Fetal chromosome abnormalities and congenital malformations: an Egyptian study

Objective: Our objective were to determine and evaluate the role of genetic counseling and amniocentesis in early detection of chromosomal abnormalities or congenital malformations among women at risk. Patients and Methods: The study was performed on 784 pregnant women. Results: The cause for seeking genetic counseling in 22.8% of the study cases was positive family history of CNS malformations, and in 17.9% was chromosomal abnormalities in previous child. Also, the results showed that the indications for amniocentesis in 60.8% were history of having previous child with Down syndrome, and in 15.3% were advanced maternal age. The results of chromosomal analysis of amniotic fluid samples; 21 cases (19.3%) had chromosomal abnormalities, where trisomy 21 (Down syndrome) was detected in 10 cases (9.2%), unbalanced translocation Down syndrome was detected in 9 cases (8.3%) and one had 46 XX, del (13-q), one had 45, XX, t (13;14) and 2.8% was 46, XX, +21, der (14;21) (q10;q10). The risk of complications of amniocentesis was associated with performing amniocentesis early in pregnancy, and with increased number of attempts. The results also showed that Multiple congenital anomalies (MCA) represented among 42.2%, congenital malformation of CNS represents 26.6%, congenital malformation of the skeletal system 20%, congenital polycystic kidney 8.8% and pyloric stenosis in 2.2%. Among the 21 women with abnormal karyotype of amniotic fluid, the decision to terminate the pregnancy was made in 3 (14.3%). Among the 45 cases with abnormal findings suggesting fetal congenital malformation, 16 (35.6%) chose termination of their pregnancy. In conclusion: Public awareness of the risks and difficulties facing a child with chromosomal anomalies or congenital malformations and the effect on their future health and living is of great importance for acceptance of prenatal screening. Prenatal diagnosis may affect the reproductive decision after genetic counseling. It is essential that genetic counseling is noncoercive and nonjudjemental. The couples decision (Even if it is different from the counselor's views) should be respected. Keywords: Genetic counselling, antenatal screening, amniocentesis. Egypt. J. Hum. Genet Vol. 8 (2) 2007: pp. 131-14

Approaching a Dysmorphic Newborn

Background: Dysmorphology combines concepts, knowledge and techniques from field of embryology, clinical genetics and pediatrics. It deals with people who have congenital abnormalities and their families. Clinical delineation of dysmorphism and dysmorphic syndromes is crucial for patient management and family counseling. Patients and Method: Forty case mothers and neonates, 83 control mothers and neonates were recruited in the study. Face to face interviews were conducted with the mothers of both cases and controls. Case's mothers and neonates were subjected to certain investigations according to dysmorphic anomaly and when needed. Results: The study showed that increased risk of having a dysmorphic child was associated with high consumption of legumes and the use of kerosene in cooking stoves. Their Odd Ratio (OR) and Confidence Interval (CI) respectively were [OR=15558.0; CI 137.0-17716.2] and [OR=186.7; CI 42.3-824.5]. Maternal demographic risk factors were, medication intake (OR=29.62; CI 3.38-112.5), diseases during pregnancy (OR=24.13; CI 5.92-114.18), maternal occupation (OR=15.4; CI 1.78-132.8), and educational attainment (OR=2.85; CI 1.19-6.86). In rural areas the rate of having dysmorphic child is higher than that in urban areas (OR=11.85; CI 3.60-38.99), (p-value=0.00). Consanguinity (OR=4.35; CI 1.927-9.796), was a key risk factor contributing to dysmorphology. Drinking water which is obtained by pumps was significant in this study (OR=27.3; CI 3.4-222.7) as well as ghee consumption (OR=6.3; CI 2.4-16.4). Conclusion: In conclusion, the considerable challenge posed by dysmorphic abnormalities calls for the development of prevention programs through the establishment of community genetic services particularly those related to maternal education and environmental exposures. These primary prevention measures should be integrated into primary health care. Keywords: Dysmorphology, morphogenesis, dysmorphic syndromes, teratology, ecogenetics Egypt. J. Hum. Genet Vol. 9 (1) 2008: pp. 23-4

Prenatal diagnosis of aneuploidy among a sample of Egyptian high risk pregnancies

Background: A number of studies have shown that aneuploidies of only 5chromosomes (13, 18, 21, X and Y) account for about 65% of all chromosomal abnormalities and 95% of chromosomal aberrations cause live-born birth defects. Fluorescent in-situ Hybridization (FISH) has been found to be highly effective for rapidly determining the number of specifi ed chromosomes in interphase cells.Patients and Methods: Prenatal diagnosis was performed on 40 high riskpregnancies chosen from mothers attending the Antenatal Clinic of Ain Shams University Medical genetics Center (ASUMGC). Early amniocentesis for conventional karyotype analysis of cultured amniocytes and interphase FISH studies of uncultured amniocytes for rapid detection of aneuploidies of chromosomes (13, 18, 21, X and Y) was performed.Results: Normal karyotype was detected in 35 cases (87.5%) and in 4 cases (10%) chromosomal abnormalities were detected by conventional karyotype. However, culture failed in one case (2.5%) due to culture contamination. FISH assay confi rmed the cytogenetic fi ndings, for the probes used, on interphase nuclei in all cases analysed, except three cases of structural chromosomal abnormalities:[46,XX, add 21(q22); 46,XX, t(5;20) mat, 46,XY, inv(9) (p11:q13)]paternal. In one case of culture contamination, FISH analysis was useful inexcluding the aberrations of specifi c chromosomes 13, 18, 21, X and Y on the uncultured/interphase nuclei.Conclusion: Molecular cytogenetic technique of FISH is very useful inurgent cases of prenatal diagnosis where it can be used on unculturedamniocytes for rapid and accurate detection of common aneuploidies.Keywords: Aneuploidy, prenatal diagnosis, chromosomal aberrations, amniocentesis, FISH

