Iraqi Journal of Biotechnology

Lymphoma refers to cancer that developed in the lymphatic system. This type of tumor cause
swelling in the lymph nodes and other parts of body. There are 35 different type of lymphoma recognized
by WHO,five of them are belong to Hodgkin,s lymphoma(HL) and other subtypes belong to non Hodgkin
lymphoma. Approximately 85% of lymphoma incidences are non-Hodgkin‘s disease and 15% are
Hodgkin lymphoma. Early epidemiologic data suggested that HL develops among persons with a delayed
exposure to a ubiquitous infectious agent, Epstein-Barr virus (EBV). A sound of biological basis
association has been established between the genetic regions and risk of HL including some
chromosomes and genes such as chromosomes 2, 6, 8, and 10 and REL and GATA3 genes. In HL there
are no known specific simple genetic aberrations that would appear to be necessary for the malignant
transformation. Alterations of chromosomes 2p, 3q, 6q, 7q, 9p, 13p, 14p and 17q are found more
frequently than expected. Several breakpoints are detected non-randomly in HL, including 3q27, 6q15,
7q22, 11q23, 14q32, but translocation partners have not yet been identified. FISH studies performed with
these samples led to the identification of gene amplifications, i.e. amplifications of the JAK2 gene on
9p23–p24 and the MDM2 gene on 12q14.

Helicobacter pylori (H. pylori) is a colonizer in the gastric mucosa of more than 50% of the
human population. Complications due to this bacterium include chronic gastritis, gastric mucosa
associated lymphoid tissue lymphoma, peptic ulcer and gastric adenocarcinoma. This study aimed to
compare molecular detection method of H. pylori by using glmM gene with another invasive detection
tests as Rapid urease test (RUT) and histopathological examination. Invasive tests has been performed for
detection H. pylori and five gastric biopsies has been taken from each individual, one biopsy from antrum
for detection of glmM gene by polymerase chain reaction (PCR) as a molecular method, another antral
biopsy for rapid urease test, whereas 3 biopsies from different parts of stomach used in histopathological
examination. A total of 123 (58.5 %) from 210 patients were positive at least in two invasive tests for H.
pylori infection. H. pylori were detected in 50% (105/210) by RUT, 54.7% (115/210 ) by histology and
85/210 (40.4%) for glmM detection by PCR as a molecular method.
In Conclusions the glmM gene it’s not suitable for H. pylori detection in compare to another tests.

This study was carried out in the laboratories of Institute of Genetic Engineering and
Biotechnology for postgraduate Studies – University of Baghdad from 1 Novmber 2018 until May 2019,
and the sample collected from several laboratories in the city of Baghdad. The total numbers of samples
are100 were collected from unmarried Iraqi female aged between (20-35) years old include (50) patients
were diagnosed with polycystic ovary syndrome and (50) apparently healthy subject (control).The DNA
was extracted and the electrical transfer was carried out for both groups and the ESR2 SNP (rs4986938)
gene were detected by qRT-PCR. The result showed there was significant difference between control and
patients in genotypes of wild allele (GG) (64.0 vs. 48.0%, respectively; odds ratio = 0.52 ; p-value =
0.0472), and that A allele frequency was significantly increased in patients compared to control (p-value =
0.038) and the wild allele G showed a significant decreased frequency in patients (p-value = 0.038). The
findings indicate that the GA genotype of rs4986938 SNP was efficient in raising the serum amount of
LH in PCOS patients relative to GG or AA genotype (P<0.05) but the distinction between GA and AA
genotypes was substantial. While the AA genotype of rs4986938 SNP was effective in increasing the
serum level of FSH in PCOS patients compared GG or GA genotype (P<0.05) and both differences were
highly significant. The GA genotype of rs4986938 SNP was effective in increasing the serum level of T3
in PCOS patients compared GG or AA genotype (P<0.05), but the difference was significant between GA
and AA genotypes. This study was concluded that the mutant allele A could be associated with an
increased risk to develop PCOS (Odds ratio= 1.88), while the wild allele G might have a protective effect.

