Real-time nucleic acid sequence-based amplification in nanoliter volumes

Real-time nucleic acid sequence-based amplification (NASBA) is an isothermal method specifically designed for amplification of RNA. Fluorescent molecular beacon probes enable real-time monitoring of the amplification process. Successful identification, utilizing the real-time NASBA technology, was performed on a microchip with oligonucleotides at a concentration of 1.0 and 0.1 microM, in 10- and 50-nL reaction chambers, respectively. The microchip was developed in a silicon-glass structure. An instrument providing thermal control and an optical detection system was built for amplification readout. Experimental results demonstrate distinct amplification processes. Miniaturized real-time NASBA in microchips makes high-throughput diagnostics of bacteria, viruses, and cancer markers possible, at reduced cost and without contamination.     

UW‐MAC: An underwater sensor network MAC protocol

As over 70% of the earth's surface is covered by water, it is desirable to deploy underwater sensor networks (UWSNs) to support oceanic research. UWSNs use acoustic waves and are characterized by long and variable propagation delays, intermittent connectivity, limited bandwidth and low bit rates. Energy savings have always been the primary concern in wireless sensor network protocols; however, there are applications where the latency and throughput are prioritized over energy efficiency and are so significant that the application would not be able to satisfy its requirements without them. Although existing duty‐cycle MAC protocols are power efficient, they introduce significant end‐to‐end delivery latency, provide poor throughput and are not suitable for the challenging environment of a UWSN. In this paper, we utilize CDMA as the underlying multiple access technique, due to its resilience to multi‐path and Doppler's effects prevalent in underwater environments. We propose UW‐MAC, a CDMA‐based power‐controlled medium access protocol that uses both transmitter‐based and receiver‐based CDMA inside a formed cluster, and uses a TDMA schedule to make the cluster heads communicate with the base station. Our MAC algorithm targets the latency and throughput needs in addition to its ability to increase the overall network lifetime. We discuss the design of UW‐MAC, and provide a head‐to‐head comparison with other protocols through extensive simulations focusing on the performance in terms of latency, throughput, and energy consumption. Copyright © 2009 John Wiley & Sons, Ltd.     

Detection of β‐Amyloid by Sialic Acid Coated Bovine Serum Albumin Magnetic Nanoparticles in a Mouse Model of Alzheimer's Disease

The accumulation and formation of β‐amyloid (Aβ) plaques in the brain are distinctive pathological hallmarks of Alzheimer's disease (AD). Designing nanoparticle (NP) contrast agents capable of binding with Aβ highly selectively can potentially facilitate early detection of AD. However, a significant obstacle is the blood brain barrier (BBB), which can preclude the entrance of NPs into the brain for Aβ binding. In this work, bovine serum albumin (BSA) coated NPs are decorated with sialic acid (NP‐BSA_x‐Sia) to overcome the challenges in Aβ imaging in vivo. The NP‐BSA_x‐Sia is biocompatible with high magnetic relaxivities, suggesting that they are suitable contrast agents for magnetic resonance imaging (MRI). The NP‐BSA_x‐Sia binds with Aβ in a sialic acid dependent manner with high selectivities toward Aβ deposited on brains and cross the BBB in an in vitro model. The abilities of these NPs to detect Aβ in vivo in human AD transgenic mice by MRI are evaluated without the need to coinject mannitol to increase BBB permeability. T₂*‐weighted MRI shows that Aβ plaques in mouse brains can be detected as aided by NP‐BSA_x‐Sia, which is confirmed by histological analysis. Thus, NP‐BSA_x‐Sia is a promising new tool for noninvasive in vivo detection of Aβ plaques.     

Reversible compression of MR images

Methods for reversible coding can be classified according to the organization of the source model as either static, semi-adaptive, or adaptive. Magnetic resonance (MR) images have different statistical characteristics in the foreground and the background and separation is thus a promising path for reversible MR image compression. A new reversible compression method, based on static source models for foreground and background separately, is presented. The method is nonuniversal and uses contextual information to exploit the fact that entropy and bit rate are reduced by increasing the statistical order of the model. This paper establishes a realistic level of expectation regarding the bit rate in reversible MR image compression, in general, and the bit rate using static modeling, in particular. The experimental results show that compression using the new method can give bit rates comparable to the best existing reversible methods.     

High cycle fatigue life estimation of materials processed by laser powder bed fusion

The fatigue life of metal components is known to depend on the surface topography. For components made by laser powder bed fusion, the roughness of the as‐built surfaces depends on the orientation of the component surface with respect to the build plate. Surface topographies of AlSi10Mg and Inconel 718 specimens built at 0° to 90° inclination, with 15° increments, were characterised by white light interferometry. Two methods for calculating the stress concentration factor using the surface roughness data are proposed, and the results of each approach are presented and compared. Moreover, a finite element model was developed, in order to analyse the stress field when subsurface porosity is present. The fatigue lifetime estimates suggest that the lifetime of components may differ up to two orders of magnitude, depending on the build orientation.     

