Nano-compositional imaging of the lanthanum silicide system at THz wavelengths

Terahertz scattering-type scanning near-field optical microscopy (THz-sSNOM) provides a noninvasive way to probe the low frequency conductivity of materials and to characterize material compositions at the nanoscale. However, the potential capability of atomic compositional analysis with THz nanoscopy remains largely unexplored. Here, we perform THz near-field imaging and spectroscopy on a model rare-earth alloy of lanthanum silicide (La-Si) which is known to exhibit diverse compositional and structural phases. We identify subwavelength spatial variations in conductivity that is manifested as alloy microstructures down to much less than 1 μm in size and is remarkably distinct from the surface topography of the material. Signal contrasts from the near-field scattering responses enable mapping the local silicon/lanthanum content differences. These observations demonstrate that THz-sSNOM offers a new avenue to investigate the compositional heterogeneity of material phases and their related nanoscale electrical as well as optical properties.

Comparative evaluation of native top feeds of western Himalayas for utilization as goat's ration in mash and block form

The current research was undertaken to scrutinize the effect of leaf meal mixture as concentrate mixture in the ration of goats. Leaf meal mixture (LMM) was prepared using equal quantities of ten top-foliages namely Acacia nilotica, Celtis australis, Ficus palmata, Ficus religiosa, Grewia optiva, Melia azadarach, Morus alba, Quercus incana, Salix alba and Zizyphus jujube obtained from district Poonch of Jammu region in western Himalayas. The LMM prepared was substituted for 15% in the concentrate mixture being fed to the goats. The study constituted of two trials. Concentrate mixture offered to the animals was in mash and multi-nutrient block in first and second trial respectively. A total of twelve non-descript, adult male goats were selected for each trial. Goats of 0-14 months age (27.71 ± 2.96 kg live body weight) of for first trial while goats of 12-16 months age (27.02 ± 2.93 kg live weight) for second trial were divided into control and treatment groups as per randomized block design and fed ad-lib wheat straw and concentrate mixture @ (20 g/kgW0.75). No significant variation was observed (p > 0.05) in body weight, feed and DM intake among all groups in both trials. Comparable intake as well as digestibility of various nutrients like DM, OM, CP, EE, CF, NFE, NDF, ADF and TDN were found between the two groups during individual trials. There was a positive nitrogen, calcium and phosphorus balance among all experimental animals in both the trials. Serum enzymes ALT, AST and haemato-biochemical parameters like total protein, albumin, globulin, albumin: globulin and blood urea nitrogen (BUN) showed no significant differences during both trials in all groups, being within normal physiological levels. However, haemoglobin concentration was significantly higher (P < 0.05) in treatment group with respect to the control group in first trial. On the basis of current results, it can be established that leaf meal mixture can successfully be used to replace concentrate mixture up to 15% in the ration of goats without expecting any adverse impacts on their growth and overall health.

Insight into molecular interaction between shrimp and white spot syndrome virus through MjsvCL-VP28 complex: an in-silico approach

White Spot disease is a devastating disease of shrimps caused by White Spot Syndrome Virus in multifarious shrimp species. At present there is no absolute medication to suppress the disease hence, there is an urgent need for development of drug against the virus. Molecular interaction between viral envelope protein VP28 and shrimp receptor protein especially chitins play a pivotal role in ingression of WSSV. In the present study, we have tried to shed light on structural aspects of lectin protein in Marsupenaeus japonicus (MjsvCL). A structural insight to the CTLD-domain of MjsvCL has facilitated the understanding of the binding mechanism between the two proteins that is responsible for entry of WSSV into shrimps. Further, incorporation of molecular dynamics simulation and MMPBSA studies revealed the affinity of binding and certain hotspot residues, which are critical for association of both the proteins. For the first time we have proposed that these amino acids are quintessential for formation of VP28-MjsvCL complex and play crucial role in entry of WSSV into shrimps. Targeting the interaction between VP28 and CTLD of MjsvCL may possibly serve as a potential drug target. The current study provides information for better understanding the interaction between VP28 and MjsvCL that could be a plausible site for future inhibitors against WSSV in shrimps.Communicated by Ramaswamy H. Sarma.

