An inexpensive and rapid diagnostic method for detection of SARS-CoV-2 RNA by loop-mediated isothermal amplification (LAMP)

SARS-CoV-2 is a public pandemic health concern globally. Nasopharyngeal and oropharyngeal swab samples are used for Covid-19 viral detection. Sample collection procedure was tedious and uncomfortable and unsuitable for biochemical and CBC analysis in swab samples. Biochemistry and CBC tests are key determinant in management of Covid-19 patients. We developed a LAMP test to detect viral RNA in blood samples. LAMP is required four specific primers targeting the internal transcribed S-region and loop primers for viral RNA amplification. RNA was extracted from blood samples by TRIzol method. LAMP reaction was performed at 60 °C for 1 hour and amplicons were visualized in HNB dye. No cross-reactivity was seen with HBV, HCV, and HIV infected sample. Out of 40 blood samples, 33 samples were positive for LAMP and Q-PCR analysis, one sample was positive for LAMP and negative for Q-PCR, two samples were negative for LAMP but positive for Q-PCR, and four blood samples were negative for LAMP and Q-PCR. LAMP method has an accuracy of 92.50%, with sensitivity and specificity of 94.28% and 80%, respectively. Thus, LAMP diagnostic test has proved reliable, fast, inexpensive and can be useful for detection where the limited resources available.•LAMP method is a potential tool for detection of SARS-CoV-2.•Blood samples are the key determinant for routine diagnostics as well as molecular diagnostics.•LAMP assay is an appropriate diagnostics method which offers greater simplicity, low cost, sensitivity, and specificity than other methods in molecular diagnostics.

Prevalence of Escherichia coli O157 and Salmonella spp. in solid bovine manure in California using real-time quantitative PCR

The occurrence of Escherichia coli O157 and Salmonella spp. in solid bovine manure was investigated through a multi-county survey in California. Solid bovine manure samples (n = 91) were collected from 13 dairy farms located in multiple counties in California between June 2016 and August 2017. To quantify pathogens, DNA was extracted from bacteria in manure samples. Afterwards, the prevalence and levels of E. coli O157 and Salmonella spp. in solid bovine manure were determined by real-time quantitative PCR (qPCR). The prevalence of E. coli O157 and Salmonella spp. in solid bovine manure was 15·4 and 6·6% respectively. Escherichia coli O157 and Salmonella spp. levels in positive samples ranged from 3·1 to 5·3 log CFU per g and from positive (the population was <3 log CFU per g) to 5·2 log CFU per g respectively. Surface samples of manure piles had higher prevalence and levels of E. coli O157 and Salmonella spp. than subsurface samples, while no seasonal effects on pathogen occurrence were observed. Our results indicated that solid bovine manure is a source of E. coli O157 and Salmonella spp. and the application of untreated manure as biological soil amendments may pose potential risks to public health. SIGNIFICANCE AND IMPACT OF THE STUDY: Our findings suggested that the presence of Escherichia coli O157 and Salmonella spp. in solid bovine manure may pose potential risks if untreated manure is applied as biological soil amendments. Considering the large-scale sampling used in this study, the observations provide a holistic assessment in terms of pathogen prevalence in solid bovine manure.

Biofloc improves water, effluent quality and growth parameters of Penaeus vannamei in an intensive culture system

Biofloc technology was evaluated with a view to analyse utilization of nitrogenous waste from the effluent and to improve water quality and growth parameters of Penaeus vannamei in intensive culture system. The experiment was carried out in two different treatment outdoor earthen ponds of 0.12 ha, one supplemented with carbon source (molasses, wheat and sugar) for biofloc formation and other was feed based control pond with a stocking density of 60 animals m^-2 in duplicate for 120 days. Water, sediment and P. vannamei were sampled at regular intervals from the both set of ponds for evaluating physico-chemical parameters, nitrogen content and growth parameters, respectively. A significant reduction in the concentration of total ammonia nitrogen (TAN) and nitrite (NO₂-N) were found in the biofloc pond than that of control pond. A significant low level of nitrogen was recorded in the effluents of biofloc pond in comparison to the control. In biofloc system, a significantly elevated heterotrophic bacterial count along with reduction in total Vibrio count was noticed. A significant improvement in the feed conversion efficiency (FCR) and growth parameters of P. vannamei was noticed in the biofloc pond. Growth of P. vannamei in the biofloc pond showed positive allometric pattern with an increased survival. The microbial biomass grown in biofloc consumes toxic inorganic nitrogen and converts it into useful protein, making it available for the cultured shrimp. This improved FCR and reduced the discharge of nitrogenous waste into adjacent environment, making intensive shrimp farming an eco-friendly enterprise.

Impact of Superior Oblique Transposition on Primary Position Deviation, a Pattern and Intorsion in Third Nerve Palsy

PURPOSE

To evaluate the role of superior oblique transposition on primary position alignment, A pattern, and intorsion in third nerve palsy.

METHODS

Ten patients with isolated, unilateral third nerve palsy were included in this prospective study. The patients were treated by conventional surgery on horizontal recti together with superior oblique transposition by Scott's procedure in the paretic eye.

RESULTS

Pre-operative primary horizontal deviation was 60-80 PD (mean 70.00±7.45 PD). Pre-operative primary hypotropia was 15-22 PD (mean 18.80±2.48 PD). Mean A-pattern was 17.80±2.65 PD. All patients included in the study had some degree of objective torsion as measured by Guyton's method. One patient had grade I objective intorsion, 2 had grade II, 6 had grade III, and 1 had grade IV objective intorsion. Primary position horizontal alignment (up to ±8 PD) was achieved in 9 patients. Primary position vertical alignment (up to ±8 PD) was achieved in all 10 patients. Only 2 of 10 patients had A-pattern of 10 PD, in the remaining 8 patients it was eliminated (P<0.05). Postoperatively, 5 patients had no objective intorsion and 5 had grade I intorsion, and none of the patients had hypertropia or paradoxical eye movements.

