Haar wavelet based approach for short tandem repeats (STR) detection

Abstract Short Tandem Repeats (STRs)/ Microsatellites are the key factors to find the individuality on a DNA. These are playing an essential role in forensic science. Existing tools for identifying the whole series of STRs/microsatellites necessitate a complex computational method such as fast fourier transform, pattern recognition etc. The study reflects, identifying the STR regions, involving signal processing most preferably Haar wavelet and covering the complete range of STRs in the long chain of DNA sequence. The process demands less computational complexity and time compared to the other tools

Detection of intra-family coronavirus genome sequences through graphical representation and artificial neural network

Abstract In this study, chaos game representation (CGR) is introduced for investigating the pattern of genome sequences. It is an image representation of the genome for the overall visualization of the sequence. The CGR representation is a mapping technique that assigns each sequence base into the respective position in the two-dimension plane to portray the DNA sequence. Importantly, CGR provides one to one mapping to nucleotides as well as sequence. A coordinate of the CGR plane can tell the corresponding base and its location in the original genome. Therefore, the whole nucleotide sequence (until the current nucleotide) can be restored from the one point of the CGR. In this study, CGR coupled with artificial neural network (ANN) is introduced as a new way to represent the genome and to classify intra-coronavirus sequences. A hierarchy clustering study is done to validate the approach and found to be more than 90% accurate while comparing the result with the phylogenetic tree of the corresponding genomes. Interestingly, the method makes the genome sequence significantly shorter (more than 99% compressed) saving the data space while preserving the genome features

Polyion complex hydrogels from chemically modified cellulose nanofibrils:structure-function relationship and potential for controlled and pH-responsive release of doxorubicin

Abstract Herein, we report the fabrication of a polyion complex hydrogel from two oppositely charged derivatives of cellulose nanofibrils (CNF). CNF was produced from dissolving pulp through subsequent periodate oxidation, chemical modification, and microfluidization. Three different durations for periodate oxidation (30 min, 120 min, and 180 min) resulted in three different aldehyde contents. Further, two types of chemical modifications were introduced to react with the resulting aldehydes: chlorite oxidation to yield anionic CNF with carboxylic acid groups (DCC) and imination with Girard’s reagent T to yield cationic CNF containing quaternary ammonium groups (CDAC). Functional group contents were assessed using conductometric titration and elemental analysis, while nanofibril morphologies were assessed using atomic force microscopy (AFM). Longer durations of periodate oxidation did not yield different width profile but was found to decrease fibril length. The formation of self-standing hydrogel through mixing of DCC and CDAC dispersions was investigated. Oscillatory rheology was performed to assess the relative strengths of different gels. Self-standing hydrogels were obtained from mixture of DCC180 and CDAC180 dispersions in acetate buffer at pH 4 and 5 at a low concentration of 0.5% w/w that displayed approximately 10-fold increase in storage and loss moduli compared to those of the individual dispersions. Self-standing gels containing doxorubicin (an anticancer drug) displayed pH-responsive release profiles. At physiological pH 7.4, approximately 65% of doxorubicin was retained past a burst release regime, while complete release was observed within 5 days at pH 4. Biocompatibility of DCC180, CDAC180, and their mixture were investigated through quantification of the metabolic activity of NIH3T3 cells in vitro. No significant cytotoxicity was observed at concentrations up to 900 µg/mL. In short, the nanocellulose-based polyion complex hydrogels obtained in this study are promising nature-derived materials for biomedical applications

Embryonic stem cells derived kidney organoids as faithful models to target programmed nephrogenesis

Abstract The kidney is a complex organ that is comprised of thousands of nephrons developing through reciprocal inductive interactions between metanephric mesenchyme (MM) and ureteric bud (UB). The MM undergoes mesenchymal to epithelial transition (MET) in response to the signaling from the UB. The secreted protein Wnt4, one of the Wnt family members, is critical for nephrogenesis as mouse Wnt4−/− mutants fail to form pretubular aggregates (PTA) and therefore lack functional nephrons. Here, we generated mouse embryonic stem cell (mESC) line lacking Wnt4 by applying the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems 9 (Cas9). We describe here, differentiation of the wild type and Wnt4 knockout mESCs into kidney progenitors, and such cells induced to undergo nephrogenesis by the mouse E11.5 UB mediated induction. The wild type three-dimensional (3D) self-organized organoids depict appropriately segmented nephron structures, while the Wnt4-deficient organoids fail to undergo the MET, as is the case in the phenotype of the Wnt4 knockout mouse model in vivo. In summary, we have established a platform that combine CRISPR/Cas9 and kidney organoid technologies to model kidney development in vitro and confirmed that mutant organoids are able to present similar actions as in the in vivo studies

3D bioprinting of the kidney:hype or hope?

Abstract Three-dimensional (3D) bioprinting is an evolving technique that is expected to revolutionize the field of regenerative medicine. Since the organ donation does not meet the demands for transplantable organs, it is important to think of another solution, which may and most likely will be provided by the technology of 3D bioprinting. However, even smaller parts of the printed renal tissue may be of help, e.g. in developing better drugs. Some simple tissues such as cartilage have been printed with success, but a lot of work is still required to successfully 3D bioprint complex organs such as the kidneys. However, few obstacles still persist such as the vascularization and the size of the printed organ. Nevertheless, many pieces of the puzzle are already available and it is just a matter of time to connect them together and 3D bioprint the kidneys. The 3D bioprinting technology provides the precision and fast speed required for generating organs. In this review, we describe the recent developments in the field of developmental biology concerning the kidneys; characterize the bioinks available for printing and suitable for kidney printing; present the existing printers and possible printing strategies. Moreover, we identify the most difficult challenges in printing of the kidneys and propose a solution, which may lead to successful bioprinting of the kidney