Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".

Pinson et al. (1) concluded that the modern human TKTL1 gene is responsible for an increased number of cortical neurons. We show that the "putative Neanderthal variant" of TKTL1 is present in modern human backgrounds. We dispute their argument that this genetic variant is responsible for brain differences in modern humans as opposed to Neanderthals.

IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing.

Splicing is one of the most important post-transcriptional processing systems and is responsible for the generation of transcriptome diversity in all living eukaryotes. Splicing is regulated by the spliceosome machinery, which is responsible for each step of primary RNA processing. However, current molecules and stages involved in RNA splicing are still spread over different studies. Thus, a curated atlas of spliceosome-related molecules and all involved stages during RNA processing can provide all researchers with a reliable resource to better investigate this important mechanism. Here, we present IARA (website access: https://pucpr-bioinformatics.github.io/atlas/), an extensively curated and constantly updated catalog of molecules involved in spliceosome machinery. IARA has a map of the steps involved in the human splicing mechanism, and it allows a detailed overview of the molecules involved throughout the distinct steps of splicing.

Response to Comment on "Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment".

Maricic et al. performed an undisclosed in silico­only whole-exome sequencing analysis of our data and found genomic alterations previously undetected in some clones. Some of the predicted alterations, if true, could change the original genotype of the clones. We failed to experimentally validate all but one of these genomic alterations, which did not affect our previous results or data interpretation.

Leaf extracts of Campomanesia xanthocarpa positively regulates atherosclerotic-related protein expression.

Atherosclerosis is caused by a monocyte-mediated inflammatory process that, in turn, is stimulated by cytokines and adhesion molecules. Monocytes are then differentiated into macrophages, leading to the formation of arterial atherosclerotic plaques. Recently, guavirova leaf extracts from Campomanesia xanthocarpa (EG) have shown potential effects on the treatment of plaque formation by reducing cholesterol, LDL levels and serum oxidative stress. We evaluated the effect of EG on the viability of human monocytic and endothelial cell lines at three time points (24, 48 and 72 hours) and whether it can modulate the migration and in vitro expression of CD14, PECAM-1, ICAM-1, HLA-DR and CD105. Cell viability was affected only at higher concentrations and times. We observed decreased ICAM-1 expression in cells treated with 50 µg/ml EG and CD14 expression with IFN-γ and without IFN-γ. CD14 also decreased endothelial cell expression in the presence of IFN-γ and GE. We also found decreased expression of PECAM-1 when treated with EG and IFN-γ. In addition, EG-treated endothelial cells showed higher migration than the control group. Reduced expression of these markers and increased migration may lead to decreased cytokines, which may be contributing to decreased chronic inflammatory response during atherosclerosis and protecting endothelial integrity.

CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages.

Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review.

The recent decrease in cost and time to sequence and assemble of complete genomes created an increased demand for data storage. As a consequence, several strategies for assembled biological data compression were created. Vertical compression tools implement strategies that take advantage of the high level of similarity between multiple assembled genomic sequences for better compression results. However, current reviews on vertical compression do not compare the execution flow of each tool, which is constituted by phases of preprocessing, transformation, and data encoding. We performed a systematic literature review to identify and compare existing tools for vertical compression of assembled genomic sequences. The review was centered on PubMed and Scopus, in which 45726 distinct papers were considered. Next, 32 papers were selected according to the following criteria: to present a lossless vertical compression tool; to use the information contained in other sequences for the compression; to be able to manipulate genomic sequences in FASTA format; and no need prior knowledge. Although we extracted performance compression results, they were not compared as the tools did not use a standardized evaluation protocol. Thus, we conclude that there's a lack of definition of an evaluation protocol that must be applied by each tool.

The Expression Profile of Dental Pulp-Derived Stromal Cells Supports Their Limited Capacity to Differentiate into Adipogenic Cells.

Mesenchymal stromal cells (MSCs) can self-renew, differentiate into specialised cells and have different embryonic origins-ectodermal for dental pulp-derived MSCs (DPSCs) and mesodermal for adipose tissue-derived MSCs (ADSCs). Data on DPSCs adipogenic differentiation potential and timing vary, and the lack of molecular and genetic information prompted us to gain a better understanding of DPSCs adipogenic differentiation potential and gene expression profile. While DPSCs differentiated readily along osteogenic and chondrogenic pathways, after 21 days in two different types of adipogenic induction media, DPSCs cultures did not contain lipid vacuoles and had low expression levels of the adipogenic genes proliferator-activated receptor gamma (PPARG), lipoprotein lipase (LPL) and CCAAT/enhancer-binding protein alpha (CEBPA). To better understand this limitation in adipogenesis, transcriptome analysis in undifferentiated DPSCs was carried out, with the ADSC transcriptome used as a positive control. In total, 14,871 transcripts were common to DPSCs and ADSCs, some were unique (DPSCs: 471, ADSCs: 1032), and 510 were differentially expressed genes. Detailed analyses of overrepresented transcripts showed that DPSCs express genes that inhibit adipogenic differentiation, revealing the possible mechanism for their limited adipogenesis.

