Journal of Life Sciences
Volume 6, Number 5, May 2012 (Serial Number 49)
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DAV ID P UBL ISH IN G
J LS
Journal of Life Sciences
Volume 6, Number 5, May 2012 (Serial Number 49)
Contents
Biochemical and Microbiology
469 The Hemochromatosis Distribution in Matera Province: A New SNP to Explain the Low Genotype-Phenotype Correlation
Maria Carmela Padula, Marilena Larocca, Rocco Rossano, Luigi Milella, Domenico Dell’Edera and Giuseppe Martelli
476 A Survey on the Methods of Primer Design Among Plant Pathologists in Australia and New Zealand
Francisco M. Ochoa Corona, Brendan Rodoni and Joe Tang
481 Low Sero-Prevalence of Toxoplasma gondii IgG and IgM Antibodies in HIV Sero-Positive Patients Attending National Hospital, Abuja, Nigeria
Tatfeng Youtchou Mirabeau and Adesua Ojo Ebikade
485 Development of Bioinfo-Portal Tool for the Analysis of Genomic and Proteomic Data
Rana Rehan Khalid, Bilal Hussain, Muhammad Ali, Muhammad Sajjad Ahmad, Asma Haque and Hira Qamar
489 Prevalence of Anti-HCV Antibodies Among Thalassemia Patients in Mosul City, Iraq
Mohammed D. Khalid and Basima A. Abdullah
492 Comparative Evaluation of Mannan Oligosaccharides and Acidifier Calcium Formate on the
Quail Digestive Tract
Eleftherios Bonos, Efterpi Christaki, Nikolaos Soultos, Amin Abrahim and Panagiota Florou-Paneri
Botany and Zoology
501 Ecology, Biology and Biometry of an Endemic Fabaceae: Genista Saharae Cosson and Durieu
Meriane Djamila and Kaabache Mohamed
505 Identification of the Far Eastern Species of Laminaria Lamouroux and Saccharina Stackhouse (Laminariales, Phaeophyceae) Based on Morphological Features
Isabel Giménez, Jacqueline Escobar, Elena Ferruz, Susana Lorán, Marta Herrera, Teresa Juan, Antonio Herrera and Agustín Ariño
518 Oribatid Use as Bioindicateur of Environment: Case of Galumna sp. and Scheloribates sp. (Acari: Oribatida)
Ghezali Djelloul and Harkat Hafsa
528 A Review of Recent Knowledge on Raptor Species in Sumatra, Indonesia
Hilda Zulkifli, Muhammad Iqbal, Adam A. Supriatna and Agus Nurza
536 The Best Dose for Sterilisation of Greenhouse Whitefly, Trialeurodes vaporariorum (Westwood) (Hem.: Aleyrodidae) by Gamma Radiation
Maryam Moradi and Mehdi Zarabi
Interdisciplinary Researches
543 Wastewater Treatment in the Oasis of Figuig (Morocco) by Facultative Lagoon System:
Physico-Chemical and Biological Aspect
Ouafae El Hachemi, Hassan Elhalouani, Antonina Torrens Armengol and Miquel Salgot
550 The Comparison of Amaranth Decolorization Ability for Two Types of Biological Consortia
Yovana Todorova, Mihaela Kirilova, Raycho Dimkov and Yana Topalova
557 The Long Term Evolution of Phosphates from the Cambic Chernozem at ARDS Caracal, Romania
Ana Maria Dodocioiu, Romulus Mocanu and Marian Dobre
563 The Research on Carbon Accumulation of Grassland Ecological System in China Tao Li, Lei Ji, Jianrong Tan, Tao Liu, Zhongqi Song, Shujing Yang and Youmin Gan
570 Study of Contributing Factors for Cure Response in Patients with Acute Myeloblastic Leukemia (AML)
Saharnaz Ahmadi, Mostafa Rezaei-Tavirani, Adeleh Divsalar, Soheila Khodakarim and Leila Tahmasebi
577 Listeria monocytogenes in Live Mytillis galloprovincialis Collected from Butrinti Lagoon Located in South Part of Albania
Kapllan Sulaj, Halit Memoci, Xhuljeta Hamiti, Kastriot Korro and Fejzo Selami
582 Depression in End Stage Renal Disease: Comparison Between Patients Treated with Hemodialysis and Peritoneal Dialysis
The Hemochromatosis Distribution in Matera Province:
A New SNP to Explain the Low Genotype-Phenotype
Correlation
Maria Carmela Padula, Marilena Larocca, Rocco Rossano, Luigi Milella, Domenico Dell’Edera and Giuseppe Martelli
Department of Biology, University of Basilicata, Potenza, Viale dell’Ateneo Lucano 85100, Italy
Received: November 24, 2011/Accepted: January 13, 2012/Published: May 30, 2012.
Abstract: The present study aims to investigate the genotype-phenotype correlation of the hereditary hemochromatosis (HH), a
genetic disorder of iron metabolism, in Matera province (Basilicata, Italy). Integrating both epidemiological and molecular approaches, the authors studied: (a) the frequency of the HH main mutations; (b) the association between mutations and HH cases. The majority of patients with HH are homozygous for the C282Y mutation of the HFEgene. A second mutation (H63D) is more widely distributed and its connection with HH isn’t clear, but a low penetrance is attributed to this variant. The population-based study consists of three steps: (1) determination of iron biochemical parameters, (2) genetic test, and (3) sequencing of HFE gene and bioinformatics studies. A case report is presented in a 41-year-old male (genotype: H63D/wt) with biochemical and clinical evidences of HH, in absence of secondary iron overload factors. In the cohort of studied patients (150M:62F), there are 18 homozygous patients; H63D/H63D genotype is found in 11 cases. In the heterozygous group, H63D/wt is the predominant genotype (61/68 subjects). All the H63D/wt residents in the same village (Mont.) show altered biochemical parameter levels. In our case study, a substitution localized into the HFE promoter (nt225A > C) is found. Results show that the H63D genotype is responsible for most cases of HH. The peculiar clinical manifestation found in Mont. suggests a founder effect. In our case, the iron overload is related to a presence of an undetected mutation, critical for the transcriptional regulation of the HFE gene.
Key words: Hereditary hemochromatosis, HFE gene variants, clinical phenotype, transcriptional regulation.
