Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

The identification of quantitative trait loci (QTLs) affecting agronomically important traits enable to understand their underlying genetic mechanisms and genetic basis of their complex interactions. The aim of the present study was to detect QTLs for 12 agronomic traits related to staygreen, plant early development, grain yield and its components, and some growth characters by analyzing replicated phenotypic datasets from three crop seasons, using the population of 168 F(7) RILs of the cross 296B x IS18551. In addition, we report mapping of a subset of genic-microsatellite markers. A linkage map was constructed with 152 marker loci comprising 149 microsatellites (100 genomic- and 49 genic-microsatellites) and three morphological markers. QTL analysis was performed by using MQM approach. Forty-nine QTLs were detected, across environments or in individual environments, with 1-9 QTLs for each trait. Individual QTL accounted for 5.2-50.4% of phenotypic variance. Several genomic regions affected multiple traits, suggesting the phenomenon of pleiotropy or tight linkage. Stable QTLs were identified for studied traits across different environments, and genetic backgrounds by comparing the QTLs in the study with previously reported QTLs in sorghum. Of the 49 mapped genic-markers, 18 were detected associating either closely or exactly as the QTL positions of agronomic traits. EST marker Dsenhsbm19, coding for a key regulator (EIL-1) of ethylene biosynthesis, was identified co-located with the QTLs for plant early development and staygreen trait, a probable candidate gene for these traits. Similarly, such exact co-locations between EST markers and QTLs were observed in four other instances. Collectively, the QTLs/markers identified in the study are likely candidates for improving the sorghum performance through MAS and map-based gene isolations.

Exploration and mapping of microsatellite markers from subtracted drought stress ESTs in Sorghum bicolor (L.) Moench

Molecular variation within defined genes underlying specific biochemical or physiological functions provide candidate gene-based markers which show very close association with the trait of interest and thus should enable to design superior genotypes. We explored microsatellite loci in a total of 9,892 subtracted drought stress ESTs of sorghum (6,295 after flowering ESTs and 3,597 before flowering ESTs) available in the NCBI dbEST database. Analysis of 9,892 ESTs identified 221 non-redundant ESTs with SSRs, from which 109 functional SSRs were developed. Among them 62 EST-microsatellites (56.8%) exhibited polymorphism for at least one sorghum genotype among the five tested and yielded a total of 161 alleles, with an average of 2.59 alleles per marker. We present a microsatellite linkage map using a RIL population derived from the cross 296B and IS18551. The map contains 128 microsatellite loci distributed over 15 linkage groups, and spanning a genetic distance of 1,074.5 cM. The map includes map positions of 28 drought EST-microsatellites developed and seven new genomic-SSRs, and are distributed throughout the map. The developed EST markers include genes coding for important regulatory proteins and functional proteins that are involved in stress related metabolism. The drought EST-microsatellites will have applications in functional diversity studies, association studies, QTL studies for drought, and other agronomically important traits in sorghum, and comparative genomics studies between sorghum and other members of the Poaceae family.

Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template. For each of the sorghum QTL regions, the reported RFLP markers were compiled, used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL, on chromosome 9 for Stg3 QTL, and on chromosome 11 for Stg4 QTL. Using the Gramene genome browsing tool, 869 non-redundant sorghum expressed sequence tags (ESTs) were selected and 50 genic-microsatellites (18, 12, 15, and 5, for Stg1, Stg2, Stg3, and Stg4 QTL, respectively) could be developed. We could experimentally establish synteny of the Stg1, Stg2, Stg3, and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers (20%) to the positions of the staygreen QTL. The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family. The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach, and create an additional option for MAS of the staygreen trait in sorghum.

Sequencing, characterization and genetic variation of the Bos indicus glucose-6-phosphate-dehydrogenase gene

The coding sequence of the bovine (Bos indicus) Glucose-6-phosphate-dehydrogenase (G6PD) gene was amplified by Reverse Transcriptase-PCR (RT-PCR), cloned, sequenced and characterized. The deduced amino acid sequence clustered the bovine G6PD sequence with the other mammalian G6PD proteins into a monophyletic group. The bovids (B. indicus and B. taurus) clustered clearly from the rodent (rat, mouse and hamster) subcluster and from humans. The multiple sequence alignment of the bovine G6PD with the mammalian species clearly revealed conservation of the substrate, coenzyme, catalytic and the dimer binding sites with the solved X-ray crystallographic structure of Homo sapiens. Also, four fragments of bovine (Bos indicus) G6PD gene viz. 118, 319, 683 and 408 bp were amplified and sequenced for the first time. A G/A and G/C single nucleotide polymorphisms in intron-9 and exon-10 were detected on PCR-RFLP of the 319 bp amplicon with Hae III and Pst I, respectively. This work is the first study on Bos indicus G6PD gene at the nucleotide level.

