Cetaceans evolution:insights from the genome sequences of common minke whales

Background: Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water. Results: We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 - 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales. Conclusions: This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth

Stable Production of a Tethered Recombinant Eel Luteinizing Hormone Analog with High Potency in CHO DG44 Cells

We produced a recombinant eel luteinizing hormone (rec-eel LH) analog with high potency in Chinese hamster ovary DG44 (CHO DG44) cells. The tethered eel LH mutant (LH-M), which had a linker comprising the equine chorionic gonadotropin (eLH/CG) β-subunit carboxyl-terminal peptide (CTP) region (amino acids 115 to 149), was inserted between the β-subunit and α-subunit of wild-type tethered eel LH (LH-wt). Monoclonal cells transfected with the tethered eel LH-wt and eel LH-M plasmids were isolated from five to nine clones of CHO DG44 cells, respectively. The secreted quantities abruptly increased on day 3, with peak levels of 5000–7500 ng/mL on day 9. The molecular weight of tethered rec-eel LH-wt was 32–36 kDa, while that of tethered rec-eel LH-M increased to approximately 38–44 kDa, indicating the detection of two bands. Treatment with the peptide N-glycanase F decreased the molecular weight by approximately 8 kDa. The oligosaccharides at the eCG β-subunit O-linked glycosylation sites were appropriately modified post-translation. The EC50 value and maximal responsiveness of eel LH-M increased by approximately 2.90- and 1.29-fold, respectively, indicating that the mutant exhibited more potent biological activity than eel LH-wt. Phosphorylated extracellular regulated kinase (pERK1/2) activation resulted in a sharp peak 5 min after agonist treatment, with a rapid decrease thereafter. These results indicate that the new tethered rec-eel LH analog had more potent activity in cAMP response than the tethered eel LH-wt in vitro. Taken together, this new eel LH analog can be produced in large quantities using a stable CHO DG44 cell system

Development of cell-laden multimodular Lego-like customizable endometrial tissue assembly for successful tissue regeneration

Abstract Background The endometrium, the inner lining of the uterine cavity, plays essential roles in embryo implantation and its subsequent development. Although some positive results were preliminarily archived, the regeneration of damaged endometrial tissues by administrating stem cells only is very challenging due to the lack of specific microenvironments and their low attachment rates at the sites of injury. In this context, various biomaterial-based scaffolds have been used to overcome these limitations by providing simple structural support for cell attachment. However, these scaffold-based strategies also cannot properly reflect patient tissue-specific structural complexity and thus show only limited therapeutic effects. Method Therefore, in the present study, we developed a customizable Lego-like multimodular endometrial tissue architecture by assembling individually fabricated tissue blocks. Results Each tissue block was fabricated by incorporating biodegradable biomaterials and certain endometrial constituent cells. Each small tissue block was effectively fabricated by integrating conventional mold casting and 3D printing techniques. The fabricated individual tissue blocks were properly assembled into a larger customized tissue architecture. This structure not only properly mimics the patient-specific multicellular microenvironment of the endometrial tissue but also properly responds to key reproductive hormones in a manner similar to the physiological functions. Conclusion This customizable modular tissue assembly allows easy and scalable configuration of a complex patient-specific tissue microenvironment, thus accelerating various tissue regeneration procedures

Segmentation of optic nerve head using warping and RANSAC

Glaucoma is the second leading cause of blindness, and the retinal nerve fiber layer (RNFL) defect is the early sign of the glaucomatous optic nerve damage. To evaluate the RNFL, segmentation of the optic nerve head on the RNFL photograph should be the first step. This paper presents segmentation of optic nerve head using warping and random sample consensus (RANSAC). Sensitivity and positive predictability of the proposed method were 91% and 78% respectively

Signatures of correlation between DEGs from Thoroughbred RNA-seq and selected genes associated with nucleotide diversity, F_ST and XP-EHH from Thoroughbred and Jeju pony DNA sequence.

<p>a) Manhattan plot of F_ST (Dotted line = cut-off value of the top 5% with empirical p-values of <0.05. Red point = common genes between the DEGs, Thoroughbred selected genes associated with F_ST and XP-EHH). b) Manhattan plot of XP-EHH value (Red point = Common genes between the DEGs and Thoroughbred selected genes associated with F_ST and XP-EHH). c) Nucleotide diversity line plot of five common genes (sky blue color line = Jeju pony, orange color line = Thoroughbred).</p

Summary of comparative analysis between <i>de novo</i> assembly and reference genome assembly from RNA-seq data of skeletal muscle from six Thoroughbreds before and after exercise (Total 12 samples).

<p>a) The number of transcripts in common between de novo assembly and reference genome assembly b) MDS plot of six Thoroughbreds before and after exercise using de novo assembly. c) The number of DEGs between de novo assembly and reference genome assembly. d) Heat-map visualization of common DEGs between de novo assembly and reference genome assembly: rows represent DEGs from skeletal muscle and columns represent assemble method from 6 horse samples (*First ‘B’ is for blood and ‘M’ is for muscle. ‘F1’, ‘F2’, ‘F3’ and ‘S3’ are horse samples. Last ‘B’ is for ‘before exercise’ and ‘P’ is for ‘after exercise’).</p

Co-matching genes between the DEGs, selected genes associated with F_st (F_st cut-off value top 5% with empirical p-value<0.05) and Thoroughbred selected genes associated with XP-EHH (XP-EHH cut-off value empirical p-value<0.01 and XP-EHH value <−3.51551 significant SNPs).

<p>Co-matching genes between the DEGs, selected genes associated with F_st (F_st cut-off value top 5% with empirical p-value<0.05) and Thoroughbred selected genes associated with XP-EHH (XP-EHH cut-off value empirical p-value<0.01 and XP-EHH value <−3.51551 significant SNPs).</p

Enriched KEGG pathways associated with DEGs in two tissue such as skeletal muscle and blood.

<p>For each set of up-regulated and down-regulated. DEG in skeletal muscle and blood, a KEGG pathway enrichment analysis was performed. Starting from the right, the table shows: tissue type, status of regulation, KEGG pathway terms, higher-level KEGG pathway terms, and the highest level of KEGG pathway terms.</p