The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes

CpG island is a GC-rich motif occurred in gene promoter region, which can play important roles in gene silencing and imprinting. Here, we present a set of discriminant functions that can recognize the structural and compositional features of CpG islands in the putative promoter regions (PPRs) of human and mouse immunoglobulin (Ig) genes. We showed that the PPRs of both human and mouse Ig genes irrespective of gene chromosomal localization are apparently CpG island poor, with a low percentage of the CpG islands overlapped with the transcription start site (TSS). The human Ig genes that have CpG islands in the PPRs show a very narrow range of CpG densities. 47% of the Ig genes fall in the range of 3.5-4 CpGs/100 bp. In contrast, the non-Ig genes examined have a wide range of the density of CpG island, with 10.5% having the density of 8.1-15 CpGs/100 bp. Meantime, five patterns of the CpG distributions within the CpG islands have been classified: Pat A, B, C, D, and E. 21.6% and 10.8% of the Ig genes fall into the Pat B and Pat D groups, respectively, which were significantly higher than the non-Ig genes examined (8.2% and 3.8%). Moreover, the length of CpG islands is shorter in human Ig genes than in non-Ig genes but is much longer than in mouse orthologues. These findings provide a clear picture of non-neutral and nonrandom occurrence of the CpG islands in the PPRs of human and mouse Ig genes, which facilitate rational recommendations regarding their nomenclature. (C) 2005 Elsevier B.V. All rights reserved.

mecA locus diversity in methicillin-resistant Staphylococcus aureus isolates in Brisbane, Australia, and the development of a novel diagnostic procedure for the Western Samoan phage pattern clone

An emerging public health phenomenon is the increasing incidence of methicillin-resistant Staphylococcus aureus (MRSA) infections that are acquired outside of health care facilities. One lineage of community-acquired MRSA (CA-MRSA) is known as the Western Samoan phage pattern (WSPP) clone. The central aim of this study was to develop an efficient genotyping procedure for the identification of WSPP isolates. The approach taken was to make use of the highly variable region downstream of mecA in combination with a single nucleotide polymorphism (SNP) defined by the S. aureus multilocus sequence typing (MLST) database. The premise was that a combinatorial genotyping method that interrogated both a highly variable region and the genomic backbone would deliver a high degree of informative power relative to the number of genetic polymorphisms-interrogated. Thirty-five MRSA isolates were used for this study, and their gene contents and order downstream of mecA were determined. The CA-MRSA isolates were found to contain a truncated mecA downstream region consisting of mecA-HVR-IS431 mec-dcs-Ins117, and a PCR-based method for identifying this structure was developed. The hospital-acquired isolates were found to contain eight different mecA downstream regions, three of which were novel. The Minimum SNPs computer software program was used to mine the S. aureus MLST database, and the arcC 2726 polymorph was identified as 82% discriminatory for ST-30. A real-time PCR assay was developed to interrogate this SNP. We found that the assay for the truncated mecA downstream region in combination with the interrogation of arcC position 272 provided an unambiguous identification of WSPP isolates.

Archaeological Identification and Significance of ÉSAG (Agricultural Storage Pits) at Kaman-Kalehöyük, Central Anatolia

Evidence for the presence of storage pits described in Hittite texts by the Sumerogram "ÉSAG" is presented from Kaman-Kalehöyük, a multi-period tell site in central Turkey occupied during the second and first millennia BC. Small earthen pits matching the description of "ÉSAG" were part of the normal suite of domestic installations at the site throughout the period. Similar to pits seen across western Eurasia, they were probably used to store seed corn or seed for trade. Large earthen pits (>7m in diameter) were also present that matched the description of the "ÉSAG" form, and in some cases contained archaeological cereal remains. Evidence from Kaman shows "ÉSAG" were part of Anatolian life for at least 4,000 years and suggests that the term was generic for lined, earthen storage pits. The presence of so many small pits at Kaman-Kalehöyük showed that it was an agricultural production site for much of its existence. The appearance of the large pits, confined to the Hittite period, reflects centralised control of grain supply, probably by the Hittite Kingdom, and fits a pattern seen at other sites in the region during the second millennium BC. /// Hitit metinlerinde Sumerogram "ÉSAG" ile tanimlanan depo çukurlarinin varliğina dair kanit, Orta Anadolu'da M.Ö. İkinci ve Birinci binde iskan edilmiş çok dönemli bir yerleşim alani olan Kaman-Kalehöyük'ten taninmaktadir. Küçük toprak çukurlar "ÉSAG" in tanimlamasina uygun olarak bu dönem süresince normal ev düzeninin bir parçasi olarak karşimiza çikmiştir. Çukurlar, Bati Avrasya'daki benzer çukurlar gibi olasilikla ticaret maksadi ile misir tohumu ya da tohum muhafaza etmişlerdir. "ÉSAG" formunun tanimina uyan büyük toprak çukurlara (çapi 7m. den büyük) rağmen bunlarin tahil depolama ile ilgili bağlantilari tam olarak belirlenmemiştir. Kaman'daki delil, "ÉSAG" in en az 4,000 yildir Anadolu yaşaminin bir parçasi olduğunu ve bu sözcüğün sivanmiş toprak çukurlar için kullanildiğini işaret etmektedir. Kaman-Kalehöyük'te ele geçen birçok küçük çukur, yerleşimin varliğini sürdürdüǧü sürecin büyük bir bölümünde zirai üretim yapildiğini göstermektedir. Hitit Döneminde büyük çukurlarin ortaya çikmasi muhtemelen Hitit Kralliği tarafindan gerçekleştirilen tahil tedarikinin merkezi kontrolünü yansitmakta ve M.Ö. İkinci binde bu bölgedeki diğer yerleşim alanlarinda görülen şekle uymaktadir.

