Isolated perinephric abscess as the initial manifestation of filariasis-an unusual presentation.

Key Clinical Message: Filariasis may present as an isolated perinephric abscess. Hence, a high index of suspicion should be maintained in endemic settings. Abstract: In cases with unexplained fever, eosinophilia and perinephric collection, it is necessary to do detailed infectious disease work up. High index of suspicion is required to diagnose filariasis due to its wide range of clinical presentation and laboratory findings. It may present as perinephric abscess, which can be diagnosed through ultrasonography.

Immediate effect of alpha-blockers in predicting LUTS improvement in BPH patients.

INTRODUCTION: Indications for treating Benign Prostatic Hyperplasia include reversing signs and symptoms or preventing the progression of the disease. Alpha-blockers are the most effective, least costly, and best tolerated of the drugs for relieving LUTS. The aim of the study is to investigate the immediate impact of alpha-blocker medications on lower urinary tract symptoms (LUTS). MATERIALS AND METHODOLOGY: About 100 patients were included in the study-50 patients in each of the groups A (tamsulosin) and B (silodosin). The first visit was the baseline examination before starting alpha-blockers and included history, DRE, UFM, USG KUBP with PVR, IPSS, serum PSA, serum creatinine, urine analysis, urine culture, and sensitivity. All above parameters were also at 1 week, 1 month, and 3 months following starting of alpha-blockers respectively, and compared with baseline. RESULT: As of the first, second, third, and fourth visits, the mean Qmax in group A was 10.3 ± 3.3 s, 15.08 ± 2.80 s, 15.66 ± 3.18 s, and 15.12 ± 3.24 s, respectively, while in group B it was 10.1 ± 3.1 s, 14.88 ± 2.80 s, 15.18 ± 3.18 s, and 15.08 ± 3.24 s, respectively (p < 0.001). The mean voiding time was 40.87 ± 23.91 s, 36.41 ± 20.73 s, 34.85 ± 21.37 s, and 32.07 ± 21.81 s, respectively in group A, and 41.27 ± 15.49 s, 37.23 ± 21.34 s, 38.59 ± 20.83 s, and 33.10 ±22.08. In group A, the mean PVR and IPSS scores were improved and also improved in group B. CONCLUSION: The first dose of tamsulosin and silodosin improves UFM and predicts the mid-term change in UFM as well as IPSS indices in the treatment of BPH-related LUTS.

Prognostic significance of preoperative pyuria & neutrophil to lymphocyte ratio in patients with non-muscle-invasive bladder cancer: A prospective cohort study.

BACKGROUND: The most prevalent cancer of the urinary system and the fourth most frequent cancer in men is bladder cancer. Up to 45% of non-muscle-invasive bladder cancers (NMIBC), may develop into muscle-invasive disease within 5 years after initial diagnosis, depending on the risk profile. The neutrophil to lymphocyte ratio (NLR), which is an emerging marker of host inflammation and can be easily calculated from routine complete blood counts (CBCs) with differentials, has shown to be an independent prognostic factor for a variety of solid malignancies, including urinary tract cancer. Pyuria is a well-documented prognostic factor in urinary tract carcinomas, according to several research. The relationship between preoperative pyuria and recurrence in patients with NMIBC is unclear, even though some studies found that pyuria was a strong predictor of poor prognosis in patients with NMIBC. Our study's objective was to compare the prognostic effect of pre-treatment pyuria and NLR on the likelihood of progression and recurrence in individuals with primary NMIBC. MATERIALS AND METHODOLOGY: Data obtained from 100 bladder cancer patients who underwent transurethral resection of bladder tumor (TURBT) from June 2021 to January 2023 were evaluated prospectively. INCLUSION CRITERIA: Age more than 18 years, having tumor size less than 3 × 3 cm, single tumor, no H/O TURBT. EXCLUSION CRITERIA: Age less than 18 years, size more than 3 × 3 cm, multiple tumors, H/O TURBT. RESULTS: We demonstrated in the current study that, compared to NLR, preoperative pyuria was more substantially linked with intravesical recurrence, higher T stage and disease progression following TURBT for NMIBC.

