Evaluation of HAL/S language compilability using SAMSO's Compiler Writing System (CWS)

NASA Technical Reports Server (NTRS)

Feliciano, M.; Anderson, H. D.; Bond, J. W., III

1976-01-01

NASA/Langley is engaged in a program to develop an adaptable guidance and control software concept for spacecraft such as shuttle-launched payloads. It is envisioned that this flight software be written in a higher-order language, such as HAL/S, to facilitate changes or additions. To make this adaptable software transferable to various onboard computers, a compiler writing system capability is necessary. A joint program with the Air Force Space and Missile Systems Organization was initiated to determine if the Compiler Writing System (CWS) owned by the Air Force could be utilized for this purpose. The present study explores the feasibility of including the HAL/S language constructs in CWS and the effort required to implement these constructs. This will determine the compilability of HAL/S using CWS and permit NASA/Langley to identify the HAL/S constructs desired for their applications. The study consisted of comparing the implementation of the Space Programming Language using CWS with the requirements for the implementation of HAL/S. It is the conclusion of the study that CWS already contains many of the language features of HAL/S and that it can be expanded for compiling part or all of HAL/S. It is assumed that persons reading and evaluating this report have a basic familiarity with (1) the principles of compiler construction and operation, and (2) the logical structure and applications characteristics of HAL/S and SPL.

Programming in HAL/S

NASA Technical Reports Server (NTRS)

Ryer, M. J.

1979-01-01

Intended as an introduction to programming in HAL/S, this manual is organized as a tutorial aid which may be used as part of a self-study program or in conjunction with a course of twenty to forty classroom hours over a period of one to two weeks. A number of corrections to the first edition are incorporated into the text along with a chapter on FIXED data and an additional appendix on FORMAT I/0.

Inhibitory action of halothane on rat masculine sexual behavior and sperm motility.

PubMed

Oropeza-Hernández, Luis F; Quintanilla-Vega, Betzabet; Albores, Arnulfo; Fernández-Guasti, Alonso

2002-07-01

Adult male rats were exposed to inhale halothane in the following regime: 15 ppm/4 h/5 days/week/9 weeks. Sexual behavior observations and sperm motility test were made before halothane exposure (0 days) and at 15, 30, 45 and 60 days of exposure. Fifteen days after halothane exposure, this anesthetic inhibited the proportion of animals displaying ejaculation. In those animals ejaculating, halothane produced an inhibition of masculine sexual behavior reflected as an increase in the intromission latency, number of mounts and postejaculatory interval. At 30 days after exposure, only an increase in the intromission latency was observed. At 45 and 60 days, the inhibitory effect of halothane on sexual behavior disappeared. Similarly, at 15 and 30 days, but not at 45 or 60 days of halothane exposure, a reduced sperm motility was observed. Such transient effects of halothane suggest the development of tolerance to the inhibitory actions of this anesthetic on sexual behavior and sperm motility. These halothane effects are in line with an inhibition of masculine sexual behavior after stimulation of the GABAergic system.

The pathology of halothane hepatotoxicity in a guinea-pig model: a comparison with human halothane hepatitis.

PubMed Central

Lunam, C. A.; Hall, P. M.; Cousins, M. J.

1989-01-01

The pathology of halothane hepatotoxicity is described in detail in a guinea-pig model. Twenty-two of 40 guinea-pigs developed liver damage after exposure to 1% halothane in 21% O2 for 4 h. The other 18 animals showed no evidence of hepatic injury. Two distinct patterns of damage were identified: mild damage, in which livers had focal areas of necrosis, and severe damage, where necrosis was confluent around the terminal hepatic venules, often extending to the portal tracts. Serum alanine aminotransferase activity was significantly elevated in guinea-pigs with severe liver damage. Hepatocytes in the damaged areas showed degenerative changes ranging from vacuolization to ballooning degeneration and necrosis. Inflammatory cells, predominantly lymphocytes, were often present in the areas of necrosis. The pathology of mild and severe liver injury in the guinea-pig closely resembles the spectrum of injury observed in non-fatal halothane hepatitis in man. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:2818932

Biodegradation of halothane, enflurane and methoxyflurane.

PubMed

Sakai, T; Takaori, M

1978-08-01

The biodegradation of halothane, enflurane and methoxyflurane was studied in 22 patients undergoing abdominal surgery, by measuring the uptake and elimination of each agent and the fluoride excretion in urine. Six control patients were anaesthetized with nitrous oxide in oxygen together with neuromuscular blocking drugs, five patients with nitrous oxide in oxygen and 0.93% halothane, five with nitrous oxide in oxygen and 1.30% enflurane, and six with nitrous oxide in oxygen and 0.31% methoxyflurane. The ratio of the fluoride excretion in urine to the total amount of fluoride contained in the amount of each anaesthetic agent absorbed during anaesthesia was estimated to be 17.7% for halothane, 2.3% for enflurane and 46.3% for methoxyflurane. The serum fluoride concentration increased to a maximum of 15.8 +/- 3.8 mumol litre-1 (mean +/- SD) at 6 h after anaesthesia with methoxyflurane, while it did not exceed 8 mumol litre-1 with the other anaesthetic agents.

Integrated verification and testing system (IVTS) for HAL/S programs

NASA Technical Reports Server (NTRS)

Senn, E. H.; Ames, K. R.; Smith, K. A.

1983-01-01

The IVTS is a large software system designed to support user-controlled verification analysis and testing activities for programs written in the HAL/S language. The system is composed of a user interface and user command language, analysis tools and an organized data base of host system files. The analysis tools are of four major types: (1) static analysis, (2) symbolic execution, (3) dynamic analysis (testing), and (4) documentation enhancement. The IVTS requires a split HAL/S compiler, divided at the natural separation point between the parser/lexical analyzer phase and the target machine code generator phase. The IVTS uses the internal program form (HALMAT) between these two phases as primary input for the analysis tools. The dynamic analysis component requires some way to 'execute' the object HAL/S program. The execution medium may be an interpretive simulation or an actual host or target machine.

SUMC/MPOS/HAL interface study

NASA Technical Reports Server (NTRS)

Saponaro, J. A.; Kosmala, A. L.

1973-01-01

The implementation of the HAL/S language on the IBM-360, and in particular the mechanization of its real time, I/O, and error control statements within the OS-360 environment is described. The objectives are twofold: (1) An analysis and general description of HAL/S real time, I/O, and error control statements and the structure required to mechanize these statements. The emphasis is on describing the logical functions performed upon execution of each HAL statement rather than defining whether it is accomplished by the compiler or operating system. (2) An identification of the OS-360 facilities required during execution of HAL/S code as implemented for the current HAL/S-360 compiler; and an evaluation of the aspects involved with interfacing HAL/S with the SUMC operating system utilizing either the HAL/S-360 compiler or by designing a new HAL/S-SUMC compiler.

Surgical suite environmental control system. [using halothane absorbing filter

NASA Technical Reports Server (NTRS)

Higginbotham, E. J.; Jacobs, M. L.

1974-01-01

Theoretical and experimental work for a systems analysis approach to the problem of surgical suit exhaust systems centered on evaluation of halothane absorbing filters. An activated charcoal-alumina-charcoal combination proved to be the best filter for eliminating halothane through multilayer absorption of gas molecules.

An Ada Linear-Algebra Software Package Modeled After HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Lawson, Charles L.

1990-01-01

New avionics software written more easily. Software package extends Ada programming language to include linear-algebra capabilities similar to those of HAL/S programming language. Designed for such avionics applications as Space Station flight software. In addition to built-in functions of HAL/S, package incorporates quaternion functions used in Space Shuttle and Galileo projects and routines from LINPAK solving systems of equations involving general square matrices. Contains two generic programs: one for floating-point computations and one for integer computations. Written on IBM/AT personal computer running under PC DOS, v.3.1.

AN ADA LINEAR ALGEBRA PACKAGE MODELED AFTER HAL/S

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

This package extends the Ada programming language to include linear algebra capabilities similar to those of the HAL/S programming language. The package is designed for avionics applications such as Space Station flight software. In addition to the HAL/S built-in functions, the package incorporates the quaternion functions used in the Shuttle and Galileo projects, and routines from LINPAK that solve systems of equations involving general square matrices. Language conventions in this package follow those of HAL/S to the maximum extent practical and minimize the effort required for writing new avionics software and translating existent software into Ada. Valid numeric types in this package include scalar, vector, matrix, and quaternion declarations. (Quaternions are fourcomponent vectors used in representing motion between two coordinate frames). Single precision and double precision floating point arithmetic is available in addition to the standard double precision integer manipulation. Infix operators are used instead of function calls to define dot products, cross products, quaternion products, and mixed scalar-vector, scalar-matrix, and vector-matrix products. The package contains two generic programs: one for floating point, and one for integer. The actual component type is passed as a formal parameter to the generic linear algebra package. The procedures for solving systems of linear equations defined by general matrices include GEFA, GECO, GESL, and GIDI. The HAL/S functions include ABVAL, UNIT, TRACE, DET, INVERSE, TRANSPOSE, GET, PUT, FETCH, PLACE, and IDENTITY. This package is written in Ada (Version 1.2) for batch execution and is machine independent. The linear algebra software depends on nothing outside the Ada language except for a call to a square root function for floating point scalars (such as SQRT in the DEC VAX MATHLIB library). This program was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

HAL/S programmer's guide. [for space shuttle project

NASA Technical Reports Server (NTRS)

Newbold, P. M.; Hotz, R. L.

1974-01-01

The structure and symbology of the HAL/S programming language are described; this language is to be used among the flight software for the space shuttle project. The data declaration, input/output statements, and replace statements are also discussed.

Vector-matrix-quaternion, array and arithmetic packages: All HAL/S functions implemented in Ada

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Kwong, David D.

1986-01-01

The HAL/S avionics programmers have enjoyed a variety of tools built into a language tailored to their special requirements. Ada is designed for a broader group of applications. Rather than providing built-in tools, Ada provides the elements with which users can build their own. Standard avionic packages remain to be developed. These must enable programmers to code in Ada as they have coded in HAL/S. The packages under development at JPL will provide all of the vector-matrix, array, and arithmetic functions described in the HAL/S manuals. In addition, the linear algebra package will provide all of the quaternion functions used in Shuttle steering and Galileo attitude control. Furthermore, using Ada's extensibility, many quaternion functions are being implemented as infix operations; equivalent capabilities were never implemented in HAL/S because doing so would entail modifying the compiler and expanding the language. With these packages, many HAL/S expressions will compile and execute in Ada, unchanged. Others can be converted simply by replacing the implicit HAL/S multiply operator with the Ada *. Errors will be trapped and identified. Input/output will be convenient and readable.

Antioxidants prevent depression of the acute hypoxic ventilatory response by subanaesthetic halothane in men

PubMed Central

Teppema, Luc J; Nieuwenhuijs, Diederik; Sarton, Elise; Romberg, Raymonda; Olievier, Cees N; Ward, Denham S; Dahan, Albert

2002-01-01

We studied the effect of the antioxidants (AOX) ascorbic acid (2 g, I.V.) and α-tocopherol (200 mg, P.O.) on the depressant effect of subanaesthetic doses of halothane (0.11 % end-tidal concentration) on the acute isocapnic hypoxic ventilatory response (AHR), i.e. the ventilatory response upon inhalation of a hypoxic gas mixture for 3 min (leading to a haemoglobin saturation of 82 ± 1.8 %) in healthy male volunteers. In the first set of protocols, two groups of eight subjects each underwent a control hypoxic study, a halothane hypoxic study and finally a halothane hypoxic study after pretreatment with AOX (study 1) or placebo (study 2). Halothane reduced the AHR by more than 50 %, from 0.79 ± 0.31 to 0.36 ± 0.14 l min−1 %−1 in study 1 and from 0.79 ± 0.40 to 0.36 ± 0.19 l min−1 %−1 in study 2, P < 0.01 for both. Pretreatment with AOX prevented this depressant effect of halothane in the subjects of study 1 (AHR returning to 0.77 ± 0.32 l min−1 %−1, n.s. from control), whereas placebo (study 2) had no effect (AHR remaining depressed at 0.36 ± 0.27 l min−1 %−1, P < 0.01 from control). In a second set of protocols, two separate groups of eight subjects each underwent a control hypoxic study, a sham halothane hypoxic study and finally a sham halothane hypoxic study after pretreatment with AOX (study 3) or placebo (study 4). In studies 3 and 4, sham halothane did not modify the control hypoxic response, nor did AOX (study 3) or placebo (study 4). The 95 % confidence intervals for the ratio of hypoxic sensitivities, (AOX + halothane):halothane in study 1 and (AOX - sham halothane):sham halothane in study 3, were [1.7, 2.6] and [1.0, 1.2], respectively. Because the antioxidants prevented the reduction of the acute hypoxic response by halothane, we suggest that this depressant effect may be caused by reactive species produced by a reductive metabolism of halothane during hypoxia or that a change in redox state of carotid body cells by the

HAL/S-360 compiler system specification

NASA Technical Reports Server (NTRS)

Johnson, A. E.; Newbold, P. N.; Schulenberg, C. W.; Avakian, A. E.; Varga, S.; Helmers, P. H.; Helmers, C. T., Jr.; Hotz, R. L.

1974-01-01

A three phase language compiler is described which produces IBM 360/370 compatible object modules and a set of simulation tables to aid in run time verification. A link edit step augments the standard OS linkage editor. A comprehensive run time system and library provide the HAL/S operating environment, error handling, a pseudo real time executive, and an extensive set of mathematical, conversion, I/O, and diagnostic routines. The specifications of the information flow and content for this system are also considered.

Halothane-induced Hypnosis Is Not Accompanied by Inactivation of Orexinergic Output in Rodents

PubMed Central

Gompf, Heinrich; Chen, Jingqiu; Sun, Yi; Yanagisawa, Masashi; Aston-Jones, Gary; Kelz, Max B.

2009-01-01

Background One underexploited property of anesthetics is their ability to probe neuronal regulation of arousal. At appropriate doses, anesthetics reversibly obtund conscious perception. However, individual anesthetic agents may accomplish this by altering the function of distinct neuronal populations. Previously we showed that isoflurane and sevoflurane inhibit orexinergic neurons, delaying reintegration of sensory perception as denoted by emergence. Herein we study the effects of halothane. As a halogenated alkane, halothane differs structurally, has a nonoverlapping series of molecular binding partners, and differentially modulates electrophysiologic properties of several ion channels when compared with its halogenated ether relatives. Methods c-Fos immunohistochemistry and in vivo electrophysiology were used to assess neuronal activity. Anesthetic induction and emergence were determined behaviorally in narcoleptic orexin/ataxin-3 mice and control siblings exposed to halothane. Results Halothane-induced hypnosis occurred despite lack of inhibition of orexinergic neurons in mice. In rats, extracellular single-unit recordings within the locus coeruleus showed significantly greater activity during halothane than during a comparable dose of isoflurane. Microinjection of the orexin-1 receptor antagonist, SB-334867-A during the active period slowed firing rates of locus coeruleus neurons in halothane-anesthetized rats, but had no effect on isoflurane-anesthetized rats. Surprisingly, orexin/ataxin-3 transgenic mice, which develop narcolepsy with cataplexy due to loss of orexinergic neurons, did not show delayed emergence from halothane. Conclusion Coordinated inhibition of hypothalamic orexinergic and locus coeruleus noradrenergic neurons is not required for anesthetic induction. Normal emergence from halothane-induced hypnosis in orexin-deficient mice suggests that additional wake-promoting systems likely remain active during general anesthesia produced by halothane

Halothane reduces the early lipopolysaccharide-induced lung inflammation in mechanically ventilated rats.

PubMed

Giraud, O; Seince, P F; Rolland, C; Leçon-Malas, V; Desmonts, J M; Aubier, M; Dehoux, M

2000-12-01

Several studies suggest that anesthetics modulate the immune response. The aim of this study was to investigate the effect of halothane and thiopental on the lung inflammatory response. Rats submitted or not to intratracheal (IT) instillation of lipopolysaccharides (LPS) were anesthetized with either halothane (0. 5, 1, or 1.5%) or thiopental (60 mg. kg(-1)) and mechanically ventilated for 4 h. Control rats were treated or not by LPS without anesthesia. Lung inflammation was assessed by total and differential cell counts in bronchoalveolar lavage fluids (BALF) and by cytokine measurements (tumor necrosis factor-alpha [TNF-alpha], interleukin-6 [IL-6], macrophage inflammatory protein-2 [MIP-2], and monocyte chemoattractant protein-1 [MCP-1]) in BALF and lung homogenates. In the absence of LPS treatment, neither halothane nor thiopental modified the moderate inflammatory response induced by tracheotomy or mechanical ventilation. Cell recruitment and cytokine concentrations were increased in all groups receiving IT LPS. However, in halothane-anesthetized rats (halothane > or = 1%), but not in thiopental-anesthetized rats, the LPS-induced lung inflammation was altered in a dose-dependent manner. Indeed, when using 1% halothane, polymorphonuclear leukocyte (PMN) recruitment was decreased by 55% (p < 0.001) and TNF-alpha, IL-6, and MIP-2 concentrations in BALF and lung homogenates were decreased by more than 60% (p < 0.001) whereas total protein and MCP-1 concentrations remained unchanged. The decrease of MIP-2 (observed at the protein and messenger RNA [mRNA] level) was strongly correlated to the decrease of PMN recruitment (r = 0.73, p < 0.05). This halothane-reduced lung inflammatory response was transient and was reversed 20 h after the end of the anesthesia. Our study shows that halothane > or = 1%, delivered during 4 h by mechanical ventilation, but not mechanical ventilation per se, alters the early LPS-induced lung inflammation in the rat, suggesting a specific

Diphenylhydantoin and lidocaine modification of A-V conduction in halothane-anesthetized dogs.

PubMed

Atlee, J L; Homer, L D; Tobey, R E

1975-07-01

The effect of halothane on A-V conduction was evaluated in gods during atrial pacing using the technique of His-bundle electrocardiography. In addition, the effects of lidocaine and diphenylkydantoin (DPH) on A-V conuction were examined during halothane anesthesia. Effects of these drugs on three subintervals of A-V conduction were compared. These included the -H (stimulus atifact of His-bundle deflection-atrioventricular conduction), H-Q (His-budnle deflection onset of QRS complex-His-Purkinje conduction), and H-S intervals(His-bundle delfection to end of QRS COmplex-total intraventricular conduction). Linear regression best described the relationship between duration of interval (P-H, H-V,and H-S) and heart rate during incremental increases in the atrial paced rate. Data from these experiments were fitted to a multiple lenear regression model that predicted the effect of increasing concentrations of halothan, lidocaine, and DPH on slope and intercept coefficients. In creasing concentrations of halothan ( 30 and 45 mg/100 ml arterial). Both lidocaine and DPH further depressed conduction at all levels of halothan anesthesia. The P-H interval was particularly sensitive todrug effefts. This may represent potentiation of the normal slowing of conduction through the AVnode in response to incremental increases in heart rate (fatigue response.) We conclude thatboth lidocaine and DPH fail to reverse the depressant effect of halothane on A-V conduction. This may explain their ineffectiveness in treating certain types of arrhythmias during halothane anesthesia.

Halothane hepatotoxicity and the reduced derivative, 1,1,1-trifluoro-2-chloroethane.

PubMed Central

Brown, B R; Sipes, I G; Baker, R K

1977-01-01

Halothane (1,1,1-trifluoro-2-bromo-2-chloroethane) is a safe, clinically useful inhalation anesthetic. Rare, unpredictable cases of liver necrosis have been reported following its use. Although the mechanism of this reaction in man is unknown the most plausible is biotransformation to reactive intermediates compounds. The oxidative metabolism of halothane appears to be benign. There is early evidence that reductive (nonoxygen dependent) may be harmful. Since the bromine atom of halothane appears to possess weak bond energy, the reduced, debrominated derivative of halothane, 1,1,1-trifluoro-2-chloroethane, was synthesized and tested for hepatotoxicity in the rat. The derivative is unstable and thus was prepared anaerobically and trapped in propylene glycol solvent. Injection of small amounts of this compound into the portal vein of rats produces extensive liver necrosis. It is postulated that biotransformation of halothane via a reductive pathway could produce this reactive intermediate metabolite. Images FIGURE 1. PMID:612444

HAL/S-360 compiler test activity report

NASA Technical Reports Server (NTRS)

Helmers, C. T.

1974-01-01

The levels of testing employed in verifying the HAL/S-360 compiler were as follows: (1) typical applications program case testing; (2) functional testing of the compiler system and its generated code; and (3) machine oriented testing of compiler implementation on operational computers. Details of the initial test plan and subsequent adaptation are reported, along with complete test results for each phase which examined the production of object codes for every possible source statement.

Respiratory reflexes in response to nasal administration of halothane to anesthetized, spontaneously breathing dogs.

PubMed

Mutoh, T; Kanamaru, A; Tsubone, H; Nishimura, R; Sasaki, N

2000-03-01

To characterize and determine the sensory innervation of respiratory reflexes elicited by nasal administration of halothane to dogs. 10 healthy Beagles. Dogs underwent permanent tracheostomy and, 2 to 3 weeks later, were anesthetized with thiopental and alpha-chloralose administered IV. The nasal passages were functionally isolated so that halothane could be administered to the nasal passages while dogs were breathing 100% O2 via the tracheostomy. Respiratory reflexes in response to administration of halothane at concentrations of 1.25, 1.75, and 2.5 times the minimum alveolar concentration (MAC), and 5% (administered in 100% O2 at a flow rate of 5 L/min) were recorded. Reflexes in response to administration of 5% halothane were also recorded following transection of the infraorbital nerve, transection of the caudal nasal nerve, and nasal administration of lidocaine. Nasal administration of halothane induced an inhibition of breathing characterized by a dose-dependent increase in expiratory time and a resultant decrease in expired volume per unit time. Effects were noticeable immediately after the onset of halothane administration and lasted until its cessation. Reflex responses to halothane administration were attenuated by transection of the caudal nasal nerve and by nasal administration of lidocaine, but transection of the infraorbital nerve had no effect. Nasal administration of halothane at concentrations generally used for mask induction of anesthesia induces reflex inhibition of breathing. Afferent fibers in the caudal nasal nerve appear to play an important role in the reflex inhibition of breathing induced by halothane administration.

[The uterotropismus of halothane, chloroform or methoxyflurane in clinical use (author's transl)].

PubMed

Fassolt, A; Schubiger, V; Hauser, G A

1976-11-01

To perform episiotomy, 89 women after childbirth were anaesthetized with either halothane (50 patients), methoxyflurane (24 patients) or chloroform (15 patients). The activity of the uterus was registered tocodynamographically. To examine the alternate influence of narcotics and uterotonica, 57 patients were pre-medicated with sintocinon and methergin i.m. as a prophylaxis. The second group (32 patients) received no premedication to stimulate labor activity, however in 18 cases towards the end of narcosis oxytocin and methergin were given i.v. In addition to these examinations 5 vaginal deliveries were anaesthetised with halothane only. Concerning our own experimental study it can be observed: 1. The relaxative properties of halothane wich suppresses completly the activity of myometrium during the deep stages of anaesthesia are superior to chloroform and methoxyflurane. 2. More rapid relaxation of the uterus with halothane compared with chloroform and methoxyflurane. 3. After the use of halothane a quicker return of the activity of the uterus compared with chloroform and methoxyflurane. 4. The value of a prophylaxis with uterotonica can be demonstrated by a comparatively reduced slowing-down of labour-activity during anaesthesia. 5. In every one of the cases, an interuption of the labour-suppressing, caused by the anaesthesia, can be obtained by injecting intravenously oxytocin or methergin. 6. During vaginal delivery, compared to the post placentar phase, there is no need for higher concentrations of halothane to be used to suppress labour contractions. The discussion deals with the intensity of reduction of the uterus contraction caused by the above mentioned narcotics, the dangers of the atony of the uterus, and the indications and contra-indications of obstetrical anaesthesia with halothane or methoxyflurane.

Determination of halothane-induced sleeping time in the rat: effect of prior administration of centrally active drugs.

PubMed Central

Turnbull, M J; Watkins, J W

1976-01-01

A method is described for the determination of halothane-induced sleeping time in the rat. 2 The sleeping time exhibited a diurnal variation which was due, at least in part, to a change in the sensitivity of the central nervous system (CNS) to the anaesthetic. 3 Tolerance to halothane did not develop in rats repeatedly exposed to the anaesthetic over a period of over 48 hours. 4 Repeated sleeping time determinations have been used to follow changes in the sensitivity of the CNS to the anaesthetic occurring with time. 5 A tolerance to halothane was induced by pretreatment of rats with doses of amylobarbitone, pentobarbitone or meprobamate sufficient to keep animals anaesthetized for approximately 12 hours. This tolerance was followed by a period of halothane-hypersensitivity. 6 Halothane-tolerant animals awakened with higher brain halothane concentrations and were also tolerant to intracerebroventricularly administered pentobarbitone. 7 Halothane-hypertensive rats awakened with lower brain halothane concentrations and were also hypersensitivity to intracerebroventricularly administered pentobarbitone. 8 The possibility that the induction of cross-tolerance to halothane may be indicative of a drug's potential to produce dependence is discussed. PMID:987820

Effects of thiopentone sodium, methoxyflurane and halothane on haematological parameters in sheep during prolonged anaesthesia.

PubMed

Edjtehadi, M

1978-01-01

1. Satisfactory surgical anaesthesia in sheep was achieved by i.v. injection of thiopentone sodium per se (20 mg/kg); and also with thiopentone/methoxyflurane and thiopentone/halothane anaesthetics (2--3% and 1.5--2%, respectively). 2. Cardiac arrhythmias were not observed during thiopentone sodium, thiopentone/methoxyflurane and thiopentone/halothane anaesthesia. However, during thiopentone anaesthesia, one sheep displayed a high degree of sinus tachycardia followed with ventricular tachycardia. 3. Pneumograms recorded during thiopentone sodium and thiopentone/methoxyflurane anaesthesia showed no irregularity, but in thiopentone/halothane anaesthesia, 30% of the sheep developed Cheyne-Stokes periodic respiration. 4. Packed cell volume (PCV) and haemoglobin (Hb) were significantly decreased in thiopentone/methoxyflurane and thiopentone anaesthetized sheep, but not in animals anaesthetized by thiopentone/halothane. 5. White blood cell count (WBC) was significantly decreased only in thiopentone/methoxyflurane anaesthetized sheep, but was not remarkable in thiopentone and thiopentone/halothane anaesthetized animals. 6. A significant lymphocytopenia occurred in thiopentone/methoxyflurane and in thiopentone/halothane anaesthetized sheep, but not in the thiopentone anaesthetized animals. This was accompanied with an increase in neutrophils. 7. Clotting time fell, but the extent and time course was different in thiopentone, thiopentone/methoxyflurane and thiopentone/halothane anaesthesia. 8. From these data, it is suggested that thiopentone sodium, thiopentone/methoxyflurane and thiopentone/halothane have different effects on different blood parameters during prolonged anaesthesia, and may be clinically significant.

Haloacyl complexes of boron, [(CF3)3BC(O)Hal]- (Hal=F, Cl, Br, I).

PubMed

Finze, Maik; Bernhardt, Eduard; Willner, Helge; Lehmann, Christian W

2005-11-04

The haloacyltris(trifluoromethyl)borate anions [(CF3)3BC(O)Hal]- (Hal=F, Cl, Br, I) have been synthesized by reacting (CF3)3BCO with either MHal (M=K, Cs; Hal=F) in SO2 or MHal (M=[nBu4N]+, [Et4N]+, [Ph4P]+; Hal=Cl, Br, I) in dichloromethane. Metathesis reactions of the fluoroacyl complex with Me3SiHal (Hal=Cl, Br, I) led to the formation of its higher homologues. The thermal stabilities of the haloacyltris(trifluoromethyl)borates decrease from the fluorine to the iodine derivative. The chemical reactivities decrease in the same order as demonstrated by a series of selected reactions. The new [(CF3)3BC(O)Hal]- (Hal=F, Cl, Br) salts are used as starting materials in the syntheses of novel compounds that contain the (CF3)3B-C fragment. All borate anions [(CF3)3BC(O)Hal]- (Hal=F, Cl, Br, I) have been characterized by multinuclear NMR spectroscopy (11B, 13C, 17O, 19F) and vibrational spectroscopy. [PPh4][(CF3)3BC(O)Br] crystallizes in the monoclinic space group P2/c (no. 13) and the bond parameters are compared with those of (CF3)3BCO and K[(CF3)3BC(O)F]. The interpretation of the spectroscopic and structural data are supported by DFT calculations [B3LYP/6-311+G(d)].

Beyond Ether and Chloroform-A Major Breakthrough With Halothane.

PubMed

Huang, Lisa; Sang, Christine N; Desai, Manisha S

2017-07-01

The use of equipment powered by electricity in the operating room increased the risk of fires in the presence of flammable agents such as ether and cyclopropane. Chloroform was associated with cardiac arrhythmias and liver damage. The introduction of halothane in the late 1950s was heralded as a solution to many problems facing the specialty of anesthesia. We explore whether the manufacturer promptly reported halothane's adverse effects to regulatory agencies and practitioners. We consulted documents submitted by Ayerst Laboratories to federal authorities through the Freedom of Information Act, promotional advertisements, package inserts, published articles, and textbooks. Two major complications associated with the use of halothane, cardiac arrhythmias and the risk of hepatotoxicity, were disclosed by the manufacturer when the drug was first introduced to the US market. Reports appeared timely and complete; there was no apparent attempt to conceal or otherwise downplay these risks. The process of drug discovery and approval for clinical use has always been a lengthy, complex, and extremely expensive undertaking, with only a small minority of compounds receiving approval. The risk of adverse effects or drug interaction directly impacts commercial viability. In the case of halothane, the manufacturer disclosed major adverse effects, and the drug enjoyed decades of popularity until it was replaced by agents with a better drug profile. Copyright © 2017 Elsevier Inc. All rights reserved.

Influence of cimetidine and diethyldithiocarbamate on the metabolism of halothane and methoxyflurane in vitro.

PubMed

Loesch, J; Siegers, C P; Younes, M

1987-06-01

The metabolism of halothane and methoxyflurane was measured in vitro by the vial equilibration method using the S-9-fraction from rat liver as source of enzymes. Kinetic values were measured for halothane: Vmax = 11.6 nmol/g.min, KM = 19.6 mumol/l and methoxyflurane: Vmax = 12.0 nmol/g.min, KM = 17.5 mumol/l. Dithiocarb showed strong inhibitory activity on halothane and methoxyflurane metabolism; inhibition constants were calculated as Ki = 0.051 mmol/l and Ki = 0.004 mmol/l, respectively. Cimetidine inhibited the metabolism of both anesthetics to a lesser extent. Inhibition constants were calculated as Ki = 16.2 mmol/l and Ki = 8.2 mmol/l for halothane and methoxyflurane, respectively. The observed inhibitory properties of dithiocarb and cimetidine on the metabolism of halothane and methoxyflurane may be of interest in connection with the problem of toxic liver and kidney injury after anesthesia with these agents.

Associations between variants of the HAL gene and milk production traits in Chinese Holstein cows.

PubMed

Wang, Haifei; Jiang, Li; Wang, Wenwen; Zhang, Shengli; Yin, Zongjun; Zhang, Qin; Liu, Jian-Feng

2014-11-25

The histidine ammonia-lyse gene (HAL) encodes the histidine ammonia-lyase, which catalyzes the first reaction of histidine catabolism. In our previous genome-wide association study in Chinese Holstein cows to identify genetic variants affecting milk production traits, a SNP (rs41647754) located 357 bp upstream of HAL, was found to be significantly associated with milk yield and milk protein yield. In addition, the HAL gene resides within the reported QTLs for milk production traits. The aims of this study were to identify genetic variants in HAL and to test the association between these variants and milk production traits. Fifteen SNPs were identified within the regions under study of the HAL gene, including three coding mutations, seven intronic mutations, one promoter region mutation, and four 3'UTR mutations. Nine of these identified SNPs were chosen for subsequent genotyping and association analyses. Our results showed that five SNP markers (ss974768522, ss974768525, ss974768531, ss974768533 and ss974768534) were significantly associated with one or more milk production traits. Haplotype analysis showed that two haplotype blocks were significantly associated with milk yield and milk protein yield, providing additional support for the association between HAL variants and milk production traits in dairy cows (P < 0.05). Our study shows evidence of significant associations between SNPs within the HAL gene and milk production traits in Chinese Holstein cows, indicating the potential role of HAL variants in these traits. These identified SNPs may serve as genetic markers used in genomic selection schemes to accelerate the genetic gains of milk production traits in dairy cattle.

Genetic predisposition to liver damage after halothane anesthesia in guinea pigs.

PubMed

Lunam, C A; Cousins, M J; Hall, P M

1986-11-01

Three 4-hr normoxic (21% oxygen) exposures to 1% halothane administered 3 days apart were associated with elevations in serum alanine aminotransferase (ALT) activity in four of 20 guinea pigs after the initial and third exposures. Serum alanine aminotransferase values were not measured after the second anesthetic. Susceptibility was defined as an ALT level greater than 300 IU/L after halothane. Nonsusceptible animals, that is, animals without significant increases in ALT values after halothane, remained nonsusceptible after reexposure. Serum alanine aminotransferase values after the first and third anesthesias were significantly correlated (rs = 0.86, P less than 0.001). Two exposures of another 30 guinea pigs at a 5-week interval resulted in high elevations of ALT in the same eight animals after both anesthetics. In contrast, after an initial exposure nonsusceptible animals remained nonsusceptible upon reexposure. Serum alanine aminotransferase levels after the first and second anesthetics were significantly correlated (rs = 0.85, P less than 0.001). The proportion of first generation (F1) males with elevated ALTs whose parents were susceptible to halothane hepatotoxicity (HH) was significantly higher than the proportion of males with elevated ALTs in a random group of 90 males (P less than 0.005). First generation males and females of nonsusceptible parents had ALTs within the normal range after halothane exposure. These studies suggest that in the guinea pig genetic predisposition is an important determinant of susceptibility to HH, although other contributing factors are not excluded.

Origin of the X-Hal (Hal = Cl, Br) bond-length change in the halogen-bonded complexes.

PubMed

Wang, Weizhou; Hobza, Pavel

2008-05-01

The origin of the X-Hal bond-length change in the halogen bond of the X-Hal...Y type has been investigated at the MP2(full)/6-311++G(d,p) level of theory using a natural bond orbital analysis, atoms in molecules procedure, and electrostatic potential fitting methods. Our results have clearly shown that various theories explaining the nature of the hydrogen bond cannot be applied to explain the origin of the X-Hal bond-length change in the halogen bond. We provide a new explanation for this change. The elongation of the X-Hal bond length is caused by the electron-density transfer to the X-Hal sigma* antibonding orbital. For the blue-shifting halogen bond, the electron-density transfer to the X-Hal sigma* antibonding orbital is only of minor importance; it is the electrostatic attractive interaction that causes the X-Hal bond contraction.

HAL/S-FC compiler system specifications

NASA Technical Reports Server (NTRS)

1976-01-01

This document specifies the informational interfaces within the HAL/S-FC compiler, and between the compiler and the external environment. This Compiler System Specification is for the HAL/S-FC compiler and its associated run time facilities which implement the full HAL/S language. The HAL/S-FC compiler is designed to operate stand-alone on any compatible IBM 360/370 computer and within the Software Development Laboratory (SDL) at NASA/JSC, Houston, Texas.

Anesthesia specific differences in a cardio-pulmonary resuscitation rat model; halothane versus sevoflurane.

PubMed

Esser, Torben; Keilhoff, Gerburg; Ebmeyer, Uwe

2016-12-01

Our asphyxia cardiac arrest (ACA) rat model is well established. The original model was designed in the 1990th using halothane and nitrous oxide for pre-insult anesthesia. Because of its hepato-toxicity and its potential to induce severe liver failures, halothane is no longer used in clinical anesthesia for several years. In order to minimize the health risk for our laboratory staff as well as to keep the experimental settings of our model on a clinically oriented basis we decided to replace halothane by sevoflurane. In this study we intended to determine if the change of the narcotic gas regiment causes changes in the neurological damage and how far our model had to be adjusted. Adult rats were subjected to 5min of ACA followed by resuscitation. There were four treatment groups: ACA - halothane, ACA - sevoflurane and with halothane or sevoflurane sham operated animals. Vital and blood parameters were monitored during the 45min post-resuscitation intensive care phase. After a survival time of 7 days histological evaluation of the hippocampus was performed. We observed that resuscitated rats anesthetized prior by sevoflurane (i) have had a lower heart rate and a higher MAP compared to halothane anesthetized animals; (ii) The neurological damaged were significantly reduced in the hippocampal CA1 region in sevoflurane treated rats. Using sevoflurane instead of halothane for anesthesia requires some physiological and experimental changes. However the model keeps its validity. Sevoflurane caused less pronounced neurodegeneration in the CA1 region of the hippocampus. This had to be considered in further resuscitation-studies containing sevoflurane as anesthetic. Institutional protocol number for animal studies: 42502-2-2-947 Uni MD. Copyright © 2016 Elsevier B.V. All rights reserved.

Circulatory and respiratory effects of methoxyflurane in dogs: comparison of halothane.

PubMed

Steffey, E P; Farver, T B; Woliner, M J

1984-12-01

Circulatory and respiratory effects of 3 alveolar concentrations (representing 1.0, 1.5, and 2.0 times the minimal alveolar concentration, MAC) of methoxyflurane in O2 were compared with similar MAC multiples of halothane in O2. Eight adult mixed breed dogs that were healthy and nonmedicated were studied in cross-over fashion with both agents during conditions of controlled ventilation (CV; PaCO2 averaged 34 to 38 mm of Hg) and spontaneous ventilation (SV). When ventilation was controlled, methoxyflurane similar to halothane caused dose-related cardiovascular depression. Except for a greater heart rate and lesser stroke volume with methoxyflurane, little difference was noticed between the anesthetics at equivalent doses during CV. There was less dose-related circulatory depression during SV with both agents but particularly with methoxyflurane. During SV, PaCO2 increased progressively with increases in alveolar concentrations of methoxyflurane and halothane. Methoxyflurane caused significantly greater (P less than 0.05) hypoventilation than halothane only at 2.0 MAC. Except for a greater respiratory gas flow and inspiratory-expiratory gas flow ratio and a lesser inspiratory-expiratory time ratio with methoxyflurane, there was no anesthetic- or dose-response effect on respiratory variables.

The differential effects of halothane and isoflurane on electroencephalographic responses to electrical microstimulation of the reticular formation.

PubMed

Orth, Mashawn; Bravo, Emigdio; Barter, Linda; Carstens, Earl; Antognini, Joseph F

2006-06-01

Isoflurane and halothane cause electroencephalographic (EEG) depression and neuronal depression in the reticular formation, a site critical to consciousness. We hypothesized that isoflurane, more than halothane, would depress EEG activation elicited by electrical microstimulation of the reticular formation. Rats were anesthetized with either halothane or isoflurane and stimulating electrodes were positioned in the reticular formation. In a crossover design, anesthetic concentration was adjusted to 0.8 and 1.2 minimum alveolar concentration (MAC) of halothane or isoflurane and electrical microstimulation was performed and the EEG responses were recorded. Microstimulation increased the spectral edge and median edge frequencies 2-2.5 Hz at 0.8 MAC for halothane and isoflurane and 1.2 MAC halothane. At 1.2 MAC isoflurane, burst suppression occurred and microstimulation decreased the period of isoelectricity (24% +/- 19% to 8% +/- 7%; P < 0.05), whereas the spectral edge and median edge frequencies were unchanged. At anesthetic concentrations required to produce immobility, the cortex remains responsive to electrical microstimulation of the reticular formation, although the EEG response is depressed in the transition from 0.8 to 1.2 MAC. These data indicate that cortical neurons remain responsive to synaptic input during isoflurane and halothane anesthesia.

GOAL-to-HAL translation study

NASA Technical Reports Server (NTRS)

Flanders, J. H.; Helmers, C. T.; Stanten, S. F.

1973-01-01

This report deals with the feasibility, problems, solutions, and mapping of a GOAL language to HAL language translator. Ground Operations Aerospace Language, or GOAL, is a test-oriented higher order language developed by the John F. Kennedy Space Center to be used in checkout and launch of the space shuttle. HAL is a structured higher order language developed by the Johnson Space Center to be used in writing the flight software for the onboard shuttle computers. Since the onboard computers will extensively support ground checkout of the space shuttle, and since these computers and the software development facilities on the ground use the HAL language as baseline, the translation of GOAL to HAL becomes significant. The issue of feasibility was examined and it was found that a GOAL to HAL translator is feasible. Special problems are identified and solutions proposed. Finally, examples of translation are provided for each category of complete GOAL statement.

Effects of halothane and methoxyflurane on the hypothalamic-pituitary-adrenal axis in rat.

PubMed

Karuri, A R; Engelking, L R; Kumar, M S

1998-10-01

Effects of acute exposure (2 h) to either 1.5% halothane or 0.5% methoxyflurane on chemical mediators of the hypothalamic-pituitary-adrenal (HPA) axis were evaluated in male Sprague-Dawley rats immediately after exposure, after the righting reflex (4 h), or 24 h postexposure. Effects of these anesthetics on hippocampal corticotropin releasing factor (CRF) were also evaluated. Methoxyflurane caused significant elevations in pituitary adrenocorticotropin hormone (ACTH)-like immunoreactivities in all three of the experiment's time groups, yet halothane failed to cause the same response immediately after exposure. Serum ACTH-like immunoreactivities were significantly elevated immediately after exposure to both anesthetics, but were not elevated at 4 and 24 h postexposure. Corticosterone (CORT)-like immunoreactivities were significantly elevated by halothane in all experimental groups, and in the 2- and 24-h groups following methoxyflurane exposure. Hippocampal CRF-like immunoreactivities remained unaffected by either anesthetic. Results indicate that a 2-h exposure to either halothane or methoxyflurane results in significant activation of the rat hypothalamic-pituitary-adrenal axis, and that the activation appears to be sustained over a 24-h period.

Propofol, more than halothane, depresses electroencephalographic activation resulting from electrical stimulation in reticular formation.

PubMed

Antognini, J F; Bravo, E; Atherley, R; Carstens, E

2006-09-01

Halothane and propofol depress the central nervous system, and this is partly manifested by a decrease in electroencephalographic (EEG) activity. Little work has been performed to determine the differences between these anesthetics with regard to their effects on evoked EEG activity. We examined the effects of halothane and propofol on EEG responses to electrical stimulation of the reticular formation. Rats (n= 12) were anesthetized with either halothane or propofol, and EEG responses were recorded before and after electrical stimulation of the reticular formation. Two anesthetic concentrations were used (0.8 and 1.2 times the amount needed to prevent gross, purposeful movement in response to supramaximal noxious stimulation), and both anesthetics were studied in each rat using a cross-over design. Electrical stimulation in the reticular formation increased the spectral edge (SEF) and median edge (MEF) frequencies by approximately 1-2 Hz during halothane anesthesia at low and high concentrations. During propofol anesthesia, MEF increased at the low propofol infusion rate, but SEF was unaffected. At the high propofol infusion rate, SEF and MEF decreased following electrical stimulation in the reticular formation. At immobilizing concentrations, propofol produces a larger decrease than halothane in EEG responses to reticular formation stimulation, consistent with propofol having a more profound depressant effect on cortical and subcortical structures.

21 CFR 868.1620 - Halothane gas analyzer.

Code of Federal Regulations, 2010 CFR

2010-04-01

... infrared or ultraviolet radiation. (b) Classification. Class II (performance standards). ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Halothane gas analyzer. 868.1620 Section 868.1620 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED...

Advancing HAL to an operational status

NASA Technical Reports Server (NTRS)

1974-01-01

The development of the HAL language and the compiler implementation of the mathematical subset of the language have been completed. On-site support, training, and maintenance of this compiler were enlarged to broaden the implementation of HAL to include all features of the language specification for NASA manned space usage. A summary of activities associated with the HAL compiler for the UNIVAC 1108 is given.

Current status of the HAL/S compiler on the Modcomp classic 7870 computer

NASA Technical Reports Server (NTRS)

Lytle, P. J.

1981-01-01

A brief history of the HAL/S language, including the experience of other users of the language at the Jet Propulsion Laboratory is presented. The current status of the compiler, as implemented on the Modcomp 7870 Classi computer, and future applications in the Deep Space Network (DSN) are discussed. The primary applications in the DSN will be in the Mark IVA network.

Effects of anesthesia with halothane and methoxyflurane on plasma corticosterone concentration in rats at rest and after exercise.

PubMed

Carlberg, K A; Gwosdow, A R; Alvin, B L

1995-10-01

To determine whether halothane and methoxyflurane are suitable anesthetics for cardiac puncture in studies of plasma corticosterone concentration in rats, four experiments were done. Blood samples were taken immediately after rats became anesthetized with halothane or methoxyflurane. Decapitation without anesthesia was used to determine baseline corticosterone concentration. Another group of rats was anesthetized with ether as a positive control (known to stimulate corticosterone secretion). Corticosterone values in halothane- and methoxyflurane-treated rats were not significantly different from those measured after decapitation. Corticosterone concentration in halothane-treated rats was significantly lower than that in either methoxyflurane- or ether-treated rats. Cardiac puncture was done after 3 min of exposure to each of the three anesthetics. The results indicated that there were no differences in corticosterone values among the three anesthetics, suggesting that corticosterone concentration was lower immediately after halothane was used as the anesthetic, because halothane induced anesthesia in less time than that required for activation of adrenocortical secretion. To determine whether there was a difference among anesthetics in stimulating corticosterone secretion when anesthesia was maintained for a period before blood sample collection, cardiac puncture was done after 15 min of exposure to each of the three anesthetics. Corticosterone values were similar, suggesting that any of the three anesthetics was acceptable in this situation. To determine whether halothane or methoxyflurane affected exercise-induced increases in corticosterone values, exercise-trained rats were run for 30 min; then blood samples were collected by cardiac puncture immediately after induction of anesthesia with halothane, methoxyflurane, or ether, or after decapitation without anesthesia. Corticosterone values were not different among the three anesthetics or decapitation.

The GOAL-to-HAL/S translator specification. [for space shuttle

NASA Technical Reports Server (NTRS)

Stanten, S. F.; Flanders, J. H.

1973-01-01

The specification sets forth a technical framework within which to deal with the transfer of specific GOAL features to HAL/S. Key technical features of the translator are described which communicate with the data bank, handle repeat statements, and deal with software interrupts. GOAL programs, databank information, and GOAL system subroutines are integrated into one GOAL in HAL/S. This output is fully compatible HAL/S source ready for insertion into the HAL/S compiler. The Translator uses a PASS1 to establish all the global data needed for the HAL/S output program. Individual GOAL statements are translated in PASS2. The specification document makes extensive use of flowcharts to specify exactly how each variation of each GOAL statement is to be translated. The specification also deals with definitions and assumptions, executive support structure and implementation. An appendix, entitled GOAL-to-HAL Mapping, provides examples of translated GOAL statements.

The effects of furosemide on remal blood flow and cortical perfusion during methoxyflurane and halothane anaesthesia.

PubMed

Leighton, K M; Bruce, C; Machin, R

1976-01-01

Nephrotoxicity due to methoxyflurane may be due in part to alterations in intra-renal perfusion. Furosemide is believed to alter the intra-renal distribution of blood flow. Studies have been carried out to observe the effects of systemic furosemide administration during methoxyflurane and halothane anaesthesia in normotensive animals and in animals made hypotensive by increasing inspired concentrations of the anaesthetics. During halothane anaesthesia normotensive dogs showed a rise in total renal blood flow during the infusion of furosemide. Hypotensive dogs showed no increase in flow. During methoxyflurane anaesthesia no change in total renal blood flow followed furosemide administration to normotensive animals. Some diminution in total blood flow followed the administration of furosemide in hypotensive dogs during methoxyflurane anaesthesia. In normotensive dogs during halothane anaesthesia there was a significant increase in deep cortical perfusion after furosemide. Furosemide, therefore, is unlikely to mitigate the potential for nephrotoxicity which methoxyflurane possesses. Furthermore, this diuretic may adversely influence renal function when administered during halothane anaesthesia.

Cryosolution infrared study of hydrogen bonded halothane acetylene complex

NASA Astrophysics Data System (ADS)

Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

2018-05-01

The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

Development of a support software system for real-time HAL/S applications

NASA Technical Reports Server (NTRS)

Smith, R. S.

1984-01-01

Methodologies employed in defining and implementing a software support system for the HAL/S computer language for real-time operations on the Shuttle are detailed. Attention is also given to the management and validation techniques used during software development and software maintenance. Utilities developed to support the real-time operating conditions are described. With the support system being produced on Cyber computers and executable code then processed through Cyber or PDP machines, the support system has a production level status and can serve as a model for other software development projects.

Hybrid Assistive Limb (HAL) Rehabilitation in Patients with Acute Hemorrhagic Stroke.

PubMed

Ogata, Toshiyasu; Abe, Hiroshi; Samura, Kazuhiro; Hamada, Omi; Nonaka, Masani; Iwaasa, Mitsutoshi; Higashi, Toshio; Fukuda, Hiroyuki; Shiota, Etsuji; Tsuboi, Yoshio; Inoue, Tooru

2015-01-01

The efficacy of hybrid assistive limb (HAL) rehabilitation in the acute phase of stroke remains unclear. The purpose of this study was to evaluate the outcomes of patients with acute intracranial hemorrhage (ICH) who were treated with or without HAL rehabilitation. Among 270 patients with acute ICH from 2009 to 2014, 91 patients with supratentorial ICH were included in this retrospective study. Of these, 14 patients (HAL group) received HAL rehabilitation at approximately 1 week after ICH occurrence, while the remaining 77 patients received usual rehabilitation without HAL (N-HAL group). We obtained various patient data from the hospitals where the patients were moved to for further rehabilitation. Statistical comparisons were performed for the characteristics of the ICH patients, and outcomes between the HAL and N-HAL groups. There were no differences in outcomes between the HAL and N-HAL groups. However, patients with right ICH in the HAL group exhibited a significant association with a functional independence measure (FIM) score of ≥ 110 compared with patients in the N-HAL group (HAL group: 81.8%, N-HAL group: 43.9%, P = 0.04). In patients with right ICH, HAL rehabilitation was associated with improved outcomes as evaluated by the FIM score. Thus, HAL rehabilitation may improve outcomes of acute ICH in appropriately selected patients.

S-HAL : safety handbook for locals.

DOT National Transportation Integrated Search

2014-01-01

The Safety Handbook for Locals (S-HAL) is intended to be a comprehensive : traffic safety resource for all local communities in Missouri, be it cities or : counties. The S-HAL mirrors the national Highway Safety Manual (HSM) : (AASHTO, 2010) in using...

Recognition of a novel type X═N-Hal···Hal (X = C, S, P; Hal = F, Cl, Br, I) halogen bonding.

PubMed

Gushchin, Pavel V; Kuznetsov, Maxim L; Haukka, Matti; Kukushkin, Vadim Yu

2013-04-04

The chlorination of the eight-membered platinum(II) chelates [PtCl2{NH═C(NR2)N(Ph)C(═NH)N(Ph)C(NR2)═NH}] (R = Me (1); R2 = (CH2)5 (2)) with uncomplexed imino group with Cl2 gives complexes bearing the ═N-Cl moiety [PtCl4{NH═C(NR2)N(Ph)C(═NCl)N(Ph)C(NR2)═NH}] (R = Me (3); R2 = (CH2)5 (4)). X-ray study for 3 revealed a novel type intermolecular halogen bonding ═N-Cl···Cl(-), formed between the Cl atom of the chlorinated imine and the chloride bound to the platinum(IV) center. The processing relevant structural data retrieved from the Cambridge Structural Database (CSDB) shows that this type of halogen bonding is realized in 18 more molecular species having X═N-Hal moieties (X = C, P, S, V, W; Hal = Cl, Br, I), but this weak ═N-Hal···Hal(-) bonding was totally neglected in the previous works. The presence of the halogen bonding in 3 was confirmed by theoretical calculations at the density functional theory (DFT, M06-2X) level, and its nature was analyzed.

Hybrid Assistive Limb (HAL) Rehabilitation in Patients with Acute Hemorrhagic Stroke

PubMed Central

OGATA, Toshiyasu; ABE, Hiroshi; SAMURA, Kazuhiro; HAMADA, Omi; NONAKA, Masani; IWAASA, Mitsutoshi; HIGASHI, Toshio; FUKUDA, Hiroyuki; SHIOTA, Etsuji; TSUBOI, Yoshio; INOUE, Tooru

2015-01-01

The efficacy of hybrid assistive limb (HAL) rehabilitation in the acute phase of stroke remains unclear. The purpose of this study was to evaluate the outcomes of patients with acute intracranial hemorrhage (ICH) who were treated with or without HAL rehabilitation. Among 270 patients with acute ICH from 2009 to 2014, 91 patients with supratentorial ICH were included in this retrospective study. Of these, 14 patients (HAL group) received HAL rehabilitation at approximately 1 week after ICH occurrence, while the remaining 77 patients received usual rehabilitation without HAL (N-HAL group). We obtained various patient data from the hospitals where the patients were moved to for further rehabilitation. Statistical comparisons were performed for the characteristics of the ICH patients, and outcomes between the HAL and N-HAL groups. There were no differences in outcomes between the HAL and N-HAL groups. However, patients with right ICH in the HAL group exhibited a significant association with a functional independence measure (FIM) score of ≥ 110 compared with patients in the N-HAL group (HAL group: 81.8%, N-HAL group: 43.9%, P = 0.04). In patients with right ICH, HAL rehabilitation was associated with improved outcomes as evaluated by the FIM score. Thus, HAL rehabilitation may improve outcomes of acute ICH in appropriately selected patients. PMID:26511112

The effect of inhalant anesthetic and body temperature on peri-anesthetic serum concentrations of transdermally administered fentanyl in dogs.

PubMed

Pettifer, Glenn R; Hosgood, Giselle

2004-04-01

To determine whether moderate hypothermia during anesthesia significantly affects the serum concentration of transdermally delivered fentanyl and whether halothane or isoflurane affect these concentrations. Randomized cross-over experimental trial. Six mature, healthy Beagles (three males, three females) weighing 10.6 +/- 0.43 kg. A 50-microg hour(-1) fentanyl patch was applied 36 hours prior to anesthesia. Anesthesia was induced at time 0 (t = 0). Each dog received four treatments: isoflurane + normothermia (ISO-NORM), isoflurane + hypothermia (ISO-HYPO), halothane + normothermia (HAL-NORM), and halothane + hypothermia (HAL-HYPO). Dogs were intubated and maintained at 1.5 times MAC. Animals in the hypothermia treatments were cooled to 35 degrees C during anesthesia. Serum fentanyl analysis was performed at -36, -24, -12, 0, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 18, and 26 hours. Direct arterial blood pressures and arterial blood gases were monitored. The mean body temperatures (+/-SEM) during the anesthetic period for the four treatments were: ISO-NORM = 37.7 +/- 0.07 degrees C, ISO-HYPO = 35.8 +/- 0.1 degrees C, HAL-NORM = 37.7 +/- 0.06 degrees C, and HAL-HYPO = 35.8 +/- 0.13 degrees C. The mean (+/-SEM) serum fentanyl concentrations (SFC) for both hypothermia treatments were significantly lower than baseline concentrations at t = 1 hour and persisted for the duration of anesthesia for the ISO-HYPO treatment but only from t = 1 to 2 hours for the HAL-HYPO treatment. Serum fentanyl concentrations returned to baseline within one hour of the end of anesthesia, regardless of body temperature. There were no significant differences between treatments for systolic or diastolic blood pressure but mean blood pressures were higher during normothermia versus hypothermia during the last hour of anesthesia. Hypothermia during inhalation anesthesia produced a significant reduction in SFC using transdermal administration and was more protracted with isoflurane

Continued advancement of the programming language HAL to an operational status

NASA Technical Reports Server (NTRS)

1971-01-01

The continued advancement of the programming language HAL to operational status is reported. It is demonstrated that the compiler itself can be written in HAL. A HAL-in-HAL experiment proves conclusively that HAL can be used successfully as a compiler implementation tool.

The current matrix elements from HAL QCD method

NASA Astrophysics Data System (ADS)

Watanabe, Kai; Ishii, Noriyoshi

2018-03-01

HAL QCD method is a method to construct a potential (HAL QCD potential) that reproduces the NN scattering phase shift faithful to the QCD. The HAL QCD potential is obtained from QCD by eliminating the degrees of freedom of quarks and gluons and leaving only two particular hadrons. Therefor, in the effective quantum mechanics of two nucleons defined by HAL QCD potential, the conserved current consists not only of the nucleon current but also an extra current originating from the potential (two-body current). Though the form of the two-body current is closely related to the potential, it is not straight forward to extract the former from the latter. In this work, we derive the the current matrix element formula in the quantum mechanics defined by the HAL QCD potential. As a first step, we focus on the non-relativistic case. To give an explicit example, we consider a second quantized non-relativistic two-channel coupling model which we refer to as the original model. From the original model, the HAL QCD potential for the open channel is constructed by eliminating the closed channel in the elastic two-particle scattering region. The current matrix element formula is derived by demanding the effective quantum mechanics defined by the HAL QCD potential to respond to the external field in the same way as the original two-channel coupling model.

