Improved subseasonal prediction of South Asian monsoon rainfall using data-driven forecasts of oscillatory modes

Predicting the temporal and spatial patterns of South Asian monsoon rainfall within a season is of critical importance due to its impact on agriculture, water availability, and flooding. The monsoon intraseasonal oscillation (MISO) is a robust northward-propagating mode that determines the active and break phases of the monsoon and much of the regional distribution of rainfall. However, dynamical atmospheric forecast models predict this mode poorly. Data-driven methods for MISO prediction have shown more skill, but only predict the portion of the rainfall corresponding to MISO rather than the full rainfall signal. Here, we combine state-of-the-art ensemble precipitation forecasts from a high-resolution atmospheric model with data-driven forecasts of MISO. The ensemble members of the detailed atmospheric model are projected onto a lower-dimensional subspace corresponding to the MISO dynamics and are then weighted according to their distance from the data-driven MISO forecast in this subspace. We thereby achieve improvements in rainfall forecasts over India, as well as the broader monsoon region, at 10- to 30-d lead times, an interval that is generally considered to be a predictability gap. The temporal correlation of rainfall forecasts is improved by up to 0.28 in this time range. Our results demonstrate the potential of leveraging the predictability of intraseasonal oscillations to improve extended-range forecasts; more generally, they point toward a future of combining dynamical and data-driven forecasts for Earth system prediction.

Need for improvement in the evaluation of pre-malignant upper gastro-intestinal lesions in India: Results of a nationwide survey

BACKGROUND AND AIM

Gastric and esophageal cancers are associated with high morbidity in India. In the absence of formal screening programs in India, it is essential that all elective esophago-gastro-duodenoscopies (EGDs), irrespective of indication, be also considered an opportunity to screen for premalignant lesions. With this premise, we tried to assess the adherence to best practices in the detection of premalignant upper gastro-intestinal lesions (PMUGIL) among endoscopists in India. We also evaluated the adequacy of training, availability of appropriate facilities, and differences between teaching and non-teaching centers.

METHODS

We disbursed a survey among endoscopists working in India, through the membership database of the Society of Gastrointestinal Endoscopists of India, by email and instant messaging. The responses were collected and subsequently analyzed.

RESULTS

We obtained a total of 422 eligible responses. The adherence to best practices assessed was lower than the set threshold in all except one parameter in both teaching centers and non-teaching centers. Only 58.5% of endoscopists had received training in the detection of PMUGIL. Appropriate image enhanced endoscopy (IEE) facilities were available to only 58.05% of surveyed endoscopists.

CONCLUSIONS

Strategies to improve detection of PMUGIL should be directed at improving adherence to best practices, ensuring adequate training of endoscopists in the evaluation of PMUGIL and improving infrastructure.

Simethicone and N-acetyl cysteine combination as premedication before esophagogastroduodenoscopy: Double-blind randomized controlled trial

Background and study aims  Esophagogastroduodenoscopy (EGD), the most common method used for diagnosing upper gastrointestinal diseases, is often limited by the presence of foam and mucous. Thus, this study was designed to detect whether the combination of simethicone with N-acetyl cysteine (NAC) as premedication before EGD improves mucosal visualization. Patients and methods  A total of 768 consenting patients were enrolled in this prospective, double-blind, randomized placebo-controlled trial in four groups (A: simethicone + N-acetyl cysteine; B: simethicone alone; C: NAC alone; and D: placebo). After 20 minutes of consuming the corresponding solution, EGD was done and multiple images were obtained from the esophagus, stomach, and duodenum. Based on the various images obtained, the study parameters were calculated. Statistical Analysis Software (SAS) was used to analyze the results using Kruskal-Wallis with the Bonferroni correction method. Results  The study population consisted of 57 % men and the mean age was 44.18 years. Each group was randomized with 192 participants. Group A (combination of simethicone + NAC) premedication had the lowest total mucosal visibility score of 8.31, a significantly lower score for mucous/bubbles obscuring the vision, and less time to complete the procedure. Also, 81 % of the participants in group A did not require flushing to clear the mucous/bubbles. There were no side effects due to this premedication in any of the groups. Conclusions  Using simethicone and NAC combined for premedication may improve the quality of EGD.

Short term response of plankton community to nutrient enrichment in central eastern Arabian Sea: Elucidation through mesocosm experiments

Oligotrophic waters (OW), generally favour longer food chain facilitated by the microbial loop. In such ecosystems, physical mixing (e.g. upwelling, and winter convection) inject nutrients and propagules from subsurface to the photic zone. Such events are expected to alter the food chain through shifts in the plankton community. Mesocosm experiments were carried out to evaluate the influence of nutrient enrichment from the deep (100-150 m) on the surface plankton community for the first time in the Arabian Sea, through custom-designed enclosures in OW of the central-eastern Arabian Sea (CEAS). Surface water was characterized by low nutrients and phytoplankton biomass (chlorophyll-a of <0.2 μg m^-3) and upon nutrient enrichment yielded differing response. Higher abundance of picophytoplankton, bacteria and protists was noticed at a depth of ~100 m than at surface. The inoculation of such a population to the surface, resulted in a significant enhancement of autotrophic (picophytoplankton) and heterotrophic (bacteria and protists) populations. However, significant changes in the abundance of larger plankton was not evident till three days of incubation. Even though autotrophic picophytoplankton responded positively, a distinct increase in chlorophyll-a was not evident. This study points out that the lack of sufficient viable microphytoplankton propagules, neither at the surface nor at the depth (inoculum) are the possible reasons for the lack of their distinct positive response. These experiments suggest the dominance of microbial community response to physical mixing in the OW regions of the Arabian Sea and the importance of propagule diversity. The insights from this experiment will serve as a precursor for appropriate modifications in ocean modelling and forecasting studies and help in building global environmental management tools.

Predictability of Weather and Climate

The past developments in the predictability of weather and climate are discussed from the point of view of nonlinear dynamical systems. The problems ahead for long-range predictability extending into the climate time scale are also presented. The sensitive dependence of chaos on initial conditions and the imperfections in the models limit reliable predictability of the instantaneous state of the weather to less than 10 days in present-day operational forecasts. The existence of slowly varying components such as the sea surface temperature, soil moisture, snow cover, and sea ice may provide basis for predicting certain aspects of climate at long range. The regularly varying nonlinear oscillations, such as the Madden-Julian Oscillation, monsoon intraseasonal oscillations, and El Niño-Southern Oscillation, are also possible sources of extended-range predictability at the climate time scale. A prediction model based on phase space reconstruction has demonstrated that monsoon intraseasonal oscillation can be better predicted at long leads.

Strongyloides hyperinfection presenting as proteinlosing enteropathy

Strongyloides stercoralis, a soil-transmitted helminth, affects many people in tropical and subtropical countries. It is known to cause asymptomatic infection in immunocompetent and hyperinfection and disseminated Strongyloides infection in immunocompromised due to autoinfection. Here, we report a case of Strongyloides hyperinfection presenting with proteinlosing enteropathy. The diagnosis was made only with duodenal biopsy as the repeated stool examinations were negative. He was treated with ivermectin and his condition improved.

Bacteriospermia and Its Impact on Basic Semen Parameters among Infertile Men

Introduction. Semen analysis is considered as the surrogate marker for male fecundity while assessing infertile men. There are several reasons for altered semen quality and bacteriospermia could be one among them. Thereby the aim of our work is to study the semen culture and its impact on semen parameters among infertile men. Materials and Methods. Semen samples were collected from men attending infertility clinic. Semen parameters were analysed based on WHO guidelines. Also, samples were subjected to culture using standard bacteriological techniques. Results. A total of 85 samples were collected. A number of 47 (55.30%) had normal sperm count, 37 (43.50%) had oligozoospermia, and one (1.17%) had azoospermia. Teratozoospermia was the most common abnormality observed (81.17%) followed by asthenozoospermia (28.23%). The prevalence of bacteriospermia was 35.3%. Enterococcus faecalis (30%) was the most common organism isolated followed by Coagulase negative Staphylococcus (23.33%), Staphylococcus aureus (20%), and E. coli (10%). Other less frequently isolated organisms were Klebsiella pneumoniae (6.66%), Proteus sp. (6.66%), and Citrobacter sp. (3.33%). Conclusion. The presence of asymptomatic bacteriospermia did not correlate with abnormal semen parameters.