Effects of administration of local aminophylline on patients undergoing ureteroscopic lithotripsy.

INTRODUCTION: The presence of ureteral stones can cause pain, infections of urinary tract and hydronephrosis, resulting in the loss of renal function. For two decades, Ureteroscopy and laser stone fragmentation (URSL) attained a big rise and is the first line management for large ureteric stones and renal stones up to 2 cm. The present study was conducted to assess the success rate of ureteroscopic lithotripsy in treatment of ureteric calculus after local administration of aminophylline. MATERIALS AND METHODS: 100 patients having ureteric calculi <20 mm in size, aged 20-60 years were included in the study and randomly divided into Group A (n = 50) with administration of local aminophylline and Group B (n = 50) with administration of saline infusion. Ureteroscopy was performed after 5 min of administration of the solution. URSL was done using pneumatic lithoclast and/or laser. Various parameters like duration of procedure, ease of ureteral access, requirement of DJ Stent and need of further operative interventions were compared between case and control groups. The data was collected and then subjected to statistical analysis using IBM SPSS 20.0 version at significance level of p < 0.05. RESULTS: The mean age of study subjects having ureteral stones was found to be between 31 and 40 years of age with males being more affected. We observed less mean duration of surgery, higher success rate, easy ureteral access (p-value < 0.05) with aminophylline use than control group. The need of ureteral stent and Auxiliary procedures was significantly higher in the control than in the case group (38%). CONCLUSION: The use of aminophylline has been found to be highly useful and effective in reducing the need of stents and secondary surgery, decreased pain, and increased success rate. Thus, the use of aminophylline is recommended during URSL procedure for the successful management of ureteral calculi.

Investigation of ultrafast carrier dynamics in curcumin dye for environment friendly dye-sensitized solar cell.

Natural dyes have been widely employed in the fabrication of dye-sensitized solar cells (DSSCs). DSSCs are favored for their cost-effective, and simple fabrication process relies on metal-based and organic dyes. The choice of dyes greatly affects the performance of DSSCs. DSSCs have found a lot of applications in indoor, solar power gadgets with reasonable efficiency up to 13%. Nonetheless, despite advances in DSSC technology, the complex photophysics and excited state dynamics associated with natural dyes employed in DSSCs remain elusive and have not been adequately investigated. This information gap emphasizes the need for more study and analysis into the behavior of these dyes, since understanding their underlying principles might lead to major improvements in DSSC performance and efficiency. In this work, we have investigated the fundamental characteristics and excited-state carrier dynamics of natural dye curcumin using ultrafast transient absorption (TA) spectroscopy technique. The curcumin dye shows delay time-dependent positive and negative signals in the TA spectra, which are related to excited state absorption and stimulated emission. We also found that hydrogen bonding and polarity effect of solvent significantly influence the carrier dynamics of curcumin. Ultrafast lifetime component indicates that hydrogen-bond rearrangements are involved in the kinetics of the relaxation process of the S1 state of curcumin photo-sensitizer.

Comparison of perineal urethrostomy versus augmentation urethroplasty in anterior urethral stricture disease.

PURPOSE: Perineal urethrostomy and urethroplasty are very good options for complex and long anterior urethral strictures. A perineal urethroplasty is usually a neglected option. To our knowledge, a comparative study between augmentation urethroplasty and perineal urethrostomy has been not conducted regarding subjective and patient reported outcome measures. We compared both these groups in a high volume tertiary care hospital. MATERIALS AND METHODS: A prospective comparative study of augmentation urethroplasty and perineal urethroplasty for long anterior urethral stricture. it was defined by strictures of more than 3 cm. We compared demographic data, urinary and sexual function; and quality of life using validated PROMs (patient-reported outcome measures) between both above groups. RESULTS: Both groups had 40 patients each. IPSS score improvement for PU and AUP were 20 and 19.6, respectively(p = 0.1223); IIEF-5 score improvement for PU and AUP at baseline and after 6 months were 14.3 and 16.7, respectively(p = 0.1433); QOL score improvement for PU and AUP were 3.45 and 3.05, respectively; which was statistically significant (p ⩽ 0.001). CONCLUSIONS: Perineal urethrostomy is a good but neglected option for complex and long anterior urethral strictures and it should be considered one of the reliable treatment option for patients with long-segment urethral strictures.

