A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

Acute renal failure due to bilateral ureteric necrosis following percutaneous chemical lumbar sympathectomy

We report a case of acute renal failure as a result of obstructive uropathy as a consequence of instillation of phenol used for chemical sympathectomy in Beurger's disease of the lower limbs. Extensive bilateral ureteral necrosis occurred as a result of phenol instillation that. Such practices are still common among the general surgeons and such a complication has not been described before.

Colorectal carcinoma in young adults: a retrospective study on Indian patients: 2000-2008

AIM

To highlight an increased incidence of colorectal cancer (CRC) amongst young Indian adults.

METHOD

A retrospective study of 305 cases of CRC admitted to SSKM Hospital, Kolkata, India during 2000-2008 was carried out.

RESULTS

The ratio (0.64) of under-40 to above-40 CRC patients reported in this study is comparable to those from premier Oncology Centers in India (∼0.52) and is higher than those in the Indian National Cancer Registry (∼0.20) and international average (0.07). Distinctive tumour characteristics in younger patients including left-sided lesion (69.7%), presentation at an advanced (III/IV) stage (60%), poor histological differentiation (50%) and predominance of mucin-secreting adenocarcinoma (80%) are similar to those reported in the international literature. Some features are suggestive of hereditary non polyposis colorectal cancer syndrome, which may be a possible reason for the high proportion of young CRC patients.

CONCLUSION

A high index of suspicion for CRC among young Indian adults is necessary.

Predictors of long-term neurological sequelae of tuberculous meningitis: a multivariate analysis

There is paucity of studies on predictors of long-term sequelae of tuberculous meningitis (TBM). We report the neurological sequelae of TBM at 1 year and their predictors. Patients with TBM who were followed up for 1 year were included. The diagnosis of TBM was based on clinical, cerebrospinal fluid (CSF) and computed tomography (CT) scan findings. Detailed neurological examinations at admission and at 1 year were carried out. All the patients received four-drug antitubercular therapy. The frequency of sequelae at 1 year were noted and the role of various demographic (age, sex, duration of illness, BCG vaccination), clinical (weakness, seizure, extra central nervous system tuberculosis, Glasgow Coma Scale (GCS) score, cranial nerve palsy, stage, corticosteroid, drug-induced hepatitis, shunt surgery), and laboratory findings (erythrocyte sedimentation rate (ESR), CSF cell and protein, CT scan evidences of hydrocephalus, basal exudates, infarctions and tuberculoma) at presentation were evaluated employing logistic regression analysis. Sixty-five patients with TBM were included in this study whose age ranged between 13 and 80 years (mean 33.2), 27 of whom were females. Complete neurological recovery at 1 year occurred in 21.5% patients only although about 50% were independent for activities of daily living. Neurological sequelae were observed in 78.5% patients, which included cognitive impairment in 55%, motor deficit in 40%, optic atrophy in 37% and other cranial nerve palsy in 23%. On logistic regression analysis, focal motor deficit at admission was the most important predictor of neurologic deficits at 1 year. GCS score predicted the cognitive and motor sequelae. Neurological sequelae at year occurred in 78.5% patients with TBM in the form of cognitive impairment, motor deficit and optic atrophy. Sequelae were common in patients who had focal motor deficit and altered sensorium at admission.

Mannitol in intracerebral hemorrhage: A randomized controlled study

OBJECTIVE

To study the usefulness of mannitol in spontaneous intracerebral hemorrhage (ICH) patients.

METHOD

128 CT proven supratentorial ICH patients within 6 days of ictus were randomized into study and control groups. The study group received mannitol 20%, 100 ml every 4 h for 5 days, tapered in the next 2 days. The control group received sham infusion. Primary endpoint was 1-month mortality and secondary endpoint functional disability at 3 months assessed by Barthel index score.

RESULTS

There were 65 patients in study and 63 in control groups. The study and control groups were evenly matched regarding age, Glasgow coma scale (GCS) score, Canadian Neurological Scale (CNS) score, pupillary asymmetry, pyramidal signs on non-hemiplegic side, and location, midline shift and ventricular extension of hematoma. At 1 month, 16 patients died in each group. The primary and secondary endpoints were not significantly different between the two groups.

