Reconstructing dynamic regulatory maps

Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein–DNA interactions that allows the specific regulation of genes needed for the response. We have developed a novel computational method that uses an input–output hidden Markov model to model these regulatory networks while taking into account their dynamic nature. Our method works by identifying bifurcation points, places in the time series where the expression of a subset of genes diverges from the rest of the genes. These points are annotated with the transcription factors regulating these transitions resulting in a unified temporal map. Applying our method to study yeast response to stress, we derive dynamic models that are able to recover many of the known aspects of these responses. Predictions made by our method have been experimentally validated leading to new roles for Ino4 and Gcn4 in controlling yeast response to stress. The temporal cascade of factors reveals common pathways and highlights differences between master and secondary factors in the utilization of network motifs and in condition-specific regulation

Mortality in Peripheral Arterial Disease: A Comparison of Patients Managed by Vascular Specialists and General Practitioners

BACKGROUND: Peripheral arterial disease (PAD) is undertreated by general practitioners (GPs). However, the impact of the suboptimal clinical management is unknown. OBJECTIVE: To assess the mortality rate of PAD patients in relation to the type of physician who provides their care (GP or vascular specialist). DESIGN: Prospective study. SETTING: Primary care practice and academic vascular laboratory. PARTICIPANTS: GP patients (n = 60) were those of the Peripheral Arteriopathy and Cardiovascular Events study (PACE). Patients managed by specialists (n = 82) were consecutive subjects with established PAD who were referred to our vascular laboratory during the enrolment period of the PACE study. MEASUREMENTS: All-cause and cardiovascular mortality. RESULTS: After 32 months of follow-up, specialist management was associated with a lower rate of all-cause mortality (RR = 0.04; 95% CI 0.01–0.34; p = .003) and cardiovascular mortality (RR = 0.07; 95% CI 0.01–0.65; p = .020), after adjustment for patients’ characteristics. Specialists were more likely to use antiplatelet agents (93% vs 73%, p < .001), statins (62% vs 25%, p < .001) and beta blockers (28% vs 3%, p < .001). Survival differences between specialists and GPs disappeared once the use of pharmacotherapies was added to the proportional hazard model. The fully adjusted model showed that the use of statins was significantly associated with a reduced risk of all-cause mortality (RR = 0.02; 95% CI 0.01–0.73, p = .034) and cardiovascular mortality (RR = 0.02; 95% CI 0.01–0.71, p = .033). CONCLUSIONS: Specialist management of patients with symptomatic PAD resulted in better survival than generalist management. This effect appears to be mainly caused by the more frequent use of effective medicines by specialists

Evaluation and optimization of a commercial enzyme linked immunosorbent assay for detection of Chlamydophila pneumoniae IgA antibodies

<p>Abstract</p> <p>Background</p> <p>Serologic diagnosis of <it>Chlamydophila pneumoniae </it>(Cpn) infection routinely involves assays for the presence of IgG and IgM antibodies to Cpn. Although IgA antibodies to Cpn have been found to be of interest in the diagnosis of chronic infections, their significance in serological diagnosis remains unclear. The microimmunofluorescence (MIF) test is the current method for the measurement of Cpn antibodies. While commercial enzyme linked immunosorbent assays (ELISA) have been developed, they have not been fully validated. We therefore evaluated and optimized a commercial ELISA kit, the SeroCP IgA test, for the detection of Cpn IgA antibodies.</p> <p>Methods</p> <p>Serum samples from 94 patients with anti-Cpn IgG titers ≥ 256 (study group) and from 100 healthy blood donors (control group) were tested for the presence of IgA antibodies to Cpn, using our in-house MIF test and the SeroCP IgA test. Two graph receiver operating characteristic (TG-ROC) curves were created to optimize the cut off given by the manufacturer.</p> <p>Results</p> <p>The MIF and SeroCP IgA tests detected Cpn IgA antibodies in 72% and 89%, respectively, of sera from the study group, and in 9% and 35%, respectively, of sera from the control group. Using the MIF test as the reference method and the cut-off value of the ELISA test specified by the manufacturer for seropositivity and negativity, the two tests correlated in 76% of the samples, with an agreement of Ƙ = 0.54. When we applied the optimized cut-off value using TG-ROC analysis, 1.65, we observed better concordance (86%) and agreement (0.72) between the MIF and SeroCP IgA tests.</p> <p>Conclusion</p> <p>Use of TG-ROC analysis may help standardize and optimize ELISAs, which are simpler, more objective and less time consuming than the MIF test. Standardization and optimization of commercial ELISA kits may result in better performance.</p

