Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase

Archaeal transcription utilizes a complex multisubunit RNA polymerase and the basal transcription factors TBP and TF(II)B, closely resembling its eukaryal counterpart. We have uncovered a tight physical and functional interaction between RNA polymerase and the single-stranded DNA-binding protein SSB in Sulfolobus solfataricus. SSB stimulates transcription from promoters in vitro under TBP-limiting conditions and supports transcription in the absence of TBP. SSB also rescues transcription from repression by reconstituted chromatin. We demonstrate the potential for promoter melting by SSB, suggesting a plausible basis for the stimulation of transcription. This stimulation requires both the single-stranded DNA-binding domain and the acidic C-terminal tail of the SSB. The tail forms a stable interaction with RNA polymerase. These data reveal an unexpected role for single-stranded DNA-binding proteins in transcription in archaea.

Single-stranded DNA-binding protein hSSB1 is critical for genomic stability

Single-strand DNA (ssDNA)-binding proteins (SSBs) are ubiquitous and essential for a wide variety of DNA metabolic processes, including DNA replication, recombination, DNA damage detection and repair1. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating nucleases, helicases and strand-exchange proteins, activating transcription and mediating protein–protein interactions. In eukaryotes, the major SSB, replication protein A (RPA), is a heterotrimer1. Here we describe a second human SSB (hSSB1), with a domain organization closer to the archaeal SSB than to RPA. Ataxia telangiectasia mutated (ATM) kinase phosphorylates hSSB1 in response to DNA double-strand breaks (DSBs). This phosphorylation event is required for DNA damage-induced stabilization of hSSB1. Upon induction of DNA damage, hSSB1 accumulates in the nucleus and forms distinct foci independent of cell-cycle phase. These foci co-localize with other known repair proteins. In contrast to RPA, hSSB1 does not localize to replication foci in S-phase cells and hSSB1 deficiency does not influence S-phase progression. Depletion of hSSB1 abrogates the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets after ionizing radiation. Cells deficient in hSSB1 exhibit increased radiosensitivity, defective checkpoint activation and enhanced genomic instability coupled with a diminished capacity for DNA repair. These findings establish that hSSB1 influences diverse endpoints in the cellular DNA damage response.

Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis

In total, 782 Escherichia coli strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal- and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.

The use of supply chain management to reduce delays : Malaysian public sector construction projects

Construction delays are a critical problem for Malaysian public sector projects. These delays have been blamed mainly on inefficient traditional construction practices that continue to dominate the current industry. This paper reports the progress to date of a Ph.D. research project aimed at developing a framework to utilize Supply Chain Management (SCM) tools to improve the time performance of Malaysian Government projects. The potential of SCM has been identified for public sector governance and its use in Malaysia is now being considered within the strategy of the Malaysian Construction Industry Master Plan (2006-2015). Encouraged by success in the UK, there is a cautious optimism concerning the successful application of SCM in Malaysia. This paper considers delay as a problem in Malaysian public sector projects, establishes the need to embrace SCM and then elucidates the need and strategies for the development of a delay reduction framework. A literature review, survey mechanism and structured interview schedule will be undertaken to achieve the research objectives. The final research outcome will be a framework that addresses root delay contributors (“pathogens”) and applies SCM tools for their mitigation.

Single crystal Raman spectroscopy of natural leiteite ZnAs2O4 and in comparison with the synthesised mineral

The oriented single crystal Raman spectrum of leiteite has been obtained and the spectra related to the structure of the mineral. The intensities of the observed bands vary according to orientation allowing them to be assigned to either Ag or Bg modes. Ag bands are generally the most intense in the CAAC spectrum, followed by ACCA, CBBC, and ABBA whereas Bg bands are generally the most intense in the CBAC followed by ABCA. The CAAC and ACCA spectra are identical, as are those obtained in the CBBC and ABBA orientations. Both cross-polarised spectra are identical. Band assignments were made with respect to bridging and non-bridging As-O bonds.