CONCLUSION

Low dose mannitol does not seem to be beneficial in patients with ICH.

Relapsing linear acantholytic dermatosis in a four-year-old boy

Linear acantholytic dermatoses are a spectrum of cutaneous disorders that form a subset of linear dermatoses with distinct clinical features and histopathologically show acantholysis. The lesions may be zosteriform or follow the lines of Blaschko. This report describes a four-year-old boy who, on a follow up of two years, exhibited a relapsing acantholytic dermatosis along the lines of Blaschko. Histopathology of a representative lesion revealed epidermal acantholysis with multiple acantholytic keratinocytes with in the prickle cell layer and an absence of corp ronds and grains, consistent with features of Hailey-Hailey disease. This, to our knowledge, is the third case of relapsing linear acantholytic dermatosis reported.

Effect of mannitol on regional cerebral blood flow in patients with intracerebral hemorrhage

AIM

To evaluate the regional cerebral blood flow (rCBF) changes following IV mannitol bolus in patients with intracerebral hemorrhage (ICH).

METHODS

In a hospital based randomized placebo controlled study, 21 CT proven ICH patients with Glasgow coma scale (GCS) score of 5 or more were subjected to clinical evaluation including GCS and Canadian Neurological stroke (CNS) scale. Cranial SPECT study was undertaken before and 60 min after 20% mannitol 100 ml IV in 20 min or sham infusion. The SPECT images were semi-quantitatively analyzed and asymmetry index of basal ganglia, frontal, parietal and occipital regions were calculated.

RESULTS

There were 12 patients in mannitol and nine in control group who were evenly matched for age, mean arterial blood pressure, GCS score and size of hematoma. Only one patient died in mannitol group. Following mannitol, GCS score improved in six, worsened in two and remained unaltered in four patients. In the control group, GCS improved in seven, worsened in none and was unchanged in two patients. SPECT studies revealed reduction in asymmetry index in basal ganglia in four, frontal region in six, parietal in four and occipital region in five patients in mannitol group. In control group, asymmetry index was reduced in basal ganglia in one, frontal and parietal region in three each and occipital region in five patients. These differences between control and study group were not significant.

CONCLUSION

Mannitol does not seem to significantly change the regional cerebral blood flow (rCBF) in ICH patients as evaluated by SPECT study.

Tuberculous meningitis with pulmonary miliary tuberculosis: a clinicoradiological study

BACKGROUND AND AIMS

This study aims at evaluating the clinical and radiological outcome of tuberculous meningitis (TBM) patients with pulmonary miliary tuberculosis.

MATERIAL AND METHODS

Diagnosis of TBM was based on clinical, CT scan or MRI and CSF criteria, and that of miliary tuberculosis on chest radiograph. Detailed clinical evaluation was done in all. Severity of meningitis was graded into Grades I, II and III. Complete hemogram, serum chemistry and Montaux tests were performed. The recovery was defined on the basis of 6 months Barthel index score as poor, partial or complete.

RESULTS

20 out of 165 patients with TBM had pulmonary miliary tuberculosis. Their mean age was 30 years; there was one child and 13 patients were females. The mean duration of symptoms was 6.3 months. Montoux test was negative in 9 patients. Six patients were in stage I, 3 in stage II, and 11 in stage III meningitis. Hemoglobin was below 12 gm% in 13 and liver dysfunction and hypocalcaemia was present in 8 and 18 patients respectively. CT scan was abnormal in 16 patients and revealed hydrocephalus (10), granuloma (7), exudates (3) and infarction (1). MRI was abnormal in 7 out of 8 patients and 3 of these patients had normal CT scan. MRI revealed multiple granuloma in 7 patients and exudates in 2. At 6 months, 2 patients died, 10 had complete, 2 had partial and 4 had poor recovery.

CONCLUSION

TBM with pulmonary miliary tuberculosis was commoner amongst females who were anemic and hypocalcaemic. MRI revealed multiple granuloma and the majority of the patients improved.