DFT study on the adsorption behavior and electronic response of AlN nanotube and nanocage toward toxic halothane gas

NASA Astrophysics Data System (ADS)

Mohammadi, R.; Hosseinian, A.; Khosroshahi, E. Saedi; Edjlali, L.; Vessally, E.

2018-04-01

We have investigated the adsorption of a halothane molecule on the AlN nanotube, and nanocage using density functional theory calculations. We predicted that the halothane molecule tends to be physically adsorbed on the surface of AlN nanotube with adsorption energy (Ead) of -4.2 kcal/mol. The electronic properties of AlN nanotube are not affected by the halothane, and it is not a sensor. But the AlN nanocage is more reactive than the AlN nanotube because of its higher curvature. The halothane tends to be adsorbed on a hexagonal ring, an Alsbnd N bond, and a tetragonal ring of the AlN nanocage. The adsorption ability order is as follows: tetragonal ring (Ead = -14.7 kcal/mol) > Alsbnd N bond (Ead = -12.3 kcal/mol) > hexagonal ring (Ead = -10.1 kcal/mol). When a halothane molecule is adsorbed on the AlN nanocage, its electrical conductivity is increased, demonstrating that it can yield an electronic signal at the presence of this molecule, and can be employed in chemical sensors. The AlN nanocage benefits from a short recovery time of about 58 ms at room temperature.

Lipopolysaccharide induces amyloid formation of antimicrobial peptide HAL-2.

PubMed

Wang, Jiarong; Li, Yan; Wang, Xiaoming; Chen, Wei; Sun, Hongbin; Wang, Junfeng

2014-11-01

Lipopolysaccharide (LPS), the important component of the outer membrane of Gram-negative bacteria, contributes to the integrity of the outer membrane and protects the cell against bactericidal agents, including antimicrobial peptides. However, the mechanisms of interaction between antimicrobial peptides and LPS are not clearly understood. Halictines-2 (HAL-2), one of the novel antimicrobial peptides, was isolated from the venom of the eusocial bee Halictus sexcinctus. HAL-2 has exhibited potent antimicrobial activity against Gram-positive and Gram-negative bacteria and even against cancer cells. Here, we studied the interactions between HAL-2 and LPS to elucidate the antibacterial mechanism of HAL-2 in vitro. Our results show that HAL-2 adopts a significant degree of β-strand structure in the presence of LPS. LPS is capable of inducing HAL-2 amyloid formation, which may play a vital role in its antimicrobial activity. Copyright © 2014 Elsevier B.V. All rights reserved.

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

The functional requirements to be met by the HAL/S-FC compiler, and the hardware and software compatibilities between the compiler system and the environment in which it operates are defined. Associated runtime facilities and the interface with the Software Development Laboratory are specified. The construction of the HAL/S-FC system as functionally separate units and the interfaces between those units is described. An overview of the system's capabilities is presented and the hardware/operating system requirements are specified. The computer-dependent aspects of the HAL/S-FC are also specified. Compiler directives are included.

Human reductive halothane metabolism in vitro is catalyzed by cytochrome P450 2A6 and 3A4.

PubMed

Spracklin, D K; Thummel, K E; Kharasch, E D

1996-09-01

The anesthetic halothane undergoes extensive oxidative and reductive biotransformation, resulting in metabolites that cause hepatotoxicity. Halothane is reduced anaerobically by cytochrome P450 (P450) to the volatile metabolites 2-chloro-1,1-difluoroethene (CDE) and 2-chloro-1,1,1-trifluoroethane (CTE). The purpose of this investigation was to identify the human P450 isoform(s) responsible for reductive halothane metabolism. CDE and CTE formation from halothane metabolism by human liver microsomes was determined by GC/MS analysis. Halothane metabolism to CDE and CTE under reductive conditions was completely inhibited by carbon monoxide, which implicates exclusively P450 in this reaction. Eadie-Hofstee plots of both CDE and CTE formation were nonlinear, suggesting multiple P450 isoform involvement. Microsomal CDE and CTE formation were each inhibited 40-50% by P450 2A6-selective inhibitors (coumarin and 8-methoxypsoralen) and 55-60% by P450 3A4-selective inhibitors (ketoconazole and troleandomycin). P450 1A-, 2B6-, 2C9/10-, and 2D6-selective inhibitors (7,8-benzoflavone, furafylline, orphenadrine, sulfaphenazole, and quinidine) had no significant effect on reductive halothane metabolism. Measurement of product formation catalyzed by a panel of cDNA-expressed P450 isoforms revealed that maximal rates of CDE formation occurred with P450 2A6, followed by P450 3A4. P450 3A4 was the most effective catalyst of CTE formation. Among a panel of 11 different human livers, there were significant linear correlations between the rate of CDE formation and both 2A6 activity (r = 0.64, p < 0.04) and 3A4 activity (r = 0.64, p < 0.03). Similarly, there were significant linear correlations between CTE formation and both 2A6 activity (r = 0.55, p < 0.08) and 3A4 activity (r = 0.77, p < 0.005). The P450 2E1 inhibitors 4-methylpyrazole and diethyldithiocarbamate inhibited CDE and CTE formation by 20-45% and 40-50%, respectively; however, cDNA-expressed P450 2E1 did not catalyze

Prevention of thiopental and thiopental/halothane cardiac sensitization to epinephrine in the sheep.

PubMed Central

Rezakhani, A; Edjtehadi, M; Szabuniewicz, M

1977-01-01

The effects of epinephrine (5 microgram/kg of body weight) on ten unanesthetized sheep were experimentally tested: all sheep displayed serious arrhythmias. Sheep anesthetized with thiopental and thiopental/halothane combination displayed cardiac arrhythmias of the order of 10% and 20% respectively. Challenge injections of epinephrine (5 microgram/kg of body weight) to ten sheep anesthetized with thiopental, and to the same number of animals after 45 minutes of anesthesia with thiopental/halothane, produced serious arrhythmias. However, following preanesthetic treatment with acepromazine maleate (0.5 mg/kg) to 15 sheep, serious arrhythmias were prevented in all of them when they were given arrhythmic doses of epinephrine. Images Fig. 2. PMID:922556

First use of halothane in the United States, C. Ronald Stephen, M.D. (1916-2006).

PubMed

Giesecke, Adolph H

2008-01-01

Anesthesia is one of the most valued discoveries in all of history. Almost immediately after the first public demonstration of ether anesthesia, a search for a better drug began. Ether, despite its flammability, persisted as the primary inhalation agent for over a hundred years. The breakthrough came with the introduction of a non-flammable volatile anesthetic called halothane in 1955. The drug was approved by the FDA in 1958 and quickly became the most commonly used agent in the United States. It was a quantum leap forward in the safety of anesthetic drugs. It became obsolete in 1988 because of hepatotoxicity. Three eminent anesthesiologists: Drs. Abajian of Vermont, Siker of Pittsburgh and Stephen of Duke could have been the first to use halothane in the USA. My review of the documents and writings of the three confirm that Dr. C. Ronald Stephen of Duke University was indeed the first to use and publish on halothane anesthesia in the USA.

Effects of halothane and methoxyflurane on regional brain and spinal cord substance P-like and beta-endorphin-like immunoreactivities in the rat.

PubMed

Karuri, A R; Agarwal, R K; Engelking, L R; Kumar, M S

1998-03-15

Effects of acute exposure (2 hr) to either 1.5% halothane or 0.5% methoxyflurane were investigated in the Sprague Dawley rat. Pituitary (PIT) and central nervous system (CNS) substance P (SP)-like and beta-endorphin (beta-end)-like immunoreactivities were evaluated immediately after anesthetic exposure (2 h), after righting reflex (4 h) or 24 hr postexposure (24 h). Only halothane significantly reduced SP-like immunoreactivity in olfactory bulbs in both the 2-h and 4-h groups. Halothane elevated SP-like immunoreactivity of hippocampus at all three time periods, and in the hypothalamus at 2 h. Both anesthetics significantly depleted thalamic concentrations of SP-like immunoreactivity. Methoxyflurane anesthesia resulted in a drastic decrease in SP-like immunoreactivity in PIT at all three time periods periods, while halothane elevated PIT concentrations of this peptide at 4 h. Both anesthetics significantly decreased beta-end-like immunoreactivity in the olfactory bulbs and thalami at 2, 4, and 24 h. However, halothane alone significantly elevated beta-end-like immunoreactivity in the spinal cord at 24 h. Halothane significantly elevated PIT beta-end-like immunoreactivity at 2 and 24 h, while methoxyflurane significantly lowered it in the 4-h group, but elevated the levels of the same in the 24-h group. Brain stem beta-end immunoreactivity were significantly reduced at 2 h by both anesthetics, and at 4 h by methoxyflurane. Results indicate that halothane and methoxyflurane may differ significantly in their actions on SP and beta-end secreting neurons in the CNS.

Development of single leg version of HAL for hemiplegia.

PubMed

Kawamoto, Hiroaki; Hayashi, Tomohiro; Sakurai, Takeru; Eguchi, Kiyoshi; Sankai, Yoshiyuki

2009-01-01

Our goal is to try to enhance the QoL of persons with hemiplegia by the mean of an active motion support system based on the HAL's technology. The HAL (Hybrid Assistive Limb) in its standard version is an exoskeleton-based robot suit to support and enhance the human motor functions. The purpose of the research presented in this paper is the development of a new version of the HAL to be used as an assistive device providing walking motion support to persons with hemiplegia. It includes the realization of the single leg version of the HAL and the redesign of the original HAL's Autonomous Controller to execute human-like walking motions in an autonomous way. Clinical trials were conducted in order to assess the effectiveness of the developed system. The first stage of the trials described in this paper involved the participation of one hemiplegic patient who has difficulties to flex his right knee. As a result, the knee flexion support for walking provided by the HAL appeared to improve the subject's walking (longer stride and faster steps). The first evaluation of the system with one subject showed promising results for the future developments.

Comparison of the effects of halothane, isoflurane and methoxyflurane on the electroencephalogram of the horse.

PubMed

Johnson, C B; Taylor, P M

1998-11-01

We have investigated in eight ponies the effects of three different end-tidal concentrations of halothane, isoflurane and methoxyflurane on median (F50) and 95% spectral edge (F95) frequencies of the EEG and the second differential (DD) of the middle latency auditory evoked potential (MLAEP). The three concentrations of each agent were chosen to represent approximately the minimum alveolar concentration (MAC), 1.25 MAC and 1.5 MAC for each agent. During halothane anaesthesia, F95 decreased progressively as halothane concentration increased, from mean 13.9 (SD 2.6) at 0.8% to 11.9 (1.1) at 1.2%. DD was lower during anaesthesia with the highest concentration (21 (6.5)) compared with the lowest (27.6 (11.4)). There were no significant changes in F50. During isoflurane anaesthesia, there was a small, but significant increase in F95 between the intermediate and highest concentrations (10.2 (1.5) to 10.8 (1.6)). There were no changes in F50 and DD. Values of F95, F50 and DD at all isoflurane concentrations were similar to those of halothane at the highest concentration. During methoxyflurane anaesthesia, F95 and F50 decreased progressively as methoxyflurane concentration was increased, from 21.3 (0.7) and 6.5 (1), respectively, at 0.26%, to 20.1 (0.6) and 5.6 (0.8), respectively, at 0.39%. DD was lower during anaesthesia with the highest concentration of methoxyflurane (25.7 (7.8)) compared with the lowest (39.7 (20.6)). Values of F95, F50 and DD at all methoxyflurane concentrations were higher than those seen with halothane at the lowest concentration. The different relative positions of the dose-response curves for EEG and MLAEP changes compared with antinociception (MAC) changes suggest differences in the mechanisms of action of these three agents. These differences may explain the incomplete adherence to the Meyer-Overton rule.

Anesthetic biotransformation and renal function in obese patients during and after methoxyflurane or halothane anesthesia.

PubMed

Young, S R; Stoelting, R K; Peterson, C; Madura, J A

1975-04-01

Anesthetic biotransformation and renal function were studied in obese adult patients (148 plus or minus 8 kg; mean plus or minus SE) anesthetized for three hours with 60 per cent nitrous oxide plus either methoxyflurane or halothane for elective jejunoileal small-bowel-bypass operations. There was no evidence of persistent renal dysfunction in any patient postoperatively, but serum osmolality was elevated 72 hours after methoxyflurane anesthesia. Urine concentrating ability was not determined. Peak serum ionic fluoride concentration was 55.8 plus or minus 5.8 muM/1 two hours after discontinuation of methoxyflurane. Urinary ionic fluoride and oxalate excretions increased postoperatively. Compared with previously reported data from nonobese patients, serum ionic fluoride concentrations in obese patients increased more rapidly during methoxyflurane anesthesia and peaked higher and sooner after discontinuation of methoxyflurane. The peak serum ionic fluoride concentration was 10.4 plus or minus 1.5 muM/1 at the conclusion of halothane anesthesia, significantly more than the corresponding value in nonobese patients. Intraoperative liver biopsies from 23 of 27 patients showed moderate to severe fatty metamorphosis. Fatty liver infiltration may have increased hepatic anesthetic uptake and exposed more methoxyflurane or halothane to hepatic microsomal enzymes. The more rapid elevation and higher peak levels of serum ionic fluoride following methoxyflurane, and to a lesser extent following halothane, may reflect increased anesthetic biotransformation in obese compared with nonobese patients. To avoid excessive serum ionic fluoride elevations the authors recommended limiting low-dose methoxyflurane anesthesia delivered to obese patients with potential fatty liver infiltration to no more than three hours.

Reduced incidence of laryngospasm with remifentanil-midazolam anaesthesia compared to halothane-fentanyl.

PubMed

Ali, Shahriari

2008-03-01

To compare the incidence of laryngospasm by using halothane-fentanyl anaesthesia and midazolam-remifentanil anaesthesia in paediatric patients undergoing eye surgery. We enrolled 120 ASA physical status I children aged 7-12 years scheduled for eye surgery from March 2004 to February 2006 in this prospective clinical trial study. Children suffering from any medical condition that could affect airway reflexes such as active upper respiratory infection, symptomatic asthma, obesity, patients with predicted difficulty in tracheal intubation were not included in the study. Patients with prolonged or difficult intubation or those who received another drug before extubation were excluded from the study. Using a random numbers table, participants were allocated to two equal groups. After induction of anaesthesia, in one group Halothane 1% was administered for the maintenance of anaesthesia in addition with intravenous fentanyl 1.5 microg kg(-1), and for the patients of the other group midazolam with a dose of 0.1 mg kg(-1) and remifentanil infusion by a dose of 0.1 microg kg(-1) min(-1) was administered. The patients were extubated in a unique plan of anaesthesia, using the sign of swallowing as a clinical indicator for extubation of patients. The incidence of laryngospasm was lower in midazolam-remifentanil group (0%) in comparison with halothane-fentanyl group (6.6%). The results of our study suggest that remifentanil combined with midazolam in children undergoing eye surgery provided a better condition for extubation of the patients.

Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, J.; Strzalka, J; Tronin, A

2009-01-01

We demonstrate that cyano-phenylalanine (PheCN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-PheCN. The Trp to PheCN mutation alters neither the a-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this PheCN mutant hbAP-PheCN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescencemore » is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-PheCN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four PheCN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-PheCN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form

Vapour growth of argyrodite-type ionic conductors Cu 6PS 5Hal

NASA Astrophysics Data System (ADS)

Fiechter, S.; Eckstein, J.; Nitsche, R.

1983-03-01

Cu 6PS 5Hal compounds (with Hal = Cl, Br or I) have been crystallized around 950 K by CVT with P, S and Hal (and combinations thereof). Chemical insight into the transport processes was gained from dissociation pressure measurements and spectroscopic vapour analysis. Lacking thermochemical data of the compounds were obtained from Cp measurements. Models, derived for the CVT mechanisms, yield transport rates and directions which agree qualitatively with experiments. The main vapour species (for Hal = C1) are PSCI 3, S 2, PCI 3, P 4S 3 and (CuCl) 3. With a surplus of CuHal, VLS growth via liquid CuHal/Cu 2S phases was observed.

Influence of halothane and methoxyflurane on regional brain and spinal cord concentrations of methionine-enkephalin in the rat.

PubMed

Agarwal, R K; Court, M; Chandna, V K; Mohan, A; Engelking, L R; Kumar, A M

1994-01-01

Rats were exposed to either oxygen (controls), 1.5% halothane in oxygen, or methoxyflurane (0.5%) in oxygen over a period of 2 h, then sacrificed at the end of exposure (2-h group), 4 h after removal from environmental chamber (4-h group), or at 24 h following anesthetic exposure (24-h group). Pituitary (excluding the neural lobe, Pit), brain, and spinal cord areas were isolated and processed with Met-enkephalin tissue concentrations determined. In halothane-exposed animals, Met-enkephalin concentrations in pit and across CNS areas studied were significantly lower at 2 h following anesthetic exposure than in control animals. Concentrations of Met-enkephalin in many areas of CNS and Pit of 4-h group approached control levels. Concentrations of Met-enkephalin in all areas studied except spinal cord returned to basal levels by 24 h following halothane exposure. Exposure to methoxyflurane resulted in less dramatic changes in Met-enkephalin concentrations across CNS regions examined. Exposure to methoxyflurane resulted in significant decreases in Met-enkephalin levels in olfactory bulb, thalamus, and hippocampus only. Met-Enkephalin levels did not change significantly in other areas of the central nervous system following methoxyflurane exposure. These results indicate that halothane and methoxyflurane may have differential effects on the endogenous opioid system.

Chemical Aspects of General Anesthesia: Part 1. From Ether to Halothane

ERIC Educational Resources Information Center

Brunsvold, Robert; Ostercamp, Daryl L.

2006-01-01

The history and evolution of general anesthesia, which invokes a variety of drugs, each compound having a specific purpose from muscle relaxation to unconsciousness is discussed. Some of the popular anesthetics discussed are ether, chloroform, halocarbons, gaseous nitrous oxide, halothane, and mixture of 70% nitrous oxide and 30% oxygen.

The programming language HAL: A specification

NASA Technical Reports Server (NTRS)

1971-01-01

HAL accomplishes three significant objectives: (1) increased readability, through the use of a natural two-dimensional mathematical format; (2) increased reliability, by providing for selective recognition of common data and subroutines, and by incorporating specific data-protect features; (3) real-time control facility, by including a comprehensive set of real-time control commands and signal conditions. Although HAL is designed primarily for programming on-board computers, it is general enough to meet nearly all the needs in the production, verification and support of aerospace, and other real-time applications.

Effects of sevoflurane anaesthesia on recovery in children: a comparison with halothane.

PubMed

Lapin, S L; Auden, S M; Goldsmith, L J; Reynolds, A M

1999-01-01

We prospectively studied one hundred ASA physical status I-II children, ages six months to six years, undergoing myringotomy surgery. Children were randomly assigned to one of four anaesthetic groups receiving either halothane or sevoflurane for anaesthesia and oral midazolam premedication or no premedication. We found that children anaesthetized with sevoflurane had significantly faster recovery times and discharge home times than those who received halothane. Patients given oral midazolam premedication had significantly longer recovery times, but no delay in discharge home compared with those not premedicated. However, children anaesthetized with sevoflurane and no premedication had an unacceptably high incidence (67%) of postoperative agitation. The use of oral midazolam preoperatively did decrease the amount of postoperative agitation seen with sevoflurane. We conclude that although sevoflurane does shorten recovery times, the degree of associated postoperative agitation makes it unacceptable as a sole anaesthetic for myringotomy surgery.

Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease.

PubMed

Yu, Bing; Li, Alexander H; Muzny, Donna; Veeraraghavan, Narayanan; de Vries, Paul S; Bis, Joshua C; Musani, Solomon K; Alexander, Danny; Morrison, Alanna C; Franco, Oscar H; Uitterlinden, André; Hofman, Albert; Dehghan, Abbas; Wilson, James G; Psaty, Bruce M; Gibbs, Richard; Wei, Peng; Boerwinkle, Eric

2015-04-01

Histidine is a semiessential amino acid with antioxidant and anti-inflammatory properties. Few data are available on the associations between genetic variants, histidine levels, and incident coronary heart disease (CHD) in a population-based sample. By conducting whole exome sequencing on 1152 African Americans in the Atherosclerosis Risk in Communities (ARIC) study and focusing on loss-of-function (LoF) variants, we identified 3 novel rare LoF variants in HAL, a gene that encodes histidine ammonia-lyase in the first step of histidine catabolism. These LoF variants had large effects on blood histidine levels (β=0.26; P=1.2×10(-13)). The positive association with histidine levels was replicated by genotyping an independent sample of 718 ARIC African Americans (minor allele frequency=1%; P=1.2×10(-4)). In addition, high blood histidine levels were associated with reduced risk of developing incident CHD with an average of 21.5 years of follow-up among African Americans (hazard ratio=0.18; P=1.9×10(-4)). This finding was validated in an independent sample of European Americans from the Framingham Heart Study (FHS) Offspring Cohort. However, LoF variants in HAL were not directly significantly associated with incident CHD after meta-analyzing results from the CHARGE Consortium. Three LoF mutations in HAL were associated with increased histidine levels, which in turn were shown to be inversely related to the risk of CHD among both African Americans and European Americans. Future investigations on the association between HAL gene variation and CHD are warranted. © 2015 American Heart Association, Inc.

Lasagna-type arrays with halide-nitromethane cluster filling. The first recognition of the Hal(-)···HCH2NO2 (Hal = Cl, Br, I) hydrogen bonding.

PubMed

Gushchin, Pavel V; Kuznetsov, Maxim L; Wang, Qian; Karasik, Andrey A; Haukka, Matti; Starova, Galina L; Kukushkin, Vadim Yu

2012-06-21

The previously predicted ability of the methyl group of nitromethane to form hydrogen bonding with halides is now confirmed experimentally based on X-ray data of novel nitromethane solvates followed by theoretical ab initio calculations at the MP2 level of theory. The cationic (1,3,5-triazapentadiene)Pt(II) complexes [Pt{HN=C(NC(5)H(10))N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [1](Hal)(2) (Hal = Cl, Br, I), and [Pt{HN=C(NC(4)H(8)O)N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [2](Cl)(2), were crystallized from MeNO(2)-containing systems providing nitromethane solvates studied by X-ray diffraction. In the crystal structure of [1][(Hal)(2)(MeNO(2))(2)] (Hal = Cl, Br, I) and [2][(Cl)(2)(MeNO(2))(2)], the solvated MeNO(2) molecules occupy vacant spaces between lasagna-type layers and connect to the Hal(-) ion through a weak hydrogen bridge via the H atom of the methyl thus forming, by means of the Hal(-)···HCH(2)NO(2) contact, the halide-nitromethane cluster "filling". The quantum-chemical calculations demonstrated that the short distance between the Hal(-) anion and the hydrogen atom of nitromethane in clusters [1][(Hal)(2)(MeNO(2))(2)] and [2][(Cl)(2)(MeNO(2))(2)] is not just a consequence of the packing effect but a result of the moderately strong hydrogen bonding.

Mechanism of Interaction Between the General Anesthetic Halothane and a Model Ion Channel Protein, I: Structural Investigations via X-Ray Reflectivity from Langmuir Monolayers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strzalka, J.; Liu, J; Tronin, A

2009-01-01

We previously reported the synthesis and structural characterization of a model membrane protein comprised of an amphiphilic 4-helix bundle peptide with a hydrophobic domain based on a synthetic ion channel and a hydrophilic domain with designed cavities for binding the general anesthetic halothane. In this work, we synthesized an improved version of this halothane-binding amphiphilic peptide with only a single cavity and an otherwise identical control peptide with no such cavity, and applied x-ray reflectivity to monolayers of these peptides to probe the distribution of halothane along the length of the core of the 4-helix bundle as a function ofmore » the concentration of halothane. At the moderate concentrations achieved in this study, approximately three molecules of halothane were found to be localized within a broad symmetric unimodal distribution centered about the designed cavity. At the lowest concentration achieved, of approximately one molecule per bundle, the halothane distribution became narrower and more peaked due to a component of {approx}19Angstroms width centered about the designed cavity. At higher concentrations, approximately six to seven molecules were found to be uniformly distributed along the length of the bundle, corresponding to approximately one molecule per heptad. Monolayers of the control peptide showed only the latter behavior, namely a uniform distribution along the length of the bundle irrespective of the halothane concentration over this range. The results provide insight into the nature of such weak binding when the dissociation constant is in the mM regime, relevant for clinical applications of anesthesia. They also demonstrate the suitability of both the model system and the experimental technique for additional work on the mechanism of general anesthesia, some of it presented in the companion parts II and III under this title.« less

QT-RR relationships and suitable QT correction formulas for halothane-anesthetized dogs.

PubMed

Tabo, Mitsuyasu; Nakamura, Mikiko; Kimura, Kazuya; Ito, Shigeo

2006-10-01

Several QT correction (QTc) formulas have been used for assessing the QT liability of drugs. However, they are known to under- and over-correct the QT interval and tend to be specific to species and experimental conditions. The purpose of this study was to determine a suitable formula for halothane-anesthetized dogs highly sensitive to drug-induced QT interval prolongation. Twenty dogs were anesthetized with 1.5% halothane and the relationship between the QT and RR intervals were obtained by changing the heart rate under atrial pacing conditions. The QT interval was corrected for the RR interval by applying 4 published formulas (Bazett, Fridericia, Van de Water, and Matsunaga); Fridericia's formula (QTcF = QT/RR(0.33)) showed the least slope and lowest R(2) value for the linear regression of QTc intervals against RR intervals, indicating that it dissociated changes in heart rate most effectively. An optimized formula (QTcX = QT/RR(0.3879)) is defined by analysis of covariance and represents a correction algorithm superior to Fridericia's formula. For both Fridericia's and the optimized formula, QT-prolonging drugs (d,l-sotalol, astemizole) showed QTc interval prolongation. A non-QT-prolonging drug (d,l-propranolol) failed to prolong the QTc interval. In addition, drug-induced changes in QTcF and QTcX intervals were highly correlated with those of the QT interval paced at a cycle length of 500 msec. These findings suggest that Fridericia's and the optimized formula, although the optimized is a little bit better, are suitable for correcting the QT interval in halothane-anesthetized dogs and help to evaluate the potential QT prolongation of drugs with high accuracy.

76 FR 19350 - Truax, Hal D.; Notice of Filing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-07

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. ID-6528-000] Truax, Hal D.; Notice of Filing Take notice that on April 1, 2011, Hal D. Truax submitted for filing, an application for...-8659. Comment Date: 5 p.m. Eastern Time on April 21, 2011. Dated: April 1, 2011. Kimberly D. Bose...

Use of intranasal fentanyl in children undergoing myringotomy and tube placement during halothane and sevoflurane anesthesia.

PubMed

Galinkin, J L; Fazi, L M; Cuy, R M; Chiavacci, R M; Kurth, C D; Shah, U K; Jacobs, I N; Watcha, M F

2000-12-01

Many children are restless, disoriented, and inconsolable immediately after bilateral myringotomy and tympanosotomy tube placement (BMT). Rapid emergence from sevoflurane anesthesia and postoperative pain may increase emergence agitation. The authors first determined serum fentanyl concentrations in a two-phase study of intranasal fentanyl. The second phase was a prospective, placebo-controlled, double-blind study to determine the efficacy of intranasal fentanyl in reducing emergence agitation after sevoflurane or halothane anesthesia. In phase 1, 26 children with American Society of Anesthesiologists (ASA) physical status I or II who were scheduled for BMT received intranasal fentanyl, 2 microg/kg, during a standardized anesthetic. Serum fentanyl concentrations in blood samples drawn at emergence and at postanesthesia care unit (PACU) discharge were determined by radioimmunoassay. In phase 2, 265 children with ASA physical status I or II were randomized to receive sevoflurane or halothane anesthesia along with either intranasal fentanyl (2 microg/kg) or saline. Postoperative agitation, Children's Hospital of Eastern Ontario Pain Scale (CHEOPS) scores, and satisfaction of PACU nurses and parents with the anesthetic technique were evaluated. In phase 1, the mean fentanyl concentrations at 10 +/- 4 min (mean +/- SD) and 34 +/- 9 min after administering intranasal fentanyl were 0.80 +/- 0.28 and 0.64 +/- 0.25 ng/ml, respectively. In phase 2, the incidence of severe agitation, highest CHEOPS scores, and heart rate in the PACU were decreased with intranasal fentanyl. There were no differences between sevoflurane and halothane in these measures and in times to hospital discharge. The incidence of postoperative vomiting, hypoxemia, and slow respiratory rates were not increased with fentanyl. Serum fentanyl concentrations after intranasal administration exceed the minimum effective steady state concentration for analgesia in adults. The use of intranasal fentanyl during

Effect of low-dose atropine administration on dobutamine dose requirement in horses anesthetized with detomidine and halothane.

PubMed

Weil, A B; Keegan, R D; Greene, S A

1997-12-01

To determine whether a low dose of atropine is associated with decreased requirement for cardiovascular supportive treatment in horses given detomidine prior to maintenance of general anesthesia with halothane. 3 groups of 10 healthy horses. Detomidine (20 micrograms/kg of body weight, i.m.) was administered to all 30 horses. Then, 10 horses received atropine (0.006 mg/kg, i.v.) 1 hour after detomidine administration, 10 horses received atropine (0.012 mg/kg, i.m.) at the time of detomidine administration, and 10 horses served as a control group. Heart rate was measured prior to detomidine administration and at fixed intervals throughout anesthesia. The dobutamine infusion rate necessary to maintain mean arterial blood pressure between 70 and 80 mm of Hg was recorded. Systemic blood pressures, end-tidal halothane, end-tidal CO2, and arterial blood gas tensions were measured at fixed intervals. Mean heart rate was higher among horses receiving atropine i.v. or i.m., compared with that in control horses. Horses that received atropine i.v. had higher systemic arterial blood pressure and required a lower dobutamine infusion rate than did horses of the other groups. Detomidine-treated, halothane-anesthetized horses given atropine i.v. required less dobutamine, compared with horses receiving or not receiving atropine i.m. Complications, such as colic and dysrhythmias, from use of higher doses of atropine, were not observed at this lower dose of atropine. i.v. administration of a low dose of atropine prior to induction of general anesthesia may result in improved blood pressure in horses that have received detomidine before anesthesia with halothane.

RevManHAL: towards automatic text generation in systematic reviews.

PubMed

Torres Torres, Mercedes; Adams, Clive E

2017-02-09

Systematic reviews are a key part of healthcare evaluation. They involve important painstaking but repetitive work. A major producer of systematic reviews, the Cochrane Collaboration, employs Review Manager (RevMan) programme-a software which assists reviewers and produces XML-structured files. This paper describes an add-on programme (RevManHAL) which helps auto-generate the abstract, results and discussion sections of RevMan-generated reviews in multiple languages. The paper also describes future developments for RevManHAL. RevManHAL was created in Java using NetBeans by a programmer working full time for 2 months. The resulting open-source programme uses editable phrase banks to envelop text/numbers from within the prepared RevMan file in formatted readable text of a chosen language. In this way, considerable parts of the review's 'abstract', 'results' and 'discussion' sections are created and a phrase added to 'acknowledgements'. RevManHAL's output needs to be checked by reviewers, but already, from our experience within the Cochrane Schizophrenia Group (200 maintained reviews, 900 reviewers), RevManHAL has saved much time which is better employed thinking about the meaning of the data rather than restating them. Many more functions will become possible as review writing becomes increasingly automated.

The effects of ryanodine receptor (RYR1) mutation on natural killer cell cytotoxicity, plasma cytokines and stress hormones during acute intermittent exercise in pigs.

PubMed

Ciepielewski, Z M; Stojek, W; Borman, A; Myślińska, D; Pałczyńska, P; Kamyczek, M

2016-04-01

Stress susceptibility has been mapped to a single recessive gene, the ryanodine receptor 1 (RYR1) gene or halothane (Hal) gene. Homozygous (Hal(nn)), mutated pigs are sensitive to halothane and susceptible to Porcine Stress Syndrome (PSS). Previous studies have shown that stress-susceptible RYR1 gene mutated homozygotes in response to restraint stress showed an increase in natural killer cell cytotoxicity (NKCC) accompanied by more pronounced stress-related hormone and anti-inflammatory cytokine changes. In order to determine the relationship of a RYR1 gene mutation with NKCC, plasma cytokines and stress-related hormones following a different stress model - exercise - 36 male pigs (representing different genotypes according to RYR1 gene mutation: NN, homozygous dominant; Nn, heterozygous; nn, homozygous recessive) were submitted to an intermittent treadmill walking. During the entire experiment the greatest level of NKCC and the greatest concentrations of interleukin (IL-) 6, IL-10, IL-12, interferon (IFN-)γ and tumor necrosis factor-α and stress-related hormones (adrenaline, prolactin, beta-endorphin) were observed in nn pigs, and the greatest concentration of IL-1 and growth hormone in NN pigs. Immunostimulatory effects of intermittent exercise on NKCC in nn pigs were concomitant with increases in IL-2, IL-12 and IFN-γ, the potent NKCC activators. Our findings suggest that stress-susceptible pigs RYR1 gene mutated pigs develop a greater level of NKCC and cytokine production in response to exercise stress. These results suggest that the heterogeneity of immunological and neuroendocrine response to exercise stress in pigs could be influenced by RYR1 gene mutation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of high-dose gentamicin sulfate on neuromuscular blockade in halothane-anesthetized horses.

PubMed

Hague, B A; Martinez, E A; Hartsfield, S M

1997-11-01

To evaluate effects of a single high dose of gentamicin on neuromuscular function in horses anesthetized with halothane. 6 healthy adult horses. Halothane-anesthetized horses were positioned in left lateral recumbency, and the right hind limb was immobilized in a reusable fiberglass cast fixed to a steel frame. The hoof was attached to a force transducer, and resting tension of 0.93 +/- 0.16 kg was maintained. A supramaximal train-of-four stimulus of 2 Hz for a duration of 0.25 millisecond was applied to the superficial peroneal nerve every 20 seconds by a square-wave stimulator. The force of the evoked digital extensor tension was recorded to determine first muscle twitch tension, compared with the baseline value (T1%) and the ratio of the force of the fourth twitch to the first twitch (T4/T1). Data were recorded at 5, 10, 15, 30, and 60 minutes after i.v. administration of vehicle or gentamicin (6 mg/kg of body weight). There was a significant (P = 0.04) treatment-time interaction for the effect of gentamicin on T1%; T1% associated with vehicle decreased from 100% to 92% during the 60- minute study period, but no decrease was associated with gentamicin. For T4/T1, there was no significant effect of treatment or time or treatment-time interaction between gentamicin and vehicle. Gentamicin did not cause a decrease in initial muscular strength, nor did it impair the muscles' ability to sustain strength. A single high dose of gentamicin does not cause significant neuromuscular blockade when administered alone to healthy horses anesthetized with halothane.

Regulation of cation transport in Saccharomyces cerevisiae by the salt tolerance gene HAL3.

PubMed Central

Ferrando, A; Kron, S J; Rios, G; Fink, G R; Serrano, R

1995-01-01

Dynamic regulation of ion transport is essential for homeostasis as cells confront changes in their environment. The gene HAL3 encodes a novel component of this regulatory circuit in the yeast Saccharomyces cerevisiae. Overexpression of HAL3 improves growth of wild-type cells exposed to toxic concentrations of sodium and lithium and suppresses the salt sensitivity conferred by mutation of the calcium-dependent protein phosphatase calcineurin. Null mutants of HAL3 display salt sensitivity. The sequence of HAL3 gives little clue to its function. However, alterations in intracellular cation concentrations associated with changes in HAL3 expression suggest that HAL3 activity may directly increase cytoplasmic K+ and decrease Na+ and Li+. Cation efflux in S. cerevisiae is mediated by the P-type ATPase encoded by the ENA1/PMR24 gene, a putative plasma membrane Na+ pump whose expression is salt induced. Acting in concert with calcineurin, HAL3 is necessary for full activation of ENA1 expression. This functional complementarity is also reflected in the participation of both proteins in recovery from alpha-factor-induced growth arrest. Recently, HAL3 was isolated as a gene (named SIS2) which when overexpressed partially relieves loss of transcription of G1 cyclins in mutants lacking the protein phosphatase Sit4p. Therefore, HAL3 influences cell cycle control and ion homeostasis, acting in parallel to the protein phosphatases Sit4p and calcineurin. PMID:7565698

A novel O2-sensing mechanism in rat glossopharyngeal neurones mediated by a halothane-inhibitable background K+ conductance.

PubMed

Campanucci, Verónica A; Fearon, Ian M; Nurse, Colin A

2003-05-01

Modulation of K+ channels by hypoxia is a common O2-sensing mechanism in specialised cells. More recently, acid-sensitive TASK-like background K+ channels, which play a key role in setting the resting membrane potential, have been implicated in O2-sensing in certain cell types. Here, we report a novel O2 sensitivity mediated by a weakly pH-sensitive background K+ conductance in nitric oxide synthase (NOS)-positive neurones of the glossopharyngeal nerve (GPN). This conductance was insensitive to 30 mM TEA, 5 mM 4-aminopyridine (4-AP) and 200 microM Cd2+, but was reversibly inhibited by hypoxia (O2 tension (PO2) = 15 mmHg), 2-5 mM halothane, 10 mM barium and 1 mM quinidine. Notably, the presence of halothane occluded the inhibitory effect of hypoxia. Under current clamp, these agents depolarised GPN neurones. In contrast, arachidonic acid (5-10 microM) caused membrane hyperpolarisation and potentiation of the background K+ current. This pharmacological profile suggests the O2-sensitive conductance in GPN neurones is mediated by a class of background K+ channels different from the TASK family; it appears more closely related to the THIK (tandem pore domain halothane-inhibited K+) subfamily, or may represent a new member of the background K+ family. Since GPN neurones are thought to provide NO-mediated efferent inhibition of the carotid body (CB), these channels may contribute to the regulation of breathing during hypoxia via negative feedback control of CB function, as well as to the inhibitory effect of volatile anaesthetics (e.g. halothane) on respiration.

Speaking Personally--With Hal Markowitz

ERIC Educational Resources Information Center

Pittman, Von

2012-01-01

This article presents an interview with Hal Markowitz, a veteran distance educator whose experience in the field is both deep and broad. Building on bachelor's and master's degrees at the University of Florida and his doctorate at Columbia University, Markowitz served in leadership roles in several professional organizations and directed distance…

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.

PubMed

Cheng, Mary Hongying; Coalson, Rob D; Tang, Pei

2010-11-24

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.

Incubation temperature effects on physical characteristics of normal, dark, firm and dry, and halothane-carrier pork longissimus.

PubMed

McCaw, J; Ellis, M; Brewer, M S; McKeith, F K

1997-06-01

Pigs (n = 18) were selected to represent three different muscle conditions (six pigs per condition): normal: dark, firm, and dry; and halothane carrier. A 45-cm-long longissimus section was excised from each side of the carcass at 30 min postmortem and cut into six sections. Right side sections were assigned to the intermediate temperature incubation (23 degrees C), and left side sections were designated high temperature incubation (40 degrees C). Sections were randomly assigned to incubation times (0, 1, 2, 4, 6, or 8 h). The 0 h section from each incubation treatment was designated as a control and was placed directly into a 4 degree C cooler. Temperature and pH were evaluated on the control section and for each loin section a the end of the incubation time. Color (L*, a*, and b* values), percentage of purge loss, water-holding capacity, and drip loss were determined. Incubation treatment did not alter pH decline in dark, firm, and dry muscle; however, high temperature increased pH decline in normal and halothane carrier samples. Results suggest that there is a strong interaction between pH and temperature that affects pork quality attributes. High incubation temperature had a negative effect on most quality variables; however, muscle condition (normal or halothane carrier) had limited effects on muscle quality.

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

PubMed

Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David

2013-05-15

Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance. We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal. hickey@soe.ucsc.edu or haussler@soe.ucsc.edu Supplementary data are available at Bioinformatics online.

A possible molecular mechanism for the pressure reversal of general anaesthetics: Aggregation of halothane in POPC bilayers at high pressure

NASA Astrophysics Data System (ADS)

Tu, K. M.; Matubayasi, N.; Liang, K. K.; Todorov, I. T.; Chan, S. L.; Chau, P.-L.

2012-08-01

We placed halothane, a general anaesthetic, inside palmitoyloleoylphosphatidylcholine (POPC) bilayers and performed molecular dynamics simulations at atmospheric and raised pressures. We demonstrated that halothane aggregated inside POPC membranes at 20 MPa but not at 40 MPa. The pressure range of aggregation matches that of pressure reversal in whole animals, and strongly suggests that this could be the mechanism for this effect. Combining these results with previous experimental data, we describe a testable hypothesis of how aggregation of general anaesthetics at high pressure can lead to pressure reversal, the effect whereby these drugs lose the efficacy at high pressure.

Chemical composition of HAL, an isotopically-unusual Allende inclusion

NASA Technical Reports Server (NTRS)

Davis, A. M.; Tanaka, T.; Grossman, L.; Lee, T.; Wasserburg, G. J.

1982-01-01

Samples of hibonite, black rim, and portions of friable rim from an unusual Allende inclusion, named HAL, were analyzed by INAA and RNAA for 37 major, minor, and trace elements. An unusually low amount of Ce was found in HAL, although it otherwise was highly enriched in REE compared to C1 chondrites. HAL is also depleted in Sr, Ba, U, V, Ru, Os, and Ir relative to other refractory elements. It is concluded that the distribution of REE between hibonite and rims was established when hibonite and other refractory minerals were removed at slightly different temperatures from a hot, oxidizing gas in which they previously coexisted as separate grains. Possible locations for the chemical and mass dependent isotopic fractionation are considered to be in ejecta from the low temperature helium-burning zone of a supernova and in the locally oxidizing environment generated by evaporation of interstellar grains of near-chondritic chemical composition.

Chemical composition of HAL, an isotopically-unusual Allende inclusion

NASA Astrophysics Data System (ADS)

Davis, A. M.; Tanaka, T.; Grossman, L.; Lee, T.; Wasserburg, G. J.

1982-09-01

Samples of hibonite, black rim, and portions of friable rim from an unusual Allende inclusion, named HAL, were analyzed by INAA and RNAA for 37 major, minor, and trace elements. An unusually low amount of Ce was found in HAL, although it otherwise was highly enriched in REE compared to C1 chondrites. HAL is also depleted in Sr, Ba, U, V, Ru, Os, and Ir relative to other refractory elements. It is concluded that the distribution of REE between hibonite and rims was established when hibonite and other refractory minerals were removed at slightly different temperatures from a hot, oxidizing gas in which they previously coexisted as separate grains. Possible locations for the chemical and mass dependent isotopic fractionation are considered to be in ejecta from the low temperature helium-burning zone of a supernova and in the locally oxidizing environment generated by evaporation of interstellar grains of near-chondritic chemical composition.

HIV-1/HAART-Related Lipodystrophy Syndrome (HALS) Is Associated with Decreased Circulating sTWEAK Levels

PubMed Central

López-Dupla, Miguel; Maymó-Masip, Elsa; Martínez, Esteban; Domingo, Pere; Leal, Manuel; Peraire, Joaquim; Viladés, Consuelo; Veloso, Sergi; Arnedo, Mireia; Ferrando-Martínez, Sara; Beltrán-Debón, Raúl; Alba, Verónica; Gatell, Josep Mª; Vendrell, Joan; Vidal, Francesc; Chacón, Matilde R.

2015-01-01

Background and Objectives Obesity and HIV-1/HAART–associated lipodystrophy syndrome (HALS) share clinical, pathological and mechanistic features. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a multifunctional cytokine that plays an important role in obesity and related diseases. We sought to explore the relationship between HALS and circulating levels of soluble (s) TWEAK and its scavenger receptor sCD163. Methods This was a cross-sectional multicenter study of 120 HIV-1-infected patients treated with a stable HAART regimen; 56 with overt HALS and 64 without HALS. Epidemiological and clinical variables were determined. Serum levels of sTWEAK and sCD163 levels were measured by ELISA. Results were analyzed with Student’s t-test, Mann-Whitney U and χ2 test. Pearson and Spearman correlation were used to estimate the strength of association between variables. Results Circulating sTWEAK was significantly decreased in HALS patients compared with non-HALS patients (2.81±0.2 vs. 2.94±0.28 pg/mL, p = 0.018). No changes were observed in sCD163 levels in the studied cohorts. On multivariate analysis, a lower log sTWEAK concentration was independently associated with the presence of HALS (OR 0.027, 95% CI 0.001–0.521, p = 0.027). Conclusions HALS is associated with decreased sTWEAK levels. PMID:26658801

HIV-1/HAART-Related Lipodystrophy Syndrome (HALS) Is Associated with Decreased Circulating sTWEAK Levels.

PubMed

López-Dupla, Miguel; Maymó-Masip, Elsa; Martínez, Esteban; Domingo, Pere; Leal, Manuel; Peraire, Joaquim; Viladés, Consuelo; Veloso, Sergi; Arnedo, Mireia; Ferrando-Martínez, Sara; Beltrán-Debón, Raúl; Alba, Verónica; Gatell, Josep Ma; Vendrell, Joan; Vidal, Francesc; Chacón, Matilde R

2015-01-01

Obesity and HIV-1/HAART-associated lipodystrophy syndrome (HALS) share clinical, pathological and mechanistic features. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a multifunctional cytokine that plays an important role in obesity and related diseases. We sought to explore the relationship between HALS and circulating levels of soluble (s) TWEAK and its scavenger receptor sCD163. This was a cross-sectional multicenter study of 120 HIV-1-infected patients treated with a stable HAART regimen; 56 with overt HALS and 64 without HALS. Epidemiological and clinical variables were determined. Serum levels of sTWEAK and sCD163 levels were measured by ELISA. Results were analyzed with Student's t-test, Mann-Whitney U and χ2 test. Pearson and Spearman correlation were used to estimate the strength of association between variables. Circulating sTWEAK was significantly decreased in HALS patients compared with non-HALS patients (2.81±0.2 vs. 2.94±0.28 pg/mL, p = 0.018). No changes were observed in sCD163 levels in the studied cohorts. On multivariate analysis, a lower log sTWEAK concentration was independently associated with the presence of HALS (OR 0.027, 95% CI 0.001-0.521, p = 0.027). HALS is associated with decreased sTWEAK levels.

Current matrix element in HAL QCD's wavefunction-equivalent potential method

NASA Astrophysics Data System (ADS)

Watanabe, Kai; Ishii, Noriyoshi

2018-04-01

We give a formula to calculate a matrix element of a conserved current in the effective quantum mechanics defined by the wavefunction-equivalent potentials proposed by the HAL QCD collaboration. As a first step, a non-relativistic field theory with two-channel coupling is considered as the original theory, with which a wavefunction-equivalent HAL QCD potential is obtained in a closed analytic form. The external field method is used to derive the formula by demanding that the result should agree with the original theory. With this formula, the matrix element is obtained by sandwiching the effective current operator between the left and right eigenfunctions of the effective Hamiltonian associated with the HAL QCD potential. In addition to the naive one-body current, the effective current operator contains an additional two-body term emerging from the degrees of freedom which has been integrated out.

[Efficiency of combined methods of hemorroid treatment using hal-rar and laser destruction].

PubMed

Rodoman, G V; Kornev, L V; Shalaeva, T I; Malushenko, R N

2017-01-01

To develop the combined method of treatment of hemorrhoids with arterial ligation under Doppler control and laser destruction of internal and external hemorrhoids. The study included 100 patients with chronic hemorrhoids stage II and III. Combined method of HAL-laser was used in study group, HAL RAR-technique in control group 1 and closed hemorrhoidectomy with linear stapler in control group 2. Сomparative evaluation of results in both groups was performed. Combined method overcomes the drawbacks of traditional surgical treatment and limitations in external components elimination which are inherent for HAL-RAR. Moreover, it has a higher efficiency in treating of hemorrhoids stage II-III compared with HAL-RAR and is equally safe and well tolerable for patients. This method does not increase the risk of recurrence, reduces incidence of complications and time of disability.

[The effect of halothane on the fructose metabolism in the liver].

PubMed

Götz, E; Scholz, R

1975-10-01

Glucose production from frutose (2 mmol) and fructolysis was studied in perfused rat liver. In the presence of halothane (0.5, 1.5, and 4.0 vol%) glucose production was inhibited, whereas lactate production was stimulated. Total fructose metabolism was unchanged. Since halogenated hydrocarbon compounds are known to inhibit the mitochondrial respiratory chain, it is concluded that glucose synthesis is inhibited due to decreased supply of energy-rich phosphates from oxidative phosphorylation. On the other hand, this depletion of energy may be partially compensated for by an increased extramitochondrial energy production due to fructolysis.

On the performance of the HAL/S-FC compiler. [for space shuttles

NASA Technical Reports Server (NTRS)

Martin, F. H.

1975-01-01

The HAL/S compilers which will be used in the space shuttles are described. Acceptance test objectives and procedures are described, the raw results are presented and analyzed, and conclusions and observations are drawn. An appendix is included containing an illustrative set of compiler listings and results for one of the test cases.

Hal: an automated pipeline for phylogenetic analyses of genomic data.

PubMed

Robbertse, Barbara; Yoder, Ryan J; Boyd, Alex; Reeves, John; Spatafora, Joseph W

2011-02-07

The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed.

The Yeast HAL1 Gene Improves Salt Tolerance of Transgenic Tomato1

PubMed Central

Gisbert, Carmina; Rus, Ana M.; Bolarín, M. Carmen; López-Coronado, J. Miguel; Arrillaga, Isabel; Montesinos, Consuelo; Caro, Manuel; Serrano, Ramon; Moreno, Vicente

2000-01-01

Overexpression of the HAL1 gene in yeast has a positive effect on salt tolerance by maintaining a high internal K+ concentration and decreasing intracellular Na+ during salt stress. In the present work, the yeast gene HAL1 was introduced into tomato (Lycopersicon esculentum Mill.) by Agrobacterium tumefaciens-mediated transformation. A sample of primary transformants was self-pollinated, and progeny from both transformed and non-transformed plants (controls) were evaluated for salt tolerance in vitro and in vivo. Results from different tests indicated a higher level of salt tolerance in the progeny of two different transgenic plants bearing four copies or one copy of the HAL1 gene. In addition, measurement of the intracellular K+ to Na+ ratios showed that transgenic lines were able to retain more K+ than the control under salt stress. Although plants and yeast cannot be compared in an absolute sense, these results indicate that the mechanism controlling the positive effect of the HAL1 gene on salt tolerance may be similar in transgenic plants and yeast. PMID:10806256

Comparative Analysis of Doppler Guided Hemorrhoidal Artery Ligation (DG-HAL) & Infrared Coagulation (IRC) in Management of Hemorrhoids.

PubMed

Ahmad, Arshad; Kant, Rama; Gupta, Avneet

2013-08-01

Both Doppler-guided hemorrhoidal artery ligation (DG-HAL) and infrared coagulation (IRC) are well-established techniques in the management of hemorrhoids. The aim of the study is to compare the clinical outcomes of DG-HAL and IRC in the patients with grade 1 and 2 hemorrhoids. A total of 296 patients were registered for the study, but 51 patients were lost in follow-up; hence, finally 245 patients were included in the analysis. Patients were randomized into two groups (mean age, 42 years; range, 19-60 years). Group A (n = 116) was treated with DG-HAL and group B (n = 129) was treated with IRC. Patients were examined at 1 week, 1 month, and 6 months after the procedure. Mean time taken for HAL was 21 min and for IRC, 12 min. The cost of the DG-HAL procedure was 1,440 rupees ($31.53) and that of IRC was 376 rupees ($8). The mean duration of hospital stay after HAL was 6 h and after IRC, 2 h. Control of symptoms with HAL was 96 %, whereas with IRC, 81 %. Postoperative complication rate for HAL was 2 %, whereas for IRC, 13 %. Requirement of repeat procedure with HAL was 9 % and with IRC, 28 %. Both the procedures are minimally invasive, associated with minimal discomfort, and suitable for day care surgery. IRC requires lesser procedure time, lesser postoperative hospital stay, and has lower procedure cost, whereas DG-HAL is more effective in controlling symptoms of hemorrhoids, has lower post operative complication rate, and has lesser requirement of repeat procedure.

HAL-2 Promotes Homologous Pairing during Caenorhabditis elegans Meiosis by Antagonizing Inhibitory Effects of Synaptonemal Complex Precursors

PubMed Central

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S.; MacQueen, Amy J.; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M.; Villeneuve, Anne M.

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification. PMID:22912597

HAL-2 promotes homologous pairing during Caenorhabditis elegans meiosis by antagonizing inhibitory effects of synaptonemal complex precursors.

PubMed

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S; MacQueen, Amy J; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M; Villeneuve, Anne M

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification.

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

Compiler organization is discussed, including overall compiler structure, internal data transfer, compiler development, and code optimization. The user, system, and SDL interfaces are described, along with compiler system requirements. Run-time software support package and restrictions and dependencies are also considered of the HAL/S-FC system.

Effects of MK-801 upon local cerebral glucose utilization in conscious rats and in rats anaesthetised with halothane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurumaji, A.; McCulloch, J.

1989-12-01

The effects of MK-801 (0.5 mg/kg i.v.), a non-competitive N-methyl-D-aspartate (NMDA) antagonist, upon local cerebral glucose utilization were examined in conscious, lightly restrained rats and in rats anaesthetised with halothane in nitrous oxide by means of the quantitative autoradiographic (14C)-2-deoxyglucose technique. In the conscious rats, MK-801 produced a heterogenous pattern of altered cerebral glucose utilization with significant increases being observed in 12 of the 28 regions of gray matter examined and significant decreases in 6 of the 28 regions. Pronounced increases in glucose use were observed after MK-801 in the olfactory areas and in a number of brain areas inmore » the limbic system (e.g., hippocampus molecular layer, dentate gyrus, subicular complex, posterior cingulate cortex, and mammillary body). In the cerebral cortices, large reductions in glucose use were observed after administration of MK-801, whereas in the extrapyramidal and sensory-motor areas, glucose use remained unchanged after MK-801 administration in conscious rats. In the halothane-anaesthetised rats, the pattern of altered glucose use after MK-801 differed qualitatively and quantitatively from that observed in conscious rats. In anaesthetised rats, significant reductions in glucose use were noted after MK-801 in 10 of the 28 regions examined, with no area displaying significantly increased glucose use after administration of the drug. In halothane-anaesthetised rats, MK-801 failed to change the rates of glucose use in the olfactory areas, the hippocampus molecular layer, and the dentate gyrus.« less

The hybrid assistive limb (HAL) for Care Support successfully reduced lumbar load in repetitive lifting movements.

PubMed

Miura, Kousei; Kadone, Hideki; Koda, Masao; Abe, Tetsuya; Kumagai, Hiroshi; Nagashima, Katsuya; Mataki, Kentaro; Fujii, Kengo; Noguchi, Hiroshi; Funayama, Toru; Kawamoto, Hiroaki; Sankai, Yoshiyuki; Yamazaki, Masashi

2018-05-03

Work-related low back pain is a serious socioeconomic problem. This study examined whether HAL for Care Support, which is a newly developed wearable robot, would decrease lumbar fatigue and improve lifting performance during repetitive lifting movements. Eighteen healthy volunteers (11 men, 7 women) performed repetitive stoop lifting movements of a cardboard box weighing 12 kg as many times as possible. The first lifting trial was executed without HAL for Care Support, and the second was with it. We evaluated the VAS of lumbar fatigue as the lumbar load and the number of lifts and the lifting time as lifting performance. Without HAL for Care Support, the mean VAS of lumbar fatigue, the number of lifts and lifting time were 68 mm, 60 and 230 s; with HAL for Care Support, they were 51 mm, 87 and 332 s, respectively. Both lifting performance measures were significantly improved by using HAL for Care Support (Fig. 2). A power analysis showed that there was sufficient statistical power for the VAS of lumbar fatigue (0.99), the number of lifts (0.92), and lifting time (0.93). All participants performed their repetitive lifting trials safely. There were no adverse events caused by using HAL for Care Support. In conclusion, the HAL for Care Support can decrease lumbar load and improve the lifting performance during repetitive stoop lifting movements in healthy adults. Copyright © 2018. Published by Elsevier Ltd.

Gait training using a hybrid assistive limb (HAL) attenuates head drop: A case report.

PubMed

Miura, Kousei; Koda, Masao; Kadone, Hideki; Kubota, Shigeki; Shimizu, Yukiyo; Kumagai, Hiroshi; Nagashima, Katsuya; Mataki, Kentaro; Fujii, Kengo; Noguchi, Hiroshi; Funayama, Toru; Abe, Tetsuya; Sankai, Yoshiyuki; Yamazaki, Masashi

2018-06-01

Dropped head syndrome (DHS) is characterized by a chin-on-chest deformity, which can severely interfere with forward vision and impair activities of daily living. A standardized treatment strategy for DHS has not been established. To our knowledge, this is the first case report describing the efficacy of gait training using a hybrid assistive limb (HAL) for DHS. A 75-year-old man showed apparent head drop in a standing position, resulting in passively reducible chin-on-chest deformity. A radiograph image showed apparent cervical kyphosis. Center of gravity of the head (CGH)-C7 SVA was +115 mm, CL was -40°, and T1S 39°. The patient underwent a treatment program using HAL, in which gait training was mainly performed, 60 min a day, 5 days a week for 2 weeks (10 sessions). After 2-3 sessions, dropped head started to attenuate. At the end of 10 sessions, the patient was able to walk with normal posture and radiograph images showed cervical kyphosis dramatically decreased because of HAL training. CGH-C7 SVA was 42 mm, CL was -1.7°, and T1S was 30°. Three months' outpatient follow-up revealed a slight deterioration of cervical alignment. However, the patient was able to maintain a better cervical alignment than before HAL training and keep walking with forward vision. There were no complications in any HAL treatment session. In conclusion, gait training using HAL is an option for treatment of DHS in addition to previously reported neck extensor muscle training. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Impact of Blue Light Cystoscopy with Hexaminolevulinate (HAL) on Progression of Bladder Cancer - A New Analysis.