Two Intra-Individual ITS1 rDNA Sequence Variants Identified in the Female and Male Rotylenchulus reniformis Populations of Alabama.

Around 300 different plant species are infected by the plant-parasitic reniform nematode (Rotylenchulus reniformis), including cotton. This is a devasting nematode with a preference for cotton; it is commonly found in Alabama farms and causes severe reduction in yields. Its first internal transcribed spacer (ITS1) region can be sequenced, and potential mutations can be found in order to study the population dynamics of the reniform nematode. The goal of our study was to sequence the ITS1 rDNA region in male and female RNs that were collected from BelleMina, Hamilton, and Lamons locations in Alabama. After separating the single male and female RNs from the samples collected from the three selected listed sites above, the ITS1 region was amplified selectively using specific primers, and the resulting products were cloned and sequenced. Two distinct bands were observed after DNA amplification of male and female nematodes at 550 bp and 730 bp, respectively. The analysis of sequenced fragments among the three populations showed variation in average nucleotide frequencies of female and male RNs. Singletons within the female and male Hamilton populations ranged from 7.8% to 10%, and the variable sites ranged from 13.4% to 26%. However, female and male BelleMina populations had singletons ranging from 7.1% to 19.7% and variable regions in the range of 13.9% to 49.3%. The female and male Lamons populations had singletons ranging from 2.5% to 8.7% and variable regions in the range of 2.9% to 14.2%. Phylogenetic (neighbor-joining) analysis for the two ITS1 fragments (ITS-550 and ITS-730) showed relatively high intra-nematode variability. Different clone sequences from an individual nematode often had greater similarity with other nematodes than with their own sequences. RNA fold analysis of the ITS1 sequences revealed varied stem and loop structures, suggesting both conserved and variable regions in the variants identified from female and male RNs, thus underscoring the presence of significant intra- and inter-nematodal variation among RN populations in Alabama.

Safety and procedural outcomes of intravascular lithotripsy in calcified coronaries in Indian patients.

OBJECTIVE: Calcified coronaries still remain a major challenge for interventional cardiologist. This study aims to evaluate safety and efficacy of intravascular lithotripsy (IVL) in management of coronary artery calcification. METHODS: This was a retrospective single centre study regarding the utility of IVL in management of calcified coronaries. Patients with hemodynamically stable acute coronary syndrome or symptomatic chronic coronary syndrome (CCS) and calcified coronaries on angiography and who underwent IVL were enrolled. Intravascular imaging was performed wherever feasible. The primary endpoint was procedural success. In addition, data regarding procedural complications were collected. RESULTS: A total of 29 patients underwent IVL with a majority being males and having comorbidities such as hypertension and diabetes. A procedural success rate of 93.1% was achieved with no patient having >50% residual stenosis. IVL catheter was successfully delivered in all patients. The mean catheter diameter was 3.3 ± 0.4 mm and mean number of delivered pulses was 70.3 ± 16.4. The arteries most commonly intervened were the left main coronary and the left anterior descending artery. Intracoronary imaging revealed a significant increase in minimum luminal cross-sectional area (MLA) post IVL (pre-MLA: 5.1 ± 2.5 mm2; post-MLA: 10.7 ± 2.9 mm2; P<0.001). Two patients had in-hospital MACE in form of peri-procedural non Q-wave MI. No patient had arrhythmias, stent thrombosis, coronary perforation, or slow flow/no-reflow. Two patients had a rupture of IVL balloon while four had coronary artery dissection. CONCLUSIONS: IVL is a safe and highly effective modality with high procedural success rate in management of calcified coronaries.