Two Unusual but Treatable Causes of Refractory Ascites After Liver Transplantation

Refractory ascites (RA) is thought to complicate the postoperative course of 5-7% (Nishida et al. in Am J Transplant. 6: 140-149, 2006; Gotthardt et al. in Ann Transplant. 18: 378-383, 2013) of liver transplant recipients. RA after liver transplantation is often a frustrating diagnostic dilemma with few good management options unless an obvious mechanical factor is identified. Supportive therapies often fail until a treatable precipitating cause is identified and removed. We describe two patients who developed RA following liver transplantation for primary sclerosing cholangitis, and hepatitis C and alcoholic liver disease, respectively. The cause for RA was hyperkinetic portal hypertension secondary to splenomegaly in the first case and a pancreatic AVM in the 2nd case. After failure of other interventions, surgical splenectomy resulted in immediate and durable resolution of the previously intractable ascites.

Defining acute ischemic stroke tissue pathophysiology with whole brain CT perfusion

BACKGROUND

This study aimed to identify and validate whole brain perfusion computed tomography (CTP) thresholds for ischemic core and salvageable penumbra in acute stroke patients and develop a probability based model to increase the accuracy of tissue pathophysiology measurements.

METHODS

One hundred and eighty-three patients underwent multimodal stroke CT using a 320-slice scanner within 6hours of acute stroke onset, followed by 24hour MRI that included diffusion weighted imaging (DWI) and dynamic susceptibility weighted perfusion imaging (PWI). Coregistered acute CTP and 24hour DWI was used to identify the optimum single perfusion parameter thresholds to define penumbra (in patients without reperfusion), and ischemic core (in patients with reperfusion), using a pixel based receiver operator curve analysis. Then, these results were used to develop a sigma curve fitted probability based model incorporating multiple perfusion parameter thresholds.

RESULTS

For single perfusion thresholds, a time to peak (TTP) of +5seconds best defined the penumbra (area under the curve, AUC 0.79 CI 0.74-0.83) while a cerebral blood flow (CBF) of < 50% best defined the acute ischemic core (AUC 0.73, CI 0.69-0.77). The probability model was more accurate at detecting the ischemic core (AUC 0.80 SD 0.75-0.83) and penumbra (0.85 SD 0.83-0.87) and was significantly closer in volume to the corresponding reference DWI (P=0.031).

CONCLUSIONS

Whole brain CTP can accurately identify penumbra and ischemic core using similar thresholds to previously validated 16 or 64 slice CTP. Additionally, a novel probability based model was closer to defining the ischemic core and penumbra than single thresholds.

Native valve Escherichia coli endocarditis following urosepsis

Gram-negative organisms are a rare cause of infective endocarditis. Escherichia coli, the most common cause of urinary tract infection and gram-negative septicemia involves endocardium rarely. In this case report, we describe infection of native mitral valve by E. coli following septicemia of urinary tract origin in a diabetic male; subsequently, he required prosthetic tissue valve replacement indicated by persistent sepsis and congestive cardiac failure.

Ethyl 3-amino-5-bromo-1-benzo-furan-2-carboxyl-ate

The title compound, C₁₁H₁₀BrNO₃, is close to planar with the benzo­furan unit and the ester group subtending a dihedral angle of 5.25 (2)°. The mol­ecular structure features an intra­molecular N—H⋯O inter­action. In the crystal, N—H⋯O hydrogen bonds involving carboxyl O-atom acceptors generate a chain extending along [201].

Ethyl 5-bromo-3-eth-oxy-carbonyl-amino-1-benzofuran-2-carboxyl-ate

In the title compound, C₁₄H₁₄BrNO₅, the ester group is disordered [occupancy ratio 0.52 (2):0.48 (2)]. The major component is nearly coplanar with the benzofuran plane, subtending a dihedral angle of 7.84 (2)°, while the amide group is twisted out of the benzofuran plane making a dihedral angle of 39.69 (2)°. An intra­molecular N—H⋯O hydrogen bond occurs. In the crystal, pairs of weak C—H⋯O hydrogen bonds link the mol­ecules into inversion dimers, which are further linked via strong N—H⋯O hydrogen bonds, generating a zigzag chain extending along [100].

