Plant metabolomics: from experimental design to knowledge extraction

Metabolomics is one of the most recent additions to the functional genomics approaches. It involves the use of analytical chemistry techniques to provide high-density data of metabolic profiles. Data is then analyzed using advanced statistics and databases to extract biological information, thus providing the metabolic phenotype of an organism. Large variety of metabolites produced by plants through the complex metabolic networks and their dynamic changes in response to various perturbations can be studied using metabolomics. Here, we describe the basic features of plant metabolic diversity and analytical methods to describe this diversity, which includes experimental workflows starting from experimental design, sample preparation, hardware and software choices, combined with knowledge extraction methods. Finally, we describe a scenario for using these workflows to identify differential metabolites and their pathways from complex biological samples.

Topography and morphological anatomy of nutrient foramina in human metacarpal bones and their clinical implications

PURPOSE

To study the morphological and topographic anatomy of nutrient foramina and to determine the foraminal index of metacarpal bones.

MATERIALS AND METHODS

The study consisted of 438 unpaired, human metacarpal bones of unknown age and sex. Nutrient foramina in each of the bones were grossly identified in relation to their number and location. The foraminal index was calculated by applying the Hughes formula. A digital vernier caliper was used to perform the measurements.

RESULTS

Among our specimens, 93.1% of metacarpals had single foramen, 2% had double foramina, 0.3% of the bones had triple foramina and in 4.6% of cases the foramen was absent. The mean foraminal indexes of the 1st, 2nd, 3rd, 4th and 5th metacarpal were 60.1, 53, 43.1, 43.7 and 45.9 respectively.

CONCLUSION

It was observed that the morphology and topography of nutrient foramina vary among different metacarpals. In 1st and 2nd metacarpals, foramina were more common at the medial surface and in other metacarpals, mostly seen on the lateral surface. The knowledge about these foramina is important in certain surgical procedures to preserve the circulation. This data is important to the plastic surgeon for microvascular bone transfer surgeries.

Green and NIR sensitized luminescent nanophosphor: preparation, characterization and application

Luminescent nanophosphor of Er, Yb: Gd(2)O(3) has been synthesized by well known combustion synthesis. Along with strong UV-Vis upconversion emission, sensor for temperature and magnetic field, nano-heater etc., it can also be used as luminescent ink by dispersing the nanophosphor in aqueous polyvinyl alcohol solution. The stability of the ink has been found to depend strongly on the mixing process of the phosphor powder in the polymer solution. The X-ray diffraction results and TEM images with diffraction pattern show that the particles are in cubic phase of Gd(2)O(3) with particles of average size <40 nm. SEM images show flaky structure which makes it suitable for dispersing in PVA and useful for luminescent ink purposes on NIR excitation. The FT-IR and the thermal analysis support the presence of PVA. Upconversion and downconversion luminescence has also been observed with 532 nm excitation and energy transfer mechanism has been explained. The NIR pumping gives strong UC emission bands in red and green regions extending up to extreme UV (240 nm) in this host.

Range of motion of the metacarpophalangeal joint in rheumatoid patients, with and without a flexible joint replacement prosthesis, compared with normal subjects

BACKGROUND

The metacarpophalangeal is commonly affected by rheumatoid arthritis. This may lead to joint replacement with a flexible prosthesis. The aims of this study were to determine the effects of rheumatoid arthritis on joint motion and to determine whether joint replacement needs to restore the full range of motion.

METHODS

Three-dimensional motion analysis was used to measure the range of motion of the metacarpophalangeal joint in rheumatoid patients with and without a flexible silicone arthroplasty, when performing pinch and key grips, when making a fist and when spreading the fingers. The results were compared with those from younger and older normal subjects.

FINDINGS

There appeared to be a trend for a decrease in range of motion from younger normal to older normal to rheumatoid (no prosthesis) to rheumatoid (with prosthesis) subject groups. However, statistically different (p<0.05) results were only observed for some movements (mostly involved in making a fist), in some fingers and between some subject groups. The only exception to this apparent trend was in flexion/extension when spreading the fingers into abduction.

