The calculation of information and organismal complexity

<p>Abstract</p> <p>Background</p> <p>It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and Shannon's information concept.</p> <p>Results</p> <p>The results demonstrate that the calculated information correlates quite well with the intuitive organismal phenotypic complexity defined by traditional taxonomy and evolutionary theory. From viruses to human beings, the effective information gradually increases, from thousands of bits to hundreds of millions of bits. The simpler the organism is, the less the information; the more complex the organism, the more the information. About 13% of human genome is estimated as effective information or functional sequence.</p> <p>Conclusions</p> <p>The effective information can be used as a quantitative measure of phenotypic complexity of living organisms and also as an estimate of functional fraction of genome.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Lavanya Kannan (nominated by Dr. Arcady Mushegian), Dr. Chao Chen, and Dr. ED Rietman (nominated by Dr. Marc Vidal).</p

بررسی نتایج حاصل از اجرای الگوی ارتقاء کیفیت مدیریت مواد زائد در بیمارستان شهید فقیهی شیراز طی سال 1384

مقدمه: رشد جمعیت و توسعه شهر نشینی افزایش بی رویه انواع ضایعات در تمامی کشورها را به همراه داشته است . امروزه دفع این پسمانده ها بویژه در بیمارستانها به عنوان یکی از مهمترین چالشهای زیست – محیطی در کشورهای توسعه یافته و در حال توسعه درآمده است. در این میان تخلیه پسمانده های خطرناک صنعتی و بیمارستانی ، بدون رعایت ملاحظات زیست محیطی و فنی به عنوان یکی از پیچیده ترین و پرهزینه ترین مشکلات مسئولان در هر کشوری محسوب می شود. لذا این پژوهش با هدف کاهش میزان تولید مواد زائد عفونی بیمارستان با استفاده از الگوی ارتقاء کیفیت مدیریت مواد زائد انجام گردید. روش بررسی: در این پژوهش مداخله ای که در یکی از بیمارستانهای آموزشی شیراز انجام گرفت تلاش شد تا با اجرای یک الگوی ارتقاء کیفیت مدیریت مواد زائد از میزان تولید مواد زائد عفونی بیمارستان کاسته شود. در این پژوهش طی دو مرحله قبل و بعد از اجرای الگو زباله های بیمارستانی وزن (بر حسب کیلوگرم) و مقایسه شدند. برای تحلیل داده ها از شاخص های آمار توصیفی استفاده شد. یافته ها: نتایج نشان داد که قبل از اجرای الگو میانگین روزانه تولید زباله در بیمارستان برای زباله های عفونی 813 کیلوگرم و برای زباله های عادی83 کیلوگرم بوده، همچنین میانگین روزانه تولید زباله عفونی در بخشهای بستری 43/3 کیلوگرم به ازاء تخت روز اشغالی بوده است . میزان تولید زباله عفونی در بیمارستان 7/90% کل زباله های بیمارستان را تشکیل می داد که بعد از اجرای الگوی ارتقاء کیفیت مدیریت مواد زائد این میزان به 6/57% کاهش یافت. نتیجه گیری: استفاده از مدل ارتقاء کیفیت مدیریت مواد زائد میزان تولید زباله عفونی را تا 1/33% کاهش داده است. بنابراین بیمارستانها می توانند با استفاده از مدل ارتقاء کیفیت مواد زائد، زباله های عفونی خود را کاهش دهند

Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models

Background Entolimod is a Salmonella enterica flagellin derivate. Previous work has demonstrated that entolimod effectively protects mice and non-human primates from ionizing radiation. However, it caused a “flu-like” syndrome after radioprotective and anticancer clinical application, indicating some type of immunogenicity and toxicity. Cyclization is commonly used to improve the in vivo stability and activity of peptides and proteins. Methods We designed and constructed cyclic entolimod using split Nostoc punctiforme DnaE intein with almost 100% cyclization efficiency. We adopted different strategies to purify the linear and circular entolimod due to their different topologies. Both of linear and circular entolimod were first purified by Ni-chelating affinity chromatography, and then the linear and circular entolimod were purified by size-exclusion and ion-exchange chromatography, respectively. Results The circular entolimod showed significantly increased both the in vitro NF-κB signaling and in vivo radioprotective activity in mice. Conclusion Our data indicates that circular entolimod might be a good candidate for further clinical investigation

