The Y chromosome pool of Jews as part of the genetic landscape of the Middle East

A sample of 526 Y chromosomes representing six Middle Eastern populations (Ashkenazi, Sephardic, and Kurdish Jews from Israel; Muslim Kurds; Muslim Arabs from Israel and the Palestinian Authority Area; and Bedouin from the Negev) was analyzed for 13 binary polymorphisms and six microsatellite loci. The investigation of the genetic relationship among three Jewish communities revealed that Kurdish and Sephardic Jews were indistinguishable from one another, whereas both differed slightly, yet significantly, from Ashkenazi Jews. The differences among Ashkenazim may be a result of low-level gene flow from European populations and/or genetic drift during isolation. Admixture between Kurdish Jews and their former Muslim host population in Kurdistan appeared to be negligible. In comparison with data available from other relevant populations in the region, Jews were found to be more closely related to groups in the north of the Fertile Crescent (Kurds, Turks, and Armenians) than to their Arab neighbors. The two haplogroups Eu 9 and Eu 10 constitute a major part of the Y chromosome pool in the analyzed sample. Our data suggest that Eu 9 originated in the northern part, and Eu 10 in the southern part of the Fertile Crescent. Genetic dating yielded estimates of the expansion of both haplogroups that cover the Neolithic period in the region. Palestinian Arabs and Bedouin differed from the other Middle Eastern populations studied here, mainly in specific high-frequency Eu 10 haplotypes not found in the non-Arab groups. These chromosomes might have been introduced through migrations from the Arabian Peninsula during the last two millennia. The present study contributes to the elucidation of the complex demographic history that shaped the present-day genetic landscape in the region.

Objective-type dark-field illumination for scattering from microbeads

We introduce a method for detecting and tracking small particles in a solution near a surface. The method is based on blocking the backreflected illumination beam in an objective-type total internal reflection microscope, leaving unhindered the light scattered by the particles and resulting in dark-field illumination. Using this method, we tracked the motion of 60-nm polystyrene beads with a signal-to-noise ratio of 6 and detected 20-nm gold particles with a signal-to-noise ratio of 5. We illustrate the method's use by following the Brownian motion of small beads attached by short DNA tethers to a substrate.

Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392

Deviation from the stepwise mutation model (SMM) at specific human microsatellite loci has implications for population genetic and forensic investigations. In the present study, data on six Y chromosome-specific microsatellites were pooled for 455 paternally unrelated males from six Middle Eastern populations. All chromosomes were assigned to three haplogroups defined by six binary polymorphisms. Two of the microsatellite loci tested, DYS388 and DYS392, displayed marked haplogroup-specific differences in their allele variability. A bimodal distribution of short and long alleles was observed for DYS388 in haplogroup 1 and for DYS392 in haplogroups 1 and 2. Further investigation showed that the short/long alleles segregated almost completely between genealogically distinct haplogroups defined by additional binary markers. Thus, these two loci have a discriminatory power similar to a binary polymorphism. DYS388 was characterised by an extremely low mutation rate in haplogroups 2 and 3, as was DYS392 in haplogroup 3. Sequence analysis of the repeat regions at the two loci revealed no irregularities, indicating that the triplet expansion in these loci is not controlled by sequence variation at the repeat level. A high frequency of long DYS388 alleles has, so far, been found only in populations originating in the Middle East, suggesting that this microsatellite is useful as a region-specific marker.

Production and purification of SV40 major capsid protein (VP1) in Escherichia coli strains deficient for the GroELS chaperone machine

Production of the major capsid protein of SV40, VP1, is of great interest for the study on capsid assembly in vitro. Production of soluble His6-VP1 in Escherichia coli strains deficient in the GroELS chaperone machine was substantially higher than in the wild-type strain. The His6-VP1 produced in a groEL mutant strain was readily purified. The protein was able to form higher-order structures as evidenced by analysis of the soluble fraction by gel filtration, by sedimentation in sucrose gradient, and by electron microscopy. We propose the use of groE mutants for the production of the major capsid protein of SV40 and perhaps also other papovaviruses.

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (approximately 14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (approximately 8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.

