High throughput functional analysis of HIV-1 env genes without cloning

Functional human immunodeficiency virus type 1 (HIV-1) env genes have been widely used for vaccine design, neutralization assays, and pathogenesis studies. However, obtaining bona fide functional env clones is a time consuming and labor intensive process. A new high throughput method has been developed to characterize HIV-1 env genes. Multiple rev/env gene cassettes were obtained from each of seven HIV-1 strains using single genome amplification (SGA) PCR. The cytomegalovirus (CMV) promoter was amplified separately by PCR. A promoter PCR (pPCR) method was developed to link both PCR products using an overlapping PCR method. Pseudovirions were generated by cotransfection of pPCR products and pSG3 Delta env backbone into 293T cells. After infecting TZM-bl cells, 75 out of 87 (86%) of the rev/env gene cassettes were functional. Pseudoviruses generated with pPCR products or corresponding plasmid DNA showed similar sensitivity to six HIV-1 positive sera and three monoclonal antibodies, suggesting neutralization properties are not altered in pPCR pseudovirions. Furthermore, sufficient amounts of pseudovirions can be obtained for a large number of neutralization assays. The new pPCR method eliminates cloning, transformation, and plasmid DNA preparation steps in the generation of HIV-1 pseudovirions. This allows for quick analysis of multiple env genes from HIV-1 infected individuals.     

Biogenesis of vaccinia: evidence for more than 100 polypeptides in the virion.

The polypeptides of vaccinia were separated and analyzed by two-dimensional (2-D) gel electrophoresis patterned after that of O'Farrell (1975). Following labeling with [³⁵S]-methionine, [³³P]phosphate, or [³H]glucosamine, pure virions were dissociated and subjected to electrophoresis using either isoelectric focussing or nonequilibrium pH gradient conditions in the first dimension and SDS-polyacrylamide slab gels in the second dimension. By this means at least 111 spots, of which 7 or more were basic proteins, were resolved in the autoradiograms. Authenticity of several single spots was established. This included a glycoprotein of molecular weight 34,000 (34 K) labeled with [³H]glucosamine; a phosphorylated basic protein of about 11 K marked with ³³PO₄; isolated purified surface tubular elements of 58 K; two major core polypeptides of 60 and 62 K derived from larger precursors after proteolytic cleavage; a precursor polypeptide of 25 K known from previous studies with a ts mutant 1085 to undergo cleavage; and an 18 K polypeptide which appears in wild type and ts 1085 infections under circumstances permissive for cleavage. The 2-D analysis therefore reveals that poxviruses are in terms of their polypeptides, even more complex than had been anticipated previously.     

Chronic multiple knee ligament injuries: epidemiological analysis of more than one hundred cases

INTRODUCTION: Diagnosis and treatment of multiple ligament injuries of the knee remain a real challenge for most surgeons. OBJECTIVE: To find out the epidemiological profile of patients surgically treated at a Reference Service with more than one chronic ligament injury in the knee joint. MATERIALS AND METHODS: Of a total of 978 operated patients, 109 presented at least two associated ligament injuries in the same knee. Demographic and clinical variables were evaluated. RESULTS: The anterior cruciate ligament group presented a larger number of cases of ligament injuries related with sports practice and falls, while the posterior cruciate ligament and anterior cruciate ligament + posterior cruciate ligament groups presented more cases related to traffic accidents and trauma with object (weight on the knee) (p<0.001). The varus group presented significantly higher values of time since injury (p<0.01). In the group with new anterior cruciate ligament injury (neoligament) associated with other ligament injuries the disruption times were higher, showing statistical significance (p<0.001). CONCLUSIONS: Anterior cruciate ligament injury associated with other ligament injuries other than posterior cruciate ligament injury are related to sports practice and falls. Posterior cruciate ligament injury associated to other ligament injuries, including or not anterior cruciate ligament injury, are related to traffic accidents and direct trauma caused by an object on the knee. Significant delay between primary ligament injuries and their reconstructions generates varus deformity of the affected knee. In spite of the large delay in seeking medical treatment, few patients with neoligament anterior cruciate ligament injury and other combined disruptions will develop varus deformity.     

