Background and aims. Open reading frames (ORFs) are sections of a reading frame that do not include any stop codons. A reading frame is a sequence of nucleotide triplets read as codons indicating amino acids; a single strand of DNA has three potential reading frames. Long ORFs in a DNA sequence may represent possible protein-coding areas. In addition to extended ORFs, which assist in gene locus prediction, there is yet another type of ORFS known as small open reading frames (smORFs), which have 100 codons or fewer. Methods. We develop an offline, cross-platform, and dependable detection tool for regular ORFs and smORFs prevalent in biomedical studies. Results. In this work, the most ORFs were found in the Bos taurus (Cattle) Insulin gene, which had 17 consecutive ORFs, while the fewest ORFs were reported in the Cani's lupus (Dog) Insulin gene, which had only 4 ORFs. Conclusion. The software meets the expected demarcation restrictions. We strongly advise more research into the detection of nested ORFs.

Exact string-matching algorithms have become very supreme in many bioinformatics tools. Despite the abundance and diversity of such algorithms, exposing them to real-time experimental analysis has been critical. This study was conducted to evaluate the efficiency of ten exact-string matching algorithms on large-scale genomic sequences from a runtime perspective. To define the most efficient algorithms are qualified to handle the short alphabet used for nucleic acid coding. The methodology promoted for this study was the factorial experiment with Randomized Complete Block Design (FRCBD). Under influence of four independent parameters, four levels of pattern lengths, four levels of pattern indices, two levels of programming languages, and ten levels of algorithmic architecture. The yield of the tested algorithms was calculated in nanoseconds. One-way ANOVA and Two-way ANOVA tests with post-hoc Games-Howell test were used separately for statistical analysis. In this study two widely accepted programming languages, C# and JAVA were used to speculate the possible effect of programing language on algorithm performance. The One-way ANOVA results revealed that the Backward-Oracle-Matching (BOM), Zhu-Takaoka (ZT), and Horspool's (HP) algorithms exhibited the highest final performance correspondingly. These algorithms have demonstrated an efficiency of up to 250% higher than other algorithms. The results of two-way ANOVA revealed a significant interaction between programing language adopted and execution time with the absence of pattern lengths and pattern index effect. The combination of the C# programing language and the Backward-Oracle-Matching algorithm produced the most effective performance on genomic sequences. 

Short Tandem Repeats (STRs) are one of the utmost mutable provinces in the human genome. They comprise tandem repeating DNA sequences ranging in length from two to six base pairs. Owing to their significant mutation rate, they exhibit considerable variation in pattern among populations and the capacity to be passed on from generation to generation. These loci are broadly employed in medicine, biology, and criminal investigation. They are pivotal in the genesis of a variety of genetic illnesses and have been intensively investigated in forensics, population genetics, and genetic genealogy. Although many implementations that manage STR loci are offered, the overwhelming majority of them rely primarily on the Command-Line Interface (CLI) inputs, which frequently necessitate the implementation of tools carried out in various scripting languages. Installing and launching programs through the Command Line (CL) is timeconsuming and/or unprofitable for many students and scholars. The fundamental intention of this project is to develop a cross-platform Graphical User Interface (GUI) package directed to the Combined DNA Index System (CODIS) STR analysis. Zenobia is a Java-based application considered as a step in consistently making CL-only programs available to more apprentices and researchers. In general, Zenobia's application outcomes satisfy the evaluation metrics for efficiency and time consumption. However, more genetic markers should be introduced to increase productivity of the application.

Three-dimensional (3D) cell culture systems have gained increasing interest in drug discovery and tissue engineering due to a number of advantages in providing more physiologically relevant information and potentially more predictive data for in vivo tests. Extracellular matrix (ECM) proteins have been developed over in recent years to simulate a natural microenvironment for cells cultured in vitro. Conventional cell culture or 2D cell culture form monolayers of cells on a solid surface, which is typically polystyrene or glass, whereas a 3D culture system employ a porous growth matrix on which the cells grow. The transition from cell culture on a flat surface 2D to a 3D model in vitro is expected to mimic more realistic culture environments. However, the major limitation of 2D culture is their lack of structural architecture and stroma and not all types of normal epithelial cell are able to adhere and grow on 2D culture. For this study, two different immortal cell lines were used (HeLa and HaCaT cells) and two commercial 3D substrates (Collagen Rat Tail and Geltrex) were used, in order to evaluate how the transition from 2D to 3D affects viability, cell cycle, live/dead cell, responses to the drug exposure and bio-spectroscopy studies. The viability of cells were monitored with the aid of the Alamar Blue assay, cellular morphology was monitored with confocal microscopy, cell cycle and cell death studies were performed with flow cytometry and viability of 3D culture in bio-spectroscopy performed with Raman spectroscopy. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to a 3D environment causing alterations to effective resazurin concentration, uptake and conversion rates. This was verified by flow cytometry, in which no significant differences in viable cell numbers between 2D and 3D systems was ii observed. Cell cycle analysis revealed cellular function could be altered by growth on the 3D substrates and the alterations were noted to be dependent on 3D membrane concentration. The use of 3D culture matrices has been widely interpreted to result in “improved viability levels” or “reduced” toxicity or cellular “resistance” compared to cells cultured on traditional 2D systems. Cells were grown on the different substrates (Collagen and CaF2), confirming that the in vitro cell culture environment impacts significantly on the cell cycle. The live cell in vitro Raman spectroscopic analysis of cells on the 2D CaF2 and 3D Collagen substrates was performed and data were analysed using principal component analysis (PCA). The spectroscopic analysis revealed differences in profiles which reflect the differences in cell cycle for both in vitro culture environments. In particular, the Raman spectra of cells grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. Doxorubicin still induced apoptosis with no difference in the population levels in 3D and 2D culture of apoptotic, necrotic and live cells. Also, cells grown on both substrates were arrested at G0/G1 phase by the Doxorubicin, Raman spectra collected from cells grown in Collagen showed that, Doxorubicin is clearly seen to be present in the nucleolus, nucleus and cytoplasm of the HaCaT cells. Statistical analysis, consisting of principal components analysis (PCA) was used to highlight the Doxorubicin interaction with HaCaT cells grown in 3D cultures. The results of this study show that Cellular health and viability levels were not altered by culture in 3D environments, but their normal cycle could be altered verified by the cell cycle studies performed and these variations must be accounted for in studies employing 3D membranes. The Raman spectra of cells grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. The bioavailability or effective concentration of the cytotoxicity assay and the chemotherapeutic agent are both affected by the iii absorptive nature of the matrix. Despite the differences in the cell cycle in cells grown in 2D and 3D cultures, the efficacies and ultimate effect of the drug on all the cultured cells are the same regardless of culture environment and the variations in the cell cycle for cells grown on different substrates must be accounted for in vitro cellular screening in particular when screening cell cycle dependant toxicants. This study has shown that the use of 3D culture systems has the potential to make a significant impact in the Raman spectroscopy field in particular Collagen is a cost effective substrate replacement for more expensive options. 

