Multiplex semi-nested RT-PCR with exogenous internal control for simultaneous detection of bovine coronavirus and group A rotavirus

Neonatal calf diarrhea is a multi-etiology syndrome of cattle and direct detection of the two major agents of the syndrome, group A rotavirus and Bovine coronavirus (BCoV) is hampered by their fastidious growth in cell culture. This study aimed at developing a multiplex semi-nested RT-PCR for simultaneous detection of BCoV (N gene) and group A rotavirus (VP1 gene) with the addition of an internal control (mRNA ND5). The assay was tested in 75 bovine feces samples tested previously for rotavirus using PAGE and for BCoV using nested RT-PCR targeted to RdRp gene. Agreement with reference tests was optimal for BCoV (kappa = 0.833) and substantial for rotavirus detection (kappa = 0.648). the internal control, ND5 mRNA, was detected successfully in all reactions. Results demonstrated that this multiplex semi-nested RT-PCR was effective in the detection of BCoV and rotavirus, with high sensitivity and specificity for simultaneous detection of both viruses at a lower cost, providing an important tool for studies on the etiology of diarrhea in cattle. (C) 2010 Elsevier B.V. All rights reserved.

GAPD and tubulin are suitable internal controls for qPCR analysis of oral squamous cell carcinoma cell lines

The selection of housekeeping genes is critical for gene expression studies. To address this issue, four candidate housekeeping genes, including several commonly used ones, were investigated in oral squamous cell carcinoma cell lines. A simple quantitative RT-PCR approach was employed by comparing relative expression of the four candidate genes within two cancerous cell tines (HN6 and HN31) and one noncancerous cell tine (HaCaT) treated or not with EGF and TGF-beta 1. Data were analyzed using ANOVA followed by the NormFinder software program. On this basis, stability of the candidate housekeeping genes was ranked and non statistical differences were found using ANOVA test. On the other hand, the NormFinder was able to show that GAPD and TUBB presented the less variable results, representing appropriated housekeeping genes for the samples and conditions anatyzed. In conclusion, this study suggests that the GAPD and the TUBB represent adequate normalizers for gene profiting studies in OSCC cell. tines, covering, respectively, high and low expression levels genes. (C) 2008 Elsevier Ltd. All rights reserved.

Effects of Orthopedic Rapid Maxillary Expansion on Internal Nasal Dimensions in Children With Cleft Lip and Palate Assessed by Acoustic Rhinometry

The objective of the current study was to characterize the internal nasal dimensions of children with repaired cleft lip and palate and transverse maxillary deficiency, using acoustic rhinometry and analyze the changes caused by rapid maxillary expansion (RME). A convenience sampling of 19 cleft lip and palate individuals, aged 14 to 18 years, of both sexes, previously submitted to primary surgeries and referred for RME were analyzed prospectively at the Hospital for Rehabilitation of Craniofacial Anomalies, University of Sao Paulo, Bauru, Sao Paulo, Brazil. All patients underwent acoustic rhinometry before installation of the expansor and at 30 and 180 days after the active expansion phase. Nasal cross-sectional areas and volumes corresponding to the nasal valve (CSA(1) and V(1)) and the turbinates (CSA(2), CSA(3), and V(2)) regions were determined before and after nasal decongestion. Rapid maxillary expansion led to a statistically significant increase (P < 0.05) in mean CSA(1), CSA(2), V(1), and V(2) (without nasal decongestion) and in CSA(1) and V(1) (with decongestion) in the group as a whole. Individual data analysis showed that 58% of the patients responded positively to RME, with an average increase in CSA(1) of 26% (with decongestion), whereas 37% of the patients had no significant change. Only 1 patient (5%) showed a decrease. The findings contribute toward the characterization of nasal deformities determined by the cleft and demonstrate the positive effect RME had on nasal morphophysiology in a significant number of the patients who underwent this procedure.

A critical comparison of the external and internal boron requirements for contrasting species in boron-buffered solution culture

Despite reports that boron (B) requirements differ among plant species there is a shortage of critical evidence to demonstrate unequivocally whether species differ in internal or external B requirements or both. The present research was conducted to establish the external and internal B requirements of three contrasting species, a woody dicot (marri), an herbaceous dicot (sunflower) and a monocot (wheat) using B-buffered solution culture. Boron-buffered solution culture provided satisfactory control of external B concentrations ranging from 0.04 to 30 muM throughout the 20- (sunflower and wheat) or 40-day (marri) growth period. At low external B concentrations (less than or equal to 0.13 muM), the growth of marri and sunflower was severely depressed but by contrast the vegetative growth of wheat plants was satisfactory and free of B deficiency symptoms. Marri and sunflower plants achieved total maximum shoot growth at greater than or equal to1.2 muM B in solutions while wheat plants did so at greater than or equal to 0.6 muM B. The critical B concentrations (mg kg(-1) dry matter) in the youngest open leaf blades of marri, sunflower and wheat plants were 17.9, 19.7 and 1.2 on 20, 10 and 10 days after transplanting (DAT), respectively. Lower internal and external B requirements of wheat were matched by a lower uptake rate of B compared to marri and sunflower.