Species distribution modeling and assessment of environmental drivers responsible for distribution and preferred niche of critically endangered and endemic ornamental freshwater fish species of the genus Sahyadria

India has different bioclimatic zones and supports diverse aquatic habitats rich in biodiversity. For effective conservation of the endangered species in its habitat, it is essential to know the distribution of fish species in the environmental range, and for this, species distribution models are the efficient and innovative tools. The present study used the MaxEnt modeling technique for developing probability distribution models highlighting the distribution of fish species by analyzing the known occurrence records of Denison barb under genus Sahyadria (Sahyadria denisonii Day 1865 and Sahyadria chalakkudiensis (Menon et al., Rec Zool Surv India 97:61-63, 1999)) in relation to environmental variables typically incorporating seasonal and temporal variability. AUC of the models for Sahyadria species depicted good fitness. Both species were found sensitive to "solar radiation," "temperature seasonality," and "temperature annual range" and assessed as significant predictors. The sensitivity and distribution of both species to these environmental variables were found correlated with their breading and spawning seasons. "Precipitation" was determined as one of the significant climatic envelopes influencing the distribution of the species associated with river flow. The models showed the distribution of S. denisonii in the higher precipitation areas compared to S. chalakkudiensis. The probability distribution model with respect to the distribution of both species indicates a lineage barrier at Palghat Gap supporting the earlier studies. At the latitudinal scale, prediction of the suitable ecological habitat provides a detailed insight into the distribution of all genetic lineages of the genus Sahyadria. Evidently, the findings of this study can assist in determining ecological niches for endangered species of other areas and may aid in field surveys as well as developing conservation plans.

Spent marigold flower meal as an alternate feed for goats

This research trial is aimed to study the nutritional qualities and significance of feeding spent marigold flower meal (SMFM) in goats. SMFM and diet containing iso-nitrogenous concentrate mixture with different levels of spent marigold flower meal (0-30%) were studied for in vitro degradation. Depending upon the in vitro results, concentrate mixture containing 15% level of SMFM was selected for in vivo trial. In vivo studies were conducted for a period of 60 days, and 12 local, non-descript, adult male goats (10-14 months age; 31.09 ± 2.91 kg body weight) were randomly assigned to two groups and were fed on ad libitum wheat straw with either conventional (control) or SMFM containing concentrate mixture (treatment). Results of the study showed that there was no variation in body weight of the goats between periods and between groups. DM and OM intake along with their digestibility were similar among the two groups. The digestibility of all other nutrients was comparable between the two groups. Nitrogen, calcium and phosphorus balance were positive in both the groups without any significant disparity. Moreover, experimental goats did not differ in biochemical parameters, without any significant difference between periods and dietary treatments except AST level which was significantly higher (P > 0.05) in treatment group. So, this study successfully demonstrates that SMFM could be incorporated in the concentrate mixture, up to 15% without any discernable difference in the performance of goats.

Magnetic ground states of Ce3TiSb5, Pr3TiSb5and Nd3TiSb5determined by neutron powder diffraction and magnetic measurements

