Slaughterdencker0903

Genome-scale metabolic models (GEMs) are comprehensive knowledge bases of cellular metabolism and serve as mathematical tools for studying biological phenotypes and metabolic states or conditions in various organisms and cell types. Given the sheer size and complexity of human metabolism, selecting parameters for existing analysis methods such as metabolic objective functions and model constraints is not straightforward in human GEMs. In particular, comparing several conditions in large GEMs to identify condition- or disease-specific metabolic features is challenging. In this study, we showcase a scalable, model-driven approach for an in-depth investigation and comparison of metabolic states in large GEMs which enables identifying the underlying functional differences. Using a combination of flux space sampling and network analysis, our approach enables extraction and visualisation of metabolically distinct network modules. Importantly, it does not rely on known or assumed objective functions. We apply this novel approach to extract the biochemical differences in adipocytes arising due to unlimited vs blocked uptake of branched-chain amino acids (BCAAs, considered as biomarkers in obesity) using a human adipocyte GEM (iAdipocytes1809). The biological significance of our approach is corroborated by literature reports confirming our identified metabolic processes (TCA cycle and Fatty acid metabolism) to be functionally related to BCAA metabolism. Additionally, our analysis predicts a specific altered uptake and secretion profile indicating a compensation for the unavailability of BCAAs. Taken together, our approach facilitates determining functional differences between any metabolic conditions of interest by offering a versatile platform for analysing and comparing flux spaces of large metabolic networks.Gene editing in C. elegans using plasmid-based CRISPR reagents requires microinjection of many animals to produce a single edit. Germline silencing of plasmid-borne Cas9 is a major cause of inefficient editing. Here, we present a set of C. elegans strains that constitutively express Cas9 in the germline from an integrated transgene. These strains markedly improve the success rate for plasmid-based CRISPR edits. For simple, short homology arm GFP insertions, 50-100% of injected animals typically produce edited progeny, depending on the target locus. Template-guided editing from an extrachromosomal array is maintained over multiple generations. We have built strains with the Cas9 transgene on multiple chromosomes. Additionally, each Cas9 locus also contains a heatshock-driven Cre recombinase for selectable marker removal and a bright fluorescence marker for easy outcrossing. These integrated Cas9 strains greatly reduce the workload for producing individual genome edits.We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.Cortical pyramidal cells (PCs) have a specialized dendritic mechanism for the generation of bursts, suggesting that these events play a special role in cortical information processing. In vivo, bursts occur at a low, but consistent rate. Theory suggests that this network state increases the amount of information they convey. However, because burst activity relies on a threshold mechanism, it is rather sensitive to dendritic input levels. In spiking network models, network states in which bursts occur rarely are therefore typically not robust, but require fine-tuning. Here, we show that this issue can be solved by a homeostatic inhibitory plasticity rule in dendrite-targeting interneurons that is consistent with experimental data. The suggested learning rule can be combined with other forms of inhibitory plasticity to self-organize a network state in which both spikes and bursts occur asynchronously and irregularly at low rate. Finally, we show that this network state creates the network conditions for a recently suggested multiplexed code and thereby indeed increases the amount of information encoded in bursts.Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.Several studies have revealed a correlation between chronic inflammation and nicotinamide adenine dinucleotide (NAD+) metabolism, but the precise mechanism involved is unknown. Here, we report that the genetic and pharmacological inhibition of nicotinamide phosphoribosyltransferase (Nampt), the rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, reduced oxidative stress, inflammation, and keratinocyte DNA damage, hyperproliferation, and cell death in zebrafish models of chronic skin inflammation, while all these effects were reversed by NAD+ supplementation. Similarly, genetic and pharmacological inhibition of poly(ADP-ribose) (PAR) polymerase 1 (Parp1), overexpression of PAR glycohydrolase, inhibition of apoptosis-inducing factor 