Evolutionary Perspectives on Human-Artificial Intelligence Convergence.

In this analytical review, we explore the potential impact of the rapid proliferation of artificial intelligence (AI) tools on the biosphere and noosphere, suggesting that the trend may lead to a transformative event that could be termed "Human-AI integration." We argue that this integration could give rise to novel lifeforms, associations, and hierarchies, resulting in competitive advantages and increased complexity of structural organizations within both the biosphere and noosphere. Our central premise emphasizes the importance of human-AI integration as a global adaptive response crucial for our civilization's survival amidst a rapidly changing environment.

Milk Formula Diet Alters Bacterial and Host Protein Profile in Comparison to Human Milk Diet in Neonatal Piglet Model.

The metaproteome profiling of cecal contents collected from neonatal piglets fed pasteurized human milk (HM) or a dairy-based infant formula (MF) from postnatal day (PND) 2 to 21 were assessed. At PND 21, a subset of piglets from each group ( = 11/group) were euthanized, and cecal contents were collected for further metaproteome analysis. Cecal microbiota composition showed predominantly more Firmicutes phyla and family in the lumen of cecum of HM-fed piglets in comparison to the MF-fed group.

Metaproteomics-An Advantageous Option in Studies of Host-Microbiota Interaction.

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. Manipulating gut microbiota is being recognized as a therapeutic target to manage various chronic diseases. The therapeutic manipulation of the intestinal microbiome is achieved through diet modification, the administration of prebiotics, probiotics, or antibiotics, and more recently, fecal microbiome transplantation (FMT).

Resistant starch slows the progression of CKD in the 5/6 nephrectomy mouse model.

Background: Resistant Starch (RS) improves CKD outcomes. In this report, we study how RS modulates host-microbiome interactions in CKD by measuring changes in the abundance of proteins and bacteria in the gut. In addition, we demonstrate RS-mediated reduction in CKD-induced kidney damage.

Integration of Flow Cytometry and Single Cell Sequencing.

Integrating cytometric analysis of cells, mitochondria, and other polynucleotide-containing biological particles with high-throughput single particle sequencing would provide an ultimate bioanalytical tool, simultaneously assessing phenotype, functionality, genome, and transcriptome of each particle in a large population. Here, we describe how such integration could be performed by adapting existing, well-established technologies.

Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study.

Gene set analysis (GSA) has become the common methodology for analyzing transcriptomics data. However, self-contained GSA techniques are rarely, if ever, used for proteomics data analysis. Here we present a self-contained proteome level GSA of four consensus molecular subtypes (CMSs) previously established by transcriptome dissection of colon carcinoma specimens.

Chronic kidney disease and the gut microbiome.

The gut microbiome is composed of a diverse population of bacteria that have beneficial and adverse effects on human health. The microbiome has recently gained attention and is increasingly noted to play a significant role in health and a number of disease states. Increasing urea concentration during chronic kidney disease (CKD) leads to alterations in the intestinal flora that can increase production of gut-derived toxins and alter the intestinal epithelial barrier.

DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA.

We identified 29 G-quadruplex binding proteins by affinity purification and quantitative LC-MS/MS. We demonstrated that the DEAD-box RNA helicases Dbp2, Ded1 and Mss116 preferentially bind to G-quadruplex nucleic acids in vitro and destabilize RNA quadruplexes, suggesting new potential roles for these helicases in disruption of quadruplex structures in RNA.

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats.

Background: Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling.

Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond.

The analysis of gene sets (in a form of functionally related genes or pathways) has become the method of choice for extracting the strongest signals from omics data. The motivation behind using gene sets instead of individual genes is two-fold. First, this approach incorporates pre-existing biological knowledge into the analysis and facilitates the interpretation of experimental results.

GSAR: Bioconductor package for Gene Set analysis in R.

Background: Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level statistics for a gene set or apply a multivariate statistic that accounts for intergene correlations. Most available methods detect complex departures from the null hypothesis but lack the ability to identify the specific alternative hypothesis that rejects the null.