Diversity of alpha-globin mutations and clinical presentation of alpha-thalassemia in Israel

Alpha-thalassemia is among the world's most common single gene disorders, caused primarily by gene deletions. In Israel, where alpha(o)-trait thalassemia is uncommon, it is of particular importance because of its phenotypic interactions with beta-thalassemia in hetero- and homozygotes. In a study of 232 individuals referred for molecular evaluation of anemia, 303 chromosomes carried alpha-globin gene abnormalities; 6 gene rearrangements and 11 point mutations were identified. This unexpected heterogeneity is in part due to the many ethnic subgroups represented by these patients. Our findings include nine unique Israeli alleles, 3 of which are described here for the first time. An equal number of point mutations was found in the alpha2-globin gene as compared to alpha1. A threonine deletion in codon 39 of the alpha1-globin gene, found frequently in Arabs, is unique to Israel and probably represents one of several indigenous alleles. Among Arabs, point mutations were more frequent than large deletions. Surprisingly, in Ashkenazi Jews, who resided for many centuries in a nonmalarial environment, a single alpha-globin gene deletion -alpha(3.7) was found in many cases. The clinical presentation of individuals carrying two or more alpha-globin lesions was highly variable. In general, the severity correlated inversely with the number of functional alpha-globin genes. In some cases, impairment of two alpha-globin genes by point mutations led to a thalassemia-intermedia-like picture which could be misdiagnosed as beta-thalassemia. We conclude that alpha-thalassemia is phenotypically and genotypically more heterogeneous than previously recognized. DNA analysis is invaluable as it provides a specific diagnosis and enables reliable genetic counseling.

Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes

Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of the Jewish Diaspora. A set of 18 biallelic polymorphisms was genotyped in 1,371 males from 29 populations, including 7 Jewish (Ashkenazi, Roman, North African, Kurdish, Near Eastern, Yemenite, and Ethiopian) and 16 non-Jewish groups from similar geographic locations. The Jewish populations were characterized by a diverse set of 13 haplotypes that were also present in non-Jewish populations from Africa, Asia, and Europe. A series of analyses was performed to address whether modern Jewish Y-chromosome diversity derives mainly from a common Middle Eastern source population or from admixture with neighboring non-Jewish populations during and after the Diaspora. Despite their long-term residence in different countries and isolation from one another, most Jewish populations were not significantly different from one another at the genetic level. Admixture estimates suggested low levels of European Y-chromosome gene flow into Ashkenazi and Roman Jewish communities. A multidimensional scaling plot placed six of the seven Jewish populations in a relatively tight cluster that was interspersed with Middle Eastern non-Jewish populations, including Palestinians and Syrians. Pairwise differentiation tests further indicated that these Jewish and Middle Eastern non-Jewish populations were not statistically different. The results support the hypothesis that the paternal gene pools of Jewish communities from Europe, North Africa, and the Middle East descended from a common Middle Eastern ancestral population, and suggest that most Jewish communities have remained relatively isolated from neighboring non-Jewish communities during and after the Diaspora.

Molecular analysis of beta-thalassemia in Vietnam

The molecular basis of the thalassemias has been studied in many of the world's populations. Here we report the results of the first screening for mutations in Vietnam. Twenty-three unrelated patients, of which 17 have Hb E/beta-thalassemia, were diagnosed and beta-globin mutations were detected in all 46 chromosomes. Four previously reported South Asian mutations were found. The most common mutations were the nonsense in codon 17 (A-->T) and the frameshift at codons 41/42 (-TTCT) (30 and 22%, respectively). The rare frameshift mutation at codon 95 (+A) was present in 9% of the 46 chromosomes studied, suggesting that it is indigenous to Vietnam. These results will serve as an initial database for DNA-based prenatal diagnosis of thalassemia in Vietnam.

From a dry bone to a genetic portrait: a case study of sickle cell anemia

The potential and reliability of DNA analysis for the identification of human remains are demonstrated by the study of a recent bone sample, which represented a documented case of sickle cell anemia. beta-globin gene sequences obtained from the specimen revealed homozygosity for the sickle cell mutation, proving the authenticity of the retrieved residual DNA. Further investigation of mitochondrial and Y chromosome DNA polymorphic markers indicated that this sample came from a male of maternal West African (possibly Yoruban) and paternal Bantu lineages. The medical record, which became available after the DNA analyses had been completed, revealed that it belonged to a Jamaican black male. These findings are consistent with this individual being a descendent of Africans brought to Jamaica during the trans-Atlantic slave trade. This study exemplifies how a "reverse population genetics" approach can be applied to reconstruct a genetic profile from a bone specimen of an unknown individual.