TheR₃TiSb₅ternary compounds, withRa light rare earth (La to Sm) have been reported to crystallize with the anti-Hf₅CuSn₃-type hexagonal structure (Pearson's symbolhP18; space-groupP6₃/mcm, N. 193). An early article that reported possible superconductivity in some of these intermetallic phases (namely those withR= La, Ce, and Nd) caught our attention. In this work, we have now refined the crystal structure of theR₃TiSb₅compounds withR= Ce, Pr and Nd by Rietveld methods using high-resolution neutron powder diffraction data. The magnetic ground states of these intermetallics have been investigated by low-temperature magnetization and high-intensity neutron diffraction. We find two different magnetic transitions corresponding to two related magnetic structures atT_N1= 4.8 K (k₁= [0, 1/2, 1/8]) andT_N2= 3.4 K (k₂= [0, 0, 1/8]), respectively for Ce₃TiSb₅. However, the magnetic ordering appears to occur following a peculiar hysteresis: thek₂-type magnetic structure develops only after thek₁-type phase fraction has first slowly ordered with time and the size of the ordered Ce³⁺magnetic moment has become large enough to induce the second magnetic transition. AtT= 1.5 K the maximum amplitude of the Ce moment in the coexisting phases amounts toμ_Ce= 2.15 μ_B. For Nd₃TiSb₅an antiferromagnetic ordering belowT_N= 5.2 K into a relatively simpler commensurate magnetic structure with a magnetic moment ofμ_Nd= 2.14(3)μ_Band magnetic propagation vector ofk= [0, 0, 0], was determined. No evidence of superconductivity has been found in Nd₃TiSb₅. Finally, Pr₃TiSb₅does not show any ordering down to 1.5 K in neutron diffraction while an antiferromagnetic ground state is detected in magnetization measurements. There is no sign of magnetic contribution from Ti atoms found in any of the studied compounds.

Isolation and characterization of hypoxia inducible heme oxygenase 1 (HMOX1) gene in Labeo rohita

The HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying ~540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.

Sensitivity Enhancement of a Concave Shaped Optical Fiber Refractive Index Sensor Covered with Multiple Au Nanowires

In the present paper, a new kind of concave shaped refractive index sensor (CSRIS) exploiting localized surface plasmon resonance (LSPR) is proposed and numerically optimized. The LSPR effect between polaritons and the core guided mode of designed CSRIS is used to enhance the sensing performance. The sensor is characterized for two types of sensing structures coated with gold (Au) film and Au nanowires (AuNWs), respectively. The influence of structural parameters such as the distance (D) of the concave shaped channel (CSC) from the core, the diameter of the nanowire (d_n) and the size (s) of the CSC are investigated here. In comparison to Au film, the AuNWs are shown to significantly enhance the sensitivity and the performance of the designed sensor. An enhanced sensitivity of 4471 nm/RIU (refractive index unit) is obtained with AuNWs, for a wide range of analytes refractive index (n_a) varying between 1.33 to 1.38. However, for conventional Au film; the sensitivity of 808.57 nm/RIU is obtained for the same range of analytes.

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements

Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (-4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.

FisOmics: A portal of fish genomic resources

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics/, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements.

Non-hysteretic first-order phase transition with large latent heat and giant low-field magnetocaloric effect

First-order magnetic transitions (FOMTs) with a large discontinuity in magnetization are highly sought in the development of advanced functional magnetic materials. Isosymmetric magnetoelastic FOMTs that do not perturb crystal symmetry are especially rare, and only a handful of material families, almost exclusively transition metal-based, are known to exhibit them. Yet, here we report a surprising isosymmetric FOMT in a rare-earth intermetallic, Eu₂In. What makes this transition in Eu₂In even more remarkable is that it is associated with a large latent heat and an exceptionally high magnetocaloric effect in low magnetic fields, but with tiny lattice discontinuities and negligible hysteresis. An active role of the Eu-5d and In-4p states and a rather unique electronic structure borne by In to Eu charge transfer, altogether result in an unusual exchange mechanism that both sets the transition in motion and unveils an approach toward developing specific magnetic functionalities ad libitum.