PubMed

Kamat, Ashish M; Cookson, Michael; Witjes, J Alfred; Stenzl, Arnulf; Grossman, H Barton

2016-04-27

Background: The International Bladder Cancer Group (IBCG) recently proposed a new definition of disease progression in non-muscle invasive bladder cancer (NMIBC), including change in T-stage, change to T2 or higher or change from low to high grade. Objective: To establish whether blue light cystoscopy with hexaminolevulinate (HAL) impacts the rate of progression and time to progression using the revised definition. Methods: An earlier long-term follow-up of a controlled Phase III study reported outcomes following blue light cystoscopy with HAL (255 patients) or white light (WL) cystoscopy (261 patients) in NMIBC patients. The data was re-analysed according to the new definition. Results: In the original analysis, after 4.5 years (median), eight HAL and 16 WL patients were deemed to have progressed (transition from NMIBC to muscle invasive bladder cancer, (T2-4)). According to the new definition, additional patients in both groups were found to have progressed: 31 (12.2%) HAL vs 46 (17.6%) WL ( p  = 0.085) with four (1.6%) HAL and 11 (4.2%) WL patients progressing from Ta to CIS. Time to progression was longer in the HAL group ( p  = 0.05). Conclusions: Applying the new IBCG definition there was a trend towards a lower rate of progression in HAL patients, particularly in those progressing from Ta to CIS. Time to progression was significantly prolonged. This suggests that patients should receive blue light cystoscopy with HAL rather than WL at resection. Adoption of the new definition could allow more patients at risk of progression to be treated appropriately earlier.

Quantitative evaluation of the neuroprotective effects of thiopental sodium, propofol, and halothane on brain ischemia in the gerbil: effects of the anesthetics on ischemic depolarization and extracellular glutamate concentration.

PubMed

Kobayashi, Motomu; Takeda, Yoshimasa; Taninishi, Hideki; Takata, Ken; Aoe, Hisami; Morita, Kiyoshi

2007-07-01

Although propofol and thiopental are commonly used as neuroprotective agents, it has not been determined which is more neuroprotective. This study was designed to quantitatively evaluate the neuroprotective effects of thiopental, propofol, and halothane on brain ischemia by determining P50, ischemic time necessary for causing 50% neuronal damage. Gerbils were anesthetized with thiopental, propofol, or halothane and underwent 2-vessel occlusion (0, 3, 5 or 10 min). Direct current potentials were measured in bilateral CA1 regions, in which histologic evaluation was performed 5 days later. In some animals, extracellular glutamate concentrations (microdialysis) were measured during 7.5 minutes of ischemia. P50 in the thiopental, propofol, and halothane groups were estimated to be 8.4, 6.5 (P<0.05, vs. thiopental), and 5.1 (P<0.05) minutes, respectively. Durations of ischemic depolarization were equally reduced in the thiopental and propofol groups compared with that in the halothane group. Severity of neuronal damage with identical duration of ischemic depolarization was attenuated by thiopental compared with the effect of propofol. Maximum glutamate concentrations in the thiopental and propofol group were significantly reduced compared with that in the halothane groups but were comparable. By using P50, we found that the neuroprotective effect of thiopental was greater than that of propofol. Although duration of ischemic depolarization was equally reduced in thiopental and propofol groups, thiopental has a greater suppressive effect on neuronal injury during identical duration of ischemic depolarization than propofol does. Glutamate concentration during brain ischemia tended to be attenuated more by thiopental than by propofol, but it was not statistically significant.

The impact of age on bispectral index values and EEG bispectrum during anaesthesia with desflurane and halothane in children.

PubMed

Tirel, O; Wodey, E; Harris, R; Bansard, J Y; Ecoffey, C; Senhadji, L

2006-04-01

The relationship between end-tidal sevoflurane concentration, bispectral index (BIS) and the EEG bispectrum in children appears to be age dependent. The aim of this study was to quantify the BIS values at 1 MAC (minimum alveolar concentration) for desflurane and halothane, and explore the relationship with age for these anaesthetic agents in children. ECG, EEG and BIS were recorded continuously in 90 children aged 6-170 months requiring anaesthesia for elective surgery. Fifty children were anaesthetized with desflurane, and 40 children with halothane. Recordings were performed through to a steady state of 2 MAC, and thereafter at 1 and 0.5 MAC, respectively. The bispectrum of the EEG was estimated using MATLAB(c) software. A multiple correspondence analysis (MCA) was used. At a steady state of 1 MAC, BIS values were significantly higher with halothane 62 (43-80) than desflurane 34 (18-64). BIS values were significantly correlated with age in both groups: DES (r(2)=0.57; P<0.01) and HALO (r(2)=0.48; P<0.01). Changes in position in the structured model of the MCA (dependent on the pattern of the EEG bispectrum) were different for the two volatile anaesthetic agents. In children, BIS values are linked to age irrespective of the volatile anaesthetic agent used. The difference in BIS values for different agents at the same MAC can be explained by the specific effect on the EEG bispectrum induced by each anaesthetic agent, bringing into question the ability of the EEG bispectrum to accurately determine the depth of anaesthesia.

A new MRI land surface model HAL

NASA Astrophysics Data System (ADS)

Hosaka, M.

2011-12-01

A land surface model HAL is newly developed for MRI-ESM1. It is used for the CMIP simulations. HAL consists of three submodels: SiByl (vegetation), SNOWA (snow) and SOILA (soil) in the current version. It also contains a land coupler LCUP which connects some submodels and an atmospheric model. The vegetation submodel SiByl has surface vegetation processes similar to JMA/SiB (Sato et al. 1987, Hirai et al. 2007). SiByl has 2 vegetation layers (canopy and grass) and calculates heat, moisture, and momentum fluxes between the land surface and the atmosphere. The snow submodel SNOWA can have any number of snow layers and the maximum value is set to 8 for the CMIP5 experiments. Temperature, SWE, density, grain size and the aerosol deposition contents of each layer are predicted. The snow properties including the grain size are predicted due to snow metamorphism processes (Niwano et al., 2011), and the snow albedo is diagnosed from the aerosol mixing ratio, the snow properties and the temperature (Aoki et al., 2011). The soil submodel SOILA can also have any number of soil layers, and is composed of 14 soil layers in the CMIP5 experiments. The temperature of each layer is predicted by solving heat conduction equations. The soil moisture is predicted by solving the Darcy equation, in which hydraulic conductivity depends on the soil moisture. The land coupler LCUP is designed to enable the complicated constructions of the submidels. HAL can include some competing submodels (precise and detailed ones, and simpler ones), and they can run at the same simulations. LCUP enables a 2-step model validation, in which we compare the results of the detailed submodels with the in-situ observation directly at the 1st step, and follows the comparison between them and those of the simpler ones at the 2nd step. When the performances of the detailed ones are good, we can improve the simpler ones by using the detailed ones as reference models.

Baryon interactions in lattice QCD: the direct method vs. the HAL QCD potential method

NASA Astrophysics Data System (ADS)

Iritani, T.; HAL QCD Collaboration

We make a detailed comparison between the direct method and the HAL QCD potential method for the baryon-baryon interactions, taking the $\\Xi\\Xi$ system at $m_\\pi= 0.51$ GeV in 2+1 flavor QCD and using both smeared and wall quark sources. The energy shift $\\Delta E_\\mathrm{eff}(t)$ in the direct method shows the strong dependence on the choice of quark source operators, which means that the results with either (or both) source are false. The time-dependent HAL QCD method, on the other hand, gives the quark source independent $\\Xi\\Xi$ potential, thanks to the derivative expansion of the potential, which absorbs the source dependence to the next leading order correction. The HAL QCD potential predicts the absence of the bound state in the $\\Xi\\Xi$($^1$S$_0$) channel at $m_\\pi= 0.51$ GeV, which is also confirmed by the volume dependence of finite volume energy from the potential. We also demonstrate that the origin of the fake plateau in the effective energy shift $\\Delta E_\\mathrm{eff}(t)$ at $t \\sim 1$ fm can be clarified by a few low-lying eigenfunctions and eigenvalues on the finite volume derived from the HAL QCD potential, which implies that the ground state saturation of $\\Xi\\Xi$($^1$S$_0$) requires $t \\sim 10$ fm in the direct method for the smeared source on $(4.3 \\ \\mathrm{fm})^3$ lattice, while the HAL QCD method does not suffer from such a problem.

Two-baryon systems from HAL QCD method and the mirage in the temporal correlation of the direct method

NASA Astrophysics Data System (ADS)

Iritani, Takumi

2018-03-01

Both direct and HAL QCD methods are currently used to study the hadron interactions in lattice QCD. In the direct method, the eigen-energy of two-particle is measured from the temporal correlation. Due to the contamination of excited states, however, the direct method suffers from the fake eigen-energy problem, which we call the "mirage problem," while the HAL QCD method can extract information from all elastic states by using the spatial correlation. In this work, we further investigate systematic uncertainties of the HAL QCD method such as the quark source operator dependence, the convergence of the derivative expansion of the non-local interaction kernel, and the single baryon saturation, which are found to be well controlled. We also confirm the consistency between the HAL QCD method and the Lüscher's finite volume formula. Based on the HAL QCD potential, we quantitatively confirm that the mirage plateau in the direct method is indeed caused by the contamination of excited states.

Hand-Assisted Laparoscopic (HAL) Multiple Segmental Colorectal Resections: Are They Feasible and Safe?

PubMed

Taggarshe, Deepa; Attuwaybi, Bashir O; Matier, Brian; Visco, Jeffrey J; Butler, Bryan N

2015-04-01

The objective of this study was to evaluate the short-term outcomes of synchronous hand-assisted laparoscopic (HAL) segmental colorectal resections. The surgical options for synchronous colonic pathology include extensive colonic resection with single anastomosis, multiple synchronous segmental resections with multiple anastomoses, or staged resections. Traditionally, multiple open, synchronous, segmental resections have been performed. There is a lack of data on HAL multiple segmental colorectal resections. A retrospective chart review was compiled on all patients who underwent HAL synchronous segmental colorectal resections by all the colorectal surgeons from our Group during the period of 1999 to 2014. Demographics, operative details, and short-term outcomes are reported. During the period, 9 patients underwent HAL synchronous multiple segmental colorectal resections. There were 5 women and 4 men, with median age of 54 (24-83) years and median BMI of 24 (19.8-38.7) kg/m(2). Two patients were on long-term corticosteroid therapy. The median operative time was 210 (120-330) minutes and median operative blood loss was 200 (75-300) mLs. The median duration for return of bowel function was 2 days and the median length of stay was 3.5 days. We had 2 minor wound infections. There were no deaths. Synchronous segmental colorectal resections with anastomoses using the hand-assisted laparoscopic technique are safe. Early conversion to open and use of stomas are advisable in challenging cases.

Mice expressing T4826I-RYR1 are viable but exhibit sex- and genotype-dependent susceptibility to malignant hyperthermia and muscle damage

PubMed Central

Yuen, Benjamin; Boncompagni, Simona; Feng, Wei; Yang, Tianzhong; Lopez, Jose R.; Matthaei, Klaus I.; Goth, Samuel R.; Protasi, Feliciano; Franzini-Armstrong, Clara; Allen, Paul D.; Pessah, Isaac N.

2012-01-01

Mutation T4825I in the type 1 ryanodine receptor (RYR1T4825I/+) confers human malignant hyperthermia susceptibility (MHS). We report a knock-in mouse line that expresses the isogenetic mutation T4826I. Heterozygous RYR1T4826I/+ (Het) or homozygous RYR1T4826I/T4826I (Hom) mice are fully viable under typical rearing conditions but exhibit genotype- and sex-dependent susceptibility to environmental conditions that trigger MH. Hom mice maintain higher core temperatures than WT in the home cage, have chronically elevated myoplasmic[Ca2+]rest, and present muscle damage in soleus with a strong sex bias. Mice subjected to heat stress in an enclosed 37°C chamber fail to trigger MH regardless of genotype, whereas heat stress at 41°C invariably triggers fulminant MH in Hom, but not Het, mice within 20 min. WT and Het female mice fail to maintain euthermic body temperature when placed atop a bed whose surface is 37°C during halothane anesthesia (1.75%) and have no hyperthermic response, whereas 100% Hom mice of either sex and 17% of the Het males develop fulminant MH. WT mice placed on a 41°C bed maintain body temperature while being administered halothane, and 40% of the Het females and 100% of the Het males develop fulminant MH within 40 min. Myopathic alterations in soleus were apparent by 12 mo, including abnormally distributed and enlarged mitochondria, deeply infolded sarcolemma, and frequent Z-line streaming regions, which were more severe in males. These data demonstrate that an MHS mutation within the S4-S5 cytoplasmic linker of RYR1 confers genotype- and sex-dependent susceptibility to pharmacological and environmental stressors that trigger fulminant MH and promote myopathy.—Yuen, B., Boncompagni, S., Feng, W., Yang, T., Lopez, J. R., Matthaei, K. I., Goth, S. R., Protasi, F., Franzini-Armstrong, C., Allen, P. D., Pessah, I. N. Mice expressing T4826I-RYR1 are viable but exhibit sex- and genotype-dependent susceptibility to malignant hyperthermia and muscle

The voluntary driven exoskeleton Hybrid Assistive Limb (HAL) for postoperative training of thoracic ossification of the posterior longitudinal ligament: a case report.

PubMed

Fujii, Kengo; Abe, Tetsuya; Kubota, Shigeki; Marushima, Aiki; Kawamoto, Hiroaki; Ueno, Tomoyuki; Matsushita, Akira; Nakai, Kei; Saotome, Kosaku; Kadone, Hideki; Endo, Ayumu; Haginoya, Ayumu; Hada, Yasushi; Matsumura, Akira; Sankai, Yoshiyuki; Yamazaki, Masashi

2017-05-01

The hybrid assistive limb (HAL) is a wearable robot suit that assists in voluntary control of knee and hip joint motion by detecting bioelectric signals on the surface of the skin with high sensitivity. HAL has been reported to be effective for functional recovery in motor impairments. However, few reports have revealed the utility of HAL for patients who have undergone surgery for thoracic ossification of the posterior longitudinal ligament (thoracic OPLL). Herein, we present a postoperative thoracic OPLL patient who showed remarkable functional recovery after training with HAL. A 63-year-old woman, who could not walk due to muscle weakness before surgery, underwent posterior decompression and fusion. Paralysis was re-aggravated after the initial postoperative rising. We diagnosed that paralysis was due to residual compression from the anterior lesion and microinstability after posterior fixation, and prescribed bed rest for a further 3 weeks. The incomplete paralysis gradually recovered, and walking training with HAL was started on postoperative day 44 in addition to standard physical therapy. The patient underwent 10 sessions of HAL training until discharge on postoperative day 73. Results of a 10-m walk test were assessed after every session, and the patient's speed and cadence markedly improved. At discharge, the patient could walk with 2 crutches and no assistance. Furthermore, no adverse events associated with HAL training occurred. HAL training for postoperative thoracic OPLL patients may enhance improvement in walking ability, even if severe impairment of ambulation and muscle weakness exist preoperatively.

Mineralogy and petrography of HAL, an isotopically-unusual Allende inclusion

NASA Technical Reports Server (NTRS)

Allen, J. M.; Grossman, L.; Lee, T.; Wasserburg, G. J.

1980-01-01

Results of a detailed mineralogical and textural study of the HAL (Hibonite ALlende) inclusion of the Allende meteorite, which has been found to exhibit no Mg-26 excesses despite very high Al-27/Mg-24 ratios and large fractionation effects with small nuclear effects in its Ca, are reported. The inclusion is found to consist of three up to 1-mm diameter hibonite crystals partially surrounded by a black rim resembling a devitrified glass and containing an anisotropic Al-Fe oxide, which is in turn surrounded by a 2-mm thick friable rim sequence consisting of five layers distinguishable by mineral composition. From the available evidence, it is concluded that each of the layers of the friable rim formed by the accretion of an assemblage of condensate grains rather than by the complete reaction of a HAL precursor with a nebular gas, thus explaining its unusual isotopic characteristics and supporting the conclusion that the solar nebular contained isotopically-distinct reservoirs.

Effects of production conditions on the properties of Cu/sub 6/PS/sub 5/Hal crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan'ko, V.V.; Studenyak, I.P.; D'ordyai, V.S.

1988-06-01

Cu/sub 6/PS/sub 5/Hal single crystals belong to the class of compounds having the argyrodite structure; they have high disordered-vacancy concentrations, so they show high ionic conductivity even at room temperature. Various values have been quoted for the conductivities of Cu/sub 6/PS/sub 5/Hal, which may be due to differing growth conditions. The authors have examined the effects of those conditions on some electrophysical and optical parameters. The crystals were grown by chemical transport reaction. Differences in Cu/sub 6/PS/sub 5/Hal production conditions were found to affect the absorption edge and broaden the exciton-impurity absorption band, whose intensity alters, as well as increasingmore » the Rayleigh flank intensity in the Raman spectrum on account of increased copper concentrations.« less

The voluntary driven exoskeleton Hybrid Assistive Limb (HAL) for postoperative training of thoracic ossification of the posterior longitudinal ligament: a case report

PubMed Central

Abe, Tetsuya; Kubota, Shigeki; Marushima, Aiki; Kawamoto, Hiroaki; Ueno, Tomoyuki; Matsushita, Akira; Nakai, Kei; Saotome, Kosaku; Kadone, Hideki; Endo, Ayumu; Haginoya, Ayumu; Hada, Yasushi; Matsumura, Akira; Sankai, Yoshiyuki; Yamazaki, Masashi

2017-01-01

Context The hybrid assistive limb (HAL) is a wearable robot suit that assists in voluntary control of knee and hip joint motion by detecting bioelectric signals on the surface of the skin with high sensitivity. HAL has been reported to be effective for functional recovery in motor impairments. However, few reports have revealed the utility of HAL for patients who have undergone surgery for thoracic ossification of the posterior longitudinal ligament (thoracic OPLL). Herein, we present a postoperative thoracic OPLL patient who showed remarkable functional recovery after training with HAL. Findings A 63-year-old woman, who could not walk due to muscle weakness before surgery, underwent posterior decompression and fusion. Paralysis was re-aggravated after the initial postoperative rising. We diagnosed that paralysis was due to residual compression from the anterior lesion and microinstability after posterior fixation, and prescribed bed rest for a further 3 weeks. The incomplete paralysis gradually recovered, and walking training with HAL was started on postoperative day 44 in addition to standard physical therapy. The patient underwent 10 sessions of HAL training until discharge on postoperative day 73. Results of a 10-m walk test were assessed after every session, and the patient's speed and cadence markedly improved. At discharge, the patient could walk with 2 crutches and no assistance. Furthermore, no adverse events associated with HAL training occurred. Conclusion HAL training for postoperative thoracic OPLL patients may enhance improvement in walking ability, even if severe impairment of ambulation and muscle weakness exist preoperatively. PMID:26856189

Risk assessments using the Strain Index and the TLV for HAL, Part I: Task and multi-task job exposure classifications.

PubMed

Kapellusch, Jay M; Bao, Stephen S; Silverstein, Barbara A; Merryweather, Andrew S; Thiese, Mathew S; Hegmann, Kurt T; Garg, Arun

2017-12-01

The Strain Index (SI) and the American Conference of Governmental Industrial Hygienists (ACGIH) Threshold Limit Value for Hand Activity Level (TLV for HAL) use different constituent variables to quantify task physical exposures. Similarly, time-weighted-average (TWA), Peak, and Typical exposure techniques to quantify physical exposure from multi-task jobs make different assumptions about each task's contribution to the whole job exposure. Thus, task and job physical exposure classifications differ depending upon which model and technique are used for quantification. This study examines exposure classification agreement, disagreement, correlation, and magnitude of classification differences between these models and techniques. Data from 710 multi-task job workers performing 3,647 tasks were analyzed using the SI and TLV for HAL models, as well as with the TWA, Typical and Peak job exposure techniques. Physical exposures were classified as low, medium, and high using each model's recommended, or a priori limits. Exposure classification agreement and disagreement between models (SI, TLV for HAL) and between job exposure techniques (TWA, Typical, Peak) were described and analyzed. Regardless of technique, the SI classified more tasks as high exposure than the TLV for HAL, and the TLV for HAL classified more tasks as low exposure. The models agreed on 48.5% of task classifications (kappa = 0.28) with 15.5% of disagreement between low and high exposure categories. Between-technique (i.e., TWA, Typical, Peak) agreement ranged from 61-93% (kappa: 0.16-0.92) depending on whether the SI or TLV for HAL was used. There was disagreement between the SI and TLV for HAL and between the TWA, Typical and Peak techniques. Disagreement creates uncertainty for job design, job analysis, risk assessments, and developing interventions. Task exposure classifications from the SI and TLV for HAL might complement each other. However, TWA, Typical, and Peak job exposure techniques all have

Risk assessments using the Strain Index and the TLV for HAL, Part II: Multi-task jobs and prevalence of CTS.

PubMed

Kapellusch, Jay M; Silverstein, Barbara A; Bao, Stephen S; Thiese, Mathew S; Merryweather, Andrew S; Hegmann, Kurt T; Garg, Arun

2018-02-01

The Strain Index (SI) and the American Conference of Governmental Industrial Hygienists (ACGIH) threshold limit value for hand activity level (TLV for HAL) have been shown to be associated with prevalence of distal upper-limb musculoskeletal disorders such as carpal tunnel syndrome (CTS). The SI and TLV for HAL disagree on more than half of task exposure classifications. Similarly, time-weighted average (TWA), peak, and typical exposure techniques used to quantity physical exposure from multi-task jobs have shown between-technique agreement ranging from 61% to 93%, depending upon whether the SI or TLV for HAL model was used. This study compared exposure-response relationships between each model-technique combination and prevalence of CTS. Physical exposure data from 1,834 workers (710 with multi-task jobs) were analyzed using the SI and TLV for HAL and the TWA, typical, and peak multi-task job exposure techniques. Additionally, exposure classifications from the SI and TLV for HAL were combined into a single measure and evaluated. Prevalent CTS cases were identified using symptoms and nerve-conduction studies. Mixed effects logistic regression was used to quantify exposure-response relationships between categorized (i.e., low, medium, and high) physical exposure and CTS prevalence for all model-technique combinations, and for multi-task workers, mono-task workers, and all workers combined. Except for TWA TLV for HAL, all model-technique combinations showed monotonic increases in risk of CTS with increased physical exposure. The combined-models approach showed stronger association than the SI or TLV for HAL for multi-task workers. Despite differences in exposure classifications, nearly all model-technique combinations showed exposure-response relationships with prevalence of CTS for the combined sample of mono-task and multi-task workers. Both the TLV for HAL and the SI, with the TWA or typical techniques, appear useful for epidemiological studies and surveillance

The effect of thiopental sodium, methoxyflurane and halothane on the acid-base status in sheep.

PubMed Central

Edjtehadi, M; Howard, B R

1978-01-01

Experiments have been carried out on 20 adult fat-tailed ewes to determine the effects of thiopental sodium, methoxyflurane and halothane on acid-base status of the saliva loss during prolonged surgical anaesthesia. The rate of loss of base in saliva depends on the volume of saliva produced, which fell sharply at the onset of anesthesia with the volatile anaesthesia. Plasma pH and plasma pvCO2 excess were both increased by the volatile anaesthetics but fell sharply during thiopental anaesthesia. Plasma pH and plasma PvCO2 showed no consistent relationship. PMID:688076

The strain index and TLV for HAL: risk of lateral epicondylitis in a prospective cohort.

PubMed

Garg, Arun; Kapellusch, Jay M; Hegmann, Kurt T; Thiese, Matthew S; Merryweather, Andrew S; Wang, Ying-Chih; Malloy, Elizabeth J

2014-03-01

This study's objective was to quantify exposure-response relationships between job physical exposure (JPE) and incidence of lateral epicondylitis (LE). A cohort of 536 workers was enrolled from 10 manufacturing facilities and followed monthly for 6 years to ascertain changes in JPE and health status. JPE was individually measured and quantified using the Strain Index (SI) and TLV for HAL. Worker demographics, medical history, psychosocial factors, and current musculoskeletal disorders were obtained. Fifty-six workers developed LE. In multivariate models JPE, age, family problems, and swimming were associated with increased risk of LE. SI showed an exposure-response relationship with maximum hazard ratio (HR) of 4.5(P = 0.04). TLV for HAL showed a non-statistically significant trend for increased risk of LE (P = 0.19). JPE is associated with increased risk of LE. The SI and TLV for HAL are useful metrics for estimating JPE. © 2013 Wiley Periodicals, Inc.

Exposure to the chlorofluorocarbon substitute 2,2-dichloro-1,1,1- trifluoroethane and the anesthetic agent halothane is associated with transient protein adduct formation in the heart

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huwyler, J.; Gut, J.

1992-05-15

Hydrochlorofluorocarbons (HCFCs) that are structural analogues of the anesthetic agent halothane may follow a common pathway of bioactivation and formation of adducts to cellular targets of distinct tissues. Exposure of rats to a single dose of HCFC 123 (2,2-dichloro- 1,1,1-trifluoroethane) or its structural analogue halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) in vivo resulted in the formation of one prominent trifluoroacetylated protein adduct (TFA-protein adduct) in the heart. In contrast, a variety of distinct TFA-protein adducts were formed in the liver and the kidney of the same animals. The TFA-protein adduct in the heart was processed rapidly; t1/2 of the intact TFA-protein adduct was lessmore » than 12 h.« less

An evaluation of the influence of medetomidine hydrochloride and atipamezole hydrochloride on the arrhythmogenic dose of epinephrine in dogs during halothane anesthesia.

PubMed Central

Pettifer, G R; Dyson, D H; McDonell, W N

1996-01-01

Alterations in the arrhythmogenic dose of epinephrine (ADE) were determined following administration of medetomidine hydrochloride (750 micrograms/M2) and a saline placebo, or medetomidine hydrochloride (750 micrograms/M2), followed by specific medetomidine reversal agent, atipamezole hydrochloride (50 micrograms/kg) 20 min later, in halothane-anesthetized dogs (n = 6). ADE determinations were made prior to the administration of either treatment, 20 min and 4 h following medetomidine/saline or medetomidine/atipamezole administration. Epinephrine was infused for 3 min at increasing dose rates (2.5 and 5.0 micrograms/kg/min) until the arrhythmia criterion (4 or more intermittent or continuous premature ventricular contractions) was reached. The interinfusion interval was 20 min. There were no significant differences in the amount of epinephrine required to reach the arrhythmia criterion following the administration of either treatment. In addition, the ADE at each determination was not different between treatment groups. In this study, the administration of medetomidine to halothane-anesthetized dogs did not alter their arrhythmogenic response to infused epinephrine. PMID:8825986

Extension of the HAL QCD approach to inelastic and multi-particle scatterings in lattice QCD

NASA Astrophysics Data System (ADS)

Aoki, S.

We extend the HAL QCD approach, with which potentials between two hadrons can be obtained in QCD at energy below inelastic thresholds, to inelastic and multi-particle scatterings. We first derive asymptotic behaviors of the Nambu-Bethe-Salpeter (NBS) wave function at large space separations for systems with more than 2 particles, in terms of the one-shell $T$-matrix consrainted by the unitarity of quantum field theories. We show that its asymptotic behavior contains phase shifts and mixing angles of $n$ particle scatterings. This property is one of the essential ingredients of the HAL QCD scheme to define "potential" from the NBS wave function in quantum field theories such as QCD. We next construct energy independent but non-local potentials above inelastic thresholds, in terms of these NBS wave functions. We demonstrate an existence of energy-independent coupled channel potentials with a non-relativistic approximation, where momenta of all particles are small compared with their own masses. Combining these two results, we can employ the HAL QCD approach also to investigate inelastic and multi-particle scatterings.

Bidirectional reporter assay using HAL promoter and TOPFLASH improves specificity in high-throughput screening of Wnt inhibitors.

PubMed

Yamaguchi, Kiyoshi; Zhu, Chi; Ohsugi, Tomoyuki; Yamaguchi, Yuko; Ikenoue, Tsuneo; Furukawa, Yoichi

2017-12-01

Constitutive activation of Wnt signaling plays an important role in colorectal and liver tumorigenesis. Cell-based assays using synthetic TCF/LEF (T-cell factor/lymphoid enhancer factor) reporters, as readouts of β-catenin/TCF-dependent transcriptional activity, have contributed greatly to the discovery of small molecules that modulate Wnt signaling. In the present study, we report a novel screening method, called a bidirectional dual reporter assay. Integrated transcriptome analysis identified a histidine ammonia-lyase gene (HAL) that was negatively regulated by β-catenin/TCF-dependent transcriptional activity. We leveraged a promoter region of the HAL gene as another transcriptional readout of Wnt signaling. Cells stably expressing both an optimized HAL reporter and the TCF/LEF reporter enabled bidirectional reporter activities in response to Wnt signaling. Increased HAL reporter activity and decreased TCF/LEF reporter activity were observed simultaneously in the cells when β-catenin/TCF7L2 was inhibited. Notably, this method could decrease the number of false positives observed when screening an inhibitor library compared with the conventional TCF/LEF assay. We found that Brefeldin A, a disruptor of the Golgi apparatus, inhibited the Wnt/β-catenin signaling pathway. The utility of our system could be expanded to examine other disease-associated pathways beyond the Wnt/β-catenin signaling pathway. © 2017 Wiley Periodicals, Inc.

I = 2 ππ scattering phase shift from the HAL QCD method with the LapH smearing

NASA Astrophysics Data System (ADS)

Kawai, Daisuke; Aoki, Sinya; Doi, Takumi; Ikeda, Yoichi; Inoue, Takashi; Iritani, Takumi; Ishii, Noriyoshi; Miyamoto, Takaya; Nemura, Hidekatsu; Sasaki, Kenji

2018-04-01

Physical observables, such as the scattering phase shifts and binding energy, calculated from the non-local HAL QCD potential do not depend on the sink operators used to define the potential. In practical applications, the derivative expansion of the non-local potential is employed, so that physical observables may receive some scheme dependence at a given order of the expansion. In this paper, we compare the I=2ππ scattering phase shifts obtained in the point-sink scheme (the standard scheme in the HAL QCD method) and the smeared-sink scheme (the LapH smearing newly introduced in the HAL QCD method). Although potentials in different schemes have different forms as expected, we find that, for reasonably small smearing size, the resultant scattering phase shifts agree with each other if the next-to-leading-order (NLO) term is taken into account. We also find that the HAL QCD potential in the point-sink scheme has a negligible NLO term for a wide range of energies, which implies good convergence of the derivative expansion, while the potential in the smeared-sink scheme has a non-negligible NLO contribution. The implications of this observation for future studies of resonance channels (such as the I=0 and 1ππ scatterings) with smeared all-to-all propagators are briefly discussed.

Helicopter Visual Segment Approach Lighting System (HALS) Test Report

DTIC Science & Technology

1988-08-01

this Pegl 23. Ne. a# Palo$ 22. Ptuco Unclassified Unclassified 316 Form DOT F 1700.7 (8-721 Reproduction of e9Isted Ppe authorized TABLE OF CONTENTS...Subject Pilot Range Rate/Vertical Position Plots lii LIST OF ILLUSTRATIONS Figure Page I Basic Heliport IFR Lighting System 4 2 Heliport Approach...Instrument Flight Rules ( IFR ) Heliport Lighting System and a centerline HALS. The Basic IFR Approach Light System is presented in figure 1. It consists of

Functional Outcome of Neurologic-Controlled HAL-Exoskeletal Neurorehabilitation in Chronic Spinal Cord Injury: A Pilot With One Year Treatment and Variable Treatment Frequency.

PubMed

Jansen, Oliver; Schildhauer, Thomas A; Meindl, Renate C; Tegenthoff, Martin; Schwenkreis, Peter; Sczesny-Kaiser, Matthias; Grasmücke, Dennis; Fisahn, Christian; Aach, Mirko

2017-12-01

Longitudinal prospective study. Whether 1-year HAL-BWSTT of chronic spinal cord injured patients can improve independent ambulated mobility further as a function of training frequency, after an initial 3-month training period. Eight patients with chronic SCI were enrolled. They initially received full standard physical therapy and neurorehabilitation in the acute/subacute posttrauma phase. During this trial, all patients first underwent a daily (5 per week) HAL-BWSTT for 12 weeks. Subsequently, these patients performed a 40-week HAL-BWSTT with a training session frequency of either 1 or 3 to 5 sessions per week. The patients' functional status including HAL-associated treadmill-walking time, -distance, and -speed with additional analysis of gait pattern, and their independent (without wearing the robot suit) functional mobility improvements, were assessed using the 10-Meter-Walk Test (10MWT), Timed-Up-and-Go Test (TUG) and 6-Minute-Walk Test (6MinWT) on admission, at 6 weeks, 12 weeks, and 1 year after enrollment. The data were analyzed separately for the 2 training frequency subgroups after the initial 12-week training period, which was identical in both groups. During the 1-year follow-up, HAL-associated walking parameters and independent functional improvements were maintained in all the patients. This result held irrespective of the training frequency. Long-term 1-year maintenance of HAL-associated treadmill walking parameters and of improved independent walking abilities after initial 12 weeks of daily HAL-BWSTT is possible and depends mainly on the patients' ambulatory status accomplished after initial training period. Subsequent regular weekly training, but not higher frequency training, seems to be sufficient to preserve the improvements accomplished.

Immediate effects of a single session of robot-assisted gait training using Hybrid Assistive Limb (HAL) for cerebral palsy.

PubMed

Matsuda, Mayumi; Mataki, Yuki; Mutsuzaki, Hirotaka; Yoshikawa, Kenichi; Takahashi, Kazushi; Enomoto, Keiko; Sano, Kumiko; Mizukami, Masafumi; Tomita, Kazuhide; Ohguro, Haruka; Iwasaki, Nobuaki

2018-02-01

[Purpose] Robot-assisted gait training (RAGT) using Hybrid Assistive Limb (HAL, CYBERDYNE) was previously reported beneficial for stroke and spinal cord injury patients. Here, we investigate the immediate effect of a single session of RAGT using HAL on gait function for cerebral palsy (CP) patients. [Subjects and Methods] Twelve patients (average age: 16.2 ± 7.3 years) with CP received a single session of RAGT using HAL. Gait speed, step length, cadence, single-leg support per gait cycle, hip and knee joint angle in stance, and swing phase per gait cycle were assessed before, during, and immediately after HAL intervention. [Results] Compared to baseline values, single-leg support per gait cycle (64.5 ± 15.8% to 69.3 ± 12.1%), hip extension angle in mid-stance (149.2 ± 19.0° to 155.5 ± 20.1°), and knee extension angle in mid-stance (137.6 ± 20.2° to 143.1 ± 19.5°) were significantly increased immediately after intervention. Further, the knee flexion angle in mid-swing was significantly decreased immediately after treatment (112.0 ± 15.5° to 105.2 ± 17.1°). Hip flexion angle in mid-swing also decreased following intervention (137.2 ± 14.6° to 129.7 ± 16.6°), but not significantly. Conversely, gait speed, step length, and cadence were unchanged after intervention. [Conclusion] A single-time RAGT with HAL improved single-leg support per gait cycle and hip and knee joint angle during gait, therapeutically improving gait function in CP patients.

Functional Outcome of Neurologic-Controlled HAL-Exoskeletal Neurorehabilitation in Chronic Spinal Cord Injury: A Pilot With One Year Treatment and Variable Treatment Frequency

PubMed Central

Schildhauer, Thomas A.; Meindl, Renate C.; Tegenthoff, Martin; Schwenkreis, Peter; Sczesny-Kaiser, Matthias; Grasmücke, Dennis; Fisahn, Christian; Aach, Mirko

2017-01-01

Study Design: Longitudinal prospective study. Objectives: Whether 1-year HAL-BWSTT of chronic spinal cord injured patients can improve independent ambulated mobility further as a function of training frequency, after an initial 3-month training period. Methods: Eight patients with chronic SCI were enrolled. They initially received full standard physical therapy and neurorehabilitation in the acute/subacute posttrauma phase. During this trial, all patients first underwent a daily (5 per week) HAL-BWSTT for 12 weeks. Subsequently, these patients performed a 40-week HAL-BWSTT with a training session frequency of either 1 or 3 to 5 sessions per week. The patients’ functional status including HAL-associated treadmill-walking time, -distance, and -speed with additional analysis of gait pattern, and their independent (without wearing the robot suit) functional mobility improvements, were assessed using the 10-Meter-Walk Test (10MWT), Timed-Up-and-Go Test (TUG) and 6-Minute-Walk Test (6MinWT) on admission, at 6 weeks, 12 weeks, and 1 year after enrollment. The data were analyzed separately for the 2 training frequency subgroups after the initial 12-week training period, which was identical in both groups. Results: During the 1-year follow-up, HAL-associated walking parameters and independent functional improvements were maintained in all the patients. This result held irrespective of the training frequency. Conclusions: Long-term 1-year maintenance of HAL-associated treadmill walking parameters and of improved independent walking abilities after initial 12 weeks of daily HAL-BWSTT is possible and depends mainly on the patients’ ambulatory status accomplished after initial training period. Subsequent regular weekly training, but not higher frequency training, seems to be sufficient to preserve the improvements accomplished. PMID:29238636

Generation and analysis of the improved human HAL9/10 antibody phage display libraries.

PubMed

Kügler, Jonas; Wilke, Sonja; Meier, Doris; Tomszak, Florian; Frenzel, André; Schirrmann, Thomas; Dübel, Stefan; Garritsen, Henk; Hock, Björn; Toleikis, Lars; Schütte, Mark; Hust, Michael

2015-02-19

Antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. From naive antibody gene libraries - in theory - antibodies against any target can be selected. Here we describe the design, construction and characterization of an optimized antibody phage display library. The naive antibody gene libraries HAL9 and HAL10, with a combined theoretical diversity of 1.5×10(10) independent clones, were constructed from 98 healthy donors using improved phage display vectors. In detail, most common phagemids employed for antibody phage display are using a combined His/Myc tag for detection and purification. We show that changing the tag order to Myc/His improved the production of soluble antibodies, but did not affect antibody phage display. For several published antibody libraries, the selected number of kappa scFvs were lower compared to lambda scFvs, probably due to a lower kappa scFv or Fab expression rate. Deletion of a phenylalanine at the end of the CL linker sequence in our new phagemid design increased scFv production rate and frequency of selected kappa antibodies significantly. The HAL libraries and 834 antibodies selected against 121 targets were analyzed regarding the used germline V-genes, used V-gene combinations and CDR-H3/-L3 length and composition. The amino acid diversity and distribution in the CDR-H3 of the initial library was retrieved in the CDR-H3 of selected antibodies showing that all CDR-H3 amino acids occurring in the human antibody repertoire can be functionally used and is not biased by E. coli expression or phage selection. Further, the data underline the importance of CDR length variations. The highly diverse universal antibody gene libraries HAL9/10 were constructed using an optimized scFv phagemid vector design. Analysis of selected antibodies revealed that the complete amino acid diversity in the CDR-H3 was also found in selected scFvs showing the functionality of the naive CDR

Immediate effects of a single session of robot-assisted gait training using Hybrid Assistive Limb (HAL) for cerebral palsy

PubMed Central

Matsuda, Mayumi; Mataki, Yuki; Mutsuzaki, Hirotaka; Yoshikawa, Kenichi; Takahashi, Kazushi; Enomoto, Keiko; Sano, Kumiko; Mizukami, Masafumi; Tomita, Kazuhide; Ohguro, Haruka; Iwasaki, Nobuaki

2018-01-01

[Purpose] Robot-assisted gait training (RAGT) using Hybrid Assistive Limb (HAL, CYBERDYNE) was previously reported beneficial for stroke and spinal cord injury patients. Here, we investigate the immediate effect of a single session of RAGT using HAL on gait function for cerebral palsy (CP) patients. [Subjects and Methods] Twelve patients (average age: 16.2 ± 7.3 years) with CP received a single session of RAGT using HAL. Gait speed, step length, cadence, single-leg support per gait cycle, hip and knee joint angle in stance, and swing phase per gait cycle were assessed before, during, and immediately after HAL intervention. [Results] Compared to baseline values, single-leg support per gait cycle (64.5 ± 15.8% to 69.3 ± 12.1%), hip extension angle in mid-stance (149.2 ± 19.0° to 155.5 ± 20.1°), and knee extension angle in mid-stance (137.6 ± 20.2° to 143.1 ± 19.5°) were significantly increased immediately after intervention. Further, the knee flexion angle in mid-swing was significantly decreased immediately after treatment (112.0 ± 15.5° to 105.2 ± 17.1°). Hip flexion angle in mid-swing also decreased following intervention (137.2 ± 14.6° to 129.7 ± 16.6°), but not significantly. Conversely, gait speed, step length, and cadence were unchanged after intervention. [Conclusion] A single-time RAGT with HAL improved single-leg support per gait cycle and hip and knee joint angle during gait, therapeutically improving gait function in CP patients. PMID:29545679

Hemorrhoidal artery ligation (HAL) and rectoanal repair (RAR): retrospective analysis of 408 patients in a single center.

PubMed

Scheyer, M; Antonietti, E; Rollinger, G; Lancee, S; Pokorny, H

2015-01-01

Rectoanal repair (RAR), which combines doppler-guided hemorrhoidal artery ligation (HAL) and mucopexy via lifting of the hemorrhoidal prolapse, offers a minimally invasive alternative to conventional hemorrhoidectomy. Patients with grade II hemorrhoids were treated with HAL, and patients with grade III and IV hemorrhoids were treated with the RAR procedure by two surgeons. Postoperative follow-up was performed clinically and by proctoscopy after 8 weeks routinely, and long-term follow-up was performed using a standardized postal questionnaire. The overall complication rate was 29% (n = 118). After short-term follow-up, 26% (n = 106) of patients reported recurrent or persistent prolapsing piles, while 21% (n = 86) of patients had recurrent bleeding. After long-term follow-up, 24% (n = 98) of patients reported prolapsing piles, 3% (n = 12) bleeding, 3% (n = 12) pruritus, and 2% (n = 8) anal pain, while 20% (n = 82) complained of persistent mixed symptoms. HAL and RAR provide prolonged relief for patients with hemorrhoidal disease whose main symptoms are bleeding, pruritus and pain but not for patients with prolapse as an initial indication.

Diatomics-in-molecules description of the Rg-Hal2 rare gas-halogen van der Waals complexes with applications to He-Cl2

NASA Astrophysics Data System (ADS)

Grigorenko, B. L.; Nemukhin, A. V.; Buchachenko, A. A.; Stepanov, N. F.; Umanskii, S. Ya.

1997-03-01

The diatomics-in-molecules (DIM) technique is applied for a description of the low-lying states of the Rg-Hal2 van der Waals complexes correlating with the lowest states of constituent atoms Rg(1S)+Hal(2Pj)+Hal(2Pj). The important feature of this approach is the construction of polyatomic basis functions as products of the Hal2 diatomic eigenstates classified within the Hund "c" scheme and the atomic rare gas wave function. Necessary transformations to the other basis set representations are described, and finally all the matrix elements are expressed in terms of nonrelativistic adiabatic energies of Hal2 and Rg Hal fragments and spin-orbit splitting constant of the halogen atom. Our main concern is to test the DIM-based approximations of different levels taking the He-Cl2 system as an example. Namely, we have compared the results obtained within a hierarchy of approaches: (1) the simplest pairwise potential scheme as a far extreme of the DIM model, (2) the same as (1) but with the different components (Σ and Π) for He-Cl interaction, (3) the accurate DIM technique without spin-orbit terms, and (4) the highest level which takes into account all these contributions. The results have been compared to the other DIM like models as well. The shapes of two-dimensional potential surfaces for the ground (X) and excited (B) states of HeCl2, binding energies De with respect to He+Cl2, stretching and bending vibrational frequencies of the complex, binding energies D0, and spectral shifts for the B←X transition are discussed.

Photodynamic therapy of bladder cancer - a phase I study using hexaminolevulinate (HAL).

PubMed

Bader, M J; Stepp, Herbert; Beyer, Wolfgang; Pongratz, Thomas; Sroka, Ronald; Kriegmair, Martin; Zaak, Dirk; Welschof, Mona; Tilki, Derya; Stief, Christian G; Waidelich, Raphaela

2013-10-01

To assess the safety and feasibility of hexaminolevulinate (HAL) based photodynamic therapy (PDT) as adjuvant treatment after transurethral resection of the bladder (TURB) in patients with intermediate or high-risk urothelial cell carcinoma (UCC) of the bladder. Seventeen patients received 50 ml of either a 16 mM (4 patients) or 8 mM HAL (13 patients) solution instilled intravesically. Bladder wall irradiation was performed using an incoherent white light source coupled via a quartz fiber assembled into a flexible transurethral irrigation catheter. Each patient received 3 treatments with HAL-PDT 6 weeks apart. After PDT, patients were followed by regular cystoscopy for up to 21 months to assess time to recurrence. Reported adverse events (AEs) were coded according the World Health Organization Adverse Reaction Terminology (WHO-ART). Efficacy was assessed by cystoscopy, cytology, and histology, and was defined as the number of patients who were tumor-free at 6 or 21 months after initial PDT treatment. Transient bladder irritability was reported by 15 of the 17 patients and resolved completely in all patients. No evidence of a cumulative effect of treatment on the incidence of AEs could be detected. PDT treatment was performed without any technical complications. Furthermore preliminary assessment of efficacy showed that of the 17 patients included, 9 (52.9%; 95% CI: 27.8-77.0) were tumor-free at 6 months, 4 (23.5%; 95% CI: 6.8-49.9) were tumor-free at 9 months, and 2 (11.8%, 95% CI: 1.5-36.4) were tumor-free after 21 months. PDT using hexaminolevulinate and an incoherent white light system with the special flexible irradiation catheter system is technically feasible and safe and may offer an alternative in the treatment of non-muscle-invasive intermediate and high-risk bladder cancer. Copyright © 2013 Elsevier Inc. All rights reserved.

A Novel for High School Seniors: Hal Borland's "When the Legends Die."

ERIC Educational Resources Information Center

Adkins, Carl A.

1968-01-01

Hal Borland's "When the Legends Die" is especially appropriate for high school seniors because its central problem--a Ute Indian boy's search for his identity and expected role in society--is exactly that faced by these students. The novel is divided into four sections, each concerned with a specific stage in the development of the…

The hybrid assisted limb (HAL) for Care Support, a motion assisting robot providing exoskeletal lumbar support, can potentially reduce lumbar load in repetitive snow-shoveling movements.

PubMed

Miura, Kousei; Kadone, Hideki; Koda, Masao; Abe, Tetsuya; Endo, Hirooki; Murakami, Hideki; Doita, Minoru; Kumagai, Hiroshi; Nagashima, Katsuya; Fujii, Kengo; Noguchi, Hiroshi; Funayama, Toru; Kawamoto, Hiroaki; Sankai, Yoshiyuki; Yamazaki, Masashi

2018-03-01

An excessive lumbar load with snow-shoveling is a serious problem in snowfall areas. Various exoskeletal robots have been developed to reduce lumbar load in lifting work. However, few studies have reported the attempt of snow-shoveling work using exoskeletal robots. The purpose of the present study was to test the hypothesis that the HAL for Care Support robot would reduce lumbar load in repetitive snow-shoveling movements. Nine healthy male volunteers performed repetitive snow-shoveling movements outdoors in a snowfall area for as long as possible until they were fatigued. The snow-shoveling trial was performed under two conditions: with and without HAL for Care Support. Outcome measures were defined as the lumbar load assessed by the VAS of lumbar fatigue after the snow-shoveling trial and the snow-shoveling performance, including the number of scoops, and snow shoveling time and distance. The mean of VAS of lumbar fatigue, the number of scoops, and snow-shoveling time and distance without HAL for Care Support were 75.4 mm, 50.3, 145 s, and 9.6 m, while with HAL for Care Support were 39.8 mm, 144, 366 s, and 35.4 m. The reduction of lumbar fatigue and improvement of snow-shoveling performance using HAL for Care Support were statistically significant. There was no adverse event during snow-shoveling with HAL for Care Support. In conclusion, the HAL for Care Support can reduce lumbar load in repetitive snow-shoveling movements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tissue Engineering in der Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie

NASA Astrophysics Data System (ADS)

Bücheler, Markus; Bootz, Friedrich

Tissue Engineering ist eine Schlüsseltechnologie für den Gewebeersatz der Zukunft. Am Beispiel der Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie werden klinisch etablierte Gewebeersatzmethoden und aktuelle Entwicklungen des Tissue Engineering gegenübergestellt. Die Besonderheiten der zu ersetzenden Gewebe im Kopf- und Halsbereich erfordert vielfältige Ersatzverfahren. Im klinischen Alltag werden heute vor allem autogene Transplantate und Implantate für den Gewebeersatz verwendet [1]. In vitro hergestellte Gewebe werden abgesehen von Einzelanwendungen zur Zeit noch nicht am Patienten eingesetzt.

The expression of the Saccharomyces cerevisiae HAL1 gene increases salt tolerance in transgenic watermelon [Citrullus lanatus (Thunb.) Matsun. & Nakai.].

PubMed

Ellul, P; Ríos, G; Atarés, A; Roig, L A; Serrano, R; Moreno, V

2003-08-01

An optimised Agrobacterium-mediated gene transfer protocol was developed in order to obtain watermelon transgenic plants [Citrullus lanatus (Thunb.) Matsun. & Nakai.]. Transformation efficiencies ranged from 2.8% to 5.3%, depending on the cultivar. The method was applied to obtain genetically engineered watermelon plants expressing the Saccharomyces cerevisiae HAL1 gene related to salt tolerance. In order to enhance its constitutive expression in plants, the HAL1 gene was cloned in a pBiN19 plasmid under control of the 35S promoter with a double enhancer sequence from the cauliflower mosaic virus and the RNA4 leader sequence of the alfalfa mosaic virus. This vector was introduced into Agrobacterium tumefaciens strain LBA4404 for further inoculation of watermelon half-cotyledon explants. The introduction of both the neomycin phosphotransferase II and HAL1 genes was assessed in primary transformants (TG1) by polymerase chain reaction analysis and Southern hybridisation. The expression of the HAL1 gene was determined by Northern analysis, and the diploid level of transgenic plants was confirmed by flow cytometry. The presence of the selectable marker gene in the expected Mendelian ratios was demonstrated in TG2 progenies. The TG2 kanamycin-resistant plantlets elongated better and produced new roots and leaves in culture media supplemented with NaCl compared with the control. Salt tolerance was confirmed in a semi-hydroponic system (EC=6 dS m(-1)) on the basis of the higher growth performance of homozygous TG3 lines with respect to their respective azygous control lines without the transgene. The halotolerance observed confirmed the inheritance of the trait and supports the potential usefulness of the HAL1 gene of S. cerevisiae as a molecular tool for genetic engineering of salt-stress protection in other crop species.

Treatment changes and long-term recurrence rates after hexaminolevulinate (HAL) fluorescence cystoscopy: does it really make a difference in patients with non-muscle-invasive bladder cancer (NMIBC)?

PubMed

Geavlete, Bogdan; Multescu, Razvan; Georgescu, Dragos; Jecu, Marian; Stanescu, Florin; Geavlete, Petrisor

2012-02-01

•  To evaluate in a prospective, randomized study the impact of hexaminolevulinate blue-light cystoscopy (HAL-BLC) on the diagnostic accuracy and treatment changes in cases of non-muscle invasive bladder cancer (NMIBC) compared with standard white-light cystoscopy (WLC). •  To compare the long-term recurrence rates in the two study arms. •  In all, 362 patients suspected of NMIBC were included in the trial based on positive urinary cytology and/or ultrasonographic suspicion of bladder tumours and underwent transurethral resection of bladder tumours. •  A single postoperative mytomicin-C instillation was performed in all cases, intravesical chemotherapy for intermediate-risk patients and BCG instillations for high-risk cases. •  The follow-up protocol consisted of urinary cytology and WLC every 3 months for 2 years. •  Only first-time recurrences after the initial diagnosis were considered. •  In the 142 patients with NMIBC in the HAL-BLC series, tumour detection rates significantly improved for carcinoma in situ, pTa andoverall cases. •  In 35.2% of the cases, additional malignant lesions were found by HAL-BLC and consequently, the recurrence- and progression-risk categories of patients and subsequent treatment improved in 19% of the cases due to fluorescence cystoscopy. •  In all, 125 patients in the HAL-BLC group and 114 of the WLC group completed the follow-up. •  The recurrence rate at 3 months was lower in the HAL-BLC series (7.2% vs 15.8%) due to fewer 'other site' recurrences when compared with the WLC series (0.8% vs 6.1%). •  The 1 and 2 years recurrence rates were significantly decreased in the HAL-BLC group compared with the WLC group (21.6% vs 32.5% and 31.2% vs 45.6%, respectively). •  HAL-BLC was better than WLC for detecting NMIBC cases and improved tumour detection rates. •  HAL-BLC significantly modified the postoperative treatment of cases. •  The 3 months, 1 and 2 years recurrence rates were

Characterization of CuHal-intercalated carbon nanotubes with x-ray absorption spectroscopy combined with x-ray photoelectron and resonant photoemission spectroscopies

NASA Astrophysics Data System (ADS)

Brzhezinskaya, M.; Generalov, A.; Vinogdradov, A.; Eliseev, A.

2013-04-01

Encapsulated single-walled carbon nanotubes (SWCNTs) with inner channels filled by different compounds present the new class of composite materials. Such CNTs give opportunity to form 1D nanocrystals as well as quantum nanowires with new physical and chemical properties inside the tubes. The present study is aimed to characterize the possible chemical interaction between CuHal (Hal=I, Cl, Br) and SWCNTs in CuHal@SWCNTs and electronic structure of the latter using high-resolution near edge X-ray absorption fine structure (NEXAFS) spectroscopy combined with high-resolution X-ray photoelectron spectroscopy and resonant photoemission spectroscopy. The present study has shown that there is a chemical interaction between the filler and π-electron subsystem of CNTs which is accompanied by changes of the atomic and electronic structure of the filler during the encapsulating it inside CNTs.

Charmonium-nucleon interactions from the time-dependent HAL QCD method

NASA Astrophysics Data System (ADS)

Sugiura, Takuya; Ikeda, Yoichi; Ishii, Noriyoshi

2018-03-01

The charmonium-nucleon effective central interactions have been computed by the time-dependent HAL QCD method. This gives an updated result of a previous study based on the time-independent method, which is now known to be problematic because of the difficulty in achieving the ground-state saturation. We discuss that the result is consistent with the heavy quark symmetry. No bound state is observed from the analysis of the scattering phase shift; however, this shall lead to a future search of the hidden-charm pentaquarks by considering channel-coupling effects.

The Strain Index (SI) and Threshold Limit Value (TLV) for Hand Activity Level (HAL): risk of carpal tunnel syndrome (CTS) in a prospective cohort.

PubMed

Garg, A; Kapellusch, J; Hegmann, K; Wertsch, J; Merryweather, A; Deckow-Schaefer, G; Malloy, E J

2012-01-01

A cohort of 536 workers was enrolled from 10 diverse manufacturing facilities and was followed monthly for six years. Job physical exposures were individually measured. Worker demographics, medical history, psychosocial factors, current musculoskeletal disorders (MSDs) and nerve conduction studies (NCS) were obtained. Point and lifetime prevalence of carpal tunnel syndrome (CTS) at baseline (symptoms + abnormal NCS) were 10.3% and 19.8%. During follow-up, there were 35 new CTS cases (left, right or both hands). Factors predicting development of CTS included: job physical exposure (American conference of governmental industrial hygienists Threshold Limit Value (ACGIH TLV) for Hand Activity Level (HAL) and the Strain Index (SI)), age, BMI, other MSDs, inflammatory arthritis, gardening outside of work and feelings of depression. In the adjusted models, the TLV for HAL and the SI were both significant per unit increase in exposure with hazard ratios (HR) increasing up to a maximum of 5.4 (p = 0.05) and 5.3 (p = 0.03), respectively; however, similar to other reports, both suggested lower risk at higher exposures. Data suggest that the TLV for HAL and the SI are useful metrics for estimating exposure to biomechanical stressors. This study was conducted to determine how well the TLV for HAL and the SI predict risk of CTS using a prospective cohort design with survival analysis. Both the TLV for HAL and the SI were found to predict risk of CTS when adjusted for relevant covariates.

Higher-order semantic structures in an African Grey parrot's vocalizations: evidence from the hyperspace analog to language (HAL) model.