INTERPRETATION

Making a fist is the most sensitive simple measure of range of motion in the metacarpophalangeal joint. Successful replacement of the metacarpophalangeal joint in patients with rheumatoid arthritis need not restore the normal range of motion.

Effects of Low Dose Vasopressin in Catecholamine Resistant Septic Shock

BACKGROUND

Septic shock commonly leads to death in critically ill patients. Severe hypotension resistant to conventional catecholamine leads to multiorgan failure. We studied the effectiveness of low dose vasopressin in resistant septic shock.

METHODS

Thirty critically ill patients with catecholamine resistant hypotension were included in the study. After adequate fluid resuscitation, infusion of norepinephrine and dobutamine was started. If the patient remained hypotensive, vasopressin was infused at a fixed rate of 0.04 unit/minute for 24 hours. Haemodynamic parameters and mortality rates were recorded.

RESULT

There was a significant improvement in systolic and mean arterial pressure within four hours of starting vasopressin. This improvement continued throughout the 24-hour period. In addition, it was possible to withdraw dopamine in all the patients and significantly reduce infusion rates of dobutamine and norepinephrine. No significant complication was noted.

CONCLUSION

Low dose vasopressin at the rate of 0.04 unit/minute is an effective vasopressor in adult patients with catecholamine resistant septic shock.

Extent of surgery in the management of phyllodes tumor of the breast: a retrospective multicenter study from India

INTRODUCTION

Phyllodes tumor (PT) is a rare tumor of the breast. Usually, difficulty in making preoperative diagnoses and unpredictable clinical outcome of this disease leads to inappropriate management. Till date, no definite conclusion regarding the appropriate surgical procedure can be drawn.

OBJECTIVES

The objective of this retrospective study is to study the clinicopathological correlation of phyllodes tumors in North-Central part of the India and also to evaluate efficacy of the various surgical options available for the management of phyllodes tumors of the breast.

MATERIALS AND METHODS

A retrospective study of 24 cases from the archives of department of surgery of three tertiary institutes of North-Central part of India. We reviewed the clinical, pathological features of this disease entity with a view to highlight relevant features. We also analyzed various surgical options done for primary as well as recurrent PT.

RESULTS

The breast masses in our study were particularly large. The mean size of the lump was 9.5 +/- 5.5 cm (range was 4.0-23 cm). Histopathological report was benign, borderline, and malignant PT in 62.4%, 20.8%, and 16.8% of the cases, respectively. Overall, 31 surgical procedures (24 in primary and 7 in recurrent) were performed. Simple lumpectomy, wide local excision and simple mastectomy were done in 25%, 27.4% and 27.4% of primary (non-recurrent) cases of PT, respectively. Modified radical mastectomy and simple mastectomy with LD flap reconstruction was done in 7.2% and 2.4% in primary cases, respectively in recurrent cases, simple mastectomy was done in four cases and modified radical mastectomy was done in one case. Overall, recurrence was seen in 29.2% of the cases. The median time for recurrence was 6 months (range 5.0-36 months). 90% (6/7) of recurrence occurred in lumpectomy patients.

CONCLUSION

The unpredictable behavior of histological types and the disputable results of particular surgical procedures have contributed to the controversies. The therapeutic issue is further compounded by an imprecise preoperative diagnosis. This study shows that wide local excision for benign and borderline and simple mastectomy with or without reconstruction for the malignant PT of the breast are acceptable best surgical options.

Small interfering RNAs inhibit infectious bursal disease virus replication in Vero cells

Small interfering RNA (siRNA) molecules are considered to be a promising antiviral therapeutics. This study was performed to analyze the application of siRNA against infectious bursal disease virus (IBDV) replication. Two siRNAs were designed to target common coding sequences of four IBDV proteins. Corresponding vectors were constructed to express anti-IBDV short hairpin RNAs (shRNA) that were tested for their antiviral effect in Vero cells. The results showed that expressed shRNA inhibited the virus replication to a significant extent (92%) as determined by the virus titration in cell culture. This outcome demonstrated the effectiveness of RNA interference (RNAi) based mechanism against the IBDV in vitro.

Direct detection and serogroup characterization of Neisseria meningitidis from outbreak of meningococcal meningitis in Delhi

BACKGROUND AND OBJECTIVES

Rapid clinical manifestation/progression of the meningococcal meningitis and lacunae in conventional bacteriological test often encourages indiscriminate use of antibiotics much before the etiology is established. Accordingly this study was planned to evaluate ctrA PCR for rapid molecular detection. In addition, multiplex PCR and sequencing was done for serogroup prediction to provide essential epidemiological and laboratory evidence for decision makers of health department of the country for choosing appropriate vaccine and phylogenetic analysis to establish its lineage.

MATERIALS AND METHODS

73 CSF samples, collected from equal number of suspected cases, were investigated by both bacteriological (microscopy, culture, LA and drug sensitivity testing) as well as molecular tests i.e. PCR targeting conserved ctrA gene, multiplex PCR for serogroup characterization and DNA sequencing.

RESULTS

ctrA PCR revealed sensitivity, specificity, positive predictive value and negative predictive values of 93.15%, 100%,100%, and 88.23% respectively. Multiplex PCR based genogrouping followed by DNA sequencing, BLAST and phylogenetic analysis revealed complete homology with earlier submitted Neisseria meningitidis serogroup A strain Z2491 to suggest the sole involvement of only serogroup A in the outbreak. Two strains showed resistance to cefuroxime, ciprofloxacin, nalidixic acid. Only one strain showed resistance to ciprofloxacin, emphasizing the need for a constant surveillance system.

CONCLUSION

These diagnostic molecular tools are of paramount importance in establishing etiology, serogrouping, and epidemiological surveillance especially in developing countries like India.

Quantum entanglement in coupled lossy waveguides

We investigate the viability of coupled waveguides as basic units of quantum circuits. We study entanglement when the waveguides are fed in by light produced by a down-converter working either in low gain limit or under large gain. We present explicit analytical results for the measure of entanglement in terms of the logarithmic negativity for a variety of input states. We also address the effect of loss on entanglement dynamics of waveguide modes. Our results indicate that the waveguide structures are reasonably robust against the effect of loss and thus quite appropriate for quantum architectures as well as for the study of coherent phenomena like random walks. Our analysis is based on realistic structures used currently.

Differential transcriptional expression following thidiazuron-induced callus differentiation developmental shifts in rice

Very little is known about molecular events associated with callus differentiation in indica rice. The genes expressed differentially during shoot meristem initiation were identified on genomic arrays applied to efficiently regenerating rice calli. A thidiazuron (TDZ; N-phenyl-N-thiadiazol-1,2,3-5,ylurea)-dependent regeneration protocol was developed for efficient embryogenesis in indica rice. The regenerating embryogenic calli induced by TDZ for 10 days showed transcriptional modulation of a number of genes associated with photosynthesis, hormone metabolism, plant development, signal transduction, light response, and plant defense. Eighteen candidate miRNAs were predicted to target the genes expressed differentially in the embryogenic calli grown in TDZ-containing medium. The majority of the photosynthesis-related genes up-regulated in differentiating calli were not expressed or were down-regulated in developing seeds and inflorescences. Most of the genes down-regulated in differentiating calli were up-regulated in developing seeds. The transcriptome of differentiating callus most closely resembled that of the germinating whole seed.

Characterization of RPO B gene for detection of rifampicin drug resistance by SSCP and sequence analysis

PURPOSE

Because of the emergence of multidrug-resistant tuberculosis in recent times, the rapid detection of resistance to the first-line anti-tuberculosis drug rifampicin was felt worldwide. Accordingly, this study was conducted to evaluate the diagnostic potential of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) for checking its utility as a rapid screening test for determination of rifampicin drug resistance.

MATERIALS AND METHODS

A total of 34 isolates of Mycobacterium tuberculosis (M. tuberculosis) (22 rifampicin resistant, 11 rifampicin sensitive and one control H37Rv) strains were analysed by PCR-SSCP and DNA sequencing within the 157-bp region of the rpo B gene (Ala 500-Val 550).