Expression of beta-globin in primary erythroid progenitors of beta-thalassemia patients using an SV40-based gene delivery system

SV40-based vectors are very efficient in gene delivery into human hematopoietic cells. In the present work, we investigated the expression of constructs carrying the human beta-globin gene that were delivered as beta-globin pseudovirions. Expression studies were performed by RNA analysis of primary human erythroid progenitors cultivated from peripheral blood of beta(0)-thalassemia patients who are unable to produce normal beta-globin RNA. This erythroid culture system recapitulates in vitro the process of growth, differentiation, and maturation of authentic erythroid precursors. The progenitors were induced to differentiate by the addition of erythropoietin (EPO). Five days later, the cells were infected with pseudovirions containing the normal beta-globin gene, and RNA was harvested on day 8. The results showed significant levels of normal beta-globin gene mRNA. A small DNA fragment derived from the 5'-region of the HSII element of the human beta-globin locus control region (LCR) enhanced expression of the linked beta-globin gene 20-30-fold. Normal beta-globin mRNA expression was in direct correlation to the multiplicity of infection. These studies suggest the potential feasibility of using the beta-globin delivery system for gene therapy of beta-thalassemia.

Evaluation of triage decisions for intensive care admission

OBJECTIVE

To assess physician decision-making in triage for intensive care and how judgments impact on patient survival.

DESIGN

Prospective, descriptive study.

SETTING

General intensive care unit, university medical center.

INTERVENTIONS

All patients triaged for admission to a general intensive care unit were studied. Information was collected for the patient's age, diagnoses, surgical status, admission purpose, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and mortality. The number of available beds at the time of triage and reasons for refused admission were obtained.

MEASUREMENTS AND MAIN RESULTS

Of 382 patients, 290 were admitted, 92 (24%) were refused admission, and 31 were admitted at a later time. Differences between admission diagnoses were found between patients admitted or not admitted (p < .001). Patients refused admission had higher APACHE II scores (15.6+/-1.5 admitted later and 15.8+/-1.4 never admitted) than did admitted patients (12.1+/-.4; p < .001). The frequency of admitting patients decreased when the intensive care unit was full (p < .001). Multivariate analysis revealed that triage to intensive care correlated with age, a full unit, surgical status, and diagnoses. Hospital mortality was lower in admitted (14%) than in refused patients (36% admitted later and 46% never admitted; p < .01) and in admitted patients with APACHE II scores of 11 to 20 (p = .02). The 28-day survival of patients was greater for admitted patients compared with patients never admitted (p = .01).

CONCLUSIONS

Physicians triage patients to intensive care based on the number of beds available, the admission diagnosis, severity of disease, age, and operative status. Admitting patients to intensive care is associated with a lower mortality rate, especially in patients with APACHE scores of 11 to 20.

Effect of haemofiltration on pathological fibrinolysis due to severe sepsis: a case report

Bleeding due to coagulopathy is a frequent complication of severe sepsis, especially in burn patients. The primary treatment is aimed at the underlying cause but additional supportive measures, consisting mainly of coagulation factor replacement, are frequently necessary. We describe the salutary effect of continuous veno-venous haemofiltration (CVVH) with predilution on diffuse haemorrhage in a patient with severe septic shock and renal failure. The diffuse haemorrhage was initially treated with replacement of coagulation factors. Prothrombin time and partial thromboplastin time became normal while diffuse bleeding continued and the thrombelastogram showed evidence of fibrinolysis. A short period of CVVH lead to the cessation of bleeding which was reflected by a normal thrombelastogram.

Rapid detection of the common Mediterranean alpha-globin deletions/rearrangements using PCR

The most frequent molecular lesions causing alpha-thalassemia are deletions of one or more alpha-globin genes. Detection of these deletions generally requires genomic Southern analysis, which is cumbersome and time consuming. We have designed new sets of primers for PCR identification of the common Mediterranean alpha-globin gene rearrangements, including the -alpha3.7 deletion and the alphaalphaalpha(anti3.7) triplication, the -alpha4.2 deletion, and the --Med allele. We have established reaction conditions that provide easily interpretable, unambiguous diagnoses. Some of the PCR reactions are multiplex, simultaneously identifying several genotypes, thus reducing the time and cost of screening and prenatal testing. The use of these methods should facilitate carrier screening and identification of couples at risk for alpha-thalassemia.