Crystal, magnetic, calorimetric and electronic structure investigation of GdScGe1-x Sb x compounds

Experimental investigations of crystal structure, magnetism and heat capacity of compounds in the pseudoternary GdScGe-GdScSb system combined with density functional theory projections have been employed to clarify the interplay between the crystal structure and magnetism in this series of RTX materials (R  =  rare-earth, [Formula: see text]  =  transition metal and X  =  p-block element). We demonstrate that the CeScSi-type structure adopted by GdScGe and CeFeSi-type structure adopted by GdScSb coexist over a limited range of compositions [Formula: see text]. Antimony for Ge substitutions in GdScGe result in an anisotropic expansion of the unit cell of the parent that is most pronounced along the c axis. We believe that such expansion acts as the driving force for the instability of the double layer CeScSi-type structure of the parent germanide. Extensive, yet limited Sb substitutions [Formula: see text] lead to a strong reduction of the Curie temperature compared to the GdScGe parent, but without affecting the saturation magnetization. With a further increase in Sb content, the first compositions showing the presence of the CeFeSi-type structure of the antimonide, [Formula: see text], coincide with the appearance of an antiferromagnetic phase. The application of a finite magnetic field reveals a jump in magnetization toward a fully saturated ferromagnetic state. This antiferro-ferromagnetic transformation is not associated with a sizeable latent heat, as confirmed by heat capacity measurements. The electronic structure calculations for [Formula: see text] indicate that the key factor in the conversion from the ferromagnetic CeScSi-type to the antiferromagnetic CeFeSi-type structure is the disappearance of the induced magnetic moments on Sc. For the parent antimonide, heat capacity measurements indicate an additional transition below the main antiferromagnetic transition.

Effect of condensed tannins from Ficus infectoria and Psidium guajava leaf meal mixture on nutrient metabolism, methane emission and performance of lambs

Objective

The study examined the effect of condensed tannins (CT) containing Ficus infectoria and Psidium guajava leaf meal mixture (LMM) supplementation on nutrient metabolism, methane emission and performance of lambs.

Methods

Twenty four lambs of ~6 months age (average body weight 10.1±0.60 kg) were randomly divided into 4 dietary treatments (CT-0, CT-1, CT-1.5, and CT-2 containing 0, 1.0, 1.5, and 2.0 percent CT through LMM, respectively) consisting of 6 lambs each in a completely randomized design. All the lambs were offered a basal diet of wheat straw ad libitum, oat hay (100 g/d) along with required amount of concentrate mixture to meet their nutrient requirements for a period of 6 months. After 3 months of experimental feeding, a metabolism trial of 6 days duration was conducted on all 24 lambs to determine nutrient digestibility and nitrogen balance. Urinary excretion of purine derivatives and microbial protein synthesis were determined using high performance liquid chromatography. Respiration chamber study was started at the mid of 5th month of experimental feeding trial. Whole energy balance trials were conducted on individual lamb one after the other, in an open circuit respiration calorimeter.

Results

Intake of dry matter and organic matter (g/d) was significantly (p<0.05) higher in CT-1.5 than control. Digestibility of various nutrients did not differ irrespective of treatments. Nitrogen retention and microbial nitrogen synthesis (g/d) was significantly (p<0.01) higher in CT-1.5 and CT-2 groups relative to CT-0. Total body weight gain (kg) and average daily gain (g) were significantly (linear, p<0.01) higher in CT-1.5 followed by CT-1 and CT-0, respectively. Feed conversion ratio (FCR) by lambs was significantly (linear, p<0.01) better in CT-1.5 followed by CT-2 and CT-0, respectively. Total wool yield (g; g/d) was linearly (p<0.05) higher for CT-1.5 than CT-0. Methane emission was linearly decreased (p<0.05) in CT groups and reduction was highest (p<0.01) in CT-2 followed by CT-1.5 and CT-1. Methane energy (kcal/d) was linearly decreased (p<0.05) in CT groups.

Conclusion

The CT supplementation at 1% to 2% of the diet through Ficus infectoria and Psidium guajava LMM significantly improved nitrogen metabolism, growth performance, wool yield, FCR and reduced methane emission by lambs.