1. Introduction
Hemochromatosis type 1 is an autosomal recessive disorder that occurs predominantly in Northern European populations, with a prevalence of approximately 3-8 in 1,000 [1, 2]. HH is characterized by excessive iron absorption, which progressively leads to multi-organ failure. In fact, if untreated, hemochromatosis patients develop hepatic cirrhosis, hepatocellular carcinoma, cardiomyopathy, arrhythmias, diabetes, arthritis and hypogonadism [3, 4]. At an early stage, non-specific symptoms,
Corresponding author: Maria Carmela Padula, Ph.D.
candidate, research fields: molecular biology, human genetic. E-mail: [email protected].
persistent fatigue and arthralgia, can appear; after a phase of latency, the first signs of biochemical expression appear, with a serum iron parameters increase (serum transferrin, iron and ferritin) [5]. The clinical manifestation occurs around the age of 40 in males and later in females, because of the protective effects of menstrual blood loss and pregnancies [6]. The clinical expression occurs more frequently in males than in females (sex ratio of 3:1). HH can be treated by phlebotomies or chelation therapy [7].
different mutations have been identified in the HFE gene worldwide, but the main mutations are known as C282Y (exon4, nt845G > A; Cys282Tyr) and H63D (exon2, nt187C > G; His63Asp) [11]. The HFE gene encodes the HFE protein, a transmembrane glycoprotein implicated in the iron uptake modulation. It forms a heterodimeric complex with
β2-microglobulin [12, 13]. The C282Y disrupts a disulfide bond in the α3 domain leading to lack of HFE-β2microglobulin association [14].
The H63D mutation is responsible for the lack of HFE protein-transferrin receptor complex [15], a critical interaction for the iron homeostasis maintenance.
Although the HFE protein role in the iron regulation is still unclear, several recent studies have emphasized a role in the regulation of intestinal iron absorption by forming complexes with: (a) transferrin receptor 1 (TfR1), in case of iron deficiency, or (b) transferrin receptor 2 (TfR2), the TfR1 liver homolog, in case of iron overload. HFE/TfR2 complex actives a signaling cascade resulting in the upregulation of hepcidin and, consequently, a decreased dietary iron uptake [16, 17].
Regarding the distribution of genotypes among iron loaded patients, most subjects are homozygous for C282Y mutation [18]. The percentages are > 90% in the UK and Brittany, > 80% in Northern European countries; it ranges from 60% and 83% in the USA [19, 20]. The C282Y/C282Y percentage in Italy is 64%; C282Y homozygous shows more severe iron overload than the other HFE genotypes [21]. The H63D role in iron overload is controversial, but this condition rarely develops iron overload [22, 23]. Compound heterozygous C282Y/H63D has a mild-moderate phenotype [6].
2. Material and Methods
The present investigation is conducted in Basilicata, a region of about six hundred thousand inhabitants located in the South of Italy. The study includes patients who have or had some symptoms related to an
altered iron metabolism or individuals belonging to families with clinical evidence of iron overload.
Biochemical parameters related to iron metabolism (serum iron, serum transferrin and serum ferritin) are determined by standard biochemical methods (including collection of serum after a 12-hour fast, confirmation by at least two measurements). Serum transferrin saturation value is calculated as follows: [serum iron/(serum transferrin × 1.2)] × 100.
The subsequent analysis of mutations related to hemochromatosis relies on amplification of the specific gene region by PCR, followed by mutation detection using reverse dot-blot (Nuclear Laser Medicine S.r.l. kit). In particular, the methodology includes three steps: (1) DNA isolation, (2) PCR amplification using biotinylated primers, (3) hybridation of amplification products to a test strip containing allele-specific oligonucleotide probes immobilized as an array of parallel lines. Bound biotinylated sequences are detected using streptavidin-alkaline phosphatase and color substrates.
The assay covers 11 HFE gene mutations (V53M, V59M, H63D, H63H, S65C, Q127H, E168X, E168Q, W169X, C282Y, Q283P), four transferrin receptor mutations (Y250X, E60X, M172K, the AVA Q 594-597) and 2 Ferroportin mutations (N144H, V162).
To evaluate the quality and quantity of extracted DNA two methods are used: (1) gel electrophoresis (1% agarose gel) in presence of standard at known concentration, and (2) spectrophotometric determination by means of NanoDrop™ spectrophotometer.
Explain the Low Genotype-Phenotype Correlation
patterns shown in Table 1 should be obtained. If the DNA test confirms the presence of mutations in a patient, family testing is proposed. It combines the collection of clinical, biochemical and genotypic information for the patient relatives.
In order to better investigate the correlation between genetic background and clinical phenotype, a second level genetic analysis is performed, considering a case-model: 41-year-old male with some early clinical signs of iron overload, such as fatigue, weakness, joint and abdominal pains and jaundiced complexion. To define the clinical picture, the patient is assayed for CBC, total bilirubin, transaminases, HBV and HCV serum markers, as well as the iron biochemical parameters. Medical history is assessed to exclude additional risk factors related to iron overload.
The presence of unknown mutations in HFE gene or an alteration of regulation mechanisms are supposed to explain a low correlation. On the basis of HFE sequences in NCBI database, the PCR primers are designed by means of NCBI Primer-Blast. After the optimization of reaction components and conditions, a series of amplifications is carried out to isolate and sequence gene fragments belonging to our case DNA. For the amplification, 25 µL of PCR reaction are used: 1.5 µL MgCl2, each of dNTP 2 mM,
1 µL of specific primers, 0.4 U/µL of AmpliTaq Gold® DNA polymerase in 1× PCR buffer (100 mM tris-HCl, pH 8.3, 500 mM KCl).The conditions of reaction are the following: (a) initial denaturation: 95 °C/7 min; (b) thermocycling: 94 °C/1 min; 58 °C/1 min; 72 °C/2 min (43 cycles); (c) final extension: 72 °C/10 min. Amplification products are analyzed by gel electrophoresis (1.5% agarose gel) in order to detect the most significant fragments. These ones are
Table 1 Pattern for Genotype Identification.
Wild type line Mutant line Genotype
Normal Positive Negative Normal
Heterogyzous Positive Positive Heterozygous Homozygous Negative Positive Homozygous
isolated from the gel using sterile needles directly placed in the band, after exposure to UV light. The DNA isolated fragments are amplified in a final amplification mix volume equal to 50 µL, to verify the quality and uniqueness. The final step consists in HFE fragment sequencing. The next bioinformatics analysis allows to verify the similarity between our sequences and HFE sequences reported in database. In particular, a multiple alignment is performed to identify conserved/non conserved nucleotides and consequently possible new variants.