Tension pneumoperitoneum after blast injury: dramatic improvement in ventilatory and hemodynamic parameters after surgical decompression

Tension pneumoperitoneum is a known although rare complication of barotrauma, which can accompany blast injury. We report two patients who suffered from severe pulmonary blast injury, accompanied by tension pneumoperitoneum, and who were severely hypoxemic, hypercarbic, and in shock. After surgical decompression of their pneumoperitoneum, respiratory and hemodynamic functions improved dramatically. Several mechanisms to explain this improvement are suggested. In such cases the release of the tension pneumoperitoneum is mandatory, and laparotomy with delayed closure can be contemplated.

Efficient transduction of human hematopoietic cells with the human multidrug resistance gene 1 via SV40 pseudovirions

Transduction of MDR1 may be of use in chemoprotection of normal bone marrow (BM) cells during treatment of malignancies, or as a selectable marker for the transfer of other genes into the BM, a critical target for the cure of many diseases. To that aim, the human multidrug resistance gene MDR1 was cloned into an SV40 pseudoviral vector containing the SV40 origin of replication (ori) and encapsidation signal (ses), and the plasmid was encapsidated in COS cells as SV40/MDR1 pseudovirions. Expression of the human MDR1 gene was demonstrated in murine MEL cells infected with SV40/MDR1 pseudovirions, using a monoclonal antibody (MPK16) specific for the human 170-kD P-glycoprotein. Functional P-glycoprotein was demonstrated by resistance to colchicine in NIH-3T3 cells infected with SV40/MDR1 pseudovirions. Activity of P-glycoprotein was assayed by rhodamine-123 dye exclusion and fluorescence-activated cell sorter analysis (FACS) in various cell types including hematopoietic cells. Highly efficient gene transfer and expression was demonstrated in all murine and human cell types tested, including primary human BM cells. Using multiplicities of infection (moi) of 1-2, over 95% of cells were found to become MDR1+. The percent of MDR1+ cells was proportional to the moi. We conclude that the SV40 pseudoviral vector is efficient for gene transmission into human hematopoietic cells.

Helium versus oxygen for tracheal gas insufflation during mechanical ventilation

OBJECTIVE

To evaluate and compare the effect of tracheal gas insufflation using two gases with different physical properties, helium and oxygen, as an adjunct to conventional mechanical ventilation in patients with respiratory failure.

DESIGN

Prospective, intervention study.

SETTING

General intensive care unit in a tertiary university medical center.

PATIENTS

Seven sedated and paralyzed patients with respiratory failure of various etiologies. All patients were ventilated in the volume-control mode (tidal volume 5 to 7 mL/kg). Inclusion criteria were PaCO2 of > or =50 torr (> or =6.7 kPa), together with peak inspiratory pressure of > or =35 cm H2O and respiratory rate of > or =14 breaths/min.

INTERVENTIONS

All patients were intubated with an endotracheal tube that had an additional lumen opening at its distal end, through which tracheal gas insufflation was administered. The tracheal gas insufflation was applied continuously throughout the respiratory cycle at three flow rates (2, 4, and 6 L/min) with two gases, oxygen and helium, while the ventilatory settings were maintained constant.

MEASUREMENTS AND MAIN RESULTS

In addition to airway pressures and arterial blood gases, the relative efficacy of tracheal gas insufflation with each gas was estimated using a "coefficient of efficiency" (which we defined as the change in PaCO2/peak inspiratory pressure) compared with baseline measurements. Tracheal gas insufflation with both gases decreased PaCO2 significantly (p < .05) at all flow rates. This effect was accompanied by an increase in airway pressure with both gases (oxygen and helium). However, at flow rates of 6 L/min, tracheal gas insufflation with helium resulted in lower peak inspiratory pressure than with oxygen. Tracheal gas insufflation with helium was more effective (as estimated by the coefficient of efficiency) than with oxygen at all flow rates (p < .05).

CONCLUSION

In volume-controlled, mechanically ventilated patients with respiratory failure, tracheal gas insufflation with helium might be suggested as an alternative to oxygen.