Prescribing pattern of antiedema therapy in stroke by neurologists and general physicians

BACKGROUND

In acute stroke, a number of drugs are used to reduce the raised intracranial pressure (ICP) although their scientific basis has not been established or shown in randomized controlled trials.

AIMS

In this communication, we report the pattern of use of antiedema therapy in acute stroke by general physicians (GPs) and neurophysicians (NPs) in India.

MATERIAL AND METHODS

A questionnaire was developed regarding the use of various antiedema measures in stroke and responses were collected either through post or when the responders were attending a national conference. The use of antiedema therapy by NPs and GPs was analyzed employing the Chi-square test.

RESULTS

We could collect responses from 102 physicians, of whom 48 were NPs and 54 GPs. More than two-thirds of the physicians managed more than three strokes per week and all used antiedema therapy at some time or the other. Thirteen used it in all the patients and the remaining used it in patients with large and moderate strokes or in patients with herniation. Twelve used only one drug, while the remaining physicians used various combinations in different doses and frequency. The prescribing pattern was significantly different between GPs and NPs with respect to the frequency of the antiedema drugs used, type of stroke where these were used, combination of drugs, timing and dose of mannitol.

CONCLUSION

This study highlights that antiedema therapy in acute stroke is practiced without any uniformity.

Serial study of clinical and CT changes in tuberculous meningitis

Clinical and radiological changes in tuberculous meningitis (TBM) have been reported but there is paucity of comprehensive serial clinicoradiological follow-up. In this prospective hospital based study, we investigated serial changes in the clinical and radiological findings and their relationships over 6 months in 31 consecutive patients with TBM, diagnosed on the basis of clinical, radiological and spinal fluid criteria. We graded the severity of the TBM as I-III. Detailed clinical examination, contrast-enhanced CT and activities of daily living (ADL) assessments were made on admission, and 3 and 6 months after therapy. Further CT was carried out as required. Patients received four-drug antituberculous therapy (RHZE) and underwent a ventriculoperitoneal shunt if necessary. Outcome was defined as poor, partial or complete recovery using the Barthel index score at 6 months. The age of the patients was 6-80 years, mean 35.2 years; four were children and 13 female. Meningitis was stage I in 5, stage II in six and stage III in 20 patients. Focal weakness was present in nine, papilloedema in six and ophthalmoplegia in ten. There were ten patients who deteriorated within first 6 weeks of therapy. Mean Glasgow coma score (GCS) deteriorated from 12.5 to 11.4; the grade of meningitis increased by two stages in one patient, one stage in another, and motor deficits appeared in four and optic atrophy in four; four patients required shunt surgery. By 3 months most patients were stable. At 6 months 17 patients had complete, four partial and nine poor recovery. Initial CT was abnormal in 28 patients, revealing hydrocephalus and exudates in 15 each, infarcts in ten and tuberculomas in 13. It was repeated in ten patients who deteriorated, showing new abnormalities such as hydrocephalus in two, infarcts in four, exudates in four and granulomas in two, with worsening of the previous findings. CT at 3 and 6 months was still abnormal in most patients. At 6 months hydrocephalus had disappeared in four, as had tuberculomas in seven and exudates in six, but infarcts did not change. Initial deterioration was related to weakness on admission and the GCS. Cognitive impairment significantly correlated with exudates and tuberculomas and motor deficits with infarcts. Thus, a third of patients with TBM may deteriorate within 6 weeks of starting treatment and CT can be helpful in managing them. Worsening on treatment was related to weakness and GCS on admission. In most patients CT remained abnormal at 6 months despite clinical recovery.

Hemichorea: a rare presentation of tuberculoma

Hemichorea due to tuberculoma has not been reported. We managed a 16-year-old girl who developed transient left hemichorea due to right sided striatal tuberculoma. Chorea regressed following 1 week of antitubercular treatment with corticosteroid therapy and disappeared at 3 months. In a patient presenting with chorea, striatal tuberculoma should also be considered especially in the area where tuberculosis is prevalent.