CONCLUSION

Superior oblique transposition by Scott's procedure along with conventional surgery on horizontal recti in third nerve palsy results in better horizontal and vertical alignment, and improves A-pattern and intorsion, thus leading to better binocular interaction.

Solving third-order boundary value problems with quartic splines

In this article, we present a novel second order numerical method for solving third order boundary value problems using the quartic polynomial splines. We establish the convergence of the method. We present numerical experiments to demonstrate the efficiency of the method and validity of our second order method, which shows that present method gives better results.

Sources, distribution and risk assessment of polycyclic aromatic hydrocarbons in the mangrove sediments of Thane Creek, Maharashtra, India

The sources, distribution and risk assessment of polycyclic aromatic hydrocarbons (PAHs) were investigated in the mangrove sediments of Trombay and Vashi, along the Thane Creek, Maharashtra, India, for a period of 6 months. The results showed that the concentration of Ʃ15 PAHs ranged from 902.58 to 1643.60 and from 930.69 to 1158.30 ng g(-1) in Trombay and Vashi, respectively. Trombay showed significantly higher PAH concentration (p < 0.05) than Vashi. The four carcinogenic PAHs, (benzo(b)fluorathene, benzo(k)fluorathene, Indeno(1,2,3-cd)pyrene and dibenz(a,h)anthracene) accounted for maximum concentration of the total PAHs. Specific PAH diagnostic indices and the molecular index indicated the presence of both pyrolytic and petrogenic sources with the predominance of pyrolytic origin. A positive correlation (r = 0.736, p < 0.05) existed between the benzo(k)fluorathene level and total PAHs, suggesting the use of this compound as a potential molecular marker for PAH pollution in mangrove sediment. Assessments of potential environmental risks associated with PAHs in this study revealed that the sediment was moderately polluted with high molecular weight PAHs. The study reports the baseline data that can be used for regular monitoring of contamination level considering the heavy industrialization and urbanization along the creek and its coastal region.

Effect of azadirachtin on haematological and biochemical parameters of Argulus-infested goldfish Carassius auratus (Linn. 1758)

Argulosis hampers aquaculture production and alters the host physiology and growth. Azadirachtin is recognized as a potential antiparasitic agent against Argulus sp. The present study aimed to investigate the effect of different concentration of azadirachtin solution on haematological and serum biochemical parameters of Argulus-infested goldfish Carassius auratus. Ninety Argulus-infested goldfish were randomly divided into six equal groups. Fish of group 1-5 were treated with azadirachtin solution through bath of 1, 5, 10, 15 and 20 mg L(-1) as T1, T2, T3, T4 and T5, respectively, and group 6 was exposed to 2% DMSO solution without azadirachtin and considered as negative control T0(-). Along with six treatment groups, a positive control T0(+) of healthy goldfish free from Argulus infestation was also maintained. Parasitic mortality was evaluated after 3 days of consecutive bath treatment. After 7 days of post-treatment, the blood and serum were drawn from each of the treatment groups and haematological and serum biochemical parameters were evaluated. Total leucocyte count (TLC), mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), blood glucose, total protein (TP), globulin, serum glutamate oxaloacetate transaminase (SGOT) and serum glutamate pyruvate transaminase (SGPT) were significantly (p < 0.05) high in negative control group when compared with positive control group. It could be concluded that Argulus infestation altered marked haematological and serum biochemical parameters. However, in treated groups complete elimination of Argulus was found in T4 and T5 groups. Also significant (p < 0.05) reduction in haematological and serum biochemical parameters of all the treatment groups were recorded in comparison with negative control group. In addition, T4 and T5 groups showed significantly (p < 0.05) high superoxide dismutase (SOD), catalase, total erythrocyte count (TEC) and haemoglobin (Hb). However, higher mean corpuscular haemoglobin concentration (MCHC), blood glucose and lactate dehydrogenase (LDH) levels in T5 group revealed that higher concentration of azadirachtin have notable effects on activity of vital tissues function and physiology of the host. Argulus spp. from infested goldfish could be eliminated using bath treatment with solution of azadirachtin having concentration of 15 mg L(-1) and that also shifted haematological and serum biochemical parameters towards homeostasis.

Effect of orally administered azadirachtin on non-specific immune parameters of goldfish Carassius auratus (Linn. 1758) and resistance against Aeromonas hydrophila

Modulation of the immune responses using active bio-ingredients as a possible prophylaxis measure has been novel prospect for aquaculture. The present study evaluated the effects of azadirachtin EC 25% on non-specific immune responses in goldfish Carassius auratus and resistance against pathogenic bacteria Aeromonas hydrophila. The experimental trial for effects of azadirachtin on immuno-haematoloical parameters in goldfish was conducted by feeding the various levels of azadirachtin as control T(0) (without azadirachtin), T(1) (0.1%), T(2) (0.2%), T(3) (0.4%), T(4) (0.8%) and T(5) (1.6%) for a period of 28 days. Fishes were challenged with A. hydrophila 28 days post feeding and relative percentage survival (%) was recorded over 14 days post infection. Immuno-haematoloical (total erythrocyte count, total leukocyte count, haemoglobin, packed cell volume, NBT activity, phagocytic activity, serum lysozyme activity, myeloperoxidase activity, total immunoglobulin) and serum biochemical parameters (serum glutamate oxaloacetate transaminase (SGOT), serum glutamate pyruvate transaminase (SGPT) and blood glucose) of fishes were examined at 14 and 28 days of feedings. Fish fed with azadirachtin, showed significantly (p < 0.05) enhanced TEC, TLC, Total Ig, total protein, NBT activity, serum lysozyme activity and myeloperoxidase level in different treatment groups in comparison with control group. Similarly, SGOT, SGPT and blood glucose level were found to be significantly (p < 0.05) high but PCV and Hb did not differ significantly (p > 0.05) in the treatment groups compared to control groups. Azadirachtin at the concentration of 4 g kg(-1) showed significantly (p < 0.05) higher relative percentage survival (42.60%) when compared with the control against A. hydrophila infection. This study indicated that azadirachtin EC 25% (4 g kg(-1)) showed higher NBT activity, serum lysozyme, protein profiles, leukocyte counts and resistance against A. hydrophila infection and thus, can be used as a potential immunostimulant in aquaculture.