3. Results
Regarding the epidemiologic data, this study involves 212 patients (median age: 53, range: 3-88), of whom 126 subjects (59%) are healthy, 68 (32%) are heterozygous (61 cases H63D/wt, 5 C282Y/wt, 2 S65C/wt). There are 13 patients with homozygosity condition (11 cases H63D/H63D, 2 C282Y/C282Y). Five individuals are compound heterozygous (3 C282Y/H63D, 1 C282Y/S65C, 1 H63D/S65C). The sex ratio is equal to 2.42M:1F (150:62). In detail, the authors observe the distribution shown in Table 2. The Fig. 1 shows the distribution of the most important mutations related to the disease (C282Y and H63D) within the population investigated. As H63D variant is more frequent than C28Y in the province of Matera, we focus our attention on the distribution of this variant: the Table 3 concerns the age distribution of H63D genotypes and controls.
Table 2 Distribution of HFE genotypes within the analyzed population.
HFE genotype Gender
Fig. 1 Distribution of H63D and C282Y mutations in the analyzed population.
Table 3 Age distribution of H63D genotypes and controls.
Age (years) H63D/H63D H63D/wt Controls Up to 24 1 (0M:1F) 6 (3M:3F) 3 (2M:1F)
25-34 0 3 (0M:3F) 11 (8M:3F)
35-44 4 (3M:1F) 8 (6M:2F) 21 (15M:6F) 45-54 5 (2M:3F) 13 (11M:2F) 33 (30M:3F) 55-64 1 (0M:1F) 11 (4M:7F) 16 (14M:2F) 65-74 1 (1M:0F) 13 (10M:3F) 30 (19M:11F) 75 and older 0 6 (5M:1F) 12 (8M:4F)
Total 12 60 126
During data collection and interpretation, we have identified a group of patients with a peculiar clinical behavior: some H63D carriers show abnormal iron biochemical parameter levels. They are inhabitants of the same village in Basilicata (Mont.). In order to investigate this particular behavior, we deeply study a peculiar case. We report the average (three measurements) biochemical iron parameter values observed in our clinical case: transferrin 312 mg/dL (normal range: 200-360 mg/dL); ferritin: 948 ng/mL (normal range: 10-291 ng/mL); iron: 129 µL/dL (normal range: 49-151 µL/dL).
About the results of the second level analysis, sequencing outcomes show a nucleotide change that could explain the clinical behavior anomaly found in our case. In particular, applying a bioinformatics approach that integrates the similarity searches (performed by BlastN of NCBI database) and the multialignment analysis (carried out using ClustalW2 Tool of EMBL-EBI database), we have established that the change A > C resides in 225 position of the
HFE promoter region (GenBank ID: Y09801).
4. Discussion
Since the discovery of the HFE gene, several studies have been performed in order to evaluate the H63D and C282Y frequencies in different populations and to provide information about the worldwide HFE mutations distribution [20, 24], but also about the genotype-phenotype correlation [25]. We have notified that no information is found about the H63D and C282Y frequencies in Basilicata. In the present study we perform a population-based study of the clinical expression of the hemochromatosis gene, in order to: (a) determine the main HFE mutation frequencies in Matera district, (b) evaluate the correlation between genotype and phenotype in our population, and (c) compare these results to other studies.
Explain the Low Genotype-Phenotype Correlation
patients heal the iron overload with periodic blood donations. One of these subjects underwent liver transplantation, evidence of H63D/H63D genotype severity, in absence of other causes of hepatic injury. The majority of H63D/H63D patients are 35-55 years-old males, according to the late HH onset and to the sex differences.
Analyzing the compound heterozygous group (sex ratio of 4M:1F), we observe that the subject C282Y/H63D, a 54 years old male, treats the iron overload with periodic phlebotomy, suggesting a synergistic effect of the two mutations on the clinical HH expression. The C282Y/S65C individual shows a value of transferrin saturation equal to 32% (n.r. 15-45%); the TS value of H63D/S65C patient is equal to 24%. In this case we don’t emphasize the H63D genotype severity, because there are no significant differences between the two TS values: they are within the normal range both in absence (C282Y/S65C genotype) and in presence (H63D/S65C genotype) of H63D variant. However, we could relate this aspect to the patient age: they are under 30 years-old. Instead the clinical manifestation of HH occurs 10 years later and the subsequent clinical signs are due to the progressive alteration of the physiology of involved organs, liver in particular.
Within the H63D/wt genotype group, we observe a particular clinical manifestation that has revealed a
low genotype-phenotype correlation: about half of the subjects (28/61) show abnormal values of iron parameters in absence of other factors. In detail, focusing our attention on the distribution of these subjects in the analyzed population, we observed that, of these 28, 18 subjects are inhabitants of the same small village in Basilicata (Mont.) and all these individuals have biochemical evidences of iron overload (serum ferritin value higher than 750 ng/mL) without evidence of secondary iron overload causes. For this reason, we report and analyze the case-model of a male who lives in Mont. village, with H63D/wt genotype. To elucidate this experimental evidence, we sequence the HFE coding region, the 5’UTR (UnTranslated Region) and the 3’UTR. No mutation has been found in HFE CDS, 3’UTR; a new polymorphic site is individuated within the promoter region (nt225 A > C). A previous study provided information about the transcriptional regulation of the human HFE gene and defined the functional organization of the HFE promoter. The putative gene regulatory element site of the 5’-flanking region has been identified and we can localize our polymorphism two nucleotides downstream of the TATA binding protein (TBP) site [28], by aligning our case model and the RefSeq as shown in Fig. 2. This transcriptional factor is essential for the promoter activation and for the assembly of transcriptional complex [29].
Our polymorphic site resides in a regulatory region within the core promoter, important for the regulation of the HFE gene. This aspect is very important because it is known that the regulation of gene expression is achieved through the interaction of several control levels including the regulation of transcription initiation.
In some cases, an association between promoter genetic variations and disease is reported, such as in lactose intolerance [30, 31], chronic hepatitis [32], and autoimmune diseases [33]. Based on these aspects, the authors could suggest that our polymorphism affects the HFE transcriptional regulation, leading to the dysregulation of the same gene. Consequently, the hemochromatosis gene is unable to perform its “iron sensing” role and the iron overload occurs.
