High-resolution cartography of recently integrated human chromosome 19-specific Alu fossils.

The recently inserted subfamilies of Alu retroposons (Ya5/8 and Yb8) are composed of approximately 2000 elements. We have screened a human chromosome 19-specific cosmid library for the presence of Ya5/8 and Yb8 Alu family members. This analysis resulted in the identification of 12 Ya5/8 Alu family members and 15 Yb8 Alu family members from human chromosome 19. The total number of Ya5/8 and Yb8 Alu family members located on human chromosome 19 does not differ from that expected based upon random integration of Alu repeats within the human genome. The distribution of both subfamilies of Alu elements along human chromosome 19 also appears to be random. DNA sequence analysis of the individual Alu elements revealed a low level of random mutations within both subfamilies of Alu elements consistent with their recent evolutionary origin. Oligonucleotide primers complementary to the flanking unique sequences adjacent to each Alu element were used in polymerase chain reaction assays to determine the phylogenetic distribution and human genomic variation associated with each Alu family member. All of the chromosome 19-specific Ya5/8 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates. Three of the Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The polymorphic Alu elements will be useful tools for the study of human population genetics.

Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus.

An analysis of 8 Alu insertion loci (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65) has been carried out in six populations from the Caucasus, including Indo-European-speaking Armenians; Altaic-speaking Azerbaijanians; North Caucasian-speaking Cherkessians, Darginians, and Ingushians; and South Caucasian (Kartvelian)-speaking Georgians. The Caucasus populations exhibit low levels of within-population variation and high levels of between-population differentiation, with the average Fst value for the Caucasus of 0.113, which is almost as large as the Fst value of 0.157 for worldwide populations. Maximum likelihood tree and principal coordinate analyses both group the Caucasus populations with European populations. Neither geographic nor linguistic relationships appear to explain the genetic relationships of Caucasus populations. Instead, it appears as if they have been small and relatively isolated, and hence genetic drift has been the dominant influence on the genetic structure of Caucasus populations.

Glomerular filtration rate estimates decrease during high altitude expedition but increase with Lake Louise acute mountain sickness scores.

AIM: Acute mountain sickness (AMS) can result in pulmonary and cerebral oedema with overperfusion of microvascular beds, elevated hydrostatic capillary pressure, capillary leakage and consequent oedema as pathogenetic mechanisms. Data on changes in glomerular filtration rate (GFR) at altitudes above 5000 m are very limited. METHODS: Thirty-four healthy mountaineers, who were randomized to two acclimatization protocols, undertook an expedition on Muztagh Ata Mountain (7549 m) in China. Tests were performed at five altitudes: Zurich pre-expedition (PE, 450 m), base camp (BC, 4497 m), Camp 1 (C1, 5533 m), Camp 2 (C2, 6265 m) and Camp 3 (C3, 6865 m). Cystatin C- and creatinine-based (Mayo Clinic quadratic equation) GFR estimates (eGFR) were assessed together with Lake Louise AMS score and other tests. RESULTS: eGFR significantly decreased from PE to BC (P < 0.01). However, when analysing at changes between BC and C3, only cystatin C-based estimates indicated a significant decrease in GFR (P = 0.02). There was a linear decrease in eGFR from PE to C3, with a decrease of approx. 3.1 mL min(-1) 1.73 m(-2) per 1000 m increase in altitude. No differences between eGFR of the two groups with different acclimatization protocols could be observed. There was a significant association between eGFR and haematocrit (P = 0.01), whereas no significant association between eGFR and aldosterone, renin and brain natriuretic peptide could be observed. Finally, higher AMS scores were significantly associated with higher eGFR (P = 0.01). CONCLUSIONS: Renal function declines when ascending from low to high altitude. Cystatin C-based eGFR decreases during ascent in high altitude expedition but increases with AMS scores. For individuals with eGFR <40 mL min(-1) 1.73 m(-2), caution may be necessary when planning trips to high altitude above 4500 m above sea level.

[Endangering of the Liechtenstein population by the early-summer meningoencephalitis virus]. / Gefährdung der Bevölkerung in Liechtenstein durch das Virus der Frühsommer-Meningoenzephalitis (FSME).

There have been a few severe cases of tick-borne encephalitis in Liechtenstein during the last 20 years. To form a better idea of the risk of infection and the potential benefit of vaccination, a total of 311 sera from different cohorts were investigated for antibodies to tick-borne encephalitis. The mean seroprevalence found was 3.6% and was not higher even in persons who were active in professional forestry. The antibodies measured derived in all groups mainly from previous vaccination and in only 2 cases (0.6%) from natural infection. It is concluded that the risk of TbE infection in Liechtenstein is very low. Therefore, a reduction in cases would probably be achieved only by mass vaccination.

[Amylase and lipase as reference values for the differential diagnosis of chronic kidney failure and pancreatitis]. / Amylase und Lipase als differentialdiagnostische Bezugsgrösse bei chronischem Nierenversagen und Pankreatitis.

To differentiate between pancreatitis in patients with chronic renal insufficiency and uremic pancreopathy we investigated 23 patients with chronic renal insufficiency, 28 patients on hemodialysis before and after treatment and 13 patients after renal transplantation. As controls served 15 healthy people. The total amylase in serum is significantly elevated in patients with chronic renal insufficiency regardless if they were treated with hemodialysis or not. This elevation is due to an elevation of the pancreatic isoenzyme. The testing of both isoamylases (pancreatic and salivary) does not contribute to a better diagnosis. Patients with chronic renal insufficiency show a lower concentration of the amylases in their urine than their healthy controls. Lipase and creatinin show a linear correlation in serum. In the individual case it is not possible to draw a definite diagnostic conclusion using the above mentioned parameters because of the wide distribution of the measured values.

Long DOP-PCR of rare archival anthropological samples.

The application of molecular DNA technologies to anthropological questions has meant that rare or archival samples of human remains, including blood, hair, and bone, can now be used as a source of material for genetic analysis. Often, these samples are irreplaceable, and/or yield very small quantities of DNA, so methods for preamplifying as much of the whole genome as possible would greatly enhance their usefulness. DOP-PCR (degenerate oligonucleotide-primed polymerase chain reaction) is an amplification method that uses a degenerate primer and very low initial annealing temperatures to amplify the whole genome. We adapted a published DOP-PCR protocol to long PCR enzyme and amplification conditions. The effectiveness of these modifications was tested by PCR amplification of DOP-PCR products at a mixture of genomic targets including 66 different microsatellites, 11 Alu insertion polymorphisms, and variable-length segments of the human lipoprotein lipase gene (LPL). The selected microsatellite markers were chosen to represent every chromosome, with expected product sizes ranging from 150 base pairs to 8,000 base pairs in length, while the 22 Alu insertion polymorphisms were selected to reveal biases in the recovery of alleles of different sizes. To determine nucleotide sequence variation, 2 kilobases (kb) of the LPL gene in 30 Mongolian individuals were sequenced. All gene-specific targets from DOP-PCR product template were amplified. No unexpected polymorphisms in the sequence results attributable to the DOP-PCR step were found, and 93% to 95% of Alu genotypes that have been amplified from total genomic DNA were replicated. The incorrect typings were all due to the preferential amplification of the shorter of two possible alleles in individuals heterozygous for an Alu insertion and were all correctly typed on subsequent reamplification of the gene-specific PCR products. This method of whole-genome amplification promises to be an efficient way to maximize the genetic use of rare anthropological samples.

Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition.

The insertion of mobile elements into the genome represents a new class of genetic markers for the study of human evolution. Long interspersed elements (LINEs) have amplified to a copy number of about 100,000 over the last 100 million years of mammalian evolution and comprise approximately 15% of the human genome. The majority of LINE-1 (L1) elements within the human genome are 5' truncated copies of a few active L1 elements that are capable of retrotransposition. Some of the young L1 elements have inserted into the human genome so recently that populations are polymorphic for the presence of an L1 element at a particular chromosomal location. L1 insertion polymorphisms offer several advantages over other types of polymorphisms for human evolution studies. First, they are typed by rapid, simple, polymerase chain reaction (PCR)-based assays. Second, they are stable polymorphisms that rarely undergo deletion. Third, the presence of an L1 element represents identity by descent, because the probability is negligible that two different young L1 repeats would integrate independently between the exact same two nucleotides. Fourth, the ancestral state of L1 insertion polymorphisms is known to be the absence of the L1 element, which can be used to root plots/trees of population relationships. Here we report the development of a PCR-based display for the direct identification of dimorphic L1 elements from the human genome. We have also developed PCR-based assays for the characterization of six polymorphic L1 elements within the human genome. PCR analysis of human/rodent hybrid cell line DNA samples showed that the polymorphic L1 elements were located on several different chromosomes. Phylogenetic analysis of nonhuman primate DNA samples showed that all of the recently integrated "young" L1 elements were restricted to the human genome and absent from the genomes of nonhuman primates. Analysis of a diverse array of human populations showed that the allele frequencies and level of heterozygosity for each of the L1 elements was variable. Polymorphic L1 elements represent a new source of identical-by-descent variation for the study of human evolution. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF242435-AF242451.]