Novel islands of GGC and GCC repeats coincide with human evolution

BACKGROUND

Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored.

RESULTS

In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions.

CONCLUSION

We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.

A Hypermutable Region in the DISP2 Gene Links to Natural Selection and Late-Onset Neurocognitive Disorders in Humans

(CCG) short tandem repeats (STRs) are predominantly enriched in genic regions, mutation hotspots for C to T truncating substitutions, and involved in various neurological and neurodevelopmental disorders. However, intact blocks of this class of STRs are widely overlooked with respect to their link with natural selection. The human neuron-specific gene, DISP2 (dispatched RND transporter family member 2), contains a (CCG) repeat in its 5' untranslated region. Here, we sequenced this STR in a sample of 448 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 203) and controls (N = 245). We found that the region spanning the (CCG) repeat was highly mutated, resulting in several flanking (CCG) residues. However, an 8-repeat of the (CCG) repeat was predominantly abundant (frequency = 0.92) across the two groups. While the overall distribution of genotypes was not different between the two groups (p > 0.05), we detected four genotypes in the NCD group only (2% of the NCD genotypes, Mid-p = 0.02), consisting of extreme short alleles, 5- and 6-repeats, that were not detected in the control group. The patients harboring those genotypes received the diagnoses of probable Alzheimer's disease and vascular dementia. We also found six genotypes in the control group only (2.5% of the control genotypes, Mid-p = 0.01) that consisted of the 8-repeat and extreme long alleles, 9- and 10-repeats, of which the 10-repeat was not detected in the NCD group. The (CCG) repeat specifically expanded in primates. In conclusion, we report an indication of natural selection at a novel hypermutable region in the human genome and divergent alleles and genotypes in late-onset NhCDs and controls. These findings reinforce the hypothesis that a collection of rare alleles and genotypes in a number of genes may unambiguously contribute to the cognition impairment component of late-onset NCDs.

Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes

BACKGROUND

GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored.

RESULTS

On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human.

CONCLUSION

In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.

A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease

Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.

Relationship between self-esteem and subjective vitality among older people in Iran

Today, aging of the population is considered one of the most fundamental challenges worldwide. One of the important factors in active aging is paying attention to psychological variables and related factors. This study was conducted aimed to determine the relationship between self-esteem and subjective vitality of the older people in Iran, Sirjan in 2020. In this descriptive-analytical study, 200 older people aged 60 years and older were selected from comprehensive health centers in Sirjan by a two-stage random sampling method. The data were collected using the validated Rosenberg Self-Esteem Scale, and validated Subjective Vitality Scale. The data were analyzed using SPSS software version 20 using descriptive and inferential statistics, including the Mann-Whitney test, Kruskal-Wallis test, Post Hoc tests, and Spearman correlation coefficient. The mean age of the older people was 65,66±3,9 years. The the mean and standard deviation of self-esteem score was 36,34±4,62 and 21,80±2,85 for subjective vitality score. There was a positive and significant correlation between self-esteem and subjective vitality R=0,58 (p˂0,001 ). Also, gender, marital status and employment status were associated with subjective vitality (p˂0,05). Therefore, planners and policymakers should consider self-esteem and subjective vitality in designing and prioritizing interventions related to improving the health of the older people.

Comparative antibacterial effects of ginger and marjoram extract versus conventional irrigants on mature Enterococcus faecalis biofilms: An in vitro study

Background

This study evaluated antibacterial effects of Ginger and Marjoram extract compared with Routine Intracanal Irrigants on Mature Enterococcus faecalis Biofilms.

Material and Methods

Sixty-six extracted human teeth, were randomly assigned to four groups 5.25% sodium hypochlorite (NaOCl), 2% chlorhexidine (CHX), chloroform extract of marjoram (Origanum majorana), and oil extract of ginger (Zingiber officinale), and two positive and negative control groups (n=11). Samples were contaminated with E. faecalis, except the negative control group. Then the root canals were irrigated with solutions above, after which dental debris was collected from each tooth separately, followed by culturing on plates containing BHI agar. The bacterial counts were finally determined with a colony counting machine.

Results

No bacterial growth was detected in the NaOCl, CHX, and negative control groups. However, some bacterial growth was observed in the ginger and marjoram groups. All four solutions successfully eliminated E. faecalis biofilms compared to the positive control group. Significant difference in the median bacterial growth between the ginger and marjoram groups and the positive control group (P<0.001) has been shown. There was no significant difference in median bacterial growth between the ginger and marjoram groups (P=0.94).

