A performant bridge between fixed-size and variable-size seeding.

BACKGROUND: Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds). The former strategy supports fast seed computation, while the latter one benefits from a high seed uniqueness. Algorithmic bridges between instances of both seeding strategies are of interest for combining their respective advantages. RESULTS: We introduce an efficient strategy for computing MEMs out of fixed-size seeds (k-mers or minimizers). In contrast to previously proposed extend-purge strategies, our merge-extend strategy prevents the creation and filtering of duplicate MEMs. Further, we describe techniques for extracting SMEMs or maximal spanning seeds out of MEMs. A comprehensive benchmarking shows the applicability, strengths, shortcomings and computational requirements of all discussed seeding techniques. Additionally, we report the effects of seed occurrence filters in the context of these techniques. Aside from our novel algorithmic approaches, we analyze hierarchies within fixed-size and variable-size seeding along with a mapping between instances of both seeding strategies. CONCLUSION: Benchmarking shows that our proposed merge-extend strategy for MEM computation outperforms previous extend-purge strategies in the context of PacBio reads. The observed superiority grows with increasing read size and read quality. Further, the presented filters for extracting SMEMs or maximal spanning seeds out of MEMs outperform FMD-index based extension techniques. All code used for benchmarking is available via GitHub at https://github.com/ITBE-Lab/seed-evaluation .

A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature.

INTRODUCTION: Glioblastoma multiform (GBM) is a neural stem cell (NSC)-derived malignant brain tumor with complex genetic alterations challenging clinical treatments. FAM72 is a NSC-specific protein comprised of four paralogous genes (FAM72 A-D) in the human genome, but its functional tumorigenic significance is unclear. METHODS: We conducted an in-depth expression and somatic mutation data analysis of FAM72 (A-D) in GBM using the comprehensive human clinical cancer study database cBioPortal [including The Cancer Genome Atlas (TCGA)]. RESULTS: We established a FAM72 transcription profile across TCGA correlated with the expression of the proliferative marker MKI67 and a tissue-specific gene-mutation signature represented by pivotal genes involved in driving the cell cycle. FAM72 paralogs are overexpressed in cancer cells, specifically correlating with the mitotic cell cycle genes ASPM, KIF14, KIF23, CENPE, CENPE, CEP55, SGO1, and BUB1, thereby contributing to centrosome and mitotic spindle formation. FAM72 expression correlation identifies a novel GBM-specific gene set (SCN9A, MXRA5, ADAM29, KDR, LRP1B, and PIK3C2G) in the de novo pathway of primary GBM predestined as viable targets for therapeutics. CONCLUSION: Our newly identified primary GBM-specific gene-mutation signature, along with FAM72, could thus provide a new basis for prognostic biomarkers for diagnostics of GBM and could serve as potential therapeutic targets.

Brain plasticity, cognitive functions and neural stem cells: a pivotal role for the brain-specific neural master gene |-SRGAP2-FAM72-|.

Due to an aging society with an increased dementia-induced threat to higher cognitive functions, it has become imperative to understand the molecular and cellular events controlling the memory and learning processes in the brain. Here, we suggest that the novel master gene pair |-SRGAP2-FAM72-| (SLIT-ROBO Rho GTPase activating the protein 2, family with sequence similarity to 72) reveals a new dogma for the regulation of neural stem cell (NSC) gene expression and is a distinctive player in the control of human brain plasticity. Insight into the specific regulation of the brain-specific neural master gene |-SRGAP2-FAM72-| may essentially contribute to novel therapeutic approaches to restore or improve higher cognitive functions.

A novel specialized single-linkage clustering algorithm for taxonomically ordered data.

