Gene Regulatory Proteins Research Articles

ITraNet: A Web-Based Platform for integrated Trans-Omics Network Visualization and Analysis

Abstract Motivation Visualization and analysis of biological networks play crucial roles in understanding living systems. Biological networks include diverse types, from gene regulatory networks and protein–protein interactions to metabolic networks. Metabolic networks include substrates, products, and enzymes, which are regulated by allosteric mechanisms and gene expression. However, the analysis of these diverse omics types is challenging due to the diversity of databases and the complexity of network analysis. Results We developed iTraNet, a web application that visualizes and analyzes trans-omics networks involving four types of networks: gene regulatory networks; protein–protein interactions; metabolic networks; and metabolite exchange networks. Using iTraNet, we found that in wild-type mice, hub molecules within the network tended to respond to glucose administration, whereas in ob/ob mice, this tendency disappeared. With its ability to facilitate network analysis, we anticipate that iTraNet will help researchers gain insights into living systems. Availability iTraNet is available at https://itranet.streamlit.app/. Supplementary information Supplementary data are available at Bioinformatics Advances online.

Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility.

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.

Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR

The 91 kDa oligomeric ring-shaped ligand binding protein TRAP (trp RNA binding attenuation protein) regulates the expression of a series of genes involved in tryptophan (Trp) biosynthesis in bacilli. When cellular Trp levels rise, the free amino acid binds to sites buried in the interfaces between each of the 11 (or 12, depending on the species) protomers in the ring. Crystal structures of Trp-bound TRAP show the Trp ligands are sequestered from solvent by a pair of loops from adjacent protomers that bury the bound ligand via polar contacts to several threonine residues. Binding of the Trp ligands occurs cooperatively, such that successive binding events occur with higher apparent affinity but the structural basis for this cooperativity is poorly understood. We used solution methyl-TROSY NMR relaxation experiments focused on threonine and isoleucine sidechains, as well as magic angle spinning solid-state NMR 13C–13C and 15N-13C chemical shift correlation spectra on uniformly labeled samples recorded at 800 and 1200 MHz, to characterize the structure and dynamics of the protein. Methyl 13C relaxation dispersion experiments on ligand-free apo TRAP revealed concerted exchange dynamics on the µs-ms time scale, consistent with transient sampling of conformations that could allow ligand binding. Cross-correlated relaxation experiments revealed widespread disorder on fast timescales. Chemical shifts for methyl-bearing side chains in apo- and Trp-bound TRAP revealed subtle changes in the distribution of sampled sidechain rotameric states. These observations reveal a pathway and mechanism for induced conformational changes to generate homotropic Trp-Trp binding cooperativity.

Zinc and Its Impact on the Function of the Testicle and Epididymis.

Zinc (Zn) is an essential trace element; it exhibits a plethora of physiological properties and biochemical functions. It plays a pivotal role in regulating the cell cycle, apoptosis, and DNA organization, as well as in protein, lipid, and carbohydrate metabolism. Among other important processes, Zn plays an essential role in reproductive health. The ZIP and ZnT proteins are responsible for the mobilization of Zn within the cell. Zn is an inert antioxidant through its interaction with a variety of proteins and enzymes to regulate the redox system, including metallothioneins (MTs), metalloenzymes, and gene regulatory proteins. The role of Zn in the reproductive system is of great importance; processes, such as spermatogenesis and sperm maturation that occur in the testicle and epididymis, respectively, depend on this element for their development and function. Zn modulates the synthesis of androgens, such as testosterone, for these reproductive processes, so Zn deficiency is related to alterations in sperm parameters that lead to male infertility.

Regulation of the expression of MHETase and TPA degradation genes involved in the degradation of PET in Ideonella sakaiensis.