Ocular tilt reaction, internuclear ophthalmoplegia, and torsional nystagmus following mitral commissurotomy

Ocular tilt reaction, a type of skew deviation, and unilateral internuclear ophthalmoplegia with torsional nystagmus resulting from an ischemic event may result from unilateral disruption of otolithic pathways in the medial longitudinal fasciculus. A subset of skew deviations is known to simulate superior oblique palsy; however, none have been reported with a coexisting internuclear ophthalmoplegia. The present report documents the rare occurrence of an ocular tilt reaction simulating a left superior oblique palsy from involvement of left medial longitudinal fasciculus at the level of interstitial nucleus of Cajal.

Antiparasitic efficacy of piperine against Argulus spp. on Carassius auratus (Linn. 1758): in vitro and in vivo study

Argulus are common aquatic ectoparasites that create one of the major threats to aquaculture due to absence of suitable therapy. Piperine, a bioactive component of Piper longum, has medicinal properties and acts as anti-inflammatory, antibacterial, and antifungal, considering eco-friendliness and cost-effectiveness. The present study aimed to evaluate antiparasitic effect of piperine against an ectoparasite Argulus spp. on Carassius auratus. Artificial Argulus infection was carried out by cohabitation method, and the fishes were selected for in vivo study when intensity of Argulus infestation was observed to be 15-20 Argulus per fish. In vitro and in vivo studies were performed at different concentration 1.0 (T (1)), 3.0 (T (2)), 5.0 (T (3)), 7.0 (T (4)), and 9.0 mg l(-1) (T (5)) of piperine solution to treat Argulus for 3 and 72 h, respectively. The acute toxicity test for piperine EC 97 % against goldfish was performed for 96 h. The 96 h median lethal concentration (LC(50)) for piperine was found to be 52.64 mg l(-1). In vitro effect of piperine solution led to 100 % mortality of Argulus at 9.0 mg l(-1) in 3 h whereas, under in vivo test, the 100 % antiparasitic efficacy of piperine solution was found at 9.0 mg l(-1) in 48 h. The EC(50) for 48 h was 9.0 mg l(-1), and thus, therapeutic index is 5.8. The results revealed that piperine at a concentration of 9.0 mg l(-1) can be used as a potential natural agent for controlling Argulus parasite.

Stoichiometric investigations of laser-ablated brass plasma

Laser-ablated brass plasma plumes expanding in various air pressures have been studied using optical emission spectroscopy and two-dimensional imaging. The velocity of the plume front calculated from the R-t plot decreases from 1.9×10(4) m/s to ~5.5×10(3) m/s as the pressure increases from 0.01 to 10(5) Pa. The estimated higher electron temperature for Cu I (510.5 nm) transition than for Zn I (481.1 nm) may be due to differences in the heat of vaporization and vaporization temperature of copper and zinc. The electron density estimated using the Stark-broadened transition 4p(2)P(3/2)→4s(2)(2)D(5/2) of Cu I (510.5 nm) is about 10 times higher than that for transition 4s5s(3)S(1)→4s4p(3)P(2) of Zn I (481.1 nm). The appearance and enhancement of the Cu(2) (A-X) band at lower ambient pressure and formation of nanoparticle clusters have been extensively discussed. Stoichiometric and morphological study of the deposited nanoparticles on carbon tape at different ambient pressure reveals a different percentage composition of copper and of nanoparticles.