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium Iodide staining and monitored by flow cytometry, was performed on cells of both types, grown on the different substrates, confirming that the in vitro cell culture environment impacts significantly on the cell cycle. Live cell in vitro Raman spectroscopic analysis of cells on the 2D CaF2 and 3D Collagen substrates was performed and data was analysed using principal components analysis (PCA). The spectroscopic analysis revealed differences in profiles which reflect the differences in cell cycle for both in vitro culture environments. In particular, the Raman spectra of cells 2 grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. This work contributes to the field of Raman spectroscopic analysis by providing a fresh look at the significance of the effect of in vitro culture environment to cell cycle and the sensitivity of Raman spectroscopy to such differences in cell metabolism. 

In this study, the cellular viability and function of immortalized human cervical and dermal cells are monitored and compared in conventional 2D and two commercial 3D membranes, Collagen and Geltrex, of varying working concentration and volume. Viability was monitored with the aid of the Alamar Blue assay, cellular morphology was monitored with confocal microscopy, and cell cycle studies and cell death mechanism studies were performed with flow cytometry. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to 3D environment causing alterations to effective resazurin concentration, uptake and conversion rates, which was dependent on exposure time, but also due to the effect of the membrane itself on cellular function. These effects were verified by flow cytometry, in which no significant differences in viable cell numbers between 2D and 3D systems were observed after 24 h culture. The results showed the observed effect was different after shorter exposure periods, was also dependent on working concentration of the 3D system and could be mediated by altering the culture vessel size. Cell cycle analysis revealed cellular function could be altered by growth on the 3D substrates and the alterations were noted to be dependent on 3D membrane concentration. The use of 3D culture matrices has been widely interpreted to result in “improved viability levels” or “reduced” toxicity or cellular “resistance” compared to cells cultured on traditional 2D systems. The results of this study show that cellular health and viability levels are not altered by culture in 3D environments, but their normal cycle can be altered as indicated in the cell cycle studies performed and such variations must be accounted for in studies employing 3D membranes for in vitro cellular screening.

The interest in the use of 3D matrices for in vitro analysis, with a view to increasing the relevance of in vitro studies and reducing the dependence on in vivo studies, has been growing in recent years. Cells grown in a 3D in vitro matrix environment have been reported to exhibit significantly different properties to those in a conventional 2D culture environment. However, comparison of 2D and 3D cell culture models have recently been noted to result in differing responses of cytotoxic assays, without any associated change in viability. The effect was attributed to differing conversion rates and effective concentrations of the resazurin assay in 2D and 3D environments, rather than differences in cellular metabolism. In this study, the efficacy of a chemotherapeutic agent, doxorubicin, is monitored and compared in conventional 2D and 3D collagen gel exposures of immortalized human cervical cells. Viability was monitored with the aid of the Alamar Blue assay and drug internalisation was verified using confocal microscopy. Drug uptake and retention within the collagen matrix was monitored by absorption spectroscopy. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to a 3D environment causing alterations to dye resazurin uptake and conversion rates. The use of 3D culture matrices has widely been interpreted to result in “reduced” toxicity or cellular “resistance” to the chemotherapeutic agent. The results of this study show that the reduced efficiency of the drug to cells grown in the 3D environment can be accounted for by a sequential reduction of the effective concentration of the test compound and assay. This is due to absorption within the collagen gel inducing a higher uptake of both drug and assay thereby influencing the toxic impact of the drug and conversion rate of resazurin, and. The increased effective surface area of the cell exposed to the drug and assay in the 3D environment. The effect was noted to be higher after shorter exposure periods and should be accounted for in in vitro 2D and 3D culture environment comparisons.