Similarities among ortholog genes for a given set of species S can be expressed by alignment matrices, where each matrix cell results from aligning a gene transcript against the genome of a species within S. Gene clusters can be computed by using single-linkage clustering in time n × m, where n denotes the number of ortholog genes and m denotes the number of inspected assemblies. Our approach can break the O(n × m) complexity of single-linkage clustering by exploiting an order among species that results from an in-order traversal of a given phylogenetic tree. The order among species allows the reduction of the inspected scope of the matrix to taxonomically related combinations of assemblies and genes, thus lowering the computational efforts necessary for creating the alignment matrix without affecting cluster quality. We present two novel approaches for clustering. First, we introduce a hierarchical clustering with, omitting the initial sorting of |S| elements, amortized O(|S|) time behavior, where it holds |S|≤n+m. Then, we propose a consecutive clustering having a linear time complexity O(|S|). Both approaches compute identical clusters, whereas dendrograms can only be obtained from the hierarchical one. We prove that our approaches deliver higher cluster densities than single linkage clustering. Additionally, we show that we compute clusters of superior quality, which ensures that our approaches are generally less error prone.

Glutamate E15 and E171 are Hotspots in p60TRP-Related Cancer.

RAS protein is a small G protein linked to multiple G protein-coupled receptor (GPCR) signaling cascades and is responsible for various types of cancer, but to this day, Ras is considered "undruggable." Multiple alternative regulators of G protein signaling (RGS) pathways have become the focus of ongoing efforts to identify new cancer therapeutics. We analyzed human cancer genome datasets and describe p60TRP, a recently identified GPCR-associated sorting protein (GPRASP), and its role in various types of cancer. We found that some regions of p60TRP were more prone to specific mutations, with two hotspots for mutations at E15 and E171.

All-or-(N)One - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci.

FAM72 is a novel neuronal progenitor cell (NPC) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. Accumulating data indicate the potential pivotal tumourigenic effects of FAM72. Our in silico human genome-wide analysis (GWA) revealed that the FAM72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. Unique asymmetric FAM72 segmental gene duplications are most likely to have occurred in conjunction with the paired genomic neighbour SRGAP2 (SLIT-ROBO Rho GTPase activating protein), as both genes have four paralogues in humans but only one vertebra-emerging orthologue in all other species. No species with two or three FAM72/SRGAP2 gene pairs could be identified, and the four exclusively human-defining ohnologues, with different mutation patterns in Homo neanderthalensis and Denisova hominin, may remain under epigenetic control through long non-coding (lnc) RNAs.

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17).

FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.

Characterization of a solvent, surfactant and temperature-tolerant laccase from Pleurotus sp. MAK-II and its dye decolorizing property.

OBJECTIVE: Laccase is industrially important but a major challenge is the production of an ideal laccase with suitable physicochemical properties to tolerate temperature, surfactants, metal ions and solvents towards its potential application in bioremediation. RESULTS: A laccase with a molecular mass of 43 kDa was purified from Pleurotus sp. MAK-II. It was optimally active at pH 4.5 and 60 °C using ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) as substrate. The laccase was susceptible to NaN3 and NaCN. Activity was strongly enhanced by Cu(2+), Mg(2+) and Ca(2+). The purified laccase showed stability towards various surfactants and solvents and decolorized, in the presence of violuric acid as redox mediator, the diazo dye Congo Red and the anthraquinone dye Remazol Brilliant Blue R to the extent of 96 and 72 %, respectively. CONCLUSION: The ideal physicochemical properties of Pleurotus sp. MAK-II-derived laccase suggest that it could be effectively used in the textile dye industry.

Deciphering the molecular landscape of the FAM72 gene family: Implications for stem cell biology and cancer.

Family with sequence similarity 72 (FAM72) is a protein-coding gene family located on chromosome 1 in humans, uniquely featuring four paralogs: FAM72A, FAM72B, FAM72C, and FAM72D. While FAM72's presence as a gene pair with the SLIT-ROBO Rho GTPase-activating protein 2 (SRGAP2) is intriguing, its functional roles, particularly in neural stem cells, remain incompletely understood. This review explores the distinct characteristics of FAM72, shedding light on its expression patterns, potential roles in cell cycle regulation, stem cell renewal and implications in neurogenesis and tumorigenesis.

MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads.

Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA .

Phytochemical Profiling in Conjunction with In Vitro and In Silico Studies to Identify Human α-Amylase Inhibitors in Leucaena leucocephala (Lam.) De Wit for the Treatment of Diabetes Mellitus.

Bioactive constituents from natural sources are of great interest as alternatives to synthetic compounds for the treatment of various diseases, including diabetes mellitus. In the present study, phytochemicals present in Leucaena leucocephala (Lam.) De Wit leaves were identified by gas chromatography-mass spectrometry and further examined by qualitative and quantitative methods. α-Amylase enzyme activity assays were performed and revealed that L. leucocephala (Lam.) De Wit leaf extract inhibited enzyme activity in a dose-dependent manner, with efficacy similar to that of the standard α-amylase inhibitor acarbose. To determine which phytochemicals were involved in α-amylase enzyme inhibition, in silico virtual screening of the absorption, distribution, metabolism, excretion, and toxicity properties was performed and pharmacophore dynamics were assessed. We identified hexadecenoic acid and oleic acid ((Z)-octadec-9-enoic acid) as α-amylase inhibitors. The binding stability of α-amylase to those two fatty acids was confirmed in silico by molecular docking and a molecular dynamics simulation performed for 100 ns. Together, our findings indicate that L. leucocephala (Lam.) De Wit-derived hexadecanoic acid and oleic acid are natural product-based antidiabetic compounds that can potentially be used to manage diabetes mellitus.

Antibacterial, Antifungal, and Antioxidant Activities of Silver Nanoparticles Biosynthesized from Bauhinia tomentosa Linn.

The biogenic synthesis of silver nanoparticles (AgNPs) has a wide range of applications in the pharmaceutical industry. Here, we synthesized AgNPs using the aqueous flower extract of Bauhinia tomentosa Linn. Formation of AgNPs was observed using ultraviolet-visible light spectrophotometry at different time intervals. Maximum absorption was observed after 4 h at 420 nm due to the reduction of Ag+ to Ag0. The stabilizing activity of functional groups was identified by Fourier-transform infrared spectroscopy. Size and surface morphology were also analyzed using scanning electron microscopy. The present study revealed the AgNPs were spherical in form with a diameter of 32 nm. The face-centered cubic structure of AgNPs was indexed using X-ray powder diffraction with peaks at 2θ = 37°, 49°, 63°, and 76° (corresponding to the planes of silver 111, 200, 220, 311), respectively. Energy-dispersive X-ray spectroscopy revealed that pure reduced silver (Ag0) was the major constituent (59.08%). Antimicrobial analyses showed that the biosynthesized AgNPs possess increased antibacterial activity (against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative), with larger zone formation against S. aureus (9.25 mm) compared with that of E. coli (6.75 mm)) and antifungal activity (against Aspergillus flavus and Candida albican (with superior inhibition against A. flavus (zone of inhibition: 7 mm) compared with C. albicans (zone of inhibition: 5.75 mm)). Inhibition of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity was found to be dose-dependent with half-maximal inhibitory concentration (IC50) values of 56.77 µg/mL and 43.03 µg/mL for AgNPs and ascorbic acid (control), respectively, thus confirming that silver nanoparticles have greater antioxidant activity than ascorbic acid. Molecular docking was used to determine the mode of antimicrobial interaction of our biosynthesized B. tomentosa Linn flower-powder extract-derived AgNPs. The biogenic AgNPs preferred hydrophobic contacts to inhibit bacterial and fungal sustainability with reducing antioxidant properties, suggesting that biogenic AgNPs can serve as effective medicinal agents.

Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing.

Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2 to prevent mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a molecule that can specifically prevent the FAM72A-UNG2 interaction by blocking its cell signaling pathways. Our results provide an excellent basis for possible therapeutic approaches in the clinical treatment of cancer.

FAM72, Glioblastoma Multiforme (GBM) and Beyond.