A New Begomovirus Species Causing Leaf Curl Disease of Radish in India

Leaf curl disease of radish (RLCD) was observed for the first time in India in commercial fields and kitchen gardens of the Varanasi District and adjoining areas of eastern Uttar Pradesh during November 2003. Infected plants exhibited typical upward and downward leaf curling, leaf distortion, reduction of leaf area, and conspicuous enations on the underside of the leaves. Incidence of RLCD was estimated to be between 10 and 40% depending on the cultivars used. Electron microscopic observation revealed typical geminate particles in infected leaf samples. The causal virus could be transmitted to radish cv. Minu Early by whiteflies (Bemisia tabaci) and grafting. Inoculated plants developed symptoms similar to those observed in naturally infected radish plants. Viral DNA was isolated from artificially inoculated symptomatic radish plants (4) followed by concentration of super-coiled DNA by alkaline denaturation (1). The presence of a geminivirus was confirmed by PCR using DNA-A degenerate primers (3), and a 1.5-kb amplified product was obtained from six artificially and three naturally infected plants. Amplification of the full-length DNA-A was achieved using a primer combination derived from sequences obtained from a 1.5-kb amplicon. Amplification of 1.3-kb DNA-β sequences was achieved using specific primers (2) in three infected plants. Sequence analysis revealed that DNA-A (GenBank Accession No. EF 175733) contained 2,756 nt and DNA-β contained 1,358 nt (GenBank Accession No. EF 175734). DNA-A of the causal virus shares 87.7% identity with Tomato leaf curl Bangladesh virus (GenBank Accession No. AF 188481) and 62% identity with Mungbean yellow mosaic India virus (GenBank Accession No. AF126406). The begomovirus DNA-A sequence associated with RLCD contained seven open reading frames (AV1, AV2, AC1, AC2, AC3, AC4, and AC5). The DNA-β associated with RLCD shared the highest nucleotide sequence identity (84.9%) with DNA-β of Tobacco leaf curl virus isolate NIB 12-1 (GenBank Accession No. AJ316033) reported from Pakistan. Despite exhaustive attempts to amplify a putative viral B-component using degenerate primers based on the intergenic region sequence of the DNA-A or sequences that are highly conserved for other begomoviruses, no DNA-B component was detected. On the basis of DNA-A sequence analysis, the ICTV species demarcation criteria of 89% sequence identity, and genome organization, the virus causing RLCD should be considered a new Begomovirus species, for which the name Radish leaf curl virus (RLCV) is proposed. To our knowledge, this is the first report of the association of a Begomovirus with a disease of radishes in India. References: (1) H. C. Birnboim and J. Doly. Nucleic Acids Res. 7:1513, 1979. (2) R. W. Briddon et al. Mol. Biotechnol. 20:315, 2002. (3) M. R. Rojas et al. Plant Dis. 77:340, 1993. (4) K. M. Srivastava et al. J. Virol. Methods 51:297, 1995.

Characterization of nanostructured PZT prepared by chemical routes

Nanostructured, crystalline Pb(Zr0.52Ti0.48)O3 (crystallite size 8-10 nm) ceramic powders were synthesized at low temperature by the hydroxide co-precipitation and aqueous solution method (water bath technique). The phase and surface morphology characterizations were carried out by XRD, SEM, and TEM analyses. XRD powder pattern exhibited the presence of a major tetragonal and a minor rhombohedral crystalline phase indicating the mixed phase composition in both the samples. SEM-EDS analysis revealed good homogeneity of the materials. From evolution of the Raman spectra the spectroscopic signature of the corresponding phases was determined. Detailed dielectric measurements (between 30 degrees C to 500 degrees C) were obtained to analyze a complete set of impedance-related functions such as dielectric constant (epsilon), loss factor (tan delta), dielectric modulus (M), and conductivity (sigma). Similar to the normal ferroelectric (FE) materials, the dielectric constant (epsilon) of synthesized PZTs was found to be increasing gradually with temperature and attains a maxima (epsilonmax) at the Curie temperature (Tc). The peaks in the dielectric constant plots are attributed to the phase transition associated with the change from tetragonal to rhombohedral structures. The higher dielectric constant of the PZT prepared by hydroxide co-precipitation make it more suitable for various applications.

Arsenic contamination in the Kanker district of central-east India: geology and health effects

This paper identifies newer areas of arsenic contamination in the District Kanker, which adjoins the District Rajnandgaon where high contamination has been reported earlier. A correlation with the mobile phase episodes of arsenic contamination has been identified, which further hinges on the complex geology of the area. Arsenic concentrations in both surface and groundwater, aquatic organisms (snail and water weeds) soil and vegetation of Kanker district and its adjoining area have been reported here. The region has been found to contain an elevated level of arsenic. All segments of the ecoysystem are contaminated with arsenic at varying degrees. The levels of arsenic vary constantly depending on the season and location. An analysis of groundwater from 89 locations in the Kanker district has shown high values of arsenic, iron and manganese (mean: 144, 914 and 371 microg L(-1), respectively). The surface water of the region shows elevated levels of arsenic, which is influenced by the geological mineralised zonation. The most prevalent species in the groundwater is As(III), whereas the surface water of the rivers shows a significant contamination with the As(V) species. The analysis shows a bio-concentration of the toxic metals arsenic, nickel, copper and chromium. Higher arsenic concentrations (groundwater concentrations greater than 50 microg L(-1)) are associated with sedimentary deposits derived from volcanic rocks, hence mineral leaching appears to be the source of arsenic contamination. Higher levels of arsenic and manganese in the Kanker district have been found to cause impacts on the flora and fauna. A case study of episodic arsenical diarrhoea is presented.

Cloning, restriction mapping and phylogenetic relationship of genomic components of MYMIV from Lablab purpureus

The present work describes cloning of genomic components of whitefly transmitted geminivirus infecting Lablab purpureus syn. Dolichos lablab (commonly known as Dolichos bean or Hyacinth bean). The genome characterization using PCR with geminiviral degenerate primers and DNA sequencing were used to describe the bipartite virus associated with yellow mosaic disease of Dolichos lablab. Full-length DNA-A and DNA-B clones were obtained. The DNA-A sequence analysis showed that the isolate was similar to other Mungbean yellow mosaic India virus (MYMIV) isolates reported earlier. The nucleotide sequence analysis of the full-length DNA-A of virus isolate revealed more than 97% homology with Mungbean yellow mosaic India virus-[Cowpea] (AF481865), while the DNA-B also showed >95% homology with MYMIV-[Cp] (AF503580) and MYMIV-[Sb] (AY049771). The phylogenetic analysis of present isolate showed close relationship to legume geminiviruses. The nucleotide sequence analysis showed presence of six open reading frames (ORFs) in DNA-A, with 2 ORFs aligned in sense and 4 ORFs in antisense orientation. Similarly, DNA-B contained two open reading frames (ORFs), one in sense and another in antisense orientation.