RESULTS

Rifampicin resistance was detected successfully by PCR-SSCP in 20/22(90.90%) of rifampicin-resistant strains showing a total of nine different mutations in seven codon positions: codon 513 (CAA-->CCA), 516 (GAC-->GTC), 507 (GGC-->GAC), 526 (CAC-->GAC, TAC), 531 (TCG-->TTG, TGG), 522 (TCG-->TGG) and 533 (GTG-->CCG). Two rifampicin-resistant strains showed an identical PCR-SSCP pattern with the wild type H37Rv; 77.27% rifampicin-resistant strains showed a single point mutation and 9.09% had no mutation. Three rifampicin-resistant strains showed characteristic double mutations at codon positions 526 and 531. Sensitivity and specificity were calculated as 90.90% and 100%.

CONCLUSIONS

Rifampicin-resistant genotypes were mainly found in codon positions 516, 526 and 531. PCR-SSCP seems to be an efficacious method of predicting rifampicin resistance and substantially reduces the time required for susceptibility testing from 4 to 6 weeks to a few weeks.

Progression of imaging in pancreatitis panniculitis polyarthritis (PPP) syndrome

Lobular panniculitis, together with a polyarthritis may complicate pancreatic disease. Abdominal symptoms are frequently absent and mis-diagnosis of the joint-skin complex can lead to inappropriate treatment in a condition with an already high mortality. We report a case of the pancreatitis panniculitis polyarthritis (PPP) syndrome, complicated by metastatic fat necrosis, with bone marrow involvement and characteristic magnetic resonance imaging (MRI) and describe the clinical characteristics, therapy and outcome of patients affected by the syndrome.

A sindbis virus replicon-based DNA vaccine encoding the rabies virus glycoprotein elicits immune responses and complete protection in mice from lethal challenge

A sindbis virus replicon-based DNA vaccine encoding rabies virus glycoprotein (G) was developed by subcloning rabies G gene into a sindbis virus replicon-based vaccine vector (pAlpha). The self-amplification of RNA transcripts and translation efficiency of rabies G was analyzed in pAlpha-Rab-G-transfected mammalian cells using RT-PCR, SDS-PAGE and Western blot analysis. The transfected cells also showed induction of apoptosis which is an important event in the enhancement of immune responses. Further, immune responses induced with replicon-based rabies DNA vaccine (pAlpha-Rab-G) was compared with conventional rabies DNA vaccine and commercial cell culture vaccine (Rabipur) in intramuscularly injected mice. The mice immunized with replicon-based rabies DNA vaccine induced humoral and cell mediated immune responses better than conventional rabies DNA vaccine however, comparable to Rabipur vaccine. On challenge with rabies virus CVS strain, replicon-based rabies DNA vaccine conferred complete protection similar to Rabipur. These results demonstrate that replicon-based rabies DNA vaccine is effective in inducing both humoral and cellular immune responses and can be considered as effective vaccine against rabies.

Modifications of ampicillin structure and its implication: an in-silico approach

Structural modifications of the existing ampicillin are much needed for saving patients from ampicillin-resistant microorganisms. A number of new molecules were generated by side chain modification of the existing ampicillin structure. Armed with molecular docking softwares like FlexiDOC, GLIDE, and AutoDOCK, a docking study was performed. Interaction between new molecules and target protein (1W2N) was also executed. Finally, we arranged new molecules according to docking scores, which directly reflects the binding affinity to the receptor protein.

Sindbis virus replicon-based DNA vaccine encoding Rabies virus glycoprotein elicits specific humoral and cellular immune response in dogs

A Sindbis virus (SINV) replicon-based DNA vaccine encoding Rabies virus (RABV) glycoprotein G developed previously (Saxena et al., Vaccine 26, 6592, 2008) was used for immunization of dogs against rabies. The intradermal injection of DNA vaccine into external ear generated protective level of virus neutralizing antibodies. The cellular immune response was specific to RABV, in particular by an increase in CD3+CD4+ and CD3+CD8+ lymphocytes. This study has demonstrated that the SINV replicon-based DNA vaccine encoding RABV G is capable of inducing the protective level of specific immune response in dogs.