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with multi drug resistance
infections and high levels of illness and the efflux pump has vital role in multi drug resistance for
antimicrobial agent in S. aureus. Four hundred and thirty nine clinical specimens (burns, blood, wounds)
were collected from patients attending different hospitals in Baghdad and Wassit City. S. aureus has been
identified using biochemical and molecular methods. Molecular method was depended on PCR in
detection specific genes, 16S rRNA to diagnos staphylococcus genus and mecA to diagnos S.aureus
species. The results demonstrated that 168 isolates belonged to S. aureus , 96 isolates of them were
related to Methicillin resistance S.aureus (MRSA). The isolation results showed that burns 51 (53.13%),
blood 18 (18.75%) and wounds 27 (28.13%) isolated out of 96 (100%). The aim of this study is to
investigate the prevelance of number of chromosomal efflux pumps genes including (norA, norB, norC,
mdeA and mepA). The results indicated the presence of mdeA gene in all isolates 96 (100 %) of MRSA.
The mepA gene has been recorded the second highest prevalence present in 89 (92.71%) isolates. The
norA and norB genes were present in 77 (80.21%) and 54 (56.25%) respectively of isolates, while the
gene norC was present in 17 (17.81%) of the total isolates. In conclusion, our results showed the role of
16S rRNA for molecular detection Staphylococcus genus and using mecA gene in S.aureus bacteria
considered one of the most important features in the description of MRSA isolates. The results of
detection efflux pump genes demonstrated the presence of MdeA gene in all multidrug resistant local
isolates of S.aureus and also high prevalence of other genes especially MepA gene.

Pseudomonas aeruginosa considered as one of the most dangerous bacteria in the world and
the studying of its resistant and virulence mechanisms is as important as the elimination of this bacteria.
One hundred and fifteen burn and wound samples were collected, from hospitals in Baghdad, diagnosed
and identified by routine tests, API 20E and VITEK-2 system. Also the identification of genus was
conducted by detection the specific gene rpsl using polymerase chain reaction (PCR) technique.
According to cultural and biochemical test results 105 of 115 were showed growth on media, however;
only 49 isolates (46.7%) of which were identified as P. aeruginosa as a most causative agent in burn.
Sensitivity test was performed for eight antibiotics by Kirby-Bauer standard disk diffusion method, the
levels of resistance against, colistin 22.4%,Ticarcillin 59.2% ,Pipracillin tazobactam 28.6%,Amikacin
49%,Cefepime 49%,Ciprofloxacin 28.6%,Ceftazidime 59.2%,Imipenem 42.9% . Minimum inhibitory
concentrations (MICs) of Colistin and mint oil were evaluated by well diffusion method (to identify
antimicrobial activity) for 5 isolates most resistance to antibiotic, appearance MIC for Colistin was 32 µg/
ml, and MIC for mint oil is 1/16 ml/ ml. At the molecular level of this study, the results of PCR reaction
showed the presence of rpsl gene in all isolates (100%) and this confirmed the role of this gene in the
identification of P. aerugionsa species and its intrinsic in this species, while the pilB gene presented in 45
isolates (91.8%). The gene expression of pilB gene was conducted by using reverse transcriptase
quantitative PCR technique. It was found that the value of gene expression fold was reduced for the burns
samples after exposure to mint oil in contrast with the untreated isolates, The rpsl gene expression results,
which were used as reference gene, demonstrated that this gene was well suited as housekeeping gene
because of the minimal variations of expression of this gene whether in Colistin and mint oil treated or
untreated isolates.

Recently, Single nucleotide polymorphisms (SNPs) located in the 3'-UTR of the KRAS (KRAS
rs712 (G>T)) which interrupts let-7 miRNA binding site was stated to be associated with the occurrence of
many human cancers. This study aimed to assess the association of KRAS rs712 polymorphism with the
occurrence of breast cancer and breast benign tumor in Iraqi women. rs712 in 3' UTR of the KRAS gene
was amplified by using specific primers, then genotype was detected after sequencing of the amplified
products. Results of genotyping showed that mutant type TT was significantly associated in women with
breast cancer versus women breast benign tumors and in women with breast benign tumors versus healthy
women. However, the results showed there is no significant association in women with breast cancer versus
healthy women. Based on the results, rs712 polymorphism in the 3' UTR of the KRAS gene was considered
as a risk factor with the occurrence of breast cancer and breast benign tumor in Iraqi women compared with
healthy women.

Methicillin-resistant Staphylococcus aureus (MRSA) is known as a key agent implicated in
infections resulting in significant morbidity and mortality among patients. MRSA can develop resistant
structure named biofilm. Among the various naturally occurring classes, chalcones are important
intermediates for the biosynthesis of flavonoids. Therefore, the current study aimed to investigate in vitro
the inhibitory effect of chalcone on MRSA planktonic cells and biofilm. Around 111 Staphylococcus
aureus locally isolated from different clinical specimens were collected in this study. Methicillin
resistance was evaluated by detection mecA amplification by PCR assay. Minimum inhibitory
concentration (MIC) of chalcone was estimated by broth microdilution method. Moreover, Atomic Force
Microscopy (AFM) technique was employed for confirming the effect of chalcone on biofilm. The
present findings revealed that MRSA constituted, nearly, (93.22 %) (55 isolates) of all S. aureus isolates.
Most of MRSA isolates were able to form biofilms, around 70.9% have the capacity to form strong
biofilm. Chalcone at MIC (5 µg/ml) significantly reduced the planktonic MRSA cells. Whereas at
Minimum Biofilm Inhibitory Concentration (MBIC) (20 µg/ml) and sub MBIC (15 µg/ml)reduced
biofilm formation significantly and this findings are confirmed by using Atomic force microscopy. In
conclusion, suggest that chalcone could be a new agent for prevention of bacterial adherence to surfaces
and could be identified as anew agent against S. aureus infection.

