Can Zipf's law be adapted to normalize microarrays?

BACKGROUND: Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. RESULTS: Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. CONCLUSION: Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays)

Placenta growth factor and vascular endothelial growth factor B expression in the hypoxic lung

<p>Abstract</p> <p>Background</p> <p>Chronic alveolar hypoxia, due to residence at high altitude or chronic obstructive lung diseases, leads to pulmonary hypertension, which may be further complicated by right heart failure, increasing morbidity and mortality. In the non-diseased lung, angiogenesis occurs in chronic hypoxia and may act in a protective, adaptive manner. To date, little is known about the behaviour of individual vascular endothelial growth factor (VEGF) family ligands in hypoxia-induced pulmonary angiogenesis. The aim of this study was to examine the expression of placenta growth factor (PlGF) and VEGFB during the development of hypoxic pulmonary angiogenesis and their functional effects on the pulmonary endothelium.</p> <p>Methods</p> <p>Male Sprague Dawley rats were exposed to conditions of normoxia (21% O₂) or hypoxia (10% O₂) for 1-21 days. Stereological analysis of vascular structure, real-time PCR analysis of vascular endothelial growth factor A (VEGFA), VEGFB, placenta growth factor (PlGF), VEGF receptor 1 (VEGFR1) and VEGFR2, immunohistochemistry and western blots were completed. The effects of VEGF ligands on human pulmonary microvascular endothelial cells were determined using a wound-healing assay.</p> <p>Results</p> <p>Typical vascular remodelling and angiogenesis were observed in the hypoxic lung. PlGF and VEGFB mRNA expression were significantly increased in the hypoxic lung. Immunohistochemical analysis showed reduced expression of VEGFB protein in hypoxia although PlGF protein was unchanged. The expression of VEGFA mRNA and protein was unchanged. <it>In vitro </it>PlGF at high concentration mimicked the wound-healing actions of VEGFA on pulmonary microvascular endothelial monolayers. Low concentrations of PlGF potentiated the wound-healing actions of VEGFA while higher concentrations of PlGF were without this effect. VEGFB inhibited the wound-healing actions of VEGFA while VEGFB and PlGF together were mutually antagonistic.</p> <p>Conclusions</p> <p>VEGFB and PlGF can either inhibit or potentiate the actions of VEGFA, depending on their relative concentrations, which change in the hypoxic lung. Thus their actions <it>in vivo </it>depend on their specific concentrations within the microenvironment of the alveolar wall during the course of adaptation to pulmonary hypoxia.</p

Differential Binding of Co(II) and Zn(II) to Metallo-β-Lactamase Bla2 from \u3cem\u3eBacillus anthracis\u3c/em\u3e

In an effort to probe the structure, mechanism, and biochemical properties of metallo-β-lactamase Bla2 from Bacillus anthracis, the enzyme was overexpressed, purified, and characterized. Metal analyses demonstrated that recombinant Bla2 tightly binds 1 equiv of Zn(II). Steady-state kinetic studies showed that mono-Zn(II) Bla2 (1Zn-Bla2) is active, while di-Zn(II) Bla2 (ZnZn-Bla2) was unstable. Catalytically, 1Zn-Bla2 behaves like the related enzymes CcrA and L1. In contrast, di-Co(II) Bla2 (CoCo-Bla2) is substantially more active than the mono-Co(II) analogue. Rapid kinetics and UV−vis, 1H NMR, EPR, and EXAFS spectroscopic studies show that Co(II) binding to Bla2 is distributed, while EXAFS shows that Zn(II) binding is sequential. To our knowledge, this is the first documented example of a Zn enzyme that binds Co(II) and Zn(II) via distinct mechanisms, underscoring the need to demonstrate transferability when extrapolating results on Co(II)-substituted proteins to the native Zn(II)-containing forms

Smad4-dependent pathways control basement membrane deposition and endodermal cell migration at early stages of mouse development