Long-term outcome of DCIS patients: p53 as a biomarker of ipsilateral recurrence

39

Background: Ductal carcinoma in situ (DCIS) is a heterogeneous and potentially curable disease with a long natural history. DCIS represents 21% of breast cancers diagnosed in 2010. The risk of dying after a diagnosis of DCIS is low, emphasizing the importance of treatment-related morbidity, yet the risk of recurrence remains substantial. Optimum individualized therapy remains elusive. We previously identified p53 overexpression as a biomarker for ipsilateral tumor recurrence (IBTR). The purpose of the current study was to investigate its prognostic validity in an expanded patient cohort with long-term follow-up.

Methods: We studied 186 consecutive pure DCIS patients from our Breast Cancer Registry and identified 142 cases with sufficient histopathologic material to perform evaluable immunostaining for p53. Median follow-up was 11 years. Statistical analysis was performed with SAS software.

Results: Median patient age was 66 (range 35-91) years and 47/153 (31%) presented with palpable disease. Median tumor size was 10 (range 2-165) mm. Predominant histologic subtype included 34 (24%) comedo, 43 (30%) solid, 50 (35%) cribiform and 15 (11%) micropapillary/papillary cases. Necrosis was present in 74/142 (52%) of tumors. Overexpression of p53 was identified in 33/142 (23%) and was associated with necrosis, but not with any other patient, tumor or treatment variables. Fifteen patients (11%) were diagnosed with an IBTR at a median of 56 (range 11-154) months after their initial diagnosis; 3 recurrences were DCIS, while 12 were invasive cancer. p53 overexpression, present in 10/15 (68%) of cases with recurrence versus 23/127 (18%) of non-recurrent tumors, p < 0.001, and no adjuvant tamoxifen, p = 0.003, were associated with IBTR. No other patient, tumor or treatment factors studied were predictive of IBTR. The type of IBTR did not correlate with the p53 status of the index tumor.

Conclusions: These data suggest that p53 may be a biomarker for elevated risk of IBTR after a diagnosis of DCIS and support the value of adjuvant tamoxifen for DCIS patients. Further investigation to validate these findings and to identify clinically useful individualized risk stratification for DCIS patients is warranted.

An asymmetric approach to modeling ion channels using finite element analysis

Biological ion channels are water filled pores in the cell membrane. They regulate the flow of ions in and out of the cell. Modeling the dynamics of these channels and relating their structure to functionality is crucial in understanding the mechanisms by which they conduct. This paper proposes a novel Finite Element Method (FEM) based simulation framework for modeling of ion channels that does not assume channel symmetry. This is the first framework that allows the use of multiple dielectric constants inside such channels without assuming geometrical symmetry thus providing a more realistic model of the channel. Due to the run-time complexity of the problem, lookup tables must be constructed in memory to store pre-calculated electric potential information. The large number of elements involved in FEM and channel resolution requirements can potentially result in very large lookup tables leading to a performance "bottleneck". This paper answers the following question: Does the accuracy introduced by using an asymmetric model outweigh the inaccuracy caused by having to reduce the size and resolution of electric-field look-up tables? This paper compares the memory footprint of an ion channel simulator that assumes a symmetric channel model versus an asymmetric model. We show that currently available personal computers are sufficient for attaining reasonable levels of accuracy for both. Our results show diminishing returns in accuracy with tables sized greater than 8.5 GB for the asymmetric model.

Assessing dust exposure in an integrated iron and steel manufacturing plant in South India

A study to monitor and estimate respirable particulate matter (RPM), toxic trace metal concentrations in the work environment was carried out in different sections of an integrated steel manufacturing industry. The average RPM concentration observed varied according to the section blast furnace was 2.41 mg/m;{3}; energy optimization furnace, 1.87 mg/m;{3}; sintering plant, 0.98 mg/m;{3}; continuous casting machine, 1.93 mg/m;{3}. The average trace metal concentration estimated from the RPM samples like iron, manganese, lead and chromium did not exceed ACGIH prescribed levels.