HRGFish: A database of hypoxia responsive genes in fishes

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Tetragonal to triclinic structural transition in the prototypical CeScSi induced by a two-step magnetic ordering: a temperature-dependent neutron diffraction study of CeScSi, CeScGe and LaScSi

An investigation on the ground state magnetism of CeScSi, CeScGe (tetragonal CeScSi-type, tI12, space group I4/mmm) by temperature-dependent powder neutron diffraction has been carried out, as debated and controversial data regarding the low temperature magnetic behaviours of these two compounds were reported. Our studies reveal that, while cooling, long-range magnetic ordering in CeScSi and CeScGe takes place by a two-step process. A first transition leads to a magnetic structure with the Ce moments aligned ferromagnetically onto two neighbouring tetragonal basal a-b planes of the CeScSi-type structure; the double layers are then antiferromagnetically coupled to each other along the c-axis. The transition temperature associated with the first ordering is T _N ~ 26 K and T _N ~ 48 K for the silicide and the germanide, respectively. Here the spin directions are rigorously confined to the basal plane, with values of the Ce magnetic moments of μ _Ce  =  0.8-1.0 μ _B. A second magnetic transition, which takes place at slightly lower temperatures, results in a canting of the ordered magnetic moments out of the basal plane which is accompanied by an increase of the magnetic moment value of Ce to μ _Ce  =  1.4-1.5 μ _B. Interestingly, the second magnetic transition leads to a structural distortion in both compounds from the higher-symmetry tetragonal space group I4/mmm to the lower-symmetry and triclinic I-1 (non-standard triclinic). Magnetic symmetry analysis shows that the canted structure would not be allowed in the I4/mmm space group; this result further confirms the structural transition. The transition temperatures T _S from I4/mmm to I-1 are about 22 K in CeScSi and 36 K in CeScGe, i.e. well below the temperature of the first onset of antiferromagnetic order observed in this work (or below the ordering temperature, previously reported as either T _C or T _N). This result, along with the synchronism of the magnetic and structural transitions, suggests a magnetostructural origin of this structural distortion. We have also carried out powder neutron diffraction for LaScSi as a non-magnetically-ordering reference compound and compared the results with those of CeScSi and CeScGe compounds.

Modelling of microalgal growth and lipid production in Dunaliella tertiolecta using nitrogen-phosphorus-potassium fertilizer medium in sintered disk chromatographic glass bubble column

A comprehensive mathematical model involving NPK-10:26:26 fertilizer, NaCl, NaHCO3, light and temperature operating variables for Dunaliella tertiolecta cultivation is formulated to predict microalgae-biomass and lipid productivity. Proposed model includes Monod/Andrews kinetics for the absorption of essential nutrients into algae-biomass and Droop model involving internal nutrient cell quota for microalgae growth, assuming algae-biomass is composed of sugar, functional-pool and neutral-lipid. Biokinetic model parameters are determined by minimizing the residual-sum-of-square-errors between experimental and computed microalgae-biomass and lipid productivity using genetic algorithm. Developed model is validated with the experiments of Dunaliella tertiolecta cultivation using air-agitated sintered-disk chromatographic glass-bubble column and the effects of operating variables on microalgae-biomass and lipid productivity is investigated. Finally, parametric sensitivity analysis is carried out to know the sensitivity of model parameters on the obtained results in the input parameter space. Proposed model may be helpful in scale-up studies and implementation of model-based control strategy in large-scale algal cultivation.

Effect of tanniferous leaf meal based multi-nutrient blocks on feed intake, hematological profile, immune response, and body weight changes in Haemonchus contortus infected goats

Aim:

The aim was to assess the effect of multi nutrient block (MNB) supplementation with and without tanniferous leaf meal mixture on feed intake, hematological profile, immune response, and body weight changes of goats that were experimentally infected with Haemonchus contortus.

