Sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. These sequences may be common in populations, and their absence in the reference genome may indicate rare variants in the genomes of individuals who served as donors for the human genome project. As the reference genome is used in probe design for microarray technology and mapping short reads in next generation sequencing (NGS), this missing sequence could be a source of bias in functional genomic studies and variant analysis. One End Anchor (OEA) and/or orphan reads from paired-end sequencing have been used to identify novel sequences that are absent in reference genome. However, there is no study to investigate the distribution, evolution and functionality of those sequences in human populations. To systematically identify and study the missing common sequences (micSeqs), we extended the previous method by pooling OEA reads from large number of individuals and applying strict filtering methods to remove false sequences. The pipeline was applied to data from phase 1 of the 1000 Genomes Project. We identified 309 micSeqs that are present in at least 1% of the human population, but absent in the reference genome. We confirmed 76% of these 309 micSeqs by comparison to other primate genomes, individual human genomes, and gene expression data. Furthermore, we randomly selected fifteen micSeqs and confirmed their presence using PCR validation in 38 additional individuals. Functional analysis using published RNA-seq and ChIP-seq data showed that eleven micSeqs are highly expressed in human brain and three micSeqs contain transcription factor (TF) binding regions, suggesting they are functional elements. In addition, the identified micSeqs are absent in non-primates and show dynamic acquisition during primate evolution culminating with most micSeqs being present in Africans, suggesting some micSeqs may be important sources of human diversity. 76% of micSeqs were confirmed by a comparative genomics approach. Fourteen micSeqs are expressed in human brain or contain TF binding regions. Some micSeqs are primate-specific, conserved and may play a role in the evolution of primates.

Gelatin-based films with an immobilized enzyme designed for extending the stability of the protein in dry, non-powder configuration with precise dosing attributes were subjected to stress conditions of temperature and relative humidity. β-galactosidase was used as model functional protein. The film configuration preserved the activity of the enzyme under the different storage conditions investigated, which include room temperature under low (ambient) and high (75%) relative humidity, and 36 °C under low (oven) and high relative humidity conditions for a period of 46 days. The influence of the enzyme and plasticizer (glycerol) on the physical and mechanical properties of the films was investigated using DMA (dynamic mechanical analysis). Films containing 5% β-galactosisdase and glycerol concentrations of 14% or greater exhibited greater tensile strength, Young’s modulus, and elongation at break than films with equal concentrations of plasticizer but devoid of any enzyme. The surface texture of the films was analyzed using scanning electron microscopy (SEM). β-galactosidase and glycerol have opposite effects on the surface morphology of the films. Increasing concentrations of the enzyme result in rougher film surface, whereas increasing the concentration of glycerol leads to films with denser and smoother surface. The results obtained suggest that the dry film configuration approach can help in facilitating the stabilization, handling, storage, and transportation of functional proteins in a cost effective manner.

Background: Vitexicarpin (VIT), an isoflavone derived from various medicinal herbs, has shown promising anti-tumor activities against multiple cancer cells. However, the understanding of the mechanisms and potential targets of VIT in treating triple-negative breast cancer (TNBC) remains limited. Methods: The potential VIT targets were searched for in the Super-PRED online database, while the TNBC targets were acquired in the DisGeNET database, and the Veeny database was used to identify the VIT and TNBC targets that overlapped. Then, GO and KEGG enrichment analyses were carried out in the DAVID database. The protein–protein interaction (PPI) network was constructed to acquire the hub targets in the STRING database, and the overall survival analysis of the hub targets was examined in the Kaplan–Meier plotter database. Afterward, molecular docking was performed to evaluate the binding capabilities between VIT and the hub targets. In order to measure the effect of VIT on proliferation, apoptosis, and cell cycle arrest in the TNBC cell lines—MDA-MB-231 and HCC-1937—the Cell Counting Kit-8 (CCK-8) assay and flow cytometry analysis were performed. The Western blot and pull-down assays were used to verify the molecular mechanisms by modulating the hub targets. Results: The network pharmacology results identified a total of 37 overlapping genes that were shared by VIT and TNBC. The results of the PPI network and molecular docking analyses showed that HSP90AA1, CREBBP, and HIF-1A were key targets of VIT against TNBC. However, the pull-down results suggested that VIT could directly bind to HSP90AA1 and HIF-1A, yet not to CREBBP. The results of the in vitro tests showed that VIT decreased proliferation and induced apoptosis in MDA-MB-231 and HCC-1937 cells, in a dose-dependent manner, while the cell cycle arrest occurred at the G2 phase. Mechanistically, the Western blot assay demonstrated that VIT decreased the expression of HSP90AA1, CREBBP, and HIF-1A. Conclusions: VIT inhibited growth and induced apoptosis of TNBC cells by modulating HIF-1A, HSP90AA1, and CREBBP expression. Our findings suggest that VIT is a potential drug for TNBC therapy.