Longest Order Conserved Exemplar Subsequences

We propose a new problem whose input data are two linear genomes together with two indexed gene subsequences of them, which asks to find a longest common exemplar subsequence of the two given genomes with a subsequence identical to the given indexed gene subsequences. We present an algorithm for this problem such that the algorithm is allowed to take diminishing time and space to solve the problem by setting the indexed genes with an incremental number. Although an incremental number of indexed genes were selected, the algorithm was verified definite to reach a solution whose length insistently comes very close to a real longest common exemplar subsequence of the two given genomes. Aiming at 23 human/gorilla chromosome pairs, the algorithm was examined for use in questing for longest common exemplar subsequences whose basic units are annotated genes as well as pseudo genes, namely consecutive DNA subsequences. By contrasting the pseudo gene common exemplar subsequences the algorithm had reached for the human chromosomes 7 and 16 and their gorilla homologues with those annotated genes in the human and gorilla chromosomes, we found more than 1000 and 500 pseudo genes in the human chromosomes 7 and 16 that occur in the same order as they are in the gorilla chromosomes 7 and 16 and, do not overlap with any annotated gene.

Long noncoding RNA AURKAPS1 potentiates malignant hepatocellular carcinoma progression by regulating miR-142, miR-155 and miR-182

The mitotic serine/threonine kinase aurora kinase-A (AURKA) has been identified as carcinogenic in hepatocellular carcinoma (HCC). AURKAPS1, a long non-coding RNA (lncRNA), is the pseudo-gene of AURKA, which play important roles in the cancer. Its underlying functions and mechanisms in liver cancer progression remain largely unknown. The mRNA expression of AURKAPS1 in HCC tumor tissues was significantly higher, which is associated with tumor size and TNM stage. The high expression of AURKAPS1 promotes cell movement, migration and invasion. AURKAPS1 can increases the protein expression of RAC1, promotes the activation of ERK, and enhance the formation of membrane ruffles by binding with miR-182, miR-155 and miR-142 competively. Thus, AURKAPS1 could be a useful marker, and the combination of AURKAPS1/miRNAs (miR-142, miR-155 and miR-182) may be a new theoretical basis for the treatment of HCC.

Gene flow from the gorilla lineage in the Late Miocene as the "missing link"

ABSTRACT: The "missing link" as a concept comes from that there is no continuous evolutionary model for the origin of the human species. There is now conclusive evidence that the speciation of the Homo lineage was caused by the common ancestor of humans and chimpanzees interbreeding with the gorilla lineage around 6 million years ago, an event that also led to the speciation of the Paranthropus lineage. The hybridization of two separate lineages explains the absence of a single continuous lineage. Evidence for an interbreeding event in the Late Miocene can be seen as introgression of around 30% of the gorilla genome into the Pan - Homo clade, with lineage sorting between Pan and Homo where 15% of the gorilla genome is closer to humans, and another 15% being closer to the chimpanzee lineage. (Scally, 2012) The interbreeding event can also be read in the genomes of both Gorilla , Pan and Homo as fragments of mitochondrial DNA that during the event 6 million years ago was inserted into the genome as a NUMT ("nuclear mitochondrial DNA segment"), a pseudo-gene, that originates from the gorilla lineage (Popadin, 2017) and has been transferred to all three lineages.

Molecular characterization of dihydroneopterin aldolase and aminodeoxychorismate synthase in common bean—genes coding for enzymes in the folate synthesis pathway

Common beans (Phaseolus vulgaris) are excellent sources of dietary folates, but different varieties contain different amounts of these compounds. Genes coding for dihydroneopterin aldolase (DHNA) and aminodeoxychorismate synthase (ADCS) of the folate synthesis pathway were characterized by PCR amplification, BAC clone sequencing, and whole genome sequencing. All DHNA and ADCS genes in the Mesoamerican cultivar OAC Rex were isolated and compared with those genes in the genome of Andean genotype G19833. Both genotypes have two functional DHNA genes and one pseudo gene. PvDHNA1 and PvDHNA2 proteins have similar secondary structures and conserved residues as DHNA homologs in Staphylococcus aureus and Arabidopsis. Sequence analysis and synteny mapping indicated that PvDHNA1 might be a duplicated and transposed copy of PvDHNA2. There is only one ADCS gene (PvADCS) identified in the bean genome and it is identical in OAC Rex and G19833. PvADCS has the conserved motifs required for catalytic activity similar to other plant ADCS homologs. DHNA and ADCS gene-specific markers were developed, mapped, and compared to their physical locations on chromosomes 1 and 7, respectively. The gene-specific markers developed in this study should be useful for detection and selection of varieties with enhanced folate contents in bean breeding programs.

Direct Molecular Diagnosis of CYP21A2 Point Mutations in Macedonian and Serbian Patients with 21-Hydroxylase Deficiency/Direktna Molekularna Dijagnoza CYP21A2 Tačkaste Mutacije Kod Makedonskih I Srpskih Pacijenata Sa Nedostatkom 21-Hidroksilaze

Summary Background: Steroid 21-hydroxylase deficiency is present in 90-95% of all cases with congenital adrenal hyperplasia (CAH), an autosomal recessive disorder. It can present as the severe classical salt wasting (SW) or simple virilising (SV) form, or the milder, nonclassical form. Nine pseudo- gene-derived point mutations account for about 80% of all defects in the CYP21A2 gene coding the 21-hydroxylase enzyme. Methods: We have studied nine CYP21A2 point mutations in 61 Macedonian and 24 Serbian patients with different clinical presentations of CAH, using the PCR/ACRS method. Results: Six different mutations were detected in 71.3% of alleles of the Macedonian patients. The most prevalent mutation was IVS2. Mutations were detected in 85.4% of the SW, 83.4% SV and 47.7% LO alleles. In the Macedonian patients the most common genotype was IVS2/IVS2. Five different mutations were detected in 64.6% of alleles of the Serbian patients. The most preva- lent was P30L. Mutations were present in 83.3% SW, 80% SV and 50% of the LO alleles. In the Serbian patients, the P30L/P30L genotype was the most frequent. Conclusions: Specific CYP21A2 mutations are involved in different clinical forms of CAH. High frequency of P30L was found in both populations. Also, high prevalence of the mild P30L mutation was found in both the Macedonian and Serbian classical SV patients. Our findings support the role of the P30L mutation in pronounced virilisation. An unusual finding is the low frequency of V281L in the Macedonian non-classical patients and its absence in the ones from Serbia.