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Byline: M. Tiwana, L. Ni, S. Saini, S. Verma, D. Doddamani, N. Jain, M. Biswas, Meenu. Gupta, Madhur. Gupta, M. Saini, N. Chauhan Introduction: To audit the survival outcomes and [...]

Aims: Extracoporeal SWL is the treatment of choice for most renal and ureteric calculi, but most patients are not immediately stone free. We prospectively evaluated the effect of forced diuresis during ESWL treatment of renal calculi of size 1.5 to 2.5 cm without the use of stents. Materials and Methods: 122 patients were randomized into two groups. Lithotripsy was performed using Dornier Compact Delta lithotriptor. The study group received 2 litres fluid infusion with frusemide 40 mg during the procedure whereas the control group received fluids only. Outcome of stone clearance in both groups was studied. Results: 62 patients of the control group were treated by standard SWL and 60 patients in study group by SWL with forced diuresis., Mean number of SWL sessions in the study group and in control group was 2.00 and 2.56 respectively. Calculated separately, mean number of SWL sessions required in calyceal and pelvic stones of the study population were 2.00 (shocks - 5016.8) and 2.04 (shocks - 8177.22) as compared to control group values of 2.6 (shocks - 5951.82) and 2.51 (shocks - 7387.87) respectively. The difference was statistically significant (p value of 0.05 and 0.04 respectively). Mean duration to stone clearance in the study group was 20.41 days and in the control group was 28.54 days which was also statistically significant. Conclusion: Forced diuresis increases the treatment response of stones sized 1.5-2.5 cm. The clearance is enhanced, number of shockwaves and SWL sessions is reduced significantly with less additional procedures. Forced diuresis is a useful, inexpensive and safe adjunct to SWL. [ABSTRACT FROM AUTHOR]

Introduction: Renal function reserve is the ability of the kidney to increase its GFR when stressed. Donor nephrectomy has been shown to demonstrate renal function reserve in remaining kidney. After unilateral nephrectomy the remaining kidney increases its GFR by 25% to 40% within four weeks. Factors affecting the renal function reserve of the remaining kidney include pre nephrectomy GFR, age, and gender. Our objective was to study these factors in the Indian donors and compare it with western literature. Methods: Kidney donors undergoing surgery in Army Hospital over a period of two years had their GFR estimated using DTPA scintigraphy at two times, pre nephrectomy and one month post nephrectomy. Data was analyzed to asses renal function reserve of the remaining kidneys and compare the increase in GFR with respect to age and gender. Results: GFR increased in 71 patients, remained same in 2 patients and decreased in 7 patients. 1 month post nephrectomy GFR of the remaining kidney increased by19.3%. GFR in male and female donors increased by17.5% and 20.43% respectively. The GFR increased by 32.14% in 18-30 yrs, 15.8% in 31-40 yrs, 12% in 41-50 yrs, 20% in 50-60yrs and by 13% in above 60 yrs group. Conclusions: Renal function reserve in Indian donors is less than their western counterparts. Primary factor predictive of post nephrectomy GFR is the pre nephrectomy GFR, age and gender are other factors. [ABSTRACT FROM AUTHOR]

Introduction: Urethral calculi are very rare and majority of them originate in the upper urinary tract or bladder. They however may get lodged in urethra during their passage if associated with a stricture or a diverticulum of the urethra. Rarely, urethral calculi may arise primarily in a urethral diverticulum or around a foreign body. Calculi in the urethral diverticulum may cause recurrent urinary tract infections or may be there without being symptomatic for years. Aim: We report a patient with two giant urethral calculi in two urethral diverticula. Case is interesting because solitary giant calculus in a diverticulum has been reported but giant calculi with multiple diverticula have not been reported in literature so far. Materials and Methods: A 42 years old male reported with dysuria,scrotal and perineal mass. He had sustained fracture pelvis and urethral injury 12 years back for which he had undergone multiple surgeries. Examination of genitalia showed two large hard lumps in penoscrotal region and perineum. Biochemical parameters were normal. RGU and MCU showed two large diverticula at penoscrotal junction and bulbar urethra with calculi measuring 6x4 cm and 4x3 cm. He underwent excision of the diverticule with reconstruction of the urethra. A voiding cystourethrogram 4 weeks later was normal. Conclusion: Acquired urethral diverticula result from trauma, suppuration, urethral calculus or a urethral stricture. Stone formation in urethral diverticulum is more common in females as compared to males. Multiple diverticula can be managed successfully with diverticulectomy. [ABSTRACT FROM AUTHOR]