PubMed

Kaufman, Allison B; Colbert-White, Erin N; Burgess, Curt

2013-09-01

Previous research has described the significant role that social interaction plays in both the acquisition and use of speech by parrots. The current study analyzed the speech of one home-raised African Grey parrot (Psittacus erithacus erithacus) across three different social contexts: owner interacting with parrot in the same room, owner and parrot interacting out of view in adjacent rooms, and parrot home alone. The purpose was to determine the extent to which the subject's speech reflected an understanding of the contextual substitutability (e.g., the word street can be substituted in context for the word road) of the vocalizations that comprised the units in her repertoire (i.e., global co-occurrence of repertoire units; Burgess in Behav Res Methods Instrum Comput 30:188-198, 1998; Lund and Burgess in Behav Res Methods Instrum Comput 28:203-208, 1996). This was accomplished via the human language model hyperspace analog to language (HAL). HAL is contextually driven and bootstraps language "rules" from input without human intervention. Because HAL does not require human tutelage, it provided an objective measure to empirically examine the parrot's vocalizations. Results indicated that the subject's vocalization patterns did contain global co-occurrence. The presence of this quality in this nonhuman's speech may be strongly indicative of higher-order cognitive skills.

The HubBLe Trial: haemorrhoidal artery ligation (HAL) versus rubber band ligation (RBL) for symptomatic second- and third-degree haemorrhoids: a multicentre randomised controlled trial and health-economic evaluation.

PubMed

Brown, Steven; Tiernan, Jim; Biggs, Katie; Hind, Daniel; Shephard, Neil; Bradburn, Mike; Wailoo, Allan; Alshreef, Abualbishr; Swaby, Lizzie; Watson, Angus; Radley, Simon; Jones, Oliver; Skaife, Paul; Agarwal, Anil; Giordano, Pasquale; Lamah, Marc; Cartmell, Mark; Davies, Justin; Faiz, Omar; Nugent, Karen; Clarke, Andrew; MacDonald, Angus; Conaghan, Phillip; Ziprin, Paul; Makhija, Rohit

2016-11-01

Optimal surgical intervention for low-grade haemorrhoids is unknown. Rubber band ligation (RBL) is probably the most common intervention. Haemorrhoidal artery ligation (HAL) is a novel alternative that may be more efficacious. The comparison of HAL with RBL for the treatment of grade II/III haemorrhoids. A multicentre, parallel-group randomised controlled trial. UK NHS and Personal Social Services. 17 NHS Trusts. Patients aged ≥ 18 years presenting with grade II/III (second- and third-degree) haemorrhoids, including those who have undergone previous RBL. HAL with Doppler probe compared with RBL. Primary outcome - recurrence at 1 year post procedure; secondary outcomes - recurrence at 6 weeks; haemorrhoid severity score; European Quality of Life-5 Dimensions, 5-level version (EQ-5D-5L); Vaizey incontinence score; pain assessment; complications; and cost-effectiveness. A total of 370 participants entered the trial. At 1 year post procedure, 30% of the HAL group had evidence of recurrence compared with 49% after RBL [adjusted odds ratio (OR) = 2.23, 95% confidence interval (CI) 1.42 to 3.51; p  = 0.0005]. The main reason for the difference was the number of extra procedures required to achieve improvement/cure. If a single HAL is compared with multiple RBLs then only 37.5% recurred in the RBL arm (adjusted OR 1.35, 95% CI 0.85 to 2.15; p  = 0.20). Persistence of significant symptoms at 6 weeks was lower in both arms than at 1 year (9% HAL and 29% RBL), suggesting significant deterioration in both groups over the year. Symptom score, EQ-5D-5L and Vaizey score improved in both groups compared with baseline, but there was no difference between interventions. Pain was less severe and of shorter duration in the RBL group; most of the HAL group who had pain had mild to moderate pain, resolving by 3 weeks. Complications were low frequency and not significantly different between groups. It appeared that HAL was not cost-effective compared with RBL. In the base

Plasma and muscle cortisol measurements as indicators of meat quality and stress in pigs.

PubMed

Shaw, F D; Trout, G R; McPhee, C P

1995-01-01

Post-slaughter blood samples and muscle samples were collected from pigs slaughtered at the completion of a live-animal performance trial. There were two lines of pigs in which the halothane allele (n) was segregating. The lines were a lean line selected for rapid lean growth and an unselected fat line. There were homozygous normal (NN), homozygous halothane positive (nn) and heterozygous (Nn) genotypes in both lnes. Cortisol was measured in the plasma of the blood samples and in muscle juice obtained by high-speed centrifugation. Meat quality was assessed using pH, colour, fibre-optic probe, drip loss and cure yield measurements. Plasma cortisol concentrations in the fat line were significantly (P < 0·05) greater than thosein the lean line but concentrations did not differ significantly for the three halothane genotypes. Carcasses classified as dark, firm and dry (DFD) had significantly (P < 0·05) greater muscle cortisol concentrations than those classified as normal. Plasma and muscle cortisol concentrations of carcases classified as pale, soft and exudative (PSE) did not differ significantly from those classified as normal. Correlations between muscle cortisol and meat quality attributes were generally highly significant (r = 0·31 to r = 0·51, P < 0·001) There was a highly significant correlation (r = 0·73, P < 0·0001) between plasma and muscle cortisol concentrations.

A Price To Pay for Relaxed Substrate Specificity: A Comparative Kinetic Analysis of the Class II Lanthipeptide Synthetases ProcM and HalM2

PubMed Central

2015-01-01

Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) that typically harbor multiple intramolecular thioether linkages. For class II lanthipeptides, these cross-links are installed in a multistep reaction pathway by a single enzyme (LanM). The multifunctional nature of LanMs and the manipulability of their genetically encoded peptide substrates (LanAs) make LanM/LanA systems promising targets for the engineering of new antibacterial compounds. Here, we report the development of a semiquantitative mass spectrometry-based assay for kinetic characterization of LanM-catalyzed reactions. The assay was used to conduct a comparative kinetic analysis of two LanM enzymes (HalM2 and ProcM) that exhibit drastically different substrate selectivity. Numerical simulation of the kinetic data was used to develop models for the multistep HalM2- and ProcM-catalyzed reactions. These models illustrate that HalM2 and ProcM have markedly different catalytic efficiencies for the various reactions they catalyze. HalM2, which is responsible for the biosynthesis of a single compound (the Halβ subunit of the lantibiotic haloduracin), catalyzes reactions with higher catalytic efficiency than ProcM, which modifies 29 different ProcA precursor peptides during prochlorosin biosynthesis. In particular, the rates of thioether ring formation are drastically reduced in ProcM, likely because this enzyme is charged with installing a variety of lanthipeptide ring architectures in its prochlorosin products. Thus, ProcM appears to pay a kinetic price for its relaxed substrate specificity. In addition, our kinetic models suggest that conformational sampling of the LanM/LanA Michaelis complex could play an important role in the kinetics of LanA maturation. PMID:25409537

The Strain Index and ACGIH TLV for HAL: risk of trigger digit in the WISTAH prospective cohort.

PubMed

Kapellusch, Jay M; Garg, Arun; Hegmann, Kurt T; Thiese, Matthew S; Malloy, Elizabeth J

2014-02-01

The objective of this study was to investigate the association between job physical exposure (JPE) and incidence of flexor tendon entrapment of the digits (FTED). FTED, commonly known as trigger digit, is associated with age, gender, and certain health disorders. Although JPE has been suggested as a risk factor for FTED, there are no prospective cohort studies. A cohort of 516 workers was enrolled from 10 diverse manufacturing facilities and followed monthly for 6 years. Worker demographics, medical history, and symptoms of FTED were assessed. JPE was individually measured using the Strain Index (SI) and American Conference of Governmental Industrial Hygienists (ACGIH) threshold limit value for hand activity level (TLV for HAL). Changes in JPE (assessed quarterly) and symptoms (assessed monthly) were recorded during follow-up. FTED was defined as demonstrated triggering on examination. Point prevalence of FTED at baseline was 3.6%. During follow-up there were 23 incident FTED cases (left and/or right hands). The incident rate for first occurrence of FTED from enrollment was 1.38 per 100 person-years. Risk factors were JPE, age, gender, diabetes mellitus, carpometacarpal osteoarthrosis, and rheumatoid arthritis. In multivariate models, the SI showed strong association with risk of FTED when treated as a continuous variable and marginal association when dichotomized (SI > 6.1). TLV for HAL showed a statistical trend of increasing risk of FTED using the ACGIH limits, but no association as a continuous variable. Both JPE and personal risk factors are associated with FTED development. The SI and TLV for HAL are useful tools for estimating JPE.

Clinical application of the Hybrid Assistive Limb (HAL) for gait training-a systematic review.

PubMed

Wall, Anneli; Borg, Jörgen; Palmcrantz, Susanne

2015-01-01

The aim of this study was to review the literature on clinical applications of the Hybrid Assistive Limb system for gait training. A systematic literature search was conducted using Web of Science, PubMed, CINAHL and clinicaltrials.gov and additional search was made using reference lists in identified reports. Abstracts were screened, relevant articles were reviewed and subject to quality assessment. Out of 37 studies, 7 studies fulfilled inclusion criteria. Six studies were single group studies and 1 was an explorative randomized controlled trial. In total, these studies involved 140 participants of whom 118 completed the interventions and 107 used HAL for gait training. Five studies concerned gait training after stroke, 1 after spinal cord injury (SCI) and 1 study after stroke, SCI or other diseases affecting walking ability. Minor and transient side effects occurred but no serious adverse events were reported in the studies. Beneficial effects on gait function variables and independence in walking were observed. The accumulated findings demonstrate that the HAL system is feasible when used for gait training of patients with lower extremity paresis in a professional setting. Beneficial effects on gait function and independence in walking were observed but data do not allow conclusions. Further controlled studies are recommended.

Comparison of the cardiopulmonary effects of anesthesia maintained by continuous infusion of romifidine, guaifenesin, and ketamine with anesthesia maintained by inhalation of halothane in horses.

PubMed

McMurphy, Rose M; Young, Lesley E; Marlin, David J; Walsh, Karen

2002-12-01

To compare cardiopulmonary responses during anesthesia maintained with halothane and responses during anesthesia maintained by use of a total intravenous anesthetic (TIVA) regimen in horses. 7 healthy adult horses (1 female, 6 geldings). Each horse was anesthetized twice. Romifidine was administered IV, and anesthesia was induced by IV administration of ketamine. Anesthesia was maintained for 75 minutes by administration of halothane (HA) or IV infusion of romifidine, guaifenesin, and ketamine (TIVA). The order for TIVA or HA was randomized. Cardiopulmonary variables were measured 40, 60, and 75 minutes after the start of HA orTIVA. Systolic, diastolic, and mean carotid arterial pressures, velocity time integral, and peak acceleration of aortic blood flow were greater, and systolic, diastolic, and mean pulmonary arterial pressure were lower at all time points for TIVA than for HA. Pre-ejection period was shorter and ejection time was longer for TIVA than for HA. Heart rate was greater for HA at 60 minutes. Minute ventilation and alveolar ventilation were greater and inspiratory time was longer for TIVA than for HA at 75 minutes. The PaCO2 was higher at 60 and 75 minutes for HA than forTIVA. Horses receiving a constant-rate infusion of romifidine, guaifenesin, and ketamine maintained higher arterial blood pressures than when they were administered HA. There was some indication that left ventricular function may be better during TIVA, but influences of preload and afterload on measured variables could account for some of these differences.

Use of a rapid brain-sampling technique in a physiologic preparation: effects of morphine, ketamine, and halothane on tissue energy intermediates.

PubMed

Dedrick, D F; Sherer, Y D; Biebuyck, J F

1975-06-01

A new method of rapid sampling of brain tissue, "freeze-blowing," has been used to compare the neurochemistry of the brain during anesthesia with that in the awake state. The method avoids anoxia associated with the sampling process. Physiologic variables, including body temperature, blood-gas tensions and blood pressure, were carefully monitored and controlled in the experimental animals. None of the agents tested (halothane, morphine, and ketamine) reduced the brain tissue high-energy phosphate reserved. All three drugs doubled glucose levels. Morphine lowered both lactate and the lactate/pyruvate ratio. Uniformly, the three anesthetic agents led to twofold increases of brain cyclic 3'-5' adenosine monophosphate concentrations. These changes suggest a possible role for cyclic nucleotides in central neurotransmission.

Doppler-guided hemorrhoidal artery ligation (DG-HAL): a safe treatment of II-III degree hemorrhoids for all patients. Could it be potentially also good prophylaxis?

PubMed

Testa, A; Torino, G

2010-06-01

Doppler-guided hemorrhoidal artery ligation (HAL Doppler) is an innovative hemorrhoid treatment mainly utilised for II-III degree where bleeding is a predominant symptom. This procedure aims at dearterialization of the internal hemorrhoidal plexus by ligation of the terminal branches of the superior rectal artery detected using a special proctoscope and ultrasound system; the procedure is performed entirely above the dentate line, so it is genuinely painless. The aim of this study was to evaluate the efficacy, safety and invasivity of HAL Doppler technique to treat II and III degree hemorrhoids. The authors treated 148 patients, from May 2002 to December 2007, principally affected by II-III degree hemorrhoids characterized by bleeding and pain at evacuation. These patients were examined in a retrospective observational study of 128 patients, 86% of the group. Follow-up varied from 5 up to 72 months with an average observation time of 36.5 months. Success was registered in 90% of patients affected by II-III degree hemorrhoids and the absence of major complications (hemorrhage, incontinence, stenosis, perforation, sepsis). The authors suggest the safety, efficacy and low invasity of HAL Doppler for treatment of II-III degree hemorrhoids, which also found in the literature, and highlight its use in treating patients with unhealthy conditions which are a contraindication to the usual surgical treatments. Moreover, they suppose the use of HAL Doppler in low degree hemorrhoids as a therapeutic and also prophylactic rule of advanced degree.

Effects of trailer design on animal welfare parameters and carcass and meat quality of three Pietrain crosses being transported over a long distance.

PubMed

Weschenfelder, A V; Torrey, S; Devillers, N; Crowe, T; Bassols, A; Saco, Y; Piñeiro, M; Saucier, L; Faucitano, L

2012-09-01

This study aimed at evaluating the effects of trailer design on stress responses and meat quality traits of 3 different pig crosses: 50% Pietrain breeding with halothane (HAL)(Nn) (50Nn); 50% Pietrain breeding with HAL(NN) (50NN); and 25% Pietrain breeding with HAL(NN) genotype (25NN). Over a 6-wk period, pigs (120 pigs/crossbreed) were transported for 7 h in either a pot-belly (PB) or flat-deck (FD) trailer (10 pigs/crossbreed(-1)·trailer(-1)·wk(-1)). Temperature (T) and relative humidity (RH) were monitored in each trailer. Behaviors during loading and unloading, time to load and unload, and latency to rest in lairage were recorded, whereas a sub-population of pigs (4 pigs/crossbreed(-1)·trailer(-1)·wk(-1)) was equipped with gastro-intestinal tract (GIT) temperature monitors. Blood samples were collected at exsanguination for measurement of cortisol, creatine kinase (CK), lactate, haptoglobin, and Pig-MAP concentrations. Meat quality data were collected at 24 h postmortem from the LM and semimembranosus (SM) and adductor (AD) muscles of all 360 pigs. Greater T were recorded in the PB trailer during transportation (P = 0.006) and unloading (P < 0.001). Delta GIT temperature was greater (P = 0.01) in pigs unloaded from the PB. At loading, pigs tended to move backwards more (P = 0.06) when loaded on the FD than the PB trailer. At unloading, an interaction was found between trailer type and crossbreed type, with a greater (P < 0.01) frequency of overlaps in 50NN and 25NN pigs and slips/falls in 50Nn and 50NN pigs from the FD than the PB trailer. Cortisol concentrations at slaughter were greater (P = 0.02) in pigs transported in the PB than FD trailer. Greater lactate concentrations were found in 50Nn and 50NN pigs (P = 0.003) and greater CK concentrations (P < 0.001) in 50Nn pigs. As expected, 50Nn pigs produced leaner (P < 0.001) carcasses, with greater (P = 0.01) dressing percentages, as well as lower (P < 0.001) ultimate pH values and greater (P < 0.001) drip

Physico-chemical characteristics of Longissimus lumborum muscle in goats subjected to halal slaughter and anesthesia (halothane) pre-slaughter.

PubMed

Sabow, Azad Behnan; Sazili, Awis Qurni; Zulkifli, Idrus; Goh, Yong Meng; Ab Kadir, Mohd Zainal Abidin; Adeyemi, Kazeem Dauda

2015-12-01

This study assessed the effect of halal slaughter and anesthesia pre-slaughter followed by bleeding on meat quality characteristics of goats. Eleven male Boer cross goats were divided into two groups and subjected to either halal slaughter (HS) or anesthesia with halothane and propofol pre-slaughter (AS). At pre-rigor, HS had significantly lower (P < 0.05) muscle pH and glycogen than AS. However, no significant difference was observed in the pH and glycogen content between the treatments on 1, 3 and 7 days post mortem. The drip loss of HS was significantly lower (P < 0.05) than that of AS at all aging periods. Treatment had no effect on sarcomere length, myofibrillar fragmentation index and shear force values, loss of thiol groups and degradation of major myofibrillar proteins. It can be concluded that HS did not have deleterious effect on meat quality traits of goat when compared to AS. © 2015 Japanese Society of Animal Science.

Cloning, expression and characterisation of P450-Hal1 (CYP116B62) from Halomonas sp. NCIMB 172: A self-sufficient P450 with high expression and diverse substrate scope.

PubMed

Porter, Joanne L; Sabatini, Selina; Manning, Jack; Tavanti, Michele; Galman, James L; Turner, Nicholas J; Flitsch, Sabine L

2018-06-01

Cytochrome P450 monooxygenases are able to catalyse a range of synthetically challenging reactions ranging from hydroxylation and demethylation to sulfoxidation and epoxidation. As such they have great potential for biocatalytic applications but are underutilised due to often-poor expression, stability and solubility in recombinant bacterial hosts. The use of self-sufficient P450 s with fused haem and reductase domains has already contributed heavily to improving catalytic efficiency and simplifying an otherwise more complex multi-component system of P450 and redox partners. Herein, we present a new addition to the class VII family with the cloning, sequencing and characterisation of the self-sufficient CYP116B62 Hal1 from Halomonas sp. NCIMB 172, the genome of which has not yet been sequenced. Hal1 exhibits high levels of expression in a recombinant E. coli host and can be utilised from cell lysate or used in purified form. Hal1 favours NADPH as electron donor and displays a diverse range of activities including hydroxylation, demethylation and sulfoxidation. These properties make Hal1 suitable for future biocatalytic applications or as a template for optimisation through engineering. Copyright © 2018 Elsevier Inc. All rights reserved.

Development of an assist controller with robot suit HAL for hemiplegic patients using motion data on the unaffected side.

PubMed

Kawamoto, Hiroaki; Kandone, Hideki; Sakurai, Takeru; Ariyasu, Ryohei; Ueno, Yukiko; Eguchi, Kiyoshi; Sankai, Yoshiyuki

2014-01-01

Among several characteristics seen in gait of hemiplegic patients after stroke, symmetry is known to be an indicator of the degree of impairment of walking ability. This paper proposes a control method for a wearable type lower limb motion assist robot to realize spontaneous symmetric gait for these individuals. This control method stores the motion of the unaffected limb during swing and then provides motion support on the affected limb during the subsequent swing using the stored pattern to realize symmetric gait based on spontaneous limb swing. This method is implemented on the robot suit HAL (Hybrid Assistive Limbs). Clinical tests were conducted in order to assess the feasibility of the control method. Our case study involved participation of one chronic stroke patient who was not able to flex his right knee. As a result, the walking support for hemiplegic leg provided by the HAL improved the subject's gait symmetry. The feasibility study showed promising basis for the future clinical study.

Epigenetische Aspekte bei Karzinomen der Kopf-Hals-Region

PubMed Central

Schmezer, Peter; Plass, Christoph

2009-01-01

Zusammenfassung Plattenepithelkarzinome der Kopf-Hals-Region (HNSCC) zählen seit Jahren zu den weltweit häufigsten Krebsarten. Trotz vieler Bemühungen hat sich das 5-Jahres-Überleben bei Patienten mit HNSCC kaum verbessert. Um einen Fortschritt zu erzielen, ist es notwendig, die der Erkrankung zugrunde liegenden biologischen Prozesse besser zu verstehen. Neben den bekannten genetischen Veränderungen haben molekular-zytogenetische Untersuchungen bei HNSCC gezeigt, dass es weitere Veränderungen gibt, die mit Vermehrung und Verlust chromosomaler Bereiche einhergehen, für die jedoch die krankheitsverursachenden Gene bisher nicht identifiziert wurden. Darüberhinaus haben jüngste Forschungsergebnisse verdeutlicht, dass epigenetische Modifikationen wie die DNA Methylierung eine wichtige Rolle spielen. So konnte gezeigt werden, dass bei HNSCC eine Reihe von Genen (z.B. das Tumorsuppressorgen CDKN2A sowie DAPK1, MGMT, TIMP3, TCF21, und C/EBPα) hypermethylierte Bereiche in regulatorischen DNA Sequenzen aufweisen, wodurch ihre Expression verringert oder unterbunden wird. Die Hypermethylierung solcher Gene könnte als Biomarker zur Früherkennung von HNSCC genutzt werden und nicht zuletzt dadurch zur Verbesserung von Prävention und Therapieerfolg beitragen. PMID:18483718

Advancing bioluminescence imaging technology for the evaluation of anticancer agents in the MDA-MB-435-HAL-Luc mammary fat pad and subrenal capsule tumor models.

PubMed

Zhang, Cathy; Yan, Zhengming; Arango, Maria E; Painter, Cory L; Anderes, Kenna

2009-01-01

Tumors grafted s.c. or under the mammary fat pad (MFP) rarely develop efficient metastasis. By applying bioluminescence imaging (BLI) technology, the MDA-MB-435-HAL-Luc subrenal capsule (SRC) model was compared with the MFP model for disease progression, metastatic potential, and response to therapy. The luciferase-expressing MDA-MB-435-HAL-Luc cell line was used in both MFP and SRC models. BLI technology allowed longitudinal assessment of disease progression and the therapeutic response to PD-0332991, Avastin, and docetaxel. Immunohistochemical analysis of Ki67 and CD31 staining in the primary tumors was compared in these models. Caliper measurement was used in the MFP model to validate the BLI quantification of primary tumors. The primary tumors in MDA-MB-435-HAL-Luc MFP and SRC models displayed comparable growth rates and vascularity. However, tumor-bearing mice in the SRC model developed lung metastases much earlier (4 weeks) than in the MFP model (>7 weeks), and the metastatic progression contributed significantly to the survival time. In the MFP model, BLI and caliper measurements were comparable for quantifying palpable tumors, but BLI offered an advantage for detecting the primary tumors that fell below a palpable threshold and for visualizing metastases. In the SRC model, BLI allowed longitudinal assessment of the antitumor and antimetastatic effects of PD-0332991, Avastin, and docetaxel, and the results correlated with the survival benefits of these agents. The MDA-MB-435-HAL-Luc SRC model and the MFP model displayed differences in disease progression. BLI is an innovative approach for developing animal models and creates opportunities for improving preclinical evaluations of anticancer agents.

Hybrid Assistive Limb Exoskeleton HAL in the Rehabilitation of Chronic Spinal Cord Injury: Proof of Concept; the Results in 21 Patients.

PubMed

Jansen, Oliver; Grasmuecke, Dennis; Meindl, Renate C; Tegenthoff, Martin; Schwenkreis, Peter; Sczesny-Kaiser, Matthias; Wessling, Martin; Schildhauer, Thomas A; Fisahn, Christian; Aach, Mirko

2018-02-01

The use of mobile exoskeletons is becoming more and more common in the field of spinal cord injury (SCI) rehabilitation. The hybrid assistive limb (HAL) exoskeleton provides a tailored support depending on the patient's voluntary drive. After a pilot study in 2014 that included 8 patients with chronic SCI, this study of 21 patients with chronic SCI serves as a proof of concept. It was conducted to provide further evidence regarding the efficacy of exoskeletal-based rehabilitation. Functional assessment included walking speed, distance, and time on a treadmill, with additional analysis of functional mobility using the following tests: 10-meter walk test (10MWT), timed up and go (TUG) test, 6-minute walk test (6MWT), and the walking index for SCI II (WISCI-II) score. After a training period of 90 days, all 21 patients significantly improved their functional and ambulatory mobility without the exoskeleton. Patients were assessed by the 6MWT, the TUG test, and the 10MWT, which also indicated an increase in the WISCI-II score along with significant improvements in HAL-associated walking speed, distance, and time. Although, exoskeletons are not yet an established treatment in the rehabilitation of spinal cord injuries, the devices will play a more important role in the future. The HAL exoskeleton training enables effective, body weight-supported treadmill training and is capable of improving ambulatory mobility. Future controlled studies are required to enable a comparison of the new advances in the field of SCI rehabilitation with traditional over-ground training. Copyright © 2017 Elsevier Inc. All rights reserved.

Repeatability of Doppler ultrasound measurements of hindlimb blood flow in halothane anaesthetised horses.

PubMed

Raisis, A L; Young, L E; Meire, H; Walsh, K; Taylor, P M; Lekeux, P

2000-05-01

The purpose of this study was to determine the repeatability of femoral blood flow recorded using Doppler ultrasound in anaesthetised horses. Doppler ultrasound of the femoral artery and vein was performed in 6 horses anaesthetised with halothane and positioned in left lateral recumbency. Velocity spectra, recorded using low pulse repetition frequency, were used to calculate time-averaged mean velocity (TAV), velocity of component a (TaVa), velocity of component b (TaVb), volumetric flow, early diastolic deceleration slope (EDDS) and pulsatility index (PI). Within-patient variability was determined for sequential Doppler measurements recorded during a single standardised anaesthetic episode. Within-patient variability was also determined for Doppler and cardiovascular measurements recorded during 4 separate standardised anaesthetic episodes performed at intervals of at least one month. Within-patient variation during a single anaesthetic episode was small. Coefficients of variation (cv) were <12.5% for arterial measurements and <17% for venous measurements. Intraclass correlation coefficient was >0.75 for all measurements. No significant change was observed in measurements of cardiovascular function suggesting that within-patient variation observed during a single anaesthetic episode was due to measurement error. In contrast, within-patient variation during 4 separate anaesthetic episodes was marked (cv>17%) for most Doppler measurements obtained from arteries and veins. Variation in measurements of cardiovascular function were marked (cv>20%), suggesting that there is marked biological variation in central and peripheral observed. Further studies are warranted to determine the ability of this technique to detect differences in blood flow during administration of different anaesthetic agents.

Evaluation of aqueous tear production in dogs after general anaesthesia with medetomidine-propofol-carprofen-halothane.

PubMed

Komnenou, A T H; Kazakos, G M; Savvas, I; Thomas, A L N

2013-08-10

The influence of an anaesthetic protocol, which included medetomidine, propofol, carprofen and halothane on tear production in the dog. There are no previous studies on the effects of this combination on tear production in dogs or in any other species. The present study included 39 dogs, which underwent non-ophthalmic surgery in our clinic. Preanaesthetically, all dogs had normal tear production (18.62±3.65 mm/minute) as this was recorded with Schirmer tear test I (STT I) and the ophthalmologic examination did not reveal anything abnormal. Tear production readings were recorded before the administration of premedication, at the end of anaesthesia, one hour and two hours postanaesthesia. No reverse agent was administrated. At the end of anaesthesia (right eye (oculus dexter, OD) P<0.0005, left eye (oculus sinister, OS) P<0.0005), as well as one hour postanaesthesia (OD P=0.020, OS P=0.001) there was a statistically significant reduction in tear production, which returned to normal values two hours postanaesthesia, regardless of the duration of the operation. This anaesthetic combination resulted in a decrease in tear production and, therefore, the use of tear substitute treatment in dogs undergoing anaesthesia with this protocol (combination) from the time the sedative is given until at least two hours after the end of anaesthesia is highly recommended.

MMW radar enhanced vision systems: the Helicopter Autonomous Landing System (HALS) and Radar-Enhanced Vision System (REVS) are rotary and fixed wing enhanced flight vision systems that enable safe flight operations in degraded visual environments

NASA Astrophysics Data System (ADS)

Cross, Jack; Schneider, John; Cariani, Pete

2013-05-01

Sierra Nevada Corporation (SNC) has developed rotary and fixed wing millimeter wave radar enhanced vision systems. The Helicopter Autonomous Landing System (HALS) is a rotary-wing enhanced vision system that enables multi-ship landing, takeoff, and enroute flight in Degraded Visual Environments (DVE). HALS has been successfully flight tested in a variety of scenarios, from brown-out DVE landings, to enroute flight over mountainous terrain, to wire/cable detection during low-level flight. The Radar Enhanced Vision Systems (REVS) is a fixed-wing Enhanced Flight Vision System (EFVS) undergoing prototype development testing. Both systems are based on a fast-scanning, threedimensional 94 GHz radar that produces real-time terrain and obstacle imagery. The radar imagery is fused with synthetic imagery of the surrounding terrain to form a long-range, wide field-of-view display. A symbology overlay is added to provide aircraft state information and, for HALS, approach and landing command guidance cuing. The combination of see-through imagery and symbology provides the key information a pilot needs to perform safe flight operations in DVE conditions. This paper discusses the HALS and REVS systems and technology, presents imagery, and summarizes the recent flight test results.

Evidence for distillation in the formation of HAL and related hibonite inclusions. [from Allende, Dhajala, and Murchison chondrites

NASA Technical Reports Server (NTRS)

Ireland, Trevor R.; Zinner, Ernst K.; Fahey, Albert J.; Esat, Tezer M.

1992-01-01

New Ca- and Ti-isotopic analyses of DH-H1, 7-404, and 7-971, and Mg-isotopic analyses on DH-H1 and 7-404 are reported. O-isotopic analyses of HAL, 7-404, 7-971, and a variety of other refractory inclusions from Murchison were made in order to establish the presence or absence of FUN O-isotopic systematics. A higonite-rich residue produced by the evaporation of kaersutite was analyzed for its trace-element and isotopic abundances to see if any of the characteristics of FUN hibonite inclusions can be produced by distillation in the laboratory. These data are then used to evaluate for all four inclusions the HAL-type formation models originally proposed by Allen et al. (1980) and Lee et al. (1980). The four inclusions were found to have very similar chemical and isotopic features. All are characterized by large Ce depletions and very low Mg, Ti, and V concentrations compared to other meteoritic hibonites. All four inclusions have delta(C-48) within error of -5 per mil. Ca-, Ti-, and O-isotopic compositions are fractionated with enrichments of the heavy isotopes, and the Ti-isotopic mass fractionation is inversely correlated with Ti concentration. It is concluded that the inclusions formed primarily as distillation residues in accord with the early conclusions.

Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

PubMed

Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

2010-08-01

There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

PubMed

Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

2016-09-17

Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

Hal Is a Bacillus anthracis Heme Acquisition Protein

PubMed Central

Balderas, Miriam A.; Nobles, Christopher L.; Honsa, Erin S.; Alicki, Embriette R.

2012-01-01

The metal iron is a limiting nutrient for bacteria during infection. Bacillus anthracis, the causative agent of anthrax and a potential weapon of bioterrorism, grows rapidly in mammalian hosts, which suggests that it efficiently attains iron during infection. Recent studies have uncovered both heme (isd) and siderophore-mediated (asb) iron transport pathways in this pathogen. Whereas deletion of the asb genes results in reduced virulence, the loss of three surface components from isd had no effect, thereby leaving open the question of what additional factors in B. anthracis are responsible for iron uptake from the most abundant iron source for mammals, heme. Here, we describe the first functional characterization of bas0520, a gene recently implicated in anthrax disease progression. bas0520 encodes a single near-iron transporter (NEAT) domain and several leucine-rich repeats. The NEAT domain binds heme, despite lacking a stabilizing tyrosine common to the NEAT superfamily of hemoproteins. The NEAT domain also binds hemoglobin and can acquire heme from hemoglobin in solution. Finally, deletion of bas0520 resulted in bacilli unable to grow efficiently on heme or hemoglobin as an iron source and yielded the most significant phenotype relative to that for other putative heme uptake systems, a result that suggests that this protein plays a prominent role in the replication of B. anthracis in hematogenous environments. Thus, we have assigned the name of Hal (heme-acquisition leucine-rich repeat protein) to BAS0520. These studies advance our understanding of heme acquisition by this dangerous pathogen and justify efforts to determine the mechanistic function of this novel protein for vaccine or inhibitor development. PMID:22865843

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction.

PubMed

Siu, Chi-Kit; Liu, Zhi-Feng; Tse, John S

2002-09-11

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

PubMed

Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

PubMed

Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

2015-01-01

The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

Activation of C-O and C-C bonds and formation of novel HAlOH-ether complexes: an EPR study of the reaction of ground-state Al atoms with methylethyl ether and diethyl ether.

PubMed

Brunet, François D; Feola, Julie C; Joly, Helen A

2012-03-15

Reaction mixtures, containing Al atoms and methylethyl ether (MEE) or diethyl ether (DEE) in an adamantane matrix, were prepared with the aid of a metal-atom reactor known as a rotating cryostat. The EPR spectra of the resulting products were recorded from 77-260 K, at 10 K intervals. Al atoms were found to insert into methyl-O, ethyl-O, and C-C bonds to form CH(3)AlOCH(2)CH(3), CH(3)OAlCH(2)CH(3), and CH(3)OCH(2)AlCH(3), respectively, in the case of MEE while DEE produced CH(3)CH(2)AlOCH(2)CH(3) and CH(3)AlCH(2)OCH(2)CH(3), respectively. From the intensity of the transition lines attributed to the Al atom C-O insertion products of MEE, insertion into the methyl-O bond is preferred. The Al hyperfine interaction (hfi) extracted from the EPR spectra of the C-O insertion products was greater than that of the C-C insertion products, that is, 5.4% greater for the DEE system and 7% greater for the MEE system. The increase in Al hfi is thought to arise from the increased electron-withdrawing ability of the substituents bonded to Al. Besides HAlOH, resulting from the reaction of Al atoms with adventitious water, novel mixed HAlOH:MEE and HAlOH:DEE complexes were identified with the aid of isotopic studies involving H(2)(17)O and D(2)O. The Al and H hfi of HAlOH were found to decrease upon complex formation. These findings are consistent with the nuclear hfi calculated using a density functional theory (DFT) method with close agreement between theory and experiment occurring at the B3LYP level using a 6-311+G(2df,p) basis set.

Genotypic variability and genotype by environment interactions in oil and fatty acids in high, intermediate, and low oleic acid peanut genotypes.

PubMed

Singkham, Nattawut; Jogloy, Sanun; Kesmala, Thawan; Swatsitang, Prasan; Jaisil, Prasit; Puppala, Naveen

2010-05-26

Variability of genotype and genotype x environment (G x E) interactions for fatty acids are important to develop high-oleic types in peanut varietal improvement programs. The objective of this study was to determine the variation in fatty acid composition among peanut genotypes and G x E interactions of fatty acids in three groups of genotypes with high, intermediate, and low-oleic acid. Twenty-one genotypes were tested in three environments consisting of two rainy seasons and one dry season. The results indicated that G x E interactions were significant for biomass, pod yield, and harvest index and also for oleic, linoleic acids, and O/L ratio. G x E interactions were less important than genotypic main effect. For oleic acid, significant interactions were found in the intermediate and low-oleic groups only. Therefore, selection for high-oleic trait in peanut breeding programs should be effective.

Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

PubMed

Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

2015-06-01

Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

Global Identification of Three Major Genotypes of Varicella-Zoster Virus: Longitudinal Clustering and Strategies for Genotyping

PubMed Central

Loparev, Vladimir N.; Gonzalez, Antonio; Deleon-Carnes, Marlene; Tipples, Graham; Fickenscher, Helmut; Torfason, Einar G.; Schmid, D. Scott

2004-01-01

By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E- and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples. PMID:15254207

Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

PubMed

Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

2016-02-18

Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide.

HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

PubMed Central

Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y. M.; Klappenbach, Joel A.; Marton, Matthew J.

2015-01-01

Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection. PMID:25830316

Decoding noises in HIV computational genotyping.

PubMed

Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

2017-11-01

Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

Performance evaluation of the Abbott RealTime HCV Genotype II for hepatitis C virus genotyping.

PubMed

Sohn, Yong-Hak; Ko, Sun-Young; Kim, Myeong Hee; Oh, Heung-Bum

2010-04-01

The Abbott RealTime hepatitis C virus (HCV) Genotype II (Abbott Molecular Inc.) for HCV genotyping, which uses real-time PCR technology, has recently been developed. Accuracy and sensitivity of detection were assessed using the HCV RNA PHW202 performance panel (SeraCare Life Sciences). Consistency with restriction fragment mass polymorphism (RFMP) data, cross-reactivity with other viruses, and the ability to detect minor strains in mixtures of genotypes 1 and 2 were evaluated using clinical samples. All performance panel viruses were correctly genotyped at levels of >500 IU/mL. Results were 100% concordant with RFMP genotypic data (66/66). However, 5% (3/66) of the samples examined displayed probable genotypic cross reactivity. No cross reactivity with other viruses was evident. Minor strains in the mixtures were not effectively distinguished, even at quantities higher than the detection limit. The Abbott RealTime HCV Genotype II assay was very accurate and yielded results consistent with RFMP data. Although the assay has the advantages of automation and short turnaround time, we suggest that further improvements are necessary before it is used routinely in clinical practice. Efforts are needed to decrease cross reactivity among genotypes and to improve the ability to detect minor genotypes in mixed infections.

HBV Genotypic Variability in Cuba

PubMed Central

Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

2015-01-01

The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

A genotype independent, full-genome reverse-transcription protocol for HCV genotyping and resistance testing.

PubMed

Walker, Andreas; Bergmann, Matthias; Camdereli, Jennifer; Kaiser, Rolf; Lübke, Nadine; Timm, Jörg

2017-06-01

HCV treatment options and cure rates have tremendously increased in the last decade. Although a pan-genotype HCV treatment has recently been approved, most DAA therapies are still genotype specific. Resistance-associated variants (RAVs) can limit the efficacy of DAA therapy and are associated with increased risk for therapy failure. With the approval of DAA regimens that recommend resistance testing prior to therapy, correct assessment of the genotype and testing for viruses with RAVs is clinically relevant. However, genotyping and resistance testing is generally done in costly and laborious separate reactions. The aim of the study was to establish a genotype-independent full-genome reverse transcription protocol to generate a template for both genotyping and resistance testing and to implement it into our routine diagnostic setup. The complete HCV genome was reverse transcribed with a pan-genotype primer binding at the 3'end of the viral RNA. This cDNA served as template for transcription of the genotyping amplicon in the core region as well as for the resistance testing of NS3, NS5A, and NS5B. With the established RT-protocol the HCV core region was successfully amplified and genotyped from 124 out of 125 (99.2%) HCV-positive samples. The amplification efficiency of RAV containing regions in NS3, NS5A, NS5B was 96.2%, 96.6% and 94.4%, respectively. We developed a method for HCV full-genome cDNA synthesis and implemented it into a routine diagnostic setup. This cDNA can be used as template for genotyping amplicons covering the core or NS5B region as well as for resistance testing amplicons in NS3, NS5A and NS5B. Copyright © 2017 Elsevier B.V. All rights reserved.

The Effect of Gas Density on Gas Transport during High Frequency Oscillation

DTIC Science & Technology

1985-04-04

found that as alveolar ventilation increased the rate of uptake of halothane increased. Papper and Kitz (1963) used conventiot~al positive pressure...coefficient (halothane) = 2.3 ( Papper and Kitz, 1963; Wylie and Churchill-Davidson, 1972; Eger, 1976) [ 11] v2 =Volume (L), (310)(22.4)/ 273...there is an increase in alveolar concentration of halothane with conventional ventilation (Kety, 1951; Papper and Kitz, 1963). Our halothane uptake

Comparison of detomidine and romifidine as premedicants before ketamine and halothane anesthesia in horses undergoing elective surgery.

PubMed

Taylor, P M; Bennett, R C; Brearley, J C; Luna, S P; Johnson, C B

2001-03-01

To compare detomidine hydrochloride and romifidine as premedicants in horses undergoing elective surgery. 100 client-owned horses. After administration of acepromazine (0.03 mg/kg, IV), 50 horses received detomidine hydrochloride (0.02 mg/kg of body weight, IV) and 50 received romifidine (0.1 mg/kg, IV) before induction and maintenance of anesthesia with ketamine hydrochloride (2 mg/kg) and halothane, respectively. Arterial blood pressure and blood gases, ECG, and heart and respiratory rates were recorded. Induction and recovery were timed and graded. Mean (+/- SD) duration of anesthesia for all horses was 104 +/- 28 minutes. Significant differences in induction and recovery times or grades were not detected between groups. Mean arterial blood pressure (MABP) decreased in both groups 30 minutes after induction, compared with values at 10 minutes. From 40 to 70 minutes after induction, MABP was significantly higher in detomidine-treated horses, compared with romifidine-treated horses, although more romifidine-treated horses received dobutamine infusions. In all horses, mean respiratory rate ranged from 9 to 11 breaths/min, PaO2 from 200 to 300 mm Hg, PaCO2 from 59 to 67 mm Hg, arterial pH from 7.33 to 7.29, and heart rate from 30 to 33 beats/min, with no significant differences between groups. Detomidine and romifidine were both satisfactory premedicants. Romifidine led to more severe hypotension than detomidine, despite administration of dobutamine to more romifidine-treated horses. Both detomidine and romifidine are acceptable alpha2-adrenoceptor agonists for use as premedicants before general anesthesia in horses; however, detomidine may be preferable when maintenance of blood pressure is particularly important.

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

PubMed

Manrubia, Susanna; Cuesta, José A

2017-04-01

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes

USDA-ARS?s Scientific Manuscript database

High-throughput SNP genotyping provides a rapid way of developing resourceful set of markers for delineating the genetic architecture and for effective species discrimination. In the presented research, we demonstrate a set of 192 SNPs for effective genotyping in sugar beet using high-throughput mar...

Rotavirus genotype shifts among Swedish children and adults-Application of a real-time PCR genotyping.

PubMed

Andersson, Maria; Lindh, Magnus

2017-11-01

It is well known that human rotavirus group A is the most important cause of severe diarrhoea in infants and young children. Less is known about rotavirus infections in other age groups, and about how rotavirus genotypes change over time in different age groups. Develop a real-time PCR to easily genotype rotavirus strains in order to monitor the pattern of circulating genotypes. In this study, rotavirus strains in clinical samples from children and adults in Western Sweden during 2010-2014 were retrospectively genotyped by using specific amplification of VP 4 and VP 7 genes with a new developed real-rime PCR. A genotype was identified in 97% of 775 rotavirus strains. G1P[8] was the most common genotype representing 34.9%, followed by G2P[4] (28.3%), G9P[8] (11.5%), G3P[8] (8.1%), and G4P[8] (7.9%) The genotype distribution changed over time, from predominance of G1P[8] in 2010-2012 to predominance of G2P[4] in 2013-2014. There were also age-related differences, with G1P[8] being the most common genotype in children under 2 years (47.6%), and G2P[4] the most common in those over 70 years of age (46.1%.). The shift to G2P[4] in 2013-2014 was associated with a change in the age distribution, with a greater number of rotavirus positive cases in elderly than in children. By using a new real-time PCR method for genotyping we found that genotype distribution was age related and changed over time with a decreasing proportion of G1P[8]. Copyright © 2017. Published by Elsevier B.V.

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

PubMed

O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

PubMed Central

Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

HAL-RAR (Doppler guided haemorrhoid artery ligation with recto-anal repair) is a safe and effective procedure for haemorrhoids. Results of a prospective study after two-years follow-up.

PubMed

Hoyuela, Carlos; Carvajal, Fernando; Juvany, Montserrat; Troyano, Daniel; Trias, Miquel; Martrat, Antoni; Ardid, Jordi; Obiols, Joan

2016-04-01

To analyse prospectively results of HAL-RAR technique by evaluating pain, perioperative complications and clinical outcome after two years followup. A prospective study design including 30 consecutive patients with haemorrhoids grade III-IV treated from June 2012. After discharge, patients received a specific questionnaire to record postoperative pain, delayed complications, evolution/disappearance of the symptoms that led to the surgical intervention (bleeding, prolapse, itching, pain and soiling). A visual analog scale (VAS) was used to measure pain. Outpatient follow-up was carried out at 7 days, and 1, 6 and 12 months and annually thereafter. Pre, intra and postoperative data (including physical examination) had been recorded prospectively. The median operating time (range) was 40 (26-60) minutes. Average hospital stay (range) was 11 (3-25) hours. No postoperative complications were observed in 29 cases (96.6%). Median follow-up was 26 (12-36) months. All the patients attended the follow-up. Mean postoperative pain was VAS = 1.7 on the seventh day and it was practically non-existent (VAS = 0.7) 1 month after the procedure. 87.5% of patients confirmed complete relief of symptoms after 30 days and 93% of patients feel free of symptoms 6 months after the procedure. No patient has experienced late complications as dyschezia, urgency, soiling or faecal incontinence. After 24 months follow-up, recurrence of bleeding and prolapse was observed in only 1 patient; 93% of patients have considered results of HAL-RAR as very good or excellent. HAL-RAR is safe and almost painless technique and it has very good results in the control of haemorrhoidal symptoms. This procedure should be considered as an effective first treatment option for haemorrhoids. Copyright © 2016 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.

Distribution of HBV genotypes in Poland.

PubMed

Świderska, Magdalena; Pawłowska, Małgorzata; Mazur, Włodzimierz; Tomasiewicz, Krzysztof; Simon, Krzysztof; Piekarska, Anna; Wawrzynowicz-Syczewska, Marta; Jaroszewicz, Jerzy; Rajewski, Paweł; Zasik, Ewelina; Murias-Bryłowska, Elżbieta; Pniewska, Anna; Halota, Waldemar; Flisiak, Robert

2015-05-01

To identify distribution of HBV genotypes in particular regions of Poland. The study included 270 treatment-naïve, HBV-infected individuals, enrolled in 7 centers of Poland. HBV genotyping was performed in 243 of them with the INNO-LiPA HBV Genotyping assay (Innogenetics). Genotype A present in 2/3 patients was demonstrated as the most predominant in Poland. It was followed by D (20%), H (5%) and mixed A + D (5%). Remaining patients were infected with genotype F, mixed D + G, A + C or D + F. Analysis of distribution demonstrated regional differences, with a higher rate of genotype D prevalence (about 30%) in the eastern (Białystok and Lublin) and south-western (Wrocław) parts compared to other regions, where the prevalence rate was below 15%. The highest prevalence of genotype A (exceeding 80%) was observed in central Poland (Bydgoszcz, Łódź). The presented data reveal the current distribution of HBV genotypes across Poland, which is the first and the largest such epidemiological analysis.

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

PubMed Central

2012-01-01

Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing information due to genotyping errors

Geographical distribution of HCV genotypes in Mexico.

PubMed

Sánchez-Avila, Juan Francisco; González, Elizabeth; Vázquez, Victoria; Suárez, Susana; Uribe, Misael

2007-01-01

Chronic hepatitis C (CHC) is the second cause of endstage liver disease in our country and one of the main indications of liver transplantation. Hepatitis C virus (HCV) genotype is the principal prognostic factor and the determinant of the therapeutic scheme. In our country few data exist regarding the prevalence of HCV infection and genotype distribution in the Mexican Republic has not been determined. The aim of this study was to characterize the prevalence of the different HCV genotypes and to explore their geographical distribution. Mexican patients with hepatitis C infection, detected throughout the country between 2003 and 2006, were included. All samples were analyzed by a central laboratory and Hepatitis C genotype was identified by Line Immuno Probe Assay in PCR positive samples (Versant Line Probe Assay Quest Diagnostics Nichols Institute, San Juan Capistrano CA). Data were analyzed according to the four geographical areas in Mexico. One thousand three hundred and ninety CHC patients were included. The most frequent genotype detected was genotype 1 (69%) followed by genotype 2 (21.4%) and genotype 3 (9.2%). Genotype 4 and 5 were infrequent. There was no subject infected with genotype 6. Genotype 1 and 2 exhibit very similar distribution in all geographical areas. Genotype 3 infected patients were more frequent in the North region (52%) compared with other areas:center-western (30%), center (17%), South-South east (1%) (p < 0.001). The most prevalent HCV genotype in Mexico is genotype 1. Geographical distribution of HCV genotypes in the four geographical areas in Mexico is not homogenous with a greater frequency of genotype3 in the north region. This difference could be related to the global changes of risk factors for HCV infection.

Hepatitis C virus genotypes in Myanmar.

PubMed

Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

2016-07-21

Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

Hepatitis C virus genotypes in Myanmar

PubMed Central

Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

2016-01-01

Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined. PMID:27468202

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

PubMed

Prilusky, Jaime; Oueillet, Eric; Ulryck, Nathalie; Pajon, Anne; Bernauer, Julie; Krimm, Isabelle; Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Liger, Dominique; Trésaugues, Lionel; Sussman, Joel L; Janin, Joël; van Tilbeurgh, Herman; Poupon, Anne

2005-06-01

Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

PubMed Central

Browning, Brian L.; Yu, Zhaoxia

2009-01-01

We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods, using genotype data from the Illumina 550K and Affymetrix 500K arrays. We show that our method has higher genotype-call accuracy and yields fewer uncalled genotypes than competing methods. We perform single-marker analysis of data from the Wellcome Trust Case Control Consortium bipolar disorder and type 2 diabetes studies. For bipolar disorder, the genotype calls in the original study yield 25 markers with apparent false-positive association with bipolar disorder at a p < 10−7 significance level, whereas genotype calls made with our method yield no associated markers at this significance threshold. Conversely, for markers with replicated association with type 2 diabetes, there is good concordance between genotype calls used in the original study and calls made by our method. Results from single-marker and haplotypic analysis of our method's genotype calls for the bipolar disorder study indicate that our method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Our new genotype-calling methods are implemented in the BEAGLE and BEAGLECALL software packages. PMID:19931040

Modification of hemiplegic compensatory gait pattern by symmetry-based motion controller of HAL.

PubMed

Kawamoto, Hiroaki; Kadone, Hideki; Sakurai, Takeru; Sankai, Yoshiyuki

2015-01-01

As one of several characteristics of hemiplegic patients after stroke, compensatory gait caused by affected limb is often seen. The purpose of this research is to apply a symmetry-based controller of a wearable type lower limb robot, Hybrid Assistive Limb (HAL) to hemiplegic patients with compensatory gait, and to investigate improvement of gait symmetry. The controller is designed respectively for swing phase and support phase according to characteristics of hemiplegic gait pattern. The controller during swing phase stores the motion of the unaffected limb and then provides motion support on the affected limb during the subsequent swing using the stored pattern to realize symmetric gait based on spontaneous limb swing. Moreover, the controller during support phase provides motion to extend hip and knee joints to support wearer's body. Clinical tests were conducted in order to assess the modification of gait symmetry. Our case study involved participation of one chronic stroke patient who performs abnormally-compensatory gait for both of the affected and unaffected limbs. As a result, the patient's gait symmetry was improved by providing motion support during the swing phase on the affected side and motion constraint during the support phase on the unaffected side. The study showed promising basis for the effectiveness of the controller for the future clinical study.

AN EVALUATION OF CRYPTOSPORIDIUM PARVUM GENOTYPING

EPA Science Inventory

We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. Genomic DNA from three species of Crytosporidium parasites (genotype 1 and genotype 2 of C. parvum, C. muris, a...

Host genotype by parasite genotype interactions underlying the resistance of anopheline mosquitoes to Plasmodium falciparum.

PubMed

Lambrechts, Louis; Halbert, Jean; Durand, Patrick; Gouagna, Louis C; Koella, Jacob C

2005-01-11

Most studies on the resistance of mosquitoes to their malaria parasites focus on the response of a mosquito line or colony against a single parasite genotype. In natural situations, however, it may be expected that mosquito-malaria relationships are based, as are many other host-parasite systems, on host genotype by parasite genotype interactions. In such systems, certain hosts are resistant to one subset of the parasite's genotypes, while other hosts are resistant to a different subset. To test for genotype by genotype interactions between malaria parasites and their anopheline vectors, different genetic backgrounds (families consisting of the F1 offspring of individual females) of the major African vector Anopheles gambiae were challenged with several isolates of the human malaria parasite Plasmodium falciparum (obtained from naturally infected children in Kenya). Averaged across all parasites, the proportion of infected mosquitoes and the number of oocysts found in their midguts were similar in all mosquito families. Both indices of resistance, however, differed considerably among isolates of the parasite. In particular, no mosquito family was most resistant to all parasites, and no parasite isolate was most infectious to all mosquitoes. These results suggest that the level of mosquito resistance depends on the interaction between its own and the parasite's genotype. This finding thus emphasizes the need to take into account the range of genetic diversity exhibited by mosquito and malaria field populations in ideas and studies concerning the control of malaria.

Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes.

PubMed

Sulyok, Kinga M; Kreizinger, Zsuzsa; Hornstra, Heidie M; Pearson, Talima; Szigeti, Alexandra; Dán, Ádám; Balla, Eszter; Keim, Paul S; Gyuranecz, Miklós

2014-05-07

Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis (MLVA). Phylogenetic relationships among MST genotypes show how these Hungarian samples are related to others collected around the world. Three MST genotypes were identified: sequence type (ST) 20 has also been identified in ruminants from other European countries and the USA, ST28 was previously identified in Kazakhstan, and the proposed ST37 is novel. All MST genotypes yielded different MLVA genotypes and three different MLVA genotypes were identified within ST20 samples alone. Two novel MLVA types 0-9-5-5-6-2 (AG) and 0-8-4-5-6-2 (AF) (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34) were defined in the ovine materials correlated with ST28 and ST37. Samples from different parts of the phylogenetic tree were associated with different hosts, suggesting host-specific adaptations. Even with the limited number of samples analysed, this study revealed high genetic diversity among C. burnetii in Hungary. Understanding the background genetic diversity will be essential in identifying and controlling outbreaks.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

PubMed

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-11-18

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

PubMed Central

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-01-01

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

Heterogeneous recombination among Hepatitis B virus genotypes.

PubMed

Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

2017-10-01

The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum.

PubMed

Grandke, Fabian; Singh, Priyanka; Heuven, Henri C M; de Haan, Jorn R; Metzler, Dirk

2016-08-24

Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. Alternatively, continuous genotype values can be used for association analysis in higher polyploids. We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method. A disease, a flowering and a growth trait with h (2) of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. The data set consisted of 55,825 probes and 228 samples. We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The identified probe sets were overlapping, but not identical between the methods. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. Linear and partial least squares regression led to numerous associating probes. Association based on genotype classes resulted in similar values, but missed several significant probes. A simulation study was used to successfully validate the number of associating markers. Association of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. Genotype calling does not improve the association and shows no advantages in this study. Instead, use of continuous genotypes simplifies the analysis, saves

[Evaluation of hepatitis B virus genotyping EIA kit].

PubMed

Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

2009-01-01

Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

Subcellular distribution of an inhalational anesthetic in situ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eckenhoff, R.G.; Shuman, H.

1990-01-01

To better understand the mechanisms and sites of anesthetic action, we determined the subcellular partitioning of halothane in a tissue model. A method was found to fix the in vivo distribution of halothane in rat atrial tissue for subsequent electron microscopy and x-ray microanalysis. Atrial strips were exposed to various concentrations of halothane, rapidly frozen, cryo-sectioned, and cryo-transferred into an electron microscope. Irradiation of the hydrated cryosections with the electron beam caused halothane radiolysis, which allowed retention of the halogen-containing fragments after dehydration of the sections. The bromine from halothane was detected and quantified with x-ray microanalysis in various microregionsmore » of atrial myocytes. Halothane (bromine) partitioned largely to mitochondria, with progressively lower concentrations in sarcolemma, nuclear membrane, cytoplasm, sarcomere, and nucleus. Partitioning could not be explained solely by distribution of cellular lipid, suggesting significant and differential physicochemical solubility in protein. However, we found no saturable compartment in atrial myocytes within the clinical concentration range, which implies little specific protein binding.« less

Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.

PubMed

Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

2014-12-11

To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference. Genotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from http://www.molgenis.org/systemsgenetics. GH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines.

Minimum Information about a Genotyping Experiment (MIGEN)

PubMed Central

Huang, Jie; Mirel, Daniel; Pugh, Elizabeth; Xing, Chao; Robinson, Peter N.; Pertsemlidis, Alexander; Ding, LiangHao; Kozlitina, Julia; Maher, Joseph; Rios, Jonathan; Story, Michael; Marthandan, Nishanth; Scheuermann, Richard H.