A new unequal DC link voltage configuration for a single phase multilevel converter to reduce low order harmonics

Multilevel converters are used in high power and high voltage applications due to their attractive benefits in generating high quality output voltage. Increasing the number of voltage levels can lead to a reduction in lower order harmonics. Various modulation and control techniques are introduced for multilevel converters like Space Vector Modulation (SVM), Sinusoidal Pulse Width Modulation (SPWM) and Harmonic Elimination (HE) methods. Multilevel converters may have a DC link with equal or unequal DC voltages. In this paper a new modulation technique based on harmonic elimination method is proposed for those multilevel converters that have unequal DC link voltages. This new technique has better effect on output voltage quality and less Total Harmonic Distortion (THD) than other modulation techniques. In order to verify the proposed modulation technique, MATLAB simulations are carried out for a single-phase diode-clamped inverter.

A forensic investigation of single human hair fibres using FTIR-ATR spectroscopy and chemometrics

Human hair fibres are ubiquitous in nature and are found frequently at crime scenes often as a result of exchange between the perpetrator, victim and/or the surroundings according to Locard's Principle. Therefore, hair fibre evidence can provide important information for crime investigation. For human hair evidence, the current forensic methods of analysis rely on comparisons of either hair morphology by microscopic examination or nuclear and mitochondrial DNA analyses. Unfortunately in some instances the utilisation of microscopy and DNA analyses are difficult and often not feasible. This dissertation is arguably the first comprehensive investigation aimed to compare, classify and identify the single human scalp hair fibres with the aid of FTIR-ATR spectroscopy in a forensic context. Spectra were collected from the hair of 66 subjects of Asian, Caucasian and African (i.e. African-type). The fibres ranged from untreated to variously mildly and heavily cosmetically treated hairs. The collected spectra reflected the physical and chemical nature of a hair from the near-surface particularly, the cuticle layer. In total, 550 spectra were acquired and processed to construct a relatively large database. To assist with the interpretation of the complex spectra from various types of human hair, Derivative Spectroscopy and Chemometric methods such as Principal Component Analysis (PCA), Fuzzy Clustering (FC) and Multi-Criteria Decision Making (MCDM) program; Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and Geometrical Analysis for Interactive Aid (GAIA); were utilised. FTIR-ATR spectroscopy had two important advantages over to previous methods: (i) sample throughput and spectral collection were significantly improved (no physical flattening or microscope manipulations), and (ii) given the recent advances in FTIR-ATR instrument portability, there is real potential to transfer this work.s findings seamlessly to on-field applications. The "raw" spectra, spectral subtractions and second derivative spectra were compared to demonstrate the subtle differences in human hair. SEM images were used as corroborative evidence to demonstrate the surface topography of hair. It indicated that the condition of the cuticle surface could be of three types: untreated, mildly treated and treated hair. Extensive studies of potential spectral band regions responsible for matching and discrimination of various types of hair samples suggested the 1690-1500 cm^-1 IR spectral region was to be preferred in comparison with the commonly used 1750-800 cm^-1. The principal reason was the presence of the highly variable spectral profiles of cystine oxidation products (1200-1000 cm^-1), which contributed significantly to spectral scatter and hence, poor hair sample matching. In the preferred 1690-1500 cm^-1 region, conformational changes in the keratin protein attributed to the α-helical to β-sheet transitions in the Amide I and Amide II vibrations and played a significant role in matching and discrimination of the spectra and hence, the hair fibre samples. For gender comparison, the Amide II band is significant for differentiation. The results illustrated that the male hair spectra exhibit a more intense β-sheet vibration in the Amide II band at approximately 1511 cm^-1 whilst the female hair spectra displayed more intense α-helical vibration at 1520-1515cm^-1. In terms of chemical composition, female hair spectra exhibit greater intensity of the amino acid tryptophan (1554 cm^-1), aspartic and glutamic acid (1577 cm^-1). It was also observed that for the separation of samples based on racial differences, untreated Caucasian hair was discriminated from Asian hair as a result of having higher levels of the amino acid cystine and cysteic acid. However, when mildly or chemically treated, Asian and Caucasian hair fibres are similar, whereas African-type hair fibres are different. In terms of the investigation's novel contribution to the field of forensic science, it has allowed for the development of a novel, multifaceted, methodical protocol where previously none had existed. The protocol is a systematic method to rapidly investigate unknown or questioned single human hair FTIR-ATR spectra from different genders and racial origin, including fibres of different cosmetic treatments. Unknown or questioned spectra are first separated on the basis of chemical treatment i.e. untreated, mildly treated or chemically treated, genders, and racial origin i.e. Asian, Caucasian and African-type. The methodology has the potential to complement the current forensic analysis methods of fibre evidence (i.e. Microscopy and DNA), providing information on the morphological, genetic and structural levels.