There are several reasons for altered semen quality and bacteriospermia could be one among
them. However, there is no complete agreement on detrimental role of the premises suggesting the
bacterial semen infection is associated with male infertility. The aim of this work is to study the semen
culture and detection of bacteria is semen as well as their association with semen quality among infertile
male. Semen samples were collected from men attending high institute for infertility diagnosis assisted
reproductive technology in Baghdad Al-Kadhmiya for the period from June-July 2019. Samples were
subjected to culture using standard bacteriological techniques according to WHO guidance. A total of
fifty samples were collected.45(90%) showed bacteriosperima .Enterococcus 32% was the most common
organism followed by Klebsiella spp. 24%, while proteus spp. and staphylococcus spp. 18%
respectively, and other less frequently organism is E.coli 16. Standard semen analysis was performed,
including volume liquefaction, pH, concentration, morphology, agglutination, round cell count and
percentage motility. Results showed the presence of bacteria growth does not impact on their parameters
concluding that no definite relationship was established between semen parameters and bacteriospermia.

Touched mobile surfaces became part of crime scene evidences which analyzed by forensic
scientists. The minimal amount of DNA required for full STR profile is 0.2-0.5ng. The aim of this work is
to quantitate the amount of DNA isolated from three touched mobiles brands (iPhone, Samsung, and
Sony) surfaces using Organic and Chelex DNA extraction methods. The results showed that organic
method extract more DNA than Chelex from Samsung mobile surface and fewer amounts from iPhone
and Sony. Quantification of DNA by Real time PCR was more accurate with quantities near the minimal
amount required for full profile analysis. STR analysis showed a partial DNA profile recovered from all
cell phones brands. The results indicate the possibility of obtain suitable quantities of DNA from cell
phone surface.

The expression of endothelial nitric oxide synthase (eNOS) gene represents one of the most
important causes that effect the male infertility. The eNOS is primarily responsible that create of NO in
the vascular endothelium, therefore eNOS is mainly expressed in the human testicular endothelial cells,
in addition of Sertoli cells and Leydig, epididymis and vas deferens which regulates the synthesis of
NO. Many study informed in the first time about the NO that is synthesized by human male gamete.
Experimental evidence has shown that NO in high concentrations can cause defective function of the
sperm and low concentrations of NO play very important role in the control of the sperm physiology. In
this study, Approximately 50 Iraqi idiopathic asthenozoospermic (AZS) patients were recruited from
Kamal Al-Samraee hospital, Baghdad, Iraq during a period from 15 November 2017 to 1 May 2018 and
50 healthy men were included for this study, Gene expression for eNOS of reverse transcription
quantitative PCR (RT-qPCR) is distinguished from other methods because of its accuracy, sensitivity.
Real time PCR quantification applied in the present experiment utilized the SYBR green, a fluorescent
dye which recognizes any double stranded DNA including cDNA, the amplification was recorded as a Ct
value (cycle threshold). The lower Ct value indicates the presence of higher copies of the target and vice
versa. In terms of gene expression, high Ct values indicate low gene expression and low Ct value
indicates a high gene expression . In this study we analyzed gene expression of eNOS genes by RT-PCR
depending Ct value to measure gene expression in AZS patients and fertile. As related with eNOS genes
the fold of gene expression in control was lower than AZS patients 4 times. Fold number in AZS patients
were 4 times for eNOS gene. In calculation of the relative expression of eNOS gene in all study groups ,
the 2-ΔΔCt results were appliedو the gene expression in fertile lower than AZS patients 4.05 times for
eNOS gene. Fold number in fertile was 1 time for eNOS gene.

Hepatitis B virus (HBV) Infection is highly widespread. Chronic hepatitis B infection (CHB)
leads to expansion of complications, like cirrhosis, hepatocellular carcinoma (HCC) and death.
microRNAs are emerging as biomarkers for liver disease development . this study aims to rated the level
of serum miR-101 alteration in patients with CHB and inactive carrier comparing with healthy control. A
total of 67 patient’s blood samples collected during the period from February 2019 to September 2019 at
Hepatology and Gastroenterology Teaching Hospital .The serum miRNA-101 expression were detected
using real time PCR. The results showed that the serum miR-101 was downregulated in the chronic
HBV and inactive carrier comparing with the healthy subjects but there was no significant difference
(P = 0.630) was observed among them.