Estrogen-dependent cell signaling and apoptosis in BRCA1-blocked BG1 ovarian cancer cells in response to plumbagin and other chemotherapeutic agents

BACKGROUND

Cellular response to chemotherapeutic drugs in the absence of BRCA1 either completely or partially had drawn less attention. The present study evaluated whether there is a differential inhibition of cell growth by selected compounds with respect to BRCA1 status in estrogen receptor (ER)-positive ovarian cancer cells.

MATERIALS AND METHODS

The BG1 ovarian cancer cells used in the experiments were antisensely blocked with BRCA1 gene. Growth inhibition and apoptotic induction were analyzed to evaluate the cytotoxic effects. Small interfering RNA (SiRNA) transfection, western blot analysis, RT-PCR analysis and molecular modeling were carried out to analyze the estrogen-dependent action of plumbagin.

RESULTS

Although we found that all the compounds studied induce apoptosis, the induction was in the order of plumbagin > doxorubicin > tamoxifen > cisplatin. Plumbagin can bind to the active site of ER-alpha. Plumbagin, however, induced ER-alpha 46 kDa truncated isoform, which was found abundantly preempted in the cytoplasm compared with a 66-kDa full-length isoform. The truncated isoform is known to inhibit classical ER-alpha signaling pathways. SiRNA-transfected cells for ER-alpha exhibited lower cytotoxicity upon plumbagin treatment than the control-transfected cells.

CONCLUSION

Taken together, this study indicates that plumbagin has chemotherapeutic potential in BRCA1-mutated/defective ER-positive cancers.

A mouse model for luminal epithelial like ER positive subtype of human breast cancer

Background

Generation of novel spontaneous ER positive mammary tumor animal model from heterozygous NIH nude mice.

Methods

Using brother-sister mating with pedigree expansion system, we derived a colony of heterozygous breeding females showing ER-Positive tumors around the age of 6 months. Complete blood picture, differential leukocyte count, and serum levels of Estrogen, Alanine amino transferase (SGPT), Aspartate amino transferase (SGOT), total protein and albumin were estimated. Aspiration biopsies and microbiology were carried out. Gross pathology of the tumors and their metastatic potential were assessed. The tumors were excised and further characterized using histopathology, cytology, electron microscopy (EM), molecular markers and Mouse mammary Tumor Virus – Long Terminal Repeats (MMTV LTR) specific RT-PCR.

Results

The tumors originated from 2^ndor 5^thor both the mammary glands and were multi-nodulated with variable central necrosis accompanied with an accumulation of inflammatory exudate. Significant increases in estrogen, SGPT, SGOT and neutrophils levels were noticed. Histopathologically, invasive nodular masses of pleomorphic tubular neoplastic epithelial cells invaded fibro-vascular stroma, adjacent dermis and subcutaneous tissue. Metastatic spread through hematogenous and regional lymph nodes, into liver, lungs, spleen, heart and dermal lymphatics was observed. EM picture revealed no viral particles and MMTV-negativity was confirmed through MMTV LTR-specific RT-PCR. High expression of ER α, moderate to high expression of proliferating cell nuclear antigen (PCNA), moderate expression of vimentin and Cytokeratin 19 (K19) and low expression of p53 were observed in tumor sections, when compared with that of the normal mammary gland.

Conclusion

Since 75% of human breast cancer were classified ER-positive and as our model mimics (in most of the characteristics, such as histopathology, metastasis, high estrogen levels) the ER-positive luminal epithelial-like human breast cancer, this model will be an attractive tool to understand the biology of estrogen-dependant breast cancer in women. To our knowledge, this is the first report of a spontaneous mammary model displaying regional lymph node involvement with both hematogenous and lymphatic spread to liver, lung, heart, spleen and lymph nodes.

Outcome of day-case inguinal hernia in elderly patients: how safe is it?

INTRODUCTION

Inguinal hernia repair is well established as a day-case procedure but little is reported about the outcome for elderly patients.

METHODS

A retrospective study was undertaken to compare a study group of patients aged 70 and above with a controlled group of patients aged less than 65 who had day-case inguinal hernia repair (Lichtenstein repair) between January 1996 and December 2004.

RESULTS

A total of 588 patients (282 in the elderly group and 306 in the control group) were studied. Although there were a larger number of higher-risk (ASA III) patients in the elderly group (P < 0.001), unplanned admission, postoperative symptoms, and satisfaction were comparable with those for the younger group.

CONCLUSION

Day-case inguinal hernia repair can be safely offered to patients aged 70 and above.

Osteopetrosis with Arnold Chiari malformation type I and brain stem compression

Osteopetrosis is a collective term for a range of sclerosing bone diseases resulting from an absence or defective function of osteoclasts. The clinical expression is variable and includes skeletal, hematological and neurological manifestations. The common neurological manifestation includes cranial neuropathies involving optic, cochlear, facial and trigeminal nerves. Spastic quadriplegia occurring as a result of brain stem compression in osteopetrosis is uncommon. The association of Type 1 Arnold Chiari malformation with osteopetrosis resulting in brain stem compression syndrome is an extremely rare entity.

Changes in cholesterol levels in the plasma membrane modulate cell signaling and regulate cell adhesion and migration on fibronectin

The number and distribution of lipid molecules, including cholesterol in particular, in the plasma membrane, may play a key role in regulating several physiological processes in cells. We investigated the role of membrane cholesterol in regulating cell shape, adhesion and motility. The acute depletion of cholesterol from the plasma membrane of cells that were well spread and motile on fibronectin caused the rounding of these cells and decreased their adhesion to and motility on fibronectin. These modifications were less pronounced in cells plated on laminin, vitronectin or plastic, indicating that cholesterol-mediated changes in adhesion and motility are more specific for adhesion mediated by fibronectin-specific integrins, such as alpha5beta1. These changes were accompanied by remodeling of the actin cytoskeleton, the spatial reorganization of paxillin in the membrane, and changes to the dynamics of alpha5 integrin and paxillin-rich focal adhesions. Levels of tyrosine phosphorylation at position 576/577 of FAK and Erk1/Erk2 MAP-kinase activity levels were both lower in cholesterol-depleted than in control cells. These levels normalized only on fibronectin when cholesterol was reincorporated into the cell membrane. Thus, membrane cholesterol content has a specific effect on certain signaling pathways specifically involved in regulating cell motility on fibronectin and organization of the actin cytoskeleton.

Strobilocercus fasciolaris infection with hepatic sarcoma and gastroenteropathy in a Wistar colony

Tapeworm cysts were identified in liver of Wistar rats and it induced fibrosarcoma in liver and gastroenteropathy in stomach and intestine. The tapeworm larva was confirmed as Strobilocercus fasciolaris by PCR linked mitochondrial DNA sequencing. Light microscopy, special staining (masson trichrome) and immunoflouresence supported the diagnosis of fibrosarcoma. Infiltration of plasma cells, macrophages and eosinophils were observed in the liver section. Gastric mucosal hyperplasia, dilation of gastric glands with secretion, intestinal mucosal cell hyperplasia, proliferation of duodenal submucosal glands were confirmed by light microscopy and supported by PAS, AB staining. The concomitant development of hepatic sarcoma and gastroenteropathy by larvae of Taenia taeniaeformis (S. fasciolaris) infection is very rare and is the first reported case in Wistar rats to our knowledge.

Neoadjuvant chemotherapy followed by surgical cytoreduction in advanced epithelial ovarian cancer

AIMS

To study the role of neoadjuvant chemotherapy (NACT) followed by surgical cytoreduction in the management of advanced epithelial ovarian cancers.

MATERIALS AND METHODS

A retrospective analysis of 82 patients with advanced epithelial ovarian cancers (stage IIIC and IV) who were treated with NACT followed by surgical cytoreduction between 1995 and 2004 was performed. Response to NACT, optimal cytoreduction rate, disease-free survival and overall survival were analyzed.

RESULTS

There were 59 patients (72%) with stage IIIC disease and 23 (28%) with stage IV disease. Diagnosis was established by imaging, ascitic fluid cytology and CA-125 estimations in 75% and by laparotomy in 25% of the patients. After NACT, complete response occurred in 17 patients (20.7%), 50 (61.0%) had partial response and no response was documented in 15 (18.3%) patients. Optimal surgical cytoreduction could be achieved in 72% of the patients. At the median follow-up of 34 months (range 6-102 months), 5-year disease-free and overall survivals were 31 and 32% respectively. The median disease free interval was 25.4 months. On multivariate analysis, degree of optimal cytoreduction was the only factor (P < 0.05) affecting survival.

CONCLUSIONS

NACT followed by surgical cytoreduction is a promising treatment strategy for the management of advanced epithelial ovarian cancers. A significant number of patients exhibit response to NACT. Downstaging following NACT leads to higher optimal cytoreduction rates and improved survival in comparison to historical controls.