Thallium poisoning: emphasis on early diagnosis and response to haemodialysis

Thallium poisoning is known for its diverse manifestations and these can delay the diagnosis if a clear history of poisoning is not forthcoming. A 42 year old man presented on the third day of illness with flaccid quadriparesis and paresthesia, which were confused with Guillain-Barré syndrome. Because of associated loose motions, skin lesions, and liver and kidney dysfunction arsenic poisoning was considered. In the second week he developed ophthalmoplegia, nystagmus, and neck tremor and later developed alopecia, and thallium poisoning was suspected. His serum thallium level on the 18th day of illness was 40 980 micro g/ml. He was subjected to haemodialysis, potassium supplementation, laxatives, and B complex supplementation. He showed significant improvement after haemodialysis and at three months he was able to walk with support. At six months of follow up he was independent for activities of daily living. Severe paresthesia, ophthalmoplegia, cerebellar and extrapyramidal signs, and alopecia are highly suggestive of thallium poisoning. Haemodialysis may be effective even in the third week of poisoning.

HYSTEROSCOPY IN POSTMENOPAUSAL BLEEDING

The purpose of the present study was to evaluate the utility of hysteroscopy as a diagnostic tool in cases of postmenopausal bleeding. The study includes 42 cases presenting with postmenopausal bleeding on which hysterscopy was performed using rigid hysteroscope (CIRCON) with glycine 1.5% as the distension medium. In 17 of the 42 cases positive hysteroscopic findings were noted which included 2 cases of endometrial carcinoma, 2 cases of postmenopausal endometritis, 4 cases of endometrial polyp, 5 cases of endometrial hyperplasia, 1 case of submucous myoma and 3 cases of endocervical polyp whereas normal postmenopausal endometrium was noticed in rest of the 25 cases. Endometrial biopsy was done in all these cases so that the hysteroscopic findings could be corroborated with tissue diagnosis. Hysteroscopy along with directed endometrial biopsy proved to be a useful diagnostic aid in cases of postmenopausal bleeding.

A comparison of carbon dioxide monitoring and oxygenation between facemask and divided nasal cannula

The divided nasal cannula is a device recently released in Australia that couples oxygen delivery and end-tidal carbon dioxide (PETCO2) monitoring. This study compares the accuracy of PETCO2 measurements by the divided nasal cannula and those measured by a modified facemask (as currently used in this institution), with arterial partial pressure of carbon dioxide (PaCO2). In this crossover study, 30 patients who had arterial lines as part of their routine monitoring were given oxygen via nasal cannula and facemask preoperatively. The PETCO2 was measured with each device and a simultaneous PaCO2 and PaO2 measured after equilibration. The results demonstrate a significant difference between the PETCO2 as measured by each technique. The divided nasal cannula more accurately reflects PaCO2 (mean arterial to end expired gradient of 5 mmHg) and provides a more representative trace when compared to a traditional facemask system. Both methods provided adequate oxygenation.

Anticancer drug-induced apoptosis in human monocytic leukemic cell line U937 requires activation of endonuclease(s)

Anticancer agents effect tumor cell killing both in vivo and in vitro through the induction of apoptosis. Endonuclease-mediated internucleosomal DNA fragmentation, the most widely used biochemical marker of apoptosis, has been shown to play a central role in apoptosis in many experimental systems. In the present investigation, we report that activation of endonuclease(s) leading to oligonucleosomal DNA fragmentation is common and an essential event in apoptosis, induced by different anticancer drugs, adriamycin, etoposide and cisplatin. The endonuclease inhibitors aurintricarboxylic acid and zinc ion prevented apoptotic cell death in human monocytic leukemic cell line U937, as documented by DNA fragmentation, morphological and nuclear alterations, and cell viability assay. Additional studies suggest endonuclease(s)-mediated DNA fragmentation may not play a central role in apoptosis in the same cell line in response to other inducers such as heat shock and cells may undergo cell death showing all morphological features of apoptosis even in the absence of DNA fragmentation.