Inhibition of Bovine herpesvirus multiplication in MDBK cells by small interfering RNAs

Small interfering RNA (siRNA) mediated gene silencing is a promising approach in antiviral therapy. To investigate the antiviral effects of siRNAs on Bovine herpesvirus 1 (BoHV-1) multiplication, we designed and in vitro synthesized two siRNAs (siRNA-1 and siRNA-2) targeting the UL25 gene that is essential for BHV-1 multiplication. siRNA-1 and siRNA-2 inhibited the BoHV-1 multiplication in MDBK cells to a different extent, namely by 11% and 40%, respectively, as demonstrated by virus titers (TCID(50)/ml) determined in cell culture. This indicates that, in general, siRNAs can inhibit BHV-1 multiplication in vitro and could be used also against a BHV-1 infection in vivo following optimization of their application.

Energy transfer between Er3+:Sm3+codoped TeO2-Li2O glass

The energy transfer in Er3+: Sm3+ codoped binary TeO2-Li2O (TLO) glass has been studied using 532 nm laser radiation on the basis of fluorescence intensity and the lifetime measurements. It is observed that the trace of erbium ion can be utilized to sensitize the samarium. The mechanism involved in the present case is found to be dipole-dipole. The energy transfer efficiencies, probabilities of energy transfer and the average donor acceptor distance has been evaluated.

Streptozotocin-induced diabetes decreases conducted vasoconstrictor response in mouse cremaster arterioles

A conducted vasomotor response (CVR) is characterized by the spread of vasoconstriction or vasodilatation both up- and downstream from a local stimulation site in the microcirculation. It is believed to coordinate vasomotor responses within the microcirculation, and to contribute to the control of the major feed arteries to a given organ or tissue. Microvascular disease is a common and severe complication in diabetes, and we therefore studied CVR in streptozotocin (STZ) diabetic mice to examine whether changes in CVR might have a role in the pathophysiology of microvascular dysfunction in diabetes. The mouse cremasteric arterioles were stimulated locally with KCl and the resulting local response as well as conducted responses at 500 microm and 1000 microm were measured in control and STZ treated mice. Diabetes (n=8) induced by intraperitoneal injection of STZ in a dose of 100 mg/kg (mean blood glucose 16.8+/-2.1 mmol/l) decreased the conduction of vasoconstriction from 27.3+/-1.1% to 21.4+/-1.6% at 500 microm (p<0.01) and from 17.4+/-1.0% to 9.8+/-1.1% at 1000 microm (p<0.01) as compared with control (n=9). Treatment with either the protein kinase C beta II inhibitor (LY341684) or the oxygen radical scavenger tempol, did not improve the decreased conduction of vasoconstriction, but when administered together, the conduction of vasoconstriction was improved from 21.4+/-1.6% to 26.5+/-0.8% at 500 microm and 9.8+/-1.1% to 16.5+/-0.7% at 1000 microm (p<0.01). We conclude that STZ induced diabetes reduces conducted vasoconstriction to KCl in mouse cremasteric arterioles, and combined treatment with both an oxygen radical scavenger and a protein kinase C beta II inhibitor improves the reduced conducted vasoconstriction.

XRD and Mössbauer spectroscopy investigation of Mn substituted CuFe2O4 nanoparticles

The effect of Mn substitution in Cu ferrite may present a challenge, as there are three transition metals ions distributed among the two available crystallographic sub lattices. This system also presents complicated super exchange interactions. In this study a series of five powdered samples with composition Cu(1-x)Mn(x)Fe2O4 were investigated using XRD and transmission Mössbauer spectroscopy. The variation of lattice parameter, crystallite size, and Mössbauer parameters of the product formed with the variation in the concentration of Mn has been studied. XRD study revealed the formation of pure phase spinels with FCC cubic structure having particle size ranging from 7.2 nm to 20 nm. Lattice constant value showed constant increase with increasing Mn concentration. AFM image confirms the formation of spherical shaped nanoparticles. Mössbauer spectroscopy proves to be an excellent tool for probing the local environment of Fe atoms present in such materials. Results show two sets of six finger patterns for all the samples with two double line pattern obtained for the composition with x = 0.75 and 1.0, indicating the presence of Fe in both A and B site. Increase in Mn concentration first increases the hyperfine field and then it gradually decreases. This effect is observed at both the sites. This effect is due to the relative strengths of Fe-O-X super exchange (X = Fe, Mn, Cu) as well as number of different nearest neighbour of A and B sites. The unexpected behaviour for the last two compositions can be explained by the presence of particle size distribution that results in superparamagnetic behaviour.

