Extensible Interface for a Compact Spectrophotometer for Teaching Molecular Absorption in the Undergraduate Laboratory

A simple computer interface for controlling a compact spectrograph for use as a spectrophotometer in an undergraduate teaching laboratory was developed. The project was implemented on a Raspberry Pi computer which permits the integration of a light source into the software. The interface was written in Python to facilitate modification by the user and because of its compatibility with several computing platforms. An implementation of the project in Linux on a Raspberry Pi computer is described

A Non-equilibrium Approach to Temperature Calibration for Tungsten Filament Atomic Spectrometry

A nonequilibrium approach to voltamperometric temperature measurement for tungsten filament atomizers was developed to facilitate the transfer of thermal conditions between instruments that possess different power supply regulation modes and filaments. Large differences in the equilibrium and instantaneous temperatures were found during the pyrolysis and atomization steps of cadmium atomic absorption spectroscopy (AAS) analysis. By using the instantaneous temperature, the pyrolysis and atomization behaviors of cadmium were shown to be equivalent regardless of the power supply regulation mode. The pyrolysis conditions optimized for a 15-V filament were readily and accurately transferred to a 12-V filament by applying the nonequilibrium voltamperometric temperature model

Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes

BACKGROUND: Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein. METHODOLOGY/PRINCIPAL FINDINGS: We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores. CONCLUSIONS: The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine

The MAPK Kinase Kinase GmMEKK1 Regulates Cell Death and Defense Responses

MAPK signaling pathways play critical roles in plant immunity. Here, we silenced multiple genes encoding MAPKs using virus-induced gene silencing mediated by Bean pod mottle virus to identify MAPK genes involved in soybean (Glycine max) immunity. Surprisingly, a strong hypersensitive response (HR) cell death was observed when soybean MAPK KINASE KINASE1 (GmMEKK1), a homolog of Arabidopsis (Arabidopsis thaliana) MEKK1, was silenced. The HR was accompanied by the overaccumulation of defense signaling molecules, salicylic acid (SA) and hydrogen peroxide. Genes involved in primary metabolism, translation/transcription, photosynthesis, and growth/development were down-regulated in GmMEKK1-silenced plants, while the expression of defense-related genes was activated. Accordingly, GmMEKK1-silenced plants were more resistant to downy mildew (Peronospora manshurica) and Soybean mosaic virus compared with control plants. Silencing GmMEKK1 reduced the activation of GmMPK6 but enhanced the activation of GmMPK3 in response to flg22 peptide. Unlike Arabidopsis MPK4, GmMPK4 was not activated by either flg22 or SA. Interestingly, transient overexpression of GmMEKK1 in Nicotiana benthamiana also induced HR. Our results indicate that GmMEKK1 plays both positive and negative roles in immunity and appears to differentially activate downstream MPKs by promoting GmMPK6 activation but suppressing GmMPK3 activation in response to flg22. The involvement of GmMPK4 kinase activity in cell death and in flg22- or SA-triggered defense responses in soybean requires further investigation

Analysis of Salmonella enterica Serotype Paratyphi A Gene Expression in the Blood of Bacteremic Patients in Bangladesh

Salmonella enterica serotype Paratyphi A is a significant and emerging global public health problem and accounts for one fifth of all cases of enteric fever in many areas of Asia. S. Paratyphi A only infects humans, and the lack of an appropriate animal model has limited the study of S. Paratyphi A infection. In this study, we report the application of an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), to evaluate which S. Paratyphi A genes are expressed directly in the blood of infected humans. Our results provide insight into the bacterial adaptations and modifications that S. Paratyphi A may need to survive within infected humans and suggest that similar approaches may be applied to other pathogens in infected humans and animals

Comparative Proteomic Analysis of the PhoP Regulon in Salmonella enterica Serovar Typhi Versus Typhimurium

Background: S. Typhi, a human-restricted Salmonella enterica serovar, causes a systemic intracellular infection in humans (typhoid fever). In comparison, S. Typhimurium causes gastroenteritis in humans, but causes a systemic typhoidal illness in mice. The PhoP regulon is a well studied two component (PhoP/Q) coordinately regulated network of genes whose expression is required for intracellular survival of S. enterica. Methodology/Principal Findings: Using high performance liquid chromatography mass spectrometry (HPLC-MS/MS), we examined the protein expression profiles of three sequenced S. enterica strains: S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2 in PhoP-inducing and non-inducing conditions in vitro and compared these results to profiles of $phoP^−/Q^−$ mutants derived from S. Typhimurium LT2 and S. Typhi Ty2. Our analysis identified 53 proteins in S. Typhimurium LT2 and 56 proteins in S. Typhi that were regulated in a PhoP-dependent manner. As expected, many proteins identified in S. Typhi demonstrated concordant differential expression with a homologous protein in S. Typhimurium. However, three proteins (HlyE, STY1499, and CdtB) had no homolog in S. Typhimurium. HlyE is a pore-forming toxin. STY1499 encodes a stably expressed protein of unknown function transcribed in the same operon as HlyE. CdtB is a cytolethal distending toxin associated with DNA damage, cell cycle arrest, and cellular distension. Gene expression studies confirmed up-regulation of mRNA of HlyE, STY1499, and CdtB in S. Typhi in PhoP-inducing conditions. Conclusions/Significance: This study is the first protein expression study of the PhoP virulence associated regulon using strains of Salmonella mutant in PhoP, has identified three Typhi-unique proteins (CdtB, HlyE and STY1499) that are not present in the genome of the wide host-range Typhimurium, and includes the first protein expression profiling of a live attenuated bacterial vaccine studied in humans (Ty800)

Dataset for Characterization of ‘Cool’ and ‘Warm’ White LEDs

The emission properties of “cool” and “warm” white LEDs were studied. The suitability of pulse-width modulation as a method to control LED brightness was examined. Both types of LED demonstrated emission standard deviation minima at a PWM frequency greater than 2000 Hz. The functional wavelength ranges of the LEDs were approximated using the linearity of brightness as a function of pulse-width modulation duty-cycle and the root mean squared deviation from mean for absorbance measurements. Both LED types demonstrated good stability in absorbance measurements over long operation times. The “warm” LED demonstrated a broader range of wavelengths useful for spectrophotometry. This is the dataset of the investigation

Extensible Interface for a Compact Spectrophotometer for Teaching Molecular Absorption in the Undergraduate Laboratory

A simple computer interface for controlling a compact spectrograph for use as a spectrophotometer in an undergraduate teaching laboratory was developed. The project was implemented on a Raspberry Pi computer which permits the integration of a light source into the software. The interface was written in Python to facilitate modification by the user and because of its compatibility with several computing platforms. An implementation of the project in Linux on a Raspberry Pi computer is described