In vitro drug sensitivity and apoptosis induction in newly diagnosed pediatric acute lymphoblastic leukemia: correlation with overall survival

The present study looked for any associations between in vitro drug sensitivity and clinical outcome in pediatric acute lymphoblastic leukemia (ALL) with the standard drugs used for leukemia therapy. A total of 72 samples were analyzed. In vitro sensitivity to drugs was tested by a methylthiazol-tetrazolium assay in 6 serial fold dilutions. Apoptosis was determined by TUNEL assay and apoptotic index was calculated for each sample. Patients sensitive to prednisone, asparginase, vincristine, and 6-mercapto purine had higher overall survival compared to patients whose tumor cells were resistant to these drugs (p < .01). For the other drugs tested, overall survival did not vary from that of the resistant patients. For doxorubicin, asparginase, vincristine, prednisone combination sensitivity, there was a significant worsening of prognosis from the extremely sensitive patients through an intermediate sensitive group to a most resistant group. The present study thus shows that in vitro drug-sensitivity testing provides significant prognostic information in childhood ALL.

A comparative study of modified radical mastectomy using harmonic scalpel and electrocautery

AIM

The harmonic scalpel is recently emerging as an alternative surgical tool for dissection and haemostasis and has been extensively used in the field of minimally invasive surgery. We studied the utility and advantages of this instrument over electrocautery for performing modified radical mastectomy.

METHODS

The operative and morbidity details of twenty-three breast cancer patients who underwent modified radical mastectomy using the harmonic scalpel were compared with 23 matched controls operated with electrocautery by the same surgical team.

RESULTS

There was no significant difference in the operating time between the harmonic scalpel and electrocautery group (104 and 100 mins, p > 0.05). The blood loss (60 +/- 35 ml and 294 +/- 155, p < 0.001) and drainage volume (590 +/- 430 ml and 1,085 +/- 690 ml, p < 0.001) were significantly lower in the harmonic scalpel group. There was a significant reduction of drain days in harmonic scalpel group (mean five and nine days, p < 0.05). There was no significant difference in the seroma rate between two groups (16% and 22%).

CONCLUSION

Modified radical mastectomy using harmonic scalpel is feasible and learning curve is short. Harmonic scalpel significantly reduces the blood loss and duration of drainage as compared to electrocautery.

Treatment-seeking behavior and compliance of diabetic patients in a rural area of south India

India, being a rural country, has unique problems regarding the treatment compliance of diabetic patients. This community-based study was undertaken in a rural primary health center area near Chennai (Madras) in order to better understand treatment-seeking behavior, compliance patterns, and reasons for noncompliance among rural diabetics. Compliance was indirectly measured through patient interviews and drug use charts. Of the 112 patients interviewed, 72% had some symptoms at the time of diagnosis, and the majority of them were diagnosed in government health centers. Noncompliance was seen in 57% of the 112 patients interviewed, and reasons were elicited. Interruption of treatment was significantly associated with lack of education. The study identified the lack of a patient-friendly, flexible health care system as the primary reason for noncompliance.

Cost-effectiveness analysis of laparoscopic versus minilaparotomy cholecystectomy for gallstone disease. A randomized trial

OBJECTIVE

To evaluate the total cost of minilaparotomy cholecystectomy (MC) and laparoscopic cholecystectomy (LC) and perform a cost-effectiveness (CE) analysis.

METHODS

One hundred adult subjects with painful gallstone disease were randomized: 59 cases for LC and 41 cases for MC. Patients with gallstones shown on ultrasound with normal common bile duct and no history of icterus were included after an informed consent. Cases with acute cholecystitis and raised alkaline phosphatase were excluded. LC was performed using CO2 insufflation and a Storz 2D video camera. MC was done by transverse rectus cutting incision. Outcome was coded as success or failure. Success was defined as operation without injury to bile duct, viscera or vessels, minimal pain and discomfort at 4 weeks, no wound infection up to 4 weeks, and resumption of work within 2 weeks of operation. The total cost of each case included cost of investigations, cost of disposable articles for operation, cost of drugs, cost of hospital stay, and cost of operation including anesthesia. LC and MC were done with reusable instruments. A "societal viewpoint" has been taken in the cost calculations.

RESULTS

There were 50/59 successful outcomes in LC and 15/40 outcomes in MC group. Total cost for LC was 386,769 rupees (Rs) and for MC was Rs 205,041. CE in LC was Rs 7,735 and in MC was Rs 13,669. Incremental CE ratio comparing LC with MC was 3,028.33.