Mutation screening of EXT1 and EXT2 by direct sequence analysis and MLPA in patients with multiple osteochondromas: splice site mutations and exonic deletions account for more than half of the mutations

Multiple osteochondromas (MO) is an autosomal dominant condition, caused by mutations in either the EXT1 or the EXT2 gene. The DNA of a cohort of 35 patients, clinically suspected to be affected with MO, was screened for mutations by a combination of direct sequence analysis and multiplex ligation-dependent probe amplification (MLPA). In this cohort, 26 pathogenic gene alterations were found (74%). With sequence analysis mutations were detected in 22 patients (63%). In total, 10 mutations were detected in the EXT1 and 12 in the EXT2 gene. The number of the splice site mutations detected was larger than expected from the literature. In addition, with the MLPA four deletions of one or more exons were found in this cohort. Two patients, of whom one had a negative family history, showed deletions of exon 1 of the EXT1 gene, which is possibly a deletion hot spot. In patients suspected to be affected by MO, we recommend a quantitative analysis such as MLPA, followed by direct sequence analysis for the screening of the EXT1 and EXT2 genes.     

High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts

Background

Recent work suggests that multiple genes and several environmental risk factors influence risk for non‐syndromic oral clefts, one of the most common birth defects in humans. Advances in high‐throughput genotyping technology now make it possible to test multiple markers in many candidate genes simultaneously.

Methods

We present findings from family based association tests of single nucleotide polymorphism (SNP) markers in 64 candidate genes genotyped using the BeadArray approach in 58 case‐parent trios from Maryland (USA) to illustrate how multiple markers in multiple genes can be analysed. To assess whether these genes were expressed in human craniofacial structures relevant to palate and lip development, we also analysed data from the Craniofacial and Oral Gene Expression Network (COGENE) consortium, and searched public databases for expression profiles of these genes.

Results

Thirteen candidate genes showed significant evidence of linkage in the presence of disequilibrium, and ten of these were found to be expressed in relevant embryonic tissues: SP100, MLPH, HDAC4, LEF1, C6orf105, CD44, ALX4, ZNF202, CRHR1, and MAPT. Three other genes showing statistical evidence (ADH1C, SCN3B, and IMP5) were not expressed in the embryonic tissues examined here.

Conclusions

This approach demonstrates how statistical evidence on large numbers of SNP markers typed in case‐parent trios can be combined with expression data to identify candidate genes for complex disorders. Many of the genes reported here have not been previously studied as candidates for oral clefts and warrant further investigation.     

Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP

Mutations in three genes (PSEN1, PSEN2, and APP) have been identified in patients with early-onset (<65 years) Alzheimer's disease (AD). We performed a screening for mutations in the coding regions of presenilins, as well as exons 16 and 17 of the APP gene in a total of 231 patients from the Iberian peninsular with a clinical diagnosis of early-onset AD (mean age at onset of 52.9 years; range 31-64). We found three novel mutations in PSEN1, one novel mutation in PSEN2, and a novel mutation in the APP gene. Four previously described mutations in PSEN1 were also found. The same analysis was carried in 121 elderly healthy controls from the Iberian peninsular, and a set of 130 individuals from seven African populations belonging to the Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Panel (CEPH-HGDP), in order to determine the extent of normal variability in these genes. Interestingly, in the latter series, we found five new non-synonymous changes in all three genes and a presenilin 2 variant (R62H) that has been previously related to AD. In some of these mutations, the pathologic consequence is uncertain and needs further investigation. To address this question we propose and use a systematic algorithm to classify the putative pathology of AD mutations.     

Pore diameter of more than 100 microm is not requisite for bone ingrowth in rabbits.

The optimal pore size for bone ingrowth is claimed to be 100-400 microm. With the use of a highly standardized experimental model, the present study reevaluated whether a pore size of 100 microm is the threshold value for bone ingrowth into porous structures under non-load-bearing conditions. Titanium triangle-shaped plates 250 or 500 microm thick were perforated with the use of a laser in order to create standard-sized holes ( 50, 75, 100, and 125 microm) in multiple rows. The amount of bone ingrowth through the implant holes was studied in the cancellous bone of the distal rabbit femur. Twelve weeks after implantation, detailed analysis of bone ingrowth was performed with computerized image analysis of backscattered electron imaging techniques of scanning electron microscopy. The results showed that the amount of ingrown new bone was independent of the pore size and implant thickness. The median value for bone ingrowth varied between 64 and 78%. A striking feature was the formation of secondary osteonal structures even in the smallest holes. Based on these results, there is no threshold value for new bone ingrowth in pore sizes ranging from 50 to 125 microm under non-load-bearing conditions.     

Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity

Genetic diagnosis of steroid-resistant nephrotic syndrome (SRNS) using Sanger sequencing is complicated by the high genetic heterogeneity and phenotypic variability of this disease. We aimed to improve the genetic diagnosis of SRNS by simultaneously sequencing 26 glomerular genes using massive parallel sequencing and to study whether mutations in multiple genes increase disease severity. High-throughput mutation analysis was performed in 50 SRNS and/or focal segmental glomerulosclerosis (FSGS) patients, a validation cohort of 25 patients with known pathogenic mutations, and a discovery cohort of 25 uncharacterized patients with probable genetic etiology. In the validation cohort, we identified the 42 previously known pathogenic mutations across NPHS1, NPHS2, WT1, TRPC6, and INF2 genes. In the discovery cohort, disease-causing mutations in SRNS/FSGS genes were found in nine patients. We detected three patients with mutations in an SRNS/FSGS gene and COL4A3. Two of them were familial cases and presented a more severe phenotype than family members with mutation in only one gene. In conclusion, our results show that massive parallel sequencing is feasible and robust for genetic diagnosis of SRNS/FSGS. Our results indicate that patients carrying mutations in an SRNS/FSGS gene and also in COL4A3 gene have increased disease severity.     

The analysis of intraclass correlation in multiple samples

A unified methodology is presented for the analysis of intraclass correlation in two or more samples, with emphasis on application to family studies. The methodology provides point and interval estimates of a common intraclass correlation in data having either fixed or variable class sizes. Tests of homogeneity for intraclass correlation coefficients are also discussed.     

Genetic algorithm for analysis of mutations in Parkinson's disease

OBJECTIVE: Mitochondrial genetics has unique features that impede analysis of the biological significance of mitochondrial mutations. Simple searches for differences in total mutational load between normal and pathological samples have been frequently unrewarding, raising the possibility that more complex patterns of mutations may be responsible for some conditions. We explore this possibility in the context of Parkinson's disease (PD). METHODS AND MATERIALS: We report the development of a modified genetic algorithm suited for detection of biologically meaningful patterns of mitochondrial mutations. The algorithm is applied to a database of mutations derived from biological samples, and verified by the use of shuffled data, and repeated leave-one-out testing. RESULTS: It is possible to derive, from a very small sample, multiple accurate classifier functions that correlate with biological features. The methodology is validated statistically through experiments with fabricated data. CONCLUSION: This algorithm might be generally applicable to conditions where interactions among multiple mitochondrial DNA mutations are important. The patterns embodied in the classifier functions obtained should be the subject of further experimental study.     

Insulin resistance and elevated triglyceride in muscle: more important for survival than 'thrifty' genes?