Effect of plasmin, plasminogen activators and a plasmin inhibitor on bovine in vitro embryo production

In the present study, four experiments were conducted to investigate the possible effects of plasminogen activators (urokinase-type plasminogen activator (u-PA) and tissue-type plasminogen activator (t-PA)), plasmin, and a plasmin inhibitor (epsilon-aminocaproic acid (epsilon-ACA)) on different stages of bovine in vitro embryo production (IVP). The concentrations of these modifiers in IVP media were conditioned according to the plasminogen activator activity of bovine preovulatory follicular fluid. Media were modified in a single phase of IVP with an 18 h or 24 h incubation for in vitro maturation (IVM) and a 24 h or 48 h incubation for the IVF or in vitro culture (IVC), respectively. After IVM the oocytes were either fixed and stained or underwent IVF and IVC. The main findings were: (1) plasmin added to the 18 h IVM medium increased maturation rate without affecting fertilisation or embryo development rates; (2) t-PA added to the IVF medium significantly increased cleavage; (3) u-PA added to the IVC medium significantly increased embryo development rates; (4) the efficiency of all phases of IVP was reduced after the addition of epsilon-ACA; and (5) plasminogen addition had no effect in any IVP phase tested. We conclude that the members of the plasminogen activator-plasmin system contribute in different ways to bovine IVM, IVF and IVC

Plasminogen activator activity and plasminogen activator inhibition in the uterus of ewes after the induction of oestrus synchronization or superovulation, involving eCG

During the preimplantation period, early mammalian embryos largely depend on uterine environment. Concurrently, uterine architecture undergoes substantial growth and remodeling under the influence of ovarian steroids. Plasminogen activators/plasmin proteolytic system that is implicated in tissue remodeling is affected by reproductive hormone variations. Thus, hormone treatments for reproductive function control possibly influence proteolytic enzyme activity in the reproductive tract and its study in uterine fluid and endometrium could demonstrate possible changes in uterine environment. This work examines (a) the effect of hormone treatment involving eCG in the dosage used for oestrus synchronization or for superovulation on plasminogen activator activity (PAA) and plasminogen activator inhibition (PAI) in the uterus of ewes before maternal recognition of pregnancy and (b) the possible relationships among blood ovarian steroid concentration, proteolytic enzyme activity and ovarian response/embryo yield. Chios ewes (n = 24) were treated with progestagen intravaginal sponges for 12 days and eCG (500 or 1000 IU) at sponge removal; ewes at the second oestrus after synchronization were used as controls. On day 6 of the oestrous cycle, after slaughter, ovarian response was assessed and embryos were collected; uterine horn flushings (UHF), caruncular endometrium (CE) and intercaruncular (ICE) endometrium samples were collected, for PAA and PAI photometrical assessment. Oestradiol-17β (E2) and progesterone (P4) concentration was assessed in blood serum samples collected before slaughter by a radioimmunoassay. A significant increase of PAA in the UHF was observed after treatment; PAA in UHF was significantly associated with the number of embryos or high-quality embryos, while PAA in UHF per embryo or high-quality embryo was not affected by treatment. No significant effect of treatment was noticed on PAA or PAI in the endometrium (CE, ICE). In UHF and in ICE, PAI against tissue-type PA had a significant positive relationship with PAI against urokinase-type PA. PAI against tissue-type PA in CE had significant negative relationship with E2 concentration. In conclusion, hormone treatment involving eCG in the dosage used for superovulation and, to a lesser degree, in the dosage used for oestrus synchronization affected PAA in the uterus of Chios ewes, before maternal recognition of pregnancy, but did not seem to disturb reproductive function. © 2022 Elsevier B.V