NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.

Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed.

Poppers-Induced Methemoglobinemia: A Curious Case of the Blues.

Methemoglobinemia (MetHb) can be a deadly condition at certain levels, presenting in a fulminant form of cyanosis or disguising itself with vague symptoms. Methemoglobinemia is an altered state of the body's hemoglobin, which can be congenital or acquired. We report a case of a 62-year-old male who presented with altered mental status and hypoxia after consuming "Jungle Juice", raising concern for methemoglobinemia.

Na controls hypoxic signalling by the mitochondrial respiratory chain.

All metazoans depend on the consumption of O by the mitochondrial oxidative phosphorylation system (OXPHOS) to produce energy. In addition, the OXPHOS uses O to produce reactive oxygen species that can drive cell adaptations, a phenomenon that occurs in hypoxia and whose precise mechanism remains unknown. Ca is the best known ion that acts as a second messenger, yet the role ascribed to Na is to serve as a mere mediator of membrane potential.

NGSEP3: accurate variant calling across species and sequencing protocols.

Motivation: Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features.

Results: Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats.

HIF1α Suppresses Tumor Cell Proliferation through Inhibition of Aspartate Biosynthesis.

Cellular aspartate drives cancer cell proliferation, but signaling pathways that rewire aspartate biosynthesis to control cell growth remain largely unknown. Hypoxia-inducible factor-1α (HIF1α) can suppress tumor cell proliferation. Here, we discovered that HIF1α acts as a direct repressor of aspartate biosynthesis involving the suppression of several key aspartate-producing proteins, including cytosolic glutamic-oxaloacetic transaminase-1 (GOT1) and mitochondrial GOT2.