Three successful pregnancies through dietary management of fructose-1,6-bisphosphatase deficiency

Fructose-1,6-bisphosphatase (FBPase) deficiency (OMIM 229700) has been characterized as the cause of life-threatening hypoglycaemia and lactic acidaemia following prolonged fasting. The patient, an adult African-American woman, presented during the second trimester of her first pregnancy with recurrent episodes of lactic acidaemia and hypoglycaemia. She had recently been admitted to a nearby intensive care unit after presentation with profound hypoglycaemia and lactic acidosis, and was found to be pregnant. The history was remarkable for approximately 30 hospitalizations for hypoglycaemia and acidosis. She had previously undergone liver biopsy at another centre and was diagnosed with a 'glycogen storage disease', although no enzyme testing had been done for confirmation. Based on clinical symptoms, a diagnosis of FBPase deficiency was accomplished through gene sequencing, which revealed homozygosity for a panethnic, common mutation, 960/961insG in exon 7. The availability of mutation testing facilitated the confirmation of FBPase deficiency in this patient, obviating liver biopsy for enzyme activity confirmation. The patient underwent three successful pregnancies by strict compliance with dietary management, including nocturnal uncooked cornstarch to manage hypoglycaemia. The pregnancies were complicated by mild gestational diabetes, increased cornstarch requirements, and hypoglycaemia at the time of discharge from the hospital. The three infants had normal birth weights and experienced no complications during the neonatal period. The patient subsequently developed sensorineural hearing loss and early-onset cognitive impairment, despite compliance with the monitoring and treatment of hypoglycaemia. The experience with multiple pregnancies in this FBPase-deficient patient provides insight into the management of hypoglycaemia in inherited disorders of gluconeogenesis.

Environmental and Biological Monitoring in a Lead Acid Battery Manufacturing Unit in India

An environmental and biological monitoring of a lead acid battery manufacturing unit was carried out to measure the respirable particulate matter, lead content in working atmosphere and blood lead levels of workers employed in different sections. The results showed high mean air lead concentration in buffing (1444.45 microg/m(3)), plate cutting (430.14 microg/m(3)) and pasting (277.48 microg/m(3)) sections. The mean blood lead levels of employees in these sections were also higher than the values prescribed by ACGIH.

Hepatocellular carcinoma in glycogen storage disease type Ia: a case series

We present a series of 8 patients (6 males, 2 females) with hepatocellular carcinoma (HCC) and glycogen storage disease type Ia (GSD Ia). In this group, the age at which treatment was initiated ranged from birth to 39 years (mean 9.9 years). All patients but one were noncompliant with treatment. Hepatic masses were first detected at an age range of 13-45 years (mean 28.1 years). Age at diagnosis of HCC ranged from 19 to 49 years (mean 36.9 years). Duration between the diagnosis of liver adenomas and the diagnosis of HCC ranged from 0 to 28 years (mean 8.8 years, SD = 11.5). Two patients had positive hepatitis serologies (one hepatitis B, one hepatitis C). Alpha-fetoprotein (AFP) was normal in 6 of the 8 patients. Carcinoembryonic antigen (CEA) was normal in the 5 patients in which it was measured. Current guidelines recommend abdominal ultrasonography with AFP and CEA levels every 3 months once patients develop hepatic lesions. Abdominal CT or MRI is advised when the lesions are large or poorly defined or are growing larger. We question the reliability of AFP and CEA as markers for HCC in GSD Ia. Aggressive interventional management of masses with rapid growth or poorly defined margins may be necessary to prevent the development of HCC in this patient population.

Behavioural and chemical confirmation of the preovulatory pheromone, (Z)-7-dodecenyl acetate, in wild Asian elephants: its relationship to musth