Materials and Methods:

Total 12 adult male goats of similar age and body weight (26.49±0.87) were allocated in 3 groups in completely randomized design. MNB supplemented in first two groups i.e. in T₁ (no infection) and T₂ (H. contortus infection @ 1500 L₃/goat) group, while, MNB-condensed tannin (CT) supplemented in T₃ (H. contortus infection @ 1500 L₃/goat + CT source). All goats were fed concentrate mixture @ 100 g/day/goat, ad lib wheat straw and MNB or MNB-CT to meet their requirement for maintenance. Body weights were recorded and blood and fecal samples were collected at 0 day and thereafter at 15 days intervals for a period of 75 days for the assessment of body weight changes, hematological profile and H. contortus loads. Both humoral and cell-mediated immune (CMI) response were assessed at the end of feeding trial.

Results:

Mean hemoglobin and packed cell volume (PCV) levels were found to be highest (p<0.001, p<0.05) in T₁ group followed by T₃ group and lowest values were observed in T₂ group. However, The PCV values between T₁ and T₃ groups were found to be statistically non-significant (p<0.05). The humoral and CMI response were significantly (p<0.036) higher in T₃ group as compared to T₂ group. MNB-CT supplementation significantly (p<0.001) reduced fecal egg counts in T₃ group as compared to MNB supplemented T₂ group.

Conclusion:

Supplementation of MNB-CT could be used as an alternative sustainable method to control H. contortus and maintained health status and performance of goats in face of parasitic challenge.

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes.

Database URL:http://mail.nbfgr.res.in/Fish_Karyome

Prevalence of lymphatic filariasis in a tea garden worker population of Dibrugarh (Assam), India after six rounds of mass drug administration

BACKGROUND & OBJECTIVES

Lymphatic filariasis (LF) is endemic in the state of Assam and mass drug administration (MDA) programme for LF elimination is being implemented in the state since 2004. A study on prevalence of microfilaria (mf), disease endemicity and vector infection was carried out in a tea garden population of Dibrugarh, Assam (India) to assess the effect of ongoing MDA programme on elimination of LF.

METHODS

Finger prick thick blood smears (20 mm3) were made from individuals aged ≥2 yr old during night blood survey in between 2000-0000 hrs during the period of November 2012 to February 2013. Blood smears were dehaemoglobinised, stained with Giemsa and examined under microscope for presence of mf. Indoor resting mosquitoes were collected during 0600-1000 hrs and female Culex quinquefasciatus were dissected and examined under microscope for larval forms of the parasite.

RESULTS

A total of 634 blood smears were collected and screened for mf and 47 (7.41%) individuals were found microfilaraemic, with predominance of males (74.5%). Highest mf rate (20.0%) was seen in the males of 30-39 yr age group while in females, age group of 10-19 yr recorded maximum mf rate (5.48%). Entomological collection and dissection of Cx. quinquefasciatus revealed presence of larval stages of the parasite and infection and infectivity rates recorded were 13.20 and 3.70%, respectively. Chronic clinical manifestations in the form of elephantiasis and hydrocele were recorded in 33 (5.73%) subjects of the 575 examined.

INTERPRETATION & CONCLUSION

Mass drug administration data showed six rounds of MDA with drug distribution coverage in between 63.42 and 95.93% in the study population. Out of 634 individuals examined 47 were found microfilaraemic giving an overall infection rate of 7.41%. Mosquito vector infection and infectivity rates were 13.20 and 3.70%, respectively. Presence of high mf rate, vector infectivity rate and clinical cases in the study population after six rounds of MDA warrants concerted efforts to be made for effective implementation and monitoring of MDA for success of LF elimination programme.

Microfilarial periodicity of Wuchereria bancrofti in Assam, Northeast India

BACKGROUND & OBJECTIVES

Wuchereria bancrofti has shown nocturnal periodicity in India and other endemic countries of the world except pacific regions where non-periodic or diurnal sub-periodic forms have been reported. Presence of sub-periodic form of W. bancrofti in Andaman and Nicobar Islands, India and a case report of sub- periodic form of W. bancrofti from Mysore, India provide basis for exploring the periodicity pattern of microfilaria of W. bancrofti prevalent in Assam, Northeastern region of India. State of Assam has unique geographical location as its Northeastern region shares international boundaries with Nepal, China, Bhutan, Myanmar and Bangladesh. Evolutionary association of W. bancrofti found in Assam is not known and possibility of its link with W. bancrofti form, prevalent in neighbouring countries may not be ruled out. Hence, this study was undertaken to know the microfilarial periodicity of W. bancrofti in Assam.