Finally, we propose a model of mechanism that underlines a partial dominance of wild type allele of the HFE gene and that could be to explain the iron overload in our clinical case.
Further investigation are needed to validate the detected mutation and to screen all individuals with a clinical manifestation that is similar to our case in the same area and in different areas, in order to confirm the clinical implications of this new variation and to evaluate the possibility that it could become a new HH marker.
5. Conclusion
The present study allows to know the distribution of the main HH mutations in Basilicata. In contrast with previous investigations, our results show that the H63D/H63D genotype is responsible for most cases of the disorder and that some H63D/wt subjects have abnormal iron biochemical parameter values. We observe that the majority of these iron loaded carriers are inhabitants of the same area, suggesting a founder effect. To explain the found low genotype-phenotype correlation, we perform the second level analysis. This study emphasizes the importance of gene sequencing in HH diagnosis and management. In addition, the
new mutation (nt225 A > C), never described before in literature, explains, at molecular level, the peculiar HH clinical expression: we demonstrate that in our clinical case, the iron overload is related to a promoter mutation that affects the transcriptional regulation of the HFE gene.
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A Survey on the Methods of Primer Design Among Plant
Pathologists in Australia and New Zealand
Francisco M. Ochoa Corona1, Brendan Rodoni2 and Joe Tang3
1. Oklahoma State University, National Institute for Microbial Forensics & Food and Agricultural Biosecurity (NIMFFAB), 127
Noble Research Center, Stillwater, OK 74078-3003, USA
2.Department of Primary Industries, Knoxfield Centre, Private Bag 15, Ferntree Gully Delivery Centre, Victoria, Australia
3.Plant Health and Environment Laboratory, Investigation and Diagnostic Centre, MAF Biosecurity New Zealand, P.O. Box 2095,
Auckland 1140, New Zealand
Received: October 14, 2011/Accepted: December 12, 2011/Published: May 30, 2012.
Abstract: Designing primers for PCR-based diagnostics was achieved by executing sight searches on DNA sequences. Visual
searching for specific DNA targets is time consuming, subjective and requires optimisation among numerous candidate primer sets. Several primer design software have been linked to useful bioinformatic packages to speed the development of PCR assays. Despite the software options available, primer design has remained a challenging aspect of incursion responses, biosecurity emergencies and microbial forensic applications. Two surveys were conducted among 45 plant virologists and 21 other plant pathologists during the 7th Australasian Plant Virology Workshop and the 16th Biennial Australasian Plant Pathology Conference in 2006 and 2007, respectively. Results show that most primer design learning occurs scientist to scientist rather than during academic teaching. This tendency matches with 16% of scientists users of PCR, who do not engage in primer design and 25% designing primers only by visual means, combining a pool of 41% who if trained, would likely enhance their performance in primer design. Only 13 out of 58 scientists ranked themselves as experts. Implementing primer design in study programs and regional training will benefit plant pathology and entomology, and the responsiveness and performance of biosecurity and microbial forensics in the South Pacific.
Key words: Primer design, PCR, education, training, biosecurity, microbial forensics, plant pathology.
1. Introduction
Since the first report of the polymerase chain reaction (PCR) [1-4], oligonucleotide primer design
has become a cornerstone step for developing PCR-based assays. The selection of oligonucleotide sequences with appropriate priming and
thermodynamic characteristics was achieved initially by executing visual searches of targeted DNA
sequences followed by tedious and time consuming rounds of PCR optimization applied to numerous primer set candidates until a robust and repeatable
Corresponding author: Francisco M. Ochoa Corona, Ph.D.,
assistant professor, research fields: plant virology, microbial forensics, diagnostics and detection, biosecurity. E-mail: [email protected].
assay was achieved. More recently, several primer design software packages have been developed, and
serve as useful bioinformatic tools to speed the development of PCR-assays [1, 5-9]. However, despite the number of options now available for
primer design, the rapid development of primer sequences required for PCR detection of exotic
micro-organisms during incursion responses, molecular detection, and other biosecurity and microbial forensic applications remain challenging for
a number of scientists.
A survey was conducted among plant pathologists
Pathologists in Australia and New Zealand
biosecurity responsiveness in this region. This survey also explored how knowledge of primer design and
new related developments in this field is communicated among scientists working on the
development of detection methods, disease diagnostics, biosecurity, microbial forensics and general molecular biology.
2. Materials and Methods
Two surveys were conducted during the 2006 7th Australasian Plant Virology Workshop held in Rottnest Island, Australia, and the 2007 16th Biennial
Australasian Plant Pathology Conference in Adelaide, Australia. The surveyed universe consisted of 66
interviews, 45 of which were of plant virologists and 21 of other plant pathologists. Eight interviews were discarded because of conflicts in the provided
answers, leaving 58 interviews. The interviewed scientists were affiliated with universities (47%),
government (37%), private industry (6%) and part time combinations such as universities-government (8.8%) and government-private (2.2%). The
interviewed universe was composed of scientists (24.4%), graduate students (24.4%), academic faculty
(15.5%), postdoctoral associates (6.6%), laboratory technicians (2.2%), managers (2.2%), as well as participants who did not state their occupation
(24.4%). Moreover, 51.1% of respondents were virologists, 2.2% mycologists, 2.2% nematologists,
and 44.5% did not specify an area of expertise. Other questions explored the preferred resources and methods used during primer design, such as how
primer design skills were learned, and the willingness to share expertise in primer design with colleagues. A
call to structure a list of experts in primer design was also included. All questions were provided in multiple choices format and percentages calculated after data
collection. Percentages were rounded to the proximal decimal.
3. Results
The survey indicates that 25% of the surveyed
scientists use only visual analysis of targeted DNA sequences for primer design, while 11% use only
software. Fifty eight percent combined both methods and 5% did not answer (Fig. 1). When these plant
pathologists were asked about what they do when requiring primers, 48% indicated to be self-designers that eventually also picks primers from literature, 28%
expressed to be only self-designers, and 8% design primers or rely on team members or contract services
to get them. The rest 16% do not engage in primer design. In this group only 6% rely on team members expertise, 4% may rely on team members but also
select primers from literature, 2% only select primers from literature, 2% only contract services, and 2% do
not know how (Fig. 2). Regarding how primer design skills are gained, 7% learned during undergraduate or graduate education, 14% during postdoctoral research,
28% through colleagues, 22% were self learners and 29% learned by themselves and with colleagues
combining more than one way of learning, but none had learned during workshops or conferences. All of whom group 79% of self learners scientists that
learned with colleagues, or by combining different learning approaches, for example combining either
with colleagues and other approaches or by self- learning plus another approach, on the contrary,
Fig. 1 Preference for primer design methods.
