[A Pipeline for the Error-free Identification of Somatic Alu Insertions in High-throughput Sequencing Data].

Retroelements are considered as one of the important sources of genomic variability in modern humans. It is known that transposition activity of retroelements in germline cells generates new insertions in various genomic loci and sometimes results in genetic diseases. Retroelements activity in somatic cells is restricted by different cellular mechanisms; however, there is an evidence for it in some tissue types. Somatic insertions can trigger tumorigenesis or participate in normal functioning such as generation of neurons' plasticity. In spite of the rapid development of high-throughput sequencing methods a confident detection of somatic insertions is still quite a challenging task. That, in part, is due to the absence of adequate bioinformatic tools for the analysis of sequencing data. Here, we propose an advanced computational pipeline for the identification of somatic insertions in datasets generated by selective amplification and high-throughput sequencing of genomic regions flanking insertions of AluYa5. Particular attention is paid for the identification of various artifacts arising in course of library preparation and the parameters for their filtration. Pipeline sensitivity is confirmed by in silico experiments with artificial datasets. Using the proposed pipeline we remove at least 80% of artifacts and preserve 75% of potentially somatic insertions. The approaches used in this work can be applied for the study of other mobile elements insertion variability.

Advanced lymphoblastic clones detection in T-cell leukemia.

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignant neoplasm of the lymphocyte precursors that suffered malignant transformation arresting the lymphoid cell differentiation. Clinical studies revealed monoor, more rarely, oligoclonal nature of the disease. A precise identification of malignant clone markers is both the crucial stage of early diagnostics and the essential prognostic factor for therapeutic treatment. Here we present an improved system for unbiased detection of lymphoblastic clones in bone marrow aspirates of T-ALL patients. The system based on multiplex PCR of rearranged T-cell receptor locus (TRB) and straightforward sequencing of the resulted PCR fragments. Testing of the system on genomic DNA from Jurkat cell line and four clinical bone marrow aspirates revealed a set of unique TRB rearrangements that precisely characterize each of tested samples. Therefore, the outcome of the system produces highly informative molecular genetic markers for further monitoring of minimal residual disease in T-ALL patients.

[A novel approach to identification of somatic retroelements' insertions in human genome].

The activity of retroelements is one of the factors leading to genetic variability of the modern humans. Insertions of retroelements may result in alteration of gene expression and functional diversity between cells. In recent years an increasing amount of data indicating an elevated level of retroelements' mobilisation in some human and animal tissues has been reported. Therefore, the development of a system for the detection of somatic retroposition events is required. Here we describe a novel approach to the whole-genome identification of somatic retroelemts' insertions in human genome. The developed approach was applied for the comparisons of somatic mosaicism levels in two tissues of the investigated individual. A total of 3410 insertions of retroelements belonging to AluYa5 subfamily were identified.

[The functional analysis of polymorphic insertions of Alu retroelements at acute lymphoblastic leukemia].

Human genome variability observed within patient cohorts is considered as a goal of functional genomics essential for personalized medicine progress. In the current research we implement functional analysis of 31 polymorphic Alu insertions located within gene introns for individual genomes of patients with acute lymphoblastic leukemia (ALL). As a result we demonstrated a decrease of the primary transcripts content for 21 Alu-containing alleles. The most strong inhibitory effect of 10 Alu insertions was observed in both mononuclear blood cells of healthy donors and B-lymphoblasts of ALL patients. Allele frequencies of three Alu insertions that are located in MEF2C (two of them) and TAX1BP1 genes significantly differ (p-value 0.027. 0.052. 0.014 accordingly) between cohorts of healthy donors and ALL patients. Prolong influence of the Alu insertions on intracellular content of mature mRNA was studied for corresponding allele of TARBP1 gene.

[Surgeon's strategy in forming large intestine anastomoses].

