A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7

Malaria is a major public health concern, and malarial parasites have developed resistance against the commonly available drugs. So now a days it is a major concern to find out a new target for drug therapy. Plasmodium falciparum 3D7, one of the strains of plasmodium species also lacks in a functional tricarboxylic acid cycle and solely dependent on glycolysis for its energy supply like other plasmodium species. Although enzymes of malarial parasite have been considered as potential antimalarial drug targets, a little is known about their structural biology. The tertiary structure of triose phosphate isomerase of P. falciparum 3D7 was determined by means of homology modeling through multiple alignment followed by intensive optimization and validation. The modeling was done by Swiss-Model Workspace. The obtained model was verified with the structure validation programs such as, PROCHECK, Verify3D, and QMEAN for reliability. The verify3D value of 0.69 indicates that the environment profile of the model is good. A self-optimized prediction method with alignment or SOPMA is employed for calculation of the secondary structural features of triose phosphate isomerase. The secondary structure indicates that the predicted 3D structure of triosephosphate isomerase of P. falciparum 3D7 contains 48.37% α-helix, 29.27% random coil, and 16.67% extended strand. Active site determination through CASTp suggests that this protein can be utilized as a potential drug target. However, these will further be tested by wet lab studies for a targeted vaccine design against P. falciparum 3D7.

Mechanisms of nuclear suppression of host immunity by effectors from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa)

Filamentous phytopathogens form sophisticated intracellular feeding structures called haustoria in plant cells. Pathogen effectors are likely to play a role in the establishment and maintenance of haustoria additional to their more characterized role of suppressing plant defense. Recent studies suggest that effectors may manipulate host transcription or other nuclear regulatory components for the benefit of pathogen development. However, the specific mechanisms by which these effectors promote susceptibility remain unclear. Of two recent screenings, we identified 15 nuclear-localized Hpa effectors (HaRxLs) that interact directly or indirectly with host nuclear components. When stably expressed in planta, nuclear HaRxLs cause diverse developmental phenotypes highlighting that nuclear effectors might interfere with fundamental plant regulatory mechanisms. Here, we report recent advances in understanding how a pathogen can manipulate nuclear processes in order to cause disease.

Mechanisms of nuclear suppression of host immunity by effectors from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa)

Filamentous phytopathogens form sophisticated intracellular feeding structures called haustoria in plant cells. Pathogen effectors are likely to play a role in the establishment and maintenance of haustoria additional to their more characterized role of suppressing plant defense. Recent studies suggest that effectors may manipulate host transcription or other nuclear regulatory components for the benefit of pathogen development. However, the specific mechanisms by which these effectors promote susceptibility remain unclear. Of two recent screenings, we identified 15 nuclear-localized Hpa effectors (HaRxLs) that interact directly or indirectly with host nuclear components. When stably expressed in planta, nuclear HaRxLs cause diverse developmental phenotypes highlighting that nuclear effectors might interfere with fundamental plant regulatory mechanisms. Here, we report recent advances in understanding how a pathogen can manipulate nuclear processes in order to cause disease.

Acute colonic diverticulitis: visualization in magnetic resonance imaging

The incidence of acute colonic diverticulitis (ACD) is increasing. To allow rational therapeutic decisions to be made, a timely diagnosis is required. The feasibility of "on-admission-MRI" to establish the diagnosis has not yet been studied. Therefore, a prospective observational study was carried out in 20 patients with an established diagnosis of ACD. The diagnostic criteria for the MRI diagnosis of ACD were the demonstration of at least one diverticulum, pericolic exudation, and edema of the colonic wall. MRI was diagnostic in all but one patient. It is concluded that MRI has considerable diagnostic potential in ACD and should be formally evaluated.

Measurement of torsion angles of long finger bones using computed tomography

OBJECTIVE

Rotational dislocation at the fracture site is a complication of long finger bone fractures of the metacarpals and phalanges. To evaluate such deformities, we performed CT of the articular surfaces of these bones to demonstrate the torsion angles.

DESIGN

We evaluated 10 pairs of cadaver hands. These were placed flat, with the bones of interest perpendicular to the gantry to acquire axial images. The torsion of the long bone axes was defined as the angle between a tangent positioned parallel to the proximal articular surface and a tangent parallel to the distal articular surface of individual bones.

RESULTS

The maximum difference between repeated measurements was 4 degrees. Intraobserver differences measured between right and left hands are less than 3 degrees.

CONCLUSION

Side differences in torsion angles exceeding 3 degrees are strongly suspicious of a malrotation after fracture. These measurements might help to plan derotational osteotomy and assess the results of therapy.

Feasibility of MRI in the diagnosis of acute diverticulitis: initial results

PURPOSE

The purpose of this study was to evaluate MRI as a diagnostic tool in patients with suspected acute sigmoid diverticulitis. Furthermore, we sought to develop an optimal imaging protocol in these patients.

PATIENTS AND METHODS

Eleven patients with suspected acute diverticulitis were included in the study. All patients were imaged in a 1.0 T clinical scanner using a body-array coil. Imaging sequences were single-shot TSE, HASTE-, STIR- and TrueFisp- sequence. All were obtained in the frontal plane. The diagnosis was verified by a single experienced investigator, using ultrasound, and overall clinicopathological outcome.

RESULTS

MRI enabled visualization of signs of an acute diverticulitis in all patients. However, the diagnosis of acute diverticulitis was obtained in 10 patients only. The mean imaging time was 17.5+/-5.5 min. STIR- and TrueFisp-sequences alone displayed all findings, e.g pericolonic exsudation, edema and segmental narrowing, whereas SSTSE and HASTE-sequences showed no additional information. Therefore, it appeared that the imaging protocol could be restricted to STIR- and TrueFisp-sequences.

CONCLUSION

MRI is feasible as a fast, accurate and investigator-independent diagnostic tool in patients with suspected acute diverticulitis. To prove its value in comparison to computed tomography or ultrasound, further studies are needed.

MR hydrometry to assess exocrine function of the pancreas: initial results of noninvasive quantification of secretion

PURPOSE

To evaluate magnetic resonance (MR) hydrometry, a method of quantifying fluid amounts by using MR imaging, for assessing the exocrine function of the pancreas after stimulation with secretin.

MATERIALS AND METHODS

Images were obtained with a single-shot turbo spin-echo sequence by using a 1.0-T magnet with a quadrature body coil. Image postprocessing and evaluation were performed at an external workstation by using a specially designed histogram algorithm that translates the MR signal intensity of duodenal filling into an actual amount of duodenal fluid. This algorithm was tested in vitro and in vivo. Finally, MR hydrometry results in five patients were correlated with those of the secretin-cerulein test.

RESULTS

The phantom measurements showed a high correlation (r = 0.99) between the actual amount of fluid in the imaging volume and the calculated results. In vivo, the ability of MR hydrometry to enable exact quantification of fluid amounts was demonstrated. In correlating the signal intensity of duodenal filling with the exact amount of additional fluid in the duodenum in volunteers, a coefficient of 0.043 gray tones per pixel per milliliter was calculated. The correlation (r) between secretin-stimulated duodenal fluid output estimated by using tube aspiration and that estimated by using MR hydrometry was 0.946 (P <.05).

CONCLUSION

MR hydrometry is a promising noninvasive method of assessing fluid output as a measure of exocrine pancreatic function.

Comparison of C-arm CT fluoroscopy and conventional fluoroscopy for percutaneous biliary drainage procedures

PURPOSE

To conduct a prospective randomized evaluation of C-arm computed tomography (CT) fluoroscopy for external biliary drainage procedures in comparison with conventional fluoroscopic guidance to reduce the number of transhepatic punctures as a primary endpoint.

MATERIALS AND METHODS

In 18 patients with biliary obstructions, 20 external percutaneous biliary drainage procedures were prospectively performed with use of either C-arm CT fluoroscopy or conventional fluoroscopy alone. The number of hepatic punctures, procedure time, and fluoroscopy time, were analyzed separately for both methods.

RESULTS

C-arm CT fluoroscopy resulted in a reduced number of transhepatic punctures, with decreased procedure and fluoroscopy times (P < .05; t test). When compared with conventional external biliary drainage procedures, a mean of 1.8+/-1 versus 4.8+/-2.8 hepatic punctures at a fluoroscopy time of 3.4+/-1.5 versus 11.4+/-7.4 minutes was required for C-arm CT fluoroscopy, while procedure times were 11+/-3.6 versus 16.2+/-9.3 minutes.

CONCLUSIONS

C-arm CT fluoroscopy is associated with decreased procedure and fluoroscopy times, while fewer transhepatic punctures are required to establish external biliary drainage.

Combination therapy with octreotide and alpha-interferon: effect on tumor growth in metastatic endocrine gastroenteropancreatic tumors

OBJECTIVE

We investigated the antiproliferative efficacy of the addition of alpha-interferon to the somatostatin analogue octreotide in patients with metastasized gastroenteropancreatic tumors unresponsive to octreotide monotherapy.

METHODS

In an open prospective trial, 21 patients with metastasized neuroendocrine gastroenteropancreatic tumors (nine patients with carcinoid syndrome, eight with nonfunctioning tumors, four with gastrinoma) were treated with 5 x 10(6) IU alpha-interferon tiw in addition to 200 microg of octreotide tid. All patients, including 16 patients with preceding monotherapy with 200 microg of octreotide tid, had tumor progression documented by computed tomography before entering the study. Growth response (computed tomography documented) and biochemical response were assessed at 3-month intervals.

RESULTS

Inhibition of tumor growth was observed in 14 patients (67%), 11 of whom had preceding octreotide monotherapy; complete regression was observed in one patient lasting for 49 months and stable disease (stand-still) in 13 patients lasting for 3 to 52 months (median, 12 months). Seven patients failing this combination therapy exhibited a significantly shorter overall survival (median, 23 months; range, 5 to 42 months) than the 14 patients responding to this regimen (median, 68 months; range, 12 to 112 months; p = 0.007). Two patients are still alive. Biochemical response was achieved in 69% of patients with functioning tumors: in three of four patients with gastrinoma and in six of nine patients with carcinoid syndrome.

CONCLUSIONS

These data suggest that the addition of alpha-interferon to octreotide has antiproliferative efficacy in a subgroup of patients with advanced metastatic disease unresponsive to octreotide monotherapy. Prolonged survival was seen in the responder group.

[Control of percutaneous biopsy with CT fluoroscopy]

PURPOSE

Clinical evaluation of CT fluoroscopy and comparison with conventional CT guidance for monitoring of non-pulmonary percutaneous biopsy procedures.

MATERIALS AND METHODS

20 non-pulmonary CT-guided biopsy procedures were prospectively performed either with CT fluoroscopy or with conventional CT guidance. CT fluoroscopy was performed using 120 kV and 50, 70 or 90 mA at a frame-rate of three or six images per second. Number of punctures and biopsies, procedure times, radiation doses and histologic results were analyzed separately for conventional CT guidance and for CT fluoroscopy.

RESULTS

With CT fluoroscopy, yield of biopsies was improved (p = 0.005, t-test) and procedure times were shorter than for conventional CT guidance (11.4 +/- 6.0 vs. 23.6 +/- 13.8 min; p = 0.03, t-test). Analysis of procedure related radiation exposure and histologic outcome showed no significant difference between conventional and fluoroscopic CT-guided procedures (p > 0.05, t-test).

CONCLUSIONS

CT fluoroscopy facilitates guidance of percutaneous biopsy procedures. Compared to conventional CT assistance, procedure times are decreased while yield of biopsies is improved.

[Epiphyseal injuries of the distal tibia. Does MRI provide useful additional information?]

Plain film radiography often underestimates the extent of injury in children with epiphyseal fracture. Especially Salter-Harris V fractures (crush fracture of the epiphyseal plate) are often primarily not detected. MRI of the ankle was performed in 10 children aged 9-17 (mean 14) years with suspected epiphyseal injury using 1.0-T Magnetom Expert. The fractures were classified according to the Salter-Harris-Rang-Odgen classification and compared with the results of plain radiography. In one case MRI could exclude epiphyseal injury; in four cases the MRI findings changed the therapeutic management. The visualisation of the fracture in three orthogonal planes and the possibility of detection of cartilage and ligamentous injury in MR imaging makes this method superior to conventional radiography and CT. With respect to radiation exposure MRI instead of CT should be used for the diagnosis of epiphyseal injuries in children.

[Pitfalls when using a contrast media injector in MRI]

PURPOSE

Using a power injector to applicate Gd-DTPA we found a contrast enhancement of the pyelo-caliceal system even in the native studies, and hence we analysed pitfalls when using power injectors in MRI.

MATERIAL AND METHODS

We used a power injector Spectris (MedRad, Maastricht, Netherlands). In vitro artifacts were achieved by the mixture of contrast media and saline solution. We substituted contrast media by red water, NaCl by clear water.

RESULTS

Using power injectors in MRI, some pitfalls must be avoided, which can render investigations useless, especially dynamic contrast-enhanced investigations.

CONCLUSION

In our study we showed an easy way to overcome some pitfalls and use a power injector in MRI in a diagnostically helpful way. The simple use of valves inhibits the mixture of contrast media and saline solution.

[Magnetic resonance phlebography (MRP) of the abdomen and pelvis]

PURPOSE

To evaluate the image quality of magnetic resonance venography (MRV) of pelvic and abdominal veins.

METHODS

A retrospective analysis of all MRV between 1993 and 1996 was conducted. A 2D-FLASH-TOF without breath hold and with arterial presaturation was used. All venous segments have been assessed for the quality of visualisation and an overall image quality was determined. 43% of our patients had malignant disease and phlebothrombosis had already been diagnosed in 64%.

RESULTS

126 examinations and 1696 venous segments were analysed. The overall quality of the examination was good, however one examination was non diagnostic because of motion artefacts. Vessels along the vertical axis were good visualised in over 90%. Most important reasons for insufficient visualisation were breathing, motion and metal artefacts as well as compression and displacement of veins due to tumour disease.

CONCLUSIONS

Magnetic resonance venography without breath hold TOF technique is practical and robust for routine clinical applications.

[Venous compression syndrome: etiology, diagnosis and therapy from the radiologic viewpoint]

Venous compression is a clinical entity distinct from deep vein thrombosis although the clinical signs may be indistinguishable. Reasons for venous compression are tumors, scars, hematomas, postoperative changes and anatomic variations. The differential diagnosis between compression and thrombosis is important because therapy and prognosis differ markedly between the two patient groups. Ultrasound, computed tomography and magnetic resonance tomography are the diagnostic tools of choice because they offer not only information about the intraluminal situation but also about the extraluminal pathology.