Publications by authors named "Benjamin R Carone"

Human satellitess(HSats) are pericentric, tandemly repeating satellite DNA sequences in the human genome. While silent in normal cells, a subset of HSat2 noncoding RNA is expressed and accumulates in the nucleus of cancer cells. We developed a FISH-based approach for identification of the distribution of three subfamilies of HSat2 (A1, A2, B) sequences on individual human chromosomes.

View Article and Find Full Text PDF

Identification of the occupancy of transcription factors (TFs) and nucleosomes across the genome yields insights into the regulation of gene expression patterns. While several independent techniques can be performed and then analyzed in composite to reveal this chromatin landscape, the use of micrococcal nuclease (MNase) digestion can resolve the footprints of nearly all chromatin proteins simultaneously. The protocol below describes the use of MNase to identify chromatin footprints of both TFs and nucleosomes in two vastly different cell types, Mouse embryonic stem cells (mESCs) and sperm, with differing levels of chromatin compaction.

View Article and Find Full Text PDF
Article Synopsis
  • Ionic liquids (ILs), especially fatty acid-based ILs (FAILs), show promise in antibiotic formulations due to their ability to permeabilize lipid bilayers with low cytotoxicity to human cells.
  • The study tested different FAILs, specifically tetramethylguanidinium (TMG) or choline combined with octanoate or decanoate, to analyze their effects on lipid bilayers and bacteria.
  • Results indicated that while octanoate-based FAILs displayed low activity, decanoate-based FAILs successfully permeabilized cell membranes and demonstrated better antibacterial activity, suggesting a non-micelle based mechanism of action.
View Article and Find Full Text PDF

The detection of differentially expressed genes (DEGs) is one of most important computational challenges in the analysis of single-cell RNA sequencing (scRNA-seq) data. However, due to the high heterogeneity and dropout noise inherent in scRNAseq data, challenges in detecting DEGs exist when using a single distribution of gene expression levels, leaving much room to improve the precision and robustness of current DEG detection methods. Here, we propose the use of a new method, DEGman, which utilizes several possible diverse distributions in combination with Bhattacharyya distance.

View Article and Find Full Text PDF

Despite considerable advances in recent years, challenges in delivery and storage of biological drugs persist and may delay or prohibit their clinical application. Though nanoparticle-based approaches for small molecule drug encapsulation are mature, encapsulation of proteins remains problematic due to destabilization of the protein. Reverse micelles composed of decylmonoacyl glycerol (10MAG) and lauryldimethylamino-N-oxide (LDAO) in low-viscosity alkanes have been shown to preserve the structure and stability of a wide range of biological macromolecules.

View Article and Find Full Text PDF

Combinations of ionic liquids (ILs) with antimicrobial compounds have been shown to produce synergistic activities in model liposomes. In this study, imidazolium chloride-based ILs with alkyl tail length variations are combined with commercially available, small-molecule antimicrobials to examine the potential for combinatorial and synergistic antimicrobial effects on and The effects of these treatments in a human cell culture model indicate the cytotoxic limits of ILs paired with antimicrobials. The analysis of these ILs demonstrates that the length of the alkyl chain on the IL molecule is proportional to both antimicrobial activity and cytotoxicity.

View Article and Find Full Text PDF
Article Synopsis
  • NPC1 deficiency impacts brain development, leading to significant changes in microglia and climbing fiber synaptic refinement during cerebellar development in mice.
  • The absence of NPC1 results in delayed radial migration, increased proliferation, and impaired differentiation of microglia precursor cells, indicating early developmental issues.
  • Findings suggest that these microglial defects and synaptic connectivity problems may contribute to the early neurodegeneration of Purkinje cells in Niemann-Pick disease type C.
View Article and Find Full Text PDF

We synthesized a combinatorial library of dendrons that display a cluster of cationic charges juxtaposed with a hydrophobic alkyl chain, using the so-called "molecular umbrella" design approach. Systematically tuning the generation number and alkyl chain length enabled a detailed study of the structure-activity relationships in terms of both hydrophobic content and number of cationic charges. These discrete, unimolecular compounds display rapid and broad-spectrum bactericidal activity comparable to the activity of antibacterial peptides.

View Article and Find Full Text PDF

Alkyl-imidazolium chloride ionic liquids (ILs) have been broadly studied for biochemical and biomedical technologies. They can permeabilize lipid bilayer membranes and have cytotoxic effects, which makes them targets for drug delivery biomaterials. We assessed the lipid-membrane permeabilities of ILs with increasing alkyl chain lengths from ethyl to octyl groups on large unilamellar vesicles using a trapped-fluorophore fluorescence lifetime-based leakage experiment.

View Article and Find Full Text PDF

Amphiphilic alpha-helices are common motifs used in numerous biological systems including membrane channels/pores and antimicrobial peptides (AMPs), and binding proteins, and a variety of synthetic biomaterials. Previously, an amphiphilic peptide with lysine-containing motifs was shown to reversibly bind the anionic porphyrin meso-Tetra(4-sulfonatophenyl)porphyrin (TPPS ) and promote the formation of excitonically coupled conductive J-aggregates. The work presented here focuses on the use of this amphiphilic peptide and derivatives as a potential antimicrobial agent.