Frequency and association of mitochondrial genetic variants with neurological disorders.

Mitochondria are small cytosolic organelles and the main source of energy production for the cells, especially in the brain. This organelle has its own genome, the mitochondrial DNA (mtDNA), and genetic variants in this molecule can alter the normal energy metabolism in the brain, contributing to the development of a wide assortment of Neurological Disorders (ND), including neurodevelopmental syndromes, neurodegenerative diseases and neuropsychiatric disorders. These ND are comprised by a heterogeneous group of syndromes and diseases that encompass different cognitive phenotypes and behavioral disorders, such as autism, Asperger's syndrome, pervasive developmental disorder, attention deficit hyperactivity disorder, Huntington disease, Leigh Syndrome and bipolar disorder. In this work we carried out a Systematic Literature Review (SLR) to identify and describe the mitochondrial genetic variants associated with the occurrence of ND. Most of genetic variants found in mtDNA were associated with Single Nucleotide Polimorphisms (SNPs), ~79%, with ~15% corresponding to deletions, ~3% to Copy Number Variations (CNVs), ~2% to insertions and another 1% included mtDNA replication problems and genetic rearrangements. We also found that most of the variants were associated with coding regions of mitochondrial proteins but were also found in regulatory transcripts (tRNA and rRNA) and in the D-Loop replication region of the mtDNA. After analysis of mtDNA deletions and CNV, none of them occur in the D-Loop region. This SLR shows that all transcribed mtDNA molecules have mutations correlated with ND. Finally, we describe that all mtDNA variants found were associated with deterioration of cognitive (dementia) and intellectual functions, learning disabilities, developmental delays, and personality and behavior problems.

Crosstalk between Hedgehog pathway and energy pathways in human adipose-derived stem cells: A deep sequencing analysis of polysome-associated RNA.

Adult stem cells are considered promising candidates for cellular therapies due to their capacity to differentiate and self-renew. Differentiation leads to changes in the metabolism, structure, and gene expression patterns of cells. Hedgehog is one of the pathways that is involved in the enhancement of osteogenesis and chondrogenesis in adult stem cells, but its mechanisms are poorly understood. In this study, we treated adipose tissue-derived stem cells (ADSC) with two well-characterized drugs, purmorphamine (Hedgehog pathway activator) and cyclopamine (Hedgehog pathway inhibitor), and identified mRNAs associated with polysomes in each treatment group to determine the post transcriptional genetic networks governed by the Hedgehog pathway. Activation of the Hedgehog pathway by purmorphamine results in significant upregulation of mRNAs associated with cellular communication and signal transduction. Furthermore, our experiments show that cyclopamine acts late downregulating GLI1 expression in ADSCs but promotes the upregulation of mRNAs associated with energy pathways and metabolism at early times. Through in silico analysis, we identified some miRNAs, such as miR-355, that could regulate these mRNAs association with polysomes and thereby modulate the Hedgehog pathway. Our results suggest that activation of the Hedgehog pathway by purmorphamine also results in a negative regulation of mRNAs in the protein translation machinery.

De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta).

BACKGROUND: Providing double-stranded RNA (dsRNA) to insects has been proven to silence target genes, and this approach has emerged as a potential method to control agricultural pests by engineering plants to express insect dsRNAs. A critical step of this technology is the screening of effective target genes essential for insect development and/or survival. The tomato leafminer (Tuta absoluta Meyrick) is a major Solanum lycopersicum (tomato) pest that causes significant yield losses and has recently invaded Europe, from where it is spreading at an alarming rate. To explore RNA interference (RNAi) against T. absoluta, sequence information on potential target genes is necessary, but only a few sequences are available in public databases. RESULTS: We sequenced six libraries from RNA samples from eggs, adults, and larvae at four stages, obtaining an overall total of around 245 million reads. The assembled T. absoluta transcriptome contained 93,477 contigs with an average size of 1,574 bp, 59.8 % of which presented positive Blast hits, with 19,995 (21.4 %) annotated by gene ontology. From the transcriptome, most of the core genes of the RNAi mechanism of Lepidoptera were identified indicating the potential suitability of T. absoluta for gene silencing. No contigs displayed significant similarity with a RNA-dependent RNA Polymerase. Genes from the juvenile hormone and ecdysteroid biosynthetic pathways were identified, representing potential target genes for systemic silencing. Comparisons of transcript profiles among stages revealed 1,577 genes differentially expressed at earlier larval stages, from which potential gene targets were identified. Five of these genes were evaluated using in vitro transcribed dsRNA absorbed by tomato leaflets, which were fed to 1(st) instar T. absoluta larvae, resulting in significant reduction of larval body weight while exhibiting significant knockdown for three of the genes. CONCLUSIONS: The transcriptome we generated represents a valuable genomic resource for screening potential gene targets that affect the development or survival of T. absoluta larvae. Five novel genes that showed greater expression at the 1(st) larval stage were demonstrated to be effective potential RNAi targets by reducing larval weight and can be considered good candidates for use in RNAi-mediated crop protection.

Is a genome a codeword of an error-correcting code?

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.