‐Cu‐O Thin Films and Superlattices of ‐Ba‐Cu‐O/Yy‐Pr1‐y ‐Ba‐Cu‐O

We have prepared epitaxial thin films of Yy‐Pr1‐y‐Ba‐Cu‐O (y= 1 to 0) and superlattices of Y‐Ba‐Cu‐O/Yy‐Pr1‐y ‐Ba‐Cu‐O using pulsed laser deposition technique. The zero resistance transition temperatures of Yy‐Pr1‐y‐Ba‐Cu‐O bulk samples are reproduced in the films. The composition oscillations in the superlattices are observed by SIMS. The films and superlattices are found to have c‐axis orientations and good crystallinity.

A Multicast Authentication Protocol (MAP) for Dynamic Multicast Groups in Wireless Networks

In this paper, we have proposed a centralized multicast authentication protocol (MAP) for dynamic multicast groups in wireless networks. In our protocol, a multicast group is defined only at the time of the multicasting. The authentication server (AS) in the network generates a session key and authenticates it to each of the members of a multicast group using the computationally inexpensive least common multiple (LCM) method. In addition, a pseudo random function (PRF) is used to bind the secret keys of the network members with their identities. By doing this, the AS is relieved from storing per member secrets in its memory, making the scheme completely storage scalable. The protocol minimizes the load on the network members by shifting the computational tasks towards the AS node as far as possible. The protocol possesses a membership revocation mechanism and is protected against replay attack and brute force attack. Analytical and simulation results confirm the effectiveness of the proposed protocol.

Wireless Aircraft Fuel Quantity Indication System

A wireless fuel quantity indication system (FQIS) has been developed using an RFID-enabled sensing platform. The system comprises a fully passive tag, modified reader protocol, capacitive fuel probe, and auxiliary antenna for additional energy harvesting. Results of fluid testing show sensitivity to changes in fluid height of less than 0.25in. An RF-DC harvesting circuit was developed, which delivers up to 5dBm of input power through a remote radio frequency (RF) source. Testing was conducted in a loaded reverberation chamber to emulate the fuel tank environment. Results demonstrate feasibility of the remote source to power the sensor with less than 1W of maximum transmit power and under 100ms dwell time (100mW average power) into the tank. This indicates adequate coverage for large transport aircraft at safe operating levels with a sample rate of up to 1 sample/s.

Estabilidad aerobica del ensilaje de marango con diferentes proporciones de Taiwan, Caña de Azucar y Melaza

El experimento se realizó en las instalaciones de la facultad de Ciencia Animal ubicada en la finca "Santa Rosa" de la Universidad Nacional Agraria, en la comunidad de Sabana Grande, Managua, Nicaragua, localizada geográficamente a los 12 o 08’ 15’’latitud norte y 86 o 09’ 36’ longitud oeste. La temperatura promedio anual es de 28 oC y una precipitación promedio anual de 1,200 mm y aproximadamente una altura de 56 msnm. El objetivo del experimento fue generar conocimientos sobre los procesos de degradación aeróbica en ensilajes de marango (Moringa oleífera)con diferentes proporciones de caña de azúcar ( Saccharum officinarum), pasto Taiwán (Penisetum purpureum), y Melaza. Se utilizaron 14 tratamientos con 3 repeticiones cada uno distribuidos en Diseño Completamente al Azar; donde se evaluó Marango en proporciones de 31.66, 33.00, 33.33, 63.33, 66.00, 66.66, 95.00 y 99.00%. Taiwán en las mismas proporciones, Caña de azúcar en proporciones de 33.33, 66.33 y 100%, y Melaza en proporción de 1 y 5% cuando la caña no estaba presente. Las variables evaluadas fueron Materia Seca (MS), Proteina Cruda (PC), Dióxido de Carbono (CO2), Tiempo al Deterioro (TAD) y pH. Se realizó Análisis de Varianza y comparaciones de medias con la Prueba de Tukey al 5% cuando se encontró diferencia s significativas entre tratamientos, paras eso se uso SAS versión 9.1. Los resultados de los análisis de varianza ( P<0,05)mostraron que el tratamiento con menor perdida de M S y PB fue el T1 (T99M1) con 4.08, menor pH el T10 (M33 C66) con 4.13, mayor TAD fue el T1 (T99M1) con 14.75 días y producción de CO2 fuel T7 (M95M5) con 43.06. En conclusión los tratamientos con diferentes proporciones de marango también demostra ron diferencias significativas con respectos a la pérdida de Proteina Cruda (PC) siend o estos viables para ser utilizados por productores como suplementos proteicos, aunque demostraron no ser estables ya en condiciones aérobicas.