Ideonella sakaiensis is a bacterium that can degrade and consume polyethylene terephthalate (PET), a plastic material that was previously considered non-biodegradable. The degradation of PET requires two enzymes, namely poly (ethylene terephthalate) hydrolase (PETase) and mono (2-hydroxyethyl) terephthalate hydrolase (MHETase), which break down PET into terephthalate (TPA) and ethylene glycol (EG), which serve as carbon sources for the bacterium. Previous studies have focused on the enzymatic properties, structure, and mechanism of action of PETase and MHETase. However, the regulation of PETase and MHETase gene expression has not been investigated. This study identified a protein that binds to the MHETase promoter DNA, MHETase gene-regulating protein (MRP) in I. sakaiensis. PET or TPA induced the expression of PETase and MHETase genes. Furthermore, the induction of the MHETase gene was abolished by the deletion of the mrp gene, while the expression of the PETase gene was maintained. In addition, the genes involved in TPA metabolism were not induced in the mrp mutant. Furthermore, the growth of the PET and TPA deteriorated due to mrp mutation. Also, MRP binds to the promoter regions of the MHETase gene and TPA metabolizing genes, but not to the PETase gene promoter. These results suggest that MRP is a transcription factor that activates MHETase and TPA-metabolizing genes.

A [formula omitted] adic approach to the TSPO gene

TSPO protein is known to be involved in various cellular functions and dysregulations of TSPO expression has been found to be associated with pathologies of different human diseases, including cardiovascular disease, cancer, neuroinflammatory, neurodegenerative, neoplastic disorders. However, there are limited studies in the literature on the effects of sequence variations in the TSPO gene on the function of the protein and their relationship with human diseases. Evaluating the pathogenicity of genetic variants is crucial in terms of prioritizing the functional importance and clinical use. Therefore, various in-silico prediction tools have been developed that combine different algorithms to predict the effects of sequence variations on protein functions or gene regulation. In this study, the p-adic distance approach in modeling the genetic code, proposed and developed by Dragovich and Dragovich, was discussed in order to obtain an alternative to the existing in-silico prediction tools. Dragovichs’ approach is expressed as follows: A 5-adic space of codons is constructed and 5-adic and 2-adic distances between codons are taken into account. As a result, two codons with the smallest value of 5-adic and 2-adic distances are obtained, encoded for the same amino acid and stop signal. This model describes well the degeneration of the genetic code. This study combined the data obtained from in-silico prediction tools and used a bioinformatics approach to determine the functional relevance of coding SNPs in the TSPO. Overall, we evaluate the potential utility of Dragovichs’ approach by comparing it with other existing prediction tools for variant classification and prioritization.

PPIH acts as a potential predictive biomarker for patients with common solid tumors

BackgroundOur previous studies have indicated that mRNA and protein levels of PPIH are significantly upregulated in Hepatocellular Carcinoma (LIHC) and could act as predictive biomarkers for patients with LIHC. Nonetheless, the expression and implications of PPIH in the etiology and progression of common solid tumors have yet to be explored, including its potential as a serum tumor marker.MethodsWe employed bioinformatics analyses, augmented with clinical sample evaluations, to investigate the mRNA and protein expression and gene regulation networks of PPIH in various solid tumors. We also assessed the association between PPIH expression and overall survival (OS) in cancer patients using Kaplan-Meier analysis with TCGA database information. Furthermore, we evaluated the feasibility and diagnostic efficacy of PPIH as a serum marker by integrating serological studies with established clinical tumor markers.ResultsThrough pan-cancer analysis, we found that the expression levels of PPIH mRNA in multiple tumors were significantly different from those in normal tissues. This study is the first to report that PPIH mRNA and protein levels are markedly elevated in LIHC, Colon adenocarcinoma (COAD), and Breast cancer (BC), and are associated with a worse prognosis in these cancer patients. Conversely, serum PPIH levels are decreased in patients with these tumors (LIHC, COAD, BC, gastric cancer), and when combined with traditional tumor markers, offer enhanced sensitivity and specificity for diagnosis.ConclusionOur findings propose that PPIH may serve as a valuable predictive biomarker in tumor patients, and its secreted protein could be a potential serum marker, providing insights into the role of PPIH in cancer development and progression.

Genome-Wide Transcriptional Roles of KSHV Viral Interferon Regulatory Factors in Oral Epithelial Cells.

