Morphometric and genetic characterization of cultured and wild populations of tilapia, Oreochromis niloticus in India

To study genetic variation in Indian populations of tilapia, Oreochromis niloticus, both truss morphometrics and genetic characterization have been performed. In the present study, 88 individuals from two farm populations (GIFT and West Bengal) and one reservoir population (Gujarat) were selected to analyse variations at ten morphometric landmarks and eight microsatellite loci. Truss morphometric analysis showed PCI, PCII, and PCIII expressing 29.1%, 21.36%, and 15.48% of the variance, respectively. Results showed no clear shift in shape between the studied populations of O. niloticus, indicating low morphological variability among them. The number of microsatellite alleles ranged from 3 to 9, while expected heterozygosity (HE) and observed heterozygosity (HO) values ranged from 0.56 (WB) to 0.68 (Guj) and 0.59 (GIFT) to 0.72 (Guj), respectively. The Gujarat and West Bengal populations had the smallest pairwise distance (0.0123) between them, indicating that they were genetically closer. Individuals from GIFT, however, showed the largest distance from the other populations. DNA marker variations revealed the highest genetic variability in the Gujarat population and the lowest variability in the GIFT population. The results of this study will help establish a base population for genetic improvement program and conservation of wild populations.

Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes

The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.

Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress

Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.

Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing

The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467 bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A + T content 53.9%. The control region contains a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cichlid fish of India.

Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita

Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time.

Complete mitochondrial genome sequence of Heteropneustes fossilis obtained by paired end next generation sequencing

In the present study, the complete mitochondrial genome sequence of Heteropneustes fossilis is reported using massive parallel sequence technology. The complete mitogenome of H. fossilis is obtained by de novo assembly of paired end Illumina sequences using CLC Genomics Workbench version 7.0.4, which is 16,489 bp in length. It comprised of 13 protein- coding genes, 22 tRNAs, 2 rRNA genes and a putative control region along with the gene order and organization, being similar to most of vertebrates. The mitogenome in the present study has 99% similarity to the complete mitogneome sequence of H. Fossilis, as reported earlier. Phylogenetic analysis of Siluriformes depicted that Heteropneustids were closer to Clariids. The mitogenome sequence of H. fossilis contributes better understanding of population genetics, phylogenetics and evolution of Indian catfish species.

Complete mitochondrial genome sequence of Labeo fimbriatus (Bloch, 1975)

The complete mitochondrial genome of Labeo fimbriatus, the fringe-lipped carp, was determined for the first time. The genome was 16,614 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on the plus strand was A: 32.35%, G: 15.46%, C: 27.54%, T: 24.647%, and the A + T content 57%. The control region contains a microsatellite, (TA)12, a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cultivable carps of India.

Complete mitochondrial genome sequence of Cirrhinus mrigala (Hamilton, 1822)

The complete mitochondrial genome of Cirrhinus mrigala was determined using the polymerase chain reaction. The mitogenome (16,594 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The overall base composition on the heavy strand was as follows: A: 32.0%, G: 15.5%, C: 28.0%, T: 24.55% and the A+T content: 56.5%. The control region contains a dinucleotide repeat motif, (TA)14, a termination-associated sequence and three conserved sequence blocks. These mitogenome sequence data would play an important role in population genetics and the molecular taxonomy of cultivable cyprinids in India.

HPLC method development and validation of chromafenozide in paddy

A simple and efficient HPLC-UV method was developed and validated for determination of chromafenozide in paddy as there was no previous report on record in this regard. The residue analysis method of chromafenozide, its dissipation and final residue in paddy along with soil were also studied after field treatment. Residues of chromafenozide were extracted and purified from paddy and soil followed by liquid/liquid partitioning, chromatographic column and determination by HPLC equipped with PDA detector. The separation was performed on a Phenomenex Luna RP C(18) (250 × 4.6 mm i.d, 5 μm particle size) column at room temperature. The mean accuracy of analytical method were 94.92 %, 95.38 %, 94.67 % and 96.90 % in straw, grain, soil and field water respectively. The precision (repeatability) was found in the range of 1.30 %-9.25 % for straw/grain, 1.27 %-11.19 % in soil; 1.0 %-9.25 % in field water. The precision (reproducibility) in straw/grain was ranging from 2.2 % to 12.1 %, in soil it from 2.0 % to 11.7 %. The minimum detectable concentration was 0.01 mg kg(-1). The degradation of chromafenozide formulation in rice, soil and water was determined and results showed that chromafenozide as wettable powder formulation degraded with the half-lives of about 4.4 and 2.9 days in paddy plant and soil respectively for double recommended dose. The results indicated that the developed method is easier and faster then could meet the requirements for determination of chromafenozide in paddy.

Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration

Complete nucleotide sequence of mitochondrial genome (mitogenome) of the Catla catla (Ostariophysi: Cypriniformes: Cyprinidae) was determined in the present study. Its length is 16,594 bp and contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs and one non-coding control region. Most of the genes were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pair of genes overlapped: ATPase 8 with 6 and ND4L with ND4 by seven nucleotides each. The main non-coding region was 929 bp, with three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and an unusual simple sequence repeat, (TA)(7). Phylogenetic analyses based on complete mitochondrial genome sequences were in favor of the traditional taxonomy of family Cyprinidae. In conclusion present mitogenome of Catla catla adds more information to our understanding of diversity and evolution of mitogenome in fishes.

Complete mitochondrial genome of Labeo rohita

The complete mitochondrial genome of Labeo rohita, an important cultivable fish, was determined for the first time. The genome is 16,611 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region. The gene organisation and its order were similar to other vertebrates. The overall base composition on heavy strand was as follows A: 32.5%, G: 15.2%, C: 27.7%, T: 24.47%, and the A+T content 56.9%. The control region contains a microsatellite, (TA)(12), a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of Indian major carps.

Degradation dynamics of chromafenozide in different types of soil

Chromafenozide is a lepidopteran insecticide. It is highly effective in controlling various lepidopteran pests. Chromafenozide technical and formulation (80WP) was applied at 2.5 and 5.0 μg g(-1) in 4 types of soils (air dried and sieved) separately in laboratory condition. Half-lives of active ingredient were calculated and found at 15.8, 21.6, 25 and 23.9 days for single dose for chromafenozide technical (99.4 %).

Degradation dynamics of chlorfenapyr residue in chili, cabbage and soil

Chlorfenapyr is a pyrrole group of insecticide, [4-bromo-2-(4-chlorophenyl)-1-ethoxymethyl-5-trifluoromethyl-1H-pyrrole-3-carbonitrile]used as broad spectrum insecticide/acaricide to control whitefly, thrips, caterpillars, mites, leafminers, aphids, etc., chlorfenapyr 10% SC formulation was applied on chili and cabbage twice @ 75 and 100 g a.i./ha along with untreated control. Chlorfenapyr was dissipated in chili, cabbage and soil following the first-order kinetics (logC/C(0) = -kt). The half lives of chlorfenapyr in chili, cabbage and soil were varying from 2.93 to 2.96 days, 2.98 to 3.62 days and 4.06 to 4.36 days respectively, according to the application rate.

The malaria severity score: a method for severity assessment and risk prediction of hospital mortality for falciparum malaria in adults

BACKGROUND

There is paucity of research to quantify the severity and to predict the mortality risk of severe falciparum malaria even if it affects multiple organ systems during the course of the disease. Therefore, the aim of the present study is to develop a severity score for assessment of disease severity and risk prediction in adult patients of severe falciparum malaria on the first day of hospitalisation.

METHODS

A cohort of 2598 patients of falciparum malaria were enrolled in this study of which 2089 patients were included as developmental sample and 509 patients as validation sample. Physiological variables were analyzed for defining and assessment of severity of organ dysfunction (OD). The severity level and corresponding severity score for each organ dysfunction were determined by logistic regression analysis that took both the relative severity among the organ systems and the degree of severity within an organ system into account. Risk of mortality has been calculated for each score.

RESULTS

Physiological variables defined dysfunction in 7 organ systems with 3 levels of severity (I to III). Neurologic and renal dysfunction had 3 levels of severity. Hematologic, cardiovascular, and respiratory dysfunction had 2 levels of severity where as hepatic and metabolic dysfunction had 1 level of severity. 1,3, and 5 points were assigned to level I, II, and III severity of organ dysfunction respectively. Malaria without any abnormal physiological variables had been considered as no organ failure and assigned 0 score. The cumulative scores in a patient is known as malaria severity score (MSS) that ranged from 0 to 21. Risk of mortality had been calculated for each score.