Simultaneous Intraocular and Bilateral Extraocular Muscle Involvement in a Case of Disseminated Cysticercosis

We report an unusual case of disseminated cysticercosis having simultaneous intraocular and extraocular involvement. This 21-year-old male presented with recent loss of vision in one eye and history of a single seizure. Examination revealed intravitreal cysticercosis with exudative retinal detachment. Computed tomographic scan showed disseminated neurocysticercosis and cysticercosis of the medial and inferior recti of both the eyes. The patient was started on albendazole and prednisolone under neurologist's supervision. Subsequent computed tomographic scan showed resolution of the extraocular muscle cysts and decrease in the number of neurocysticerci. The patient has had no further seizures. This is the first report of simultaneous intraocular and extraocular cysticercosis.

Removal of arsenic(III) from aqueous solutions using fresh and immobilized plant biomass

The ability of Garcinia cambogia, an indigenous plant found in many parts of India, to remove trivalent arsenic from solution was assessed. Batch experiments were carried out to characterize the As(III) removal capability of fresh and immobilized biomass of G. cambogia. It was found that the kinetic property and uptake capacity of fresh biomass were significantly enhanced by the immobilization procedure. The uptake of As(III) by fresh and immobilized biomass was not greatly affected by solution pH with optimal biosorption occurring at around pH 6--8. The presence of common ions such as Ca and Mg at concentrations up to 100mg/l had no effect on As(III) removal. However, the presence of Fe(III) at 100mg/l caused a noticeable drop in the extent of As(III) removal but the effect was minimal when Fe(III) was present at 10mg/l. The adsorption isotherms quantitatively predicted the extent of As(III) removal in groundwater samples collected from an arsenic-contaminated site in India. Immobilized biomass loaded with As(III) was amenable to efficient regeneration with NaOH solution. Column studies showed that immobilized biomass could be reused over five cycles of loading and elution. The excellent As(III) sequestering capability of fresh and immobilized G. cambogia biomass could lead to the development of a viable and cost-effective technology for arsenic removal in groundwater.

Tomato leaf curl Gujarat virus, a New Begomovirus Species Causing a Severe Leaf Curl Disease of Tomato in Varanasi, India

ABSTRACT The biological and molecular properties of Tomato leaf curl Gujarat virus from Varanasi, India (ToLCGV-[Var]) were characterized. ToLCGV-[Var] could be transmitted by grafting and through whitefly transmission in a persistent manner. The full-length genome of DNA-A and DNA-B of ToLCGV-[Var] was cloned in pUC18. Sequence analysis revealed that DNA-A (AY190290) is 2,757 bp and DNA-B (AY190291) is 2,688 bp in length. ToLCGV-[Var] could infect and cause symptoms in tomato, pepper, Nicotiana benthamiana, and N. tabacum when partial tandem dimeric constructs of DNA-A and DNA-B were co-inoculated by particle bombardment. DNA-A alone also is infectious, but symptoms were milder and took longer to develop. ToLCGV-Var virus can be transmitted through sap inoculation from infected tomato plants to the above-mentioned hosts causing the same symptoms. Open reading frames (ORFs) in both DNA-A and DNA-B are organized similarly to those in other begomoviruses. DNA-A and DNA-B share a common region of 155 bp with only 60% sequence identity. DNA-B of ToLCGV-[Var] shares overall 80% identity with DNA-B of Tomato leaf curl New Delhi virus-Severe (ToLCNDV-Svr) and 75% with ToLCNDV-[Lucknow] (ToLCNDV-[Luc]). Comparison of DNA-A sequence with different begomoviruses indicates that ToLCGV-[Var] shares 84% identity with Tomato leaf curl Karnataka virus (ToLCKV) and 66% with ToLCNDV-Svr. ToLCGV-[Var] shares a maximum of 98% identity with another isolate of the same region (ToLCGV-[Mir]; AF449999) and 97% identity with one isolate from Gujarat (ToLCGV-[Vad]; AF413671). All three viruses belong to the same species that is distinct from all the other geminivirus species described so far in the genus Begomovirus of the family Geminiviridae. The name Tomato leaf curl Gujarat virus is proposed because the first sequence was taken from an isolate of Gujarat, India.