Restoration of CpG Methylation in The Egf Promoter Region during Rat Liver Regeneration

Epidermal growth factor (EGF) is an important factor for healing after tissue damage in diverse experimental models. It plays an important role in liver regeneration (LR). The objective of this experiment is to investigate the methylation variation of 10 CpG sites in the Egf promoter region and their relevance to Egf expression during rat liver regeneration. As a follow up of our previous study, rat liver tissue was collected after rat 2/3 partial hepatectomy (PH) during the re-organization phase (from days 14 to days 28). Liver DNA was extracted and modified by sodium bisulfate. The methylation status of 10 CpG sites in Egf promoter region was determined using bisulfite sequencing polymerase chain reaction (PCR), as BSP method. The results showed that 3 (sites 3, 4 and 9) out of 10 CpG sites have strikingly methylation changes during the re-organization phase compared to the regeneration phase (from 2 hours to 168 hours, P=0.002, 0.048 and 0.018, respectively). Our results showed that methylation modification of CpGs in the Egf promoter region could be restored to the status before PH operation and changes of methylation didn’t affect Egf mRNA expression during the re-organization phase

The novel protein C3orf43 accelerates hepatocyte proliferation

Abstract Background Our previous study found that single-pass membrane protein with coiled-coil domains 1 (C3orf43; XM_006248472.3) was significantly upregulated in the proliferative phase during liver regeneration. This indicates that C3orf43 plays a vital role in liver cell proliferation. However, its physiological functions remains unclear. Methods The expressions of C3orf43 in BRL-3A cells transfected with C3orf43-siRNA (C3-siRNA) or overexpressing the vector plasmid pCDH-C3orf43 (pCDH-C3) were measured via RT-qPCR and western blot. Cell growth and proliferation were determined using MTT and flow cytometry. Cell proliferation-related gene expression was measured using RT-qPCR and western blot. Results It was found that upregulation of C3orf43 by pCDH-C3 promoted hepatocyte proliferation, and inhibition of C3orf43 by C3-siRNA led to the reduction of cell proliferation. The results of qRT-PCR and western blot assay showed that the C3-siRNA group downregulated the expression of cell proliferation-related genes like JUN, MYC, CCND1 and CCNA2, and the pCDH-C3 group upregulated the expression of those genes. Conclusion These findings reveal that C3orf43 may contribute to hepatocyte proliferation and may have the potential to promote liver repair and regeneration

Rat hepatocytes weighted gene co-expression network analysis identifies specific modules and hub genes related to liver regeneration after partial hepatectomy.

The recovery of liver mass is mainly mediated by proliferation of hepatocytes after 2/3 partial hepatectomy (PH) in rats. Studying the gene expression profiles of hepatocytes after 2/3 PH will be helpful to investigate the molecular mechanisms of liver regeneration (LR). We report here the first application of weighted gene co-expression network analysis (WGCNA) to analyze the biological implications of gene expression changes associated with LR. WGCNA identifies 12 specific gene modules and some hub genes from hepatocytes genome-scale microarray data in rat LR. The results suggest that upregulated MCM5 may promote hepatocytes proliferation during LR; BCL3 may play an important role by activating or inhibiting NF-kB pathway; MAPK9 may play a permissible role in DNA replication by p38 MAPK inactivation in hepatocytes proliferation stage. Thus, WGCNA can provide novel insight into understanding the molecular mechanisms of LR

DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy

Epidermal growth factor (EGF), a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH) rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration