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PubMed2025

CNV-Finder: Streamlining Copy Number Variation Discovery.

Copy Number Variations (CNVs) play pivotal roles in the etiology of complex diseases and are variable across diverse populations. Understanding the association between CNVs and disease susceptibility is significant in disease genetics research and often requires analysis of large sample sizes. One of the most cost-effective and scalable methods for detecting CNVs is based on normalized signal intensity values, such as Log R Ratio (LRR) and B Allele Frequency (BAF), from Illumina genotyping arrays. In this study, we present CNV-Finder, a novel pipeline integrating deep learning techniques on array data, specifically a Long Short-Term Memory (LSTM) network, to expedite the large-scale identification of CNVs within predefined genomic regions. This facilitates efficient prioritization of samples for time-consuming or costly subsequent analyses such as Multiplex Ligation-dependent Probe Amplification (MLPA), short-read, and long-read whole genome sequencing. We incorporate four genes to establish our methods-Parkin (PRKN), Leucine Rich Repeat And Ig Domain Containing 2 (LINGO2), Microtubule Associated Protein Tau (MAPT), and alpha-Synuclein (SNCA)-which may be relevant to neurological diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Progressive Supranuclear Palsy (PSP), or related disorders such as essential tremor (ET). By training our models on expert-annotated samples and validating them across diverse cohorts, including those from the Global Parkinson's Genetics Program (GP2) and additional dementia-specific databases, we demonstrate the efficacy of CNV-Finder in accurately detecting deletions and duplications. Our pipeline outputs app-compatible files for visualization within CNV-Finder's interactive web application. This interface enables researchers to review predictions and filter displayed samples by model prediction values, LRR range, and variant count in order to explore or confirm results. Our pipeline integrates this human feedback to enhance model performance and reduce false positive rates. Through a series of comprehensive analyses and validations using visual inspection, MLPA, short-read, and long-read sequencing data, we demonstrate the robustness and adaptability of CNV-Finder in identifying CNVs with regions of varied size, probe density, and noise. Our findings highlight the significance of contextual understanding and human expertise in enhancing the precision of CNV identification, particularly in complex genomic regions like 17q21.31. The CNV-Finder pipeline is a scalable, publicly available resource for the scientific community, available on GitHub (https://github.com/GP2code/CNV-Finder; DOI 10.5281/zenodo.14182563). CNV-Finder not only expedites accurate candidate identification but also significantly reduces the manual workload for researchers, enabling future targeted validation and downstream analyses in regions or phenotypes of interest.

Copy Number Variation (CNV)↗
PubMed2005

Inheritance of the F4ab, F4ac and F4ad E. coli receptors in swine and examination of four candidate genes for F4acR.

Susceptibility to enterotoxigenic Escherichia coli with fimbriae F4ac is dominantly inherited in the pig. A three-generation pedigree was created to refine the position of F4acR on chromosome 13 comprising 202 pigs: eight parents, 18 F1 and 176 F2 pigs. The 17-point analysis indicates that F4acR lies between Sw207 and S0283. Recombinant offspring specify that the most probable order is Sw207-S0075-F4acR-Sw225-S0283. We observed six phenotypes for the three fimbrial variants F4ab, F4ac and F4ad. The two missing phenotypes F4abR-/F4acR+/F4adR+ and F4abR-/F4acR+/F4adR- indicate that pigs susceptible to F4ac are always susceptible to F4ab. Furthermore, a weak and a strong adhesion of F4ab and F4ad bacteria was observed. The weak receptor F4abR (F4abRw) was present only in pigs devoid of the receptor F4acR (F4abR+/F4acR-). In contrast, in pigs with the phenotype F4abR+/F4acR+, F4ab bacteria adhered to the majority of enterocytes. F4abRw constitutes a frequently observed phenotype whose inheritance is still unclear. Strong adhesion of F4ab and F4ac bacteria is most likely influenced by the same receptor that we name F4bcR. The number of F4ad bacteria that adhered to enterocytes was very variable in the adhesion test. Moreover, expression of F4adR was independent of age. Our segregation analyses indicated a dominant inheritance of F4adR, although the number of susceptible pigs was smaller than expected. We examined four genes as candidates for the F4acR locus: the transferrin receptor gene (TFRC) and three genes members of the glucosyl/galactosyltransferase family (B3GnT5, B3GALT3 and B4GALT4). Comparison of sequences from resistant and homozygous susceptible F4ac pigs did not reveal any causative single nucleotide polymorphism in the four genes. Two silent mutations at the positions 295 (C/T) and 313 (T/C) in B3GALT3 were found. Using the somatic cell hybrid panel, B3GnT5 and B3GALT3 were assigned to the chromosomal region SSC13q23-q41. No mutations were found in the cDNA sequences of these genes associated with the F4acR genotypes.

Animals↗
PubMed2005

Effect of acute body positional changes on the haemodynamics of rats with and without myocardial infarction.

In humans, the lateral recumbent position has a beneficial effect on haemodynamics. If this effect is substantial in small animals too, there is a risk of misinterpretation in preclinical investigations. Therefore, the aim of this study was to analyse the impact of acute changes in body position on haemodynamics in rats. Healthy rats (n=21) and rats post myocardial infarction (n=20) were randomly positioned supine, prone, or on the right or left side. In each position, we measured haemodynamic parameters by pressure-tip catheter and thermodilution. We found that left ventricular contractility (dP/dtmax) was significantly elevated in both lateral positions as compared to the supine position in healthy rats. In healthy rats and following infarction, cardiac index (CI) and stroke volume index (SVI) were significantly higher in both lateral positions as compared to the supine or prone position. Of importance, if SVI values in the supine position in healthy rats (0.095 +/- 0.003 ml (100 g)(-1)) are compared to SVI values measured in different positions after myocardial infarction, the SVI can be either significantly lower in the supine (0.084 +/- 0.003 ml (100 g)(-1)) or significantly higher in the left lateral position (0.105 +/- 0.003 ml (100 g)(-1)). We conclude that post myocardial infarction and in healthy control rats, important haemodynamic values are increased in lateral positions as compared to prone or supine positions. Analysing haemodynamic data in rats may therefore result in misinterpretation if the body position is inconsistent.

Algorithms↗
PubMed1996

Identification of yeast Rho1p GTPase as a regulatory subunit of 1,3-beta-glucan synthase.

1,3-beta-D-glucan synthase [also known as beta(1-->3) glucan synthase] is a multi-enzyme complex that catalyzes the synthesis of 1,3-beta-linked glucan, a major structural component of the yeast cell wall. Temperature-sensitive mutants in the essential Rho-type guanosine triphosphatase (GTPase), Rho1p, displayed thermolabile glucan synthase activity, which was restored by the addition of recombinant Rho1p. Glucan synthase from mutants expressing constitutively active Rho1p did not require exogenous guanosine triphosphate for activity. Rho1p copurified with beta(1-->3)glucan synthase and associated with the Fks1p subunit of this complex in vivo. Both proteins were localized predominantly at sites of cell wall remodeling. Therefore, it appears that Rho1p is a regulatory subunit of beta(1-->3)glucan synthase.

GTP Phosphohydrolases↗
PubMed2005

Prevalence of victims of violence admitted to an emergency department.

OBJECTIVE: To collect data on the consultation frequency and demographic profile of victims of violence attending an emergency department (ED) in Switzerland. METHODS: We undertook screening of all admitted adult patients (>16 years) in the ED of the CHUV, Lausanne, Switzerland, over a 1 month period, using a modified version of the Partner Violence Screen questionnaire. Exclusionary criteria were: life threatening injury (National Advisory Committee on Aeronautics score > or =4), or inability to understand or speak French, to give oral informed consent, or to be questioned without a family member or accompanying person being present. Data were collected on history of physical and/or psychological violence during the previous 12 months, the type of violence experienced by the patient, and if violence was the reason for the current consultation. Sociodemographic data were obtained from the registration documents. RESULTS: The final sample consisted of 1602 patients (participation rate of 77.2%), with a refusal rate of 1.1%. Violence during the past 12 months was reported by 11.4% of patients. Of the total sample, 25% stated that violence was the reason for the current consultation; of these, 95% of patients were confirmed as victims of violence by the ED physicians. Patients reporting violence were more likely to be young and separated from their partner. Men were more likely to be victims of public violence and women more commonly victims of domestic violence. CONCLUSIONS: Based on this monthly prevalence rate, we estimate that over 3000 adults affected by violence consult our ED per annum. This underlines the importance of the problem and the need to address it. Health services organisations should establish measures to improve quality of care for victims. Guidelines and educational programmes for nurses and physicians should be developed in order to enhance providers' skills and basic knowledge of all types of violence, how to recognise and interact appropriately with victims, and where to refer these patients for follow up care in their local networks.

Adolescent↗
PubMed1999

Psychogenetically selected (Roman high- and low-avoidance) rats differ in 24-hour sleep organization.

A comparison of sleep organization in Roman high-(RHA/Verh) and low-(RLA/Verh) avoidance rats, which differ in the way they respond to environmental stimuli and in several neuroendocrine and neurochemical parameters, was carried out. EEG-sleep recordings were obtained from adult males over 12:12 light-dark periods to determine how these two psychogenetically selected rat lines might also differ in their sleep-wake cycle. There was no significant difference in total sleep time between the two lines. However, the (hypoemotional) RHA/Verh rats showed an overall increase (percentage of total sleep) in paradoxical sleep (PS) duration, with a concomitant decrease in slow-wave sleep (SWS). During the dark phase, RHA/Verh rats showed a shorter PS latency and a larger number of PS episodes. Hourly sleep scoring also revealed a more discontinuous pattern (total sleep and PS vs. SWS) during the dark phase in RHA/Verh rats. In relation to recognized neurochemical and neuroendocrine differences between them, these rat lines may prove useful in investigations of the neurobiological mechanisms underlying sleep regulation.

Animals↗
PubMed1993

Blocking T-type calcium channels with tetrandrine inhibits steroidogenesis in bovine adrenal glomerulosa cells.

Tetrandrine, an alkaloid extracted from a Chinese medicinal herb traditionally used in hypertension treatment, inhibited aldosterone production induced in bovine adrenal glomerulosa cells by either potassium ion, angiotensin II, or ACTH in a concentration-dependent manner (IC50 = 10 microM). The inhibition of the response to potassium by tetrandrine had a pattern very similar to that of nickel, a blocker of T-type calcium channels. In addition, tetrandrine prevented calcium influx induced by potassium or angiotensin II without affecting the calcium release phase stimulated by the hormone. The effect of tetrandrine on voltage-activated barium currents was investigated using the whole cell configuration of the patch clamp technique. T-type currents were isolated by recording the slowly deactivating currents elicited during repolarization of the cell to -65 mV after various depolarizing pulses. These currents were blocked by micromolar concentrations of the drug. The voltage sensitivity of channel activation was not affected by tetrandrine; nevertheless, the drug significantly slowed the deactivation of the current. The action of tetrandrine did not require the activation of the channel. Tetrandrine also affected L-type currents, as assessed after inactivating T channels for 100 msec, but at higher concentrations of the drug. Thus, tetrandrine affects with a similar potency aldosterone production, calcium influx, and T-type calcium channel activity. This finding strongly suggests a role for these channels in calcium signaling and control of steroidogenesis in adrenal glomerulosa cells.

Adrenocorticotropic Hormone↗
PubMed1993

Peripheral-type benzodiazepines inhibit calcium channels and aldosterone production in adrenal glomerulosa cells.

Angiotensin-II (Ang-II), K+, and ACTH are important stimulators of aldosterone secretion that require Ca2+ influx to be active. However, Ang-II and K+ are linked to the Ca2+ messenger system, while ACTH is coupled to the cAMP pathway. Peripheral-type binding sites for benzodiazepines are particularly abundant in steroidogenic tissues and have been proposed to be involved in the steroidogenic action of ACTH in Y-1 adrenocortical cells. We report here that in adrenal glomerulosa cells, peripheral-type [4'-chlor-diazepam (CDZ), 1-(2-chlorophenyl)N-methyl-N-(1-methylpropyl)3-isoquinolinecarboxamid e (RP 52028), and flunitrazepam], but not a central-type (flumazenil) benzodiazepine reversibly abolished the stimulation of aldosterone output induced by Ang-II or K+, while they had no significant effect on basal aldosterone secretion. This inhibitory effect depended upon drug concentration (IC50 30 microM for CDZ) and affected the potencies of both stimulators, without altering their respective EC50 values. Similar results were obtained when aldosterone production was stimulated with ACTH, forskolin, or (Bu)2cAMP. Aldosterone production from exogenous 25-hydroxycholesterol or progesterone was partially inhibited by CDZ. In glomerulosa cells loaded with a fluorescent Ca2+ probe, benzodiazepines blocked Ca2+ influx triggered by K+ or Ang-II without affecting the release of Ca2+ from intracellular stores induced by Ang-II. T- and L-type Ca2+ channel activities, monitored with the patch-clamp technique, were both inhibited within the same range of concentrations as aldosterone synthesis and Ca2+ influx. These results indicate that in adrenal zona glomerulosa cells, peripheral-type benzodiazepines block Ca2+ influx through voltage-activated channels. The combined action of peripheral-type benzodiazepines on calcium influx and precursor conversion may be responsible for the observed inhibition of Ang-II-, K(+)-, or ACTH-induced aldosterone secretion.