Fig. 2 How scientists as users of PCR obtain primer sequences.
Sixteen percent do not engage in primer design (6% relay on team members expertise, 4% may rely on team members but also select
primers from literature, 2% only select primers from literature, 2% only contract services, and 2% do not know how) in contrast to
48% that either design or pick primers from literature. Twenty eight percent claimed to only design the primers they need.
Fig. 3 How scientist learned primer design.
Seventy nine percent of surveyed scientists comprise self learners, scientists that learned with colleagues, or scientist combining different approaches for learning (combining either with colleagues and other approach or by self-learning plus another approach), in contrast to 21% who had learned during postdoctoral research, undergraduate or graduate studies. No learning during attendance at scientific conferences or meetings was reported.
21% had learned during formal education (postdoctoral research, undergraduate or graduate
studies) (Fig. 3). When asked about their willingness to share expertise and whether sharing their
expertise.or skills could make them less competitive, 72% were willing to share their expertise, 14% were not, and 14% did not answer. Similarly, 72% did not
think that sharing their expertise would make them
less competitive, 7% think that sharing expertise would make them less competitive and 19% did not
answer. Only 13 out of the 58 scientists interviewed at the two conferences ranked themselves as experts.
Seven of these were from Australia, three from New Zealand and the remaining three respondents were from South Africa, the UK and the USA. The software
used by scientists to assist the design of primer 1.78 5.3% Post‐graduate
course
14.2%
Doctoral Res.
0%
Workshops/Conf.
28.5%
with colleagues
21.4%
Self‐learner
1.78 1.78 1.78 1.78 3.571.78
1.78 10.71%
With colleagues & ‐learner
1.78
self
Self ‐design 28%
Only literature
2%
Only relay in
team 6%
Only
contract 2%
Don’t
know how
2%
Self‐ design & literature
48%
Literature or
relay on team
member
4 %
Self‐design or
relay on team
or contract
them
Pathologists in Australia and New Zealand
sequences include (in alphabetical order): Amplify 1.2, Gprime, DNAMAN, Oligo, Primer Express, Primer3,
Primo, Premier3, PCR/DNA detective [1, 5-8, 10, 11].
4. Discussion
A number of interpretations can be derived from
this survey. However, the aim of this survey was to
obtain elements for discussion toward training and
education needs, and the implementation of measures
for improving primer design as a catalytic factor for
the improvement of responsiveness and awareness of
biosecurity and microbial forensics in the South Pacific. The surveyed plant pathologists were not
equally comfortable with sharing some information.
For example, 44.5% did not provide details about their
specialty field and 24.4% of the respondents declined
to provide details about their type of appointment.
Some survey questions not answered by the whole
universe of interviewed scientists were not evaluated
during this survey (not shown). Yet, the information
obtained depicts the preferences of a group of scientists in Australia and New Zealand regarding
methods used for primer design, and for learning and
communicating their expertise. Two major tendencies
were observed regarding how primer design skills are
learned. Seventy nine percent of surveyed scientists
describe themselves as self learners, or learned with
colleagues, or combined these two learning
approaches (Fig. 3), on the contrary, 21% had learned
during postdoctoral research, undergraduate or graduate studies (Fig. 3). No learning during
attendance at scientific conferences or meetings was
reported (Fig. 3). This result suggests that most of the
primer design learning occurs scientist to scientist
rather than during academic teaching. These
tendencies match with additional results indicating
that 16% of these scientists who are users of PCR, do
not engage in formal primer design (Fig. 2) and 25%
design primers only by visual means (Fig. 1), combining a pool of 41% who if trained, would likely
enhance their level of performance in primer design.
Similarly, 14% of these plant pathologists rely on
team members or contract services for primer design
or select primers from the literature (Fig. 2).
The results obtained from PCR based procedures during initial phases of detection and investigation are
of fundamental value to downstream the presumptive diagnosis that lead to a definitive diagnosis [12]. Design of optimal primers is paramount for the
successful development of effective PCR detection procedures. This survey shows that improvements in
primer design performance can be gained by incorporating primer design principles in plant pathology, entomology, microbial forensics and
biosecurity training programs.
Primer design strategies comprise a relatively new
area of knowledge and skills, and involve a
conglomerate of knowledge from molecular biology,
bioinformatics, thermodynamics, biochemistry,
mathematics and chemistry among other basic
sciences. Techniques of primer design can be fit
logically into a variety of curricula as either a
curriculum component or part of course works in plant pathology, entomology, forensics and biosecurity.
5. Conclusions
This survey showed that 74% of a selected group of
plant pathologists in the South Pacific are willing to
share their primer design expertise, and at least ten self-described primer design experts are located in this
region. Incorporation of primer design into curricula
and study programs and the implementation of
regional training workshops will benefit current
programs in plant pathology and entomology, and will
improve the responsiveness and performance of
programs in biosecurity, microbial forensics in the
South Pacific.
Acknowledgments
The authors acknowledge Professors Jacqueline
affiliated to the National Institute for Microbial Forensics & Food and Agricultural Biosecurity
(NIMFFAB) for the review of the manuscript and valuable comments.
References
[1] L. Ping, K.C. Kupfer, C.J. Davies, D. Burbee, G.A. Evans, H.R. Garner, Primo: A primer design program that applies base quality statistics for automated large-scale DNA sequencing,Genomics 40 (1997) 476-485.
[2] K. Mullis, F. Faloona, S. Schar, R. Saiki, G. Horn, H. Erlich, Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction, Cold Spring Harbor Symp. Quant. Biol. 51 (1986) 263-273.
[3] R. Saiki, D.H. Gelfand, S. Stoffel, S.J. Scharf, R. Higuchi, G.T. Horn, et al., Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase, Science 239 (1988) 487-491.
[4] R. Saiki, S.J. Scharf, F. Faloona, K.B. Mullis, G.T. Horn, H. Erlich, Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia, Science 230 (1985) 1350-1354.
[5] M.D. Gadberry, S.T. Malcomber, A.N. Doust, E.A. Kellogg, Primaclade—A flexible tool to find primers across multiple species, Bioinformatics 21 (2005) 1263-1264.
[6] A. Gibbs, J. Armstrong, A.M. Mackenzie, G.F. Weiller, The GPRIME package: Computer programs for identifying the best regions of aligned genes to target in nucleic acid hybridisation-based diagnostic tests, and their use with plant viruses, Journal of Virological
Methods 74 (1998) 67-76.
[7] T.M. Rose, E.R. Schultz, J.G. Henikoff, S. Pietrokovski, C.M. McCallum, S. Henikoff, Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences, Nucleic Acids Research 26 (1998) 1628-1635.
[8] S. Rozen, H.J. Skaletsky, Primer3 on the WWW for general users and for biologist programmers, in: S. Krawetz, S. Misener (Eds), Bioinformatics Methods and Protocols: Methods in Molecular Biology, Humana Press, Totowa, NJ, 2000, pp. 365-386.
[9] K. Mullis, F. Faloona, Specific synthesis of DNA in vitro
via a polymerase-catalyzed chain reaction, Methods Enzymol. 155 (1987) 335-350.
[10] Lynnon corporation, DNAMAN, available online at: http://www.lynnon.com/.
[11] Molecular biology insights, Oligo, available online at: http://www.oligo.net/.
Low Sero-Prevalence of
Toxoplasma gondii
IgG and IgM
Antibodies in HIV Sero-Positive Patients Attending
National Hospital, Abuja, Nigeria
Tatfeng Youtchou Mirabeau1 and Adesua Ojo Ebikade2
1, Department of Medical Laboratory Science, College of Health Sciences, Niger Delta University, Wilberforce Island, Bayelsa State,
Nigeria
2, Department of Chemical Pathology, National Hospital, Abuja, Nigeria
Received: September 04, 2011/Accepted: October 22, 2011/Published: May 30, 2012.
Abstract: Several researchers have investigated the association of numerous opportunistic pathogens with HIV, little is documented
on its association with T. gondii in our environment. We investigated the prevalence of T. gondii immunoglobulins G and M (IgG and IgM) in HIV positive individuals in relation to their cluster of differentiation 4 (CD4) cells count. IgG, IgM and CD4 were assayed using enzyme immunoassay (EIA) and flowcytometry respectively. 341 HIV positive individuals were studied in the present research, 30 (8.7%) of them had T. gondii IgG and IgM, 297 subjects had CD4 cells count a range of 200-400 cells/μL, 27 (9.7%) and 2 (0.6%) of which had T. gondii IgG and IgM respectively. Of the 44 HIV positive subjects with CD4 > 400 cells/μL, one (2.2%) was positive for T. gondii IgG. In the control group, all the 177 had CD4 > 400 cells/μL of which, one (0.5%) had T. gondii IgG. The prevalence of T. gondii infection was significantly higher in HIV positive individuals than in controls (P < 0.05). Male subjects in the age bracket 18-30 years had significantly higher prevalence when compared to other groups (P < 0.05). Although the present findings revealed a low prevalence of T. gondii antibodies in HIV infection, this suggests that a differential toxoplasmosis diagnosis is also necessary in cases of encephalitis in HIV infection.
Key words:Toxoplasma gondii, IgG, IgM, CD4, HIV-sero-positive.
1. Introduction
Toxoplasma gondii is an obligate intracellular protozoan of worldwide distribution. Development of cell-mediated immunity after acute infection with T. gondii results in control but not eradication of the infection [1]. The ensuing chronic or latent phase of infection is characterized by the persistence of the organism in tissues of the infected individual (primarily brain, skeletal muscle, and heart). Indeed, T. gondii is one of the most common causes of chronic infection with an intracellular organism in humans. A chronically infected individual who develops defects in
Corresponding author: Tatfeng Youtchou Mirabeau, Ph.D.,
research fields: malaria, HIV, immunology. E-mail: [email protected].
cell-mediated immunity is at risk for reactivation of the infection [1, 2]. Toxoplasmosis in this setting manifests primarily as toxoplasmic encephalitis. The prevalence of serologic evidence of T. gondii infection varies depending on geographic locale and population group. About 3%-67% of adults in the United Sates are sero-positive for antibodies against T. gondii [1]. The rate of seroprevalence can be as high as 90% in Western Europe and tropical countries.
transfusion, and organ transplantation. Acute infection in immunocompetent individuals is usually asymptomatic.
Toxoplasmic encephalitis usually occurs in HIV-infected patients with CD4 T-cell counts < 100/µL
[2]. T. encephalitis in AIDS patients in the United States is almost always caused by reactivation of a chronic infection. Thus, the incidence of this disease correlates directly with the prevalence of anti-T. gondii antibodies. 10%-40% of HIV-infected patients in the United Sates have antibodies against T. gondii [2, 3]. Early studies indicated that 24%-47% of T. gondii-sero-positive AIDS patients ultimately developed toxoplasmic encephalitis [2-4]. The risk of toxoplasmosis decreased after introduction of primary prophylaxis against T. gondii and effective antiretroviral therapy (ART). The incidence in the United States of toxoplasmic encephalitis among patients diagnosed with AIDS declined from 2.1/100 person-years in 1992 to 0.7/100 person-years in 1997 [5].
2. Methods
2.1 Study Design
This study was conducted at the special treatment clinic (STC) of the National Hospital, Abuja. Abuja is a mega city and political capital of the Federal Republic of Nigeria. It accounts among the cities with the highest prevalence of HIV in Nigeria.
2.2 Sample Collection and Sample Size
10 mL of blood were collected from a total of 341 HIV confirmed sero-positive individuals (172 males and 169 females) attending the STC of the National Hospital and 177 apparently health controls. 5 mL of blood were dispensed in plain anticoagulant bottle, while remaining 5 mL of blood sample was dispensed into EDTA for CD4 cells count.
HIV-sero-positive individuals on antiretroviral therapy or with neurological disorders, pregnant women and those on any anti-T. gondii prophylaxis
were excluded.
Verbal consent of the patients was sought and ethical approval was obtained from the management of the National Hospital Abuja.