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress.

Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA).

Protein-protein interaction analysis for functional characterization of helicases.

Helicases are enzymes involved in nucleic acid metabolism, playing major roles in replication, transcription, and repair. Defining helicases oligomerization state and transient and persistent protein interactions is essential for understanding of their function. In this article we review current methods for the protein-protein interaction analysis, and discuss examples of its application to the study of helicases: Pif1 and DDX3.

Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry.

Defining protein-protein contacts is a challenging problem and cross-linking is a promising solution. Here, we present a case of mitochondrial single strand binding protein Rim1 and helicase Pif1, an interaction first observed in immuno-affinity pull-down from yeast cells using Pif1 bait. We found that only the short succinimidyl-diazirine cross-linker or formaldehyde captured the interaction between recombinant Rim1 and Pif1.

Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA.

Using a G-quadruplex bait, we identified the transcription co-activator Sub1 as a G-quadruplex binding protein by quantitative LC-MS/MS and demonstrated in vivo G-quadruplex binding by ChIP. In vitro, Sub1, and its human homolog PC4, bind preferentially to G-quadruplexes. This provides a possible mechanism by which G-quadruplexes can influence gene transcription.

XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry.

Background: Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, and to the overall low-abundance of cross-link species in the background of linear peptides.

[G4-quadruplexes and genome instability].

A comparative analysis in silico of distribution of nucleotide sequences that predispose to formation of non-canonical DNA structure of G-quadruplexes, closely related with gene expression regulation and double strand DNA breaks, within vertebrata and yeast nuclear and mitochondrial genomes was carried out. Data on preferable localization of potential quadruplexes within non-coding sequences, their evolutionary conservation, and existing homology between them in mitochondrial and nuclear genomes were obtained. A possible interrelation between quadruplexes, Pif1 helicase and genomic instability is discussed.

Large Scale Chemical Cross-linking Mass Spectrometry Perspectives.

The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one's attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces.

Computational prediction of polycomb-associated long non-coding RNAs.

Among thousands of long non-coding RNAs (lncRNAs) only a small subset is functionally characterized and the functional annotation of lncRNAs on the genomic scale remains inadequate. In this study we computationally characterized two functionally different parts of human lncRNAs transcriptome based on their ability to bind the polycomb repressive complex, PRC2. This classification is enabled by the fact that while all lncRNAs constitute a diverse set of sequences, the classes of PRC2-binding and PRC2 non-binding lncRNAs possess characteristic combinations of sequence-structure patterns and, therefore, can be separated within the feature space.

The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis.

Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies.

Workflow for large scale detection and validation of peptide modifications by RPLC-LTQ-Orbitrap: application to the Arabidopsis thaliana leaf proteome and an online modified peptide library.

Post-translational modifications (PTMs) of proteins add to the complexity of proteomes, thereby complicating the task of proteome characterization. An efficient strategy to identify this peptide heterogeneity is important for determination of protein function, as well as for mass spectrometry-based protein quantification. Furthermore, studies of allelic variation or single nucleotide polymorphisms (SNPs) at the proteome level, as well as mRNA editing, are increasingly relevant, but validation and determination of false positive rates are challenging.

Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis.

The plastid ClpPR protease complex in Arabidopsis thaliana consists of five catalytic ClpP and four noncatalytic ClpR subunits. An extensive analysis of the CLPR family and CLPP5 is presented to address this complexity. Null alleles for CLPR2 and CLPR4 showed delayed embryogenesis and albino embryos, with seedling development blocked in the cotyledon stage; this developmental block was overcome under heterotrophic conditions, and seedlings developed into small albino to virescent seedlings.

Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism.

The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast.

PPDB, the Plant Proteomics Database at Cornell.

The Plant Proteomics Database (PPDB; http://ppdb.tc.cornell.

Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells.

Chloroplasts of maize leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C(4) photosynthesis. Chloroplasts contain thylakoid and envelope membranes that contain the photosynthetic machineries and transporters but also proteins involved in e.g.