Elevated intramyocellular triglyceride (IMTG) is strongly associated with insulin resistance, though a cause and effect relationship has not been fully described. Insulin sensitivity and IMTG content are both dynamic and can alter rapidly in response to dietary variation, physical activity and thermoregulatory response. Physically active humans (athletes) display elevated IMTG content, but in contrast to obese persons, are insulin sensitive. This paradox has created confusion surrounding the role of IMTG in the development of insulin resistance. In this review we consider the modern athlete as the physiological archetype of the Late Palaeolithic hunter–gatherer to whom the selection pressures of food availability, predation and fluctuating environmental conditions applied and to whom the genotype of modern man is virtually identical. As food procurement by the hunter–gatherer required physical activity, 'thrifty' genes that encouraged immediate energy storage upon refeeding after food deprivation ( Neel, 1962 ) must have been of secondary importance in survival to genes that preserved physical capacity during food deprivation. Similarly genes that enabled survival during cold exposure whilst starved would be of primary importance. In this context, we discuss the advantage afforded by an elevated IMTG content, and how under these conditions, a concomitant muscle resistance to insulin-mediated glucose uptake would also be advantageous. In sedentary modern man, adiposity is high and skeletal muscle appears to respond as if a state of starvation exists. In this situation, elevated plasma lipids serve to accrue lipid and induce insulin resistance in skeletal muscle. Reversal of this physiological state is primarily dependant on adequate contractile activity, however, in modern Western society, physical inactivity combined with abundant food and warmth has rendered IMTG a redundant muscle substrate.     

Detection of more than 94% cystic fibrosis mutations in a sample of belgian population and identification of four novel mutations

We have analysed 194 Belgian CF chromosomes using a variety of techniques: ΔF508 was detected by polyacrylamide gel electrophoresis; dot blotting of PCR products was used to identify the mutations G542X, 1717-1 G → A, and N1303K; molecular defects in exons 2, 3, 4, 5, 6b, 7, 11, 12, 13, 14a, 14b, 17b, 19, 20, and 21 were screened for by DGGE. We identified 17 mutations, which accounted for 94.3% of the Belgian CF chromosomes. Four novel mutations and a novel polymorphism were characterized. The detection of such a high proportion of Belgian CF mutations is important in understanding the functional role of the molecule and in improving prenatal and genetic diagnosis of CF. © 1993 Wiley-Liss, Inc.     

Sequence analysis of cDNAs for the human and bovine ATP synthase β subunit: mitochondrial DNA genes sustain seventeen times more mutations

We have cloned and sequenced human and bovine cDNAs for the subunit of the ATP synthase (ATP-synß), a nuclear DNA (nDNA) encoded oxidative phosphorylation (OXPHOS) gene. The two cDNAs were found to share 99% amino acid homology and 94% nucleotide homology. The evolutionary rate of ATPsynß was then compared with that of two mitochondrial DNA (mtDNA) ATP synthase genes (ATPase 6 and 8), seven other mtDNA OXPHOS genes, and a number of nuclear genes. The synonymous substitution rate for ATPsynß proved to be 1.9 × 10^–9 substitutions per site per year (substitutions × site^–1 × year^–1) (SSY). This is less than 1/2 that of the average nDNA gene, 1/12 the rate of ATPase 6 and 8, and 1/17 the rate of the average mtDNA gene. The synonymous and replacement substitution rates were used to calculate a new parameter, the selective constraint ratio. This revealed that even the most variable mtDNA protein was more constrained than the average nDNA protein. Thus, the high substitution mutation rate and strong selective constraints of mammalian mtDNA proteins suggest that mtDNA mutations may result in a disproportionately large number of human hereditary diseases of OXPHOS.     

Closely spaced multiple mutations as potential signatures of transient hypermutability in human genes

Data from diverse organisms suggests that transient hypermutability is a general mutational mechanism with the potential to generate multiple synchronous mutations, a phenomenon probably best exemplified by closely spaced multiple mutations (CSMMs). Here we have attempted to extend the concept of transient hypermutability from somatic cells to the germline, using human inherited disease‐causing multiple mutations as a model system. Employing stringent criteria for data inclusion, we have retrospectively identified numerous potential examples of pathogenic CSMMs that exhibit marked similarities to the CSMMs reported in other systems. These examples include (1) eight multiple mutations, each comprising three or more components within a sequence tract of <100 bp; (2) three possible instances of “mutation showers”; and (3) numerous highly informative “homocoordinate” mutations. Using the proportion of CpG substitution as a crude indicator of the relative likelihood of transient hypermutability, we present evidence to suggest that CSMMs comprising at least one pair of mutations separated by ≤100 bp may constitute signatures of transient hypermutability in human genes. Although this analysis extends the generality of the concept of transient hypermutability and provides new insights into what may be considered a novel mechanism of mutagenesis underlying human inherited disease, it has raised serious concerns regarding current practices in mutation screening.Hum Mutat 30:1–14, 2009. © 2009 Wiley‐Liss, Inc.     