Recurrent gains and losses of large (84-109 bp) repeats in the rDNA internal transcribed spacer 2 (ITS2) of rhipicephaline ticks

We studied the internal transcribed spacer 2 (ITS2) in twenty-two spp. of ticks from the subfamily Rhipicephalinae. A 104-109 base pair (bp) region was Imperfectly repeated In most ticks studied. Mapping the number of repeat copies on to a phylogeny from the ITS2 showed that there have been many Independent gains and losses of repeats. Comparison of the sequences of the repeat copies Indicated that in most taxa concerted evolution had played little if any role in the evolution of these regions, as the copies clustered by sequence position rather than species, In our putative secondary structure, each repeat copy can fold into a distinct and almost identical stem-loop complex; a gain or loss of a repeat copy apparently does not impair the function of the ITS2 in these ticks.

Low intraspecific variation in the rRNA internal transcribed spacer 2 (ITS2) of the Australian paralysis tick, Ixodes holocyclus

Ixodes holocyclus has a narrow, discontinuous distribution along the east coast of Australia. We studied ticks from 17 localities throughout the geographic range of this tick. The ITS2 of I. holocyclus is 793 bp long. We found nucleotide variation at eight of the 588 nucleotide positions (1.4%) that were compared for all ticks. There were eight different nucleotide sequences. Most sequences were not restricted to a particular geographic region. However, sequences F, G and H, which had an adenine at position 197, were found only in the far north of Queensland - all other ticks had a guanine at this position. The low level of intraspecific variation in this tick (0.7%) contrasts with the sequence divergence between L holocyclus and its close relative, I. cornuatus (13.1 %). These data indicate that L holocyclus does not contain cryptic species despite possible geographic isolation of some populations. We conclude that variation in the ITS2 is likely to be informative about the phylogeny of the group.

Vitamin B12 stalls the 80 S ribosomal complex on the hepatitis C internal ribosome entry site

The effect of cyanocobalamin (CNCbl, vitamin 1312) on hepatitis C virus internal ribosome entry site (HCV IRES)-dependent initiation of translation was studied by ribosomal toeprinting and sucrose gradient centrifugation analysis. These results suggested that CNCbl did not inhibit HCV IRES-dependent translation by a competitive binding mechanism. CNCbl allowed 80 S elongation complex formation on the mRNA, but stalled the initiation at that point, effectively trapping the 80 S ribosomal complexes on the HCV TRES. CNCbl had no effect on cap-dependent mRNA, consistent with the known mRNA specificity of this translational inhibitor. To help elucidate the mechanism, comparative data were collected for the well-characterised translation inhibitors cycloheximide and 5'-guanylyl-imidophosphate, Although CNCbl stalled HCV IRES-dependent translation at approximately the same step in initiation as cycloheximide, the mechanisms of these two inhibitors are distinct. (C) 2002 Elsevier Science Ltd. All rights reserved.

Cross-national comparison of internal migration: issues and measures

Our objectives are to identify the issues that researchers encounter when measuring internal migration in different countries and to propose key indicators that analysts can use to compare internal migration at the 'national' level. We establish the benefits to be gained by a rigorous approach to cross-national comparisons of internal migration and discuss issues that affect such comparisons. We then distinguish four dimensions of internal migration on which countries can be compared and, for each dimension, identify a series of summary measures. We illustrate the issues and measures proposed by comparing migration in Australia and Great Britain.

Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda)

ITS2 sequences are used extensively in molecular taxonomy and population genetics of arthropods and other animals yet little is known about the molecular evolution of ITS2. We studied the secondary structure of ITS2 in species from each of the six main lineages of hard ticks (family Ixodidae). The ITS2 of these ticks varied in length from 679 bp in Ixodes scapularis to 1547 bp in Aponomma concolor. Nucleotide content varied also: the ITS2 of ticks from the Prostriata lineage (Ixodes spp.) had 46-49% GC whereas ITS2 sequences of ticks from the Metastriata lineage (all other hard ticks) had 61-62% GC. Despite variation in nucleotide sequence, the secondary structure of the ITS2 of all of these ticks apparently has five domains. Stems 1, 3, 4 and 5 of this secondary structure were obvious in all of the species studied. However, stem 2 was not always obvious despite the fact that it is flanked by highly conserved sequence motifs in the adjacent stems, stems 1 and 3. The ITS2 of hard ticks has apparently evolved mostly by increases and decreases in length of the nucleotide sequences, which caused increases, and decreases in the length of stems of the secondary structure. This is most obvious when stems of the secondary structures of the Prostriata (Ixodes spp.) are compared to those of the Metastriata (all other hard ticks). Increases in the size of the ITS2 may have been caused by replication slippage which generated large repeats, like those seen in Haemaphysalis humerosa and species from the Rhipicepalinae lineage, and the small repeats found in species from the other lineages of ticks.

Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences

The entire internal transcribed spacer ( ITS) region, including the 5.8S subunit of the nuclear ribosomal DNA ( rDNA), was sequenced by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified fragments. The study included 40 Sporobolus ( Family Poaceae, subfamily Chloridoideae) seed collections from 14 putative species ( all 11 species from the S. indicus complex and three Australian native species). These sequences, along with those from two out-group species [ Pennisetum alopecuroides ( L.) Spreng. and Heteropogon contortus ( L.) P. Beauv. ex Roemer & Schultes, Poaceae, subfamily Panicoideae], were analysed by the parsimony method (PAUP; version 4.0b4a) to infer phylogenetic relationships among these species. The length of the ITS1, 5.8S subunit and ITS2 region were 222, 164 and 218 base pairs ( bp), respectively, in all species of the S. indicus complex, except for the ITS2 region of S. diandrus P. Beauv. individuals, which was 217 bp long. Of the 624 characters included in the analysis, 245 ( 39.3%) of the 330 variable sites contained potential phylogenetic information. Differences in sequences among the members of the S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur & Schinz and S. jacquemontii Kunth. collections were 0%, while differences ranged from 0 to 2% between these and other species of the complex. Similarly, differences in sequences among collections of S. laxus B. K. Simon, S. sessilis B. K. Simon, S. elongatus R. Br. and S. creber De Nardi were 0%, compared with differences of 1-2% between these four species and the rest of the complex. When comparing S. fertilis ( Steud.) Clayton and S. africanus (Poir.) Robyns & Tourney, differences between collections ranged from 0 to 1%. Parsimony analysis grouped all 11 species of the S. indicus complex together, indicating a monophyletic origin. For the entire data set, pair-wise distances among members of the S. indicus complex varied from 0.00 to 1.58%, compared with a range of 20.08-21.44% among species in the complex and the Australian native species studied. A strict consensus phylogenetic tree separated 11 species of the S. indicus complex into five major clades. The phylogeny, based on ITS sequences, was found to be congruent with an earlier study on the taxonomic relationship of the weedy Sporobolus grasses revealed from random amplified polymorphic DNA ( RAPD). However, this cladistic analysis of the complex was not in agreement with that created on past morphological analyses and therefore gives a new insight into the phylogeny of the S. indicus complex.

Soil profile internal drainage for a central pivot fertigated coffee crop

Coffee cultivation via central-pivot fertigation can lead to fertilizer losses by soil profile internal drainage when water application is excessive and soils have low water retention and cation adsorption capacities. This study analyses the deep water losses from the top 1 m sandy soil layer of east Bahia, Brazil, cultivated with coffee at a high technology level (central-pivot fertigation), using above normal N fertilizer rates. The deep drainage (Q) estimation is made through the application of a climatologic water balance (CWB) program having as input direct measures of irrigation and rainfall, climatological data from weather stations, and measured soil water retention characteristics. The aim of the study is to contribute to the understanding of the hydric regime of coffee crops managed by central-pivot irrigation, analyzing three scenarios (Sc): i) rainfall only, ii) rainfall and irrigation full year, and iii) rainfall and irrigation dry season only. Annual Q values for the 2008/2009 agricultural year were: Sc i = 811.5 mm; Sc ii = 1010.5 mm; and Sc iii = 873.1 mm, so that the irrigation interruption in the wet season reduced Q by 15.7%, without the appearance of water deficit periods. Results show that the use of the CWB program is a convenient tool for the evaluation of Q under the cited conditions.

Limiting Internal Supply Voltage Spikes in DC-DC Converters

Implementing monolithic DC-DC converters for low power portable applications with a standard low voltage CMOS technology leads to lower production costs and higher reliability. Moreover, it allows miniaturization by the integration of two units in the same die: the power management unit that regulates the supply voltage for the second unit, a dedicated signal processor, that performs the functions required. This paper presents original techniques that limit spikes in the internal supply voltage on a monolithic DC-DC converter, extending the use of the same technology for both units. These spikes are mainly caused by fast current variations in the path connecting the external power supply to the internal pads of the converter power block. This path includes two parasitic inductances inbuilt in bond wires and in package pins. Although these parasitic inductances present relative low values when compared with the typical external inductances of DC-DC converters, their effects can not be neglected when switching high currents at high switching frequency. The associated overvoltage frequently causes destruction, reliability problems and/or control malfunction. Different spike reduction techniques are presented and compared. The proposed techniques were used in the design of the gate driver of a DC-DC converter included in a power management unit implemented in a standard 0.35 mu m CMOS technology.