The viral interferon regulatory factors (vIRFs) of KSHV are known to dysregulate cell signaling pathways to promote viral oncogenesis and to block antiviral immune responses to facilitate infection. However, it remains unknown to what extent each vIRF plays a role in gene regulation. To address this, we performed a comparative analysis of the protein structures and gene regulation of the four vIRFs. Our structure prediction analysis revealed that despite their low amino acid sequence similarity, vIRFs exhibit high structural homology in both their DNA-binding domain (DBD) and IRF association domain. However, despite this shared structural homology, we demonstrate that each vIRF regulates a distinct set of KSHV gene promoters and human genes in epithelial cells. We also found that the DBD of vIRF1 is essential in regulating the expression of its target genes. We propose that the structurally similar vIRFs evolved to possess specialized transcriptional functions to regulate specific genes.

A Novel Approach for Glioblastoma Treatment by Combining Apoptosis Inducers (TMZ, MTX, and Cytarabine) with E.V.A. (Eltanexor, Venetoclax, and A1210477) Inhibiting XPO1, Bcl-2, and Mcl-1.

Adjuvant treatment for Glioblastoma Grade 4 with Temozolomide (TMZ) inevitably fails due to therapeutic resistance, necessitating new approaches. Apoptosis induction in GB cells is inefficient, due to an excess of anti-apoptotic XPO1/Bcl-2-family proteins. We assessed TMZ, Methotrexate (MTX), and Cytarabine (Ara-C) (apoptosis inducers) combined with XPO1/Bcl-2/Mcl-1-inhibitors (apoptosis rescue) in GB cell lines and primary GB stem-like cells (GSCs). Using CellTiter-Glo® and Caspase-3 activity assays, we generated dose-response curves and analyzed the gene and protein regulation of anti-apoptotic proteins via PCR and Western blots. Optimal drug combinations were examined for their impact on the cell cycle and apoptosis induction via FACS analysis, paralleled by the assessment of potential toxicity in healthy mouse brain slices. Ara-C and MTX proved to be 150- to 10,000-fold more potent in inducing apoptosis than TMZ. In response to inhibitors Eltanexor (XPO1; E), Venetoclax (Bcl-2; V), and A1210477 (Mcl-1; A), genes encoding for the corresponding proteins were upregulated in a compensatory manner. TMZ, MTX, and Ara-C combined with E, V, and A evidenced highly lethal effects when combined. As no significant cell death induction in mouse brain slices was observed, we conclude that this drug combination is effective in vitro and expected to have low side effects in vivo.

The landscape and predicted roles of structural variants in Fusarium graminearum genomes.

Structural rearrangements, such as inversions, translocations, duplications, and large insertions and deletions, are large-scale genomic variants that can play an important role in shaping phenotypic variation and in genome adaptation and evolution. We used chromosomal-level assemblies from eight Fusarium graminearum isolates to study structural variants and their role in fungal evolution. We generated the assemblies of four of these genomes after Oxford Nanopore sequencing. A total of 87 inversions, 159 translocations, 245 duplications, 58,489 insertions, and 34,102 deletions were detected. Regions of high recombination rate are associated with structural rearrangements, and a significant proportion of inversions, translocations, and duplications overlap with the repeat content of the genome, suggesting recombination and repeat elements are major factors in the origin of structural rearrangements in F. graminearum. Large insertions and deletions introduce presence-absence polymorphisms for many genes, including secondary metabolite biosynthesis cluster genes and predicted effectors genes. Translocation events were found to be shuffling predicted effector-rich regions of the genomes and are likely contributing to the gain and loss of effectors facilitated by recombination. Breakpoints of some structural rearrangements fall within coding sequences and are likely altering the protein products. Structural rearrangements in F. graminearum thus have an important role to play in shaping pathogen-host interactions and broader evolution through genome reorganization, the introduction of presence-absence polymorphisms, and changing protein products and gene regulation.

Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

BackgroundThere are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions.ResultsIn this study, we examined genome-wide EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Computational predictions based on hTF motifs and subsequent ChIP-seq experiments revealed that both type 1 and 2 EBNA2 co-occupy the genome with SPI1 and AP-1 (BATF and JUNB) hTFs. However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 preferred RBPJ. These differences in hTF co-occupancy revealed possible mechanisms underlying type-specific gene expression of known EBNA2 human target genes: MYC (shared), CXCR7 (type 1 specific), and CD21 (type 2 specific). Both type 1 and 2 EBNA2 binding events were enriched at systemic lupus erythematosus (SLE) and multiple sclerosis (MS) risk loci, while primary biliary cholangitis (PBC) risk loci were specifically enriched for type 2 peaks.ConclusionsThis study reveals extensive type-specific EBNA2 interactions with the human genome, possible differences in EBNA2 interaction partners, and a possible new role for type 2 EBNA2 in autoimmune disorders. Our results highlight the importance of considering EBV type in the control of human gene expression and disease-related investigations.

Induced acute hyperglycemia modifies the barrier function of the intestinal epithelium by tissue inflammation and tight junction disruption resulting in hydroelectrolytic secretion in an animal model.

Diabetic-metabolic syndrome (MetS-D) has a high prevalence worldwide, in which an association with the rupture of the intestinal epithelium barrier function (IEBF) has been pointed out, but the functional and morphological properties are still not well understood. This study aimed to evaluate the impact of acute hyperglycemia diabetes on intestinal tight junction proteins, metabolic failure, intestinal ion and water transports, and IEBF parameters. Diabetes was induced in male Rattus norvegicus (200-310 g) with 0.5 mL of streptozotocin (70 mg/kg). Glycemic and clinical parameters were evaluated every 7 days, and intestinal parameters were evaluated on the 14th day. The MetS-D animals showed a clinical pattern of hyperglycemia, with increases in the area of villi and crypts, lactulose:mannitol ratio, myeloperoxidase (MPO) activity, and intestinal tissue concentrations of malondialdehyde (MDA), but showed a reduction in reduced glutathione (GSH) when these parameters were compared to the control. The MetS-D group had increased secretion of Na+, K+, Cl-, and water compared to the control group in ileal tissue. Furthermore, we observed a reduction in mRNA transcript of claudin-2, claudin-15, and NHE3 and increases of SGLT-1 and ZO-1 in the MetS-D group. These results showed that MetS-D triggered intestinal tissue inflammation, oxidative stress, complex alterations in gene regulatory protein transcriptions of intestinal transporters and tight junctions, damaging the IEBF and causing hydroelectrolyte secretion.

Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy.

In pathogens, a unique class of metalloregulator proteins, called gene regulatory proteins, sense specific metal ions that initiate gene transcription of proteins that export metal ions from the cell, thereby preventing toxicity and cell death. CsoR is a metalloregulator protein found in various bacterial systems that "sense" Cu(I) ions with high affinity. Upon copper binding, CsoR dissociates from the DNA promoter region, resulting in initiation of gene transcription. Crystal structures of CsoR in the presence and absence of Cu(I) from various bacterial systems have been reported, suggesting either a dimeric or tetrameric structure of these helical proteins. However, structural information about the CsoR-DNA complex is missing. Here, we applied electron paramagnetic resonance (EPR) spectroscopy to follow the conformational and dynamical changes that Mycobacterium tuberculosis CsoR undergoes upon DNA binding in solution. We showed that the quaternary structure is predominantly dimeric in solution, and only minor conformational and dynamical changes occur in the DNA bound state. Also, labeling of the unresolved C- terminus revealed no significant change in dynamics upon DNA binding. These observations are unique, since for other bacterial copper metalloregulators, such as the MerR and CopY families, major conformational changes were observed upon DNA binding, indicating a different mode of action for this protein family.

Using machine learning to predict protein–protein interactions between a zombie ant fungus and its carpenter ant host

Parasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of “effector,” often act via protein–protein interactions (PPIs). The fungal parasite Ophiocordyceps camponoti-floridani (zombie ant fungus) manipulates Camponotus floridanus (carpenter ant) behavior to promote transmission. The most striking aspect of this behavioral change is a summit disease phenotype where infected hosts ascend and attach to an elevated position. Plausibly, interspecific PPIs drive aspects of Ophiocordyceps infection and host manipulation. Machine learning PPI predictions offer high-throughput methods to produce mechanistic hypotheses on how this behavioral manipulation occurs. Using D-SCRIPT to predict host–parasite PPIs, we found ca. 6000 interactions involving 2083 host proteins and 129 parasite proteins, which are encoded by genes upregulated during manipulated behavior. We identified multiple overrepresentations of functional annotations among these proteins. The strongest signals in the host highlighted neuromodulatory G-protein coupled receptors and oxidation–reduction processes. We also detected Camponotus structural and gene-regulatory proteins. In the parasite, we found enrichment of Ophiocordyceps proteases and frequent involvement of novel small secreted proteins with unknown functions. From these results, we provide new hypotheses on potential parasite effectors and host targets underlying zombie ant behavioral manipulation.

Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression

Human Histone Locus Bodies (HLBs) are nuclear subdomains comprised of clustered histone genes that are coordinately regulated throughout the cell cycle. We addressed temporal-spatial higher-order genome organization for time-dependent chromatin remodeling at HLBs that supports control of cell proliferation. Proximity distances of specific genomic contacts within histone gene clusters exhibit subtle changes during the G1 phase in MCF10 breast cancer progression model cell lines. This approach directly demonstrates that the two principal histone gene regulatory proteins, HINFP (H4 gene regulator) and NPAT, localize at chromatin loop anchor-points, denoted by CTCF binding, supporting the stringent requirement for histone biosynthesis to package newly replicated DNA as chromatin. We identified a novel enhancer region located ∼ 2 MB distal to histone gene sub-clusters on chromosome 6 that consistently makes genomic contacts with HLB chromatin and is bound by NPAT. During G1 progression the first DNA loops form between one of three histone gene sub-clusters bound by HINFP and the distal enhancer region. Our findings are consistent with a model that the HINFP/NPAT complex controls the formation and dynamic remodeling of higher-order genomic organization of histone gene clusters at HLBs in early to late G1 phase to support transcription of histone mRNAs in S phase.

Polycomb-like Proteins in Gene Regulation and Cancer.

Polycomb-like proteins (PCLs) are a crucial group of proteins associated with the Polycomb repressive complex 2 (PRC2) and are responsible for setting up the PRC2.1 subcomplex. In the vertebrate system, three homologous PCLs exist: PHF1 (PCL1), MTF2 (PCL2), and PHF19 (PCL3). Although the PCLs share a similar domain composition, they differ significantly in their primary sequence. PCLs play a critical role in targeting PRC2.1 to its genomic targets and regulating the functionality of PRC2. However, they also have PRC2-independent functions. In addition to their physiological roles, their dysregulation has been associated with various human cancers. In this review, we summarize the current understanding of the molecular mechanisms of the PCLs and how alterations in their functionality contribute to cancer development. We particularly highlight the nonoverlapping and partially opposing roles of the three PCLs in human cancer. Our review provides important insights into the biological significance of the PCLs and their potential as therapeutic targets for cancer treatment.

Epigenetic and epitranscriptomic regulation of axon regeneration.

Effective axonal regeneration in the adult mammalian nervous system requires coordination of elevated intrinsic growth capacity and decreased responses to the inhibitory environment. Intrinsic regenerative capacity largely depends on the gene regulatory network and protein translation machinery. A failure to activate these pathways upon injury is underlying a lack of robust axon regeneration in the mature mammalian central nervous system. Epigenetics and epitranscriptomics are key regulatory mechanisms that shape gene expression and protein translation. Here, we provide an overview of different types of modifications on DNA, histones, and RNA, underpinning the regenerative competence of axons in the mature mammalian peripheral and central nervous systems. We highlight other non-neuronal cells and their epigenetic changes in determining the microenvironment for tissue repair and axon regeneration. We also address advancements of single-cell technology in charting transcriptomic and epigenetic landscapes that may further facilitate the mechanistic understanding of differential regenerative capacity in neuronal subtypes. Finally, as epigenetic and epitranscriptomic processes are commonly affected by brain injuries and psychiatric disorders, understanding their alterations upon brain injury would provide unprecedented mechanistic insights into etiology of injury-associated-psychiatric disorders and facilitate the development of therapeutic interventions to restore brain function.

Significantly higher expression of high-mobility group AT hook protein 2 (HMGA2) in the border zone of glioblastoma.