2.3 Sample Analysis
The blood collected in the plane containers was allowed to clot at room temperature, ringed and centrifuged at 3,000 rev/min for 5 minutes; the serum was carefully separated with a clean Pasteur pipette into another sterile plain container and frozen at 20 °C until required for T. gondii IgG and IgM, antibodies assays whereas the blood collected into EDTA was properly mixed, using a mixer and was used for CD4
cells count.
2.4 T. gondii IgG and IgM, Antibodies Assay and CD4
Cells Count
T. gondii IgG and IgM, antibodies were assayed using the indirect solid-phase enzyme immunoassay (EIA) reagent following the manufacturer’s instructions while CD4 cells count was done using
flowcytometry.
2.5 Statistical Analysis
Data obtained from this study were analyzed using the statistical formulae Chi-square.
3. Results
Our findings revealed that of a total of 341 HIV sero-positive individuals studied, 297 subjects recorded a CD4 cells count raging between 200 and
400 cells/μL of whole blood, 29 (9.7%) and 2 (0.6%) had T. gondii IgG and IgM antibodies respectively. Of the 44 HIV sero-positive subjects with CD4 > 400
cells/μL of whole blood, one (2.2%) was positive for T. gondii IgG and none for IgM. In the control group, of the 177 recorded, all had CD4 > 400 cells/μL of
HIV Sero-Positive Patients Attending National Hospital, Abuja, Nigeria
Table 1 Sero-prevalence of Toxoplasma gondii IgG and IgM antibodies in HIV sero-positive by CD4 cells count.
CD4 cells
HIV sero-positive (341)
Total (%) Control (177) Total (%)
No examined IgG (%) IgM (%) No examined IgG (%) IgM (%)
200-400 297 27 (9.0) 2 (0.6) 29 (9.7) - - - -
> 400 44 1 (2.2) - 1 (2.2) 177 1 (0.5) - 1 (0.5)
Total 341 28 (8.2) 2 (0.5) 30 (8.7)* 177 1 (0.5) - 1 (0.5)**
*,**
Chi-square = 4.034, P < 0.05.
Table 2 Prevalence of Toxoplasma Gondii infection in HIV sero-positive by age and sex.
Age Males Females
No examined No infected (%) No examined No infected (%)
18-30 37 7 (18.9)* 50 3 (6.0)**
31- 40 46 5 (10.8) 57 5 (8.7)
41-50 48 2 (4.1) 37 3 (8.1)
> 50 41 3 (7.3) 25 2 (8.0)
Total 172 17 (9.8) 169 13 (7.6)
*,**
Chi-square = 2.091, P < 0.05.
The age and sex distribution showed that male subjects within the age bracket 18-32 years had a significantly elevated prevalence rate when compared to subject in other groups (P < 0.05), however, no significant difference was obtained in the overall prevalence in male and female (P > 0.05) (Table 2).
4. Discussion and Conclusion
Toxoplasmosis associated with HIV infection is typically caused by reactivation of a chronic infection and manifests primarily as toxoplasmic encephalitis. This disease is an important cause of focal brain lesions in HIV-infected patients [2]. Characteristically, toxoplasmic encephalitis has a subacute onset with focal neurologic abnormalities frequently accompanied by headache, altered mental status, and fever [6-8]. Our findings revealed a significantly higher prevalence of T. gondii antibodies in HIV sero-positive than the control group. This obviously could be due to the immuno-compromised status of HIV infected individuals. Luft et al. [2] argued that toxoplasmic encephalitis usually occurs in HIV-infected patients with CD4 T-cell counts < 100/µL. In this study, all the
anti-T. gondii antibodies positive HIV individuals had a CD4 cell count > 200/µL, thus indicated that if further
decline in their CD4 count was not interrupted, these
patients were seriously at risk of developing T. encephalitis. The overall sero-prevalence in the studied population was 4.6%; this was similar to the findings of Montoya and Remington [1] who reported that 3%-67% of adults in the United Sates are sero-positive for antibodies against T. gondii. They further reported that the prevalence of serologic evidence of T. gondii infection varies depending on geographic locale and population group. The rate of sero-prevalence can be as high as 90% in Western Europe and tropical countries. The differences in these seroprevalence could be due to different feeding habits such as eating of undercooked pork or lamb meat, poorly processed vegetables contaminated with oocysts of the parasite and practices such as using cat as pet.
On the other hand, our study also revealed a higher prevalence of anti-T. gondii antibodies in the male subjects within 18-30-year-old. Undoubtedly, this represents a very active group in the population and their social habits may expose them to serious health risks.
Conclusively, our results showed that T. gondii is also associated to HIV infection in our environment, therefore the need to screen for its antibodies in HIV infected individuals may assist tremendously in improving management strategies and further reduce the health burden on HIV infected individuals.
References
[1] J.G. Montoya, J.S. Remington, Toxoplasma gondii, in: G.L. Mandell, J.E. Bennett, R. Dolin (Eds.), Principles and Practice of Infectious Diseases, Churchill Livingstone, Philadelphia, 2000, pp. 2858-2888.
[2] B.J. Luft, J.S. Remington, Toxoplasmic encephalitis in AIDS, Clin. Infect. Dis. 15 (2) (1992) 211-222.
[3] I.H. Grant, J.W. Gold, M. Rosenblum, D. Niedzwiecki,
D. Armstrong, Toxoplasma gondii serology in HIV-infected patients: The development of central nervous system toxoplasmosis in AIDS, AIDS 4 (6) (1990) 519-521.
[4] R. Zangerle, F. Allerberger, P. Pohl, P. Fritsch, M.P. Dierich, High risk of developing toxoplasmic encephalitis in AIDS patients sero-positive to
Toxoplasma gondii, Med. Microbiol. Immunol. 180 (2)
(1991) 59-66.
[5] J.L. Jones, D.L. Hanson, M.S. Dworkin, D.L. Alderton, P.L. Fleming, J.E. Kaplan, et al., Surveillance for AIDS-defining opportunistic illnesses, 1992-1997, MMWR CDC Surveill Summ. 48 (2) (1999) 1-22.
[6] B.A. Navia, C.K. Petito, J.W. Gold, E.S. Cho, B.D. Jordan, R.W. Price, Cerebral toxoplasmosis complicating the acquired immune deficiency syndrome: Clinical and neuropathological findings in 27 patients, Ann. Neurol. 19 (3) (1986) 224-238.