View Article and Find Full Text PDF

A library of functionalized oligo(thiophene)s with precisely controlled chain length, regioregularity, sequence, and pendant moieties in the side chains was prepared by iterative convergent/divergent organometallic couplings. The cationic and facially amphiphilic structures were designed to mimic the salient physiochemical features of host defense peptides (HDPs) while concurrently exerting a photodynamic mechanism of antibacterial activity. In the dark, the oligothiophenes exert broad-spectrum and rapid bactericidal activity in the micromolar regime, which is the typical range of HDP activity.

View Article and Find Full Text PDF

Antimicrobial peptides (AMPs) have been an area of great interest, due to the high selectivity of these molecules toward bacterial targets over host cells and the limited development of bacterial resistance to these molecules throughout evolution. The peptide C18G has been shown to be a selective, broad spectrum AMP with a net +8 cationic charge from seven lysine residues in the sequence. In this work, the cationic Lys residues were replaced with other natural or non-proteinogenic cationic amino acids: arginine, histidine, ornithine, or diaminopropionic acid.

View Article and Find Full Text PDF

Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs).

View Article and Find Full Text PDF
Article Synopsis
  • Paternal diet influences metabolic traits in offspring, but the exact mechanisms of this transmission are not fully understood.
  • Researchers analyzed sperm methylation patterns from mice on different diets, creating comprehensive methylation maps to study variations.
  • They found that variations in sperm cytosine methylation were more strongly linked to random or environmental factors rather than the diet, suggesting that sperm methylation doesn't directly affect the dietary influence on offspring metabolism.
View Article and Find Full Text PDF

Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, many noncoding RNAs (ncRNAs) are rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from ∼57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs).

View Article and Find Full Text PDF

Mammalian embryonic stem cells (ESCs) and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ESCs and sperm. In ESCs, we recover well-characterized features of chromatin such as promoter nucleosome depletion and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies.

View Article and Find Full Text PDF

The spontaneous incidence of chloramphenicol (Cam) resistant mutant bacteria is at least ten-fold higher in cultures of enterohemorrhagic Escherichia coli O157:H7 strain EDL933 than in E. coli K-12. It is at least 100-fold higher in the dam (DNA adenine methyltransferase) derivative of EDL933, compared to the dam strain of E.

View Article and Find Full Text PDF

Down's syndrome is a common disorder with enormous medical and social costs, caused by trisomy for chromosome 21. We tested the concept that gene imbalance across an extra chromosome can be de facto corrected by manipulating a single gene, XIST (the X-inactivation gene). Using genome editing with zinc finger nucleases, we inserted a large, inducible XIST transgene into the DYRK1A locus on chromosome 21, in Down's syndrome pluripotent stem cells.

View Article and Find Full Text PDF

The proper functioning of centromeres requires a complex cascade of epigenetic events involving chromatin and kinetochore assembly; however, the precise mechanism by which this cascade proceeds is unknown. The pivotal event during kinetochore formation is the "loading," or deposition, of CENP-A. This histone H3 variant is specific to centromeres and replaces conventional H3 in centromeric chromatin.

View Article and Find Full Text PDF

The eukaryotic genome is packaged into a highly ordered chromatin structure, with specific domains regulating the transcription patterns of local genes. Hathaway et al. now present a breakthrough technique in the artificial induction of chromatin marks and use this experimental model to test the properties of an induced heterochromatic domain.

View Article and Find Full Text PDF

Epigenetic information can be inherited through the mammalian germline and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet. Offspring of males fed a low-protein diet exhibited elevated hepatic expression of many genes involved in lipid and cholesterol biosynthesis and decreased levels of cholesterol esters, relative to the offspring of males fed a control diet.

View Article and Find Full Text PDF

The transcriptional framework of the eukaryotic centromere core has been described in budding yeast and rice, but for most eukaryotes and all vertebrates it remains largely unknown. The lack of large pericentric repeats in the tammar wallaby has made it possible to map and identify the transcriptional units at the centromere in a mammalian species for the first time. We show that these transcriptional units, comprised of satellites and a retrovirus, are bound by centromere proteins and that they are the source of a novel class of small RNA.

View Article and Find Full Text PDF

Background: Parent-specific methylation of specific CpG residues is critical to imprinting in eutherian mammals, but its importance to imprinting in marsupials and, thus, the evolutionary origins of the imprinting mechanism have been the subject of controversy. This has been particularly true for the imprinted Insulin-like Growth Factor II (IGF2), a key regulator of embryonic growth in vertebrates and a focal point of the selective forces leading to genomic imprinting. The presence of the essential imprinting effector, DNMT3L, in marsupial genomes and the demonstration of a differentially methylated region (DMR) in the retrotransposon-derived imprinted gene, PEG10, in tammar wallaby argue for a role for methylation in imprinting, but several studies have found no evidence of parent-specific methylation at other imprinted loci in marsupials.

View Article and Find Full Text PDF

Certain neurobehavioral deficiencies associated with Turner Syndrome have been attributed to brain volumetric abnormalities, particularly of the amygdala. Haplo-insufficiency of a non-dosage compensated gene or genes on the X chromosome has been hypothesized to be the cause of the neuroanatomical defect. We examined gene expression levels of 6,628 genes in developing amygdalae of late-stage embryos of a mouse model for Turner Syndrome.

View Article and Find Full Text PDF