motaz kabadaya - Academia.edu (original) (raw)

Papers by motaz kabadaya

Research paper thumbnail of The Epidemiology of Hematogenous Candidiasis Caused by Different Candida Species

Clinical Infectious Diseases, 1997

The medical records of patients with hematogenous candidiasis at M. D. Anderson Cancer Center (Ho... more The medical records of patients with hematogenous candidiasis at M. D. Anderson Cancer Center (Houston) between 1988 and 1992 were retrospectively reviewed. There were 491 episodes of infection (6 per 1,000 admissions), 79% of which occurred outside the intensive care unit setting. A significant decrease in incidence was observed among patients with leukemia over the study period, together with a relative decrease in Candida albicans and Candida tropicalis infections and an increase in Candida krusei and possibly Candida glabrata infections. In the multivariate analysis, fluconazole prophylaxis provided strong protection against the development of C. tropicalis infection (odds ratio [OR] Å 0.08) and C. albicans infection (OR Å 0.15), in comparison with protection against infections due to other species, but it was the single most important determinant for the relative increase in C. krusei (OR Å 27.07) and C. glabrata (OR Å 5.08) infections. In conclusion, there has been a substantial shift in the epidemiology of hematogenous candidiasis caused by different Candida species in recent years. Fluconazole appears to be playing a major role in this observed shift.

Research paper thumbnail of Isogenic Strain Construction and Gene Mapping in Candida albicans

Genetic manipulation of Candida albicans is constrained by its diploid genome and asexual life cy... more Genetic manipulation of Candida albicans is constrained by its diploid genome and asexual life cycle. Recessive mutations are not expressed when heterozygous and undesired mutations introduced in the course of random mutagenesis cannot be removed by genetic back-crossing. To circumvent these problems, we developed a genotypic screen that permitted identification of a heterozygous recessive mutation at the URA3 locus. The mutation was introduced by targeted mutagenesis, homologous integration of transforming DNA, to avoid introduction of extraneous mutations. The ura3 mutation was rendered homozygous by a second round of transformation resulting in a Urastrain otherwise isogenic with the parental clinical isolate. Subsequent mutation of the Ura-strain was achieved by targeted mutagenesis using the URA3 gene as a selectable marker. URA3 selection was used repeatedly for the sequential introduction of mutations by flanking the URA3 gene with direct repeats of the Salmonella typhimurium hisC gene. Spontaneous intrachromosomal recombination between the flanking repeats excised the URA3 gene restoring a Ura-phenotype. These Urasegregants were selected on 5-fluoroorotic acid-containing medium and used in the next round of mutagenesis. T o permit the physical mapping of disrupted genes, the 18-bp recognition sequence of the endonuclease ISceI was incorporated into the hisG repeats. Site-specific cleavage of the chromosome with I-SceI revealed the position of the integrated sequences.

Research paper thumbnail of Resistance of Candida species to 炉uconazole

Research paper thumbnail of Gene Expression Programming: a New Adaptive Algorithm for Solving Problems

Computing Research Repository, 2001

Gene expression programming (GEP) is, like genetic algorithms (GAs) and genetic programming (GP),... more Gene expression programming (GEP) is, like genetic algorithms (GAs) and genetic programming (GP), a genetic algorithm as it uses populations of individuals, selects them according to fitness, and introduces genetic variation using one or more genetic operators . The fundamental difference between the three algorithms reside in the nature of the individuals: in GAs the individuals are linear strings of fixed length (chromosomes); in GP the individuals are non-linear entities of different sizes and shapes (parse trees); and in GEP the individuals are encoded as linear strings of fixed length (the genome or chromosomes) which are afterwards expressed as non-linear entities of different sizes and shapes (simple diagram representations or expression trees).

Research paper thumbnail of Novel 5-Flucytosine-Resistant Clade of Candida dubliniensis from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting

DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previou... more DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30 C. dubliniensis oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [S AB ] value, 0.86). The second population of 20 isolates was much more heterogeneous (average S AB value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (n ‫؍‬ 13) and the other of genotype 4 isolates (n ‫؍‬ 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC > 128 g/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC < 0.125 g/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of C. dubliniensis (Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.

Research paper thumbnail of Novel 5-Flucytosine-Resistant Clade of Candida dubliniensis from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting

Journal of Clinical Microbiology, 2005

DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previou... more DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30 C. dubliniensis oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [S AB ] value, 0.86). The second population of 20 isolates was much more heterogeneous (average S AB value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (n ‫؍‬ 13) and the other of genotype 4 isolates (n ‫؍‬ 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC > 128 g/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC < 0.125 g/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of C. dubliniensis (Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.