2011-01-01

Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genetic variations and normal/abnormal phenotypes. Genotyping assay techniques vary from single genomic regions that are interrogated using PCR reactions to high throughput assays examining genome-wide sequence and structural variation. The resulting genotype data may include millions of markers of thousands of individuals, requiring various statistical, modeling or other data analysis methodologies to interpret the results. To date, there are no standards for reporting genotyping experiments. Here we present the Minimum Information about a Genotyping Experiment (MIGen) standard, defining the minimum information required for reporting genotyping experiments. MIGen standard covers experimental design, subject description, genotyping procedure, quality control and data analysis. MIGen is a registered project under MIBBI (Minimum Information for Biological and Biomedical Investigations) and is being developed by an interdisciplinary group of experts in basic biomedical science, clinical science, biostatistics and bioinformatics. To accommodate the wide variety of techniques and methodologies applied in current and future genotyping experiment, MIGen leverages foundational concepts from the Ontology for Biomedical Investigations (OBI) for the description of the various types of planned processes and implements a hierarchical document structure. The adoption of MIGen by the research community will facilitate consistent genotyping data interpretation and independent data validation. MIGen can also serve as a framework for the development of data models for capturing and storing genotyping results and experiment metadata in a structured way, to facilitate the exchange of metadata. PMID:22180825

The epigenetic landscape in the course of time: Conrad Hal Waddington's methodological impact on the life sciences.

PubMed

Baedke, Jan

2013-12-01

It seems that the reception of Conrad Hal Waddington's work never really gathered speed in mainstream biology. This paper, offering a transdisciplinary survey of approaches using his epigenetic landscape images, argues that (i) Waddington's legacy is much broader than is usually recognized--it is widespread across the life sciences (e.g. stem cell biology, developmental psychology and cultural anthropology). In addition, I will show that (ii) there exist as yet unrecognized heuristic roles, especially in model building and theory formation, which Waddington's images play within his work. These different methodological facets envisioned by Waddington are used as a natural framework to analyze and classify the manners of usage of epigenetic landscape images in post-Waddingtonian 'landscape approaches'. This evaluation of Waddington's pictorial legacy reveals that there are highly diverse lines of traditions in the life sciences, which are deeply rooted in Waddington's methodological work. Copyright © 2013 Elsevier Ltd. All rights reserved.

Toward high-throughput genotyping: dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers.

PubMed

Li, J L; Deng, H; Lai, D B; Xu, F; Chen, J; Gao, G; Recker, R R; Deng, H W

2001-07-01

To efficiently manipulate large amounts of genotype data generated with fluorescently labeled dinucleotide markers, we developed a Microsoft database management system, named. offers several advantages. First, it accommodates the dynamic nature of the accumulations of genotype data during the genotyping process; some data need to be confirmed or replaced by repeat lab procedures. By using, the raw genotype data can be imported easily and continuously and incorporated into the database during the genotyping process that may continue over an extended period of time in large projects. Second, almost all of the procedures are automatic, including autocomparison of the raw data read by different technicians from the same gel, autoadjustment among the allele fragment-size data from cross-runs or cross-platforms, autobinning of alleles, and autocompilation of genotype data for suitable programs to perform inheritance check in pedigrees. Third, provides functions to track electrophoresis gel files to locate gel or sample sources for any resultant genotype data, which is extremely helpful for double-checking consistency of raw and final data and for directing repeat experiments. In addition, the user-friendly graphic interface of renders processing of large amounts of data much less labor-intensive. Furthermore, has built-in mechanisms to detect some genotyping errors and to assess the quality of genotype data that then are summarized in the statistic reports automatically generated by. The can easily handle >500,000 genotype data entries, a number more than sufficient for typical whole-genome linkage studies. The modules and programs we developed for the can be extended to other database platforms, such as Microsoft SQL server, if the capability to handle still greater quantities of genotype data simultaneously is desired.

The HAL 9000 Space Operating System Real-Time Planning Engine Design and Operations Requirements

NASA Technical Reports Server (NTRS)

Stetson, Howard; Watson, Michael D.; Shaughnessy, Ray

2012-01-01

In support of future deep space manned missions, an autonomous/automated vehicle, providing crew autonomy and an autonomous response planning system, will be required due to the light time delays in communication. Vehicle capabilities as a whole must provide for tactical response to vehicle system failures and space environmental effects induced failures, for risk mitigation of permanent loss of communication with Earth, and for assured crew return capabilities. The complexity of human rated space systems and the limited crew sizes and crew skills mix drive the need for a robust autonomous capability on-board the vehicle. The HAL 9000 Space Operating System[2] designed for such missions and space craft includes the first distributed real-time planning / re-planning system. This paper will detail the software architecture of the multiple planning engine system, and the interface design for plan changes, approval and implementation that is performed autonomously. Operations scenarios will be defined for analysis of the planning engines operations and its requirements for nominal / off nominal activities. An assessment of the distributed realtime re-planning system, in the defined operations environment, will be provided as well as findings as it pertains to the vehicle, crew, and mission control requirements needed for implementation.

Comparison between genotyping by sequencing and SNP-chip genotyping in QTL mapping in wheat

USDA-ARS?s Scientific Manuscript database

Array- or chip-based single nucleotide polymorphism (SNP) markers are widely used in genomic studies because of their abundance in a genome and cost less per data point compared to older marker technologies. Genotyping by sequencing (GBS), a relatively newer approach of genotyping, suggests equal or...

Distribution of HCV genotypes in Poland.

PubMed

Panasiuk, Anatol; Flisiak, Robert; Mozer-Lisewska, Iwona; Adamek, Agnieszka; Tyczyno, Małgorzata; Halota, Waldemar; Pawłowska, Małgorzata; Stańczak, Janusz; Berak, Hanna; Wawrzynowicz-Syczewska, Marta; Boroń-Kaczmarska, Anna; Łapiński, Tadeusz Wojciech; Grzeszczuk, Anna; Piekarska, Anna; Tomasiewicz, Krzysztof; Jabłkowski, Maciej; Kryczka, Wiesław; Zarebska-Michaluk, Dorota; Stepień, Piotr; Garlicki, Aleksander Michał; Kozłowska, Joanna; Wiercińska-Drapało, Alicja; Zasik, Ewelina; Mazur, Waldemar; Dobracka, Bozena; Dobracki, Witold; Simon, Krzysztof; Ryzko, Józef; Pawłowska, Joanna; Dzierzanowska-Fangrat, Katarzyna; Januszkiewicz-Lewandowska, Danuta; Szenborn, Leszek; Zaleska, Izabela; Rokitka, Maria; Strawińska, Elzbieta; Balinowska, Katarzyna; Smiatacz, Tomasz; Stalke, Piotr; Sikorska, Katarzyna; Lakomy, Anna; Zdrojewski, Maciej; Lachowicz, Anna

2013-01-01

Available data on prevalence of HCV genotypes in Poland are insufficient. The aim of the study was the analysis of distribution of HCV genotypes in Poland over the period of recent 10 years regarding the age of patients and the regions of the country. Analysis of HCV genotypes in Poland was carried out between 2003 and 2012, and included 14 651 patients from 22 centers where patients with chronic viral hepatitis C are diagnosed and treated. Genotypes were analyzed in age groups (< 20 years of age, 20-40 years of age, > 40 years of age) as well as in populations of HBV and HIV co-infections. Genotype (G) 1 infection was demonstrated in 79.4%, G2 -0.1%, G3- 13.8%, G4- 4.9%, G6-0.09% and mixed infections in 1.6%. There was no infection with genotype 5. The highest prevalence of G1 was observed in the Łódzkie voivodship (89.2%) and the Slaskie voivodship (86.7%) while the lowest one in the Warmińsko-mazurskie (62.0%) and the Podlaskie voivodships (68.2%). Genotype 3 most commonly occurs in the Warmińsko-mazurskie (28.1%), and the Podlaskie voivodships (23.0%) and is least common in the Małopolskie (7.9%) and the Łódzkie voivodships (9.0%). Genotype 4 is more common in the Kujawsko-pomorskie (11.7%) and the Podlaskie voivodships (8.6%) and relatively less common in the Lubelskie (1.1%) and the Łódzkie voivodships (1.8%). Prevalence of G1 infection in 2003-2004 was 72% and increased up to 85.6% in 2011-2012, that was accompanied by decrease of G3 prevalence from 17% to 8% in this period. In HBV co-infected (n = 83), G1 infection was demonstrated in 85.5%, G3 - in 7.2%, G4 -4.8%, and mixed genotypes in 6%. Among HIV co-infected (n = 391), a much lower prevalence of G1 (33.0%) and a high of G3 (40.4%) as well as G4 (24.0%) were observed. There is a geographic variability of HCV genotypes prevalence in Poland. Increase of HCV G1 infections and decrease of G3 and G4 were observed in the last 10 years. Genotypes G3 and G4 occur more often in HCV/HIV co-infected than

Genotype imputation in the domestic dog

PubMed Central

Meurs, K. M.

2016-01-01

Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels. PMID:27129452

Computational strategies for alternative single-step Bayesian regression models with large numbers of genotyped and non-genotyped animals.

PubMed

Fernando, Rohan L; Cheng, Hao; Golden, Bruce L; Garrick, Dorian J

2016-12-08

Two types of models have been used for single-step genomic prediction and genome-wide association studies that include phenotypes from both genotyped animals and their non-genotyped relatives. The two types are breeding value models (BVM) that fit breeding values explicitly and marker effects models (MEM) that express the breeding values in terms of the effects of observed or imputed genotypes. MEM can accommodate a wider class of analyses, including variable selection or mixture model analyses. The order of the equations that need to be solved and the inverses required in their construction vary widely, and thus the computational effort required depends upon the size of the pedigree, the number of genotyped animals and the number of loci. We present computational strategies to avoid storing large, dense blocks of the MME that involve imputed genotypes. Furthermore, we present a hybrid model that fits a MEM for animals with observed genotypes and a BVM for those without genotypes. The hybrid model is computationally attractive for pedigree files containing millions of animals with a large proportion of those being genotyped. We demonstrate the practicality on both the original MEM and the hybrid model using real data with 6,179,960 animals in the pedigree with 4,934,101 phenotypes and 31,453 animals genotyped at 40,214 informative loci. To complete a single-trait analysis on a desk-top computer with four graphics cards required about 3 h using the hybrid model to obtain both preconditioned conjugate gradient solutions and 42,000 Markov chain Monte-Carlo (MCMC) samples of breeding values, which allowed making inferences from posterior means, variances and covariances. The MCMC sampling required one quarter of the effort when the hybrid model was used compared to the published MEM. We present a hybrid model that fits a MEM for animals with genotypes and a BVM for those without genotypes. Its practicality and considerable reduction in computing effort was

Inhibition of spinal protein kinase C-epsilon or -gamma isozymes does not affect halothane minimum alveolar anesthetic concentration in rats.

PubMed

Shumilla, Jennifer A; Sweitzer, Sarah M; Eger, Edmond I; Laster, Michael J; Kendig, Joan J

2004-07-01

Anesthetic effects on receptor or ion channel phosphorylation by enzymes such as protein kinase C (PKC) have been postulated to underlie some aspects of anesthesia. In vitro studies show that anesthetic effects on several receptors are mediated by PKC. To test the importance of PKC for the immobility produced by inhaled anesthetics, we measured the effect of intrathecal injections of PKC-epsilon and -gamma inhibitors on halothane minimum alveolar anesthetic concentration (MAC) in 7-day-old and 21-day-old Sprague-Dawley rats. The inhibitors were made as solutions of 100 pmol/5 microL and were given in a volume of 5 microL (7-day-old [P7] rats) or 10 microL (21-day-old [P21] rats). Controls were saline injections or injections of the peptide carrier at the same concentration and volumes; there were six animals in each group. In P7 rats, MAC values (in percentage of an atmosphere) were 1.63 +/- 0.0727 (mean +/- SEM) in saline controls, 1.55 +/- 0.141 in carrier controls, 1.54 +/- 0.0800 in rats given PKC-epsilon, and 1.69 +/- 0.0554 in rats given PKC-gamma. In P21 animals, the values were 1.20 +/- 0.0490, 1.31 +/- 0.0124, 1.27 +/- 0.0367, and 1.15 +/- 0.0483, respectively. Injection of the inhibitors did not change MAC in either age group. These results do not support an anesthetic effect on phosphorylation as a mechanism underlying the capacity of inhaled anesthetics to prevent movement in response to noxious stimulation, and they indirectly support a direct action on receptors or ion channels.

Additive-Multiplicative Approximation of Genotype-Environment Interaction

PubMed Central

Gimelfarb, A.

1994-01-01

A model of genotype-environment interaction in quantitative traits is considered. The model represents an expansion of the traditional additive (first degree polynomial) approximation of genotypic and environmental effects to a second degree polynomial incorporating a multiplicative term besides the additive terms. An experimental evaluation of the model is suggested and applied to a trait in Drosophila melanogaster. The environmental variance of a genotype in the model is shown to be a function of the genotypic value: it is a convex parabola. The broad sense heritability in a population depends not only on the genotypic and environmental variances, but also on the position of the genotypic mean in the population relative to the minimum of the parabola. It is demonstrated, using the model, that GXE interaction rectional may cause a substantial non-linearity in offspring-parent regression and a reversed response to directional selection. It is also shown that directional selection may be accompanied by an increase in the heritability. PMID:7896113

Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

PubMed

Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

2012-01-01

Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

Prevalence of hepatitis C virus (HCV) genotypes in Balochistan.

PubMed

Afridi, Sarwat; Naeem, Muhammad; Hussain, Abid; Kakar, Naseebullah; Babar, Masroor Ellahi; Ahmad, Jamil

2009-07-01

A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

Echinococcus granulosus genotypes in Iran

PubMed Central

Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

2014-01-01

Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

Experimental evidence for competitive growth advantage of genotype VII over VI: implications for foot-and-mouth disease virus serotype A genotype turnover in nature.

PubMed

Mohapatra, J K; Subramaniam, S; Singh, N K; Sanyal, A; Pattnaik, B

2012-04-01

In India, systematic genotype replacement has been observed for serotype A foot-and-mouth disease virus. After a decade of co-circulation of genotypes VI and VII, genotype VII emerged as the single dominant genotype since 2001. To derive possible explanations for such epochal evolution dynamics, in vitro intergenotype growth competition experiments involving both co- and superinfection regimes were conducted. Coinfection of BHK-21 cells demonstrated abrupt loss in the genotype VI viral load with commensurate increase in the load of genotype VII as measured by the genotype differentiating ELISA, RT-PCR and real-time RT-PCR. The superinfection dynamics was shaped by temporal spacing of infection, where the invading genotype VII took more number of passages than coinfection to eventually overtake the resident genotype VI. It was speculated that such superior replicative fitness of genotype VII could have been a possible factor for the ultimate dominance of genotype VII in nature. Copyright © 2011 Elsevier Ltd. All rights reserved.

Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing

PubMed Central

Mack, Steven J.; Milius, Robert P.; Gifford, Benjamin D.; Sauter, Jürgen; Hofmann, Jan; Osoegawa, Kazutoyo; Robinson, James; Groeneweg, Mathijs; Turenchalk, Gregory S.; Adai, Alex; Holcomb, Cherie; Rozemuller, Erik H.; Penning, Maarten T.; Heuer, Michael L.; Wang, Chunlin; Salit, Marc L.; Schmidt, Alexander H.; Parham, Peter R.; Müller, Carlheinz; Hague, Tim; Fischer, Gottfried; Fernandez-Viňa, Marcelo; Hollenbach, Jill A; Norman, Paul J.; Maiers, Martin

2015-01-01

The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information – message annotation, reference context, full genotype, consensus sequence and novel polymorphism – and references to three categories of accessory information – NGS platform documentation, read processing documentation and primary data. These eight categories of information ensure the long-term portability and broad application of this NGS data for all current histocompatibility and immunogenetics use cases. In addition, MIRING can be extended to allow the reporting of genotype data generated using pre-NGS technologies. Because genotyping results reported using MIRING are easily updated in accordance with reference and nomenclature databases, MIRING represents a bold departure from previous methods of reporting HLA and KIR genotyping results, which have provided static and less-portable data. More information about MIRING can be found online at miring.immunogenomics.org. PMID:26407912

The Physiological Bases for Microbial Barotolerance.

DTIC Science & Technology

1981-03-31

in general like halothane or methoxyflurane in its inhibitory action and has approximately the same potency. Ketamine at a 6 mM concentration can...Moreover, the inhibitory action of ketamine was increased by hydrostatic pressure, as is the action of halothane or methoxyflurane . {See Table 1 for...exemplified by ketamine, halothane and methoxyflurane . Their actions are enhanced by hydrostatic pressure and also by helium pressure, as indicated by the

Occupational Exposure of Veterinarians to Waste Anesthetic Gases

DTIC Science & Technology

1987-05-07

The two most frequently used anesthetic gases, methoxyflurane and halothane. were chosen to be studied.) Exposures during 38 surgeries were /"studied...use of anesthetic agent for small animals. The halothane concentrations were higher than the methoxyflurane concentrations because of the out of - ,&t...exposures by 2.7 fold for methoxyflurane and 43 fold for halothane. However, during back to back surgeries a gradual build-up of anesthetic gas was found

Compressed Genotyping

PubMed Central

Erlich, Yaniv; Gordon, Assaf; Brand, Michael; Hannon, Gregory J.; Mitra, Partha P.

2011-01-01

Over the past three decades we have steadily increased our knowledge on the genetic basis of many severe disorders. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, mainly due to the relatively tedious and expensive process of genotyping. Since the genetic variations that underlie the disorders are relatively rare in the population, they can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol to detect carriers for severe genetic disorders. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies. The mathematical framework presented here has some important distinctions from the ’traditional’ compressed sensing and group testing frameworks in order to address biological and technical constraints of our setting. PMID:21451737

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

PubMed

Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

2011-02-01

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

Helicobacter pylori Genotypes May Determine Gastric Histopathology

PubMed Central

Nogueira, Cristina; Figueiredo, Céu; Carneiro, Fátima; Taveira Gomes, António; Barreira, Raul; Figueira, Paulo; Salgado, Céu; Belo, Luis; Peixoto, António; Bravo, Juan C.; Bravo, Luis E.; Realpe, Jose L.; Plaisier, Anton P.; Quint, Wim G. V.; Ruiz, Bernardo; Correa, Pelayo; van Doorn, Leen-Jan

2001-01-01

The outcome of Helicobacter pylori infection has been associated with specific virulence-associated bacterial genotypes. The present study aimed to investigate the gastric histopathology in Portuguese and Colombian patients infected with H. pylori and to assess its relationship with bacterial virulence-associated vacA, cagA, and iceA genotypes. A total of 370 patients from Portugal (n = 192) and Colombia (n = 178) were studied. Corpus and antrum biopsy specimens were collected from each individual. Histopathological features were recorded and graded according to the updated Sydney system. H. pylori vacA, cagA, and iceA genes were directly genotyped in the gastric biopsy specimens by polymerase chain reaction and reverse hybridization. Despite the significant differences between the Portuguese and Colombian patient groups, highly similar results were observed with respect to the relation between H. pylori genotypes and histopathology. H. pylori vacA s1, vacA m1, cagA+ genotypes were significantly associated with a higher H. pylori density, higher degrees of lymphocytic and neutrophilic infiltrates, atrophy, the type of intestinal metaplasia, and presence of epithelial damage. The iceA1 genotype was only associated with epithelial damage in Portuguese patients. These findings show that distinct H. pylori genotypes are strongly associated with histopathological findings in the stomach, confirming their relevance for the development of H. pylori-associated gastric pathology. PMID:11159201

Relationship of some upland rice genotype after gamma irradiation

NASA Astrophysics Data System (ADS)

Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

2018-02-01

The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

New Measles Genotype, Uganda

PubMed Central

Muwonge, Apollo; Nanyunja, Miriam; Bwogi, Josephine; Lowe, Luis; Liffick, Stephanie L.; Bellini, William J.; Sylvester, Sempala

2005-01-01

We report the first genetic characterization of wildtype measles viruses from Uganda. Thirty-six virus isolates from outbreaks in 6 districts were analyzed from 2000 to 2002. Analyses of sequences of the nucleoprotein (N) and hemagglutinin (H) genes showed that the Ugandan isolates were all closely related, and phylogenetic analysis indicated that these viruses were members of a unique group within clade D. Sequences of the Ugandan viruses were not closely related to any of the World Health Organization reference sequences representing the 22 currently recognized genotypes. The minimum nucleotide divergence between the Ugandan viruses and the most closely related reference strain, genotype D2, was 3.1% for the N gene and 2.6% for the H gene. Therefore, Ugandan viruses should be considered a new, proposed genotype (d10). This new sequence information will expand the utility of molecular epidemiologic techniques for describing measles transmission patterns in eastern Africa. PMID:16318690

Histotype-genotype correlation in 36 high-grade endometrial carcinomas.

PubMed

Hoang, Lien N; McConechy, Melissa K; Köbel, Martin; Han, Guangming; Rouzbahman, Marjan; Davidson, Ben; Irving, Julie; Ali, Rola H; Leung, Sam; McAlpine, Jessica N; Oliva, Esther; Nucci, Marisa R; Soslow, Robert A; Huntsman, David G; Gilks, C Blake; Lee, Cheng-Han

2013-09-01

Endometrioid, serous, and clear cell carcinomas are the major types of endometrial carcinoma. Histologic distinction between these different tumor types can be difficult in high-grade cases, in which significant interobserver diagnostic disagreement exists. Endometrioid and clear cell carcinomas frequently harbor ARID1A and/or PTEN mutations. Serous carcinoma acquires TP53 mutations/inactivation at onset, with a significant subset harboring an additional mutation in PPP2R1A. This study examines the correlation between tumor histotype and genotype in 36 previously genotyped high-grade endometrial carcinomas. This included 23 endometrioid/clear cell genotype and 13 serous genotype tumors. Eight subspecialty pathologists reviewed representative online slides and rendered diagnoses before and after receiving p53, p16, and estrogen receptor immunostaining results. κ statistics for histotype-genotype concordance were calculated. The average κ values for histotype-genotype concordance was 0.55 (range, 0.30 to 0.67) on the basis of morphologic evaluation alone and it improved to 0.68 (range, 0.54 to 0.81) after immunophenotype consideration (P<0.001). Genotype-incompatible diagnoses were rendered by at least 2 pathologists in 12 of 36 cases (33%) (3 cases by 2/8 pathologists, 2 by 3/8, 2 by 4/8, 3 by 6/8, 1 by 7/8, and 1 case by 8/8 pathologists). Six of the 12 were endometrioid/clear cell genotype tumors, and the other 6 were serous genotype tumors. The histopathologic features associated with histotype-genotype-discordant cases were reviewed, and specific diagnostic recommendations were made to improve concordance. This study found that although the majority of morphologic diagnoses are genotype concordant, genotype-incompatible diagnoses are made in a significant subset of cases. Judicious use and interpretation of p53 immunohistochemistry in selected scenarios can improve histotype-genotype concordance.

Systems properties of the Haemophilus influenzae Rd metabolic genotype.

PubMed

Edwards, J S; Palsson, B O

1999-06-18

Haemophilus influenzae Rd was the first free-living organism for which the complete genomic sequence was established. The annotated sequence and known biochemical information was used to define the H. influenzae Rd metabolic genotype. This genotype contains 488 metabolic reactions operating on 343 metabolites. The stoichiometric matrix was used to determine the systems characteristics of the metabolic genotype and to assess the metabolic capabilities of H. influenzae. The need to balance cofactor and biosynthetic precursor production during growth on mixed substrates led to the definition of six different optimal metabolic phenotypes arising from the same metabolic genotype, each with different constraining features. The effects of variations in the metabolic genotype were also studied, and it was shown that the H. influenzae Rd metabolic genotype contains redundant functions under defined conditions. We thus show that the synthesis of in silico metabolic genotypes from annotated genome sequences is possible and that systems analysis methods are available that can be used to analyze and interpret phenotypic behavior of such genotypes.

Genotyping of Coxiella burnetii from domestic ruminants in northern Spain.

PubMed

Astobiza, Ianire; Tilburg, Jeroen J H C; Piñero, Alvaro; Hurtado, Ana; García-Pérez, Ana L; Nabuurs-Franssen, Marrigje H; Klaassen, Corné H W

2012-12-10

Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). A total of 45 samples from 4 goat herds (placentas, N = 4), 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20) and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21) were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM) samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several European countries, but some of the MLVA

Changing prevalence of hepatitis B virus genotypes in Iceland.

PubMed

Björnsdottir, Thora B; Stanzeit, Barbara; Sällberg, Matti; Löve, Arthur; Hultgren, Catharina

2005-12-01

At present eight hepatitis B virus (HBV) genotypes have been characterized: A to H. The most common genotype in Northern Europe is genotype A. So far there is no record of the specific HBV genotype distribution in Iceland. Iceland has a small population whose homogeneity has changed due to increasing migration during the past decades. The distribution of HBV genotypes in Iceland was analyzed using sera from 170 Icelandic patients. The samples were obtained before 1989, during an HBV epidemic among intravenous drug users in 1989 to 1992 and after 1994. A fragment of the HBV S-gene was amplified, sequenced and subjected to phylogenetic analysis. Among samples derived before 1989 genotypes A, C, and D were found. Most of the samples diagnosed during the epidemic belonged to genotype D and a smaller portion to genotype A. This suggests that the epidemic was most likely caused either by an endogenous HBV strain or by a strain imported from Europe or the USA. Among samples obtained after 1994, genotypes A to E and G were found, but the majority were of genotypes A, C, and D. This is consistent with an increase in migration and immigration from regions in Asia and Africa during the past 10 years. Thus, the changing prevalence of HBV genotypes in a small isolated community such as Iceland reflects the influence of migration and increasing contacts with regions outside the Western World. Copyright (c) 2005 Wiley-Liss, inc.

Cardiohemodynamic and electrophysiological effects of a selective EP4 receptor agonist ONO--AE1--329 in the halothane-anesthetized dogs.

PubMed

Nomura, Hiroaki; Nakamura, Yuji; Cao, Xin; Honda, Atsushi; Katagi, Jun; Ohara, Hiroshi; Izumi-Nakaseko, Hiroko; Satoh, Yoshioki; Ando, Kentaro; Sugiyama, Atsushi

2015-08-15

Cardiovascular effects of a highly selective prostaglandin E2 type 4 (EP4) receptor agonist ONO-AE1-329 were assessed with the halothane-anesthetized dogs (n=6). ONO-AE1-329 was intravenously infused in three escalating doses of 0.3, 1 and 3ng/kg/min for 10min with a pause of 20min between the doses. The low dose of 0.3ng/kg/min significantly increased maximum upstroke velocity of left ventricular pressure by 18% at 20min, indicating increase of ventricular contractility. The middle dose of 1ng/kg/min significantly decreased total peripheral resistance by 24% and left ventricular end-diastolic pressure by 32% at 10min, indicating dilation of arteriolar resistance vessels and venous capacitance ones, respectively; and increased cardiac output by 25% at 10min in addition to the change induced by the low dose. The high dose of 3ng/kg/min increased heart rate by 34% at 10min; decreased mean blood pressure by 14% at 10min and atrioventricular nodal conduction time by 13% at 5min; and shortened left ventricular systolic period by 8% at 10min and electromechanical coupling defined as an interval from completion of repolarization to the start of ventricular diastole by 39% at 10min in addition to the changes induced by the middle dose. No significant change was detected in a ventricular repolarization period. These results indicate that ONO-AE1-329 may possess a similar cardiovascular profile to typical phosphodiesterase 3 inhibitors as an inodilator, and suggest that EP4 receptor stimulation can become an alternative strategy for the treatment of congestive heart failure. Copyright © 2015 Elsevier B.V. All rights reserved.

Cholesterol, APOE genotype, and Alzheimer disease

PubMed Central

Hall, K.; Murrell, J.; Ogunniyi, A.; Deeg, M.; Baiyewu, O.; Gao, S.; Gureje, O.; Dickens, J.; Evans, R.; Smith-Gamble, V.; Unverzagt, F.W.; Shen, J.; Hendrie, H.

2010-01-01

Objective To examine the relationship between cholesterol and other lipids, APOE genotype, and risk of Alzheimer disease (AD) in a population-based study of elderly Yoruba living in Ibadan, Nigeria. Methods Blood samples and clinical data were collected from Yoruba study participants aged 70 years and older (N = 1,075) as part of the Indianapolis-Ibadan Dementia Project, a longitudinal epidemiologic study of AD. Cholesterol, low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglyceride levels were measured in fasting blood samples. DNA was extracted and APOE was genotyped. Diagnoses of AD were made by consensus using National Institute of Neurologic Disorders/Stroke-Alzheimer's Disease and Related Disorders Association criteria. Results Logistic regression models showed interaction after adjusting for age and gender between APOE-ε4 genotype and biomarkers in the risk of AD cholesterol*genotype (p = 0.022), LDL*genotype (p = 0.018), and triglyceride*genotype (p = 0.036). Increasing levels of cholesterol and LDL were associated with increased risk of AD in individuals without the APOE-ε4 allele, but not in those with APOE-ε4. There was no significant association between levels of triglycerides and AD risk in those without APOE-ε4. Conclusions There was a significant interaction between cholesterol, APOE-ε4, and the risk of Alzheimer disease (AD) in the Yoruba, a population that has lower cholesterol levels and lower incidence rates of AD compared to African Americans. APOE status needs to be considered when assessing the relationship between lipid levels and AD risk in population studies. PMID:16434658

Relationships between genotype x environment interactions and rank orders for a set of genotypes tested in different environments.

PubMed

Hühn, M; Lotito, S; Piepho, H P

1993-09-01

Multilocation trials in plant breeding lead to cross-classified data sets with rows=genotypes and columns=environments, where the breeder is particularly interested in the rank orders of the genotypes in the different environments. Non-identical rank orders are the result of genotype x environment interactions. Not every interaction, however, causes rank changes among the genotypes (rank-interaction). From a breeder's point of view, interaction is tolerable only as long as it does not affect the rank orders. Therefore, the question arises of under which circumstances does interaction become rank-interaction. This paper contributes to our understanding of this topic. In our study we emphasized the detection of relationships between the similarity of the rank orders (measured by Kendall's coefficient of concordance W) and the functions of the diverse variance components (genotypes, environments, interaction, error). On the basis of extensive data sets on different agricultural crops (faba bean, fodder beet, sugar beet, oats, winter rape) obtained from registration trials (1985-1989) carried out in the Federal Republic of Germany, we obtained the following as main result: W ≅ σ 2 (g) /(σ 2 (g) + σ 2 (v) ) where σ 2 (g) =genotypic variance and σ 2 (v) = σ 2 (ge) + σ 2 (o) /L with σ 2 (ge) =interaction variance, σ 2 (o) =error variance and L=number of replications.

Global Distribution of Rubella Virus Genotypes

PubMed Central

Zheng, Du-Ping; Icenogle, Joseph; Katow, Shigetaka; Abernathy, Emily S.; Song, Ki-Joon; Xu, Wen-Bo; Yarulin, Vitaly; Desjatskova, R.G.; Aboudy, Yair; Enders, Gisela; Croxson, Margaret

2003-01-01

Phylogenetic analysis of a collection of 103 E1 gene sequences from rubella viruses isolated from 17 countries from 1961 to 2000 confirmed the existence of at least two genotypes. Rubella genotype I (RGI) isolates, predominant in Europe, Japan, and the Western Hemisphere, segregated into discrete subgenotypes; intercontinental subgenotypes present in the 1960s and 1970s were replaced by geographically restricted subgenotypes after ~1980. Recently, active subgenotypes include one in the United States and Latin America, one in China, and a third that apparently originated in Asia and spread to Europe and North America, starting in 1997, indicating the recent emergence of an intercontinental subgenotype. A virus that potentially arose as a recombinant between two RGI subgenotypes was discovered. Rubella genotype II (RGII) showed greater genetic diversity than did RGI and may actually consist of multiple genotypes. RGII viruses were limited to Asia and Europe; RGI viruses were also present in most of the countries where RGII viruses were isolated. PMID:14720390

Newcastle Disease Virus in Madagascar: Identification of an Original Genotype Possibly Deriving from a Died Out Ancestor of Genotype IV

PubMed Central

Maminiaina, Olivier F.; Gil, Patricia; Briand, François-Xavier; Albina, Emmanuel; Keita, Djénéba; Andriamanivo, Harentsoaniaina Rasamoelina; Chevalier, Véronique; Lancelot, Renaud; Martinez, Dominique; Rakotondravao, R.; Rajaonarison, Jean-Joseph; Koko, M.; Andriantsimahavandy, Abel A.; Jestin, Véronique; Servan de Almeida, Renata

2010-01-01

In Madagascar, Newcastle disease (ND) has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed. PMID:21085573

Newcastle disease virus in Madagascar: identification of an original genotype possibly deriving from a died out ancestor of genotype IV.

PubMed

Maminiaina, Olivier F; Gil, Patricia; Briand, François-Xavier; Albina, Emmanuel; Keita, Djénéba; Andriamanivo, Harentsoaniaina Rasamoelina; Chevalier, Véronique; Lancelot, Renaud; Martinez, Dominique; Rakotondravao, R; Rajaonarison, Jean-Joseph; Koko, M; Andriantsimahavandy, Abel A; Jestin, Véronique; Servan de Almeida, Renata

2010-11-15

In Madagascar, Newcastle disease (ND) has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed.

Evidence for two koi herpesvirus (KHV) genotypes in South Korea.

PubMed

Kim, Hyoung Jun; Kwon, Se Ryun

2013-06-13

The geographic distribution of koi herpesvirus (KHV) has recently been analyzed by polymerase chain reaction (PCR, based on the alleles of 3 domains) and sequence analysis using 3 regions of KHV genomic DNA (SphI-5, 9/5, and the thymidine kinase gene). In this study, samples from 6 carp showing symptoms of KHV infection in 2008 were examined for the presence of KHV by using PCR and cell culture isolation methods. KHV was detected in 2 (Pyeongtaek and Buan) of the samples. Sequence analysis revealed that the genotype of the KHV PT-08 isolate was Asia genotype variant 1 (A1), and the genotype of the KHV BA-08 isolate was European genotype variant 4 (E4). In addition, PCR patterns and sequence analysis based on the alleles of 3 domains of an alternate KHV classification system confirmed that the genotype of the KHV PT-08 isolate was CyHV3-J, and the genotype of the KHV BA-08 isolate was CyHV3-third genotype. To our knowledge, this is the first study to demonstrate the presence of 2 genotypes of KHV (genotype A1/CyHV3-J; genotype E4/CyHV3-third genotype) in South Korea.

Strategies for genotype imputation in composite beef cattle.

PubMed

Chud, Tatiane C S; Ventura, Ricardo V; Schenkel, Flavio S; Carvalheiro, Roberto; Buzanskas, Marcos E; Rosa, Jaqueline O; Mudadu, Maurício de Alvarenga; da Silva, Marcos Vinicius G B; Mokry, Fabiana B; Marcondes, Cintia R; Regitano, Luciana C A; Munari, Danísio P

2015-08-07

Genotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R(2)). The highest imputation accuracy scenario consisted of a reference population with males and females and a target population with young females. Among the SNP panels in the tested scenarios, from the 50K, GGP75Ki and GGP80K were the most adequate to impute to HD in Canchim cattle. FImpute reduced computation run-time to impute genotypes from 20 to 100 times when compared to BEAGLE. The genotyping panels possessing at least 50 thousands markers are suitable for genotype imputation to HD with acceptable accuracy. The FImpute algorithm demonstrated a higher efficiency of

Genotype imputation efficiency in Nelore Cattle

USDA-ARS?s Scientific Manuscript database

Genotype imputation efficiency in Nelore cattle was evaluated in different scenarios of lower density (LD) chips, imputation methods and sets of animals to have their genotypes imputed. Twelve commercial and virtual custom LD chips with densities varying from 7K to 75K SNPs were tested. Customized L...

Porphyromonas gingivalis Fim-A genotype distribution among Colombians

PubMed Central

Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

2015-01-01

Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

Plant genotypic diversity reduces the rate of consumer resource utilization.

PubMed

McArt, Scott H; Thaler, Jennifer S

2013-07-07

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

Norovirus genotypes causing gastroenteritis outbreaks in Finland 1998-2002.

PubMed

Maunula, L; Von Bonsdorff, C-H

2005-11-01

Outbreak investigation methods for enteric viruses were improved in 1990s when gene amplification techniques were established in viral laboratories. The objective of the study was to determine the causative agents for Finnish viral gastroenteritis outbreaks. Our aim was also to further characterise the norovirus strains, reveal the temporal occurrence of norovirus (NV) genotypes and to study some epidemiological aspects concerning the outbreaks. A total of 416 Finnish viral gastroenteritis outbreaks that occurred during 5 years (1998-2002), excluding those among hospitalised children, were investigated for enteric viruses. Stool samples were screened by electron microscopy as well as analyzed by specific noro- and astrovirus RT-PCR tests. Amplicon sequence analysis was used to find out norovirus genotypes. Noroviruses caused 252 (60.6%) of the outbreaks; other viruses, astro- or rotavirus, caused four epidemics. Norovirus epidemics occurred in all kinds of settings, most often in hospitals (30.6%) and in restaurants and canteens (14.3%). Both NV genogroups were found every year, but NV GGII outbreaks always outnumbered those of GGI. All but one outbreak at hospitals and nursing homes were of genotype GII. Polymerase sequence analysis revealed a variety of NV genotypes; six GI and at least eight GII genotypes. The GI.3 Birmingham-like and GII.4 Bristol-like genotype appeared every year, whereas the other types were circulating for shorter periods or sporadically. During the study period the genotypes GII.4 (Bristol), GII.1 (Hawaii), an emerging genotype GIIb, and a new variant of GII.4 predominated in that order. Indication for rapid genetic changes in the genotype GII.4 was also noticed. Noroviruses were the most prevalent causative agents in the outbreaks. Many NV genotypes were circulating, and a shift in the predominant genotypes was evident between epidemic seasons.

Genotype-Specific Measles Transmissibility: A Branching Process Analysis.

PubMed

Ackley, Sarah F; Hacker, Jill K; Enanoria, Wayne T A; Worden, Lee; Blumberg, Seth; Porco, Travis C; Zipprich, Jennifer

2018-04-03

Substantial heterogeneity in measles outbreak sizes may be due to genotype-specific transmissibility. Using a branching process analysis, we characterize differences in measles transmission by estimating the association between genotype and the reproduction number R among postelimination California measles cases during 2000-2015 (400 cases, 165 outbreaks). Assuming a negative binomial secondary case distribution, we fit a branching process model to the distribution of outbreak sizes using maximum likelihood and estimated the reproduction number R for a multigenotype model. Genotype B3 is found to be significantly more transmissible than other genotypes (P = .01) with an R of 0.64 (95% confidence interval [CI], .48-.71), while the R for all other genotypes combined is 0.43 (95% CI, .28-.54). This result is robust to excluding the 2014-2015 outbreak linked to Disneyland theme parks (referred to as "outbreak A" for conciseness and clarity) (P = .04) and modeling genotype as a random effect (P = .004 including outbreak A and P = .02 excluding outbreak A). This result was not accounted for by season of introduction, age of index case, or vaccination of the index case. The R for outbreaks with a school-aged index case is 0.69 (95% CI, .52-.78), while the R for outbreaks with a non-school-aged index case is 0.28 (95% CI, .19-.35), but this cannot account for differences between genotypes. Variability in measles transmissibility may have important implications for measles control; the vaccination threshold required for elimination may not be the same for all genotypes or age groups.

Hepatitis C Virus: Viral Quasispecies and Genotypes.

PubMed

Tsukiyama-Kohara, Kyoko; Kohara, Michinori

2017-12-22

Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

Plant genotypic diversity reduces the rate of consumer resource utilization

PubMed Central

McArt, Scott H.; Thaler, Jennifer S.

2013-01-01

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore—the Japanese beetle (Popillia japonica)—increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore. PMID:23658201

Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Guangzhou, China: Predominance of Genotype 1b and Increasing Incidence of Genotype 6a.

PubMed

Yuan, Guosheng; Liu, Junwei; Hu, Chengguang; Huang, Huaping; Qi, Minghua; Wu, Tao; Liang, Weifang; Li, Yi-Ping; Zhang, Yong-Yuan; Zhou, Yuanping

2017-01-01

Distribution of Hepatitis C virus (HCV) genotypes vary geographically and may associate with the mode of transmission. Little is known about the molecular epidemiology of HCV infection in Guangzhou, China. A cross-sectional survey included 561 subjects with chronic HCV infection registered at Nanfang Hospital, Southern Medical University, was performed. All residents were invited for a questionnaire interview to collect information about their personal status and commercial blood donation history. A total of 463 chronic hepatitis C (CHC) patients were finally enrolled. Among the 463 samples, 426 were characterized by partial core-E1 sequences and classified into 7 subtypes: 1b (n=263, 61.7%), 6a (n=86, 20.2%), 2a (n=26, 6.1%), 3b (n=26, 6.1%), 3a (n=22, 5.2%), 6u (n=2, 0.5%), and 4a (n=1, 0.2%). Analysis of genotype-associated risk factors revealed that blood donation and transfusion were strongly associated with subtypes 1b and 2a, while genotype 3b and 6a were more frequent in intravenous drug users. Phylogeographic analyses demonstrated that the distribution of HCV genotypes in Guangzhou is complex. Interestingly, 6a has become a local endemic in Guangzhou and may be the second source region to disseminate 6a to other provinces. The Author(s). Published by S. Karger AG, Basel.

Genotypic and Phenotypic Characterization of Chikungunya Virus of Different Genotypes from Malaysia

PubMed Central

Sam, I-Ching; Loong, Shih-Keng; Michael, Jasmine Chandramathi; Chua, Chong-Long; Wan Sulaiman, Wan Yusoff; Vythilingam, Indra; Chan, Shie-Yien; Chiam, Chun-Wei; Yeong, Yze-Shiuan; AbuBakar, Sazaly; Chan, Yoke-Fun

2012-01-01

Background Mosquito-borne Chikungunya virus (CHIKV) has recently re-emerged globally. The epidemic East/Central/South African (ECSA) strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. Methods and Findings CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36). Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. Conclusions The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species. PMID:23209750

Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

PubMed

Sam, I-Ching; Loong, Shih-Keng; Michael, Jasmine Chandramathi; Chua, Chong-Long; Wan Sulaiman, Wan Yusoff; Vythilingam, Indra; Chan, Shie-Yien; Chiam, Chun-Wei; Yeong, Yze-Shiuan; AbuBakar, Sazaly; Chan, Yoke-Fun

2012-01-01

Mosquito-borne Chikungunya virus (CHIKV) has recently re-emerged globally. The epidemic East/Central/South African (ECSA) strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36). Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

Genotypic diversity of porcine circovirus type 2 (PCV2) and genotype shift to PCV2d in Korean pig population.

PubMed

Kwon, Taeyong; Lee, Dong-Uk; Yoo, Sung J; Je, Sang H; Shin, Jeong Y; Lyoo, Young S

2017-01-15

Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease (PCVAD), which leads to enormous economic losses in the swine industry worldwide. A high nucleotide substitution rate allows for the continuous evolution of PCV2 and the emergence of novel PCV2 strains. However, the distribution of emerging PCV2 genotypes and the co-existence of multiple genotypes in Korea have not been elucidated. The objective of this study was to determine the genetic diversity of PCV2 in Korean pig herds between 2009 and 2016. The overall prevalence of PCV2, from various samples originating from commercial pigs, was 53.8% (325/604). Two cases of a genotype shift to PCV2d at the farm level showed that the genotype shift started before 2012. In addition, genotype-specific PCR, on pen-based oral fluid samples for nationwide PCV2 surveillance in 2016, indicated that the infection pattern of PCV2 genotypes at the farm level was as follows; none (6/69), PCV2a (6/69), PCV2b (2/69), PCV2d (33/69), PCV2a/b (2/69), PCV2a/d (4/69), PCV2b/d (11/69), and PCV2a/b/d (2/69), respectively. This suggests that the genotype shift to PCV2d occurred on a nationwide scale and that the co-existence of different genotypes is common in Korean pig herds. In addition, seven sites on the capsid protein of Korean PCV2 were identified as being under positive selection pressure, all of which are related to the epitope region and neutralization activity. These data provide evidence of increased genetic diversity and shifts among Korean PCV2 isolates. Copyright © 2016 Elsevier B.V. All rights reserved.

Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010.

PubMed

Shak, Emma B; France, Anne Marie; Cowan, Lauren; Starks, Angela M; Grant, Juliana

2015-01-01

Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009-December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups.

Cryptosporidium genotyping in Europe: The current status and processes for a harmonised multi-locus genotyping scheme.

PubMed

Chalmers, Rachel M; Pérez-Cordón, Gregorio; Cacció, Simone M; Klotz, Christian; Robertson, Lucy J

2018-06-13

Due to the occurrence of genetic recombination, a reliable and discriminatory method to genotype Cryptosporidium isolates at the intra-species level requires the analysis of multiple loci, but a standardised scheme is not currently available. A workshop was held at the Robert Koch Institute, Berlin in 2016 that gathered 23 scientists with appropriate expertise (in either Cryptosporidium genotyping and/or surveillance, epidemiology or outbreaks) to discuss the processes for the development of a robust, standardised, multi-locus genotyping (MLG) scheme and propose an approach. The background evidence and main conclusions were outlined in a previously published report; the objectives of this further report are to describe 1) the current use of Cryptosporidium genotyping, 2) the elicitation and synthesis of the participants' opinions, and 3) the agreed processes and criteria for the development, evaluation and validation of a standardised MLG scheme for Cryptosporidium surveillance and outbreak investigations. Cryptosporidium was characterised to the species level in 7/12 (58%) participating European countries, mostly for human outbreak investigations. Further genotyping was mostly by sequencing the gp60 gene. A ranking exercise of performance and convenience criteria found that portability, biological robustness, typeability, and discriminatory power were considered by participants as the most important attributes in developing a multilocus scheme. The major barrier to implementation was lack of funding. A structured process for marker identification, evaluation, validation, implementation, and maintenance was proposed and outlined for application to Cryptosporidium, with prioritisation of Cryptosporidium parvum to support investigation of transmission in Europe. Copyright © 2018 Elsevier Inc. All rights reserved.

Cotton genotypes selection through artificial neural networks.

PubMed

Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

2017-09-27

Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

Hepatitis C Virus: Viral Quasispecies and Genotypes

PubMed Central

Tsukiyama-Kohara, Kyoko; Kohara, Michinori

2017-01-01

Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance. PMID:29271914

Inhalational anaesthetics and n-alcohols share a site of action in the neuronal Shaw2 Kv channel

PubMed Central

Bhattacharji, Aditya; Klett, Nathan; Go, Ramon Christopher V; Covarrubias, Manuel

2010-01-01

Background and purpose: Neuronal ion channels are key targets of general anaesthetics and alcohol, and binding of these drugs to pre-existing and relatively specific sites is thought to alter channel gating. However, the underlying molecular mechanisms of this action are still poorly understood. Here, we investigated the neuronal Shaw2 voltage-gated K+ (Kv) channel to ask whether the inhalational anaesthetic halothane and n-alcohols share a binding site near the activation gate of the channel. Experimental approach: Focusing on activation gate mutations that affect channel modulation by n-alcohols, we investigated n-alcohol-sensitive and n-alcohol-resistant Kv channels heterologously expressed in Xenopus oocytes to probe the functional modulation by externally applied halothane using two-electrode voltage clamping and a gas-tight perfusion system. Key results: Shaw2 Kv channels are reversibly inhibited by halothane in a dose-dependent and saturable manner (K0.5= 400 µM; nH= 1.2). Also, discrete mutations in the channel's S4S5 linker are sufficient to reduce or confer inhibition by halothane (Shaw2-T330L and Kv3.4-G371I/T378A respectively). Furthermore, a point mutation in the S6 segment of Shaw2 (P410A) converted the halothane-induced inhibition into halothane-induced potentiation. Lastly, the inhibition resulting from the co-application of n-butanol and halothane is consistent with the presence of overlapping binding sites for these drugs and weak binding cooperativity. Conclusions and implications: These observations strongly support a molecular model of a general anaesthetic binding site in the Shaw2 Kv channel. This site may involve the amphiphilic interface between the S4S5 linker and the S6 segment, which plays a pivotal role in Kv channel activation. PMID:20136839

Dissolution of root canal sealer cements in volatile solvents.

PubMed

Whitworth, J M; Boursin, E M

2000-01-01

There are few published data on the solubility profiles of endodontic sealers in solvents commonly employed in root canal retreatment. This study tested the hypothesis that root canal sealer cements are insoluble in the volatile solvents chloroform and halothane. Standardized samples (n = 5) of glass ionomer (Ketac Endo), zinc oxide-eugenol (Tubli-Seal EWT), calcium hydroxide (Apexit) and epoxy resin (AH Plus) based sealers were immersed in chloroform or halothane for 30 s, 1 min, 5 min and 10 min. Mean loss of weight was plotted against time of exposure, and differences in behaviour assessed by multiple paired t-tests (P < 0.01). Clear differences were shown in the solubility profiles of major classes of root canal sealer cements in two common volatile solvents. In comparison with other classes of material, Ketac Endo was the least soluble in chloroform and halothane (P < 0.01), with less than 1% weight loss after 10 min exposure to either solvent. Apexit had low solubility with 11.6% and 14.19% weight loss after 10 min exposure to chloroform and halothane, respectively. The difference between solvents was not significant (P > 0.01). Tubli-Seal EWT was significantly less soluble in halothane than chloroform (5.19% and 62.5% weight loss after 10 min exposure, respectively (P < 0.01)). Its solubility in halothane was not significantly different from that of Apexit. AH Plus was significantly more soluble than all other materials in both chloroform and halothane (96% and 68% weight loss after 10 min exposure, respectively (P < 0.01)). There are significant differences in the solubility profiles of major classes of root canal sealer in common organic solvents. Efforts should continue to find a more universally effective solvent for use in root canal treatment.

Intramuscular injection of malignant hyperthermia trigger agents induces hypermetabolism in susceptible and nonsusceptible individuals.

PubMed

Metterlein, Thomas; Schuster, Frank; Kranke, Peter; Roewer, Norbert; Anetseder, Martin

2010-01-01

A new minimally invasive metabolic test for the diagnosis of susceptibility for malignant hyperthermia measuring intramuscular p(CO(2)) and lactate following local application of caffeine and halothane in humans was recently proposed. The present study tested the hypothesis that a more simplified test protocol allows a differentiation between malignant hyperthermia susceptible (MHS) and malignant hyperthermia nonsusceptible (MHN) and control individuals. With approval of the local ethics committee and informed consent, microdialysis and p(CO(2)) probes with attached microtubing were placed into the lateral vastus muscle of six MHS, seven MHN and seven control individuals. Following equilibration, boluses of 500 microl caffeine 80 mmol l(-1) and halothane 10 vol% dissolved in soybean oil were injected locally. p(CO(2)) and lactate were measured spectrophotometrically. The maximal rate of p(CO(2)) increase was significantly higher in MHS than in MHN and control individuals following application of halothane and caffeine, respectively. Intramuscular caffeine injection leads to a significantly higher increase of local lactate levels in MHS than in MHN and control individuals, whereas halothane increased local lactate levels in all investigated groups. Haemodynamic and systemic metabolic parameters did not differ between the investigated groups. Local caffeine and halothane injection increased intramuscular metabolism in MHS individuals significantly more than in the two other groups. In contrast to previous investigations, direct injection of the concentrations of halothane described here increased lactate and p(CO(2)) even in MHN skeletal muscle.

Canine Malignant Hyperthermia: Diagnosis of Susceptibility in a Breeding Colony

PubMed Central

O'Brien, P. J.; Cribb, P. H.; White, R. J.; Olfert, E. D.; Steiss, J. E.

1983-01-01

Fifteen related dogs were studied for susceptibility to malignant hyperthermia using halothane challenge and caffeine contracture tests. These dogs had hypertrophied muscles, were of a nervous temperament and had rectal temperatures at the upper limit of the normal range. Clinical pathology findings were mild elevations of serum aspartate transaminase and mean corpuscular hemoglobin. In vitro caffeine contracture tests were performed on muscle biopsies from five of these dogs. The concentration of caffeine required to increase resting tension by 1 g in biopsy specimens of these dogs was significantly lower than that required for control dogs: 7.6 ± 1.38 (x̄ ± SEM) versus 15.5 ± 2.52 mM (P < 0.025), and in the presence of 1% halothane, 3.6 ± 1.44 versus 10.6 ± 2.19 mM (P < 0.05). Internal nuclei, fiber caliber variation and fiber hypertrophy were found in histological studies of muscle biopsies. Two other dogs possibly died of a canine stress syndrome analagous to the porcine stress syndrome which occurs in malignant hyperthermia susceptible swine. Eight others of this family were anesthetized with halothane or methoxyflurane. Methoxyflurane did not trigger the syndrome. The first exposure to halothane caused death from malignant hyperthermia in two dogs and a third died on the second exposure to halothane. Postmortem findings were nonspecific. The other three dogs exposed to halothane recovered uneventfully. Inheritance of the defect conforms to a multifactorial pattern, with gradations of susceptibility. PMID:17422267

Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

Treesearch

Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens

2013-01-01

in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

Genotypic richness predicts phenotypic variation in an endangered clonal plant

PubMed Central

Sinclair, Elizabeth A.; Poore, Alistair G.B.; Bain, Keryn F.; Vergés, Adriana

2016-01-01

Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

To Genotype or Phenotype for Personalized Medicine? CYP450 Drug Metabolizing Enzyme Genotype-Phenotype Concordance and Discordance in the Ecuadorian Population.

PubMed

De Andrés, Fernando; Terán, Santiago; Hernández, Francisco; Terán, Enrique; LLerena, Adrián

2016-12-01

Genetic variations within the cytochrome P450 (CYP450) superfamily of drug metabolizing enzymes confer substantial person-to-person and between-population differences in pharmacokinetics, and by extension, highly variable clinical effects of medicines. In this context, "personalized medicine," "precision medicine," and "stratified medicine" are related concepts attributed to what is essentially targeted therapeutics and companion diagnostics, aimed at improving safety and effectiveness of health interventions. We report here, to the best of our knowledge, the first comparative clinical pharmacogenomics study, in an Ecuadorian population sample, of five key CYP450s involved in drug metabolism: CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4. In 139 unrelated, medication-free, and healthy Ecuadorian subjects, we measured the phenotypic activity of these drug metabolism pathways using the CEIBA multiplexed phenotyping cocktail. The subjects were genotyped for each CYP450 enzyme gene as well. Notably, based on the CYP450 metabolic phenotypes estimated by the genotype data, 0.75% and 3.10% of the subjects were genotypic poor metabolizers (gPMs) for CYP2C19 and CYP2D6, respectively. Additionally, on the other extreme, genotype-estimated ultrarapid metabolizer (gUMs) phenotype was represented by 15.79% of CYP2C19, and 5.43% of CYP2D6. There was, however, considerable discordance between directly measured phenotypes (mPMs and mUMs) and the above genotype-estimated enzyme phenotypes. For example, among individuals genotypically carrying enhanced activity alleles (gUMs), many showed a lower actual drug metabolism capacity than expected by their genotypes, even lower than individuals with reduced or no activity alleles. In conclusion, for personalized medicine in the Ecuadorian population, we recommend CYP450 multiplexed phenotyping, or genotyping and phenotyping in tandem, rather than CYP450 genotypic tests alone. Additionally, we recommend, in consideration of equity, ethical

An imputed genotype resource for the laboratory mouse

PubMed Central

Szatkiewicz, Jin P.; Beane, Glen L.; Ding, Yueming; Hutchins, Lucie; de Villena, Fernando Pardo-Manuel; Churchill, Gary A.

2009-01-01

We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 49 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrate that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org/. PMID:18301946

Identification of genotypes of Influenza A virus in Malaysia.

PubMed

Mm, Rahman; Kk, Wong; I, Isahak; Zz, Rashid; H, Alfizah

2014-09-01

Influenza is considered as an emerging disease until today. The present study was undertaken to determine the prevalent genotypes of Influenza A virus in Malaysia. Influenza A virus was identified from respiratory specimens by real-time reverse transcriptase polymerase chain reaction (rRT-PCR). Phylogenetic analysis of the identified isolates was performed and genotypes were detected. A total number of 505 throat swabs and nasopharyngeal aspirates were examined by rRT-PCR at Universiti Kebangsaan Malaysia Medical Centre (UKMMC) in which 65(12.87%) were positive for influenza A. The identified isolates were successfully genotyped by phylogenetic analysis. The identified influenza A genotypes were: H1N1 (42), H3N2 (20) and H5N1 (3). The findings indicated that 3 genotypes were circulating in Malaysia during 2011 in which H1N1 was the predominant. RESULTS added new genotype (H5N1) identification record in Malaysia that may be added in data base of WHO and CDC.

High-throughput mouse genotyping using robotics automation.

PubMed

Linask, Kaari L; Lo, Cecilia W

2005-02-01

The use of mouse models is rapidly expanding in biomedical research. This has dictated the need for the rapid genotyping of mutant mouse colonies for more efficient utilization of animal holding space. We have established a high-throughput protocol for mouse genotyping using two robotics workstations: a liquid-handling robot to assemble PCR and a microfluidics electrophoresis robot for PCR product analysis. This dual-robotics setup incurs lower start-up costs than a fully automated system while still minimizing human intervention. Essential to this automation scheme is the construction of a database containing customized scripts for programming the robotics workstations. Using these scripts and the robotics systems, multiple combinations of genotyping reactions can be assembled simultaneously, allowing even complex genotyping data to be generated rapidly with consistency and accuracy. A detailed protocol, database, scripts, and additional background information are available at http://dir.nhlbi.nih.gov/labs/ldb-chd/autogene/.