Genetic Affinities within a Large Global Collection of Pathogenic Leptospira: Implications for Strain Identification and Molecular Epidemiology

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently circulating between the islands and the mainland

Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API

BACKGROUND: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. METHODOLOGY/PRINCIPAL FINDINGS: We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. CONCLUSIONS/SIGNIFICANCE: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/)

The Human Nasal Microbiota and Staphylococcus aureus Carriage

BACKGROUND: Colonization of humans with Staphylococcus aureus is a critical prerequisite of subsequent clinical infection of the skin, blood, lung, heart and other deep tissues. S. aureus persistently or intermittently colonizes the nares of approximately 50% of healthy adults, whereas approximately 50% of the general population is rarely or never colonized by this pathogen. Because microbial consortia within the nasal cavity may be an important determinant of S. aureus colonization we determined the composition and dynamics of the nasal microbiota and correlated specific microorganisms with S. aureus colonization. METHODOLOGY/PRINCIPAL FINDINGS: Nasal specimens were collected longitudinally from five healthy adults and a cross-section of hospitalized patients (26 S. aureus carriers and 16 non-carriers). Culture-independent analysis of 16S rRNA sequences revealed that the nasal microbiota of healthy subjects consists primarily of members of the phylum Actinobacteria (e.g., Propionibacterium spp. and Corynebacterium spp.), with proportionally less representation of other phyla, including Firmicutes (e.g., Staphylococcus spp.) and Proteobacteria (e.g. Enterobacter spp). In contrast, inpatient nasal microbiotas were enriched in S. aureus or Staphylococcus epidermidis and diminished in several actinobacterial groups, most notably Propionibacterium acnes. Moreover, within the inpatient population S. aureus colonization was negatively correlated with the abundances of several microbial groups, including S. epidermidis (p = 0.004). CONCLUSIONS/SIGNIFICANCE: The nares environment is colonized by a temporally stable microbiota that is distinct from other regions of the integument. Negative association between S. aureus, S. epidermidis, and other groups suggests microbial competition during colonization of the nares, a finding that could be exploited to limit S. aureus colonization

Inactivation of DltA Modulates Virulence Factor Expression in Streptococcus pyogenes

D-alanylated lipoteichoic acid is a virtually ubiquitous component of gram-positive cell walls. Mutations in the dltABCD operon of numerous species exhibit pleiotropic effects, including reduced virulence, which has been attributed to increased binding of cationic antimicrobial peptides to the more negatively charged cell surface. In this study, we have further investigated the effects that mutating dltA has on virulence factor expression in Streptococcus pyogenes.Isogenic Delta dltA mutants had previously been created in two distinct M1T1 isolates of S. pyogenes. Immunoblots, flow cytometry, and immunofluorescence were used to quantitate M protein levels in these strains, as well as to assess their ability to bind complement. Bacteria were tested for their ability to interact with human PMN and to grow in whole human blood. Message levels for emm, sic, and various regulatory elements were assessed by quantitative RT-PCR. Cell walls of Delta dltA mutants contained much less M protein than cell walls of parent strains and this correlated with reduced levels of emm transcripts, increased deposition of complement, increased association of bacteria with polymorphonuclear leukocytes, and reduced bacterial growth in whole human blood. Transcription of at least one other gene of the mga regulon, sic, which encodes a protein that inactivates antimicrobial peptides, was also dramatically reduced in Delta dltA mutants. Concomitantly, ccpA and rofA were unaffected, while rgg and arcA were up-regulated.This study has identified a novel mechanism for the reduced virulence of dltA mutants of Streptococcus pyogenes in which gene regulatory networks somehow sense and respond to the loss of DltA and lack of D-alanine esterification of lipoteichoic acid. The mechanism remains to be determined, but the data indicate that the status of D-alanine-lipoteichoic acid can significantly influence the expression of at least some streptococcal virulence factors and provide further impetus to targeting the dlt operon of gram-positive pathogens in the search for novel antimicrobial compounds

Regulation of Hemolysin Expression and Virulence of Staphylococcus aureus by a Serine/Threonine Kinase and Phosphatase

Exotoxins, including the hemolysins known as the alpha (α) and beta (β) toxins, play an important role in the pathogenesis of Staphylococcus aureus infections. A random transposon library was screened for S. aureus mutants exhibiting altered hemolysin expression compared to wild type. Transposon insertions in 72 genes resulting in increased or decreased hemolysin expression were identified. Mutations inactivating a putative cyclic di-GMP synthetase and a serine/threonine phosphatase (Stp1) were found to reduce hemolysin expression, and mutations in genes encoding a two component regulator PhoR, LysR family transcriptional regulator, purine biosynthetic enzymes and a serine/threonine kinase (Stk1) increased expression. Transcription of the hla gene encoding α toxin was decreased in a Δstp1 mutant strain and increased in a Δstk1 strain. Microarray analysis of a Δstk1 mutant revealed increased transcription of additional exotoxins. A Δstp1 strain is severely attenuated for virulence in mice and elicits less inflammation and IL-6 production than the Δstk1 strain. In vivo phosphopeptide enrichment and mass spectrometric analysis revealed that threonine phosphorylated peptides corresponding to Stk1, DNA binding histone like protein (HU), serine-aspartate rich fibrinogen/bone sialoprotein binding protein (SdrE) and a hypothetical protein (NWMN_1123) were present in the wild type and not in the Δstk1 mutant. Collectively, these studies suggest that Stk1 mediated phosphorylation of HU, SrdE and NWMN_1123 affects S. aureus gene expression and virulence