Aldosterone↗
PubMed1993

Angiotensin-II induces changes in the cytosolic sodium concentration in bovine adrenal glomerulosa cells: involvement in the activation of aldosterone biosynthesis.

The homeostasis of cytosolic free calcium ([Ca2+]i) and intracellular free sodium ([Na+]i) are linked in many cell types. We, therefore, studied the effect on [Na+]i of two physiological stimulators of aldosterone synthesis that trigger the calcium messenger system, angiotensin-II (Ang II) and potassium ion (K+), in cultured bovine adrenal glomerulosa cells, using the intracellular fluorescent probe for sodium, sodium benzofuran isophthalate. Ang II induced a concentration-dependent and sustained increase in [Na+]i, from a resting value of 9.2 +/- 3.5 to a maximum of 48.5 +/- 5.5 mM (n = 14). This [Na+]i response was mediated by receptors of the AT1 subtype, because it was abolished by losartan (DuP 753). K+ (15 mM) induced a weaker [Na+]i response, from 5.9 +/- 2.6 to 16.8 +/- 2.5 mM (n = 9). In freshly prepared cells, basal [Na+]i was significantly higher (23.9 +/- 1.8 mM; n = 14; P < 0.01) than in cultured cells. Atrial natriuretic peptide, which is known to affect sodium transport in various cell types, did not alter the [Na+]i response elicited by Ang II. Ethylisopropylamiloride, an inhibitor of Na+/H+ exchange, and dichlorobenzamyl, an inhibitor of Na+/Ca2+ exchange, both inhibited in a concentration-dependent manner the Ang II- and K(+)-induced aldosterone response. Isoosmotic replacement of extracellular Na+ markedly reduced basal aldosterone synthesis. Under these conditions, the concentration-response curve for Ang II-induced aldosterone synthesis was shifted to the right, and its maximum was strikingly diminished. These results show that Ang II and, to a lesser extent, K+ induce significant changes in [Na+]i in bovine glomerulosa cells. These [Na+]i changes probably occur through the Na+/H+ and Na+/Ca2+ exchangers and are likely to play a role in activation of the steroidogenic cascade.

Aldosterone↗
PubMed1994

Role of the capacitative calcium influx in the activation of steroidogenesis by angiotensin-II in adrenal glomerulosa cells.

Angiotensin-II (AngII)-induced Ca2+ influx in adrenal glomerulosa cells, a signal necessary for the stimulation of steroidogenesis by the hormone, is believed to involve two distinct mechanisms: 1) opening of voltage-operated Ca2+ channels, and 2) activation of a capacitative Ca2+ entry pathway that is dependent on calcium release from intracellular stores. Nicardipine, a dihydropyridine calcium antagonist, has been used to investigate the role of these Ca2+ entry mechanisms in the steroidogenic response to AngII. As demonstrated with the patch-clamp technique, micromolar concentrations of nicardipine completely blocked voltage-operated Ca2+ channel activity of both T- and L-types. This agent similarly inhibited the rise of cytosolic free calcium concentration induced by potassium, but did not significantly affect the response to thapsigargin, an activator of the capacitative pathway. Nicardipine reduced by only 22% the calcium influx stimulated by AngII, and the nicardipine-insensitive part of this response was abolished after exhausting the intracellular Ca2+ stores with thapsigargin. Similarly, aldosterone secretion induced by AngII was only partially inhibited (40%) by nicardipine at concentrations that completely abolished the steroidogenic response to potassium. Thapsigargin by itself was able to stimulate aldosterone production, an action highly potentiated by physiological concentrations of extracellular potassium. These data strongly suggest that the major part of the calcium influx response to AngII, leading to aldosterone formation, involves a capacitative calcium entry pathway activated by the release of calcium from intracellular stores. This mechanism of calcium influx could be responsible for some features of aldosterone response to the hormone, such as its poor sensitivity to dihydropyridines or its potentiation by potassium.

Aldosterone↗
PubMed1996

Possible role for mitochondrial calcium in angiotensin II- and potassium-stimulated steroidogenesis in bovine adrenal glomerulosa cells.