EphA4 regulates central nervous system vascular formation

Molecules involved in axon guidance have recently also been shown to play a role in blood vessel guidance. To examine whether axon guidance molecules, such as the EphA4 receptor tyrosine kinase, might also play a role in development of the central nervous system (CNS) vasculature and repair following CNS injury, we examined wild-type and EphA4 null mutant (-/-) mice. EphA4-/- mice exhibited an abnormal CNS vascular structure in both the cerebral cortex and the spinal cord, with disorganized branching and a 30% smaller diameter. During development, EphA4 was expressed on endothelial cells. This pattern of expression was not maintained in the adult. After spinal cord injury in wild-type mice, expression of EphA4 was markedly up-regulated on activated astrocytes, many of which were tightly associated with blood vessels. In EphA4-/- spinal cord following injury, astrocytes were not as tightly associated with blood vessels as the wild-type astrocytes. In uninjured EphA4-/- mice, the blood-brain barrier (BBB) appeared normal, but it showed prolonged leakage following spinal cord injury. These results support a role for EphA4 in CNS vascular formation and guidance during development and an additional role in BBB repair.

Screening of obstructive and central apnoea/hypopnoea in children using variability: A preliminary study

Aim: Polysomnography (PSG) is the current standard protocol for sleep disordered breathing (SDB) investigation in children. Presently, there are limited reliable screening tests for both central (CE) and obstructive (OE) respiratory events. This study compared three indices, derived from pulse oximetry and electrocardiogram ( ECG), with the PSG gold standard. These indices were heart rate (HR) variability, arterial blood oxygen de-saturation (SaO(2)) and pulse transit time (PTT). Methods: 15 children (12 male) from routine PSG studies were recruited (aged 3 - 14 years). The characteristics of the three indices were based on known criteria for respiratory events (RPE). Their estimation singly and in combination was evaluated with simultaneous scored PSG recordings. Results: 215 RPE and 215 tidal breathing events were analysed. For OE, the obtained sensitivity was HR (0.703), SaO(2) (0.047), PTT (0.750), considering all three indices (0) and either of the indices (0.828) while specificity was (0.891), (0.938), (0.922), (0.953) and (0.859) respectively. For CE, the sensitivity was HR (0.715), SaO(2) (0.278), PTT (0.662), considering all indices (0.040) and either of the indices (0.868) while specificity was (0.815), (0.954), (0.901), (0.960) and (0.762) accordingly. Conclusions: Preliminary findings herein suggest that the later combination of these non-invasive indices to be a promising screening method of SDB in children.

Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22

The base composition pattern (BCP) in the putative promoter region (PPRs) up to 5 Kb lengths of 682 human genes on Chromosome 22 (Chr22) was examined. Two-dimensional (2D) and three-dimensional (3D) functions were designed to delineate the DNA base composition, with four major patterns identified. It is found that 17.6% genes include TATA box, 28.0% GC box, 18.9% CAAT box and 38.4% CpG islands, and approximately 10% genes have one of four putative initiator (Inr) motifs. The occurrence of the promoter elements is tightly associated with the base composition features in the promoter regions, and the associations of the base composition features with occurrence of the promoter elements in the promoter regions mediate tissue-wide expression of the genes in human. The occurrence of two or more promoter elements in the promoter regions is required for the medium- and wide-range expression profiles of the human genes on Chr22. Thus, the reported data shed light on the characteristics of the PPRs of the human genes on Chr22, which may improve our understanding of regulatory roles of the PPRs with occurrence of the promoter elements in gene expression.

Motivations for second position: Evidence from North-Central Australia

It has long been observed that many languages from all over the world require that certain grammatical categories (e.g., person, number, tense, modality) occur in the "second position" of a clause. Much of the research into second position has developed formal explanations for this recurring pattern, based on interactions between morphosyntax and phonology. In this article I explore how pragmatics of information packaging interacts with these other features in the development of such morphosyntactic architecture in three North-Central Australian languages: Warlpiri, Wambaya, and Garrwa.

High fidelity radiation pattern measurement system for small antennas

The paper describes a high fidelity system for measuring a radiation pattern of an electrically small antenna. In this system, the Antenna Under Test (AUT) equipped with a battery powered signal generator is suspended by a dielectric foam in the centre of a pair of dielectric rings that are supported by a pedestal of a spherical positioning mechanical sub-system. Radiation patterns are obtained directly in spherical format using a suitably constructed probe antenna of linear or circular polarization. Measurements are controlled by a computer, which also stores and processes the measured data. The results reveal considerable differences between the radiation patterns of a small antenna obtained using the proposed wireless approach and the conventional one, in which the antenna is connected with a cable to the receiver.