Nephrotic syndrome in ulcerative colitis

Complicating disorders in various organs outside the intestinal tract are common in ulcerative colitis. This report deals with the occurrence of nephrotic syndrome in two patients with long-standing ulcerative colitis. In the patient studied in most detail, 2 episodes have taken place, the first developing into uremia. After colectomy had been performed, rapid improvement of renal function took place. The morphological changes in kidney biopsies were compatible with the presence of focal glomerular sclerosis. Activity in the complement system and a favorable response to steroid treatment indicate that humoral immune mechanisms are of pathogenetic importance with regard to the renal disease in these two patients. To our knowledge nephrotic syndrome has not previously been described as a complication to ulcerative colitis.     

A BRCA1 founder mutation, identified with haplotype analysis, allowing genotype/phenotype determination and predictive testing

We searched for a founder mutation in a population from one geographic region of Norway with prevalent breast/ovarian cancer families. We sampled 33 breast/ovarian cancer families and determined haplotypes of four markers linked to the BRCA1 region. Of the affected 33 index women, 13 (39.4%) shared one haplotype. In five (15% of total), an identical mutation was indicated by an abnormal truncated protein test (PTT) of exon 11 and shown to represent a 1675delA mutation. In the other index women, PTT of exon 11 showed no abnormality. No other BRCA1 founder mutation of this prevalence is likely because no other haplotype was more frequent in affecteds than in controls. All families with the 1675delA mutation in this geographic region may be considered as part of one large kindred. This allows a genotype-phenotype correlation to be precisely determined and used in genetic counselling for predictive testing within this kindred. Identification of identical haplotypes between unrelated affected individuals may be used to estimate the extent of founder effects for any mapped disease, without knowledge of the specific founder mutation.     

The effects of cholesterol/fat feeding on lipid levels and morphological structures in liver, kidney and spleen in guinea pigs

Guinea pigs were fed a semisynthetic diet containing 10 per cent (by weight) cottonseed oil with or without 1 per cent cholesterol. In the animals fed fat, the lipid levels and the morphology remained normal in all tissues studied. Concomitantly with a marked accumulation of cholesteryl ester (CE) in the liver, however, many microscopical changes occurred in guinea pigs fed cholesterol/fat. A prominent deposition of lipids in vacuoles, mostly without delimitating membranes, where observed at centrilobular sites. Multivacuolated, secondary lysosomes, membrane bound lipid vacuoles (lipolysosomes) and myelin figures were found both in hepatocytes and Kupffer cells. Myelin figures and crystalline clefts were observed more often in Kupffer cells than in hepatocytes. The granular endoplasmic reticulum in the Kupffer cells was grossly dilated and filled with an amorphous material. Both the biochemical and the morphological findings in hepatocytes and Kupffer cells are very similar to those observed in cholesteryl ester storage disease and in Wolman's disease. These two lipid storage diseases are both related to deficiency of an acid lipase in the liver. Measurement of the acid liver CE hydrolase in guinea pigs fed fat and in those fed cholesterol/fat showed similar activity. A relative deficiency of this enzyme activity could be the reason for the development of the enormous CE storage in guinea pig livers. These findings suggest that guinea pigs fed cholesterol/fat, in some respects, can be used as a model for Wolman's disease and cholesteryl ester storage disease. We did not find any microscopical changes in the kidneys from animals fed cholesterol/fat, thus indicating that the experimental condition it not useful as a model for studies of the kidney changes in lecithin:cholesterol acyltransferase (LCAT) deficiency.     

Determination of hereditary mutations in the BRCA1 gene using archived serum samples and capillary electrophoresis

Analysis of DNA variation in biological samples most frequently utilizes the polymerase chain reaction (PCR) performed on extracted genomic DNA, followed by visualization of alleles using various methodologies. Few reports have demonstrated that amplification of DNA from plasma and serum samples is possible. We have performed DNA amplification on a large set of serum samples (n = 2955). Here, we report that known hereditary mutations in the BRCA gene can efficiently be analyzed in serum samples collected and stored over several decades. Fragments were PCR-amplified following a short initial denaturation of the serum sample in a standard microwave oven. Fragment analysis was subsequently performed using a DNA capillary-sequencing instrument. The PCR success rates were fragment- and size-dependent ranging from 83.2% to 97.9%. Of the 11,820 polymerase chain reactions performed, the overall PCR success rate was 91.3% (10,796/11,820), which is comparable to PCR performed on genomic DNA. The advantage of the method described herein is its ability to utilize archival material stored in serum biobanks for long periods of time.