Conclusions

Chloroform extract of marjoram and oil extract of ginger were effective in eliminating 6-week-old biofilms of E. faecalis in vitro; however, their effect was not as favorable as CHX and NaOCl. These herbal extracts yielded promising results in the present study; therefore, they can be used as intracanal irrigants instead of chemical agents. Key words:Biofilm, Chlorhexidine, E. faecalis, Ginger, Marjoram, Sodium hypochlorite.

Factors Affecting the Life Satisfaction of the older adult: The Role of Place attachment

This study examined the association between life satisfaction and place attachment in the older adult. A total of 200 subjects of Kerman city, Iran, responded to questionnaires on life satisfaction and place attachment. The data were analyzed using chi-square, analysis of variance, correlation, and hierarchical multiple regression analysis by the SPSS software version 18. Approximately 51,4% of the subjects had intermediate life satisfaction. The Life satisfaction mean was significantly lower in subjects over 80 of the male gender, single marital status, with more than 3 chronic diseases and bad self-rated health. The majority of respondents had intermediate levels of place attachment (56,6%). There was a significant correlation between life satisfaction and place attachment. Independent variables accounted for 34,2% of the variance in life satisfaction. Individuals with higher attachment had higher levels of life satisfaction than those with lower place attachment. Place attachment is an appropriate strategy to increase life satisfaction in aging.

Survey of clinical and pathological characteristics and outcomes of patients with prostate cancer

INTRODUCTION

The importance of implementation: Prostate cancer is the most common malignancy in men and the second leading cause of cancer death in developed countries. Therefore, further studies about the protests of disease, diagnosis and timely treatment are essential.

STUDY METHOD

In this study, 80 prostate cancer patients admitted to Imam Khomeini Hospital, Urmia in Iran from 2000 to 2008 were reviewed. Patients were studied according to their age, clinical protests, Gleason scoring, positive family history, smoking, type of treatment and post-treatment conditions. Questionnaires were adjusted based on the objectives and the data were extracted from the medical records of patients and the desired results were achieved.

RESULTS

In this study, the most common age group for prostate cancer is older than 60 years (92/5%). The most common type of pathology for prostate cancer is adenocarcinoma that 93.75% of cases are included. Secondary TCC with secondary source is present in 5% and sarcoma in 1.25% of cases. 46.25% of patients with prostate cancer are smokers. The most common clinical symptoms among patients are obstructive symptoms (56.25%), and irritation of the urinary tract (52.81%). Hematuria in 26.25% and urinary incontinence in 5% of cases have been recorded. 16.3% of patients referred with metastatic symptoms. Most patients with prostate cancer have Gleason score 5-7 (40%). All patients were undergoing prostatectomy (82.5% TURP and 17.5% SPP) and 47.5% of cases were bilateral orchiectomy. The cases reviewed, 22 were followed that included 27.5% of cases. Among them, 6 people have died due prostate cancer (27.27%) that the mean age of the patients after diagnosis until death was 34.4 months. 2 others died from other causes (9.09%). The remaining 14 cases were elder patients with a mean follow-up duration of 44 months.

CONCLUSION

According to the results obtained in the present study, the most common type of prostate cancer pathology is adenocarcinoma that is included 93.75% of cases. Prostate sarcoma is present at 1.25% and secondary bladder TCC at 5% of cases more over the incidence of prostate sarcoma is reported in a lower age group than adenocarcinoma, which the results obtained in a similar study in Iran in other centers. Regarding the relationship between smoking and prostate cancer it can be considered one of the important factors in this regard. 

Current understanding in diagnosis and management of factor XIII deficiency

Factor XIII or "fibrin-stabilizing factor," is a transglutaminase circulates in the blood circulation as a hetero tetramer with two catalytic A subunits and two carrier B subunits. This important coagulation factor has a crucial role in clotting cascade and produces strong covalent bonds between soluble formed fibrin monomers during coagulation. This stable cross linked fibrin strands are resistanttodegradationby thefibrinolyticsystem that enablesthe bodyto stoppotential bleeding episodes. In the absence or severe decrease of factor XIII, although the clot is formed, but is rapidly degraded by the fibrinolytic system, and delayed bleedingoccurs.Factor XIII deficiency is an extremely rare bleeding disorder with estimated incidence of 1/2-3000, 000 in the general population. Presumptive diagnosis of factor XIII deficiency was by clot solubility test in 5M urea or 1% monochloroacetic acid environments. In patients with abnormal screening clot solubility test, the disease can be confirmedbymore specifictestssuch as quantitative factor XIII activity assay andFXIIIAgassay.After diagnosis of disease all patients with severe factor XIII deficiency(<1 U/dl) shouldreceive prophylactic substitution therapywith fresh frozen plasma (FFP) and cryoprecipitate as traditional choices or purified concentrateof blood coagulation factor XIII (Fibrogammin P) inorder to control severe and life-threatening clinical complications of factor XIII deficiency.