Reference interval of platelet counts and other platelet indices in apparently healthy blood donors in North India according to Clinical and Laboratory Standards Institute guidelines: Need to redefine the platelet count cutoffs for repeat plateletpheresis donation?

BACKGROUND: In clinical practice, laboratory results are of great importance for the diagnosis and treatment. Reference intervals of different parameters aid health-care professionals in the interpretation of results. There are very few studies on reference intervals from India. This prospective study was conducted to determine the reference intervals for platelet count (PLT) and PLT indices; mean PLT volume (MPV), PLT distribution width (PDW), and PLT large cell ratio (P-LCR). These values can be obtained as a part of a routine complete blood count (CBC) and have diagnostic and prognostic significance in certain diseases. PLT count is an important criterion for the selection of donors for repeat plateletpheresis donation. MATERIALS AND METHODS: Sixteen hundred and thirty-four first-time healthy volunteer plateletpheresis donors were enrolled for the study. CBC was done, values of PLT, MPV, PDW, and P-LCR were noted, and the results were analyzed. The 95% of the reference distribution was estimated using the 2.5th and 97.5th percentiles following Clinical and Laboratory Standards Institute guidelines. Adverse donor reactions, if any and quality parameters of single donor PLTs (SDP) were also studied. RESULTS: Reference range values of PLT, MPV, PDW, and P-LCR were 137,825-355,175/µl, 8.1-13.9/fl, 9.1-22.5/fl, and 11.7%-52.9%, respectively, and compared well with other published studies from India. It was observed that reference values of PLT count obtained in the study were lower than reference values that are currently used in most laboratories (150,000-450,000/µl) in India. CONCLUSION: Based on our results, we are of the opinion that the PLT count cutoffs for repeat plateletpheresis donation may need to be revised downwards for our country which would also mitigate the scarcity of apheresis donors.

Efficacy of tranexamic acid in decreasing primary hemorrhage in transurethral resection of the prostate: A novel combination of intravenous and topical approach.

BACKGROUND: Transurethral resection of the prostate (TURP) is the gold standard for benign prostatic enlargement; however, hemorrhage still remains one of the major complications. OBJECTIVE: The primary aim of this study was to evaluate the effect of tranexamic acid (TXA) in reducing intraoperative blood loss and need for blood transfusion. Secondary parameters compared were operating time, volume of irrigation fluid used, and reduction in hemoglobin concentration. SUBJECTS AND METHODS: A total of 70 eligible patients undergoing TURP were randomized based on computer generated table into two groups. The study group (1) received IV TXA 500 mg after induction of anesthesia and 500 mg in each irrigation fluid bottle (dual mode) and the control group (2) received none. RESULTS: The mean age (68.20 vs. 66.5 years), prostate size (57 vs. 51 g), and preoperative hemoglobin (13.3 vs. 13.5 g/dl) were similar between the groups. Intraoperative blood loss in the TXA group was found to be significantly reduced (174.60 ± 125.38 ml vs. 232.47 ± 116.8; P = 0.04). Blood transfusion was required in 2.8% of cases as compared to 14.2% in controls. Operating time, volume of irrigation fluid, and postoperative reduction of hemoglobin were not significant between the groups. No complications were observed in both groups. CONCLUSION: In this study, we observed that TXA, when used as a combination of Intravenous and topical route, effectively reduced intra-operative blood loss and the need for transfusion.

Novel predictive risk factor for Erectile Dysfunction: Serum folic acid.