Efecto de la densidad de siembra y nivel de fertilizacion nitrogenada sobre el rendimiento de Moringa oleifera en suelo franco arcilloso. Universidad Nacional Agraria (UNA). Managua, Nicaragua

El presente trabajo se realizó con el objetivo de evaluar el efecto de dos densidades de siembra y cuatro niveles nitrogenados sobre la producción de Moringa oleífera. El ensayo se llevó a cabo en la finca Santa Rosa, localizada geográficamente de 12°08’15’’ a latitud Norte y 86°09’36’’ a longitud e ste, municipio de Managua, de mayo 2008 a septiembre 2009; el diseño experimental fue un bifactorial con parcela dividida usando las densidades como parcela principal (100,000 plantas ha-1 y 166,666 plantas ha-1) y los niveles de fertilización (0 kg N ha año-1, 446 kg N ha año-1, 906.2 kg N ha año-1, 1334 kg N ha año-1)como sub -parcela. Las variables de estudio fueron: rendimiento de materia fresca total (RMFT), rendimiento de materia fresca fracción fina (RMFFF), rendimiento de materia fresca fracción gruesa (RMFFG), rendimiento de materia seca total (RMST), rendimiento de materia seca fracción fina (RMSFF), rendimiento de materia seca fracción gruesa (RMFFG), a ltura promedio de plantas, Mortalidad de plantas y Tasa de crecimiento (TC). Se realizó análisis de varianza (ANDEVA) y comparaciones con la prueba de Tukey utilizando MINITAB, versión 13.0. Los resultados en el ANDEVA, mostraron que la fertilización presentó efecto significativo (P<0.05) con los mejores rendimientos el nivel 150 %, con RMFT (69.17 to n ha año-1), RMFFF (60.72 ton ha año-1), RMFG (8.45 ton ha año-1), RMST (10.81 ton ha año-1), RMSFF (9.69 ton ha año -1), RMSFG (1.12 ton ha año-1), Altura de las plantas(1.33 m) y TC( 28.91), la densidad de siembra presentó efectos significativos (P<0.05)sólo para la variable Mortalidad con (18.08 %).

Nemátodos fitoparásitos en palma africana Elaeis guineensis (Jacq) y cocotero Cocos nucifera L. en el Atlántico Sur, Nicaragua

Este estudio se llevó a cabo en plantaciones de Palma africana y cocotero de las regiones de Río San Juan y en la Región Autónoma del Atlántico Sur (R.A.A.S), con el objetivo de identificar nematodos asociados en ambos cultivos, contribuir a la actualización del listado nacional de nemátodos y determinar las infestación de Rhadinaphelencus cocophilus Cobb. en picudos (Rhynchophorus palmarum L.) de la palma y el cocotero Este trabajo se realizó en dos etapas; la primera consistió de dos muestreos (uno por región) y la última etapa fue de procesamiento y análisis de muestras. El primer muestreo se realizó en los lotes de las cooperativas Luisa A. Espinoza, El Borbollón y Teodoro Martinez en Kukra Hill para la palma africana y en coco se muestreo un lote del INTA, posteriormente se muestrearon las fincas; San Nicolás y San Mariano, luego se realizó un segundo muestreo en palma africana en el lote de la cooperativa Luisa A. Espinoza en Boca de Sábalos, Rio San Juan. La segunda etapa consistió en el análisis de las muestras; el cual se realizó inmediatamente después del muestreo. Se identificaron los géneros; Rotylenchulus, Trichodorus, Psilenchus, Aphe/enchoides, Paratylenchus, He/icotylenchus, Tylenchus, Xiphinema y Meloidogyne en el cultivo de palma africana y en cocotero se lograron identificar los siguientes géneros; Psílenchus, Aphelenchoides, Paratylenchus, Pratylenchus, Helicoty/enchus, Ty/enchus, Xiphinema y Rhadinaphelenchus. Para el cultivo de la palma africana, los géneros; Roty/enchus, Gracilacus, Psilenchus, Aphelenchoides, Paratylenchus y Meloidogyne fueron reportados por primera vez por lo que deberán ser agregados al listado nacional de plagas del MAG­FOR de la misma manera para el cultivo de coco, con los géneros; Aphelenchoides, Paratylenchus y Psilenchus. En los muestreos realizados en palma africana y coco en las localidades de Boca de Sábalos y en Kukra Hill se encontró la presencia de Rhynchophorus palmarum Linnaeus. En las fincas "San Nicolás" y "San Mariano", mas del 50 por ciento de los insectos (Rhynchophorus pa/marum Linnaeus) se encontraron infestados con el género Rhadinaphelenchus.