Studies of Circulatory and Metabolic Changes during Ketamine Narcosis,

DTIC Science & Technology

1985-03-13

Braun, U., Hensel, I., Kettler, D., Lohr, B.: The effects of methoxyflurane , halothane, dipiritramide, barbiturate and ketamine on the total oxygen...narcosis caus- ed by ether, halothane, methoxyflurane , ketamine and piritranide, as well as neuroleptanalgesia. Lecture at the XIIth. General Con

Generation of recombinant European bat lyssavirus type 1 and inter-genotypic compatibility of lyssavirus genotype 1 and 5 antigenome promoters.

PubMed

Orbanz, Jeannette; Finke, Stefan

2010-10-01

Bat lyssaviruses (Fam. Rhabdoviridae) represent a source for the infection of terrestial mammals and the development of rabies disease. Molecular differences in the replication of bat and non-bat lyssaviruses and their contribution to pathogenicity, however, are unknown. One reason for this is the lack of reverse genetics systems for bat-restricted lyssaviruses. To investigate bat lyssavirus replication and host adaptation, we developed a reverse genetics system for European bat lyssavirus type 1 (EBLV-1; genotype 5). This was achieved by co-transfection of HEK-293T cells with a full-length EBLV-1 genome cDNA and expression plasmids for EBLV-1 proteins, resulting in recombinant EBLV-1 (rEBLV-1). Replication of rEBLV-1 was comparable to that of parental virus, showing that rEBLV-1 is a valid tool to investigate EBLV-1 replication functions. In a first approach, we tested whether the terminal promoter sequences of EBLV-1 are genotype-specific. Although genotype 1 (rabies virus) minigenomes were successfully amplified by EBLV-1 helper virus, in the context of the complete virus, only the antigenome promoter (AGP) sequence of EBLV-1 was replaceable, as indicated by comparable replication of rEBLV-1 and the chimeric virus. These analyses demonstrate that the terminal AGPs of genotype 1 and genotype 5 lyssaviruses are compatible with those of the heterologous genotype.

Allele-Specific PCR for Determination of IL28B Genotype

PubMed Central

Cook, Linda; Diem, Kurt; Kim, Woo; Scott, John D.

2012-01-01

The IL28B genotype is a critical determinant of interferon response in patients infected with hepatitis C virus genotype 1. We describe an allele-specific PCR assay for the IL28B genotype. The assay is simple and robust, uses commonly available real-time PCR instrumentation, and is well suited for clinical laboratories offering IL28B genotyping. PMID:23052312

Effects of tramadol or morphine in dogs undergoing castration on intra-operative electroencephalogram responses and post-operative pain.

PubMed

Kongara, K; Chambers, J P; Johnson, C B; Dukkipati, V S R

2013-11-01

To compare the effects of pre-operatively administered tramadol with those of morphine on electroencephalographic responses to surgery and post-operative pain in dogs undergoing castration. Dogs undergoing castration were treated with either pre-operative morphine (0.5 mg/kg S/C, n = 8) or tramadol (3 mg/kg S/C, n = 8). All dogs also received 0.05 mg/kg acepromazine and 0.04 mg/kg atropine S/C in addition to the test analgesic. Anaesthesia was induced with thiopentone administered I/V to effect and maintained with halothane in oxygen. Respiratory rate, heart rate, end-tidal halothane tension (EtHal) and end-tidal CO2 tension (EtCO2) were monitored throughout surgery. Electroencephalograms (EEG) were recorded continuously using a three electrode montage. Median frequency (F50), total power (Ptot) and 95% spectral edge frequency (F95) derived from EEG power spectra recorded before skin incision (baseline) were compared with those recorded during ligation of the spermatic cords of both testicles. Post-operatively, pain was assessed after 1, 3, 6 and 9 h using the short form of the Glasgow composite measure pain scale (CMPS-SF). Dogs premedicated with tramadol had higher mean F50 (12.2 (SD 0.2) Hz) and lower Ptot (130.39 (SD 12.1) µv(2)) compared with those premedicated with morphine (11.5 (SD 0.2) Hz and 161.8 (SD 15.1) µv(2), respectively; p<0.05) during ligation of testicle 1. There were no differences in EEG responses between the two treatment groups during ligation of testicle 2 (p>0.05). The F95 of the EEG did not differ between the two groups during the ligation of either testicle (p > 0.05). Post-operatively, no significant differences in the CMPS-SF score were found between animals premedicated with tramadol and morphine at any time during the post-operative period. No dog required rescue analgesia. Tramadol and morphine administered pre-operatively provided a similar degree of post-operative analgesia in male dogs at the doses tested.

The genotype-phenotype map of an evolving digital organism.

PubMed

Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

2017-02-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

The genotype-phenotype map of an evolving digital organism

PubMed Central

Zaman, Luis; Wagner, Andreas

2017-01-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

COMT genotype, gambling activity, and cognition.

PubMed

Grant, Jon E; Leppink, Eric W; Redden, Sarah A; Odlaug, Brian L; Chamberlain, Samuel R

2015-09-01

Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate significantly different from the Val/Met (13.2%) group (p = 0.001). The Val/Val COMT group was also associated with significantly more gambling disorder diagnostic criteria being met, greater frequency of gambling behavior, and significantly worse cognitive performance on the Cambridge Gamble Task (risk adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble, in the absence of differences on demographic measures and other cognitive domains. Future work should consider using genotyping to explore whether certain polymorphisms predict subsequent development of impulsive behaviors including gambling disorder, and treatment outcomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characteristics of Streptococcus mutans genotypes and dental caries in children

PubMed Central

Cheon, Kyounga; Moser, Stephen A.; Wiener, Howard W.; Whiddon, Jennifer; Momeni, Stephanie S.; Ruby, John D.; Cutter, Gary R.; Childers, Noel K.

2013-01-01

This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5 and 6 yr-old children, considered being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping with repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, filled surfaces (dmfs/DMFS) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity) and 13 genotypes were shared by at least 2 children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and was negatively associated with p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high caries risk community, which suggest fewer decayed surfaces are significantly associated with lower diversity and stability of S. mutans genotypes. PMID:23659236

Prior infection of pigs with a genotype 3 swine hepatitis E virus (HEV) protects against subsequent challenges with homologous and heterologous genotypes 3 and 4 human HEV

PubMed Central

Sanford, Brenton J.; Dryman, Barbara A.; Huang, Yao-Wei; Feagins, Alicia R.; LeRoith, Tanya; Meng, Xiang-Jin

2011-01-01

Hepatitis E virus (HEV) is an important human pathogen. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Genotypes 3 and 4 swine HEV is widespread in pigs and known to infect humans. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In this study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. The control group was inoculated and challenged with PBS buffer. Weekly sera from all pigs were tested for HEV RNA and IgG anti-HEV, and weekly fecal samples were also tested for HEV RNA. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia and fecal virus shedding of challenge viruses were not detected, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenges with homologous and heterologous genotypes 3 and 4 HEV. The results from this study have important implications for future development of an effective HEV vaccine. PMID:21536085

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

PubMed Central

Money, Daniel; Gardner, Kyle; Migicovsky, Zoë; Schwaninger, Heidi; Zhong, Gan-Yuan; Myles, Sean

2015-01-01

Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates. PMID:26377960

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.

PubMed

Money, Daniel; Gardner, Kyle; Migicovsky, Zoë; Schwaninger, Heidi; Zhong, Gan-Yuan; Myles, Sean

2015-09-15

Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates. Copyright © 2015 Money et al.

Identification of genotypes of Influenza A virus in Malaysia

PubMed Central

MM, Rahman; KK, Wong; I, Isahak; ZZ, Rashid; H, Alfizah

2014-01-01

Objective: Influenza is considered as an emerging disease until today. The present study was undertaken to determine the prevalent genotypes of Influenza A virus in Malaysia. Methods: Influenza A virus was identified from respiratory specimens by real-time reverse transcriptase polymerase chain reaction (rRT-PCR). Phylogenetic analysis of the identified isolates was performed and genotypes were detected. Results: A total number of 505 throat swabs and nasopharyngeal aspirates were examined by rRT-PCR at Universiti Kebangsaan Malaysia Medical Centre (UKMMC) in which 65(12.87%) were positive for influenza A. The identified isolates were successfully genotyped by phylogenetic analysis. The identified influenza A genotypes were: H1N1 (42), H3N2 (20) and H5N1 (3). Conclusion: The findings indicated that 3 genotypes were circulating in Malaysia during 2011 in which H1N1 was the predominant. Results added new genotype (H5N1) identification record in Malaysia that may be added in data base of WHO and CDC. PMID:25225528

SNP discovery and genotyping using Genotyping-by-Sequencing in Pekin ducks.

PubMed

Zhu, Feng; Cui, Qian-Qian; Hou, Zhuo-Cheng

2016-11-15

Genomic selection and genome-wide association studies need thousands to millions of SNPs. However, many non-model species do not have reference chips for detecting variation. Our goal was to develop and validate an inexpensive but effective method for detecting SNP variation. Genotyping by sequencing (GBS) can be a highly efficient strategy for genome-wide SNP detection, as an alternative to microarray chips. Here, we developed a GBS protocol for ducks and tested it to genotype 49 Pekin ducks. A total of 169,209 SNPs were identified from all animals, with a mean of 55,920 SNPs per individual. The average SNP density reached 1156 SNPs/MB. In this study, the first application of GBS to ducks, we demonstrate the power and simplicity of this method. GBS can be used for genetic studies in to provide an effective method for genome-wide SNP discovery.

Prevalence of IL-28B and ITPA genotypes in Chinese Han population infected persistently with hepatitis C virus genotype 6 or HCV-1.

PubMed

Zhang, Xiao-Hong; Cai, Qing-Xian; Hong, Chun-Xia; Lin, Chao-Shuang; Zhao, Zhi-Xin

2013-07-01

The geographic distribution, demographics, epidemiology, host factors, and clinical characteristics of persistent HCV-6 infection in China need further characterization. This multicenter study enrolled 63 patients with persistent HCV-6 infection and 63 patients with persistent HCV-1 infection as controls. Blood biochemistry, quantitation of HCV RNA levels, and identification of host IL-28B genotypes (rs12979860, rs8099917, and rs12980275) and ITPA genotype (rs1127354) were performed to estimate potential variability in host factors that may affect response to treatment. The mean HCV-6 RNA level (3.8E6 IU/ml) was significantly higher than that in patients infected with HCV-1 (1.7E6 IU/ml; P < 0.001). Patients persistently infected with HCV-6 had a high prevalence of IL-28B rs12979860 CC genotype (92.1%), rs8099917 TT genotype (93.7%), and rs12980275 AA genotype (90.5%). Their prevalence in patients infected with HCV-1 was only modestly lower (82.5%, 84.1%, and 82.5%, respectively; P > 0.05). The inosine triphosphate pyrophosphatase (ITPA) SNP rs1127354 CC genotype was present in 66.7% of patients infected with HCV-6, comparable to that of patients infected with HCV-1 (65.1%; P > 0.05). There were no differences in the liver function, proportion of hepatic cirrhosis patients or patients with increased serum glucose between these two groups. Persistent HCV-6 infection in Chinese Han is found mainly in the southern China. Chinese Han with chronic HCV-1 or HCV-6 infection have IL-28B genotypes, suggesting responsiveness to interferon-based pharmacotherapy. Most patients (67%) possess the ITPA genotype associated with susceptibility to ribavirin-induced hemolysis. The routes of transmission for HCV-6 genotype were more diversified than HCV-1 genotype. The outbreak of HCV-6 infection through blood transfusion progressed faster than HCV-1. Copyright © 2013 Wiley Periodicals, Inc.

Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification

PubMed Central

2013-01-01

Background Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study conducted in 2006–2007 demonstrated a predominant EU genotype in Canada and United States. The objective of the present study was to monitor the dynamic of PepMV genetic composition and its current status in North America. Results Through yearly monitoring efforts in 2009–2012, we detected a dramatic shift in the prevalent genotype of PepMV from the genotype EU to CH2 in North America since early 2010, with another shift from CH2 to US1 occurring in Mexico only two years later. Through genetic diversity analysis using the coat protein gene, such genotype shifting of PepMV in North America was linked to the positive identification of similar sequence variants in two different commercial tomato seed sources used for scion and rootstock, respectively. To allow for a quick identification, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) system was developed and demonstrated to achieve a rapid identification for each of the three genotypes of PepMV, EU, US1 and CH2. Conclusion Through systemic yearly monitoring and genetic diversity analysis, we identified a linkage between the field epidemic isolates and those from commercial tomato seed lots as the likely sources of initial PepMV inoculum that resulted in genetic shifting as observed on greenhouse tomatoes in North America. Application of the genotype-specific RT-LAMP system would allow growers to efficiently determine the genetic diversity on their crops. PMID:23587202

New description of Toxoplasma gondii genotypes from French Polynesia.

PubMed

Yera, Hélène; Ajzenberg, Daniel; Lesle, Florence; Eyrolle-Guignot, Dominique; Besnard, Marianne; Baud, Alain; Georges, Amandine; Dupouy-Camet, Jean; Dardé, Marie Laure

2014-06-01

We report here the first isolation and genotyping of two human Toxoplasma gondii strains from French Polynesia. The parasites had new and atypical genotypes, and were responsible for asymptomatic congenital toxoplasmosis. Both genotypes were divergent from the common strains isolated in Europe, North America, South America, Africa and China. Copyright © 2014 Elsevier B.V. All rights reserved.

Sex and PRNP genotype determination in preimplantation caprine embryos.

PubMed

Guignot, F; Perreau, C; Cavarroc, C; Touzé, J-L; Pougnard, J-L; Dupont, F; Beckers, J-F; Rémy, B; Babilliot, J-M; Bed'Hom, B; Lamorinière, J M; Mermillod, P; Baril, G

2011-08-01

The objective of this study was to test the accuracy of genotype diagnosis after whole amplification of DNA extracted from biopsies obtained by trimming goat embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer. Whole genome amplification (WGA) was performed using Multiple Displacement Amplification (MDA). Sex and prion protein (PRNP) genotypes were determined. Sex diagnosis was carried out by PCR amplification of ZFX/ZFY and Y chromosome-specific sequences. Prion protein genotype determination was performed on codons 142, 154, 211, 222 and 240. Embryos were collected at day 7 after oestrus and biopsied either immediately after collection (blastocysts and expanded blastocysts) or after 24 h of in vitro culture (compacted morulae). Biopsied embryos were frozen by vitrification. Vitrified whole embryos were kept as control. DNA of biopsies was extracted and amplified using MDA. Sex diagnosis was efficient for 97.4% of biopsies and PRNP genotyping was determined in 78.7% of biopsies. After embryo transfer, no significant difference was observed in kidding rate between biopsied and vitrified control embryos, whereas embryo survival rate was different between biopsied and whole vitrified embryos (p = 0.032). At birth, 100% of diagnosed sex and 98.2% of predetermined codons were correct. Offspring PRNP profiles were in agreement with parental genotype. Whole genome amplification with MDA kit coupled with sex diagnosis and PRNP genotype predetermination are very accurate techniques to genotype goat embryos before transfer. These novel results allow us to plan selection of scrapie-resistant genotypes and kid sex before transfer of cryopreserved embryo. © 2010 Blackwell Verlag GmbH.

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

PubMed Central

da Silva, Joaquim Manoel; Giachetto, Poliana Fernanda; da Silva, Luiz Otávio Campos; Cintra, Leandro Carrijo; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues; Yamagishi, Michel Eduardo Beleza

2015-01-01

High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. PMID:26305794

Chemical composition, dietary fibre, tannins and minerals of grain amaranth genotypes.

PubMed

Mustafa, Arif F; Seguin, Philippe; Gélinas, Bruce

2011-11-01

The objective of this study was to determine the chemical composition of 28 white and coloured grain amaranth (Amaranthus spp.) genotypes. Neutral detergent fibre (NDF) concentration was greater while strach concentration was lower for coloured seeds genotypes than white seeds genotypes. Total dietary fibre followed a similar trend to that observed for NDF. Total tannin concentrations ranged between 20.7 and 0 g/kg with total and hydrolysed tannin concentrations being higher for white than for coloured seeds genotypes. Coloured seeds genotypes contained higher Mg and Ca concentrations than white seeds genotypes. However, seed colour had no influence on K, Na and P concentrations. Copper and Fe were the most variable micro-minerals in the evaluated genotypes with no significant effect of seed colour on the concentration of either mineral.

HAL/S-FC and HAL/S-360 compiler system program description

NASA Technical Reports Server (NTRS)

1976-01-01

The compiler is a large multi-phase design and can be broken into four phases: Phase 1 inputs the source language and does a syntactic and semantic analysis generating the source listing, a file of instructions in an internal format (HALMAT) and a collection of tables to be used in subsequent phases. Phase 1.5 massages the code produced by Phase 1, performing machine independent optimization. Phase 2 inputs the HALMAT produced by Phase 1 and outputs machine language object modules in a form suitable for the OS-360 or FCOS linkage editor. Phase 3 produces the SDF tables. The four phases described are written in XPL, a language specifically designed for compiler implementation. In addition to the compiler, there is a large library containing all the routines that can be explicitly called by the source language programmer plus a large collection of routines for implementing various facilities of the language.

Prior infection of pigs with a genotype 3 swine hepatitis E virus (HEV) protects against subsequent challenges with homologous and heterologous genotypes 3 and 4 human HEV.

PubMed

Sanford, Brenton J; Dryman, Barbara A; Huang, Yao-Wei; Feagins, Alicia R; Leroith, Tanya; Meng, Xiang-Jin

2011-07-01

Hepatitis E virus (HEV) is an important human pathogen. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Genotypes 3 and 4 swine HEV is widespread in pigs and known to infect humans. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In this study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. The control group was inoculated and challenged with PBS buffer. Weekly sera from all pigs were tested for HEV RNA and IgG anti-HEV, and weekly fecal samples were also tested for HEV RNA. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia was not detected and only two pigs challenged with swine HEV had 1-week fecal virus shedding, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenges with homologous and heterologous genotypes 3 and 4 HEV. The results from this study have important implications for future development of an effective HEV vaccine. Copyright © 2011 Elsevier B.V. All rights reserved.

A genotype probability index for multiple alleles and haplotypes.

PubMed

Percy, A; Kinghorn, B P

2005-12-01

We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

Experimental infection of bovine mammary gland with prototheca zopfii genotype 1.

PubMed

Ito, Takaaki; Kano, Rui; Sobukawa, Hideto; Ogawa, Jin; Honda, Yayoi; Hosoi, Yoshihiro; Shibuya, Hisashi; Sato, Tsuneo; Hasegawa, Atsuhiko; Kamata, Hiroshi

2011-01-01

Prototheca zopfii is divided into three genotypes, one of which, P. zopfii genotype 2, appears to be the main causative agent of bovine protothecal mastitis. However, the difference in pathogenicity between genotypes 1 and 2 has not been well investigated. In the present study, we experimentally infected normal bovine mammary gland with P. zopfii genotype 1 to investigate its pathogenicity. The mammary gland infected with P. zopfii genotype 1 showed no clinical signs. However, the histopathologic features of the infected mammary gland consisted of interstitial infiltrates of macrophages, plasma cells, lymphocytes, and fibroblasts with neutrophils in acinar lumens. Algae were present in macrophages and free in the alveolar lumens and the interstitium. Histopathology of the resultant tissue samples revealed that genotype 1 also induced a granulomatous lesion in the cow teat, similar to the mastitis lesion due to genotype 2.

Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009–2010

PubMed Central

Shak, Emma B.; Cowan, Lauren; Starks, Angela M.; Grant, Juliana

2015-01-01

Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009–December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups. PMID:26556930

Differential survival among sSOD-1* genotypes in Chinook Salmon

USGS Publications Warehouse

Hayes, Michael C.; Reisenbichler, Reginald R.; Rubin, Stephen P.; Wetzel, Lisa A.; Marshall , Anne R.

2011-01-01

Differential survival and growth were tested in Chinook salmon Oncorhynchus tshawytscha expressing two common alleles, *–100 and *–260, at the superoxide dismutase locus (sSOD-1*). These tests were necessary to support separate studies in which the two alleles were used as genetic marks under the assumption of mark neutrality. Heterozygous adults were used to produce progeny with –100/–100, –100/–260, and –260/–260 genotypes that were reared in two natural streams and two hatcheries in the states of Washington and Oregon. The latter also were evaluated as returning adults. In general, the genotype ratios of juveniles reared at hatcheries were consistent with high survival and little or no differential survival in the hatchery. Adult returns at one hatchery were significantly different from the expected proportions, and the survival of the –260/–260 genotype was 0.56–0.89 times that of the –100/–100 genotype over four year-classes. Adult returns at a second hatchery (one year-class) were similar but not statistically significant: survival of the –260/–260genotype relative to the –100/–100 genotype was 0.76. The performance of the heterozygote group was intermediate at both hatcheries. Significant differences in growth were rarely observed among hatchery fish (one year-class of juveniles and one age-class of adult males) but were consistent with greater performance for the –100/–100 genotype. Results from two groups of juveniles reared in streams (one year-class from each stream) suggested few differences in growth, but the observed genotype ratios were significantly different from the expected ratios in one stream. Those differences were consistent with the adult data; survival for the –260/–260 genotype was 76% of that of the –100/–100 genotype. These results, which indicate nonneutrality among sSOD-1* genotypes, caused us to modify our related studies and suggest caution in the interpretation of results and analyses in

Shared Mycobacterium avium Genotypes Observed among Unlinked Clinical and Environmental Isolates

PubMed Central

Weigel, Kris M.; Yakrus, Mitchell A.; Becker, Annie L.; Chen, Hui-Ling; Fridley, Gina; Sikora, Arthur; Speake, Cate; Hilborn, Elizabeth D.; Pfaller, Stacy

2013-01-01

Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates of M. avium from geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in isolates from apparently unlinked patients in two or more geographic locations. Six of the 12 were also observed in environmental isolates. A subset of these isolates was further analyzed by alternative strain genotyping methods, pulsed-field gel electrophoresis and MIRU-VNTR, which confirmed the existence of geographically dispersed strain genotypes. These results suggest that caution should be exercised in interpreting high-resolution genotypic matches as evidence for an acquisition event. PMID:23851084

Intergenotypic chimeric hepatitis E viruses (HEVs) with the genotype 4 human HEV capsid gene in the backbone of genotype 3 swine HEV are infectious in pigs.

PubMed

Feagins, Alicia R; Córdoba, Laura; Sanford, Brent J; Dryman, Barbara A; Huang, Yao-Wei; LeRoith, Tanya; Emerson, Suzanne U; Meng, Xiang-Jin

2011-03-01

Genotypes 1 and 2 hepatitis E virus (HEV) infect only humans whereas genotypes 3 and 4 HEV infect both humans and pigs. To evaluate the mechanism of cross-species HEV infection between humans and swine, in this study we constructed five intergenotypic chimeric viruses and tested for their infectivity in vitro and in pigs. We demonstrated that chimeric viruses containing the ORF2 capsid gene either alone or in combination with its adjacent 5' junction region (JR) and 3' noncoding region (NCR) from a genotype 4 human HEV in the backbone of a genotype 3 swine HEV are replication-competent in Huh7 cells and infectious in HepG2/C3A cells and in pigs, and thus supporting the hypothesis that genotypes 3 and 4 human HEV are of swine origin. However, chimeric viruses containing the JR+ORF2+3' NCR of genotypes 3 or 4 HEV in the backbone of genotype 1 human HEV failed to infect pigs, suggesting that other genomic regions such as 5' NCR and ORF1 may also be involved in HEV cross-species infection. The results from this study provide the first experimental evidence of the exchangeability of the capsid gene between genotype 3 swine HEV and genotype 4 human HEV, and have important implications for understanding the mechanism of HEV cross-species infection. Copyright © 2010 Elsevier B.V. All rights reserved.

Genotyping of bovine Prototheca mastitis isolates from Poland.

PubMed

Jagielski, Tomasz; Lassa, Henryka; Ahrholdt, Jennifer; Malinowski, Edward; Roesler, Uwe

2011-04-21

Bovine mastitis due to unicellular, achlorophyllous algae of the genus Prototheca is a serious and complex ailment that accounts for high economic losses in the dairy industry. Bovine protothecal mastitis has been almost exclusively associated with only one species Prototheca zopfii. Recently, based on the 18S rDNA sequence analysis, P. zopfii has been divided into three genotypes (1-3), of which P. zopfii genotype 3 has been given the status of a new species Prototheca blaschkeae sp. nov. The aim of this study was to investigate the genotypic composition of the population of P. zopfii bovine mastitis isolates from Poland, according to that threefold classification. Of the 44 isolates tested, 43 (98%) were identified as P. zopfii genotype 2. Only one isolate was assigned to the newly established P. blaschkeae species. These findings clearly show the predominance of the P. zopfii genotype 2 in the etiology of bovine mammary protothecosis in Poland, but also underline the involvement of P. blaschkeae in the disease. The study is the first to provide molecular characterization of Polish P. zopfii mastitis isolates, collected from different regions of Poland. Copyright © 2010 Elsevier B.V. All rights reserved.

HLA genotyping by next-generation sequencing of complementary DNA.

PubMed

Segawa, Hidenobu; Kukita, Yoji; Kato, Kikuya

2017-11-28

Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA. Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database. The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology. The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of

Plant genotypes affect aboveground and belowground herbivore interactions by changing chemical defense.

PubMed

Li, Xiaoqiong; Guo, Wenfeng; Siemann, Evan; Wen, Yuanguang; Huang, Wei; Ding, Jianqing

2016-12-01

Spatially separated aboveground (AG) and belowground (BG) herbivores are closely linked through shared host plants, and both patterns of AG-BG interactions and plant responses may vary among plant genotypes. We subjected invasive (USA) and native (China) genotypes of tallow tree (Triadica sebifera) to herbivory by the AG specialist leaf-rolling weevil Heterapoderopsis bicallosicollis and/or the root-feeding larvae of flea beetle Bikasha collaris. We measured leaf damage and leaves rolled by weevils, quantified beetle survival, and analyzed flavonoid and tannin concentrations in leaves and roots. AG and BG herbivores formed negative feedbacks on both native and invasive genotypes. Leaf damage by weevils and the number of beetle larvae emerging as adults were higher on invasive genotypes. Beetles reduced weevil damage and weevils reduced beetle larval emergence more strongly for invasive genotypes. Invasive genotypes had lower leaf and root tannins than native genotypes. BG beetles decreased leaf tannins of native genotypes but increased root tannins of invasive genotypes. AG herbivory increased root flavonoids of invasive genotypes while BG herbivory decreased leaf flavonoids. Invasive genotypes had lower AG and BG herbivore resistance, and negative AG-BG herbivore feedbacks were much stronger for invasive genotypes. Lower tannin concentrations explained overall better AG and BG herbivore performances on invasive genotypes. However, changes in tannins and flavonoids affected AG and BG herbivores differently. These results suggest that divergent selection on chemical production in invasive plants may be critical in regulating herbivore performances and novel AG and BG herbivore communities in new environments.

Introduction to a special issue on genotype by environment interaction

USDA-ARS?s Scientific Manuscript database

Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

Multivariate Analysis of Genotype-Phenotype Association.

PubMed

Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

2016-04-01

With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

In Vitro Conservation of Sweet Potato Genotypes

PubMed Central

Arrigoni-Blank, Maria de Fátima; Tavares, Fernanda Ferreira; dos Santos, Maria Clézia; Menezes, Thays Saynara Alves; de Santana, Aléa Dayane Dantas

2014-01-01

The aim of this study was to develop a protocol for the in vitro conservation of sweet potato genotypes using the slow growth technique. The first experiment was conducted in a 4 × 5 × 2 factorial scheme, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137), five concentrations of abscisic acid (ABA) (0.0, 1.0, 2.0, 4.0, and 8.0 mg·L−1), and two temperatures (18 and 25°C). The second experiment was conducted in a 4 × 3 × 3 factorial scheme at 18°C, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137), three variations of MS salts (50, 75, and 100%), and three concentrations of sucrose (10, 20, and 30 g·L−1). Every three months, we evaluated the survival (%), shoot height, and shoot viability. In vitro conservation of the sweet potato genotypes IPB-052 and IPB-007 was obtained over three and six months, respectively, using MS medium plus 2.0 mg·L−1 of ABA at either 18 or 25°C. Genotypes IPB-072 and IPB-137 can be kept for three and six months, respectively, in MS medium without ABA at 18°C. It is possible to store IPB-052 and IPB-072 for six months and IPB-007 and IPB-137 for nine months using 30 g·L−1 of sucrose and 50% MS salts. PMID:24563627

Precise genotyping and recombination detection of Enterovirus

PubMed Central

2015-01-01

Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation.

PubMed

Matthijnssens, Jelle; Miño, Samuel; Papp, Hajnalka; Potgieter, Christiaan; Novo, Luis; Heylen, Elisabeth; Zeller, Mark; Garaicoechea, Lorena; Badaracco, Alejandra; Lengyel, György; Kisfali, Péter; Cullinane, Ann; Collins, P J; Ciarlet, Max; O'Shea, Helen; Parreño, Viviana; Bányai, Krisztián; Barrandeguy, María; Van Ranst, Marc

2012-04-01

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes.

PubMed

Creel, Scott; Spong, Goran; Sands, Jennifer L; Rotella, Jay; Zeigle, Janet; Joe, Lawrence; Murphy, Kerry M; Smith, Douglas

2003-07-01

Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias.

Noninvasive fetal RhCE genotyping from maternal blood.

PubMed

Geifman-Holtzman, O; Grotegut, C A; Gaughan, J P; Holtzman, E J; Floro, C; Hernandez, E

2009-01-01

The successful prevention of RhD disease has brought attention to other red blood cells' antigens causing alloimmunisation including RhC/c and RhE/e. Prenatal diagnosis of fetal Rh genotype from maternal blood is in clinical use in Europe but not in the USA. To estimate the collective reported diagnostic accuracy of fetal RhCE genotyping from peripheral maternal blood and compare the results of genotyping when fetal cells and free fetal DNA (FfDNA) are used. English-written literature describing fetal RhCE determination from maternal blood using fetal cells or FfDNA was performed using medical subject headings and text words. The sources included Pubmed (1966-2007), Ovid (1966-2007), CINAHL, The Cochrane Library, ACP Journal Club and OCLC. Key words were prenatal diagnosis, fetal RhCE, fetal DNA in maternal blood and alloimmunisation. A study was considered eligible if it described fetal RhCE type determination using maternal peripheral blood reported in the English literature. Abstracts were excluded. From each study, we determined the number of samples tested, fetal RhCE genotype, the source of the fetal DNA, gestational age, presence of alloimmunisation and confirmation of fetal RhCE type. Exclusions and inclusions were noted. We calculated composite estimates of accuracy using a weighted random effects model. We assessed the papers against an international quality, STARD checklist which is standards for reporting studies of diagnostic accuracy. We identified 20 protocols in six English-written publications reporting fetal RhC/c (seven protocols) and/or E/e (13 protocols) genotyping using DNA obtained from maternal blood for a total of 369 samples. For RhC/c, 176 samples were tested and for RhE/e, 193 samples were tested. Accuracy was determined for each study and for all studies. The combined accuracy of fetal genotype was 96.3% for RhC/c and 98.2% for RhE/e. Only a few samples of the sorted cells were found to be a source for accurate diagnosis, but plasma was

Molecular genotyping of HCV infection in seropositive blood donor

NASA Astrophysics Data System (ADS)

Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

2013-11-01

This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

Blood group genotyping: from patient to high-throughput donor screening.

PubMed

Veldhuisen, B; van der Schoot, C E; de Haas, M

2009-10-01

Blood group antigens, present on the cell membrane of red blood cells and platelets, can be defined either serologically or predicted based on the genotypes of genes encoding for blood group antigens. At present, the molecular basis of many antigens of the 30 blood group systems and 17 human platelet antigens is known. In many laboratories, blood group genotyping assays are routinely used for diagnostics in cases where patient red cells cannot be used for serological typing due to the presence of auto-antibodies or after recent transfusions. In addition, DNA genotyping is used to support (un)-expected serological findings. Fetal genotyping is routinely performed when there is a risk of alloimmune-mediated red cell or platelet destruction. In case of patient blood group antigen typing, it is important that a genotyping result is quickly available to support the selection of donor blood, and high-throughput of the genotyping method is not a prerequisite. In addition, genotyping of blood donors will be extremely useful to obtain donor blood with rare phenotypes, for example lacking a high-frequency antigen, and to obtain a fully typed donor database to be used for a better matching between recipient and donor to prevent adverse transfusion reactions. Serological typing of large cohorts of donors is a labour-intensive and expensive exercise and hampered by the lack of sufficient amounts of approved typing reagents for all blood group systems of interest. Currently, high-throughput genotyping based on DNA micro-arrays is a very feasible method to obtain a large pool of well-typed blood donors. Several systems for high-throughput blood group genotyping are developed and will be discussed in this review.

Clinical and epidemiological characteristics of Korean patients with hepatitis C virus genotype 6

PubMed Central

Seong, Mun Hyuk; Kil, Ho; Kim, Jong Yeop; Lee, Sang Soo; Jang, Eun Sun; Kim, Jin-Wook; Kim, Young Seok; Bae, Si Hyun; Lee, Youn Jae; Lee, Han Chu; Yun, Haesun; Kang, Byung Hak; Kim, Kisang

2013-01-01

Background/Aims The distribution of hepatitis C virus (HCV) genotypes varies geographically. In Korea, genotypes 1 and 2 comprise more than 90% of HCV infections, while genotype 6 is very rare. This study compared the clinical and epidemiological characteristics of patients with genotype 6 HCV infection with those infected with HCV genotypes 1 and 2. Methods This was a prospective, multicenter HCV cohort study that enrolled 1,173 adult patients, of which 930 underwent HCV genotype analysis, and only 9 (1.0%) were found to be infected with genotype 6 HCV. The clinical and epidemiological parameters of the genotypes were compared. Results The patients with genotype 6 HCV had a mean age of 41.5 years, 77.8% were male, and they had no distinct laboratory features. A sustained virologic response (SVR) was observed in four (67%) of six patients who received antiviral therapy. Risk factors such as the presence of a tattoo (n=6, 66.7%), more than three sexual partners (n=3, 33.3%), and injection drug use (n=3, 33.3%) were more common among genotype 6 patients than among genotypes 1 or 2. Conclusions The epidemiology and treatment response of patients infected with genotype 6 HCV differed significantly from those with genotypes 1 or 2, warranting continuous monitoring. PMID:23593609

Different Duck Species Infected Intramuscularly with Duck-Origin Genotype IX APMV-1 Show Discrepant Mortality and Indicate Another Fatal Genotype APMV-1 to Ducks.

PubMed

Fu, Guanghua; Cheng, Longfei; Fu, Qiuling; Qi, Baomin; Chen, Cuiteng; Shi, Shaohua; Chen, Hongmei; Wan, Chunhe; Liu, Rongchang; Huang, Yu

2017-03-01

Isolations of genotype IX (gIX) avian paramyxovirus type 1 (APMV-1) from various bird species have been more common recently, with isolates showing variable pathogenicity in different species of poultry. Here we sequenced the genome of a Muscovy duck origin gIX virus strain XBT14 and characterized the virulence and pathogenicity of this isolate in chickens and ducks. The genome sequence of strain XBT14 is 15,192 nt in length, containing multiple basic amino acids at the fusion protein cleavage site. The XBT14 strain shared 91.6%-91.9% nucleotide identities with early-genotype viruses (such as genotype III and IV) and shared 85.3%-85.9% nucleotide homologies with later genotype viruses (such as genotype VII). Pathogenicity tests showed that strain XBT14 could cause death in different duck breeds with a mortality rate of 44.4% in Muscovy duck, 25.9% in Sheldrake, and 11.1% in Cherry Valley duck, respectively. Similar mortality discrepancies were also observed in different ducks when infected with chicken-origin gIX virus strain F48E8. These results indicate that XBT14-like velogenic gIX APMV-1 (such as XBT14, F48E8, and GD09-2) could cause fatal infection in duck, and genotype IX is another genotype velogenic to duck as well as genotype VII. Accompanied by genetic differences in the vaccine strains or dominant strains prevailing in poultry, the virulent XBT14-like gIX viruses might become potentially endemic strains in poultry in the future.

Development of hepatitis C virus genotype 3a cell culture system.

PubMed

Kim, Sulyi; Date, Tomoko; Yokokawa, Hiroshi; Kono, Tamaki; Aizaki, Hideki; Maurel, Patrick; Gondeau, Claire; Wakita, Takaji

2014-12-01

Hepatitis C virus (HCV) genotype 3a infection poses a serious health problem worldwide. A significant association has been reported between HCV genotype 3a infections and hepatic steatosis. Nevertheless, virological characterization of genotype 3a HCV is delayed due to the lack of appropriate virus cell culture systems. In the present study, we established the first infectious genotype 3a HCV system by introducing adaptive mutations into the S310 strain. HCV core proteins had different locations in JFH-1 and S310 virus-infected cells. Furthermore, the lipid content in S310 virus-infected cells was higher than Huh7.5.1 cells and JFH-1 virus-infected cells as determined by the lipid droplet staining area. This genotype 3a infectious cell culture system may be a useful experimental model for studying genotype 3a viral life cycles, molecular mechanisms of pathogenesis, and genotype 3a-specific antiviral drug development. © 2014 by the American Association for the Study of Liver Diseases.

Variation of meat quality traits among five genotypes of chicken.

PubMed

Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K

2009-10-01

The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

Tuberculosis genotyping information management system: enhancing tuberculosis surveillance in the United States.

PubMed

Ghosh, Smita; Moonan, Patrick K; Cowan, Lauren; Grant, Juliana; Kammerer, Steve; Navin, Thomas R

2012-06-01

Molecular characterization of Mycobacterium tuberculosis complex isolates (genotyping) can be used by public health programs to more readily identify tuberculosis (TB) transmission. The Centers for Disease Control and Prevention's National Tuberculosis Genotyping Service has offered M. tuberculosis genotyping for every culture-confirmed case in the United States since 2004. The TB Genotyping Information Management System (TB GIMS), launched in March 2010, is a secure online database containing genotype results linked with case characteristics from the national TB registry for state and local TB programs to access, manage and analyze these data. As of September 2011, TB GIMS contains genotype results for 89% of all culture-positive TB cases for 2010. Over 400 users can generate local and national reports and maps using TB GIMS. Automated alerts on geospatially concentrated cases with matching genotypes that may represent outbreaks are also generated by TB GIMS. TB genotyping results are available to enhance national TB surveillance and apply genotyping results to conduct TB control activities in the United States. Published by Elsevier B.V.

Genotypes of hepatitis a virus in Turkey: first report and clinical profile of children infected with sub-genotypes IA and IIIA.

PubMed

Yilmaz, Huseyin; Karakullukcu, Asiye; Turan, Nuri; Cizmecigil, Utku Y; Yilmaz, Aysun; Ozkul, Ayse A; Aydin, Ozge; Gunduz, Alper; Mete, Mahmut; Zeyrek, Fadile Y; Kirazoglu, Taner T; Richt, Juergen A; Kocazeybek, Bekir

2017-08-11

Hepatitis A virus (HAV) is a food and water-borne virus causing clinical (mainly hepatitis) and subclinical disease in humans. It is important to characterize circulating strains of HAV in order to prevent HAV infections using efficacious vaccines. The aim of this study was the detection and characterization of the circulating strains of HAV in Turkey by performing serology, RT-PCR, sequencing and phylogenetic analysis. In this study, 355 HAV suspected cases were analysed by ELISA for the presence of antibodies to HAV. RNA was extracted from 54 HAV IgM positive human sera. None of the suspect cases were vaccinated against HAV and they never received blood transfusions. Samples found positive by RT-PCR using primers targeting the VP1/VP2A junction and VP1/VP3 capsid region of HAV, were subjected to sequencing and phylogenetic analyses. IgM type antibodies to HAV were detected in 54 patients. Twenty one of them were students. The age of IgM positive cases was between 3 and 60 years. IgM positivity differed in age groups and was higher in the age group 3 to 10 years. Phylogenetic analysis showed that the majority of HAV strains detected in this study belong to the "HAV 1B" cluster. In addition, the HAV sub-genotypes IA (KT874461.1) and IIIA (KT222963.1) were found in 2 children. These sub-genotypes were not previously reported in Turkey. The child who carried sub-genotype IIIA travelled to Afghanistan and presented with abdominal pain, icterus and vomitus. He was positive for anti-HAV IgM and IgG but negative for hepatitis B and C. Liver enzymes like aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma-glutamyl transferase and lactate dehydrogenase were severely elevated. Bilirubin levels were also increased. White blood cells, neutrophils and hemoglobin were decreased while lymphocytes and monocytes were increased. Similar clinical signs and laboratory findings were reported for the child infected with sub-genotype IA but aspartate

Hepatitis C virus genotypes in Southern Brazil.

PubMed

Krug, L P; Lunge, V R; Ikuta, N; Fonseca, A S; Cheinquer, H; Ozaki, L S; Barros, S G

1996-12-01

The prevalence of hepatitis C virus (HCV) genotypes in Southern Brazil was studied in the plasma of 100 HCV-RNA-positive patients attended in Porto Alegre, South of Brazil. Reverse transcription-polymerase chain reaction (RT-PCR) products from the 5' noncoding region were double digested with RsaI-HaeIII and BstNI-HinfI and analyzed by restriction fragment length polymorphism (RFLP). Three genotypes (1, 2 and 3) were demonstrable, the most prevalent being HCV type 1 (55 of 100 patients, 55%), followed by HCV type 3 (37 of 100 patients, 37%) and HCV type 2 (8 of 100 patients, 8%). There was an unusual high prevalence of genotype 3, in contrast to the majority of published data from the Southeast region.

The action of volatile anaesthetics on stimulus-secretion coupling in bovine adrenal chromaffin cells.

PubMed Central

Pocock, G.; Richards, C. D.

1988-01-01

1. The action of four volatile anaesthetics, ethrane, halothane, isoflurane and methoxyflurane on stimulus-secretion coupling has been studied in isolated bovine adrenal medullary cells. All four agents inhibited the secretion of adrenaline and noradrenaline evoked by 500 microM carbachol at concentrations within the anaesthetic range. Total catecholamine secretion induced by stimulation with 77 mM potassium was also inhibited but at higher concentrations. All four agents inhibited the 45Ca influx evoked by stimulation with 500 microM carbachol and the 45Ca influx in response to K+-depolarization. 2. When total catecholamine secretion in response to potassium or carbachol was modulated by varying extracellular calcium or by adding halothane or methoxyflurane to the incubation medium, the amount of catecholamine secretion for a given Ca2+ entry was the same. 3. The action of methoxyflurane on the relationship between intracellular free Ca and exocytosis was examined using electropermeabilised cells, which were suspended in solutions containing a range of concentrations of ionised calcium between 10(-8) and 10(-4)M. The anaesthetic had no effect on the activation of exocytosis by intracellular free calcium. 4. Halothane and methoxyflurane inhibited the carbachol-induced secretion of catecholamines in a non-competitive manner. 5. Halothane and methoxyflurane inhibited the increase in 22Na influx evoked by carbachol. For halothane and methoxyflurane this inhibition of Na influx appears to be sufficient to account for the inhibition of the evoked catecholamine secretion. 6. We conclude that the volatile anaesthetics ethrane, halothane, isoflurane and methoxyflurane inhibit the secretion of adrenaline and noradrenaline induced by carbachol at concentrations that lie within the range encountered during general anaesthesia.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2464384

Restoration of gait for spinal cord injury patients using HAL with intention estimator for preferable swing speed.

PubMed

Tsukahara, Atsushi; Hasegawa, Yasuhisa; Eguchi, Kiyoshi; Sankai, Yoshiyuki

2015-03-01

This paper proposes a novel gait intention estimator for an exoskeleton-wearer who needs gait support owing to walking impairment. The gait intention estimator not only detects the intention related to the start of the swing leg based on the behavior of the center of ground reaction force (CoGRF), but also infers the swing speed depending on the walking velocity. The preliminary experiments categorized into two stages were performed on a mannequin equipped with the exoskeleton robot [Hybrid Assistive Limb: (HAL)] including the proposed estimator. The first experiment verified that the gait support system allowed the mannequin to walk properly and safely. In the second experiment, we confirmed the differences in gait characteristics attributed to the presence or absence of the proposed swing speed profile. As a feasibility study, we evaluated the walking capability of a severe spinal cord injury patient supported by the system during a 10-m walk test. The results showed that the system enabled the patient to accomplish a symmetrical walk from both spatial and temporal standpoints while adjusting the speed of the swing leg. Furthermore, the critical differences of gait between our system and a knee-ankle-foot orthosis were obtained from the CoGRF distribution and the walking time. Through the tests, we demonstrated the effectiveness and practical feasibility of the gait support algorithms.

Genotypic Distribution of Hepatitis C Virus in Thailand and Southeast Asia

PubMed Central

Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

2015-01-01

The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world’s population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5’ untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27–36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

Genotyping of acute HBV isolates from England, 1997-2001.

PubMed

Sloan, Richard D; Strang, Angela L; Ramsay, Mary E; Teo, Chong-Gee

2009-02-01

Increasing data shows the relevance of HBV genotypes in the outcome of infection. Most studies investigating the relationship between the genotypic characteristics of hepatitis B virus (HBV) and the clinical or epidemiological aspects of HBV infection originate from studies of patients with chronic rather than acute hepatitis B. To study a convenience sample representing ca. 5% of reported acute hepatitis B in England between 1997 and 2001 to investigate the distribution of HBV genotypes and specific HBV variants with epidemiological risk factors, thereby providing baseline data for ongoing surveillance. From 160 serum samples, PCR was carried out to amplify the first 600 bases of the HBV S gene. Amplicons were sequenced and subjected to phylogenetic analysis and risk factor analysis. Fifty-seven percent of the study samples carried HBV belonging to subtype A2, 13% to subtype D2, and the rest to genotype E (8%) and subtypes C2 and D3 (each 6%), D1 and D4 (each 3%) and B4 (1%). One particular A2 isolate was dominant, accounting for 23% of the total sample set. Drug use and homosexual transmission were equally implicated as risks within genotype A2. No mutations associated with vaccine escape or resistance to antiviral therapy were identified. Immigration and travel likely shape the observed genotype distribution and consequent prevalence of genotypes other than A2 or D in this population. Data suggests no genetic separation of parenteral and sexually transmitted virus. These data demonstrate the value in pursuing more extensive and recent surveillance.

Spectral reflectance models for characterizing winter wheat genotypes

USDA-ARS?s Scientific Manuscript database

Optimum wheat yield can be achieved by developing and growing the best genotype in the most suited environment. However, exhaustive field measurements are required to characterize plants in breeder plots for screening genotypes with desirable traits. Remote sensing tools have been shown to provide r...

Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge.

PubMed

Alvarez Rojas, Cristian A; Romig, Thomas; Lightowlers, Marshall W

2014-01-01

Genetic variability in the species group Echinococcus granulosus sensu lato is well recognised as affecting intermediate host susceptibility and other biological features of the parasites. Molecular methods have allowed discrimination of different genotypes (G1-10 and the 'lion strain'), some of which are now considered separate species. An accumulation of genotypic analyses undertaken on parasite isolates from human cases of cystic echinococcosis provides the basis upon which an assessment is made here of the relative contribution of the different genotypes to human disease. The allocation of samples to G-numbers becomes increasingly difficult, because much more variability than previously recognised exists in the genotypic clusters G1-3 (=E. granulosus sensu stricto) and G6-10 (Echinococcus canadensis). To accommodate the heterogeneous criteria used for genotyping in the literature, we restrict ourselves to differentiate between E. granulosus sensu stricto (G1-3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and E. canadensis (G6-7, G8, G10). The genotype G1 is responsible for the great majority of human cystic echinococcosis worldwide (88.44%), has the most cosmopolitan distribution and is often associated with transmission via sheep as intermediate hosts. The closely related genotypes G6 and G7 cause a significant number of human infections (11.07%). The genotype G6 was found to be responsible for 7.34% of infections worldwide. This strain is known from Africa and Asia, where it is transmitted mainly by camels (and goats), and South America, where it appears to be mainly transmitted by goats. The G7 genotype has been responsible for 3.73% of human cases of cystic echinococcosis in eastern European countries, where the parasite is transmitted by pigs. Some of the samples (11) could not be identified with a single specific genotype belonging to E. canadensis (G6/10). Rare cases of human cystic echinococcosis have been identified as having been caused by

Hepatitis C virus genotypes in the Middle East and North Africa: Distribution, diversity, and patterns

PubMed Central

Mahmud, Sarwat; Al‐Kanaani, Zaina; Chemaitelly, Hiam; Chaabna, Karima; Kouyoumjian, Silva P.

2017-01-01

Our objective was to characterize the distribution, diversity and patterns of hepatitis C virus (HCV) genotypes in the Middle East and North Africa (MENA). Source of data was a database of HCV genotype studies in MENA populated using a series of systematic literature searches. Pooled mean proportions were estimated for each genotype and by country using DerSimonian‐Laird random‐effects meta‐analyses. Genotype diversity within countries was assessed using Shannon Diversity Index. Number of chronic infections by genotype and country was calculated using the pooled proportions and country‐specific numbers of chronic infection. Analyses were conducted on 338 genotype studies including 82 257 genotyped individuals. Genotype 1 was dominant (≥50%) in Algeria, Iran, Morocco, Oman, Tunisia, and UAE, and was overall ubiquitous across the region. Genotype 2 was common (10‐50%) in Algeria, Bahrain, Libya, and Morocco. Genotype 3 was dominant in Afghanistan and Pakistan. Genotype 4 was dominant in Egypt, Iraq, Jordan, Palestine, Qatar, Saudi Arabia, and Syria. Genotypes 5, 6, and 7 had limited or no presence across countries. Genotype diversity varied immensely throughout MENA. Weighted by population size, MENA's chronic infections were highest among genotype 3, followed by genotype 4, genotype 1, genotype 2, genotype 5, and genotype 6. Despite ubiquitous presence of genotype 1, the vast majority of chronic infections were of genotypes 3 or 4, because of the sizable epidemics in Pakistan and Egypt. Three sub‐regional patterns were identified: genotype 3 pattern centered in Pakistan, genotype 4 pattern centered in Egypt, and genotype 1 pattern ubiquitous in most MENA countries. PMID:28842995

PCR-RFLP genotypes associated with quinolone resistance in isolates of Flavobacterium psychrophilum.

PubMed

Izumi, S; Ouchi, S; Kuge, T; Arai, H; Mito, T; Fujii, H; Aranishi, F; Shimizu, A

2007-03-01

A novel genotyping method for epizootiological studies of bacterial cold-water disease caused by Flavobacterium psychrophilum and associated with quinolone resistance was developed. Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) was performed on 244 F. psychrophilum isolates from various fish species. PCR was performed with primer pair GYRA-FP1F and GYRA-FP1R amplifying the A subunit of the DNA gyrase (GyrA) gene, which contained the quinolone resistance determining region. Digestion of PCR products with the restriction enzyme Mph1103I showed two genotypes, QR and QS. The difference between these genotypes was amino acid substitutions at position 83 of GyrA (Escherichia coli numbering). The genotype QR indicated an alanine residue at this position associated with quinolone resistance in F. psychrophilum isolates. Of the 244 isolates tested in this study, the number of QR genotype isolates was 153 (62.7%). In isolates from ayu (n=177), 146 (82.5%) were genotype QR. With combination of this technique and previously reported PCR-RFLP genotyping, eight genotypes were observed in F. psychrophilum isolates. Using this genotyping system, the relationships between genotype and host fish species, or locality of isolation, were analysed and are discussed.

Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

PubMed

Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

2010-10-01

The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

Multiple HPV genotype infection impact on invasive cervical cancer presentation and survival

PubMed Central

Martins, Toni Ricardo; Mendoza Lopez, Rossana V.; Sadalla, José Carlos; de Carvalho, João Paulo Mancusi; Baracat, Edmund Chada

2017-01-01

Background Invasive cervical cancer (ICC) is the third most common malignant neoplasm affecting Brazilian women. Little is known about the impact of specific HPV genotypes in the prognosis of ICC. We hypothesized that HPV genotype would impact ICC clinical presentation and survival. Methods Women diagnosed with ICC at the Instituto do Câncer do Estado de São Paulo (ICESP) between May 2008 and June 2012 were included in the study and were followed until December 2015. HPV genotype was detected from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples using Onclarity™ system (BD Viper™ LT automated system). Results 292 patients aged 50±14 years were analyzed. HPVDNA was detected in 84% of patients. The HPV genotypes studied were: HPV16 (64%), HPV18 (10%), HPV33-58 (7%), HPV45 (5%), HPV31 (4%) and other high-risk HPV genotypes (11%). HPV genotypes showed different distributions regarding histological type and clinical stage. Patients were followed for 35±21 months. The overall survival at 5 years after diagnosis of cervical cancer was 54%. Age, clinical staging, histological type and multiple HPV genotypes infection detected in the same tumor specimen were associated with poorer overall survival on multivariate Cox proportional hazard analysis (p<0.05). No specific HPV genotype affected survival. Conclusion Multiple HPV genotype infection was associated with poorer ICC survival in our study, compared with single genotype infection. HPV genotyping from FFPE tumor tissue using an automated assay such as the Onclarity BD™ assay provides a simpler alternative for routine clinical use. Impact This is the largest study employing an automated HPV genotyping assay using FFPE of ICC. Multiple HPV genotype infection adversely influenced survival. PMID:28829791

The effects of volatile anesthetics on the extracellular accumulation of [(3)H]GABA in rat brain cortical slices.

PubMed

Diniz, Paulo H C; Guatimosim, Cristina; Binda, Nancy S; Costa, Flávia L P; Gomez, Marcus V; Gomez, Renato S

2014-01-01

GABA is an inhibitory neurotransmitter that appears to be associated with the action of volatile anesthetics. These anesthetics potentiate GABA-induced postsynaptic currents by synaptic GABAA receptors, although recent evidence suggests that these agents also significantly affect extrasynaptic GABA receptors. However, the effect of volatile anesthetics on the extracellular concentration of GABA in the central nervous system has not been fully established. In the present study, rat brain cortical slices loaded with [(3)H]GABA were used to investigate the effect of halothane and sevoflurane on the extracellular accumulation of this neurotransmitter. The accumulation of [(3)H]GABA was significantly increased by sevoflurane (0.058, 0.11, 0.23, 0.46, and 0.93 mM) and halothane (0.006, 0.012, 0.024, 0.048, 0072, and 0.096 mM) with an EC50 of 0.26 mM and 35 μM, respectively. TTX (blocker of voltage-dependent Na(+) channels), EGTA (an extracellular Ca(2+) chelator) and BAPTA-AM (an intracellular Ca(2+) chelator) did not interfere with the accumulation of [(3)H]GABA induced by 0.23 mM sevoflurane and 0.048 mM halothane. SKF 89976A, a GABA transporter type 1 (GAT-1) inhibitor, reduced the sevoflurane- and halothane-induced increase in the accumulation of GABA by 57 and 63 %, respectively. Incubation of brain cortical slices at low temperature (17 °C), a condition that inhibits GAT function and reduces GABA release through reverse transport, reduced the sevoflurane- and halothane-induced increase in the accumulation of [(3)H]GABA by 82 and 75 %, respectively, relative to that at normal temperature (37 °C). Ouabain, a Na(+)/K(+) ATPase pump inhibitor, which is known to induce GABA release through reverse transport, abolished the sevoflurane and halothane effects on the accumulation of [(3)H]GABA. The effect of sevoflurane and halothane did not involve glial transporters because β-alanine, a blocker of GAT-2 and GAT-3, did not inhibit the effect of the anesthetics

Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and Swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, ...

Preference of red mite Tetranychus ludeni Zacher (Acari: Tetranychidae) to sweet potato genotypes.

PubMed

Castro, B M C; Soares, M A; Andrade Júnior, V C; Santos Júnior, V C; Fontes, P C R; Wilcken, C F; Serrão, J E; Zanuncio, J C

2018-06-21

Tetranychus ludeni damages the sweet potato. Pest development can vary between plant genotypes. The objective was to identify the preference of Tetranychus ludeni for Ipomoea batatas genotypes, from the germplasm bank at the Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM). Natural infestations of this mite were observed on 54 sweet potato genotypes in potted, in a greenhouse. Three mite-infested leafs of each genotype were collected and analyzed. The red mite showed different population density rate in genotypes. The BD 29 genotype was found to be highly susceptible, the BD 08, BD 57, BD 17 and Espanhola genotypes were moderately susceptible, and the others forty-nine genotypes showed low susceptibility to the mite.

MMP-8 genotypes influence the inflammatory response in human endotoxemia.