[7] R.M. Levy, D.E. Bredesen, Central nervous system dysfunction in acquired immunodeficiency syndrome, J. Acquir. Immune. Defic. Syndr. 1 (1) (1988) 41-64. [8] C. Renold, A. Sugar, J.P. Chave, L. Perrin, J. Delavelle,
Development of Bioinfo-Portal Tool for the Analysis of
Genomic and Proteomic Data
Rana Rehan Khalid1, Bilal Hussain1, Muhammad Ali1, Muhammad Sajjad Ahmad1, Asma Haque1 and Hira
Qamar2
1. Department of Bioinformatics and Biotechnology, Govt College University, Faisalabad, Punjab 38000, Pakistan
2. Department of Computer Science , Riphah International University, Islamabad, Punjab 44000, Pakistan
Received: October 19, 2011/Accepted: December 09, 2011/Published: May 30, 2012.
Abstract: The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for
biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal (tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction). The sequences that user obtained from portal’s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.
Key words: Bioinfo-Portal, analytic tools, flexible and usable web environment, tertiary structure prediction, domain analysis, motif
detection, alignments.
1. Introduction
Bioinfo-Portal means that it is the hub of nucleotide and amino acid sequence analyzing platform. With the
help of it, different analytical tools like motif detection, InterProScan, etc., can be used in no time at the single interface. Sequencing technologies
advancements and subsequent improvement in the repertoire of biological information are posing serious
data-management challenges. The amount of these data is expected to continue to grow exponentially [1]. Projects such as SNP Consortium, GenBank [2], and
HapMap are prime examples of the high-throughput data-management challenges that we are experiencing.
Corresponding author: Rana Rehan Khalid, M.Sc.,
research fellow, research fields: bioinformatics and biotechnology. E-mail: [email protected].
The implementation of large-scale data analysis initiatives, the volume of information in terms of biological data availability is overwhelming, as
reflected by the hundreds of databases [3] and web servers [4] described in the literature [5]. These
resources have a great value to bioinformatician for proposing novel hypotheses and delineating further research.
Efforts to implement integration and standardization have been developed in different
frameworks. To mention a few, the VISTA [6] (http://genome.lbl.gov/vista.) and MicrobesOnline [7] (http://www.microbesonline.org) projects aim to
leverage the retrieval and integration of biological data served from distributed resources at the machine
The general proliferation of databases has necessitated the development of new approaches for
integrating and accessing the data they contain. A popular idea in the biosciences is the idea of a
bioinformatics nation [8], wherein many databases are linked by providing computational access via web services, which allows the mining of data from
multiple databases by a single portal [9]. Portals based around core databases but bringing in data from other
related databases in real time via web services may be the way forward in providing easy access to diverse datasets [10].
Bioinfo-Portal seeks to take advantage of this approach in a particular context. The major data
provider in this portal are nucleotide databases includes GenBank [11], EMBL [12], DDBJ [13] and protein databases includes ExPaSy [14], UniProt [15],
PIR [16], PDB [17]. And the data of different formats for example FASTA format can be analyzed 26
different types of tools that are divided into six categories includes: sequence analysis tools [18], alignment dotplots [19], motif detection tools [20],
profile searching tools [21], domain analysis tools [22], and tertiary structure prediction tools [23]
according to their functions which they performed over genomics and proteomic data.
2. Materials and Methods
The portal system is developed under the adobe flex
3 platform. The central database is established by SQLight, and is used only in the portal. We use Action Script 3.0 (http://www.actionscript.org/) and
MXML (http://www.adobe.com/) as the major programming languages. MXML is used for mainly
front-end interface designing and Action Script is used in all programming logics. Database is also established in action script. Action Script is also used
for communication with internet for using online resources in our software. We have already tested the
system on computation node(s) with Linux, Windows XP and MAC platform.
A number of services are already available through the bioinfo-portal. To validate the feasibility,
reliability, stabilization and compatibility of our system schema, we built it in flex, integrate many
tools which provide the analysis of genomic and proteomic data means (FASTA sequences of nucleotide and amino acid analysis), and facilitate the
portal to find the homology between the sequences, phylogenetic relationship, tertiary structure prediction,
alignment dot plots, motif finding, domain analysis, profile searching, etc.. For each function, some well-known packages are provided for users, e.g.,
Clustal W [24] and LALIGN for multiple sequence alignment, tertiary structure prediction by SWISS
Model [25], Geno3d [26] and Fundp [27], profile searching by BLOCK [28], InterProScan [29], motif detection by MEME [30], MAST [31], Gibbs Sampler
(DNA & Protein), domain analysis by SMART [21] and lots more are integrated in it. We also used the
software Transeq from the EMBOSS package to provide a DNA translation service. These services could run independently. Other services, which could
be supported by bioinfo-portal system, are being developed and will be provided in the future.
3. Results and Discussion
Bioinfo-portal provides the scientist with a global
and integrated view of all the elements needed to perform his or her analysis. At one glance, the user
can see which programs are available and which analysis have already been run. The portal is organized in two main parts as shown in Fig. 1. The
merge of the nucleotide and protein resources includes accessibility of the combined data through portal. The
availability of multiple resources at the same interface will save the researcher’s navigation time. This desktop application is providing multiple functions
like accessing different databases at same interface, saving the time in navigating the database, and so on.
Fig. 1 A flow diagram of databases includes protein and nucleotide databases from left to right.
Fig. 2 The integrated tools in the portal.
also a beneficial part of this application. Amino acid
and nucleotide sequences which are helpful in domain
analysis, profile searching and prediction of protein
tertiary structure, detection of motifs along with
graphical alignment respectively are also a component
of this portal.
Portals are used for the integration of data. They considered as the hub within the institute. If data
within the portals are relevant to single field, then the
portal becomes more helpful and effective in that
particular area. This portal is also an effort for the
bioinformatics and molecular biology scientist to
analyze genomic and proteomic data according to
their need and user can also take advantages from the
other features of the portal.
4. Conclusions
The design of bioinfo-portal, which provides an effective way to make a large panel of curated bioinformatics tools available in a homogeneous
environment, has been driven with the concern to meet the requirements of different researchers,
biologists and bioinformaticians mostly. Our objective was thus to facilitate the access to databases and
analysis tools by a design that suits the work of biologists, which we were able to observe and understand during a number of interviews and
workshops.
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