The article includes experience with treatment of 103 patients with the formed different large intestine anastomoses. Primary operations for cancer of the rectum were made on 76 patients, restorative operations--on 27 patients. The following techniques were used: manual formation of the large intestine anastomosis, apparatus anastomoses using AKA-2, "ETHICON CDH" and double apparatuses method using "CONTOUR" and "ETHICON CDH". It was found that the application of stitching apparatuses required shorter time necessary for applying large intestine anastomosis and for operation. When forming the large intestine anastomoses in the abdominal cavity the manual method should be preferred. The formation of anastomosis in the small pelvis cavity is accompanied by technical problems and requires using stitching apparatuses. The method using apparatuses "CONTOUR" and "ETHICON CDH" decreases the number of postoperative complications and can extend the list of indications for performing sphincter-sparing operations.

[Retroposons in modern human genome evolution].

The ascertainment of the rates and driving forces of human genome evolution along with the genetic diversity of populations or separate population groups remains a topical problem of fundamental and applied genomics. According to the results of comparative analysis, the most numerous human genome structure peculiarities are connected with the distribution of mobile genetic retroelements - LTR, LINE1, SVA, and Alu repeats. Due to the wide distribution in different genome loci, conversed retropositional activity, and the retroelements regulatory potential, let us regard them as one of the significant evolutionary driving forces and the source of human genome variability. In the current review, we summarize published data and recent results of our research aimed at the analysis of the evolutionary impact of the young retroelements group on the function and variability of the human genome. We examine modern approaches of the polygenomic identification of polymorphic retroelements inserts. Using an original Internet resource, we analyze special features of the genomic polymorphic inserts of Alu repeats. We thoroughly characterize the strategy of large-scale functional analysis of polymorphic retroelement inserts. The presented results confirm the hypothesis of the roles of retroelements as active cis regulatory elements that are able to modulate surrounding genes.

Effect of dietary sodium intake on glomerular filtration rate in partially nephrectomized dogs.

Exogenous creatinine clearance rate was determined in 8 partially (approx 75%) nephrectomized dogs fed 2 concentrations of dietary sodium, beginning 9 weeks after partial nephrectomy was performed. In a double crossover design, dogs were then fed low-sodium diet (0.18% sodium on a dry-weight basis) or high-sodium diet (1.3% sodium on a dry-weight basis) in 2 sequences (L/H/L or H/L/H) for 3 consecutive 4-week observation periods. Glomerular filtration rate (GFR) was measured by exogenous creatinine clearance before and after partial nephrectomy, and every 2 weeks during the experimental diet periods. Initial mean +/- SD GFR (3.76 +/- 0.78 ml/min/kg of body weight) decreased precipitously after nephrectomy (1.25 +/- 0.45 ml/min/kg); however, during the postnephrectomy and experimental diet periods, GFR gradually increased in all dogs to nearly half the prenephrectomy values (1.87 +/- 0.22 ml/min/kg). Significant differences in GFR were not observed when dogs were fed the L/H/L or the H/L/H sequence. Therefore, it was concluded that abrupt changes from high dietary sodium (1.3%) to restricted dietary sodium (0.18%), or vice versa, does not cause deterioration of renal function in dogs with moderate renal impairment. However, caution should be used in extrapolating these findings to dogs with clinically evident (azotemia, isosthenuria) renal failure.

Tracheal mucociliary transport rate in awake dogs.

To measure tracheal mucociliary transport rate (TMTR) in awake dogs, restrained in dorsal recumbency, 99mtechnetium-labeled macroaggregated albumin was administered by tracheal injection, and the cephalic movement of boluses containing the radiopharmaceutical was detected by a gamma camera positioned lateral to the dog's head and neck. The distance traveled by each bolus was measured, relative to external markers placed a known distance apart. Tracheal mucociliary transport rates were calculated by dividing the measured distance of radiopharmaceutical movement by elapsed time. The technique was efficient and well tolerated. Mean (+/- SD) TMTR was 35.3 +/- 15.9 mm/min. Significant (P = 0.029) difference in TMTR was found between males and females, but significant difference attributable to age of the dog was not detected. This method of measuring TMTR in awake dogs has potential for evaluation of clinical animal patients with suspected tracheal mucociliary abnormalities.