PubMed

Rella, Judith M; Jilma, Bernd; Fabry, Astrid; Kaynar, A Murat; Mayr, Florian B

2014-04-01

Clinical studies have reported associations between MMP-8 genotypes and clinical outcomes without exploring underlying mechanisms. This study aims to understand the influence of the rs1940475 SNP on downstream chemokine and cytokine response in human endotoxemia. Rs1940475 was genotyped in 44 healthy Caucasian males, who were challenged with an intravenous bolus of 2 ng/kg lipopolysaccharide (LPS). Plasma levels of tumor necrosis factor (TNF), interleukin (IL)-6, IL-8, and macrophage inflammatory protein (MIP)-1α were measured at baseline and 2, 4, 6, and 24 h after LPS infusion with high-sensitivity enzyme immunoassays. Peak TNF levels at 2 h after LPS infusion were significantly higher in subjects with AA genotype compared to subjects with AG or GG genotypes (185 pg/mL [IQR, 154-234] vs. 94 pg/mL [IQR, 65-125] vs. 107 pg/mL [IQR, 80-241], respectively; p = 0.03 between groups). Peak IL-6 levels were trend-wise higher in subjects with AA genotype compared to those with AG or GG genotypes (566 pg/mL [IQR, 294-644] vs. 278 pg/mL [IQR, 184-539] and 329 pg/mL [IQR, 240-492], respectively; p = 0.15 between groups). In contrast, peak MIP-1α at 2 h was highest in GG genotype carriers compared to those with AG or AA genotypes (602 pg/mL [IQR, 449-727] vs. 389 pg/mL [IQR, 375-490] and 510 pg/mL [425-813], respectively; p < 0.03 between groups). AA genotype carriers had highest peak TNF and IL-6 levels after LPS challenge, whereas peak MIP-1α levels were highest in GG carriers. This indicates that the rs1940475 SNP modifies the host response to inflammatory stimuli, which may in part explain previously shown associations with clinical outcomes.

Host specificity of Enterocytozoon bieneusi genotypes in Bactrian camels (Camelus bactrianus) in China.

PubMed

Qi, Meng; Li, Junqiang; Zhao, Aiyun; Cui, Zhaohui; Wei, Zilin; Jing, Bo; Zhang, Longxian

2018-04-02

Enterocytozoon bieneusi is an obligate, intracellular fungus and is commonly reported in humans and animals. To date, there have been no reports of E. bieneusi infections in Bactrian camels (Camelus bactrianus). The present study was conducted to understand the occurrence and molecular characteristics of E. bieneusi in Bactrian camels in China. Of 407 individual Bactrian camel fecal specimens, 30.0% (122) were E. bieneusi-positive by nested polymerase chain reaction (PCR) based on internal transcriber spacer (ITS) sequence analysis. A total of 14 distinct E. bieneusi ITS genotypes were obtained: eight known genotypes (genotype EbpC, EbpA, Henan-IV, BEB6, CM8, CHG16, O and WL17), and six novel genotypes (named CAM1 to CAM6). Genotype CAM1 (59.0%, 72/122) was the most predominant genotype in Bactrian camels in Xinjiang, and genotype EbpC (18.9%, 23/122) was the second-most predominant genotype. Phylogenetic analysis revealed that six known genotypes (EbpC, EbpA, WL17, Henan-IV, CM8 and O) and three novel genotypes (CAM3, CAM5 and CAM6) fell into the human-pathogenic group 1. Two known genotypes (CHG16 and BEB6) fell into the cattle host-specific group 2. The novel genotypes CAM1, CAM 2 and CAM4 cluster into group 8. To our knowledge, this is the first report of E. bieneusi in Bactrian camels. The host-specific genotype CAM1 was the predominant genotype, which plays a negligible role in the zoonotic transmission of E. bieneusi. However, the second-most predominant genotype, EbpC, has greater zoonotic potential.

Prototheca zopfii genotypes isolated from cow barns and bovine mastitis in Japan.

PubMed

Osumi, Takafumi; Kishimoto, Yuji; Kano, Rui; Maruyama, Haruhiko; Onozaki, Masanobu; Makimura, Koichi; Ito, Takaaki; Matsubara, Kiyoshi; Hasegawa, Atsuhiko

2008-10-15

This study is the first investigation on Japanese isolates of Prototheca zopfii from bovine mastitis and the cow-barn surroundings by molecular characterization to clarify routes of infection for bovine protothecal mastitis. We performed isolation of Prototheca from cow-barn surroundings (drinking water, sewage and feces) and milk samples from cases of bovine mastitis. Genotypes of the 32 isolates of P. zopfii from cow-barn surroundings and 67 isolates from mastitis were analyzed by genotype-specific PCR assays and restriction fragment length polymorphism (RFLP) assays. All mastitis isolates were identified as P. zopfii genotype 2. Conversely, 29 isolates from cow-barn surroundings were identified as P. zopfii genotypes 1 and 3 isolates as genotype 2, respectively. Given these results, both genotypes of P. zopfii could exist in cow-barn surroundings, but no sites were identified as frequent sources of P. zopfii genotype 2. P. zopfii isolates should thus be further explored with regard to genotype to clarify the reservoir of etiological agents in bovine Prototheca mastitis.

A Survey of Waste Anesthetic Gas Levels in Selected USAF Veterinary Surgeries.

DTIC Science & Technology

1979-02-01

Gases and Vapors (19) that certain concentration levels should not be exceeded. These levels are: (1) 2 ppm for halothane and methoxyflurane . (2) 25 ppm...Soc. J. 22:330-337. 10. Chenoweth, M. B., Leong, B. K. J., Sparschu, G. L. and Torkelson, T. R. 1972. Toxicities of methoxyflurane , halothane and

Comparison of Abbott RealTime genotype II, GeneMatrix restriction fragment mass polymorphism and Sysmex HISCL HCV Gr assays for hepatitis C virus genotyping.

PubMed

Han, Mi-Soon; Park, Yongjung; Kim, Hyon-Suk

2017-07-26

Hepatitis C virus (HCV) genotype is a predictive marker for treatment response. We sequentially evaluated the performances of two nucleic acid amplification tests (NAATs) and one serology assay for HCV genotype: Abbott RealTime genotype II (RealTime II), GeneMatrix restriction fragment mass polymorphism (RFMP), and Sysmex HISCL HCV Gr (HISCL Gr). We examined 281 clinical samples with three assays. The accuracy was assessed using the HCV Genotype Performance Panel PHW204 (SeraCare Life Sciences) for two NAATs. Discrepant cases were re-genotyped by the Versant HCV v.2.0 (line probe 2.0) assay. With the RealTime II assay, clinic samples were analyzed as follows: genotypes 1b (43.1%), 2 (40.2%), 1 subtypes other than 1a and 1b (12.5%), 3 (1.8%), 4 (1.4%), 1a (0.7%), 6 (0.4%), and mixed (1.1%). The RealTime II and RFMP assays showed a type concordance rate of 97.5% (274/281) (κ=0.80) and no significant discordance (p=0.25). Both assays accurately genotyped all samples in the Performance Panel by the subtype level. The HISCL Gr assay showed concordance rates of about 91% (κ<0.40) and statistically significant discordances with two NAATs (p<0.05). In confirmation tests, the results of RFMP assay were the most consistent with those of Versant 2.0 assay. The three HCV assays provided genotyping and serotyping results with good concordance rates. The two NAATs (RealTime II and RFMP) showed comparable performance and good agreement. However, the results of the HISCL Gr assay showed statistically significant differences with those of the NAATs.

Distribution of hepatitis C virus genotypes in a diverse US integrated health care population.

PubMed

Manos, M Michele; Shvachko, Valentina A; Murphy, Rosemary C; Arduino, Jean Marie; Shire, Norah J

2012-11-01

Hepatitis C virus (HCV) genotypes influence response to therapy, and recently approved direct-acting antivirals are genotype-specific. Genotype distribution information can help to guide antiviral development and elucidate infection patterns. HCV genotype distributions were studied in a diverse cross-section of patients in the Northern California Kaiser Permanente health plan. Associations between genotype and race/ethnicity, age, and sex were assessed with multivariate logistic regression models. The 10,256 patients studied were median age 56 years, 62% male, 55% White non-Hispanic. Overall, 70% were genotype 1, 16% genotype 2, 12% genotype 3, 1% genotype 4, <1% genotype 5, and 1% genotype 6. Blacks (OR 4.5 [3.8-5.5]) and Asians (OR 1.2 [1.0-1.4]) were more likely to have genotype 1 than 2/3 versus non-Hispanic Whites. Women less likely had genotype 1 versus 2/3 than did men (OR 0.86 [0.78-0.94]). Versus non-Hispanic Whites, Asians (OR 0.38 [0.31-0.46]) and Blacks (OR 0.73 [0.63-0.84]) were less likely genotype1a than 1b; Hispanics (OR 1.3 [1.1-1.5]) and Native Americans (OR 1.9 [1.2-2.8]) more likely had genotype 1a than 1b. Patients age ≥65 years less likely had genotype 1a than 1b versus those age 45-64 (OR 0.34 [0.29-0.41]). The predominance of genotype 1 among all groups studied reinforces the need for new therapies targeting this genotype. Racial/ethnic variations in HCV genotype and subtype distribution must be considered in formulating new agents and novel strategies to successfully treat the diversity of hepatitis C patients. Copyright © 2012 Wiley Periodicals, Inc.

Tag-mediated cooperation with non-deterministic genotype-phenotype mapping

NASA Astrophysics Data System (ADS)

Zhang, Hong; Chen, Shu

2016-01-01

Tag-mediated cooperation provides a helpful framework for resolving evolutionary social dilemmas. However, most of the previous studies have not taken into account genotype-phenotype distinction in tags, which may play an important role in the process of evolution. To take this into consideration, we introduce non-deterministic genotype-phenotype mapping into a tag-based model with spatial prisoner's dilemma. By our definition, the similarity between genotypic tags does not directly imply the similarity between phenotypic tags. We find that the non-deterministic mapping from genotypic tag to phenotypic tag has non-trivial effects on tag-mediated cooperation. Although we observe that high levels of cooperation can be established under a wide variety of conditions especially when the decisiveness is moderate, the uncertainty in the determination of phenotypic tags may have a detrimental effect on the tag mechanism by disturbing the homophilic interaction structure which can explain the promotion of cooperation in tag systems. Furthermore, the non-deterministic mapping may undermine the robustness of the tag mechanism with respect to various factors such as the structure of the tag space and the tag flexibility. This observation warns us about the danger of applying the classical tag-based models to the analysis of empirical phenomena if genotype-phenotype distinction is significant in real world. Non-deterministic genotype-phenotype mapping thus provides a new perspective to the understanding of tag-mediated cooperation.

Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test.

PubMed

Mokhtari, Camelia; Ebel, Anne; Reinhardt, Birgit; Merlin, Sandra; Proust, Stéphanie; Roque-Afonso, Anne-Marie

2016-02-01

Hepatitis C virus (HCV) genotyping continues to be relevant for therapeutic strategies. Some samples are reported as genotype 1 (gt 1) without subtype by the Abbott RealTime HCV Genotype II (GT II) test. To characterize such samples further, the Abbott HCV Genotype Plus RUO (Plus) assay, which targets the core region for gt 1a, gt 1b, and gt 6 detection, was evaluated as a reflex test in reference to NS5B or 5'-untranslated region (UTR)/core region sequencing. Of 3,626 routine samples, results of gt 1 without subtype were received for 171 samples (4.7%), accounting for 11.5% of gt 1 specimens. The Plus assay and sequencing were applied to 98 of those samples. NS5B or 5'-UTR/core region sequencing was successful for 91/98 specimens (92.9%). Plus assay and sequencing results were concordant for 87.9% of specimens (80/91 samples). Sequencing confirmed Plus assay results for 82.6%, 85.7%, 100%, and 89.3% of gt 1a, gt 1b, gt 6, and non-gt 1a/1b/6 results, respectively. Notably, 12 gt 6 samples that had been identified previously as gt 1 without subtype were assigned correctly here; for 25/28 samples reported as "not detected" by the Plus assay, sequencing identified the samples as gt 1 with subtypes other than 1a/1b. The genetic variability of HCV continues to present challenges for the current genotyping platforms regardless of the applied methodology. Samples identified by the GT II assay as gt 1 without subtype can be further resolved and reliably characterized by the new Plus assay. Copyright © 2016 Mokhtari et al.

Molecular epidemiology of mumps virus in Japan and proposal of two new genotypes.

PubMed

Inou, Yoko; Nakayama, Tetsuo; Yoshida, Naoko; Uejima, Hajime; Yuri, Kenji; Kamada, Makoto; Kumagai, Takuji; Sakiyama, Hiroshi; Miyata, Akiko; Ochiai, Hitoshi; Ihara, Toshiaki; Okafuji, Teruo; Okafuji, Takao; Nagai, Takao; Suzuki, Eitaro; Shimomura, Kunihisa; Ito, Yuhei; Miyazaki, Chiaki

2004-05-01

We isolated 872 strains of mumps virus from naso-pharyngeal secretions in seven different districts of Japan from January 2000 to July 2001. Among them, 57 strains were geno-typed by nucleotide sequencing in part of the hemagglutinin-neuraminidase (HN) and small hydrophobic (SH) protein regions. Four different genotypes (B, G, K, and L) of mumps virus were co-circulating in Japan and the distribution of genotypes varied in geographically different districts. Two new clusters designated as genotypes K and L had more than 7% nucleotide variation in the SH gene. Among the 57 strains, 11 were classified as B, 35 as G, three as K, and eight as L, which was mainly isolated in Tokyo. We also examined 104 stains isolated in a clinic in Mie prefecture from 1993 to 2003. Genotype B was the indigenous strain and genotype K was introduced in 1994. Genotypes B and K co-circulated in the 1990s and were replaced by genotype G in 2000. There was no significant change in neutralizing test antibody titers against genotypes B, G, K, and L using seven post-vaccination sera with Hoshino strain (genotype B) and these four genotypes had a different antigenicity from genotype A. We should continue to watch on mumps virus molecular epidemiology. Copyright 2004 Wiley-Liss, Inc.

Genotypic distribution of hepatitis C virus in voluntary blood donors of northern Thailand.

PubMed

Jutavijittum, Prapan; Jiviriyawat, Yupa; Yousukh, Amnat; Pantip, Chansom; Maneekarn, Niwat; Toriyama, Kan

2009-05-01

The purpose of this study was to determine the prevalence and distribution of HCV genotypes among voluntary blood donors in northern Thailand. From 1998 to 2000, 167 serum samples which tested positive for anti-HCV antibodies in the screening of voluntary blood donors from 5 provinces in northern Thailand were selected for genotyping. Viral RNA was extracted from the sera. The core-E1 region of the HCV-RNA genome was amplified using a OneStep RT-PCR kit. The core-E1 amplicon was sequenced and the HCV genotype was assigned by comparing with the reference sequences available in the GenBank database. Of 167 anti-HCV positive serum samples, 126 (75.4%) contained HCV RNA as detected by PCR. HCV genotype 3 was the most predominant genotype (39.6%), of which 33.3% belonged to genotype 3a and 6.3% to 3b. Genotype 6 was detected in 31%, and genotype 1 was detected in 27.8%. Of the genotype 1 isolates, 14.3% were la, 12.7% were 1b, and 0.8% were 1c. Two HCV isolates detected in the present study were untypeable. About 75% of anti-HCV positive blood donors had chronic HCV infection. In northern Thailand, genotype 3a was the most predominant genotype, while genotype 6, 1a and 1b were also commonly found. The genotypic distribution of HCV isolates from various regions of Thailand were more or less similar. Nevertheless, in this study, the prevalence of HCV genotype 6 (31%) was higher than previously reported by others (8-18%). Phylogenetic analysis of the HCV isolates detected in the present study was also performed.

Sugarcane Genotype Selection for Sand Soils in Florida

USDA-ARS?s Scientific Manuscript database

Selection of high yielding sugarcane (Saccharum spp.) genotypes for organic (muck) soils in Florida has been more successful than for sand soils. The purpose of this study was to compare the performance of 31 sugarcane genotypes on sand soils with and without mill mud added at the rate of 1510 cubic...

Clusters of incompatible genotypes evolve with limited dispersal

Treesearch

Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

2015-01-01

Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

Identification of polymorphic inversions from genotypes

PubMed Central

2012-01-01

Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data [1], utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS). Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model [2]. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU) and Yoruba (YRI) HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions previously predicted by

Interrelationship of hepatitis C virus genotypes with patient characteristics in Bahrain

PubMed Central

Abdulla, Maheeba A; Murad, Eman A; Aljenaidi, Hend A; Aljowder, Duha R; Aljeeran, Omar IK; Farid, Eman; Al Qamish, Jehad R

2017-01-01

Aim Hepatitis C virus (HCV) shows genotype-based variation in prevalence across geographical regions. This study was conducted to understand the clinical interrelationship of HCV genotypes with patient characteristics. Methods Medical records of 122 patients positive for HCV RNA test collected during 2013 and 2014 were included for analysis. Only adults were included in the study. HCV RNA extraction and genotyping was done as part of the routine diagnostic requirements. The association of continuous and categorical variables with genotypes was analyzed through analysis of variance and chi-square tests, respectively. Results Of the 122 patients selected, 103 were Bahrainis, 18 non-Bahrainis, and 1 was unregistered. Genotype 1 was the predominant (53%) one, followed by types 3 (23%) and 4 (20%). Classical symptoms, clinical signs, liver function test, and ultrasonographic results were recorded. Cirrhosis and ascites showed significant variation across genotypes. Although alanine transaminase, total bilirubin, and albumin levels were increased, gamma-glutamyltransferase and alkaline phosphatase levels were normal. About 12% of the subjects were alcohol users, 4% were positive for HIV infection and 2.4% were positive for hepatitis B virus infection. The circulating HCV RNA load was at medium-level in the study cohort and showed significant association with the HCV genotypes and subtypes. Patients with genotype 1a had 6 times more load than patients with type 4 (P<0.05). Conclusion This study reconfirmed the incidence and distribution of different genotypes in Bahrain population, and delineated the relationship of HCV RNA viral load with the severity of liver disease in our cohort. PMID:28280398

Genotype analysis, using PCR with type-specific primers, of hepatitis B virus isolates from patients coinfected with hepatitis delta virus genotype II from Miyako Island, Japan.

PubMed

Moriyama, Moriyama; Taira, Masaaki; Matsumura, Hiroshi; Aoki, Hiroshi; Mikuni, Morio; Kaneko, Miki; Shioda, Atsuo; Iwaguchi, Kayo; Arai, Shinobu; Ichijima, Sagiri; Iwasaki, Hiroko; Tanaka, Naohide; Abe, Kenji; Arakawa, Yasuyuki

2003-01-01

The aims of this study were to determine the hepatitis B virus (HBV) genotypes in hepatitis delta virus (HDV) RNA-positive patients and to characterize the HBV nucleotide sequences that may be found on a distant island of Japan. This study included three patients with chronic hepatitis who were positive for hepatitis B surface antigen (enzyme-linked immunosorbent assay; ELISA), HDV antibody (ELISA) and HDV RNA by polymerase chain reaction (PCR). The HBV genotype was determined by nested PCR using type-specific primers. The first-round PCR products from two patients were sequenced, followed by an investigation of nucleotide homology. Viruses from all three patients in this study were classified as HBV genotype B. Comparison with HBV isolates from geographically neighboring regions revealed that the two HBV isolates had 97.9-98.6% identity at the nucleotide level to a Chinese isolate, 98.3-98.6% identity to the Okinawa isolate and 98.6-98.8% identity to a Japanese isolate of genotype B. On phylogenetic analysis, the HBV isolates from the two patients were classified as HBV genotype B. The HBV isolates of cases 1 and 3 clustered in the same group as isolates from the Chinese mainland and Japanese mainland, which are geographically near Miyako Island. The HBV isolates coinfected with HDV found on Miyako Island were of genotype B. The PCR method based on genotype-specific primers was useful in determining HBV genotypes. Copyright 2003 S. Karger AG, Basel

Tannerella forsythensis prtH genotype and association with periodontal status.

PubMed

Hamlet, Stephen M; Taiyeb-Ali, Tara B; Cullinan, Mary P; Westerman, Bill; Palmer, Janet E; Seymour, Gregory J

2007-02-01

The prtH gene of Tannerella forsythensis encodes for a cysteine protease possessing virulent properties. Subgingival colonization by T. forsythensis with this genotype has been suggested to be a discriminator between periodontal health and disease. This study examined the prevalence of T. forsythensis prtH genotype in subgingival plaque and its association with periodontal disease progression and current disease status. Subjects harboring T. forsythensis in their subgingival plaque were identified using real-time polymerase chain reaction (PCR). The presence or absence of the prtH genotype was assessed by conventional PCR. Probing depths and relative attachment levels were also assessed. The prtH genotype was detected in 13 of 56 (23.2%) subjects harboring T. forsythensis in their subgingival plaque. Periodontal disease progression was defined as two or more sites with > or = 2 mm attachment loss in the previous 2-year period; current disease was defined as four or more sites with probing depths > or = 4 mm. The odds of periodontal disease (progression and/or current disease) were 1.55 times greater in subjects harboring prtH genotype T. forsythensis than in subjects in whom prtH was not detected. The prtH genotype was associated with higher numbers of T. forsythensis. In subjects with high levels of T. forsythensis, prtH genotype was associated with an increased extent of periodontal disease 2 years subsequently. These results show that T. forsythensis prtH genotype is associated with high levels of T. forsythensis. However, further work is needed to determine whether it also is a useful marker of periodontal disease progression in T. forsythensis-infected subjects.

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata.

PubMed

Gallart, Marta; Adair, Karen L; Love, Jonathan; Meason, Dean F; Clinton, Peter W; Xue, Jianming; Turnbull, Matthew H

2018-02-01

A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities.

Zoonotic potential of Enterocytozoon genotypes in humans and pigs in Thailand.

PubMed

Prasertbun, Rapeepun; Mori, Hirotake; Pintong, Ai-Rada; Sanyanusin, Suparut; Popruk, Supaluk; Komalamisra, Chalit; Changbunjong, Tanasak; Buddhirongawatr, Ruangrat; Sukthana, Yaowalark; Mahittikorn, Aongart

2017-01-15

Enterocytozoon bieneusi is an opportunistic intestinal pathogen infecting humans and a variety of animals. Its mode of transmission and zoonotic potential are not completely understood. E. bieneusi has been frequently identified in pigs. The objective of our study was to investigate E. bieneusi in pigs and humans in Western and Central Thailand to determine its presence, genetic diversity, and zoonotic potential. A total of 277 human and 210 pig faecal samples were collected and analysed. E. bieneusi was found in 5.4% and 28.1% of human and pig samples, respectively, by nested PCR. Genotyping based on the internal transcribed spacer regions of the small subunit ribosomal RNA demonstrated three known genotypes (D, H, PigEb10) and eight novel genotypes (TMH1-8) in humans, and five known genotypes (D, EbpA, EbpC, H, O) and 11 novel genotypes (TMP1-11) in pigs. All known genotypes identified in humans and pigs had zoonotic potential. Further studies are needed to evaluate zoonotic risk of novel genotypes, as pigs may play an important role in the transmission of E. bieneusi. Copyright © 2016 Elsevier B.V. All rights reserved.

Horticultural Performance of Eight American Elderberry Genotypes at Three Missouri Locations.

PubMed

Thomas, A L; Byers, P L; Avery, J D; Kaps, M; Gu, S

2015-01-12

American elderberry ( Sambucus nigra subsp. canadensis ) is being increasingly cultivated in North America for its edible and medicinal fruit and flowers, yet remains largely undeveloped as a horticultural crop. Productive genotypes with desirable horticultural attributes, including disease and insect resistance, precocity, uniform fruit ripening, and large berry size are needed in order to advance the commercial production of elderberries. A four-year study of eight elderberry genotypes was established in 2008 at three diverse Missouri (USA) locations. Phenology, plant morphology, pest susceptibility, productivity, and fruit characteristics data were collected over three growing seasons, 2009-2011. Significant differences for most phenological, horticultural, and fruit juice characteristics were observed among the three sites, three years, and eight genotypes. The genotype 'Ozark' was the earliest to break bud, produced fruit with high levels of soluble solids, and out-yielded most other genotypes at the three sites over the three-year study. None of the new genotypes produced berries as large as or larger than the standard 'York' which is known for its large fruit. Some of the genotypes tested, especially 'Ozark' show promise as potential cultivars and as breeding stock for further development of elderberry as a commercially-viable horticultural crop.

Hepatitis C virus genotypes in 1,504 patients in Slovenia, 1993-2007.

PubMed

Seme, Katja; Vrhovac, Maja; Mocilnik, Tina; Maticic, Mojca; Lesnicar, Gorazd; Baklan, Zvonko; Volkar, Jelka Meglic; Rajter, Mojca; Stepec, Srecko; Lunar, Maja; Poljak, Mario

2009-04-01

In order to identify the main routes of hepatitis C (HCV) transmission and to determine the HCV genotype distribution and its dynamics during a 15-year period in Slovenia, HCV genotypes were detected using the INNO-LiPA HCV II (Innogenetics) test for serum samples obtained from 1,504 patients representing 72.6% of all patients with chronic hepatitis C diagnosed from 1993 to 2007. HCV genotype 1 was predominant (56%), followed by genotypes 3, 2, and 4, with a prevalence of 37.8%, 5%, and 1.2%, respectively. HCV genotypes 5 and 6 were not detected in any patient. Patients infected with HCV genotype 3 were significantly younger (mean age 28.9 +/- 8.5 years) than those infected with genotype 1 (mean age 38.9 +/- 14.8 years; P < 0.0001) and those infected with HCV genotype 2 (mean age 50.3 +/- 18.2 years; P < 0.0001). Intravenous drug use was identified as the most frequent possible HCV transmission route (34.3%), followed by medical-related transmission such as transfusion of HCV-contaminated blood or blood products, and hemodialysis (12.5%). Being an intravenous drug user was found to be strongly associated with HCV genotype 3 (OR, 3.71 [95% CI, 2.97-4.65]; P < 0.0001) and reporting infection by transfusion of blood or blood products was found to be strongly associated with HCV genotype 1 (OR, 3.28 [95% CI, 2.18-4.95]; P < 0.0001). During the 15-year period, the proportion of genotype 3 increased substantially, reflecting the fact that the HCV epidemic in Slovenia is driven mostly by intravenous drug use. (c) 2009 Wiley-Liss, Inc.

Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations.

PubMed

McLeod, K A; Scascitelli, M; Vellend, M

2012-08-01

Studies of genotype × environment interactions (G × E) and local adaptation provide critical tests of natural selection's ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here, we tested for G × E in asexual dandelions (Taraxacum officinale) by subjecting six genotypes to experimental drought, mown and benign (control) conditions and subsequently using microsatellites to assess genotype-environment associations in the field. We found strong G × E, with genotypes that performed poorly under benign conditions showing the highest performance under stressful conditions (drought or mown). Our six focal genotypes comprise > 80% of plants in local populations. The most common genotype in the field showed its highest relative performance under mown conditions (the most common habitat in our study area), and almost all plants of this genotype in the field were found growing in mowed lawns. Genotypes performing best under benign experimental conditions were found most frequently in unmown conditions in the field. These results are strongly indicative of local adaptation at a very small scale, with unmown microsites of only a few square metres typically embedded within larger mown lawns. By studying an asexual species, we were able to map genotypes with known ecological characteristics to environments with high spatial precision. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Measles virus genotypes circulating in India, 2011-2015.

PubMed

Vaidya, Sunil R; Chowdhury, Deepika T

2017-05-01

The Government of India is accepted to participate in the measles elimination and rubella control goal 2020, hence genetic characterization of measles viruses (MeV) becomes essential. At National Reference Laboratory (National Institute of Virology, Pune), the throat swabs/urine specimens (n = 380) or PCR products (n = 219) obtained from the suspected measles cases were referred for the molecular testing and subsequently, MeV nucleoprotein (N) gene sequencing/genotyping. In addition, 2,449 suspected measles cases, mainly from the Maharashtra state were referred for the laboratory diagnosis. A detailed study was performed on N gene sequences obtained during last two decades. Indian MeV sequences obtained during 2011-2015 were compared with 1996-2010 sequences and genetic divergence was studied. Circulation of measles genotypes B3 (n = 3), D4 (n = 49), and D8 (n = 351) strains were observed in 19 States and three Union Territories of India. In addition, 64 measles viruses were isolated from 253 throat swab or urine specimens obtained from the suspected measles cases. During 2011-2015, 67.9% (1,663/2,449) suspected measles cases were laboratory confirmed. Molecular studies showed circulation of measles genotype B3 in India along with prominently circulating genotypes D4 and D8 except D7 strains. The genetic diversion within Indian B3, D4, and D8 genotypes was 0.3%, 1.1%, and 2.1%, respectively. The genetic divergence of Indian B3, D4, and D8 measles strains with the WHO reference sequences was 2.5%, 2.6%, and 1.8%, respectively. It is crucial data for national immunization program. More measles/rubella genotyping studies are necessary to track transmission and to support measles elimination and rubella control. J. Med. Virol. 89:753-758, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Identifying traits for genotypic adaptation using crop models.

PubMed

Ramirez-Villegas, Julian; Watson, James; Challinor, Andrew J

2015-06-01

Genotypic adaptation involves the incorporation of novel traits in crop varieties so as to enhance food productivity and stability and is expected to be one of the most important adaptation strategies to future climate change. Simulation modelling can provide the basis for evaluating the biophysical potential of crop traits for genotypic adaptation. This review focuses on the use of models for assessing the potential benefits of genotypic adaptation as a response strategy to projected climate change impacts. Some key crop responses to the environment, as well as the role of models and model ensembles for assessing impacts and adaptation, are first reviewed. Next, the review describes crop-climate models can help focus the development of future-adapted crop germplasm in breeding programmes. While recently published modelling studies have demonstrated the potential of genotypic adaptation strategies and ideotype design, it is argued that, for model-based studies of genotypic adaptation to be used in crop breeding, it is critical that modelled traits are better grounded in genetic and physiological knowledge. To this aim, two main goals need to be pursued in future studies: (i) a better understanding of plant processes that limit productivity under future climate change; and (ii) a coupling between genetic and crop growth models-perhaps at the expense of the number of traits analysed. Importantly, the latter may imply additional complexity (and likely uncertainty) in crop modelling studies. Hence, appropriately constraining processes and parameters in models and a shift from simply quantifying uncertainty to actually quantifying robustness towards modelling choices are two key aspects that need to be included into future crop model-based analyses of genotypic adaptation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Precision medicine: does ethnicity information complement genotype-based prescribing decisions?

PubMed Central

Shah, Rashmi R.; Gaedigk, Andrea

2017-01-01

Inter-ethnic differences in drug response are all too well known. These are underpinned by a number of factors, including pharmacogenetic differences across various ethnic populations. Precision medicine relies on genotype-based prescribing decisions with the aim of maximizing efficacy and mitigating the risks. When there is no access to genotyping tests, ethnicity is frequently regarded as a proxy of the patient’s probable genotype on the basis of overall population-based frequency of genetic variations in the ethnic group the patient belongs to, with some variations being ethnicity-specific. However, ever-increasing transcontinental migration of populations and the resulting admixing of populations have undermined the utility of self-identified ethnicity in predicting the genetic ancestry, and therefore the genotype, of the patient. An example of the relevance of genetic ancestry of a patient is the inadequate performance of European-derived pharmacogenetic dosing algorithms of warfarin in African Americans, Brazilians and Caribbean Hispanics. Consequently, genotyping a patient potentially requires testing for all known clinically actionable variants that the patient may harbour, and new variants that are likely to be identified using state-of the art next-generation sequencing-based methods. Furthermore, self-identified ethnicity is associated with a number of ethnicity-related attributes and non-genetic factors that potentially influence the risk of phenoconversion (genotype–phenotype discordance), which may adversely impact the success of genotype-based prescribing decisions. Therefore, while genotype-based prescribing decisions are important in implementing precision medicine, ethnicity should not be disregarded. PMID:29318005

Prevalence of HCV genotypes in Poland - the EpiTer study.

PubMed

Flisiak, Robert; Pogorzelska, Joanna; Berak, Hanna; Horban, Andrzej; Orłowska, Iwona; Simon, Krzysztof; Tuchendler, Ewelina; Madej, Grzegorz; Piekarska, Anna; Jabłkowski, Maciej; Deroń, Zbigniew; Mazur, Włodzimierz; Kaczmarczyk, Marcin; Janczewska, Ewa; Pisula, Arkadiusz; Smykał, Jacek; Nowak, Krzysztof; Matukiewicz, Marek; Halota, Waldemar; Wernik, Joanna; Sikorska, Katarzyna; Mozer-Lisewska, Iwona; Rozpłochowski, Błażej; Garlicki, Aleksander; Tomasiewicz, Krzysztof; Krzowska-Firych, Joanna; Baka-Ćwierz, Barbara; Kryczka, Wiesław; Zarębska-Michaluk, Dorota; Olszok, Iwona; Boroń-Kaczmarska, Anna; Sobala-Szczygieł, Barbara; Szlauer, Bronisława; Korcz-Ondrzejek, Bogumiła; Sieklucki, Jerzy; Pleśniak, Robert; Ruszała, Agata; Postawa-Kłosińska, Barbara; Citko, Jolanta; Lachowicz-Wawrzyniak, Anna; Musialik, Joanna; Jezierska, Edyta; Dobracki, Witold; Dobracka, Beata; Hałubiec, Jan; Krygier, Rafał; Strokowska, Anna; Chomczyk, Wojciech; Witczak-Malinowska, Krystyna

2016-12-01

Was to assess current prevalence of hepatitis C virus (HCV) genotypes in Poland, including their geographic distribution and changes in a given period of time. Data were collected with questionnaires from 29 Polish centers and included data of patients diagnosed with HCV infection between 1 January 2013 and 31 March 2016. In total, data of 9800 patients were reported. The highest prevalence was estimated for genotype 1b (81.7%), followed by 3 (11.3%), 4 (3.5%), 1a (3.2%) and 2 (0.2%). Genotype 5 or 6 was reported in 6 patients only (0.1%). The highest prevalence of genotype 1 was observed in central (łódzkie, mazowieckie, świętokrzyskie), eastern (lubelskie) and southern (małopolskie, śląskie) Poland. The highest rate for genotype 3 was observed in south-western (dolnośląskie, lubuskie) and eastern (podlaskie, warmińsko-mazurskie and podkarpackie) Poland. Compared to historical data, we observed an increasing tendency of G1 prevalence from 72.0% in 2003 to 87.5% in 2016, which was accompanied by a decrease of G3 (17.9% vs. 9.1%) and G4 (9.0% vs. 3.1%). Almost 85% of patients with HCV in Poland are infected with genotype 1 (almost exclusively subgenotype 1b), and its prevalence shows an increasing tendency, accompanied by a decrease of genotypes 3 and 4.

[National Database of Genotypes--ethical and legal issues].

PubMed

Franková, Vera; Tesínová, Jolana; Brdicka, Radim

2011-01-01

National Database of Genotypes--ethical and legal issues The aim of the project National Database of Genotypes is to outline structure and rules for the database operation collecting information about genotypes of individual persons. The database should be used entirely for health care. Its purpose is to enable physicians to gain quick and easy access to the information about persons requiring specialized care due to their genetic constitution. In the future, another introduction of new genetic tests into the clinical practice can be expected thus the database of genotypes facilitates substantial financial savings by exclusion of duplicates of the expensive genetic testing. Ethical questions connected with the creating and functioning of such database concern mainly privacy protection, confidentiality of personal sensitive data, protection of database from misuse, consent with participation and public interests. Due to necessity of correct interpretation by qualified professional (= clinical geneticist), particular categorization of genetic data within the database is discussed. The function of proposed database has to be governed in concordance with the Czech legislation together with solving ethical problems.

Effects of a prostagrandin EP4-receptor agonist ONO-AE1-329 on the left ventricular pressure-volume relationship in the halothane-anesthetized dogs.

PubMed

Honda, Atsushi; Nakamura, Yuji; Ohara, Hiroshi; Cao, Xin; Nomura, Hiroaki; Katagi, Jun; Wada, Takeshi; Izumi-Nakaseko, Hiroko; Ando, Kentaro; Sugiyama, Atsushi

2016-03-15

Cardiac effects of a prostagrandin EP4-receptor agonist ONO-AE1-329 were assessed in the halothane-anesthetized dogs under the monitoring of left ventricular pressure-volume relationship, which were compared with those of clinically recommended doses of dopamine, dobutamine and milrinone (n=4-5 for each treatment). ONO-AE1-329 was intravenously administered in doses of 0.3, 1 and 3 ng/kg/min for 10 min with a pause of 20 min. Dopamine in a dose of 3 µg/kg/min for 10 min, dobutamine in a dose of 1 µg/kg/min for 10 min and milrinone in a dose of 5 µg/kg/min for 10 min followed by 0.5 µg/kg/min for 10 min were intravenously administered. Low dose of ONO-AE1-329 increased the stroke volume. Middle dose of ONO-AE1-329 increased the cardiac output, left ventricular end-diastolic volume, ejection fraction, maximum upstroke/downstroke velocities of the left ventricular pressure and external work, but decreased the end-systolic pressure and internal work besides the change by the low dose. High dose of ONO-AE1-329 increased the heart rate and maximum elastance, but decreased the end-systolic volume besides the changes by the middle dose. Dopamine, dobutamine and milrinone exerted essentially similar cardiac effects to ONO-AE1-329, but they did not significantly change the end-diastolic volume, end-systolic volume, stroke volume, ejection fraction, end-systolic pressure, maximum elastance, external work or internal work. Thus, EP4-receptor stimulation by ONO-AE1-329 may have potential to better promote the passive ventricular filling than the conventional cardiotonic drugs, which could become a candidate of novel therapeutic strategy for the treatment of heart failure with preserved ejection fraction. Copyright © 2016 Elsevier B.V. All rights reserved.

Warfarin genotyping in a single PCR reaction for microchip electrophoresis.

PubMed

Poe, Brian L; Haverstick, Doris M; Landers, James P

2012-04-01

Warfarin is the most commonly prescribed oral anticoagulant medication but also is the second leading cause of emergency room visits for adverse drug reactions. Genetic testing for warfarin sensitivity may reduce hospitalization rates, but prospective genotyping is impeded in part by the turnaround time and costs of genotyping. Microfluidics-based assays can reduce reagent consumption and analysis time; however, no current assay has integrated multiplexed allele-specific PCR for warfarin genotyping with electrophoretic microfluidics hardware. Ideally, such an assay would use a single PCR reaction and, without further processing, a single microchip electrophoresis (ME) run to determine the 3 single-nucleotide polymorphisms (SNPs) affecting warfarin sensitivity [i.e., CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9) *2, CYP2C9 *3, and the VKORC1 (vitamin K epoxide reductase complex 1) A/B haplotype]. We designed and optimized primers for a fully multiplexed assay to examine 3 biallelic SNPs with the tetraprimer amplification refractory mutation system (T-ARMS). The assay was developed with conventional PCR equipment and demonstrated for microfluidic infrared-mediated PCR. Genotypes were determined by ME on the basis of the pattern of PCR products. Thirty-five samples of human genomic DNA were analyzed with this multiplex T-ARMS assay, and 100% of the genotype determinations agreed with the results obtained by other validated methods. The sample population included several genotypes conferring warfarin sensitivity, with both homozygous and heterozygous genotypes for each SNP. Total analysis times for the PCR and ME were approximately 75 min (1-sample run) and 90 min (12-sample run). This multiplexed T-ARMS assay coupled with microfluidics hardware constitutes a promising avenue for an inexpensive and rapid platform for warfarin genotyping.

The genetic diversity of hepatitis A genotype I in Bulgaria

PubMed Central

Cella, Eleonora; Golkocheva-Markova, Elitsa N.; Trandeva-Bankova, Diljana; Gregori, Giulia; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Costantino, Angela; Spoto, Silvia; Curtis, Melissa; Ciccaglione, Anna Rita; Ciccozzi, Massimo; Angeletti, Silvia

2018-01-01

Abstract The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia. PMID:29504993

The genetic diversity of hepatitis A genotype I in Bulgaria.

PubMed

Cella, Eleonora; Golkocheva-Markova, Elitsa N; Trandeva-Bankova, Diljana; Gregori, Giulia; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Costantino, Angela; Spoto, Silvia; Curtis, Melissa; Ciccaglione, Anna Rita; Ciccozzi, Massimo; Angeletti, Silvia

2018-01-01

The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

Mineral Composition of Organically Grown Wheat Genotypes: Contribution to Daily Minerals Intake

PubMed Central

Hussain, Abrar; Larsson, Hans; Kuktaite, Ramune; Johansson, Eva

2010-01-01

In this study, 321 winter and spring wheat genotypes were analysed for twelve nutritionally important minerals (B, Cu, Fe, Se, Mg, Zn, Ca, Mn, Mo, P, S and K). Some of the genotypes used were from multiple locations and years, resulting in a total number of 493 samples. Investigated genotypes were divided into six genotype groups i.e., selections, old landraces, primitive wheat, spelt, old cultivars and cultivars. For some of the investigated minerals higher concentrations were observed in selections, primitive wheat, and old cultivars as compared to more modern wheat material, e.g., cultivars and spelt wheat. Location was found to have a significant effect on mineral concentration for all genotype groups, although for primitive wheat, genotype had a higher impact than location. Spring wheat was observed to have significantly higher values for B, Cu, Fe, Zn, Ca, S and K as compared to winter wheat. Higher levels of several minerals were observed in the present study, as compared to previous studies carried out in inorganic systems, indicating that organic conditions with suitable genotypes may enhance mineral concentration in wheat grain. This study also showed that a very high mineral concentration, close to daily requirements, can be produced by growing specific primitive wheat genotypes in an organic farming system. Thus, by selecting genotypes for further breeding, nutritional value of the wheat flour for human consumption can be improved. PMID:20948934

Evolutionary analysis of rubella viruses in mainland China during 2010-2012: endemic circulation of genotype 1E and introductions of genotype 2B.

PubMed

Zhu, Zhen; Rivailler, Pierre; Abernathy, Emily; Cui, Aili; Zhang, Yan; Mao, Naiyin; Xu, Songtao; Zhou, Shujie; Lei, Yue; Wang, Yan; Zheng, Huanying; He, Jilan; Chen, Ying; Li, Chongshan; Bo, Fang; Zhao, Chunfang; Chen, Meng; Lu, Peishan; Li, Fangcai; Gu, Suyi; Gao, Hui; Guo, Yu; Chen, Hui; Feng, Daxing; Wang, Shuang; Tang, Xiaomin; Lei, Yake; Feng, Yan; Deng, Lili; Gong, Tian; Fan, Lixia; Xu, Wenbo; Icenogle, Joseph

2015-01-23

Rubella remains a significant burden in mainland China. In this report, 667 viruses collected in 24 of 31 provinces of mainland China during 2010-2012 were sequenced and analyzed, significantly extending previous reports on limited numbers of viruses collected before 2010. Only viruses of genotypes 1E and 2B were found. Genotype 1E viruses were found in all 24 provinces. Genotype 1E viruses were likely introduced into mainland China around 1997 and endemic transmission of primarily one lineage became established. Viruses reported here from 2010-2012 are largely in a single cluster within this lineage. Genotype 2B viruses were rarely detected in China prior to 2010. This report documents a previously undetected 2B lineage, which likely became endemic in eastern provinces of China between 2010 and 2012. Bayesian analyses were performed to estimate the evolutionary rates and dates of appearance of the genotype 1E and 2B viral linages in China. A skyline plot of viral population diversity did not provide evidence of reduction of diversity as a result of vaccination, but should be useful as a baseline for such reductions as vaccination programs for rubella become widespread in mainland China.

Axiom turkey genotyping array

USDA-ARS?s Scientific Manuscript database

The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

Hepatitis B among immigrants from Myanmar: Genotypes and their clinical relevance.

PubMed

Schulz, Thomas R; Edwards, Rosalind; Thurnheer, M Christine; Yuen, Lilly; Littlejohn, Margaret; Revill, Peter; Chu, Melissa; Tanyeri, Firuz; Wade, Amanda; Biggs, Beverley-Ann; Sasadeusz, Joseph

2018-02-01

Hepatitis B virus (HBV) from 76 adult immigrants in Australia from Myanmar was characterized to determine the prevalence of different HBV genotypes and subgenotypes. A mutational analysis was then performed to determine the presence of clinically significant mutations and correlate them to clinical outcomes. Initial genotyping revealed 68 patients with genotype C (89.5%) and eight patients with genotype B (10.5%). Phylogenetic analysis revealed the large majority of the genotype C infections were of subgenotype C1 (67/68). Sequencing of the HBV polymerase gene (and overlapping surface gene) revealed no mutations associated with antiviral resistance. HBV surface gene mutations were detected in 10 patients with subgenotype C1. HBV BCP/PC sequencing was obtained for 71/76 (93%) patients. BCP and/or PC mutations were identified in 57/71 (80%) of PCR positive patients. Treatment had been commenced for 15/76 (18%) patients, a further 26 untreated patients were in a stage of disease where HBV treatment would be considered standard of care. It was identified that genotype C1 is the predominant sub-genotype in this population. Genotype C is known to be associated with increased risk of development of HCC. This highlights the need for screening for HCC given the potential for the development of liver cancer. It was also identified that people with HBV were potentially not receiving optimal therapy in a timely fashion. © 2017 Wiley Periodicals, Inc.

Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain.

PubMed

Esteves, F; Montes-Cano, M A; de la Horra, C; Costa, M C; Calderón, E J; Antunes, F; Matos, O

2008-04-01

Pneumonia caused by the opportunistic organism Pneumocystis jirovecii is a clinically important infection affecting AIDS and other immunocompromised patients. The present study aimed to compare and characterise the frequency pattern of DNA sequences from the P. jirovecii mitochondrial large-subunit rRNA (mtLSU rRNA) gene, the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA operon in specimens from Lisbon (Portugal) and Seville (Spain). Total DNA was extracted and used for specific molecular sequence analysis of the three loci. In both populations, mtLSU rRNA gene analysis revealed an overall prevalence of genotype 1. In the Portuguese population, genotype 2 was the second most common, followed by genotype 3. Inversely, in the Spanish population, genotype 3 was the second most common, followed by genotype 2. The DHPS wild-type sequence was the genotype observed most frequently in both populations, and the DHPS genotype frequency pattern was identical to distribution patterns revealed in other European studies. ITS types showed a significant diversity in both populations because of the high sequence variability in these genomic regions. The most prevalent ITS type in the Portuguese population was Eg, followed by Cg. In contrast to other European studies, Bi was the most common ITS type in the Spanish samples, followed by Eg. A statistically significant association between mtLSU rRNA genotype 1 and ITS type Eg was revealed.

Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data

PubMed Central

2016-01-01

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted ‘glmnet’). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the

Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data.

PubMed

Chan, Ariel W; Hamblin, Martha T; Jannink, Jean-Luc

2016-01-01

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted 'glmnet'). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the

Methods for MHC genotyping in non-model vertebrates.

PubMed

Babik, W

2010-03-01

Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems. © 2009 Blackwell Publishing Ltd.

PEPA-1* genotype affects return rate for hatchery steelhead

USGS Publications Warehouse

Reisenbichler, R.R.; Hayes, M.C.; Rubin, S.P.; Wetzel, L.A.; Baker, B.M.

2006-01-01

Allozymes continue to be useful as genetic markers in a variety of studies; however, their utility often hinges on the selective neutrality of the allelic variation. Our study tested for neutrality between the two most common alleles (*100 and *110) at the cytosol nonspecific dipeptidase locus (PEPA-1*) in steelhead Oncorhynchus mykiss from Dworshak National Fish Hatchery in Idaho. We tested for differential growth and survival among fish with the * 100/100, *100/ 110, and *110/110 genotypes rearing in a hatchery or a natural stream. We repeated the study for two year-classes, using heterozygous (*100/110) adults to make the experimental crosses. This design avoided differences in family contribution among genotypes because each cross produced all three genotypes. We divided the progeny from each family into two groups. One group was reared in a hatchery for 1 year and then released for migration to the sea and subsequent return to the hatchery as adults. The other group was released into a natural stream and monitored for 3 years. We found no significant differences in size or survival among PEPA-1* genotypes for either the naturally reared fish or the hatchery-reared fish immediately prior to release as smolts. For females, survival to returning adult also was similar among genotypes; however, hatchery-reared males with the *110/110 genotype returned at a higher rate than did males with the *100/ 100 genotype; heterozygous males were intermediate. These results indicate that selection occurs at the PEPA-1* locus or at one or more loci tightly linked to it. The finding of nearly equal frequencies for these two alleles in the source population suggests that selection differentials among genotypes reverse or vary from year to year; otherwise, steady directional selection would drive the *100 allele to low frequencies or extinction. Locus PEPA-1* seems inappropriate for genetic marks in studies of steelhead that span the full life cycle and probably should be avoided

RT-PCR for detection of all seven genotypes of Lyssavirus genus.

PubMed

Vázquez-Morón, S; Avellón, A; Echevarría, J E

2006-08-01

The Lyssavirus genus includes seven species or genotypes named 1-7. Rabies genotypes correlate with geographical distribution and specific hosts. Co-circulation of different lyssaviruses, imported cases, and the presence of unknown viruses, such as Aravan, Khujand, Irkut and West Caucasian Bat Virus, make it necessary to use generic methods able to detect all lyssaviruses. Primer sequences were chosen from conserved regions in all genotypes in order to optimise a generic RT-PCR. Serial dilutions of 12 RNA extracts from all seven Lyssavirus genotypes were examined to compare the sensitivity of the RT-PCR standardised in this study with a published RT-PCR optimised for EBLV1 detection and capable of amplifying RNA from all seven lyssaviruses. All seven genotypes were detected by both RT-PCRs, however, the sensitivity was higher with the new version of the test. Twenty samples submitted for rabies diagnosis were tested by the new RT-PCR. Eight out of 20 samples from six dogs, one horse and one bat were found positive, in agreement with immunofluorescence results. Seven samples from terrestrial mammals were genotype 1 and one from a bat was genotype 5. In conclusion, this method can be used to complement immunofluorescence for the diagnosis of rabies, enabling the detection of unexpected lyssaviruses during rabies surveillance.

Horticultural Performance of Eight American Elderberry Genotypes at Three Missouri Locations

PubMed Central

Thomas, A.L.; Byers, P.L.; Avery, J.D.; Kaps, M.; Gu, S.

2016-01-01

American elderberry (Sambucus nigra subsp. canadensis) is being increasingly cultivated in North America for its edible and medicinal fruit and flowers, yet remains largely undeveloped as a horticultural crop. Productive genotypes with desirable horticultural attributes, including disease and insect resistance, precocity, uniform fruit ripening, and large berry size are needed in order to advance the commercial production of elderberries. A four-year study of eight elderberry genotypes was established in 2008 at three diverse Missouri (USA) locations. Phenology, plant morphology, pest susceptibility, productivity, and fruit characteristics data were collected over three growing seasons, 2009–2011. Significant differences for most phenological, horticultural, and fruit juice characteristics were observed among the three sites, three years, and eight genotypes. The genotype ‘Ozark’ was the earliest to break bud, produced fruit with high levels of soluble solids, and out-yielded most other genotypes at the three sites over the three-year study. None of the new genotypes produced berries as large as or larger than the standard ‘York’ which is known for its large fruit. Some of the genotypes tested, especially ‘Ozark’ show promise as potential cultivars and as breeding stock for further development of elderberry as a commercially-viable horticultural crop. PMID:27158183

Efficient genotype compression and analysis of large genetic variation datasets

PubMed Central

Layer, Ryan M.; Kindlon, Neil; Karczewski, Konrad J.; Quinlan, Aaron R.

2015-01-01

Genotype Query Tools (GQT) is a new indexing strategy that expedites analyses of genome variation datasets in VCF format based on sample genotypes, phenotypes and relationships. GQT’s compressed genotype index minimizes decompression for analysis, and performance relative to existing methods improves with cohort size. We show substantial (up to 443 fold) performance gains over existing methods and demonstrate GQT’s utility for exploring massive datasets involving thousands to millions of genomes. PMID:26550772

Comparison of Lipoprotein Electrophoresis and Apolipoprotein E Genotyping in Investigating Dysbetalipoproteinemia.

PubMed

Ahmed, Farhan; El-Kadiki, Alia; Gibbons, Stephen

2017-06-01

Dysbetalipoproteinemia is often associated with apolipoprotein E2E2 homozygosity; however, lipoprotein electrophoresis may also be used to assist in the diagnosis. The aim of this study was to compare apolipoprotein E (apo E) genotyping and lipoprotein electrophoresis in investigating dysbetalipoproteinemia. Data were collected over a three-year period from a lipid clinic in a tertiary referral centre and reviewed for apo E genotyping and lipoprotein electrophoresis. Sixty-two patients had both apo E genotyping and lipoprotein electrophoresis. Of these, 16 patients showed broad beta band on electrophoresis. However, only 3 of them had apo E2E2 homozygosity on genotyping. Lipoprotein electrophoresis and apo E genotyping results showed poor concordance. This was primarily due to visual interpretation error of lipoprotein electrophoresis which may over diagnose dysbetalipoproteinemia.

An innovative SNP genotyping method adapting to multiple platforms and throughputs.

PubMed

Long, Y M; Chao, W S; Ma, G J; Xu, S S; Qi, L L

2017-03-01

An innovative genotyping method designated as semi-thermal asymmetric reverse PCR (STARP) was developed for genotyping individual SNPs with improved accuracy, flexible throughputs, low operational costs, and high platform compatibility. Multiplex chip-based technology for genome-scale genotyping of single nucleotide polymorphisms (SNPs) has made great progress in the past two decades. However, PCR-based genotyping of individual SNPs still remains problematic in accuracy, throughput, simplicity, and/or operational costs as well as the compatibility with multiple platforms. Here, we report a novel SNP genotyping method designated semi-thermal asymmetric reverse PCR (STARP). In this method, genotyping assay was performed under unique PCR conditions using two universal priming element-adjustable primers (PEA-primers) and one group of three locus-specific primers: two asymmetrically modified allele-specific primers (AMAS-primers) and their common reverse primer. The two AMAS-primers each were substituted one base in different positions at their 3' regions to significantly increase the amplification specificity of the two alleles and tailed at 5' ends to provide priming sites for PEA-primers. The two PEA-primers were developed for common use in all genotyping assays to stringently target the PCR fragments generated by the two AMAS-primers with similar PCR efficiencies and for flexible detection using either gel-free fluorescence signals or gel-based size separation. The state-of-the-art primer design and unique PCR conditions endowed STARP with all the major advantages of high accuracy, flexible throughputs, simple assay design, low operational costs, and platform compatibility. In addition to SNPs, STARP can also be employed in genotyping of indels (insertion-deletion polymorphisms). As vast variations in DNA sequences are being unearthed by many genome sequencing projects and genotyping by sequencing, STARP will have wide applications across all biological organisms in

Phenotype- and Genotype-Specific Structural Alterations in Spasmodic Dysphonia

PubMed Central

Bianchi, Serena; Battistella, Giovanni; Huddleston, Hailey; Scharf, Rebecca; Fleysher, Lazar; Rumbach, Anna F.; Frucht, Steven J.; Blitzer, Andrew; Ozelius, Laurie J.; Simonyan, Kristina

2017-01-01

Background Spasmodic dysphonia is a focal dystonia characterized by involuntary spasms in the laryngeal muscles that occur selectively during speaking. Although hereditary trends have been reported in up to 16% of patients, the causative etiology of spasmodic dysphonia is unclear, and the influences of various phenotypes and genotypes on disorder pathophysiology are poorly understood. In this study, we examined structural alterations in cortical gray matter and white matter integrity in relationship to different phenotypes and putative genotypes of spasmodic dysphonia to elucidate the structural component of its complex pathophysiology. Methods Eighty-nine patients with spasmodic dysphonia underwent high-resolution magnetic resonance imaging and diffusion-weighted imaging to examine cortical thickness and white matter fractional anisotropy in adductor versus abductor forms (distinct phenotypes) and in sporadic versus familial cases (distinct genotypes). Results Phenotype-specific abnormalities were localized in the left sensorimotor cortex and angular gyrus and the white matter bundle of the right superior corona radiata. Genotype-specific alterations were found in the left superior temporal gyrus, supplementary motor area, and the arcuate portion of the left superior longitudinal fasciculus. Conclusions Our findings suggest that phenotypic differences in spasmodic dysphonia arise at the level of the primary and associative areas of motor control, whereas genotype-related pathophysiological mechanisms may be associated with dysfunction of regions regulating phonological and sensory processing. Identification of structural alterations specific to disorder phenotype and putative genotype provides an important step toward future delineation of imaging markers and potential targets for novel therapeutic interventions for spasmodic dysphonia. PMID:28186656

Phenotype- and genotype-specific structural alterations in spasmodic dysphonia.

PubMed

Bianchi, Serena; Battistella, Giovanni; Huddleston, Hailey; Scharf, Rebecca; Fleysher, Lazar; Rumbach, Anna F; Frucht, Steven J; Blitzer, Andrew; Ozelius, Laurie J; Simonyan, Kristina

2017-04-01

Spasmodic dysphonia is a focal dystonia characterized by involuntary spasms in the laryngeal muscles that occur selectively during speaking. Although hereditary trends have been reported in up to 16% of patients, the causative etiology of spasmodic dysphonia is unclear, and the influences of various phenotypes and genotypes on disorder pathophysiology are poorly understood. In this study, we examined structural alterations in cortical gray matter and white matter integrity in relationship to different phenotypes and putative genotypes of spasmodic dysphonia to elucidate the structural component of its complex pathophysiology. Eighty-nine patients with spasmodic dysphonia underwent high-resolution magnetic resonance imaging and diffusion-weighted imaging to examine cortical thickness and white matter fractional anisotropy in adductor versus abductor forms (distinct phenotypes) and in sporadic versus familial cases (distinct genotypes). Phenotype-specific abnormalities were localized in the left sensorimotor cortex and angular gyrus and the white matter bundle of the right superior corona radiata. Genotype-specific alterations were found in the left superior temporal gyrus, supplementary motor area, and the arcuate portion of the left superior longitudinal fasciculus. Our findings suggest that phenotypic differences in spasmodic dysphonia arise at the level of the primary and associative areas of motor control, whereas genotype-related pathophysiological mechanisms may be associated with dysfunction of regions regulating phonological and sensory processing. Identification of structural alterations specific to disorder phenotype and putative genotype provides an important step toward future delineation of imaging markers and potential targets for novel therapeutic interventions for spasmodic dysphonia. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

Allelopathic interference of alfalfa (Medicago sativa L.) genotypes to annual ryegrass (Lolium rigidum).