Neural stem cells (NSCs) offer great potential for regenerative medicine due to their excellent ability to differentiate into various specialized cell types of the brain. In the central nervous system (CNS), NSC renewal and differentiation are under strict control by the regulation of the pivotal SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)-Family with sequence similarity 72 (FAM72) master gene (i.e., |-SRGAP2-FAM72-|) via a divergent gene transcription activation mechanism. If the gene transcription control unit (i.e., the intergenic region of the two sub-gene units, SRGAP2 and FAM72) gets out of control, NSCs may transform into cancer stem cells and generate brain tumor cells responsible for brain cancer such as glioblastoma multiforme (GBM). Here, we discuss the surveillance of this |-SRGAP2-FAM72-| master gene and its role in GBM, and also in light of FAM72 for diagnosing various types of cancers outside of the CNS.

Proteomic Atomics Reveals a Distinctive Uracil-5-Methyltransferase.

Carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and sulfur (S) atoms intrigue as they are the foundation for amino acid (AA) composition and the folding and functions of proteins and thus define and control the survival of a cell, the smallest unit of life. Here, we calculated the proteomic atom distribution in >1500 randomly selected species across the entire current phylogenetic tree and identified uracil-5-methyltransferase (U5MTase) of the protozoan parasite Plasmodium falciparum (Pf, strain Pf3D7), with a distinct atom and AA distribution pattern. We determined its apicoplast location and in silico 3D protein structure to refocus attention exclusively on U5MTase with tremendous potential for therapeutic intervention in malaria. Around 300 million clinical cases of malaria occur each year in tropical and subtropical regions of the world, resulting in over one million deaths annually, placing malaria among the most serious infectious diseases. Genomic and proteomic research of the clades of parasites containing Pf is progressing slowly and the functions of most of the ∼5300 genes are still unknown. We applied a 'bottom-up' comparative proteomic atomics analysis across the phylogenetic tree to visualize a protein molecule on its actual basis - i. e., its atomic level. We identified a protruding Pf3D7-specific U5MTase, determined its 3D protein structure, and identified potential inhibitory drug molecules through in silico drug screening that might serve as possible remedies for the treatment of malaria. Besides, this atomic-based proteome map provides a unique approach for the identification of parasite-specific proteins that could be considered as novel therapeutic targets.

Accurate high throughput alignment via line sweep-based seed processing.

Accurate and fast aligners are required to handle the steadily increasing volume of sequencing data. Here we present an approach allowing performant alignments of short reads (Illumina) as well as long reads (Pacific Bioscience, Ultralong Oxford Nanopore), while achieving high accuracy, based on a universal three-stage scheme. It is also suitable for the discovery of insertions and deletions that originate from structural variants. We comprehensively compare our approach to other state-of-the-art aligners in order to confirm its performance with respect to accuracy and runtime. As part of our algorithmic scheme, we introduce two line sweep-based techniques called "strip of consideration" and "seed harmonization". These techniques represent a replacement for chaining and do not rely on any specially tailored data structures. Additionally, we propose a refined form of seeding on the foundation of the FMD-index.

Establishing a human adrenocortical carcinoma (ACC)-specific gene mutation signature.

Adrenocortical carcinoma (ACC) is a rare and aggressive tumor whose molecular signaling pathways are not fully understood. Using an in-silico clinical data analysis approach we retrieved human gene mutation data from the highly reputed Cancer Genome Atlas (TCGA). ACC-specific gene mutations were correlated with proliferation marker FAM72 expression and Mutsig along with the algorithmic implementation of the 20/20 rule were used to validate their oncogenic potential. The newly identified oncogenic driver gene set (ZFPM1, LRIG1, CRIPAK, ZNF517, GARS and DGKZ), specifically and most repeatedly mutated in ACC, is involved in tumor suppression and cellular proliferation and thus could be useful for the prognosis and development of therapeutic approaches for the treatment of ACC.