Mammalian breeding strategies vary depending on particular social contexts and sensory systems emphasized in various species. Among sexually dimorphic non-territorial Asian elephants, Elephas maximus, a multiplex olfactory chemical signaling system has been implicated in ensuring effective reproduction. This study explores how, using chemosensory mechanisms, widely roaming, wild male elephants locate periovulatory females in matriarchal-led female family units and precisely assess their ovulatory status. In this species, the dual obstacles of separately living sexes and infrequent oestrus are overcome by lengthy female cycles. During an extended preovulatory period captive females release increasing concentrations of the urinary pheromone (Z)-7-dodecenyl acetate, timed to reach a maximum just before ovulation. The current field studies combined chemical identification and quantification of female urinary (Z)-7-dodecenyl acetate with behavioural observations, monitoring the frequencies of chemosensory responses and premating behaviours by various categories of males. The results suggest the temporal extension of the preovulatory period effectively provides a synchrony between sexes for successful reproduction. Male elephants undergo a two-decade-long maturation process that involves physical, sexual, social, and physiological maturation. Males older than 30 years are generally large, sexually active, socially adept and capable of sustaining long periods of musth, during which they release secretions distinctive of adult musth. These older adult males in musth demonstrated significantly more chemosensory responses and premating behaviours than their younger or nonmusth counterparts; they apparently are more skilled at detecting the precise ovulatory status of females. Male–male interactions are affected by size, age, and musth; the winners gain greater access to females, as indicated by the high incidence of mate guarding. The Asian elephant shares some breeding tactics common to other mammals including some primates (e.g. orangutans) and whales, while the musth parameter adds a unique feature. Fusion–fission events are influenced by elephant reproductive strategies, as roving males join female groups while tracking preovulatory pheromone concentrations.

Mammalian breeding strategies vary depending on particular social contexts and sensory systems emphasized in various species. Among sexually dimorphic non-territorial Asian elephants,

Elephas maximus

, a multiplex olfactory chemical signaling system has been implicated in ensuring effective reproduction. This study explores how, using chemosensory mechanisms, widely roaming, wild male elephants locate periovulatory females in matriarchal-led female family units and precisely assess their ovulatory status. In this species, the dual obstacles of separately living sexes and infrequent oestrus are overcome by lengthy female cycles. During an extended preovulatory period captive females release increasing concentrations of the urinary pheromone (

Z

)-7-dodecenyl acetate, timed to reach a maximum just before ovulation. The current field studies combined chemical identification and quantification of female urinary (

Z

)-7-dodecenyl acetate with behavioural observations, monitoring the frequencies of chemosensory responses and premating behaviours by various categories of males. The results suggest the temporal extension of the preovulatory period effectively provides a synchrony between sexes for successful reproduction. Male elephants undergo a two-decade-long maturation process that involves physical, sexual, social, and physiological maturation. Males older than 30 years are generally large, sexually active, socially adept and capable of sustaining long periods of musth, during which they release secretions distinctive of adult musth. These older adult males in musth demonstrated significantly more chemosensory responses and premating behaviours than their younger or nonmusth counterparts; they apparently are more skilled at detecting the precise ovulatory status of females. Male–male interactions are affected by size, age, and musth; the winners gain greater access to females, as indicated by the high incidence of mate guarding. The Asian elephant shares some breeding tactics common to other mammals including some primates (e.g. orangutans) and whales, while the musth parameter adds a unique feature. Fusion–fission events are influenced by elephant reproductive strategies, as roving males join female groups while tracking preovulatory pheromone concentrations.

Diagnostic and treatment challenges of neuronopathic Gaucher disease: two cases with an intermediate phenotype

Gaucher disease (GD) is a lysosomal storage disorder with a broad, overlapping clinical spectrum. The presented two case reports highlight the clinical evaluation required in neuronopathic GD to assist with medical management and genetic counselling.

Mellifluous matures to malodorous in musth

Male Asian elephants in musth--an annual period of heightened sexual activity and intensified aggression--broadcast odoriferous, behaviourally influential messages from secretions of the temporal gland. From our observations in the wild, together with instantaneous chemical sampling and captive-elephant playback experiments, we have discovered that young, socially immature males in musth signal their naivety by releasing honey-like odours to avoid conflict with adult males, whereas older musth males broadcast malodorous combinations to deter young males, facilitating the smooth functioning of male society. As elephant--human conflicts can upset this equilibrium, chemically modulating male behaviour may be one way to help the conservation of wild elephants.

S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes

The requirement of S-adenosyl-L-methionine (AdoMet) in the cleavage reaction carried out by type III restriction-modification enzymes has been investigated. We show that DNA restriction by EcoPI restriction enzyme does not take place in the absence of exogenously added AdoMet. Interestingly, the closely related EcoP15I enzyme has endogenously bound AdoMet and therefore does not require the addition of the cofactor for DNA cleavage. By employing a variety of AdoMet analogs, which differ structurally from AdoMet, this study demonstrates that the carboxyl group and any substitution at the epsilon carbon of methionine is absolutely essential for DNA cleavage. Such analogs could bring about the necessary conformational change(s) in the enzyme, which make the enzyme proficient in DNA cleavage. Our studies, which include native polyacrylamide gel electrophoresis, molecular size exclusion chromatography, UV, fluorescence and circular dichroism spectroscopy, clearly demonstrate that the holoenzyme and apoenzyme forms of EcoP15I restriction enzyme have different conformations. Furthermore, the Res and Mod subunits of the EcoP15I restriction enzyme can be separated by gel filtration chromatography in the presence of 2 M NaCl. Reconstitution experiments, which involve mixing of the isolated subunits, result in an apoenzyme form, which is restriction proficient in the presence of AdoMet. However, mixing the Res subunit with Mod subunit deficient in AdoMet binding does not result in a functional restriction enzyme. These observations are consistent with the fact that AdoMet is required for DNA cleavage. In vivo complementation of the defective mod allele with a wild-type mod allele showed that an active restriction enzyme could be formed. Furthermore, we show that while the purified c2-134 mutant restriction enzyme is unable to cleave DNA, the c2-440 mutant enzyme is able to cleave DNA albeit poorly. Taken together, these results suggest that AdoMet binding causes conformational changes in the restriction enzyme and is necessary to bring about DNA cleavage.

ATP-dependent restriction enzymes

The phenomenon of restriction and modification (R-M) was first observed in the course of studies on bacteriophages in the early 1950s. It was only in the 1960s that work of Arber and colleagues provided a molecular explanation for the host specificity. DNA restriction and modification enzymes are responsible for the host-specific barriers to interstrain and interspecies transfer of genetic information that have been observed in a variety of bacterial cell types. R-M systems comprise an endonuclease and a methyltransferase activity. They serve to protect bacterial cells against bacteriophage infection, because incoming foreign DNA is specifically cleaved by the restriction enzyme if it contains the recognition sequence of the endonuclease. The DNA is protected from cleavage by a specific methylation within the recognition sequence, which is introduced by the methyltransferase. Classic R-M systems are now divided into three types on the basis of enzyme complexity, cofactor requirements, and position of DNA cleavage, although new systems are being discovered that do not fit readily into this classification. This review concentrates on multisubunit, multifunctional ATP-dependent restriction enzymes. A growing number of these enzymes are being subjected to biochemical and genetic studies that, when combined with ongoing structural analyses, promise to provide detailed models for mechanisms of DNA recognition and catalysis. It is now clear that DNA cleavage by these enzymes involves highly unusual modes of interaction between the enzymes and their substrates. These unique features of mechanism pose exciting questions and in addition have led to the suggestion that these enzymes may have biological functions beyond that of restriction and modification. The purpose of this review is to describe the exciting developments in our understanding of how the ATP-dependent restriction enzymes recognize specific DNA sequences and cleave or modify DNA.

Rule-based programming paradigm: a formal basis for biological, chemical and physical computation

A rule-based programming paradigm is described as a formal basis for biological, chemical and physical computations. In this paradigm, the computations are interpreted as the outcome arising out of interaction of elements in an object space. The interactions can create new elements (or same elements with modified attributes) or annihilate old elements according to specific rules. Since the interaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward an equilibrium or unstable or chaotic state. Such an evolution may retain certain invariant properties of the attributes of the elements. The object space resembles Gibbsian ensemble that corresponds to a distribution of points in the space of positions and momenta (called phase space). It permits the introduction of probabilities in rule applications. As each element of the ensemble changes over time, its phase point is carried into a new phase point. The evolution of this probability cloud in phase space corresponds to a distributed probabilistic computation. Thus, this paradigm can handle tor deterministic exact computation when the initial conditions are exactly specified and the trajectory of evolution is deterministic. Also, it can handle probabilistic mode of computation if we want to derive macroscopic or bulk properties of matter. We also explain how to support this rule-based paradigm using relational-database like query processing and transactions.