CONCLUSION

LC is a more cost-effective method for treatment of gallstone disease.

Reentrant behavior of relaxation time with viscosity at varying composition in binary mixtures

In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamics simulations. In these models, the two molecular species (A and B) have the same diameter and mass. In model I the interspecies interaction is more attractive than that between the pure components, while the reverse is true for model II. Simulations and mode coupling theory calculations reveal that the models can capture a wide variety of behavior observed in experiments, including the reentrant viscosity dependence of relaxation time.

Colorectal cancers--experience at a regional cancer centre in India

BACKGROUND

The incidence of colorectal cancer (CRC) shows a wide geographic variation and India along with other Asian and African countries has a low incidence. Most patients present with advanced disease and no uniform treatment guidelines are followed at present.

PATIENTS AND METHODS

An audit of 91 patients treated as per IRCH protocol between June 1994 and Jun 2000 in a single surgical unit was performed.

RESULTS

The mean age of patients was 45.3 years (18-90 years) and there was a predominance of rectal cancer patients (Rectal vs Colon = 76% vs 24%). Majority of the rectal cancers were low rectal cancers (67%) and abdominoperineal resection was the commonest surgical procedure performed(40). The inoperability rate was 24% and sphincter salvage rate was 13%. Seventy nine percent of patients had adenocarcinoma and 90% of CRC patients belonged to Astler-Collers stage B2 and C. A total of 37 patients also received adjuvant radiotherapy and only 39 out of 60 patients planned for adjuvant chemotherapy could complete the treatment. The operative mortality was 2.2% and morbidity was 18%. A total of 13 (14%) patients had relapse of disease (local 5, regional 3, distant 5).

CONCLUSIONS

A significant number of CRC patients in India present with advanced stage of disease and probably due to referral bias majority had low rectal cancers. By advocating multimodality protocols a good locoregional and systemic control can be achieved despite the advanced stage of presentation.

Mutant p53 protein, Bcl-2/Bax ratios and apoptosis in paediatric acute lymphoblastic leukaemia

PURPOSE

The Bcl-2 family of proteins regulates a late step in the apoptosis pathway. Bcl-2 protein is believed to be involved in imparting resistance to programmed cell death or apoptosis induced by chemotherapeutic agents and radiation. The anti-apoptotic function of the Bcl-2 protein appears to be modulated by its ability to heterodimerize with other members of the gene family, predominantly Bax, a protein favouring induction of apoptosis. Susceptibility to undergoing apoptosis may, therefore, be dependent on the ratio between Bcl-2 and Bax. Both Bax and Bcl-2 are regulated by the tumour-suppressor protein p53. The present study therefore aims to study the significance of the Bcl-2:Bax ratio, p53 expression and apoptosis in paediatric acute lymphoblastic leukaemia (ALL).

METHODS

Expression of Bax, Bcl-2 and p53 was determined by immunocytochemistry, and apoptosis was evaluated by an enzymatic end-labelling technique using biotin-dUTP and further confirmed by annexin binding. The presence of mutant p53 was determined using a mutant-p53-specific enzyme-linked immunosorbent assay (ELISA).

RESULTS

A total of 32 cases and 20 controls were evaluated. Bcl-2 was found to be expressed in 22/32 of the ALL cases. Pretreatment (spontaneous) apoptosis was observed in 23/32 cases. The mean pretreatment apoptotic index was 11.34 +/- 2.04% with a median value of 7.5%.

CONCLUSIONS

There was a positive correlation between apoptosis and Bax expression (r = 0.5044; P = 0.0038). There was good correlation between the immunoreactivity of p53 and detection of mutant p53 by ELISA (r = 0.4605; P = 0.0079). The apoptosis index showed a negative borderline correlation to the expression of Bcl-2 protein (r = -0.3181; P = 0.076). There was an inverse correlation between extent of apoptosis and the presence of mutant p53 protein (r = -0.4732; P = 0.006). p53 protein expression also showed a correlation with both Bcl-2 (r = 0.4647; P = 0.007) and Bax (r = 0.4128; P = 0.018). The Bcl-2/Bax ratio, however, showed no significant correlation with apoptosis (r = -0.3131; P = 0.08) or with p53 expression. No significant association was evident between clinical and laboratory parameters with the Bcl-2/Bax protein expression except lymphadenopathy (r = 0.5774; P = 0.03). However, Bax expression showed a borderline correlation with the immediate tumour response to chemotherapy (r = -0.338; P = 0.0628). These patients are being followed-up to look for any association between clinical outcome, Bcl-2/Bax ratio and apoptosis.