CONCLUSION

This prospective study provides an objective tool for assessing severity levels for organ dysfunction and prediction of risk of mortality in severe falciparum malaria which can be used for treatment and research. It has been observed that no two patients of falciparum malaria are same in severity. The severity varies over time and malaria can affect single or multiple organs with different levels of severity which can be quantified as level I, II, and III. Neurologic and renal dysfunction were the most severe with level III severity, followed by haematologic, cardiovascular, and respiratory dysfunction with level-II severity, as well as hepatic and metabolic dysfunction the least severe with level-I severity. Patient of malaria can be stratified as low, intermediate, and high risk depending on the MSS. With the help of MSS daily risk estimates and recovery time of OD can be determined.

Structural relaxation and frequency-dependent specific heat in a supercooled liquid

We have studied the relation between the structural relaxation and the frequency-dependent thermal response or the specific heat, c(p)(omega), in a supercooled liquid. The mode coupling theory (MCT) results are used to obtain c(p)(omega) corresponding to different wave vectors. Due to the two-step relaxation process present in the MCT, an extra peak, in addition to the low-frequency peak, is predicted in specific heat at high frequency.

Heterogeneities in supercooled liquids: a density-functional study

A metastable state, characterized by a low degree of mass localization, is identified using density-functional theory (DFT). This free energy minimum, located through the proper evaluation of competing terms in the free energy functional, is independent of the specific form of the DFT used. Computer simulation results on particle motion indicate that this heterogeneous state corresponds to the deeply supercooled state.

Metastable state dynamics and power law relaxation in a supercooled liquid

We consider glassy relaxation by using a model for supercooled liquid where the usual set of hydrodynamic variables is extended to include the presence of very slowly decaying defect densities. The long time limit of the density correlation function, the nonergodicity parameter, is studied in the vicinity of the dynamic transition point, and scaling exponents with respect to the distance from the critical point are obtained. In addition to the usual square root cusp, we also see a linear dependence on distance from transition with respect to the metastability parameters. We analyze the power law relaxation of the density correlation function at the initial stage of the dynamics, and obtain an exponent dependent on temperature. Results are compared with data obtained from light scattering experiments.

Elastic behavior in a supercooled liquid: analysis of viscoelasticity using an extended mode coupling model

The transverse current correlations are analyzed using the formalism of extended mode coupling theory. The undercooled liquid can sustain shear waves up to a minimum wave number. With the increase of density this wave number decreases, indicating a growing length scale that is related to the dynamics. The speed of the propagating shear waves goes to zero approaching a critical wave number. The maximum wavelength shows an initial enhancement approaching the mode coupling transition and finally grows at a slower rate as the sharp transition is cut off.

Juvenile T waves (a study of 100 normal subjects)

"Juvenile pattern" of T wave inversion in the precordial leads of electrocardiogram was studied in 100 normal healthy Indians of 0 to 70 years of age in both sexes. Incidence of such pattern was observed in 25 subjects upto 19 years of age. Persons of weight/height ratio less than 30% had higher incidence of juvenile T waves. Maximum incidence (48%) of juvenile T waves was observed in the annual income group of Rs. 15000/-. Exercise ECC showed slight flattening of the inverted T waves in V1 to V3 leads in eight subjects only.

[Prosthetic management of urinary incontinence following prostatectomy with special reference to Kaufman's prosthesis]

Issuing from the pathophysiological fundaments of the incontinence after operative sanation of the outlet of the urinary bladder the principal surgico-prosthetic possibilities for the removal of this complication are describes: 1. artificial systems of the sphincter with arbitrary increase and decrease of the occlusion pressure of the proximal urethra, 2. permanent compression of the bulbar urethra. On the last mentioned principle is based the incontinence prosthesis after Kaufman, which in its rate of success corresponds to the artificial sphincter systems.

[The Small-Carrion penile prosthesis for erectile impotence (author's transl)]

The insertion of two silicone rods into the penile corpora cavernosa (Small-Carrion penile prosthesis) is a considerable procedure for operative management of erectile impotence. Of 61 treated patients, 55 had a satisfactory anatomical and functional result, most of them regained the same sexual activity as prior to onset of impotence. Their partners were satisfied, too. Preoperative evaluation of causes of impotence is particularly important. Type and number of complications in this operative procedure are reported in detail.

Aneurysm of a polar renal artery

A patient with a saccular aneurysm arising from the left superior polar renal artery is presented together with a review of two further reports from the literature. The importance of selective arteriography and the interpretation of the "naked calyx" sign in the diagnosis of supernumerary renal arteries has been emphasized. We feel that this is the only report of an aneurysm of a polar artery successfully treated by excision and end-to-end arterial anastomosis.