Effect of thyroid dysfunctions on blood cell count and red blood cell indice

BACKGROUND

Thyroid hormones have a crucial role in metabolism and proliferation of blood cells. Thyroid dysfunction induces different effects on blood cells such as anemia, erythrocytosis leukopenia, thrombocytopenia, and in rare cases causes' pancytopenia. It also alter RBC indices include MCV, MCH, MCHC and RDW. Thus this study attempted to evaluate effect of hypo & hyperthyroidism on blood cell count and RBC indices.

MATERIALS AND METHODS

This study performed on 102 patients with hypothyroid (14.1 years), 84 with hyperthyroid (15.6 years) and 118 healthy individuals (15.2 years) as control group. Initially patients TSH level of patients was determined by ELISA method, and then according to TSH ranges (0.3-5.5µIU/mL) patients were divided into two Hyperthyroidism (TSH<0.3µIU/mL) and hypothyroidism (TSH>5.5µIU/mL) groups. Then, complete blood count was measured by cell counter. Finally, obtained results were analyzed by SPSS software.

RESULTS

Analyzes of obtained data revealed statistically significant difference between two groups of patients in RBC count, MCH, MCHC, RDW, HB and HCT(P-value<0.05), but the difference was not significant for WBC and PLT counts and MCV (P-value>0.05).

CONCLUSION

In case of patients with unknown hematological dysfunctions, must be evaluated for thyroid hormones.

Effects of combination of intrathecal lidocaine and two doses of intrathecal midazolam on post-operative pain in patients undergoing herniorrhaphy: a randomized controlled trial

Assessment of the effect of combination of intrathecal midazolam and lidocaine on postoperative pain was the aim of this study. This randomized controlled trial was performed during 2007 in a teaching hospital of Arak University of Medical Sciences. Forty five male patients who were candidates for elective inguinal herniorrhaphy entered the study and randomly divided into three groups of control (lidocaine 5% plus normal saline), M 0.5 (lidocaine 5% and midazolam 0.5 mg) and M 1.0 (lidocaine 5% and midazolam 1 mg) according intrathecal solution injected for spinal anesthesia. Mean arterial blood pressure, heart rate, post-operative pain, narcotic requirements and complications (nausea, vomiting, pruritic, headache, hypotension and bradycardia) were recorded. The severity of post-operative pain was lowest in M 1.0 group in all postoperative measurements except at 2 h after operation. With regard of complications, only there was significant difference in vomiting between three groups which had the highest frequency in M 0.5 group. No severe hypotension was seen; though, bradycardia occurred in one patient in M 0.5 group which needed treatment. Present findings suggest that administration of intrathecal midazolam (especially 1 mg) together with lidocaine is effective in reducing post-operative pain in patients undergoing open inguinal herniorrhaphy and is not associated with adverse effect.

Isolation and characterisation of the Photosystem two reaction centre complex from a double mutant of Chlamydomonas reinhardtii

A rapid procedure has been developed for the isolation of the photosystem two reaction centre complex (PS II RC) from a double mutant of Chlamydomonas reinhardtii, F54-14, which lacks the Photosystem one complex and the chloroplast ATPase. Thylakoid membranes are solubilised with 1.5% (w/v) Triton X-100 and the PS II RC purified by anion-exchange chromatography using TSK DEAE-650(S) (Merck). The complex has a pigment stoichiometry of approximately six chlorophyll a: two pheophytin a: one cytochrome b-559: one to two β-carotene. It photoaccumulates reduced pheophytin and oxidised P680 in the presence of sodium dithionite and silicomolybdate, respectively. Immunoblotting experiments have confirmed the presence of the D1 and D2 polypeptides in this complex. The α-subunit of cytochrome b-559 was identified by N-terminal sequencing. Comparison of the complex with the PS II RC from pea using SDS-polyacrylamide gel electrophoresis showed that their polypeptide compositions were similar. However, the α-subunit of cytochrome b-559 from C. reinhardtii has a lower apparent molecular weight than the pea counterpart whereas the β-subunit is larger.

Nucleotide sequence of the psbE, psbF and trnM genes from the chloroplast genome of Chlamydomonas reinhardtii

We have determined the nucleotide sequences of the psbE and psbF genes, which encode the alpha and beta subunits, respectively, of cytochrome b-559, from the chloroplast genome of the green alga Chlamydomonas reinhardtii. In contrast to other organisms psbE is not co-transcribed with psbF. The primary structures of the gene products are very similar to the equivalent proteins in cyanobacteria and plants. Each subunit contains a single histidine residue that is thought to ligate haem. Upstream of the psbE gene, a trnM gene is located which encodes an elongator tRNA(Met) molecule.