The purpose of this study was to compare the serum Folic Acid (FA) levels in patients with Erectile Dysfunction (ED) and healthy controls and whether levels vary with its severity. The study was carried out on 77 sexually active individuals, out of which 41 complained of ED and 36 were apparently normal. Patients were excluded if they had any diseases known to cause ED. The severity was further categorised based on IIEF-5 scores. Blood serum levels of testosterone, lipid profile, random blood sugar, liver function test, renal function test and FA levels were obtained in each patient. Independent-samples t test of significance was used when comparing between two means. Pearson's correlation coefficient (r) test was used for correlating data. All clinical and biochemical parameters except FA were comparable in both the groups. FA levels were significantly decreased in ED group (5.29 vs. 10.8; p value = .004). Smoking habits were comparable between the groups, and FA levels did not vary among smokers and nonsmokers (p value = .46). Serum FA levels significantly declined with increasing severity of ED (8.28 vs. 5.56 vs. 4.37 vs. 3.5; p value < .001). Thus, decreased FA might possibly be one of the novel risk factors for ED.

A Comparative Study of Antegrade Air Pyelogram and Retrograde Air Pyelogram for Initial Puncture Access during Percutaneous Nephrolithotomy.

INTRODUCTION: Access into the collecting system is considered to be the most critical step for Percutaneous Nephrolithotomy (PCNL). AIM: The present study provides a comparative view into antegrade air pyelography and retrograde air pyelography procedures for percutaneous renal access. MATERIALS AND METHODS: A cross-sectional study was conducted on 100 patients with radiopaque renal calculi indicated for PCNL procedure. These patients were randomly assigned to two groups namely antegrade air pyelogram group (Group I) and retrograde air pyelogram group (Group II). In antegrade air pyelogram group, the collecting system was delineated by targeting the renal stone using a 22 gauge spinal needle where the patients were in the prone position. In another group, the collecting system was delineated by retrograde air pyelogram under fluoroscopy guidance. The method of tract dilatation and stone extraction were the same in both groups for comparison of outcome and complication. RESULTS: The mean age of patients was 41.7±13 and 41.4±13.6 years in Group-I and Group-II respectively. The male to female ratio in Groups I and II was 35/15 (70.00%) and 38/12 (76.00%) respectively. In Group-I the average duration of access was 2.66±1.0 minutes after prone positioning whereas it was recorded to be 19.48±5.0 minutes in Group-II, after lithotomy followed by prone positioning of the patient. Duration of radiation exposure was almost similar in both groups. Additional procedural cost was significantly higher in Group II. CONCLUSION: Our study indicated that access for PCNL using antegrade air pyelogram can be a cost-effective and acceptable alternative to retrograde air pyelogram with decreased access time.

Principal Component Analysis and Molecular Characterization of Reniform Nematode Populations in Alabama.

U.S. cotton production is suffering from the yield loss caused by the reniform nematode (RN), Rotylenchulus reniformis. Management of this devastating pest is of utmost importance because, no upland cotton cultivar exhibits adequate resistance to RN. Nine populations of RN from distinct regions in Alabama and one population from Mississippi were studied and thirteen morphometric features were measured on 20 male and 20 female nematodes from each population. Highly correlated variables (positive) in female and male RN morphometric parameters were observed for body length (L) and distance of vulva from the lip region (V) (r = 0.7) and tail length (TL) and c' (r = 0.8), respectively. The first and second principal components for the female and male populations showed distinct clustering into three groups. These results show pattern of sub-groups within the RN populations in Alabama. A one-way ANOVA on female and male RN populations showed significant differences (p ≤ 0.05) among the variables. Multiple sequence alignment (MSA) of 18S rRNA sequences (421) showed lengths of 653 bp. Sites within the aligned sequences were conserved (53%), parsimony-informative (17%), singletons (28%), and indels (2%), respectively. Neighbor-Joining analysis showed intra and inter-nematodal variations within the populations as clone sequences from different nematodes irrespective of the sex of nematode isolate clustered together. Morphologically, the three groups (I, II and III) could not be distinctly associated with the molecular data from the 18S rRNA sequences. The three groups may be identified as being non-geographically contiguous.

RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.).

RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.

Retro-renal colon: role in percutaneous access.