<p>Abstract</p> <p>Background</p> <p>Smad4 mutant embryos arrest shortly after implantation and display a characteristic shortened proximodistal axis, a significantly reduced epiblast, as well as a thickened visceral endoderm layer. Conditional rescue experiments demonstrate that bypassing the primary requirement for Smad4 in the extra-embryonic endoderm allows the epiblast to gastrulate. Smad4-independent TGF-β signals are thus sufficient to promote mesoderm formation and patterning. To further analyse essential Smad4 activities contributed by the extra-embryonic tissues, and characterise Smad4 dependent pathways in the early embryo, here we performed transcriptional profiling of Smad4 null embryonic stem (ES) cells and day 4 embryoid bodies (EBs).</p> <p>Results</p> <p>Transcripts from wild-type versus Smad4 null ES cells and day 4 EBs were analysed using Illumina arrays. In addition to several known TGF-β/BMP target genes, we identified numerous Smad4-dependent transcripts that are mis-expressed in the mutants. As expected, mesodermal cell markers were dramatically down-regulated. We also observed an increase in non-canonical potency markers (<it>Pramel7</it>, <it>Tbx3</it>, <it>Zscan4</it>), germ cell markers (<it>Aire</it>, <it>Tuba3a</it>, <it>Dnmt3l</it>) as well as early endoderm markers (<it>Dpp4</it>, <it>H19</it>, <it>Dcn</it>). Additionally, expression of the extracellular matrix (ECM) remodelling enzymes <it>Mmp14 </it>and <it>Mmp9 </it>was decreased in Smad4 mutant ES and EB populations. These changes, in combination with increased levels of <it>laminin alpha1</it>, cause excessive basement membrane deposition. Similarly, in the context of the Smad4 null E6.5 embryos we observed an expanded basement membrane (BM) associated with the thickened endoderm layer.</p> <p>Conclusion</p> <p>Smad4 functional loss results in a dramatic shift in gene expression patterns and in the endodermal cell lineage causes an excess deposition of, or an inability to breakdown and remodel, the underlying BM layer. These structural abnormalities probably disrupt reciprocal signalling between the epiblast and overlying visceral endoderm required for gastrulation.</p

Proceedings - U.S.A Agroecology Summit 2023

This docket is a memory of the meeting held in Kansas City from May 22-25 called the 2023 USA Agroecology Summit and contains all the documents generated before, during, and after the meeting

Elevated plasma CXCL12 alpha is associated with a poorer prognosis in pulmonary arterial hypertension.

Recent work in preclinical models suggests that signalling via the pro-angiogenic and proinflammatory cytokine, CXCL12 (SDF-1), plays an important pathogenic role in pulmonary hypertension (PH). The objective of this study was to establish whether circulating concentrations of CXCL12α were elevated in patients with PAH and related to mortalit

Utilization of inhaled nitric oxide after surgical repair of truncus arteriosus: A multicenter analysis

BackgroundElevated pulmonary vascular resistance (PVR) is common following repair of truncus arteriosus. Inhaled nitric oxide (iNO) is an effective yet costly therapy that is frequently implemented postoperatively to manage elevated PVR.ObjectivesWe aimed to describe practice patterns of iNO use in a multicenter cohort of patients who underwent repair of truncus arteriosus, a lesion in which recovery is often complicated by elevated PVR. We also sought to identify patient and center factors that were more commonly associated with the use of iNO in the postoperative period.DesignRetrospective cohort study.Setting15 tertiary care pediatric referral centers.PatientsAll infants who underwent definitive repair of truncus arteriosus without aortic arch obstruction between 2009 and 2016.InterventionsDescriptive statistics were used to demonstrate practice patterns of iNO use. Bivariate comparisons of characteristics of patients who did and did not receive iNO were performed, followed by multivariable mixed logistic regression analysis using backward elimination to identify independent predictors of iNO use.Main ResultsWe reviewed 216 patients who met inclusion criteria, of which 102 (46%) received iNO in the postoperative period: 69 (68%) had iNO started in the operating room and 33 (32%) had iNO initiated in the ICU. Median duration of iNO use was 4 days (range: 1‐21 days). In multivariable mixed logistic regression analysis, use of deep hypothermic circulatory arrest (odds ratio: 3.2; 95% confidence interval: 1.2, 8.4) and center (analyzed as a random effect, p = .02) were independently associated with iNO use.ConclusionsIn this contemporary multicenter study, nearly half of patients who underwent repair of truncus arteriosus received iNO postoperatively. Use of iNO was more dependent on individual center practice rather than patient characteristics. The study suggests a need for collaborative quality initiatives to determine optimal criteria for utilization of this important but expensive therapy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152533/1/chd12849_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152533/2/chd12849.pd