Virus neutralizing antibody response in mice and dogs with a bicistronic DNA vaccine encoding rabies virus glycoprotein and canine parvovirus VP2

A bicistronic DNA vaccine against rabies and parvovirus infection of dogs was developed by subcloning rabies glycoprotein and canine parvovirus (CPV) VP2 genes into a bicistronic vector. After characterizing the expression of both the proteins in vitro, the bicistronic DNA vaccine was injected in mice and induced immune response was compared with monocistronic DNA vaccines. There was no significant difference in ELISA and virus neutralizing (VN) antibody responses against rabies and CPV in mice immunized with either bicistronic or monocistronic DNA vaccine. Further, there was significantly similar protection in mice immunized with either bicistronic or monocistronic rabies DNA vaccine on rabies virus challenge. Similarly, dogs immunized with monocistronic and bicistronic DNA vaccines developed comparable VN antibodies against rabies and CPV. This study indicated that bicistronic DNA vaccine can be used in dogs to induce virus neutralizing immune responses against both rabies and CPV.

Hyponatremia, arginine vasopressin dysregulation, and vasopressin receptor antagonism

Hyponatremia is often associated with arginine vasopressin (AVP) dysregulation that is regulated by the hypothalamo-neurohypophyseal tract in response to changes in plasma osmolality, commonly in patients with the syndrome of inappropriate antidiuretic hormone secretion (SIADH). Potentially lethal complications of hyponatremia most frequently involve the central nervous system and include anorexia, fatigue, lethargy, delirium, seizures, hypothermia and coma, and require prompt treatment. Chronic hyponatremia also complicates patient care and is associated with increased morbidity and mortality, particularly among patients with congestive heart failure. Conventional treatments for hyponatremia (e.g. fluid restriction, diuretic treatment, and sodium replacement) may not be effective in all patients and can lead to significant adverse events. Preclinical and clinical trial results have shown that AVP receptor antagonism is a promising approach to the treatment of hyponatremia that directly addresses the effects of increased AVP and consequent decreased aquaresis, the electrolyte-sparing excretion of free water. Agents that antagonize V(2) receptors promote aquaresis and can lead to increased serum sodium. Dual-receptor antagonism, in which both V(2) and V(1A) receptors are blocked, may provide additional benefits in patients with hyponatremia.

Allosensitization to HLA and MICA is an important measure of renal graft outcome

The objective of this study was to evaluate the donor-specific antibody repertoire against T and B cells and monocytes, as well as the non-donor anti-HLA, and MICA (MHC class I-related chain A) antibodies in recipients of the live related donor renal transplantation. Sera collected before and after transplantation were tested by ELISA for the presence of HLA class I- and class II-specific antibodies and by Luminex MICA single-antigen bead assay for the detection of MICA antibodies. Patients having a combination of both anti-HLA and MICA antibodies had worse graft survival and more rejection episodes as compared to the group without antibodies. Further, presence of IgG antibodies against the donor cells (T, B & monocytes) led to a compromised graft survival along with higher incidence of acute rejection as compared to the negative groups. These results suggest that a comprehensive assessment of anti-donor antibody repertoire and monitoring of anti-HLA, MICA antibodies following transplantation is a useful exercise to detect the sensitization status of the recipient and this can prove to be of immense prognostic value in renal transplantation.

Incarcerated inguinal hernia presenting as spontaneous scrotal fecal fistula

We report a case of neglected, strangulated, inguinal hernia in a middle-aged male, which presented as a scrotal fecal fistula. This is the first such case reported in an adult. The patient was treated by resection and anastamosis of the ileum, local debridement of the scrotum and Shouldice repair for the inguinal defect.