Genomic rearrangements account for more than one-third of the BRCA1 mutations in northern Italian breast/ovarian cancer families

The recent identification of major genomic rearrangements in breast and breast/ovarian cancer families has widened the mutational spectrum of the BRCA1 gene, thus increasing the number of informative patients who can benefit from molecular screening. Numerous types of alterations have been identified in different populations with variable frequencies, probably due to both ethnic diversity and the technical approach employed. In fact, although several methods have been successfully used to detect large genomic deletions and insertions, most are laborious, time-consuming, and of variable sensitivity. In order to estimate the contribution of BRCA1 genomic rearrangements to breast/ovarian cancer predisposition in Italian families, we applied, for the first time as a diagnostic tool, the recently described multiplex ligation-dependent probe amplification (MLPA) methodology. Among the 37 hereditary breast/ovarian cancer (HBOC) families selected, all had a high prior probability of BRCA1 mutation, and 15 were previously shown to carry a mutation in either the BRCA2 (five families) or BRCA1 gene (10 families, including one genomic rearrangement). The application of BRCA1-MLPA to the remaining 22 uninformative families allowed the identification of five additional genomic rearrangements. Moreover, we observed that loss of constitutive heterozygosity of polymorphic markers in linkage disequilibrium is predictive of such BRCA1 alterations. By means of this approach, we demonstrate that BRCA1 genomic deletions account for more than one-third (6/15) of the pathogenic BRCA1 mutations in our series. We therefore propose to systematically include MLPA in the BRCA1 mutational analysis of breast/ovarian cancer families.     

Somatic mutations in familial adenomatous polyps. Nuclear translocation of beta-catenin requires more than biallelic APC inactivation

Germline mutations of the APC gene cause familial adenomatous polyposis coli (FAP). APC inactivation results in dysregulation of wnt/wingless signaling and contributes to chromosomal instability in vitro. To investigate somatic alterations that follow a known germline mutation and contribute to the transition from normal to neoplastic mucosa, we studied 10 adenomatous polyps from a 27-year-old patient with an APC germline mutation at codon 554. Chromosomal imbalances were analyzed by comparative genomic hybridization; APC and K-ras were screened for somatic mutations. Before DNA analysis, the polyps were bisected to compare the genetic alterations with the corresponding immunohistologic phenotype of beta-catenin, a proto-oncogene product degraded by the APC tumor suppressor. Gains at chromosome 20 were the most frequent chromosomal alterations (6 polyps). Losses were found predominantly at chromosome 4q (3 polyps). A K-ras mutation was seen in 1 polyp, while all polyps displayed somatic intragenic APC mutations. Comparative immunohistologic analysis revealed strong membranous staining for beta-catenin in all adenomatous polyps, but only 1 adenoma showed nuclear accumulation. Our results suggest chromosomal aberrations contribute early to the progression of adenomatous polyps after biallelic APC inactivation. APC inactivation itself is insufficient for immunohistochemically detectable nuclear translocation of beta-catenin.     

Applications of heteroduplex analysis for mutation detection in disease genes

Double-stranded heteroduplex molecules that form between a mutant and wild-type DNA strand are often distinguished from homoduplex molecules upon gel electrophoresis. This method, heteroduplex analysis (HA), can be performed rapidly without radioisotopes or specialized equipment. Modifications and enhancements of the HA method have been developed that increase the sensitivity of detection of single-base pair alterations. © 1995 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.