Single crystal Raman spectroscopy of brandholzite Mg[Sb(OH)6]2•6H2O and bottinoite Ni[Sb(OH)6]2•6H2O and the polycrystalline Raman spectrum of mopungite Na[Sb(OH)6]

The single crystal Raman spectra of minerals brandholzite and bottinoite, formula M[Sb(OH)6]2•6H2O, where M is Mg+2 and Ni+2 respectively, and the non-aligned Raman spectrum of mopungite, formula Na[Sb(OH)6], are presented for the first time. The mixed metal minerals comprise of alternating layers of [Sb(OH)6]-1 octahedra and mixed [M(H2O)6]+2 / [Sb(OH)6]-1 octahedra. Mopungite comprises hydrogen bonded layers of [Sb(OH)6]-1 octahedra linked within the layer by Na+ ions. The spectra of the three minerals were dominated by the Sb-O symmetric stretch of the [Sb(OH)6]-1 octahedron, which occurs at approximately 620 cm-1. The Raman spectrum of mopungite showed many similarities to spectra of the di-octahedral minerals informing the view that the Sb octahedra gave rise to most of the Raman bands observed, particularly below 1200 cm-1. Assignments have been proposed based on the spectral comparison between the minerals, prior literature and density field theory calculations of the vibrational spectra of the free [Sb(OH)6]-1 and [M(H2O)6]+2 octahedra by a model chemistry of B3LYP/6-31G(d) and lanl2dz for the Sb atom. The single crystal data spectra showed good mode separation, allowing the majority of the bands to be assigned a symmetry species of A or E.

Single-crystal Raman spectroscopy of natural schafarzikite FeSb2O4 from Pernek, Slovak Republic

The single crystal Raman spectra of natural mineral schafarzikite FeSb2O4 from the Pernek locality of the Slovak Republic are presented for the first time. Raman spectra of natural mineral apuanite Fe2+Fe43+Sb4O12S, originating from the Apuan Alps in Italy, as well as spectra of synthetic ZnSb2O4 and arsenite mineral trippkeite CuAs2O4 are also presented for the first time. The spectra of the antimonite minerals are characterized by a strong band in the region 660 – 680 cm-1 with shoulders on either side, and a band of medium intensity near 300 cm-1. The spectrum of the arsenite mineral is characterized by a medium band near 780 cm-1 with a shoulder on the high wavenumber side and a strong band at 370 cm-1. Assignments are proposed based on the spectral comparison between the compounds, symmetry modes of the bands and prior literature. The single crystal spectra of schafarzikite showed good mode separation, allowing bands to be assigned a symmetry species of A1g, B1g, B2g or Eg.

Drivers of supply chain collaboration among Finnish manufacturers

This paper focuses on data exchange relationships and ways to improve collaboration in the supply chain. Initially, the paper examines the information needs and alternatives in supply chain management. In the second part, the paper identifies different sets of factors that are likely to influence information sharing with suppliers, from the manufacturers’ point of view. Results from a Finnish Manufacturing industry survey show that manufacturers provided substantial information on demand data, production schedules, and inventories to their suppliers. Respondents perceived delivery performance measured by the timeliness, accuracy, and defect rate of deliveries as the primary incentives for supplier collaboration. On the other hand, supplier image and the market in which the supplier operates were found to be less relevant in determining the intensity of collaboration.