High-mobility group AT-hook protein 2 (HMGA2) is a gene regulatory protein that is correlated with metastatic potential and poor prognosis. It has been shown that HMGA2 is overexpressed in various tumors such as lung cancer or pancreatic cancer. The invasive character and highly aggressive structure of glioblastoma let us to investigate HMGA2 expression in the border zone of the tumor more closely. We compared HMGA2 expression between glioblastoma and normal brain tissue. In addition, we analyzed and compared HMGA2 expression in the border and center zones of tumors. Correlation tests between HMGA expression and clinical parameters such as MGMT-status and survival were performed. Samples from 23 patients with WHO grade 4 glioblastomas were analyzed for HMGA2 expression using quantitative real-time polymerase chain reaction (qPCR) and immunohistochemistry (IHC) and correlated with clinical parameters. The areas from the tumor center and border were analyzed separately. Two normal brain tissue specimens were used as the controls. Our results confirm that HMGA2 is higher expressed in glioblastoma compared to healthy brain tissue (qPCR, P=0.013; IHC, P=0.04). Moreover, immunohistochemistry revealed significantly higher HMGA2 expression in the border zone of the tumor than in the tumor center zone (P=0.012). Survival analysis revealed a tendency for shorter survival when HMGA2 was highly expressed in the border zone. The results reveal an overexpression of HMGA2 in the border zone of glioblastomas; thus, the expression cluster of HMGA2 seems to be heterogenous and thorough borough surgical resection of the vital and aggressive border cells might be important to inhibit the invasive character of the tumor.

Core-Shell Magnetic Imprinted Polymers for the Recognition of FLAG-Tagpeptide

FLAG® tag (DYKDDDDK) is a small epitope peptide employed for the purification of recombinant proteins such as immunoglobulins, cytokines, and gene regulatory proteins. It provides superior purity and recoveries of fused target proteins when compared to the commonly used His-tag. Nevertheless, the immunoaffinity-based adsorbents required for their isolation are far more expensive than the ligand-based affinity resin used in combination with the His-tag. In order to overcome this limitation we report herein the development of molecularly imprinted polymers (MIPs) selective to the FLAG® tag. The polymers were prepared by the epitope imprinting approach using a four amino acids peptide, DYKD, including part of the FLAG® sequence as template molecule. Different kinds of magnetic polymers were synthesised in aqueous and organic media also using different sizes of magnetite core nanoparticles. The synthesised polymers were used as solid phase extraction materials with excellent recoveries and high specificity for both peptides. The magnetic properties of the polymers confer a new, effective, simple, and fast method in the purification using FLAG® tag.

Learning in Transcriptional Network Models: Computational Discovery of Pathway-Level Memory and Effective Interventions.

Trainability, in any substrate, refers to the ability to change future behavior based on past experiences. An understanding of such capacity within biological cells and tissues would enable a particularly powerful set of methods for prediction and control of their behavior through specific patterns of stimuli. This top-down mode of control (as an alternative to bottom-up modification of hardware) has been extensively exploited by computer science and the behavioral sciences; in biology however, it is usually reserved for organism-level behavior in animals with brains, such as training animals towards a desired response. Exciting work in the field of basal cognition has begun to reveal degrees and forms of unconventional memory in non-neural tissues and even in subcellular biochemical dynamics. Here, we characterize biological gene regulatory circuit models and protein pathways and find them capable of several different kinds of memory. We extend prior results on learning in binary transcriptional networks to continuous models and identify specific interventions (regimes of stimulation, as opposed to network rewiring) that abolish undesirable network behavior such as drug pharmacoresistance and drug sensitization. We also explore the stability of created memories by assessing their long-term behavior and find that most memories do not decay over long time periods. Additionally, we find that the memory properties are quite robust to noise; surprisingly, in many cases noise actually increases memory potential. We examine various network properties associated with these behaviors and find that no one network property is indicative of memory. Random networks do not show similar memory behavior as models of biological processes, indicating that generic network dynamics are not solely responsible for trainability. Rational control of dynamic pathway function using stimuli derived from computational models opens the door to empirical studies of proto-cognitive capacities in unconventional embodiments and suggests numerous possible applications in biomedicine, where behavior shaping of pathway responses stand as a potential alternative to gene therapy.