METHODS

Ten microfilaria positive adult male individuals having moderate to high microfilaraemia were selected. Informed written consent from each participant was obtained. The presence of microfilaria was observed at two hourly intervals over a period of 24 h using 50 μl of finger prick peripheral blood samples. Peripheral blood smears were processed, stained and examined under microscope and microfilaria counts were recorded.

RESULTS

Data collected were calculated and analyzed using modified statistical method, and the periodicity curve was prepared. Typical nocturnal periodicity was observed at a peak time of 0003 hrs with a periodicity index of 136.2.

INTERPRETATION & CONCLUSION

Analysis of the data revealed nocturnal periodicity of the W. bancrofti prevalent in the Assam with peak periodicity about one hour ahead of the other states in India. Findings will be helpful in evaluation and monitoring of ongoing MDA programme for elimination of LF in Assam.

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.

In silico analysis of SSRs in mitochondrial genomes of fishes

The availability of fish mitochondrial (mt) genomes provides an opportunity to explore the simple sequence repeats. In the present study, mt genomes of 85 fish species reported from Indian subcontinent were downloaded from NCBI and computationally analysed for finding SSRs types, frequency of occurrence, mutation and evolutionary adaptation across species. A total of 92 microsatellites in different nucleotide combinations were detected in 59 species. 26 interspersed SSRs, mostly poly (AT)n were found in the D-loop regions in the species of Cyprinidae. Fifty-six SSRs of 12 bp fixed length were observed in eight genes only. Further, identical repeat motifs were found on the same location in ATP6 and ND4 genes, which were biased towards particular habitat. The comparison of ATP6 and ND4 gene sets to other homologous sequences showed point mutations. This study explores the SSRs discovery and their utility as marker for species and population identification.

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent

Background

Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.

Description

FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview.

Conclusions

FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

Biodiversity of freshwater fish of a protected river in India: comparison with unprotected habitat

In India, freshwater environments are experiencing serious threats to biodiversity, and there is an urgent priority for the search of alternative techniques to promote fish biodiversity conservation and management. With this aim, the present study was undertaken to assess the fish biodiversity within and outside a river protected area, and to evaluate whether the protected river area provides some benefits to riverine fish biodiversity. To assess this, the pattern of freshwater fish diversity was studied in river Gerua, along with some physicochemical conditions, from April 2000 to March 2004. For this, a comparison was made between a 15km stretch of a protected area (Katerniaghat Wildlife Sanctuary), and an unprotected one 85km downstream. In each site some physicochemical conditions were obtained, and fish were caught by normal gears and the diversity per site described. Our results showed that water temperature resulted warmest during the pre-monsoon season (25 degreeC) and low during the winter (14-15 degreeC); turbidity considerably varied by season. In the protected area, a total of 87 species belonging to eight orders, 22 families and 52 genera were collected; while a maximum of 59 species belonging to six orders, 20 families and 42 genera were recorded from the unprotected areas. Cyprinids were found to be the most dominant genera and Salmostoma bacaila was the most numerous species in the sanctuary area. Other numerous species were Eutropiichthys vacha, Notopterus notopterus, Clupisoma garua and Bagarius bagarius. The results indicated more species, greater abundances, larger individuals, and higher number of endangered fishes within the sanctuary area when compared to the unprotected area. Analysis on the mean abundance of endangered and vulnerable species for the evaluated areas in the sanctuary versus unprotected ones indicated significant differences in fish abundance (p<0.05). These results showed that this riverine protected area could be important for conservation and management of fish diversity in the region, especially for resident and threatened species.