A Novel Divergent Gene Transcription Paradigm-the Decisive, Brain-Specific, Neural |-Srgap2-Fam72a-| Master Gene Paradigm.

Brain development and repair largely depend on neural stem cells (NSCs). Here, we suggest that two genes, i.e., Srgap2 (SLIT-ROBO Rho GTPase-activating protein 2) and Fam72a (family with sequence similarity to 72, member A), constitute a single, NSC-specific, |-Srgap2-Fam72a-| master gene pair co-existing in reciprocal functional dependency. This gene pair has a dual, commonly used, intergenic region (IGR) promotor, which is a prerequisite in controlling human brain plasticity. We applied fluorescence cellular microscopy and fluorescence-activated cell sorting (FACS) to assess rat |-Srgap2-Fam72a-| master gene IGR promotor activity upon stimulation with two contrary growth factors: nerve growth factor (Ngf, a differentiation growth factor) and epidermal growth factor (Egf, a mitotic growth factor). We found that Ngf and Egf acted on the same IGR gene promotor element of the |-Srgap2-Fam72a-| master gene to mediate cell differentiation and proliferation, respectively. Ngf mediated Srgap2 expression and neuronal survival and differentiation while Egf activated Fam72a transcription and cell proliferation. Our data provide new insights into the specific regulation of the |-Srgap2-Fam72a-| master gene with its dual IGR promotor that controls two reverse-oriented functional-dependent genes located on opposite DNA strands. This structure represents a novel paradigm for controlling transcription of divergent genes in regulating NSC gene expression. This paradigm may allow for novel therapeutic approaches to restore or improve higher cognitive functions and cure cancers.

Livebearing or egg-laying mammals: 27 decisive nucleotides of FAM168.

In the present study, we determine comprehensive molecular phylogenetic relationships of the novel myelin-associated neurite-outgrowth inhibitor (MANI) gene across the entire eukaryotic lineage. Combined computational genomic and proteomic sequence analyses revealed MANI as one of the two members of the novel family with sequence similarity 168 member (FAM168) genes, consisting of FAM168A and FAM168B, having distinct genetic differences that illustrate diversification in its biological function and genetic taxonomy across the phylogenetic tree. Phylogenetic analyses based on coding sequences of these FAM168 genes revealed that they are paralogs and that the earliest emergence of these genes occurred in jawed vertebrates such as Callorhinchus milii. Surprisingly, these two genes are absent in other chordates that have a notochord at some stage in their lives, such as branchiostoma and tunicates. In the context of phylogenetic relationships among eukaryotic species, our results demonstrate the presence of FAM168 orthologs in vertebrates ranging from Callorhinchus milii to Homo sapiens, displaying distinct taxonomic clusters, comprised of fish, amphibians, reptiles, birds, and mammals. Analyses of individual FAM168 exons in our sample provide new insights into the molecular relationships between FAM168A and FAM168B (MANI) on the one hand and livebearing and egg-laying mammals on the other hand, demonstrating that a distinctive intermediate exon 4, comprised of 27 nucleotides, appears suddenly only in FAM168A and there in the livebearing mammals only but is absent from all other species including the egg-laying mammals.

Cognitive Functions: Human vs. Animal - 4:1 Advantage |-FAM72-SRGAP2-|.

With the advent of computational genomics, an intensive search is underway for unique biomarkers for Homo sapiens that could be used to differentiate taxa within the Hominoidea, in particular to distinguish Homo from the apes (Pan, Gorilla, Pongo, and Hylobates) and species or subspecies within the genus Homo (H. sapiens, H. heidelbergensis, H. neanderthalensis, H. erectus, and the Denisovans). Here, we suggest that the |-FAM72-SRGAP2-| (family with sequence similarity 72/SLIT-ROBO Rho GTPase activating protein 2) gene pair is a unique molecular biomarker for the genus Homo that could also help to place Australopithecus at its most appropriate place within the phylogenetic tree and may explain the distinctive higher brain cognitive functions of humans.