In adrenal zona glomerulosa cells, the action of angiotensin II (Ang II) and of potassium (K+) on aldosterone synthesis is mediated by the Ca2+ messenger system. The major part of the steroidogenic pathway takes place inside the mitochondria, and Ca2+ must enter the mitochondrial matrix to stimulate the steroidogenic cascade. To examine how changes in the cytosolic free calcium concentration ([Ca2+]c) induced by Ang II and K+ are relayed into the mitochondrial matrix, we transfected bovine adrenal zona glomerulosa cells in primary culture with a chimeric complementary DNA encoding for the signal presequence targeting human cytochrome c oxidase subunit VIII to the matrix, linked to a complementary DNA coding for the Ca2+-sensitive photoprotein aequorin. Resting mitochondrial free calcium concentration ([Ca2+]m) amounted to 0.41 +/- 0.18 microM (n = 40). Ang II induced a concentration-dependent (EC50 = 11.3 +/- 6.0 nM), biphasic rise of [Ca2+]m. After a large transient initial peak (5.13 +/- 0.89 microM, n = 28), [Ca2+]m decreased to a plateau that remained higher than basal [Ca2+]m for several minutes in the presence of the hormone. By contrast, studies in cells transfected with cytosolic aequorin indicated that the rise of [Ca2+]c triggered by Ang II was confined to 1.34 +/- 0.26 microM (n = 17). In Ca2+-free medium, a reduced peak [Ca2+]m response to Ang II occurred without a secondary plateau. On readdition of extracellular Ca2+, in the presence of the hormone, the resulting Ca2+ influx was accompanied by small rise of [Ca2+]m. The mitochondrial uncoupler, carbonyl cyanide p-(trifluoro-methoxy)phenyl-hydrazone, prevented the Ang II-induced [Ca2+]m rise but not the [Ca2+]c response, thus demonstrating the mitochondrial location of transfected aequorin. In contrast to Ang II, K+ (13 mM) induced a sustained [Ca2+]c response, which was relayed without amplification into the mitochondrial matrix as a plateau of[Ca2+]m. This plateau of[Ca2+]m was suppressed by the addition of the dihydropyridine, nifedipine (200 nM). The inhibitor of the mitochondrial Na+/Ca2+ exchanger, CGP37157, reduced significantly the rate of decrease of [Ca2+]m following the peak induced by Ang II. In cells whose [Ca2+]c was clamped at various levels (0.05-0.860 microM) with ionomycin, a concentration-dependent stimulation of pregnenolone output was induced by Ca2+. Under these conditions, the output of pregnenolone--the early product of steroidogenesis--was markedly potentiated by CGP37157. These results suggest the existence of microdomains of high [Ca2+]c elicited by Ang II in the proximity of mitochondria. Moreover, our observations are consistent with a mitochondrial site of action for calcium in the activation of the steroidogenic cascade.

Aequorin↗
PubMed2002

[Local resources in management of adult victims of violence and abuse: a method of presentation and diffusion].

Always more health problems require integrated care. So professionals needs to be aware of local and regional network resources (social, legal, home care, etc.) and specific offers of each individual institution. This article present a method used for creating a register of institutions involved in adults violence and elder abuse, for health professionals. Dates collected by interviewing professionals permitted to class institutions by intervention domain and offer. Five utility indicators (POUCE method) were selected for the register. A score has been attributed to each institution according to their problematic-related offers. Professional in charge of each institution validated information. This map, available in paper or CDrom, affords general practitioneer a quick and targeted access to a large number of dates, according to patient needs. This method could be useful for other health problems requiring exhaustive and targeted information about local and regional community resources (alcoholism, addiction, palliatives care, etc.)

Adult↗
PubMed2005

[Prevalence of violence reported by patients consulting an emergency service].

Violence and their consequences on health is increasingly part of the daily activities of health professionals. A large proportion of victims of violence do use emergency services according to the literature. Those services are often the first contact in the health care system for victims of violence. This potential opportunity to follow the victims, make necessary to improve the quality of the screening, thus because persons concerned by violence will not easily reveal their past or current history of violence. This delicate problem leads often to under diagnosis. This paper presents the research protocol developed to assess the prevalence of violence in an emergency unit in a University hospital. We obtained a high participation rate of 77% and a high proportion of violence (11.40%) confirming the public health importance of this health problem.

Adult↗