PubMed

Zubair, Hasan Muhammad; Pratley, James E; Sandral, G A; Humphries, A

2017-07-01

Alfalfa (Medicago sativa L.) genotypes at varying densities were investigated for allelopathic impact using annual ryegrass (Lolium rigidum) as the target species in a laboratory bioassay. Three densities (15, 30, and 50 seedlings/beaker) and 40 alfalfa genotypes were evaluated by the equal compartment agar method (ECAM). Alfalfa genotypes displayed a range of allelopathic interference in ryegrass seedlings, reducing root length from 5 to 65%. The growth of ryegrass decreased in response to increasing density of alfalfa seedlings. At the lowest density, Q75 and Titan9 were the least allelopathic genotypes. An overall inhibition index was calculated to rank each alfalfa genotype. Reduction in seed germination of annual ryegrass occurred in the presence of several alfalfa genotypes including Force 10, Haymaster7 and SARDI Five. A comprehensive metabolomic analysis using Quadruple Time of Flight (Q-TOF), was conducted to compare six alfalfa genotypes. Variation in chemical compounds was found between alfalfa root extracts and exudates and also between genotypes. Further individual compound assessments and quantitative study at greater chemical concentrations are needed to clarify the allelopathic activity. Considerable genetic variation exists among alfalfa genotypes for allelopathic activity creating the opportunity for its use in weed suppression through selection.

Evidence for host specificity of Theileria capreoli genotypes in cervids.

PubMed

Hornok, Sándor; Sugár, László; Horváth, Gábor; Kovács, Tibor; Micsutka, Attila; Gönczi, Enikő; Flaisz, Barbara; Takács, Nóra; Farkas, Róbert; Meli, Marina L; Hofmann-Lehmann, Regina

2017-10-10

Data on the prevalence of piroplasms in buffaloes and large game animal species are lacking from several central European countries. Therefore, to investigate the presence of Babesia/Theileria DNA in these hosts, 239 blood and 270 spleen samples were taken from cervids (red, fallow, and roe deer), as well as from water buffaloes, mouflons, and wild boars in southwestern Hungary, followed by DNA extraction and molecular analysis for piroplasms. All samples from buffaloes and wild boars were PCR negative. Based on spleen samples, the prevalence of piroplasms was significantly higher in red deer (41.7%) than in fallow deer (23.5%). Two genotypes of Theileria capreoli were identified, which showed significant association with their host species (i.e. genotype "capreoli-CE1" was exclusively found in roe deer, whereas red and fallow deer harbored only genotype "elaphi-CE1"). Genotype "elaphi-CE1" of T. capreoli was also detected in one mouflon. No Babesia spp. were identified. In conclusion, in the evaluated region, genotypes of T. capreoli show host-associations among cervids, and at least one of these genotypes may infect mouflons.

Genotyping of Mycobacterium intracellulare isolates and clinical characteristics of lung disease.

PubMed

Kim, S-Y; Lee, S-T; Jeong, B-H; Park, H Y; Jeon, K; Kim, J-W; Shin, S J; Koh, W-J

2013-05-01

Variable number of tandem repeats (VNTR) loci were recently identified in Japanese isolates of Mycobacterium intracellulare. We hypothesised that some mycobacterial genotypes are more virulent than others, resulting in particular genotypes being associated with disease phenotype and progression. To evaluate the VNTR loci of M. intracellulare in clinical isolates from Korean patients, and investigate the association between mycobacterial genotype and disease phenotype and progression. In total, 70 M. intracellulare clinical isolates were genotyped using 16 M. intracellulare VNTR loci. VNTR typing showed strong discriminatory power and genetic diversity for molecular epidemiological studies of M. intracellulare. In a phylogenetic tree, the M. intracellulare clinical isolates were divided into two clusters (A and B). Cluster A was observed more frequently (77%) than Cluster B; however, there was no association between the clinical characteristics, disease progression, drug susceptibility and clusters based on VNTR genotyping. VNTR typing could be used for epidemiological studies of M. intracellulare lung disease; however, no association was found between the specific VNTR genotypes of M. intracellulare and the clinical characteristics of Korean patients.

Genetic mapping in the presence of genotyping errors.

PubMed

Cartwright, Dustin A; Troggio, Michela; Velasco, Riccardo; Gutin, Alexander

2007-08-01

Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders.

Genetic Mapping in the Presence of Genotyping Errors

PubMed Central

Cartwright, Dustin A.; Troggio, Michela; Velasco, Riccardo; Gutin, Alexander

2007-01-01

Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders. PMID:17277374

Genotyping of polyomavirus BK by Real Time PCR for VP1 gene.

PubMed

Gambarino, Stefano; Costa, Cristina; Astegiano, Sara; Piasentin, Elsa Alessio; Segoloni, Giuseppe P; Cavallo, Rossana; Bergallo, Massimiliano

2011-10-01

Polyomavirus BK latently persist in different sites, including the renourinary tract, and may reactivate causing nephropathy in renal transplant recipients or hemorrhagic cystitis in bone marrow recipients. Based on the sequence of the VP1 gene, four genotypes have been described, corresponding to the four serologically differentiated subtypes I-IV, with different prevalence and geographic distribution. In this study, the development and clinical validation of four different Real-Time PCR assays for the detection and discrimination of BKV genotypes as a substitute of DNA sequencing are described. 379 BK VP1 sequences, belonging to the main four genotypes, were aligned and "hot spots" of mutation specific for all the strains or isolates were identified. Specific primers and probes for the detection and discrimination of each genotype by four Real-Time PCR assays were designed and technically validated. Subsequently, the four Real-Time PCR assays were used to test 20 BK-positive urine specimens from renal transplant patients, and evidenced a prevalence of BK genotype I, as previously reported in Europe. Results were confirmed by sequencing. The availability of a rapid and simple genotyping method could be useful for the evaluation of BK genotypes prevalence and studies on the impact of the infecting genotype on viral biological behavior, pathogenic role, and immune evasion strategies.

A real time genotyping PCR assay for polyomavirus BK.

PubMed

Gard, Lilli; Niesters, Hubert G M; Riezebos-Brilman, Annelies

2015-09-01

Polyomavirus BK (BKV) may cause nephropathy in renal transplant recipients and hemorrhagic cystitis in bone marrow recipients. We developed real-time PCRs (RT-PCR) to determine easily and rapidly the different BKV genotypes (BKGT) (I-IV). On the VP1 gene a duplex of RT-PCRs was developed and validated to differentiate the four main BKGT. 212 BKV positive samples (21 plasma, 191 urine) were tested with these specific PCRs. Of these 212 samples, 55 PCR results were additionally confirmed by sequencing a VP1 gene fragment (nucleotide 1630-1956). For every genotype, a highly specific, precise and internally controlled assay was developed with a limit of detection of log 3 copies per ml. In 18 (8.5%) of these samples genotyping was not successful due to a low viral load. By sequence analysis, the genotype of 46 out of 55 and 2 out of 4 samples with double infection could be confirmed. This study describes RT-PCRs for detection of the main BKGT. It proved to be rapid, cheap and sensitive compared to sequencing. Double infections can also be detected. This method will be of value to investigate the role of BKV infection in relation to the genotype. Copyright © 2015 Elsevier B.V. All rights reserved.

Using Genotype Abundance to Improve Phylogenetic Inference

PubMed Central

Mesin, Luka; Victora, Gabriel D; Minin, Vladimir N; Matsen, Frederick A

2018-01-01

Abstract Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this article, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation. PMID:29474671

ACE ID genotype affects blood creatine kinase response to eccentric exercise.

PubMed

Yamin, Chen; Amir, Offer; Sagiv, Moran; Attias, Eric; Meckel, Yoav; Eynon, Nir; Sagiv, Michael; Amir, Ruthie E

2007-12-01

Unaccustomed exercise may cause muscle breakdown with marked increase in serum creatine kinase (CK) activity. The skeletal muscle renin-angiotensin system (RAS) plays an important role in exercise metabolism and tissue injury. A functional insertion (I)/deletion (D) polymorphism in the angiotensin I-converting enzyme (ACE) gene (rs4646994) has been associated with ACE activity. We hypothesized that ACE ID genotype may contribute to the wide variability in individuals' CK response to a given exercise. Young individuals performed maximal eccentric contractions of the elbow flexor muscles. Pre- and postexercise CK activity was determined. ACE genotype was significantly associated with postexercise CK increase and peak CK activity. Individuals harboring one or more of the I allele had a greater increase and higher peak CK values than individuals with the DD genotype. This response was dose-dependent (mean +/- SE U/L: II, 8,882 +/- 2,362; ID, 4,454 +/- 1,105; DD, 2,937 +/- 753, ANOVA, P = 0.02; P = 0.009 for linear trend). Multivariate stepwise regression analysis, which included age, sex, body mass index, and genotype subtypes, revealed that ACE genotype was the most powerful independent determinant of peak CK activity (adjusted odds ratio 1.3, 95% confidence interval 1.03-1.64, P = 0.02). In conclusion, we indicate a positive association of the ACE ID genotype with CK response to strenuous exercise. We suggest that the II genotype imposes increased risk for developing muscle damage, whereas the DD genotype may have protective effects. These findings support the role of local RAS in the regulation of exertional muscle injury.

Giardia and Cryptosporidium species and genotypes in coyotes (Canis latrans).

PubMed

Trout, James M; Santín, Mónica; Fayer, Ronald

2006-06-01

Feces and duodenal scrapings were collected from 22 coyotes (Canis latrans) killed in managed hunts in northeastern Pennsylvania. Polymerase chain reaction (PCR) methods were used to detect Giardia and Cryptosporidium spp. PCR-amplified fragments of Giardia and Cryptosporidium spp. SSU-rRNA genes were subjected to DNA sequence analysis for species/genotype determination. Seven coyotes (32%) were positive for G. duodenalis: three assemblage C, three assemblage D, and one assemblage B. Six coyotes (27%) were positive for Cryptosporidium spp. One isolate shared 99.7% homology with C. muris, whereas five others (23%) shared 100% homology with C. canis, coyote genotype. This is the first report on multiple genotypes of Giardia spp. in coyotes and on the prevalence of Cryptosporidium spp. genotypes in coyotes.

Population growth of the floricolous yeast Metschnikowia reukaufii: effects of nectar host, yeast genotype, and host × genotype interaction.

PubMed

Herrera, Carlos M

2014-05-01

Genetic diversity and genotypic diversity of wild populations of the floricolous yeast Metschnikowia reukaufii exhibit a strong host-mediated component, with genotypes being nonrandomly distributed among flowers of different plant species. To unravel the causal mechanism of this pattern of host-mediated genetic diversity, this paper examines experimentally whether floral nectars of different host plants differ in their quality as a growing substrate for M. reukaufii and also whether genetically distinct yeast strains differ in their relative ability to thrive in nectars of different species (host × genotype interaction). Genetically distinct M. reukaufii strains were grown in natural nectar of different hosts under controlled conditions. Population growth varied widely among nectar hosts, revealing that different host plants provided microhabitats of different quality for M. reukaufii. Different M. reukaufii strains responded in different ways to interspecific nectar variation, and variable growth responses were significantly associated with genetic differences between strains, thus leading to a significant host × genotype interaction. Results of this study provide support for the diversifying selection hypothesis as the underlying mechanism preserving high genetic diversity in wild M. reukaufii populations and also suggest that consequences of functional plant-pollinator diversity may surpass the domain of the mutualistic organisms to implicate associated microorganisms. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Distribution of Candida albicans genotypes among family members

NASA Technical Reports Server (NTRS)

Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

1999-01-01

Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

Prevalence and genotypes of Enterocytozoon bieneusi in China.

PubMed

Wang, Sha-Sha; Wang, Rong-Jun; Fan, Xian-Cheng; Liu, Ting-Li; Zhang, Long-Xian; Zhao, Guang-Hui

2018-07-01

Enterocytozoon bieneusi has been considered as the most frequently diagnosed microsporidian species in humans and various animal species, accounting for more than 90% of the cases of human microsporidiosis. Spores of this pathogen excreted from both symptomatic and asymptomatic hosts into environment also would be an important source of waterborne outbreak of microsporidiosis. Due to limited effective drugs available but with too much side effects to mammals (eg. toxic), accurate characterization of E. bieneusi in both humans and animals is essential to implement effective control strategies to this pathogen. In China, E. bieneusi infection was presented in humans and some animals with high prevalence. Analysis of genetic variations of the internal transcribed spacer (ITS) sequences found 361 genotypes in China, and some novel genotypes were identified in some specific hosts. Additionally, associations between infections and some risk factors were also observed. In the present article, we reviewed the current status of prevalence, genotypes, multilocus genotypes (MLGs) in humans, various animals and waters in China. These findings will provide basic information for developing effective control strategies against E. bieneusi infection in China as well as other countries. Copyright © 2018 Elsevier B.V. All rights reserved.

snpAD: An ancient DNA genotype caller.

PubMed

Prüfer, Kay

2018-06-21

The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. The C ++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary data are available at Bioinformatics online.

Treatment switch guided by HIV-1 genotyping in Brazil.

PubMed

Tupinambás, Unaí; Ribeiro, Flávia Andrade; Aleixo, Agdemir; Greco, Dirceu

2006-04-01

We assessed the performance of HIV-1 genotyping tests in rescue therapy. Patients were divided into two groups: group 1 (genotyped), included those switching to new antiretroviral drugs based on HIV-1 genotyping data, and group 2 (standard of care -SOC), comprised those in rescue therapy who had not used this test. This was an open and non-randomized study, with 74 patients, followed up for a mean period of 12 months, from February 2002 to May 2003. The groups differed in the duration of antiretroviral use, experience with diverse drug classes (non-nucleoside reverse transcriptase inhibitors and protease inhibitors) and viral load <2.6 log10 copies/mL at any time during treatment. In 23 patients (group 1), the switch in antiretroviral (ARV) regimen was based on genotyping data; this test was not used for 51 patients (group 2). Two CD4 + lymphocyte counts and viral load counts were made for each patient during the study. Data from the pharmacy where patients received antiretroviral agents, medical charts, and direct interviews with patients to assess compliance to treatment, were analyzed. In the genotyped group, the average drop in viral load was 2.8 log10, compared with a 1.5 log10 difference in group 2; the difference was significant in the first assessment performed six months after switching (p=0.001). Considering the patients with viral load < 2.6 log10 (400 copies/mL) after switching, the patients in group 1 had a better performance in the first assessment (73.9% versus 31.1% in groups 1 and 2, respectively); this difference was significant (p=0.001). In multivariate analysis, the variables associated with a greater drop in viral load in the first assessment were the patients whose switching was based on genotyping (group 1), those with a past history of viral load < 2.6 log10 and correct use of antiretroviral agents. In conclusion, the genotyping test and adherence were found to be independent factors for success in the management of patients who failed

High prevalence of Hepatitis C virus genotype 6 in Vietnam.

PubMed

Pham, Duc Anh; Leuangwutiwong, Pornsawan; Jittmittraphap, Akanitt; Luplertlop, Nattanej; Bach, Hoa Khanh; Akkarathamrongsin, Srunthron; Theamboonlers, Apiradee; Poovorawan, Yong

2009-01-01

This study aimed to update the prevalence of the various Hepatitis C virus genotypes in Vietnamese blood donors. One hundred and three HCV antibody-positive plasma samples were collected from blood donors at the National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam. All specimens were subjected to RT-PCR of the 5' untranslated region (UTR) to confirm the presence of HCV RNA. The core and NS5B regions of thh positive samples were subsequently amplified by RT-PCR followed by direct sequencing and phylogenetic analysis. Seventy out of 103 samples (68.0%) were RNA positive. Core and NS5B were successfully amplified and sequences were obtained for 70 and 65 samples, respectively. Phylogenetic analysis revealed that genotype 6a was the most predominant among Vietnamese blood donors with a prevalence of 37.1% (26/70), followed by genotype 1a at 30.0% (21/70) and genotype 1b at 17.1% (12/70). The prevalence of two other genotype 6 variants, 6e and 61 was 8.6% and 1.4%, respectively. Further analysis of recent studies showed that the geographic distribution of genotype 6 covered mainly southern China and the mainland of Southeast Asia including Vietnam, Laos, Thailand, and Myanmar. The GenBank accession numbers for the sequences reported in this study are FJ768772-FJ768906.

Genetic diversity of popcorn genotypes using molecular analysis.

PubMed

Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

2015-08-19

In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

Echinococcus granulosus genotypes in Iran: a systematic review.

PubMed

Khademvatan, S; Majidiani, H; Foroutan, M; Hazrati Tappeh, K; Aryamand, S; Khalkhali, H R

2018-04-02

Cystic echinococcosis (CE) caused by Echinococcus granulosus sensu lato (s.l.) is a significant zoonosis, especially in developing countries of the Middle East, with many studies focusing on CE genotypes in Iran. We performed a systematic review to determine the exact status of E. granulosus genotypes in the country. We explored English (Pubmed, Scopus, ISI Web of Science and Science Direct) and Persian (Magiran, Iran Medex and Scientific Information Database) databases along with Google Scholar. Our review included 73 studies published prior to the end of 2015. In total, 2952 animal (intermediate and definitive) hosts were examined, and the prevalent genotypes comprised G1 (92.75%) and G6 (4.53%) in sheep, cattle, camels, goats and buffaloes; G3 (2.43%) in five herbivore hosts and dogs; G7 (0.2%) in sheep and goats; and G2 (0.06%) in dogs. G1 was mostly dominant in West Azerbaijan, whereas G3 and G6 were identified most frequently in the provinces of Isfahan and Fars, respectively. Regarding human CE infection, 340 cases were reported from Iran, with the identified genotypes G1 (n = 320), G6 (n = 13) and G3 (n = 7). Most CE-infected humans originated from Isfahan province (168 cases), whereas the lowest number of infected persons was noted in Kerman province (two cases). The information obtained from this systematic review is central to better understanding the biological and epidemiological characteristics of E. granulosus s.l. genotypes in Iran, leading to more comprehensive control strategies.

BCL2 genotypes and prostate cancer survival.

PubMed

Renner, Wilfried; Langsenlehner, Uwe; Krenn-Pilko, Sabine; Eder, Petra; Langsenlehner, Tanja

2017-06-01

The antiapoptotic B‑cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients.

Folate supplementation in schizophrenia: a possible role for MTHFR genotype.

PubMed

Hill, Michele; Shannahan, Kelsey; Jasinski, Sarah; Macklin, Eric A; Raeke, Lisa; Roffman, Joshua L; Goff, Donald C

2011-04-01

Folate deficiency and the methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphism have been linked to negative symptoms in schizophrenia both independently and synergistically. This study examined the effect of folate supplementation on negative symptoms overall and in relation to MTHFR 677C>T genotype. Forty-six stable adult schizophrenia outpatients were enrolled and 32 were randomised, double-blind, in a parallel-group, twelve week add-on trial of folate 2mg/d or matching placebo. The primary outcome measure was change from baseline to week 12 on the modified SANS total score using a mixed-model analysis. In addition, we measured the effect of MTHFR genotype on treatment effects and on changes in serum folate by grouping participants with T/T genotype together with C/T genotype and comparing their interactions to patients with C/C genotype. Twenty-eight participants completed the trial. Folate supplementation did not significantly affect negative symptoms compared to placebo across the entire cohort. However, there was a significant genotype×treatment effect on negative symptoms (F=7.13, df=1,39, p=0.01). In addition, MTHFR status significantly moderated the relationship between change in serum folate and change in negative symptoms: among participants with at least one copy of the T allele negative symptoms were more likely to improve with increased serum folate (p=0.03). We did not detect a therapeutic benefit of folate supplementation in a sample of patients with residual negative symptoms. However, a possible association between genotypes associated with reduced MTHFR activity and benefit from folate supplementation should be investigated further. Copyright © 2010 Elsevier B.V. All rights reserved.

Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA▿

PubMed Central

Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

2010-01-01

Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

Impact of locomotion training with a neurologic controlled hybrid assistive limb (HAL) exoskeleton on neuropathic pain and health related quality of life (HRQoL) in chronic SCI: a case study (.).

PubMed

Cruciger, Oliver; Schildhauer, Thomas A; Meindl, Renate C; Tegenthoff, Martin; Schwenkreis, Peter; Citak, Mustafa; Aach, Mirko

2016-08-01

Chronic neuropathic pain (CNP) is a common condition associated with spinal cord injury (SCI) and has been reported to be severe, disabling and often treatment-resistant and therefore remains a clinical challenge for the attending physicians. The treatment usually includes pharmacological and/or nonpharmacological approaches. Body weight supported treadmill training (BWSTT) and locomotion training with driven gait orthosis (DGO) have evolved over the last decades and are now considered to be an established part in the rehabilitation of SCI patients. Conventional locomotion training goes along with improvements of the patients' walking abilities in particular speed and gait pattern. The neurologic controlled hybrid assistive limb (HAL®, Cyberdyne Inc., Ibraki, Japan) exoskeleton, however, is a new tailored approach to support motor functions synchronously to the patient's voluntary drive. This report presents two cases of severe chronic and therapy resistant neuropathic pain due to chronic SCI and demonstrates the beneficial effects of neurologic controlled exoskeletal intervention on pain severity and health-related quality of life (HRQoL). Both of these patients were engaged in a 12 weeks period of daily HAL®-supported locomotion training. In addition to improvements in motor functions and walking abilities, both show significant reduction in pain severity and improvements in all HRQoL domains. Although various causal factors likely contribute to abatement of CNP, the reported results occurred due to a new approach in the rehabilitation of chronic spinal cord injury patients. These findings suggest not only the feasibility of this new approach but in conclusion, demonstrate the effectiveness of neurologic controlled locomotion training in the long-term management of refractory neuropathic pain. Implications for Rehabilitation CNP remains a challenge in the rehabilitation of chronic SCI patients. Locomotion training with the HAL exoskeleton seems to improve CNP

Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

USDA-ARS?s Scientific Manuscript database

A number of Bangladeshi wheat genotypes (varieties and advanced lines) have been tested for boron efficiency through sand culture experiments over two years (2007-08 & 2008-09) against two Thai check varieties ‘Fang 60’ (boron efficient) and ‘SW41’ (boron inefficient). Performances of the genotypes ...

A latent modeling approach to genotype-phenotype relationships: maternal problem behavior clusters, prenatal smoking, and MAOA genotype.

PubMed

McGrath, L M; Mustanski, B; Metzger, A; Pine, D S; Kistner-Griffin, E; Cook, E; Wakschlag, L S

2012-08-01

This study illustrates the application of a latent modeling approach to genotype-phenotype relationships and gene × environment interactions, using a novel, multidimensional model of adult female problem behavior, including maternal prenatal smoking. The gene of interest is the monoamine oxidase A (MAOA) gene which has been well studied in relation to antisocial behavior. Participants were adult women (N = 192) who were sampled from a prospective pregnancy cohort of non-Hispanic, white individuals recruited from a neighborhood health clinic. Structural equation modeling was used to model a female problem behavior phenotype, which included conduct problems, substance use, impulsive-sensation seeking, interpersonal aggression, and prenatal smoking. All of the female problem behavior dimensions clustered together strongly, with the exception of prenatal smoking. A main effect of MAOA genotype and a MAOA × physical maltreatment interaction were detected with the Conduct Problems factor. Our phenotypic model showed that prenatal smoking is not simply a marker of other maternal problem behaviors. The risk variant in the MAOA main effect and interaction analyses was the high activity MAOA genotype, which is discrepant from consensus findings in male samples. This result contributes to an emerging literature on sex-specific interaction effects for MAOA.

Genonets server-a web server for the construction, analysis and visualization of genotype networks.

PubMed

Khalid, Fahad; Aguilar-Rodríguez, José; Wagner, Andreas; Payne, Joshua L

2016-07-08

A genotype network is a graph in which vertices represent genotypes that have the same phenotype. Edges connect vertices if their corresponding genotypes differ in a single small mutation. Genotype networks are used to study the organization of genotype spaces. They have shed light on the relationship between robustness and evolvability in biological systems as different as RNA macromolecules and transcriptional regulatory circuits. Despite the importance of genotype networks, no tool exists for their automatic construction, analysis and visualization. Here we fill this gap by presenting the Genonets Server, a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education. The Genonets Server is freely available at http://ieu-genonets.uzh.ch. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

PubMed

Money, Daniel; Migicovsky, Zoë; Gardner, Kyle; Myles, Sean

2017-07-10

Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from

Expanding the Genotypic Spectrum of Bathing Suit Ichthyosis

PubMed Central

Marukian, Nareh V.; Hu, Rong-Hua; Craiglow, Brittany G.; Milstone, Leonard M.; Zhou, Jing; Theos, Amy; Kaymakcalan, Hande; Akkaya, Deniz A.; Uitto, Jouni J.; Vahidnezhad, Hassan; Youssefian, Leila; Bayliss, Susan J.; Paller, Amy S.; Boyden, Lynn M.

2017-01-01

Importance Bathing suit ichthyosis (BSI) is a rare congenital disorder of keratinization characterized by restriction of scale to sites of relatively higher temperature such as the trunk, with cooler areas remaining unaffected. Fewer than 40 cases have been reported in the literature. Bathing suit ichthyosis is caused by recessive, temperature-sensitive mutations in the transglutaminase-1 gene (TGM1). Clear genotype-phenotype correlations have been difficult to establish because several of the same TGM1 mutations have been reported in BSI and other forms of congenital ichthyosis. We identify novel and recurrent mutations in 16 participants with BSI. Objective To expand the genotypic spectrum of BSI, identifying novel TGM1 mutations in patients with BSI, and to use BSI genotypes to draw inferences about the temperature sensitivity of TGM1 mutations. Design, Setting, and Participants A total of 16 participants with BSI from 13 kindreds were identified from 6 academic medical centers. A detailed clinical history was obtained from each participant, including phenotypic presentation at birth and disease course. Each participant underwent targeted sequencing of TGM1. Main Outcomes and Measures Phenotypic and genotypic characteristics in these patients from birth onward. Results Of the 16 participants, 7 were male, and 9 were female (mean age, 12.6 years; range, 1-39 years). We found 1 novel TGM1 indel mutation (Ile469_Cys471delinsMetLeu) and 8 TGM1 missense mutations that to our knowledge have not been previously reported in BSI: 5 have been previously described in non–temperature-sensitive forms of congenital ichthyosis (Arg143Cys, Gly218Ser, Gly278Arg, Arg286Gln, and Ser358Arg), and 3 (Tyr374Cys, Phe495Leu, and Ser772Arg) are novel mutations. Three probands were homozygous for Arg264Trp, Arg286Gln, or Arg315Leu, indicating that these mutations are temperature sensitive. Seven of 10 probands with a compound heterozygous TGM1 genotype had a mutation at either arginine

Rotavirus genotypes associated with acute diarrhea in Egyptian infants.

PubMed

Ahmed, Salwa F; Mansour, Adel M; Klena, John D; Husain, Tupur S; Hassan, Khaled A; Mohamed, Farag; Steele, Duncan

2014-01-01

Before the introduction of rotavirus vaccine in Egypt, information on the burden of disease and the circulating rotavirus genotypes is critical to monitor vaccine effectiveness. A cohort of 348 Egyptian children was followed from birth to 2 years of age with twice-weekly home visits to detect diarrheal illness. VP7 and VP4 genes were genotyped by reverse-transcription polymerase chain reaction and DNA sequencing. Forty percentage of children had rotavirus-associated diarrhea at least once by their second birthday. One hundred and twelve children experienced a single rotavirus diarrheal episodes (RDE) at a median age of 9 months; while 27 infants had their second RDE at a median age of 15 months and 1 infant had 3 RDE at the age of 2, 16 and 22 months. Of the 169 RDE, 82% could be assigned a G-type, while 58% had been identified a P-type. The most prevalent genotype was G2 (32%), followed by G1 (24%) and G9 (19%). G2P[4] rotavirus episodes were significantly associated with fever (P = 0.03) and vomiting (P = 0.06) when compared with other genotypes. G2 strains were the predominant genotype causing 50% of the second RDE while G9 represented 25% of the second RDE. Genotypes identified are similar to those detected globally except for absence of G4. Our finding that 75% of the second RDE were due to G2 and G9 indicates a possible reduction in natural protection afforded by these types compared with G1, where 90% of G1 cases did not experience a second xposure, indicating greater protection against recurrent symptomatic infection.

Joint effect of MCP-1 genotype GG and MMP-1 genotype 2G/2G increases the likelihood of developing pulmonary tuberculosis in BCG-vaccinated individuals.

PubMed

Ganachari, Malathesha; Ruiz-Morales, Jorge A; Gomez de la Torre Pretell, Juan C; Dinh, Jeffrey; Granados, Julio; Flores-Villanueva, Pedro O

2010-01-25

We previously reported that the -2518 MCP-1 genotype GG increases the likelihood of developing tuberculosis (TB) in non-BCG-vaccinated Mexicans and Koreans. Here, we tested the hypothesis that this genotype, alone or together with the -1607 MMP-1 functional polymorphism, increases the likelihood of developing TB in BCG-vaccinated individuals. We conducted population-based case-control studies of BCG-vaccinated individuals in Mexico and Peru that included 193 TB cases and 243 healthy tuberculin-positive controls from Mexico and 701 TB cases and 796 controls from Peru. We also performed immunohistochemistry (IHC) analysis of lymph nodes from carriers of relevant two-locus genotypes and in vitro studies to determine how these variants may operate to increase the risk of developing active disease. We report that a joint effect between the -2518 MCP-1 genotype GG and the -1607 MMP-1 genotype 2G/2G consistently increases the odds of developing TB 3.59-fold in Mexicans and 3.9-fold in Peruvians. IHC analysis of lymph nodes indicated that carriers of the two-locus genotype MCP-1 GG MMP-1 2G/2G express the highest levels of both MCP-1 and MMP-1. Carriers of these susceptibility genotypes might be at increased risk of developing TB because they produce high levels of MCP-1, which enhances the induction of MMP-1 production by M. tuberculosis-sonicate antigens to higher levels than in carriers of the other two-locus MCP-1 MMP-1 genotypes studied. This notion was supported by in vitro experiments and luciferase based promoter activity assay. MMP-1 may destabilize granuloma formation and promote tissue damage and disease progression early in the infection. Our findings may foster the development of new and personalized therapeutic approaches targeting MCP-1 and/or MMP-1.

Joint Effect of MCP-1 Genotype GG and MMP-1 Genotype 2G/2G Increases the Likelihood of Developing Pulmonary Tuberculosis in BCG-Vaccinated Individuals

PubMed Central

Ganachari, Malathesha; Ruiz-Morales, Jorge A.; Gomez de la Torre Pretell, Juan C.; Dinh, Jeffrey; Granados, Julio; Flores-Villanueva, Pedro O.

2010-01-01

We previously reported that the – 2518 MCP-1 genotype GG increases the likelihood of developing tuberculosis (TB) in non-BCG-vaccinated Mexicans and Koreans. Here, we tested the hypothesis that this genotype, alone or together with the – 1607 MMP-1 functional polymorphism, increases the likelihood of developing TB in BCG-vaccinated individuals. We conducted population-based case-control studies of BCG-vaccinated individuals in Mexico and Peru that included 193 TB cases and 243 healthy tuberculin-positive controls from Mexico and 701 TB cases and 796 controls from Peru. We also performed immunohistochemistry (IHC) analysis of lymph nodes from carriers of relevant two-locus genotypes and in vitro studies to determine how these variants may operate to increase the risk of developing active disease. We report that a joint effect between the – 2518 MCP-1 genotype GG and the – 1607 MMP-1 genotype 2G/2G consistently increases the odds of developing TB 3.59-fold in Mexicans and 3.9-fold in Peruvians. IHC analysis of lymph nodes indicated that carriers of the two-locus genotype MCP-1 GG MMP-1 2G/2G express the highest levels of both MCP-1 and MMP-1. Carriers of these susceptibility genotypes might be at increased risk of developing TB because they produce high levels of MCP-1, which enhances the induction of MMP-1 production by M. tuberculosis-sonicate antigens to higher levels than in carriers of the other two-locus MCP-1 MMP-1 genotypes studied. This notion was supported by in vitro experiments and luciferase based promoter activity assay. MMP-1 may destabilize granuloma formation and promote tissue damage and disease progression early in the infection. Our findings may foster the development of new and personalized therapeutic approaches targeting MCP-1 and/or MMP-1. PMID:20111728

Resistance of Collard Green Genotypes to Bemisia tabaci Biotype B: Characterization of Antixenosis.

PubMed

Domingos, G M; Baldin, E L L; Canassa, V F; Silva, I F; Lourenção, A L

2018-08-01

Bemisia tabaci (Genn.) biotype B (Hemiptera: Aleyrodidae) is an important pest of vegetable crops, including collard greens Brassica oleracea var. acephala (Brassicaceae). The use of resistant genotypes is an interesting option to reduce insect populations and can be used as an important tool for integrated pest management (IPM). This study evaluated 32 genotypes of collard greens against the attack of silver leaf whitefly, with the aim to characterize antixenosis. Initially, a multiple-choice trial was conducted using all genotypes, in which the adult attractiveness was assessed on two leaves per genotype at 24 and 48 h after infestation. After 48 h, one leaf of each genotype was randomly selected for the determination of the number of eggs per square centimeter. From the results of the multiple-choice trial, 13 genotypes were selected for a no-choice oviposition test, following the same method of the previous test. Colorimetric analyses were also performed to establish possible correlations between leaf color and insect colonization. Genotypes HS-20, OE, and VA were less attractive, demonstrating antixenosis. Genotypes LG, VE, J, MG, MOP, HS-20, VA, and MT had less oviposition in the multiple-choice test, which indicated expression of antixenosis. In the no-choice test, genotypes VE, P1C, CCB, RI-919, H, and J had less oviposition, which also characterized antixenosis. Therefore, genotypes VE and J showed the highest resistance stability because both had less oviposition in both test modalities. Thus, the resistance to B. tabaci biotype B indicates the genotypes HS-20, OE, VA, VE, and J are promising for use in breeding programs to develop resistance to whitefly.

[Detection and genotyping of human papillomavirus in biopsies of uterine cervical adenocarcinoma].

PubMed

Brebi M, Priscilla; Ili G, Carmen Gloria; López M, Jaime; García M, Patricia; Melo A, Angélica; Montenegro H, Sonia; Leal R, Pamela; Guzmán G, Pablo; Roa S, Juan Carlos

2009-03-01

The genotyping of Human Papillomavirus (HPV) will improve knowledge about the local epidemiological association of this virus with adenocarcinoma. To determine the frequency of HPV genotypes in biopsies of women with uterine cervical adenocarcinoma in a geographic region of Chile. Forty-one cervical biopsies with a pathological diagnosis of adenocarcinoma, corresponding to all women diagnosed with this cancer between 2002 and 2004, were analyzed. Viral gene Ll was amplified by PCRfor viral detection. HPV genotyping was carried out by a Reverse Line Blot technique. Seventy one percent of biopsies were positive for HPV. The most common genotypes found were HPV 16 (61%), followed by HPV 18 (19.5%). Eighty seven percent of biopsies had a single HPV infection. Three patients had a multiple HPV infection. All of the latter were infected by HPV 16, associated with other three viral genotypes (45, 52 and 66). No low-risk HPV genotypes were found. In this sample of biopsies, there was a high prevelence of HPV 16 and a low prevalence of HPV 18, which historically has been related to adenocarcinoma. The genotypes found correspond to those described in South America.

Genetic Diversity Analysis of Highly Incomplete SNP Genotype Data with Imputations: An Empirical Assessment

PubMed Central

Fu, Yong-Bi

2014-01-01

Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

First genotype identification of Trichosporon asahii in Sfax, Tunisia.

PubMed

Sellami, Hayet; Trabelsi, Houaida; Neji, Sourour; Amouri, Imen; Cheikhrouhou, Fatma; Makni, Fattouma; Ayadi, Ali

2017-04-01

The objectives of our study were species identification and genotyping of Trichosporon isolates collected at the Parasitology and Mycology Laboratory in Sfax, Tunisia. Molecular identification was carried out by analysing the IGS1 regions of the rDNA of 30 Trichosporon isolates. Trichosporon asahii was the most frequent species detected. Furthermore, four genotypes were identified in Tunisia: 1 (46.4 %), 4 (35.7 %), 7 (14.3 %) and 3 (3.6 %). In vitro antifungal susceptibility testing of the isolates showed that voriconazole exhibited the highest activity. This is the first reported study of genotype identification of T. asahii in Tunisia and even in the African continent.

Cookie-Ases: Interactive Models for Teaching Genotype-Phenotype Relationships

ERIC Educational Resources Information Center

Seipelt, Rebecca L.

2006-01-01

Several hands-on and wet laboratory activities have been proposed to model the genetic concepts of genotypes and phenotypes and their relationship. The exercise presented in this article is a novel, time effective, student-centered, role-playing activity in which students learn about the intricate connection between genotype and phenotype by…

High Risk Human Papilloma Virus Genotypes in Kurdistan Region in Patients with Vaginal Discharge.

PubMed

Hussein, Nawfal R; Balatay, Amer A; Assafi, Mahde S; AlMufty, Tamara Abdulezel

2016-01-01

The human papilloma virus (HPV) is considered as the major risk factor for the development of cervical cancer. This virus is of different genotypes and generally can be classified into high and low risk types. To determine the rate of high risk HPV genotypes in women with vaginal discharge and lower abdominal pain in Kurdistan region, Iraq. Cervical swabs were taken from 104 women. DNA was extracted and the polymerase chain reaction (PCR) technique was used to determine the presence of high risk genotypes. It was found that 13/104 (12.5%) of the samples were positive for high risk HPV genotypes. Amongst those who were positive, 4/13 (30.7%) were typed as genotype 16 and 7/13 (53.8%) showed mixed genotyping. On the other hand, genotypes 53 and 56 were found in only one sample each. High risk HPV genotypes are not uncommon and further community based study is needed to determine the prevalence of HPV and its genotypes and plan for prevention of infection.

Hepatitis B Virus Genotyping: Is the Time Ripe for Routine Clinical Use?

PubMed Central

Madan, Kaushal; Tyagi, Pankaj

2012-01-01

Hepatitis B is one of the major causes of end-stage liver disease and liver cancer worldwide. A number of host and viral factors influence the disease course and outcomes. One such viral factor is hepatitis B virus (HBV) genotypes. There are eight major HBV genotypes described from various geographic regions of the world. Although direct sequencing appears to be the gold standard for HBV genotyping, it is expensive and laborintensive and therefore cannot be applied for routine clinical use. The newer molecular methods including serotyping have made genotyping easier and simple to apply to large number of samples rapidly. The data collected mainly over the last decade have suggested that HBV genotypes may have a bearing over the natural course of the disease and its response to therapy. This review summarizes the available literature and highlights how genotyping could be incorporated into routine clinical practice in order to improve delivery of care to HBV-infected individuals. PMID:25755425

Prevalence of HCV genotypes in Poland – the EpiTer study

PubMed Central

Pogorzelska, Joanna; Berak, Hanna; Horban, Andrzej; Orłowska, Iwona; Simon, Krzysztof; Tuchendler, Ewelina; Madej, Grzegorz; Piekarska, Anna; Jabłkowski, Maciej; Deroń, Zbigniew; Mazur, Włodzimierz; Kaczmarczyk, Marcin; Janczewska, Ewa; Pisula, Arkadiusz; Smykał, Jacek; Nowak, Krzysztof; Matukiewicz, Marek; Halota, Waldemar; Wernik, Joanna; Sikorska, Katarzyna; Mozer-Lisewska, Iwona; Rozpłochowski, Błażej; Garlicki, Aleksander; Tomasiewicz, Krzysztof; Krzowska-Firych, Joanna; Baka-Ćwierz, Barbara; Kryczka, Wiesław; Zarębska-Michaluk, Dorota; Olszok, Iwona; Boroń-Kaczmarska, Anna; Sobala-Szczygieł, Barbara; Szlauer, Bronisława; Korcz-Ondrzejek, Bogumiła; Sieklucki, Jerzy; Pleśniak, Robert; Ruszała, Agata; Postawa-Kłosińska, Barbara; Citko, Jolanta; Lachowicz-Wawrzyniak, Anna; Musialik, Joanna; Jezierska, Edyta; Dobracki, Witold; Dobracka, Beata; Hałubiec, Jan; Krygier, Rafał; Strokowska, Anna; Chomczyk, Wojciech; Witczak-Malinowska, Krystyna

2016-01-01

The aim of the study Was to assess current prevalence of hepatitis C virus (HCV) genotypes in Poland, including their geographic distribution and changes in a given period of time. Material and methods Data were collected with questionnaires from 29 Polish centers and included data of patients diagnosed with HCV infection between 1 January 2013 and 31 March 2016. Results In total, data of 9800 patients were reported. The highest prevalence was estimated for genotype 1b (81.7%), followed by 3 (11.3%), 4 (3.5%), 1a (3.2%) and 2 (0.2%). Genotype 5 or 6 was reported in 6 patients only (0.1%). The highest prevalence of genotype 1 was observed in central (łódzkie, mazowieckie, świętokrzyskie), eastern (lubelskie) and southern (małopolskie, śląskie) Poland. The highest rate for genotype 3 was observed in south-western (dolnośląskie, lubuskie) and eastern (podlaskie, warmińsko-mazurskie and podkarpackie) Poland. Compared to historical data, we observed an increasing tendency of G1 prevalence from 72.0% in 2003 to 87.5% in 2016, which was accompanied by a decrease of G3 (17.9% vs. 9.1%) and G4 (9.0% vs. 3.1%). Conclusions Almost 85% of patients with HCV in Poland are infected with genotype 1 (almost exclusively subgenotype 1b), and its prevalence shows an increasing tendency, accompanied by a decrease of genotypes 3 and 4. PMID:28856279

Methods for discovering and validating relationships among genotyped animals

USDA-ARS?s Scientific Manuscript database

Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, t...

Genomic imputation and evaluation using high density Holstein genotypes

USDA-ARS?s Scientific Manuscript database

Genomic evaluations for 161,341 Holsteins were computed using 311,725 of the 777,962 markers on the Illumina high-density (HD) chip. Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Usable Holstein genotypes included 1,510 an...

The Correlation between Different Risk Factors of Hepatitis C and Different Genotypes

PubMed Central

Mokhtari, Mozhgan; Basirkazeruni, Hanieh; Rostami, Mojtaba

2017-01-01

Background: Hepatitis C infection is one of the health problems in the world. Several known risk factors are responsible in transmission of this infection. We are going to study the prevalence of these risk factors for different genotypes of hepatitis C and if possible, specify probable relations between each risk factor and transmission of each genotype. Materials and Methods: This is a cross-sectional study done on 270 people who had positive anti-hepatitis C virus (HCV) antibody and HCV RNA. Demographic specificity and possible risk factors were collected using a questionnaire, and statistical analysis was done by SPSS software (version 20). Chi-square test used to estimate the prevalence and relation between each qualitative risk factor and HCV genotype transmitted. Analysis of variance was used for studying the prevalence and relation between quantitative risk factors and HCV genotypes. Results: The sample size was 270 persons. Of these, 217 (80.4%) were men and 185 (68.5%) were infected with genotype Type III. Most people were in age range of 31–40 years old 92 (34%). Single people were 126 (46.7%) and 169 (62.6%) were high school and university graduated. Tattooing as a risk factor had a meaningful relation with hepatitis C genotype (P < 0.001). Conclusions: According to the findings, most people in central provinces of Iran with hepatitis C are carrying genotype III, with most prevalent risk factors such as intravenous drug use and unsafe sexual activity. Besides, tattooing had a significant association with hepatitis C genotype, so that in these groups of people, genotype I was more frequent isolated virus. PMID:28503500

Effects of ghrelin gene genotypes on the growth traits in Chinese cattle.

PubMed

Zhang, Ai-ling; Zhang, Li; Zhang, Liang-zhi; Zhang, Cun-fang; Lan, Xian-yong; Zhang, Chun-lei; Chen, Hong

2012-06-01

Ghrelin is an important peptide that stimulates food intake and regulates energy balance of animals. Single nucleotide polymorphisms of ghrelin gene in three Chinese cattle populations were investigated through PCR-SSCP and DNA sequencing. Five over-lapped DNA fragments were analyzed and a total of three ones exhibited different genotypes. Three genotypes and four SNPs (-415 A > G, -414 T > C, -321 C > A, and -172 A > G) were found on the -544 to +35 bp region (G-1) of ghrelin gene. On the locus of -1037 to -509 bp (G-2), two genotypes and one SNP (-726 A > T) were discovered. And in the exon1, exon2, and intron1 (G-4 locus, (+4 to +427)), two genotypes and one SNP were detected (+205 C > T, located in intron1). Positions of the five SNPs in the 5′ regulatory region might be the transcription factor binding sites. The SNPs at -415 and -414 in the core binding sequence were found to cause the change of the site. Though the SNP at -172 did not change the binding site, it generated one new site at the same time. The frequencies of the genotypes varied differently in the three breeds. Results of ANOVA showed that G-1 was correlative to the ischium width (IW) of Nanyang cattle aged 18 months (p = 0.043). The least square analysis between genotypes at G-1 locus and growth traits in Nanyang cattle showed that the individuals (aged 18 months) with C genotype had greater IW than that of the other two genotypes. The C genotype might serve as one potential candidate genetic marker for cattle growth and development.

Novel genotype of Tritrichomonas foetus from cattle in Southern Africa.

PubMed

Casteriano, Andrea; Molini, Umberto; Kandjumbwa, Kornelia; Khaiseb, Siegfried; Frey, Caroline F; Šlapeta, Jan

2016-12-01

Bovine trichomonosis caused by Tritrichomonas foetus is a significant reproductive disease of cattle. Preputial samples were collected using sheath washing technique in bulls in Namibia. Thirty-six trichomonad cultures were characterized using the TaqMan-probe commercial real-time polymerase chain reaction (PCR) diagnostic assay (VetMAX™-Gold Trich Detection Kit) and CYBR real-time PCR assay based on TFR3/4 primers. Diagnostic real-time PCRs and DNA sequencing of the internal transcribed region confirmed presence of T. foetus in 35 out of 36 samples. Multilocus genotyping using cysteine proteases (CP1, CP2, CP4, CP5, CP6, CP7, CP8, CP9) and malate dehydrogenase (MDH1) gene sequences demonstrate that the T. foetus in Namibia are genetically distinct from those characterized elsewhere. We report the discovery of a novel genotype of T. foetus in Namibian cattle, distinct from other T. foetus genotypes in Europe, South and North America and Australia. We suggest recognition of a 'Southern African' genotype of T. foetus. Identification of the new genotype of T. foetus demonstrates the need for wider global sampling to fully understand the diversity and origin of T. foetus causing disease in cattle or cats.

Number of repetitions for evaluating technological traits in cotton genotypes.

PubMed

Carvalho, L P; Farias, F J C; Morello, C L; Rodrigues, J I S; Teodoro, P E

2016-08-19

With the changes in spinning technology, technological cotton traits, such as fiber length, fiber uniformity, fiber strength, fineness, fiber maturity, percentage of fibers, and short fiber index, are of great importance for selecting cotton genotypes. However, for accurate discrimination of genotypes, it is important that these traits are evaluated with the best possible accuracy. The aim of this study was to determine the number of measurements (repetitions) needed to accurately assess technological traits of cotton genotypes. Seven experiments were conducted in four Brazilian States (Ceará, Rio Grande do Norte, Goiás, and Mato Grosso do Sul). We used nine brown and two white colored fiber lines in a randomized block design with four replications. After verifying the assumptions of residual normality and homogeneity of variances, analysis of variance was performed to estimate the repeatability coefficient and calculating the number of repetitions. Trials with four replications were found to be sufficient to identify superior cotton genotypes for all measured traits except short fiber index with a selective accuracy >90% and at least 81% accuracy in predicting their actual value. These results allow more accurate and reliable results in future researches with evaluating technological traits in cotton genotypes.

Sofosbuvir and Velpatasvir for HCV Genotype 1, 2, 4, 5, and 6 Infection.

PubMed

Feld, Jordan J; Jacobson, Ira M; Hézode, Christophe; Asselah, Tarik; Ruane, Peter J; Gruener, Norbert; Abergel, Armand; Mangia, Alessandra; Lai, Ching-Lung; Chan, Henry L Y; Mazzotta, Francesco; Moreno, Christophe; Yoshida, Eric; Shafran, Stephen D; Towner, William J; Tran, Tram T; McNally, John; Osinusi, Anu; Svarovskaia, Evguenia; Zhu, Yanni; Brainard, Diana M; McHutchison, John G; Agarwal, Kosh; Zeuzem, Stefan

2015-12-31

A simple treatment regimen that is effective in a broad range of patients who are chronically infected with the hepatitis C virus (HCV) remains an unmet medical need. We conducted a phase 3, double-blind, placebo-controlled study involving untreated and previously treated patients with chronic HCV genotype 1, 2, 4, 5, or 6 infection, including those with compensated cirrhosis. Patients with HCV genotype 1, 2, 4, or 6 were randomly assigned in a 5:1 ratio to receive the nucleotide polymerase inhibitor sofosbuvir and the NS5A inhibitor velpatasvir in a once-daily, fixed-dose combination tablet or matching placebo for 12 weeks. Because of the low prevalence of genotype 5 in the study regions, patients with genotype 5 did not undergo randomization but were assigned to the sofosbuvir-velpatasvir group. The primary end point was a sustained virologic response at 12 weeks after the end of therapy. Of the 624 patients who received treatment with sofosbuvir-velpatasvir, 34% had HCV genotype 1a, 19% genotype 1b, 17% genotype 2, 19% genotype 4, 6% genotype 5, and 7% genotype 6. A total of 8% of patients were black, 19% had cirrhosis, and 32% had been previously treated for HCV. The rate of sustained virologic response among patients receiving sofosbuvir-velpatasvir was 99% (95% confidence interval, 98 to >99). Two patients receiving sofosbuvir-velpatasvir, both with HCV genotype 1, had a virologic relapse. None of the 116 patients receiving placebo had a sustained virologic response. Serious adverse events were reported in 15 patients (2%) in the sofosbuvir-velpatasvir group and none in the placebo group. Once-daily sofosbuvir-velpatasvir for 12 weeks provided high rates of sustained virologic response among both previously treated and untreated patients infected with HCV genotype 1, 2, 4, 5, or 6, including those with compensated cirrhosis. (Funded by Gilead Sciences; ClinicalTrials.gov number, NCT02201940.).

Epigenomics and bolting tolerance in sugar beet genotypes.

PubMed

Hébrard, Claire; Peterson, Daniel G; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

2016-01-01

In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

General Anesthetics Have Additive Actions on Three Ligand-Gated Ion Channels

PubMed Central

Jenkins, Andrew; Lobo, Ingrid A.; Gong, Diane; Trudell, James R.; Solt, Ken; Harris, R. Adron; Eger, Edmond I

2008-01-01

Background The purpose of this study was to determine whether pairs of compounds, including general anesthetics, could simultaneously modulate receptor function in a synergistic manner, thus demonstrating the existence of multiple intra-protein anesthetic binding sites. Methods Using standard electrophysiologic methods, we measured the effects of at least one combination of benzene, isoflurane, halothane, chloroform, flunitrazepam, zinc and pentobarbital on at least one of the following ligand gated ion channels: N-methyl-D-aspartate receptors (NMDARs), glycine receptors (GlyRs) and γ-aminobutyric acid type A receptors (GABAARs). Results All drug-drug-receptor combinations were found to exhibit additive, not synergistic modulation. Isoflurane with benzene additively depressed NMDAR function. Isoflurane with halothane additively enhanced GlyR function, as did isoflurane with zinc. Isoflurane with halothane additively enhanced GABAAR function as did all of the following: halothane with chloroform, pentobarbital with isoflurane, and flunitrazepam with isoflurane. Conclusions The simultaneous allosteric modulation of ligand gated ion channels by general anesthetics is entirely additive. Where pairs of general anesthetic drugs interact synergistically to produce general anesthesia, they must do so on systems more complex than a single receptor. PMID:18633027

Approaches to genotyping individual miracidia of Schistosoma japonicum

PubMed Central

Xiao, Ning; Remais, Justin V.; Brindley, Paul J.; Qiu, Dong-chuan; Carlton, Elizabeth J.; Li, Rong-zhi; Lei, Yang; Blair, David

2013-01-01

Molecular genetic tools are needed to address questions as to the source and dynamics of transmission of the human blood fluke Schistosoma japonicum in regions where human infections have re-emerged, and to characterize infrapopulations in individual hosts. The life-stage that interests us as a target for collecting genotypic data is the miracidium, a very small larval stage that consequently yields very little DNA for analysis. Here, we report the successful development of a multiplex format permitting genotyping of 17 microsatellite loci in four sequential multiplex reactions using a single miracidium held on a Whatman Classic FTA indicating card. This approach was successful after short storage periods, but after long storage (>4 years) considerable difficulty was encountered in multiplex genotyping, necessitating the use of whole genome amplification (WGA) methods. WGA applied to cards stored for long periods of time resulted in sufficient DNA for accurate and repeatable genotyping. Trials and tests of these methods, as well as application to some field-collected samples, are reported, along with discussion of the potential insights to be gained from such techniques. These include recognition of sibships among miracidia from a single host, and inference of the minimum number of worm pairs that might be present in a host. PMID:24013341

Approaches to genotyping individual miracidia of Schistosoma japonicum.

PubMed

Xiao, Ning; Remais, Justin V; Brindley, Paul J; Qiu, Dong-Chuan; Carlton, Elizabeth J; Li, Rong-Zhi; Lei, Yang; Blair, David

2013-12-01

Molecular genetic tools are needed to address questions as to the source and dynamics of transmission of the human blood fluke Schistosoma japonicum in regions where human infections have reemerged, and to characterize infrapopulations in individual hosts. The life stage that interests us as a target for collecting genotypic data is the miracidium, a very small larval stage that consequently yields very little DNA for analysis. Here, we report the successful development of a multiplex format permitting genotyping of 17 microsatellite loci in four sequential multiplex reactions using a single miracidium held on a Whatman Classic FTA indicating card. This approach was successful after short storage periods, but after long storage (>4 years), considerable difficulty was encountered in multiplex genotyping, necessitating the use of whole genome amplification (WGA) methods. WGA applied to cards stored for long periods of time resulted in sufficient DNA for accurate and repeatable genotyping. Trials and tests of these methods, as well as application to some field-collected samples, are reported, along with the discussion of the potential insights to be gained from such techniques. These include recognition of sibships among miracidia from a single host, and inference of the minimum number of worm pairs that might be present in a host.

Choosing tree genotypes for phytoremediation of landfill leachate using phyto-recurrent selection

Treesearch

Jill A. Zalesny; Ronald S., Jr. Zalesny; Adam H. Wiese; Richard B. Hall

2007-01-01

Information about the response of poplar (Populus spp.) genotypes to landfill leachate irrigation is needed, along with efficient methods for choosing genotypes based on leachate composition. Poplar clones were irrigated during three cycles of phyto-recurrent selection to test whether genotypes responded differently to leachate and water, and to test...

Effect of hereditary haemochromatosis genotypes and iron overload on other trace elements.

PubMed

Beckett, Jeffrey M; Ball, Madeleine J

2013-02-01

Hereditary haemochromatosis is a common genetic disorder involving dysregulation of iron absorption. There is some evidence to suggest that abnormal iron absorption and metabolism may influence the status of other important trace elements. In this study, the effect of abnormal HFE genotypes and associated iron overload on the status of other trace elements was examined. Dietary data and blood samples were collected from 199 subjects (mean age = 55.4 years; range = 21-81 years). Dietary intakes, serum selenium, copper and zinc concentrations and related antioxidant enzymes (glutathione peroxidase and superoxide dismutase) in subjects with normal HFE genotype (n = 118) were compared to those with abnormal HFE genotype, with both normal iron status (n = 42) and iron overload (n = 39). For most dietary and biochemical variables measured, there were no significant differences between study groups. Red cell GPx was significantly higher in male subjects with normal genotypes and normal iron status compared to those with abnormal genotypes and normal iron status (P = 0.03) or iron overload (P = 0.001). Red cell GPx was also highest in normal women and significantly lower in the abnormal genotype and normal iron group (P = 0.016), but not in the iron overload group (P = 0.078). Although it may not be possible to exclude a small effect between the genotype groups on RBC GPx, overall, haemochromatosis genotypes or iron overload did not appear to have a significant effect on selenium, copper or zinc status.