INTRODUCTION: Upper urinary tract is accessed for various procedures. The maximum numbers of procedures are carried out in prone position. Perforation of the colon is a well-known complication. The incidence of retrorenal colon varies from 10-20% in prone position, but the chances of injury is around <1%. These facts lead us to review the occurrence of retrorenal colon. The CT scan is imaging test of choice. OBJECTIVE: The aim of this study was to find out the occurrence of retrorenal colon at our centre and potential risk of injury to colon when kidney is punctured at various levels by percutaneous route. MATERIALS AND METHODS: It is a hospital-based descriptive type of observational study. We reviewed CT abdomen in supine and prone position in patients with different problems from January 2013 to December 2013. Inclusion and exclusion criteria applied. Colon posterior to the line as described by Prassopoulos and coworkers is regarded as retrorenal colon and being at risk. RESULTS: A total number of 700 patients were included, 350 each in supine and prone position. Patients had CT scan as a part of workup for pain abdomen in 27% cases, calculus disease in 25% cases, carcinoma bladder in 16% cases and rest were of different diagnoses. Retrorenal colon was found in 2% patients in supine and 6.8% patients in prone position. CONCLUSION: Considering the low incidence, the sample size in our study is small. We recommend multicentric large population-based study to establish the true incidence of retrorenal colon and chances of injury to colon.

Ensemble Empirical Mode Decomposition based methodology for ultrasonic testing of coarse grain austenitic stainless steels.

A signal processing methodology is proposed in this paper for effective reconstruction of ultrasonic signals in coarse grained high scattering austenitic stainless steel. The proposed methodology is comprised of the Ensemble Empirical Mode Decomposition (EEMD) processing of ultrasonic signals and application of signal minimisation algorithm on selected Intrinsic Mode Functions (IMFs) obtained by EEMD. The methodology is applied to ultrasonic signals obtained from austenitic stainless steel specimens of different grain size, with and without defects. The influence of probe frequency and data length of a signal on EEMD decomposition is also investigated. For a particular sampling rate and probe frequency, the same range of IMFs can be used to reconstruct the ultrasonic signal, irrespective of the grain size in the range of 30-210 µm investigated in this study. This methodology is successfully employed for detection of defects in a 50mm thick coarse grain austenitic stainless steel specimens. Signal to noise ratio improvement of better than 15 dB is observed for the ultrasonic signal obtained from a 25 mm deep flat bottom hole in 200 µm grain size specimen. For ultrasonic signals obtained from defects at different depths, a minimum of 7 dB extra enhancement in SNR is achieved as compared to the sum of selected IMF approach. The application of minimisation algorithm with EEMD processed signal in the proposed methodology proves to be effective for adaptive signal reconstruction with improved signal to noise ratio. This methodology was further employed for successful imaging of defects in a B-scan.

Characterization of the reniform nematode genome by shotgun sequencing.

The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States, is among the major plant-parasitic nematodes for which limited genomic information exists. In this study, over 380 Mb of sequence data were generated from pooled DNA of four adult female RNs and assembled into 67,317 contigs, including 25,904 (38.5%) predicted coding contigs and 41,413 (61.5%) noncoding contigs. Most of the characterized repeats were of low complexity (88.9%), and 0.9% of the contigs matched with 53.2% of GenBank ESTs. The most frequent Gene Ontology (GO) terms for molecular function and biological process were protein binding (32%) and embryonic development (20%). Further analysis showed that 741 (1.1%), 94 (0.1%), and 169 (0.25%) RN genomic contigs matched with 1328 (13.9%), 1480 (5.4%), and 1330 (7.4%) supercontigs of Meloidogyne incognita, Brugia malayi, and Pristionchus pacificus, respectively. Chromosome 5 of Caenorhabditis elegans had the highest number of hits to the RN contigs. Seven putative detoxification genes and three carbohydrate-active enzymes (CAZymes) involved in cell wall degradation were studied in more detail. Additionally, kinases, G protein-coupled receptors, and neuropeptides functioning in physiological, developmental, and regulatory processes were identified in the RN genome.

BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton.

Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.

Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic nematode, Rotylenchulus reniformis.

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene.