A metabolomics approach exploring the function of the ESX-3 type VII secretion system of M. smegmatis

The genome of Mycobacterium, including Mycobacterium tuberculosis, contains five copies of a cluster of genes encoding a novel type VII secretion system, named the ESX gene cluster region. This ESX-3 gene cluster is essential for in vitro growth and is thought to play a role in iron and zinc homeostasis, however, its exact functionality remains an enigma. A metabolomics research approach was subsequently used to compare the metabolite profiles of a M. smegmatis ESX-3 knockout strain to that a wild type parental strain, in order to elucidate its functionality from a metabolic perspective. Statistical analysis of the GC–MS generated data showed a clear separation between the wild type and knockout sample groups, based on the analysed metabolite profiles of these organisms. Of all the metabolite markers identified, various amino acids and metabolite pathways related to these, appeared to be most affected by the ESX-3 knockout, especially those with enzymes regulated by iron and zinc, supporting previous genomics and proteomics generated hypotheses and findings. This study is the first to demonstrate the capacity of using metabolomics, in conjunction with previous genomics and proteomic findings, to identify underlying metabolic changes and confirm previous hypotheses related to the functionality of ESX-3 in Mycobacterium growth and survival.     

Molecular coupling of S4 to a K(+) channel's slow inactivation gate

The mechanism by which physiological signals regulate the conformation of molecular gates that open and close ion channels is poorly understood. Voltage clamp fluorometry was used to ask how the voltage-sensing S4 transmembrane domain is coupled to the slow inactivation gate in the pore domain of the Shaker K(+) channel. Fluorophores attached at several sites in S4 indicate that the voltage-sensing rearrangements are followed by an additional inactivation motion. Fluorophores attached at the perimeter of the pore domain indicate that the inactivation rearrangement projects from the selectivity filter out to the interface with the voltage-sensing domain. Some of the pore domain sites also sense activation, and this appears to be due to a direct interaction with S4 based on the finding that S4 comes into close enough proximity to the pore domain for a pore mutation to alter the nanoenvironment of an S4-attached fluorophore. We propose that activation produces an S4-pore domain interaction that disrupts a bond between the S4 contact site on the pore domain and the outer end of S6. Our results indicate that this bond holds the slow inactivation gate open and, therefore, we propose that this S4-induced bond disruption triggers inactivation.     

The influence of vessel wall elasticity and peripheral resistance on the carotid artery flow wave form: a CFD model compared to in vivo ultrasound measurements

The Doppler flow wave form and its derived measures such as the pulsatility index provide clinically important tools for the investigation of arterial disease. The typical shape of Doppler flow wave forms is physiologically known to be largely determined by both peripheral resistance and elastic properties of the arterial wall. In the present study we systematically investigate the influence of both vessel wall elasticity and peripheral resistance on the flow wave form obtained from a CFD-simulation of blood flow in the carotid bifurcation. Numerical results are compared to in vivo ultrasound measurements. The in vivo measurement provides a realistic geometry, local elasticities and an input flow wave form for the numerical experiment. Numerical and experimental results are compared at three different sites in the carotid branches. Peripheral resistance has a profoundly decreasing effect on velocities in the external carotid artery. If elasticity is taken into account, the computed peak systolic velocities are considerably lower and a more realistic smoothing of the flow wave form is found. Together, the results indicate that only if both vessel wall elasticity and positive peripheral resistance are taken into account, experimentally obtained Doppler flow wave forms can be reproduced numerically.     

The building stones of Roman Sagalassos (SW Turkey): Facies analysis and provenance

Summary Different types of builing stones have been macro-scopically and petrographically characterized at the ancient city of Sagalassos (SW Turkey). The natural building stones include limestone, conglomerate, breccia, marble, travertine, granite and sand-to siltstone of different qualities. The provenance of most of the building stones may be related to local lithological units, both in the immediate area of the city and on its territory. Also, some stone types were clearly imported from considerable distance. Throughout the history of the city, local beige and pink good quality limestone remained the most important building stone. Both the high quality white limestone from the territory of the city and the marbles imported from a distance of 250 km, represent only a small fraction of the total amount of building stones used. While the use of the white limestone can be considered to form a clear but limited trend from the Trajanic period (98–117 AD) onwards, the import of the marbles must be considered as a rare event. The selection of building stone went hand in hand with the appreciation for structural strength and suitability for carving complex architectural decoration, together with the desire to obtain a polychrome architecture.     

Uncovering the metabolic response of abalone (<Emphasis Type="Italic">Haliotis midae)</Emphasis> to environmental hypoxia through metabolomics

Introduction

Oxygen is essential for metabolic processes and in the absence thereof alternative metabolic pathways are required for energy production, as seen in marine invertebrates like abalone. Even though hypoxia has been responsible for significant losses to the aquaculture industry, the overall metabolic adaptations of abalone in response to environmental hypoxia are as yet, not fully elucidated.

Objective

To use a multiplatform metabolomics approach to characterize the metabolic changes associated with energy production in abalone (Haliotis midae) when exposed to environmental hypoxia.

Methods

Metabolomics analysis of abalone adductor and foot muscle, left and right gill, hemolymph, and epipodial tissue samples were conducted using a multiplatform approach, which included untargeted NMR spectroscopy, untargeted and targeted LC–MS spectrometry, and untargeted and semi-targeted GC-MS spectrometric analyses.

Results

Increased levels of anaerobic end-products specific to marine animals were found which include alanopine, strombine, tauropine and octopine. These were accompanied by elevated lactate, succinate and arginine, of which the latter is a product of phosphoarginine breakdown in abalone. Primarily amino acid metabolism was affected, with carbohydrate and lipid metabolism assisting with anaerobic energy production to a lesser extent. Different tissues showed varied metabolic responses to hypoxia, with the largest metabolic changes in the adductor muscle.

Conclusions

From this investigation, it becomes evident that abalone have well-developed (yet understudied) metabolic mechanisms for surviving hypoxic periods. Furthermore, metabolomics serves as a powerful tool for investigating the altered metabolic processes in abalone.

     

Inheritance of phenotypic traits in the progeny of a Ceratocystis interspecific cross

Ceratocystis fimbriata is a fungal plant pathogen that causes black rot on Ipomoea batatas. Based on inoculation studies on numerous tree species, the pathogen is known to be host specific. The closely related species, Ceratocystis manginecans, causes severe wilt on a broad range of tree hosts, including Mangifera indica, Acacia mangium and other leguminous tree species. The genetic factors underlying the pathogenicity and host specificity of Ceratocystis species have rarely been investigated. In this study, an F₁ population of 70 recombinant progeny from a cross between C. fimbriata and C. manginecans was generated and the inheritance of various phenotypic traits was investigated. Results showed that colony colour, growth rate, asexual spore production and aggressiveness to I. batatas and A. mangium are all quantitative traits with high levels of heritability. However, conidia production and aggressiveness appeared to be regulated by a small number of genes. No correlation could be found between aggressiveness and other phenotypic traits, suggesting that these are inherited independently. This is the first study to consider genetic inheritance of pathogenicity and host specificity in Ceratocystis species and the results will contribute, in future, to the identification of quantitative trait loci and candidate genes associated with the traits investigated.     

The Pretoria Bone Collection: a modern South African skeletal sample.

The Pretoria Bone Collection began with the inception of the Department of Anatomy and the Medical School at the University of Pretoria in August 1942. Since then the collection has grown from a student aid to a resource for research. In the year 2000, the Pretoria Bone Collection was reorganised. The research material was divided into skulls, complete postcranial and incomplete postcranial remains. The collection presently contains 290 complete skeletons, 704 complete skulls and 541 complete postcranial remains. This paper presents information on the composition of this collection and hopes to heighten both national and international awareness of the collection and research opportunities in South Africa.