Introduction and Objective: A long forgotten JJ stent is encountered rarely in urological practice. Management of such a case is difficult due to stent encrustation. We report the longest forgotten stent to the best of our knowledge after a comprehensive literature search. Methods: A 48 years old lady underwent right ureterolithotomy with JJ stenting 15 years back at Mumbai. She presented with right flank pain and Dysuria. Plain radiograph revealed a right JJ stent in situ with heavy stone encrustation along its whole length. IVU revealed bilaterally normally functioning renal units with mild right hydronephrosis. She underwent right ureteric meatotomy and URS with intracorporeal lithotripsy and JJ stent removal with JJ stenting. A plain radiograph after one month revealed stone fragments aggregated at the lower end of right Ureter with JJ stent in position. She underwent URS with intracorporeal lithotripsy with JJ stenting again. Results: Repeat radiograph showed some fragments still in the lower ureter and she has been planned for third stage surgery. Conclusion: Long forgotten JJ stents can be managed using minimally invasive surgery. Morbidity is reduced but multiple staged procedures may be required. We propose that a stent registry should be maintained at every urological centre so that every stent is accounted for. [ABSTRACT FROM AUTHOR]

Introduction: Haemorrhagic cystitis is not an uncommon complication after radiation treatment or due to cyclophosphamide for Pelvic malignancy. The incidence is about 10%. At time it can be severe and necessitate cystectomy. We present our experience of management of 22 cases. Materials and Methods: From Jan 2003 to Dec 2006, we treated 22 cases of haemorrhagic cystitis with mild to severe haematuria. All patients were female in the age range of 35 to 78 years. 19 patients had radiotherapy for carcinoma cervix, one had carcinoma rectum and the rest 2 had received cyclophosphamide for other malignancies. Haematuria usually started after 6 months to 3 years of receiving the therapy. None had active malignancy at the time of haematuria. 3 had clot retention which required evacuation. Results: Six patients had resolution of haematuria with saline irrigation alone. Five required 1% Alum irrigation lasting from 24 to 72 hrs for haematuria to resolve. Two patients had small bleeders on cystoscopy which could be controlled by diathermy coagulation. Seven patients required 1% formalin instillation for 5 to 20 minutes under anaesthesia. A cystogram was done before formalin instillation to exclude reflux. Two patients continued to bleed even after formalin and one required simple cystectomy and ideal conduit diversion and the other could be controlled with selective angioembolisation. Conclusion: Haemorrhagic cystitis is a sequel to radiation therapy and rarely cyclophosphamide chemotherapy that may cause potentially troublesome haematuria. Theses cases are managed by various ways and occasionally cystectomy may be required. [ABSTRACT FROM AUTHOR]

Introduction: Benign prostatic hyperplasia (BPH) affects more than 50% of men older than 60 years. A large number of these undergo transurethral resection of the prostate (TURP). There has been a search for other minimally invasive treatment options for BPH. Laser therapy for BPH has undergone rapid development. Among the recent innovations is photoselective vaporization of prostate (PVP) with the 80 . watt Potassium Titanyl Phosphate (KTP) laser. Objective: To assess the outcome and adverse effects of Photoselective vaporization of prostate in the treatment of BPH. Materials and Methods: From Jan 2005 to Aug 2007, 80 patients have been treated with 80 watt KTP laser. AUA symptom score, prostate size, maximum flow rate (Qmax) and post void residual (PVR) were compared preoperatively and postoperatively. All complications were recorded. From Jan 2007 patients of coronary artery disease who have had drug eluting stents placed in coronary arteries were operated with their anti-platelet medication continuing during the peri-operative period. Results: Significant improvement was observed in all parmeters. Mean improvement of Qmax was more than 100% while prostate volume reduced by 45%. Complications consisted of transient dysuria, and stress incontinence. There was minimal bleeding. Conclusion: PVP is a unique, safe and effective modality for the treatment of BPH. [ABSTRACT FROM AUTHOR]

Primordial germ cells (PGCs) are germline-restricted embryonic cells that form the functional gametes of the adult animal. The use of avian PGCs in biobanking and producing genetically modified birds has driven research on the in vitro propagation and manipulation of these embryonic cells. In avian species, PGCs are hypothesized to be sexually undetermined at an early embryonic stage and undergo differentiation into an oocyte or spermatogonial fate dictated by extrinsic factors present in the gonad. However, chicken male and female PGCs require different culture conditions, suggesting that there are sex-specific differences, even at early stages. To understand potential differences between male and female chicken PGCs during migratory stages, we studied the transcriptomes of circulatory stage male and female PGCs propagated in a serum-free medium. We found that in vitro cultured PGCs were transcriptionally similar to their in ovo counterparts, with differences in cell proliferation pathways. Our analysis also revealed sex-specific transcriptome differences between male and female cultured PGCs, with notable differences in Smad7 and NCAM2 expression. A comparison of chicken PGCs with pluripotent and somatic cell types identified a set of genes that are exclusive to germ cells, enriched in the germplasm, and associated with germ cell development.

Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the 'A 10234287911 ' allele may promote better processing vis-à-vis the structure conferred by 'G 10234287911 ' allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression., (© 2023. The Author(s).)

Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells., (© 2022. The Author(s).)

Background: Nasoalveolar molding (NAM) is a presurgical orthopedic procedure, mainly focusing upon the aesthetic outcome of the treatment goal by reducing the number of reconstructive surgeries performed later for the purpose of esthetics. It was reported a very small proportion of pediatric dentists are providing presurgical intervention and the practice of NAM still side stepping among various dental practitioners., Objectives: The study was aimed to assess the knowledge and attitude among various dental specialties regarding NAM procedure in cleft patients., Materials and Methods: A questionnaire-based cross-sectional survey was carried out among 180 dental professionals (pedodontists, orthodontists, prosthodontists, oral surgeons). A total of 180 questionnaires were prepared, out of which 98 were filled through direct personal interview and 82 were circulated via Google forms. Results were analyzed using chi-square test, Mann-Whitney U test, and Kruskal-Wallis test., Results: There was statistically significant difference in the cumulative knowledge scores between specialty with P < .001; 99% of the participants think one should opt for NAM before cleft lip and palate surgery and 39% participants prefer pedodontists to carry out NAM procedure., Conclusion: Dental specialists in India have a positive attitude toward presurgical orthopedics. Majority of them agreed that there is great improvement in the aesthetic outcomes of surgeries after NAM intervention.

Poultry is the most abundant livestock species with over 60 billion chickens raised globally per year. The majority of chicken are produced from commercial flocks, however many indigenous chicken breeds play an important role in rural economies as they are well adapted to local environmental and scavenging conditions. The ability to make precise genetic changes in chicken will permit the validation of genetic variants responsible for climate adaptation and disease resilience, and the transfer of beneficial alleles between breeds. Here, we generate a novel inducibly sterile surrogate host chicken. Introducing donor genome edited primordial germ cells into the sterile male and female host embryos produces adult chicken carrying only exogenous germ cells. Subsequent direct mating of the surrogate hosts, Sire Dam Surrogate (SDS) mating, recreates the donor chicken breed carrying the edited allele in a single generation. We demonstrate the introgression and validation of two feather trait alleles, Dominant white and Frizzle into two pure chicken breeds using the SDS surrogate hosts.

In plants, the biosynthesis of the phenylpropanoid, flavonoid and fatty acid pathway monomers, polymers and conjugated metabolites play a vital role in disease resistance. These are generally deposited to reinforce cell walls to contain the pathogen to the site of infection. Identification of sequence variants in genes that biosynthesise these resistance metabolites can explain the mechanisms of disease resistance. The resistant and susceptible genotypes inoculated with Phytophthora infestans were RNA sequenced to identify the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variations. The SNPs/InDels were annotated and classified into different categories based on their effect on gene functions. In the selected 25 biosynthetic genes overlapping 39 transcripts, a total of 52 SNPs/InDels were identified in the protein-coding (CDS) regions. These were categorised as deleterious based on prediction of their effects on protein structure and function. The SNPs/InDels data obtained in this study can be used in genome editing to enhance late blight resistance in Russet Burbank and other potato cultivars.

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform 'Axiom ® CicerSNP Array' has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p-convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom ® CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications., (© 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1 -P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Biotic stress in legume crops is one of the major threats to crop yield and productivity. Being sessile organisms, plants have evolved a myriad of mechanisms to combat different stresses imposed on them. One such mechanism, deciphered in the last decade, is small RNA (sRNA) mediated defense in plants. Small RNAs (sRNAs) have emerged as one of the major players in gene expression regulation in plants during developmental stages and under stress conditions. They are known to act both at transcriptional and post-transcriptional levels. Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDR) constitute the major components of sRNA biogenesis machinery and are known to play a significant role in combating biotic and abiotic stresses. This study is, therefore, focused on identification and characterization of sRNA biogenesis proteins in three important legume crops, namely chickpea, pigeonpea, and groundnut. Phylogenetic analysis of these proteins between legume species classified them into distinct clades and suggests the evolutionary conservation of these genes across the members of Papillionidoids subfamily. Variable expression of sRNA biogenesis genes in response to the biotic stresses among the three legumes indicate the possible existence of specialized regulatory mechanisms in different legumes. This is the first ever study to understand the role of sRNA biogenesis genes in response to pathogen attacks in the studied legumes.

In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.

APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca&#95;02170 and Ca&#95;16631) and three HSP90 genes (Ca&#95;23016, Ca&#95;09743 and Ca&#95;25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan&#95;27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan&#95;41905 and C.cajan&#95;41951, were identified as leads for further investigation in response to FW stress in pigeonpea., (© 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot&#95;a" (15 genes) and "QTL-hotspot&#95;b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.