Use of hepatobiliary scintigraphy in the diagnosis of extrahepatic biliary obstruction in dogs and cats: 25 cases (1982-1989).

Twenty-five animals (21 dogs and 4 cats) in which hepatobiliary scintigraphy (HBS) was performed between 1982 and 1989 were included in a retrospective study to determine the utility of HBS for diagnosis of extrahepatic biliary obstruction. Final diagnoses, which were based on liver biopsy results and surgical findings in all animals, were hepatocellular disease alone (n = 17), hepatocellular disease and extrahepatic biliary obstruction (n = 7), and normal liver (n = 1). Hepatobiliary scintigraphy was performed by use of 99mTc-diisopropyl iminodiacetic acid in all cases. All 7 cases of extrahepatic biliary obstruction were confirmed at surgery. In animals with biliary obstruction, HBS failed to demonstrate radiolabel within either the gallbladder or intestine at any time. Using nonvisualization of the intestine by 180 minutes as the scintigraphic criterion for diagnosis of biliary obstruction, sensitivity was 83% and specificity was 94% in this series. Hepatobiliary scintigraphy was concluded to be an accurate indicator of extrahepatic biliary obstruction in this group of animals. High serum bilirubin concentration at the time HBS was performed did not appear to reduce the diagnostic usefulness of the scintigraphic findings.

Lymphoscintigraphy in healthy dogs and dogs with experimentally created thoracic duct abnormalities.

Lymphoscintigraphic evaluation of the thoracic duct (TD) was performed in 10 healthy and 12 dogs with experimentally created TD abnormalities (6 dogs with TD lacerations and 6 dogs with cranial vena ligations). Complete imaging took 4 hours and caused no adverse effects or complications. Lymphoscintigraphy of healthy dogs failed to image the TD; however, background activity in the abdomen and thorax, and radioactivity in the kidneys, bladder, liver, and heart were noticed. Lacerations and transections of the TD were experimentally created in 6 dogs to ascertain whether TD rupture could be detected with lymphoscintigraphy. Lymphoscintigraphy was performed within 48 hours of creating the TD defect. There was no significant difference in the scintigraphic pattern of healthy dogs and those with experimentally created TD defects. Ligation of the cranial vena cava was performed in 6 dogs; 3 dogs developed chylothorax. In those 3 dogs, diffuse radioactivity was imaged in the thorax and was compatible with thoracic lymphangiectasia. In one of these dogs, linear activity consistent with the TD and localized regions of radioactivity cranial to the heart (compatible with the mediastinal lymph nodes) were noticed. Lymphoscintigraphic findings in these dogs correlated with lymphangiographic findings.

Comparison of four methods of estimating glomerular filtration rate in cats.

Four methods of evaluating renal function were performed in 6 cats anesthetized with halothane in oxygen. Glomerular filtration rate (GFR) was measured simultaneously in each cat by exogenous creatinine clearance (ECC), bolus inulin clearance, and 99mTc(Sn)-diethylene-triaminepentaacetic acid (DTPA) clearance determined by 2 different methods. In the first DTPA clearance method (DTPA-1), we measured radioactivity in serial blood specimens to construct plasma disappearance curves for calculation of GFR. In the second DTPA clearance method (DTPA-2), we used serial external head counts of radioactivity and a single blood specimen to construct plasma disappearance curves for calculation of GFR. Bolus inulin clearance was calculated from plasma disappearance curves using a 1-compartment open pharmacokinetic model (IN-1) and a 2-compartment open pharmacokinetic model (IN-2). Glomerular filtration rates were measured over 3 hours, for creatinine and DTPA methods, and over 4 hours for the inulin methods. The GFR obtained with the reference method (ECC) was 2.56 +/- 0.61 ml/min/kg of body weight (mean +/- SD). Values for GFR determined by ECC and DTPA-1 were significantly correlated (r = 0.852; P less than or equal to 0.05). Correlation between ECC and DTPA 2 was not as good (r = 0.783; P less than or equal to 0.10), but the 2 DTPA methods significantly correlated with one another (r = 0.897; P less than or equal to 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