The SV40 capsid protein VP3 cooperates with the cellular transcription factor Sp1 in DNA-binding and in regulating viral promoter activity

Chromatin structure and protein-protein interactions play an important role in eukaryotic gene function. Nucleosomal rearrangement at the simian virus 40 (SV40) regulatory region occurs at the late stages of the viral life cycle preceding viral assembly. The SV40 capsid proteins are required for this nucleosomal rearrangement suggesting that they participate in turning-off the viral promoters. In aiming to elucidate the role of the capsid proteins in gene regulation, we studied the interaction between VP3, an internal capsid protein, and the cellular transcription factor Sp1, a major regulator of both the early and late viral promoters. Our results showed that VP3 repressed transcription from the viral early promoter in vitro. We found significant cooperativity between Sp1 and VP3 in specific DNA-binding to the Sp1 binding site. In addition, protein-protein interactions between VP3 and Sp1 in the absence of DNA were observed. These findings have led us to conclude that the novel host-viral Sp1-VP3 complex down regulates viral transcription and further suggest that Sp1 participates in recruiting VP3 to the SV40 minichromosome in SV40 assembly.

Self-assembly and protein-protein interactions between the SV40 capsid proteins produced in insect cells

Soluble SV40 capsid proteins were obtained by expression of the three late genes, VP1, VP2, and VP3, in Sf9 cells using baculovirus expression vectors. Coproduction of the capsid proteins VP1, VP2, and VP3 was achieved by infecting Sf9 cells with the three recombinant baculovirus species at equal multiplicities. All three proteins were found to be localized in the nuclear fraction. Electron microscopy of nuclear extracts of the infected cells showed an abundance of SV40-like capsid structures and heterogeneous aggregates of variable size, mostly 20-45 nm. Under the same staining conditions wild-type SV40 virions are 45 nm. The capsid-like particles sedimented in glycerol gradients similarly to authentic wild-type SV40 virions. Pentamers of the major capsid protein VP1 were also seen. Protein analysis on sucrose gradients demonstrated that the capsid-like particles can be disrupted by treatment with the reducing agent dithiothreitol and the calcium chelator EGTA. The capsid-like particles were found to be significantly less stable than SV40 virions and were partially stabilized by calcium ions. Understanding the complex interactions between the capsid proteins is important for the development of an efficient in vitro packaging system for SV40 virions and pseudovirions.

A novel mechanism generating short deletion/insertions following slippage is suggested by a mutation in the human alpha2-globin gene

A novel mechanism generating short deletion/insertions is described based on a mutation in the human alpha2-globin gene. A deletion of 9 bp (codons 39-41) is replaced by an eight nucleotide insertion, duplicating the adjacent downstream sequence. We propose that the mutation arose by slipped strand mispairing (SSM), creating a single-stranded loop, followed by DNA elongation, strand breathing and the formation of a mismatch bubble. An extensive literature search has revealed six additional deletion/insertion mutations in humans in which the inserted nucleotides come from the same DNA strand. Our model explains all six mutations, suggesting that rearrangement of a mismatch loop or bubble during DNA replication may be not uncommon.

Positive end-expiratory pressure increases pulmonary venous vascular resistance in patients after coronary artery surgery

OBJECTIVE

To investigate the effect of positive and-expiratory pressure (PEEP) on the longitudinal distribution of pulmonary vascular resistance in patients immediately after coronary artery bypass grafting.

DESIGN

Prospective, intervention study.

SETTING

Postcardiac surgery intensive care unit in a teaching institution.

PATIENTS

Twenty patients after elective coronary artery bypass grafting.

INTERVENTION

The effect of PEEP on pulmonary circulation, at four different levels (0, 5, 10, and 15 cm H2O), was analyzed in 20 patients.

MEASUREMENTS AND MAIN RESULTS

Mean pulmonary arterial pressure, left atrial pressure, pulmonary artery occlusion pressure, and pulmonary capillary pressure were measured at each PEEP level. A model consisting of two resistances in series was used to analyze the effect of PEEP on the pulmonary circulation. The pulmonary vascular resistance for each area (arterial and venous) of the circulation was calculated. Pulmonary vascular resistance increased from 216 +/- 70 dyne.sec/cm5 at a PEEP of 0 cm H2O to 308 +/- 125 dyne.sec/cm5 at a PEEP of 15 cm H2O (p < .001). This increase, however, resulted solely from an increase in the resistance of the venous part of the pulmonary circulation from 66 +/- 29 to 134 +/- 69 dyne.sec/cm5 (p < .001), without any change in pulmonary arterial resistance.

CONCLUSIONS

PEEP increases pulmonary vascular resistance solely by increasing pulmonary venous resistance. When applying PEEP, changes in pulmonary vascular resistance may impede the resorption of pulmonary edema fluid.