Functional analysis of conserved motifs in type III restriction-modification enzymes

EcoP1I and EcoP15I are members of type III restriction-modification enzymes. EcoPI and EcoP15I DNA methyltransferases transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the N6 position of the second adenine residues in their recognition sequences, 5'-AGACC-3' and 5'-CAGCAG-3' respectively. We have altered various residues in two highly conserved sequences, FxGxG (motif I) and DPPY (motif IV) in these proteins by site-directed mutagenesis. Using a mixture of in vivo and in vitro assays, our results on the mutational analysis of these methyltransferases demonstrate the universal role of motif I in AdoMet binding and a role for motif IV in catalysis. All six cysteine residues in EcoP15I DNA methyltransferase have been substituted with serine and the role of cysteine residues in EcoP15I DNA methyltransferase catalysed reaction assessed. The Res subunits of type III restriction enzymes share a distant sequence similarity with and contain the motifs characteristic of the DEAD box proteins. We have carried out site-directed mutagenesis of the conserved residues in two of the helicase motifs of the EcoP1I restriction enzyme in order to investigate the role of motifs in DNA cleavage by this enzyme. Our findings indicate that certain conserved residues in these motifs are involved in ATP hydrolysis while the other residues are involved in coupling restriction of DNA to ATP hydrolysis. Taken collectively, these results form the basis for a detailed structure-function analysis of EcoP1I and EcoP15I restriction enzymes.

Essential thrombocythemia and epidural analgesia in the parturient. Does thromboelastography help?

BACKGROUND AND OBJECTIVES

It is often considered that essential thrombocythemia contraindicates placement of an epidural catheter because of the danger of epidural hematoma. Thromboelastography offers a possible means of determining the appropriateness of epidural analgesia in a patient with this disorder.

METHODS

A pregnant woman with essential thrombocythemia and a history of spontaneous abortions was evaluated by thromboelastography at 38 weeks of gestation to determine the safety of using epidural analgesia for labor pain management. On the basis of the thermoelastography findings, the patient was given epidural analgesia with bupivacaine and fentanyl during her labor.

RESULTS

The patient experienced good pain relief, delivered a healthy infant vaginally, and suffered no complications.

CONCLUSIONS

Thromboelastography may be a useful diagnostic test in determining the suitability of regional techniques for labor analgesia in parturients with essential thrombocythemia. However, success in one patient does not prove the general safety of this approach.

DNA recognition by the EcoP15I and EcoPI modification methyltransferases

The DNA-binding properties of the EcoP15I DNA methyltransferase (M.EcoP15I; MTase) were studied using electrophoretic mobility shift assays. We show by molecular size-exclusion chromatography and dimethyl suberimidate cross-linking that M.EcoP15I is a dimer in solution. While M.EcoP15I binds approx. threefold more tightly to its recognition sequence, 5'-CAGCAG-3', than to non-specific sequences in the presence of AdoMet or its analogs, the discrimination between specific and non-specific sequences significantly increases in presence of ATP. These results suggest for the first time a role for ATP in DNA recognition by type-III restriction-modification enzymes. Furthermore, we show that although c2 EcoPI mutant MTases are defective in AdoMet binding, they are still able to bind DNA in a sequence-specific manner.

Interaction of EcoP1 modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study

EcoP1 modification methylase was radioactively labeled when incubated with S-adenosyl-L-[methyl-3H]methionine in the presence of ultraviolet light. Crosslinking of the enzyme as detected by electrophoresis on sodium dodecyl sulfate-polyacrylamide gel followed by fluorography and autoradiography, was shown to be specific by a number of criteria. More importantly, EcoP1 modification methylase was also radioactively labeled with S-adenosyl-L-[carboxyl-14C]methionine demonstrating that labeling involved binding of the entire AdoMet molecule rather than methylation of the protein. Further, c2 EcoP1 mutant DNA modification methylases which show negligible or very little methylation activity, correspondingly formed a weak or no adduct upon crosslinking. These results suggest that photolabeling of EcoP1 DNA modification methylase occurs at the AdoMet binding site.

Wave digital matched filter for electrocardiogram preprocessing

Digital filters play an important role in electrocardiography. Digital filter algorithms having low sensitivity to finite word-length errors are generally desirable. Wave digital filters (WDFs) are a class of filters having excellent sensitivity properties. A wave digital matched filter (WDMF) for ECG preprocessing is presented here.