Genome-wide identification of human- and primate-specific core promoter short tandem repeats

Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation.

An exceptionally long CA-repeat in the core promoter of SCGB2B2 links with the evolution of apes and Old World monkeys

We have recently reported a genome-scale catalog of human protein-coding genes that contain "exceptionally long" STRs (≥6-repeats) in their core promoter, which may be of selective advantage in this species. At the top of that list, SCGB2B2 (also known as SCGBL), contains one of the longest CA-repeat STRs identified in a human gene core promoter, at 25-repeats. In the study reported here, we analyzed the conservation status of this CA-STR across evolution. The functional implication of this STR to alter gene expression activity was also analyzed in the HEK-293 cell line. We report that the SCGB2B2 core promoter CA-repeat reaches exceptional lengths, ranging from 9- to 25-repeats, across Apes (Hominoids) and the Old World monkeys (CA>2-repeats were not detected in any other species). The longest CA-repeats and highest identity in the SCGB2B2 protein sequence were observed between human and bonobo. A trend for increased gene expression activity was observed from the shorter to the longer CA-repeats (p<0.009), and the CA-repeat increased gene expression activity, per se (p<0.02). We propose that the SCGB2B2 gene core promoter CA-repeat functions as an expression code for the evolution of Apes and the Old World monkeys.

Prevalence and risk factors of Pediculus (humanus) capitis (Anoplura: Pediculidae), in primary schools in Sanandaj City, Kurdistan Province, Iran

Human head lice, Pediculus (humanus) capitis, infest people worldwide and are most prevalent in children. The aim of this study was to determine the prevalence of head lice, in relation to socioeconomic status of the family and hygienic practices in the home. The prevalence rate was determined in 27 primary schools that had 810 students in Sanandaj city who were selected by multistage, systematic random sampling. A total of 38 students from all grades were infested with different rates of infestations. In addition, standard questionnaire recorded information about demographic features of each student were fulfilled. Children aged 10-11 years were the most frequently affected, there was a significant relationship between head louse infestation, family income and parents education level (α=5%). Pediculosis is a public health problem in many parts of the world. Pediculosis was found to be more prevalent among children of fathers with lower level of education and socioeconomic status, it is necessary to give health education to families in order to prevent pediculosis in this area.

Laboratory colonization of Lucilia sericata Meigen (Diptera: Caliphoridae) strain from Hashtgerd, Iran

BACKGROUND & OBJECTIVES

The treatment of wounds with live green bottle fly larvae is receiving considerable attention in many countries. Laboratory rearing of Lucilia sericata is crucially important for the treatment of wounds.

STUDY DESIGN

The study was carried out for mass rearing of green bottle flies from April to November 2010. Hand catch and net trap baited with beef and cattle liver were used to collect adult flies from the field. The collected samples were placed in appropriately labeled tubes and sent to the laboratory. Adult stage flies reared in the insectary were used for species identification using specific keys.

RESULTS

A total of 89 flies (55 females and 34 males) were collected from Hashtgerd area. In the first generation, 299 flies were produced in the laboratory including 105 (35.12%) males, and 194 (64.88%) females. The female/male sex ratio was 1.61 for parents, whereas it was 1.84, 1.30 for F1 and F2 generations respectively. In total, 432 flies were reared in F3 generation including 173 (40.04%) males, and 259 (59.96%) females, and the sex ratio was 1.49.

CONCLUSION

Setting up the mass rearing of sheep blowfly at the School of Public Health, Tehran University of Medical Sciences is an important step in producing candidate flies for the treatment of myiasis by maggot therapy in future.

Application of artificial neural network in predicting the survival rate of gastric cancer patients

BACKGROUND

The aim of this study was to predict the survival rate of Iranian gastric cancer patients using the Cox proportional hazard and artificial neural network models as well as comparing the ability of these approaches in predicting the survival of these patients.

METHODS

In this historical cohort study, the data gathered from 436 registered gastric cancer patients who have had surgery between 2002 and 2007 at the Taleghani Hospital (a referral center for gastrointestinal cancers), Tehran, Iran, to predict the survival time using Cox proportional hazard and artificial neural network techniques.

RESULTS

The estimated one-year, two-year, three-year, four-year and five-year survival rates of the patients were 77.9%, 53.1%, 40.8%, 32.0%, and 17.4%, respectively. The Cox regression analysis revealed that the age at diagnosis, high-risk behaviors, extent of wall penetration, distant metastasis and tumor stage were significantly associated with the survival rate of the patients. The true prediction of neural network was 83.1%, and for Cox regression model, 75.0%.

CONCLUSION

The present study shows that neural network model is a more powerful statistical tool in predicting the survival rate of the gastric cancer patients compared to Cox proportional hazard regression model. Therefore, this model recommended for the predicting the survival rate of these patients.