A New Begomovirus Species Causing Tomato Leaf Curl Disease in Varanasi, India

In November 2001, a leaf curl disease of tomato, manifested by yellowing of leaf lamina, upward leaf curling, leaf distortion, shrinking of leaf surface, and stunted plant growth was observed in tomato-growing areas in the Varanasi and Mirzapur districts of eastern Uttar Pradesh, India, which caused yield losses up to 100%. The causal agent was infective to tomato cv. Punjab Chuhara by whiteflies and grafting. Inoculated plants developed symptoms observed in naturally infected tomatoes. Viral DNA was isolated from artificially inoculated tomato plants using 1% CTAB (2) followed by a concentration of supercoiled DNA by alkaline denaturation (1). A geminivirus was confirmed by polymerase chain reaction using DNA-A degenerate primers (3), and a 550-bp amplified product was obtained from artificially and naturally infected plants. Full-length viral genomes of DNA-A and DNA-B were cloned in plasmid pUC18 at HindIII and XbaI sites, respectively. Partial tandem dimers of the viral clones were infective to Nicotiana benthamiana and tomato cv. Organ Spring through particle bombardment. Infected N. benthamiana plants exhibited downward and upward leaf curling, big veins, leaf puckering with interveinal chlorosis, and stunting. On tomato, symptoms were the same as those seen on naturally infected plants. Cloned DNA also infected Capsicum annuum cv. California Wonder (upward leaf curling and stunting) and tobacco cv. Xanthi (leaf curling and crinkling) but failed to infect Phaseolus vulgaris, okra, cotton, and N. glutinosa. The Varanasi isolate was sap transmissible (0.1 M potassium phosphate buffer, pH 7.0) from the bombarded plants to N. benthamiana and tomato cv. Organ Spring. DNA-A alone infected N. benthamiana (upward leaf curling and big veins) and tomato cv. Organ Spring (mild leaf curl), but symptoms were delayed and milder. Full-length genome sequencing revealed DNA-A (AY190290) contained 2,757 nt and DNA-B (AY190291) contained 2,688 nt. DNA-A of the Varanasi isolate shares 98.4% identity with a DNA-A sequence (AF449999) obtained from a tomato showing leaf curl symptoms from the same region and 97.1% identity with an isolate from Gujarat (900 km from Varanasi). All three sequences represent isolates of the same species, herein called Tomato leaf curl Gujarat virus, based on the priority of submission of the DNA sequence for the Gujarat region (ToLCGV; AF 413671). All isolates noted were obtained from GenBank. However, except for the DNA-A sequence, no other information is available for these ToLCGV isolates. DNA-A of the ToLCGV-Varanasi isolate shares 66.8% identity with Tomato leaf curl New Delhi virus, severe strain (ToLCNdV-Svr) (U15015), and 84.1% with Tomato leaf curl Karnataka virus (U38239). No DNA-B has been reported for these two ToLCGV isolates, and no infectious clone proving the etiology of the disease has been constructed, except for ToLCGV-Varanasi. DNA-B of ToLCGV-Varanasi shares 79.2% homology with ToLCNdV-Svr and 84.1% with ToLCNdV-Luc (X89653). These results suggest that the isolate from Varanasi belongs to ToLCGV, a previously undescribed geminivirus species causing a devastating tomato leaf curl disease in Gujarat and Uttar Pradesh. References: (1) H. C. Birnboim and J. Doly. Nucleic Acids Res. 7:1513, 1979. (2) K. M. Srivastava et al. J. Virol. Methods 51:297, 1995. (3) S. D. Wyatt and J. K. Brown. Phytopathology 86:1288, 1996.

Physiological and biochemical alterations in Anabaena 7120 under iron stress

Various physiological and biochemical process like growth, NO3- -uptake, nitrate reductase, glutamine synthetase and ATPases (Mg2+ and Ca2+ dependent) in the cyanobacterium Anabaena 7120 were observed under iron stress. Growth was found to be maximum in 50 microM Fe3+ added cells however, 20 microM Fe3+ (the Fe3+ concentration generally used for routine culturing of cyanobacterial cell in Chu 10 medium) incubation resulted in lower growth. Fe3+ starvation on the other hand showed very poor growth up to 4th day but once the growth started it reached at significant level on 7th day. Higher Fe3+ concentration reflected reduced growth with lethality at 500 microM Fe3+. Chlorophyll a fluorescence under Fe3+ stress reflected almost the similar results as in case of growth. However, the pigment was found to be more sensitive as compared to protein under Fe3+ stress. Similar results have been observed in case of NO3-uptake with only 80% reduction in nutrient uptake in 500 microM Fe3+ incubated cells. Nitrate reductase activity was lower in Fe3+ starved cells as compared to significant enzyme activity in 20 and 50 microM Fe3+ incubated cells. Similar to nitrate reductase, glutamine synthetase also showed maximum level in 50 microM Fe3+ added cells, however, higher Fe3+ concentration (300-500 microM ) resulted in reduced enzymatic activity. Glutamine synthetase activity was less sensitivity as compared to nitrate reductase activity under Fe3+ stress. ATPase (Mg2+ and Ca2+ dependent) always showed higher level with increasing Fe3+ concentration.

Effect of levodopa and carbidopa in human amblyopia

BACKGROUND

To assess the role of continuous therapy for 3 weeks with levodopa and carbidopa in the management of human amblyopia in children and adults.

METHOD

There were 88 amblyopic eyes of 82 subjects included in this double masked randomized prospective clinical trial. Levodopa and carbidopa combination in 2 different dosage schedules were given to both adults and children. The response was monitored of the improvement in visual acuity, contrast sensitivity, and visually evoked potentials.

RESULT

Patients receiving higher dosages of levodopa and carbidopa in both adults and children showed a better response to treatment. However, the effect did not last beyond 9 weeks of stopping treatment.

CONCLUSION

Though levodopa and carbidopa therapy may not be able to ameliorate amblyopia on its own on a long-term basis, it may be considered nonetheless to be an important adjunct to conventional therapy because it may improve patient compliance for occlusion by improving visual acuity in the amblyopic eye. Thus, it offers promise of improving the functional outcome in these cases. However, longer follow-up trials are needed to substantiate these conclusions.

Insertion of a peptide from MuLV RT into the connection subdomain of HIV-1 RT results in a functionally active chimeric enzyme in monomeric conformation