Research paper thumbnail of The Epidemiology of Hematogenous Candidiasis Caused by Different Candida Species

Clinical Infectious Diseases, 1997

The medical records of patients with hematogenous candidiasis at M. D. Anderson Cancer Center (Ho... more The medical records of patients with hematogenous candidiasis at M. D. Anderson Cancer Center (Houston) between 1988 and 1992 were retrospectively reviewed. There were 491 episodes of infection (6 per 1,000 admissions), 79% of which occurred outside the intensive care unit setting. A significant decrease in incidence was observed among patients with leukemia over the study period, together with a relative decrease in Candida albicans and Candida tropicalis infections and an increase in Candida krusei and possibly Candida glabrata infections. In the multivariate analysis, fluconazole prophylaxis provided strong protection against the development of C. tropicalis infection (odds ratio [OR] Å 0.08) and C. albicans infection (OR Å 0.15), in comparison with protection against infections due to other species, but it was the single most important determinant for the relative increase in C. krusei (OR Å 27.07) and C. glabrata (OR Å 5.08) infections. In conclusion, there has been a substantial shift in the epidemiology of hematogenous candidiasis caused by different Candida species in recent years. Fluconazole appears to be playing a major role in this observed shift.

Research paper thumbnail of Isogenic Strain Construction and Gene Mapping in Candida albicans

Genetic manipulation of Candida albicans is constrained by its diploid genome and asexual life cy... more Genetic manipulation of Candida albicans is constrained by its diploid genome and asexual life cycle. Recessive mutations are not expressed when heterozygous and undesired mutations introduced in the course of random mutagenesis cannot be removed by genetic back-crossing. To circumvent these problems, we developed a genotypic screen that permitted identification of a heterozygous recessive mutation at the URA3 locus. The mutation was introduced by targeted mutagenesis, homologous integration of transforming DNA, to avoid introduction of extraneous mutations. The ura3 mutation was rendered homozygous by a second round of transformation resulting in a Urastrain otherwise isogenic with the parental clinical isolate. Subsequent mutation of the Ura-strain was achieved by targeted mutagenesis using the URA3 gene as a selectable marker. URA3 selection was used repeatedly for the sequential introduction of mutations by flanking the URA3 gene with direct repeats of the Salmonella typhimurium hisC gene. Spontaneous intrachromosomal recombination between the flanking repeats excised the URA3 gene restoring a Ura-phenotype. These Urasegregants were selected on 5-fluoroorotic acid-containing medium and used in the next round of mutagenesis. T o permit the physical mapping of disrupted genes, the 18-bp recognition sequence of the endonuclease ISceI was incorporated into the hisG repeats. Site-specific cleavage of the chromosome with I-SceI revealed the position of the integrated sequences.

Research paper thumbnail of Resistance of Candida species to 炉uconazole

Research paper thumbnail of Gene Expression Programming: a New Adaptive Algorithm for Solving Problems

Computing Research Repository, 2001

Gene expression programming (GEP) is, like genetic algorithms (GAs) and genetic programming (GP),... more Gene expression programming (GEP) is, like genetic algorithms (GAs) and genetic programming (GP), a genetic algorithm as it uses populations of individuals, selects them according to fitness, and introduces genetic variation using one or more genetic operators . The fundamental difference between the three algorithms reside in the nature of the individuals: in GAs the individuals are linear strings of fixed length (chromosomes); in GP the individuals are non-linear entities of different sizes and shapes (parse trees); and in GEP the individuals are encoded as linear strings of fixed length (the genome or chromosomes) which are afterwards expressed as non-linear entities of different sizes and shapes (simple diagram representations or expression trees).

Research paper thumbnail of Novel 5-Flucytosine-Resistant Clade of Candida dubliniensis from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting

DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previou... more DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30 C. dubliniensis oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [S AB ] value, 0.86). The second population of 20 isolates was much more heterogeneous (average S AB value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (n ‫؍‬ 13) and the other of genotype 4 isolates (n ‫؍‬ 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC > 128 g/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC < 0.125 g/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of C. dubliniensis (Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.

Research paper thumbnail of Novel 5-Flucytosine-Resistant Clade of Candida dubliniensis from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting

Journal of Clinical Microbiology, 2005

DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previou... more DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30 C. dubliniensis oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [S AB ] value, 0.86). The second population of 20 isolates was much more heterogeneous (average S AB value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (n ‫؍‬ 13) and the other of genotype 4 isolates (n ‫؍‬ 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC > 128 g/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC < 0.125 g/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of C. dubliniensis (Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.