[Physiological properties of Saccharomyces cerevisiae during sine-modulated and stepwise changes in the medium pH]. / Fiziologicheskie svoistva Saccharomyces cerevisiae pri sinusoidal'nykh i stupenchatykh izmeneniiakh pH sredy.

The responses of a chemostat Saccharomyces cerevisiae culture (D = 0.1 h-1) to a stepwise increase or decrease in the pH of the medium were shown to be asymmetric. When the pH was lowered from 6.5 to a value above 0.3, the rates of oxygen uptake and carbon dioxide evolution rose for a sort period of time whereas the optical density of the culture fell down. The detected changes in the properties of the culture were identical with those which had been observed in the course of spontaneous undamped oscillations in the physiological parameters of the continuous C. cerevisiae culture. Apparently, in both cases, the energy status of cells changed when the oxidative type of metabolism was substituted by fermentation. When the pH of the medium was elevated within the same range (4.7-6.5), the response of the culture was three times as low and its properties changed in the opposite direction. When the pH of the medium was changed in a cyclic sinusoidal manner, oscillations in the physiological characteristics of the culture, identical with spontaneous oscillations were induced at certain values of the amplitude and the frequency of pH changes.

Time of onset of estrus in gilts.

An experiment was conducted to determine when, during a 24-h period, gilts show the onset of behavioral estrus. Beginning on Day 16 of their first estrous cycle, 42 crossbred gilts were observed at 0600, 1200, 1800, and 2400 h for the onset of their second estrus. Fifty-five percent of the gilts had shown onset of estrus by 0600 h. None of the gilts showed the onset of estrus from 0600 to 1200 h, whereas 24% and 21% of the gilts had shown onset of estrus by 1800 and 2400 h, respectively. Chi-square analysis demonstrated that more (P < 0.025) gilts had shown onset of estrus by 0600 than by 1200, 1800, and 2400 h. When the data were combined for estrous checks by 0600 and 1800 h, 76% of the gilts had their onset of estrus by 0600 h as compared to 24% of the gilts by 1800 h (P < 0.005). In conclusion, more gilts had shown onset of estrus by 0600 h than at any other 6-h period.

Effects of parity, season, gonadotropin releasing hormone and altered suckling intensity on the interval to rebreeding in sows.

Two experiments were conducted to determine the effects of a) parity and season of the year on the interval from weaning to rebreeding in sows and b) altered suckling intensity (ASI) and gonadotropin releasing hormone (GnRH) on the postpartum interval in primiparous and multiparous sows. Experiment I included 406 weaning-to-rebreeding intervals in 172 primiparous and multiparous sows. Primiparous sows returning to estrus during the spring and summer months had a longer (P<0.001) rebreeding interval (11.0 d) than the other groups (5.7 d). In Experiment II, 32 sows were assigned to a factorially designed experiment. The factors were ASI, GnRH and parity. Treatments were begun 7 d before weaning (about 4 wk of age). The ASI was accomplished by separating the sow from her litter for 12 h each day. The average interval from the beginning of treatment to the onset of estrus was 13.4 d and was not affected (P>0.33) by ASI, GnRH, parity or their interactions. None of the factors was found to affect the average weaning weight of the piglets (P>0.05); however, piglets in the ASI group were heavier (P<0.03) at 1-wk postweaning than those in the no-ASI group. The results showed that primiparous sows returning to estrus during the spring and summer months had the longest rebreeding interval. Additionally, neither GnRH nor ASI, separately or in conjunction, decreased the postpartum interval in sows.