The natural form of the human immunodeficiency virus type one reverse transcriptase (HIV-1 RT) found in virion particles is a heterodimer composed of the p66 and p51 subunits. The catalytic activity resides in the larger subunit in the heterodimeric (p66/p51) enzyme while in the monomeric form it is inactive. In contrast, Murine leukemia virus RT (MuLV RT) is functionally active in the monomeric form. In the primary amino acid sequence alignment of MuLV RT and HIV-1 RT, we have identified three specific regions in MuLV RT, that were missing in HIV-1 RT. In a separate study, we have shown that a chimeric RT construct comprising of the polymerase domain of HIV-1 RT and RNase-H domain of MuLV RT is functionally active as monomer [20]. In this communication, we demonstrate that insertion of a peptide (corresponding to amino acid residues 480-506) from the connection subdomain of MuLV RT into the connection subdomain of HIV-1 RT (between residues 429 and 430) results in a functionally active monomeric chimeric RT. Furthermore, this chimeric enzyme does not dimerize with exogenously added p51 subunit of HIV-1RT. Functional analysis of the chimeric RT revealed template specific variations in its catalytic activity. The chimeric enzyme catalyzes DNA synthesis on both heteropolymeric DNA and homopolymeric RNA (poly rA) template but curiously lacks reverse transcriptase ability on heteropolymeric RNA template. Similar to MuLV RT, the polymerase activity of the chimeric enzyme is not affected by acetonitrile, a reagent which dissociates dimeric HIV-1 RT into inactive monomers. These results together with a proposed 3-D molecular model of the chimeric enzyme suggests that the insertion of the missing region may induce a change in the spatial position of RNase H domain such that it is functionally active in monomeric conformation.

The beta7-beta8 loop of the p51 subunit in the heterodimeric (p66/p51) human immunodeficiency virus type 1 reverse transcriptase is essential for the catalytic function of the p66 subunit

The heterodimeric human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is composed of p66 and p51 subunits, p66 being the catalytic subunit. Our earlier investigation on the role of p51 in the catalytic process has shown that the p51 subunit facilitates the loading of the p66 subunit onto the template primer (TP). We had postulated that the beta7-beta8 loop of the p51 subunit may be involved in opening the polymerase cleft of p66 for DNA binding [Pandey, V. N., et al. (1996) Biochemistry 35, 2168]. We report here that deletion or alanine substitution of four residues of the beta7-beta8 loop results in severe impairment of the polymerase function of the heterodimeric enzyme. The enzyme activity was restored to the wild-type levels when the mutant p66 subunit was dimerized with the wild-type p51, suggesting that the intact beta7-beta8 loop in the p51 subunit is indispensable for the catalytic function of p66. Further, the template primer binding ability of the enzyme was significantly reduced upon deletion or alanine substitution in the beta7-beta8 loop. Interestingly, the loss of the TP binding ability of the mutant p66 was restored upon dimerization with wild-type p51. Examination of the glycerol gradient ultracentrifugation analysis revealed that while the wild-type HIV-1 RT sediments as a dimeric protein, the mutant enzymes carrying deletion or alanine substitution in both the subunits sediment predominantly as monomeric proteins, suggesting their inability to form stable dimers. In contrast, mutant p66 dimerized with wild-type p51 (p66delta/p51WT and p66Ala/p51WT) sedimented at the dimeric position. Taken together, these results clearly implicate the importance of the beta7-beta8 loop of p51 in the formation of stable functional heterodimers.

Extraocular muscle cysticercosis presenting as Brown syndrome

PURPOSE

Report of a case of acquired Brown syndrome caused by infestation of the superior oblique muscle by Cysticercus cellulosae.

METHOD

Case seen in a referral practice. A 20-year-old man presented with recurrent attacks of conjunctivitis and diplopia in upgaze. Clinical examination of ocular motility established a diagnosis of acquired Brown syndrome of the right eye. Computed tomography of the right orbit unequivocally established the diagnosis of superior oblique muscle cysticercosis. The patient was started on systemic steroids and albendazole in the prescribed doses for a month.

RESULT

Serial computed tomography scans of the orbit revealed resolution of the cystic lesion after a month. Clinically, although there was restoration of ocular motility in upgaze, mild restriction of movement of the right eye in levoelevation persisted. However, the patient was symptomatically better with amelioration of the recurrent conjunctivitis and diplopia in primary gaze.

CONCLUSION

Extraocular muscle cysticercosis should be considered in the differential diagnosis of acquired motility disorder. The presentation of extraocular muscle cysticercosis as an acquired Brown syndrome is unusual. Response to medical therapy was satisfactory.

Inhibition of Tat-mediated transactivation of HIV-1 LTR transcription by polyamide nucleic acid targeted to TAR hairpin element

Tat, an essential human immunodeficiency virus type 1 protein interacts with the transactivation response element (TAR) and stimulates transcription from the viral long-terminal repeat (LTR). Blockage of Tat-TAR interaction halts viral transcription and hence replication. We have found that polyamide nucleic acid (PNA), targeted to the TAR sequences of viral RNA genome is able to prevent Tat-TAR interaction by efficient sequestration of the TAR. Anti-TAR PNA competes for TAR and prevents Tat-mediated stimulation of HIV-1 LTR transcription in vitro but has no influence on the basal level of transcription in the absence of Tat. Using a reporter gene construct pHIV LTR-CAT and pCMV-Tat in cell culture, we have further shown that anti-TAR PNA is able to block Tat-mediated transactivation of HIV-1 LTR transcription in vivo as judged by the extent of LTR driven CAT gene expression in the absence and presence of anti-TAR PNA. Supplementation of 100 nM of anti-TAR PNA into the culture medium further enhances the suppression of transactivation. Nonspecific scrambled PNA had no influence on Tat-TAR interaction and LTR-driven CAT gene expression in cell culture. These results suggest that PNA targeted to the TAR sequence of the viral genome may be a potential inhibitor of HIV-1 gene expression.

Extraocular muscle cysticercosis: a clinical masquerade

PURPOSE

To highlight the different presentations of extraocular muscle cysticercosis, which can result in acquired ocular motility disorders.

METHODS

Ten cases of acquired motility disorders examined between January 1998 and January 1999 were diagnosed as extraocular muscle cysticercosis with computed tomography (CT). All patients were treated with corticosteroid therapy and albendazole. Repeat CT scans were performed in 5 patients.