Supply chain sustainability : a relationship management approach moderated by culture and commitment

This research explores the nature of relationship management on construction projects in Australia and examines the effects of culture, by means of Schwarz’s value survey, on relationships under different contract strategies. The research was based on the view that the development of a sustainable supply chain depends on the transfer of knowledge and capabilities from the larger players in the supply chain through collaboration brought about by relationship management. The research adopted a triangulated approach in which quantitative data were collected by questionnaire, interviews were conducted to explore and enrich the quantitative data and case studies were undertaken in order to illustrate and validate the findings. The aim was to investigate how values and attitudes enhance or reduce the incorporation of the supply chain into the project. From the research it was found that the degree of match and mismatch between values and contract strategy impacts commitment and the engagement and empowerment of the supply chain.

The measurement of applied forces during anterior single rod surgical correction of adolescent idiopathic scoliosis

INTRODUCTION. Following anterior thoracoscopic instrumentation and fusion for the treatment of thoracic AIS, implant related complications have been reported as high as 20.8%. Currently the magnitudes of the forces applied to the spine during anterior scoliosis surgery are unknown. The aim of this study was to measure the segmental compressive forces applied during anterior single rod instrumentation in a series of adolescent idiopathic scoliosis patients. METHODS. A force transducer was designed, constructed and retrofitted to a surgical cable compression tool, routinely used to apply segmental compression during anterior scoliosis correction. Transducer output was continuously logged during the compression of each spinal joint, the output at completion converted to an applied compression force using calibration data. The angle between adjacent vertebral body screws was also measured on intra-operative frontal plane fluoroscope images taken both before and after each joint compression. The difference in angle between the two images was calculated as an estimate for the achieved correction at each spinal joint. RESULTS. Force measurements were obtained for 15 scoliosis patients (Aged 11-19 years) with single thoracic curves (Cobb angles 47˚- 67˚). In total, 95 spinal joints were instrumented. The average force applied for a single joint was 540 N (± 229 N)ranging between 88 N and 1018 N. Experimental error in the force measurement, determined from transducer calibration was ± 43 N. A trend for higher forces applied at joints close to the apex of the scoliosis was observed. The average joint correction angle measured by fluoroscope imaging was 4.8˚ (±2.6˚, range 0˚-12.6˚). CONCLUSION. This study has quantified in-vivo, the intra-operative correction forces applied by the surgeon during anterior single rod instrumentation. This data provides a useful contribution towards an improved understanding of the biomechanics of scoliosis correction. In particular, this data will be used as input for developing patient-specific finite element simulations of scoliosis correction surgery.

Maintenance chain integration using Petri-net enabled multiagent system modeling and implementation approach

Engineering asset management (EAM) is a broad discipline and the EAM functions and processes are characterized by its distributed nature. However, engineering asset nowadays mostly relies on self-maintained experiential rule bases and periodic maintenance, which is lacking a collaborative engineering approach. This research proposes a collaborative environment integrated by a service center with domain expertise such as diagnosis, prognosis, and asset operations. The collaborative maintenance chain combines asset operation sites, service center (i.e., maintenance operation coordinator), system provider, first tier collaborators, and maintenance part suppliers. Meanwhile, to realize the automation of communication and negotiation among organizations, multiagent system (MAS) technique is applied to enhance the entire service level. During the MAS design processes, this research combines Prometheus MAS modeling approach with Petri-net modeling methodology and unified modeling language to visualize and rationalize the design processes of MAS. The major contributions of this research include developing a Petri-net enabled Prometheus MAS modeling methodology and constructing a collaborative agent-based maintenance chain framework for integrated EAM.