Multicenter Analysis of Early Childhood Outcomes Following Repair of Truncus Arteriosus

Background Literature describing morbidity and mortality following truncus arteriosus repair is predominated by single-center reports. We created and analyzed a multicenter dataset to identify risk factors for late mortality and right ventricle-to-pulmonary artery (RV-PA) conduit reintervention for this patient population. Methods We retrospectively collected data on children who underwent repair of truncus arteriosus without concomitant arch obstruction at 15 centers between 2009 and 2016. Cox regression survival analysis was conducted to determine risk factors for late mortality, defined as death occurring after hospital discharge and greater than 30 days after surgery. Probability of any RV-PA conduit reintervention was analyzed over time using Fine-Gray modelling. Results We reviewed 216 patients, with median follow-up of 2.9 years (range:0.1-8.8). Operative mortaility occurred in 15 patients (7%). Of the 201 survivors, there were 14 (7%) late deaths. DiGeorge syndrome (HR:5.4; 95%CI:1.6-17.8) and need for postoperative tracheostomy (HR:5.9; 95%CI:1.8-19.4) were identified as independent risk factors for late mortality. At least one RV-PA conduit catheterization or surgical reintervention was performed in 109 patients (median time to reintervention:23 months, range:0.3-93). Risk factors for reintervention included use of pulmonary or aortic homografts versus Contegra® bovine jugular vein conduits (HR:1.9; 95%CI:1.2,3.1) and smaller conduit size (HR per mm/m2:1.05; 95%CI:1.03,1.08). Conclusions In a multicenter dataset, DiGeorge syndrome and need for tracheostomy postoperatively were found to be independent risk factors for late mortality after repair of truncus arteriosus, while risk of conduit reintervention was independently influenced by both initial conduit type and size

Proceedings of the Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) Oligodendroglioma Workshop.

Background: Oligodendroglioma is a rare primary central nervous system (CNS) tumor with highly variable outcome and for which therapy is usually not curative. At present, little is known regarding the pathways involved with progression of oligodendrogliomas or optimal biomarkers for stratifying risk. Developing new therapies for this rare cancer is especially challenging. To overcome these challenges, the neuro-oncology community must be particularly innovative, seeking multi-institutional and international collaborations, and establishing partnerships with patients and advocacy groups thereby ensuring that each patient enrolled in a study is as informative as possible. Methods: The mission of the National Cancer Institute\u27s NCI-CONNECT program is to address the challenges and unmet needs in rare CNS cancer research and treatment by connecting patients, health care providers, researchers, and advocacy organizations to work in partnership. On November 19, 2018, the program convened a workshop on oligodendroglioma, one of the 12 rare CNS cancers included in its initial portfolio. The purpose of this workshop was to discuss scientific progress and regulatory challenges in oligodendroglioma research and develop a call to action to advance research and treatment for this cancer. Results: The recommendations of the workshop include a multifaceted and interrelated approach covering: biology and preclinical models, data sharing and advanced molecular diagnosis and imaging; clinical trial design; and patient outreach and engagement. Conclusions: The NCI-CONNECT program is well positioned to address challenges in oligodendroglioma care and research in collaboration with other stakeholders and is developing a list of action items for future initiatives