RESULTS

The inferior rectus muscle was most commonly affected with double elevator palsy the most common clinical presentation. Response to treatment was satisfactory with complete resolution of the ocular motility disorder in 8 patients. Initiating therapy with corticosteroids prior to the addition of cysticidal drugs prevented severe inflammatory reactions and residual strabismus.

CONCLUSION

A high index of suspicion should be entertained for extraocular muscle cysticercosis in every case of recent acquired ocular motility disorder. Response to medical therapy is satisfactory.

Sensory deviations subsequent to senile cataract

PURPOSE

To evaluate the effect of extracapsular cataract extraction with posterior chamber intraocular lens (IOL) implantation in patients with sensory deviations subsequent to senile cataract.

METHODS

Twenty patients with dense cataract and associated sensory deviations underwent follow-up between April 1996 and April 1998 after extracapsular cataract extraction with posterior chamber IOL implantation in the deviating eye. All patients underwent follow-up for a minimum period of 6 months.

RESULTS

Preoperatively, all patients had a visual acuity of PL positive (perception of light present) and PR (projection of rays) accurate in the deviating eye. Two patients had an esodeviation, and 18 patients had an exodeviation. Postoperatively, all patients had a corrected visual acuity of 20/40 or better in the operated eye at 12 weeks. Nineteen patients had ocular alignment within +/-8 prism diopters of orthophoria at 12 weeks.

CONCLUSION

Sensory deviations subsequent to senile cataract usually resolve spontaneously after cataract surgery if visual gains are 20/40 or better. The prognosis for binocular vision is good.

Role of glutamine 151 of human immunodeficiency virus type-1 reverse transcriptase in substrate selection as assessed by site-directed mutagenesis

A natural mutation at codon 151 (Gln --> Met; Q151M) of HIV-1 RT has been shown to confer resistance to the virus against dideoxy nucleoside analogues [Shirasaka, T., et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 2398], suggesting that Gln 151 may be involved in conferring sensitivity to nucleoside analogues. To understand its functional implication, we generated two mutant derivatives of this residue (Q151M and Q151N) and examined their sensitivities to ddNTPs and their ability to discriminate against rNTPs versus dNTP substrates on natural U5-PBS HIV-1 RNA template. We found that Q151M was highly discriminatory against all four ddNTPs but was able to incorporate rNTPs as efficiently as the wild type enzyme. In contrast, the Q151N mutant was only moderately resistant to ddNTPs but exhibited a higher level of discrimination against rNTPs. The fidelity of misinsertion was found to be highest for the Q151N mutant followed by Q151M and the wild type enzyme. These results point toward the importance of the amino acid side chain at position 151 in influencing the ability of the enzyme in recognition and discrimination against the sugar moieties of nucleotide substrates.

Functional analysis of amino acid residues constituting the dNTP binding pocket of HIV-1 reverse transcriptase

In order to understand the functional implication of residues constituting the dNTP-binding pocket of human immunodeficiency virus type 1 reverse transcriptase, we performed site-directed mutagenesis at positions 65, 72, 113, 115, 151, 183, 184, and 219, and the resulting mutant enzymes were examined for their biochemical properties and nucleotide selectivity on RNA and DNA templates. Mutations at positions 65, 115, 183, 184, and 219 had negligible to moderate influence on the polymerase activity, while Ala substitution at positions 72 and 151 as well as substitution with Ala or Glu at position 113 severely impaired the polymerase function of the enzyme. The K219A, Y115F, and Q151M mutants had no influence on the fidelity; Y183A, Y183F, K65A, and Q151N mutants exhibited higher fidelity on both RNA and DNA templates, while Y115A was less error-prone selectively on a DNA template. Analysis of the three-dimensional model of the enzyme-template primer-dNTP ternary complex suggests that residues Tyr-183, Lys-65, and Gln-151 may have impact on the flexibility of the dNTP-binding pocket by virtue of their multiple interactions with the dNTP, template, primer, and other neighboring residues constituting the pocket. Recruitment of the correct versus incorrect nucleotides may be a function of the flexibility of this pocket. A relatively rigid pocket would provide greater stringency, resulting in higher fidelity of DNA synthesis in contrast to a flexible pocket. Substitution of a residue having multiple interactions with a residue having reduced interaction capability will alter the internal geometry of the pocket, thus directly influencing the fidelity.

The p51 subunit of human immunodeficiency virus type 1 reverse transcriptase is essential in loading the p66 subunit on the template primer

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is a dimeric enzyme consisting of p66 and p51 subunits. The functional role of the p51 subunit remains elusive since all the catalytic functions appear to be executed through the p66 subunit. We report here that the p51 subunit, in addition to providing structural support to the p66 subunit, may be involved in facilitating the loading of the p66 subunit on to the template-primer (TP). This possibility is supported by following observations: (i) Upon binding to the TP, the p51 subunit can be dissociated by acetonitrile treatment and the template-primer-bound p66 monomer alone is capable of catalyzing DNA synthesis. (ii) Photo-cross-linking of template-primer to HIV-1 RT is abolished by dissociation of the p51 subunit prior to the TP binding but remains unaffected after the TP binding step. (iii) The p66-TP covalent complex selectively generated by UV irradiation and separated by gel electrophoresis can incorporate a single nucleotide in situ upon its renaturation in the gel. (iv) Treatment of HIV-1 RT with (tert-butyldimethylsilyl)spiroaminooxathioledioside (TSAO), an inhibitor that specifically binds to the beta7 beta8 loop of p51, destabilizes the heterodimeric enzyme, resulting in the subsequent loss of DNA binding.