1, inhibition of NADPH oxidases, and reactive oxygen species (ROS) scavenging all phenocopied the effects of Nampt inhibition. Pharmacological inhibition of NADPH oxidases/NAMPT/PARP/AIFM1 axis decreased the expression of pathology-associated genes in human organotypic 3D skin models of psoriasis. Consistently, an aberrant induction of NAMPT and PARP activity, together with AIFM1 nuclear translocation, was observed in lesional skin from psoriasis patients. selleck products In conclusion, hyperactivation of PARP1 in response to ROS-induced DNA damage, fueled by NAMPT-derived NAD+, mediates skin inflammation through parthanatos cell death.BACKGROUND Renal lymphangiectasia is a rare benign disorder with unknown pathophysiology. Renal lymphangiectasia can affect both males and females with no known age predilection. Its diagnosis can be accomplished with radiological images and confirmed by aspiration of lymphatic fluid in certain cases. However, there is no clear presentation to be relied on, apart from incidental findings or presentation of complications, such as hypertension due to mass effect on the kidney or renal failure from chronic compression and obstruction or renal vein thrombosis. Management is directed toward symptomatic relief and protection of the kidneys from failure or obstruction. The timing of possible complications and the duration of conservative therapy are undetermined. CASE REPORT Here, we present a case of a healthy 39-year-old woman with bilateral renal lymphangiectasia. It was initially discovered and confirmed to be lymphangiectasia when she was 13 years old and underwent bilateral renal aspiration. She recently presented to the Emergency Department with abdominal symptoms that were found to be caused by diverticulitis. The radiological images showed the persistence of her previous diagnosis of bilateral renal lymphangiectasia. She has had the same condition for more than 25 years, with no related complications or further intervention beyond conservative management. CONCLUSIONS Renal lymphangiectasia has a benign long-term course with insignificant and minor effects in certain patients regardless of the considerable size of cysts and bilateral involvement of the kidneys. The findings of our case could reassure patients with a diagnosis of a similar condition.Background Overweight and obesity are strongly implicated in breast cancer (BC) development and are also a risk factor for BC-related lymphedema (BCRL). Materials and Methods An online cross-sectional survey was conducted between November 2017 and January 2018. Analyses were restricted to women with localized BC, who provided information about BCRL (n = 238). Most women were not experiencing BCRL (55.46%). Results Mean self-reported weight at diagnosis was 68.55 kg for women without BCRL and 74.43 kg for women with BCRL (p = 0.0021). In this study, 50.9% with BCRL were overweight/obese at diagnosis (body mass index [BMI] ≥25) compared with 36.4% of women without BCRL (p = 0.003). For women without BCRL, 12.12% were classified as obese (BMI ≥30) versus 20.75% with BCRL. Women with BCRL were more likely to have gained >5% of body weight (p = 0.03), be currently overweight or obese (p = 0.004), and less active (48.11%) than they were at diagnosis than women without BCRL (33.33%) (p = 0.042). Having a structured exercise program, following a prescribed diet, and being accountable to someone else were identified as the main facilitators to successful weight loss and weight maintenance. Conclusions Clinicians should consider obesity when personalizing axillary treatment and encourage lifestyle interventions and lymphedema screening after BC treatment.Background The Nuss procedure has provided a minimally invasive surgical solution for pectus excavatum with excellent long-term outcomes. However, opioid avoidance, cost reduction, and length of stay (LOS) still offer room for improvement. The focus of this study is to identify the impact of Bupivacaine liposome injectable suspension (Exparel) on outcomes. Methods A retrospective review at a Pediatric specialty hospital from October 1, 2014 to December 31, 2019 was performed. All patients underwent a Nuss procedure (n = 19) for pectus excavatum. The cohort comprised a control group that did not use liposomal Bupivacaine (Standard, n = 9) and an interventional group that received liposomal Bupivacaine (n = 10). Nonparametric Wilcoxon rank-sum tests and chi-squared or Fisher's exact tests were used to assess significance (P  less then  .05). Results Overall, the entire population was 68.4% male and had an average age of 15 years. There was a significant difference between the Standard and Liposomal Bupivacaine groups for total cost ($60,746 versus $13,289), total Morphine Milligram Equivalents (MME) (282 versus 76.