Occurrence of COVID-19 in Kolkata slums during second surge

Background: The clobber of COVID-19 brought a coup-de-grace to humanity in this modern era. New-norms of COVID-19 prevention although appear promising yet often adjunct with non-congruent compliance. The WHO has advocated house-to-house case-linked study to acquire facts on epidemiological and transmissibility traits of COVID-19 in low-income communities. Kolkata experienced the first wave of COVID-19 till November 20, expected second splatter in March 21. Aims and Objectives: Thinking through a probable upswing of COVID-19 in Kolkata, it was felt prudent to study the occurrence of COVID-19 among residents of two different slums inter-alia study allied factors, if any. Materials and Methods: The study was carried out in two different slums having 395 and 428 members, respectively, in South Kolkata from March 21 to August 21. Sanction was obtained from administrative authority as well from each individual. Questionnaire containing personal details, awareness, and observance of personal protective measures (PPM) on COVID-19 were sent to members through e-mode; those demurred, contacted in-person under new-norm. Data assembled was coded, tabulated and analyzed. Details of COVID-19 (RT-PCR+ve) cases confirmed by Government/private hospitals were incorporated as and when surfaced. Results: Communities studied had comparable socio-demographic attributes including education, employment, and economic stand. About 93% of subjects from each slum knew most of the facets of PPM and stated practiced the same. Occurrence rates of COVID-19 were 15.2 and 16.2 per 1000 people of respective communities during study tenure. Majority of indisposed were smoker male (92%) from the lowest SES (53.8%), educated to primary/middle school (46%), and worked as vegetable seller (53.8%). All afflicted stated followed PPM except social distancing (77%) and sanitizer use (53.8%). All affected were smokers/quid-users and shared tobacco sticks/hand-smothered quid for mutual use regularly. The study unveiled unequivocal heterogeneity of COVID-19 transmission in Kolkata slums because of certain unattended socio-graphics besides optimistic reflective of PPM awareness/observance. PPM proffers protection no doubt but its effective role necessitates consistent conformity in the background of certain contextual considerations. Conclusion: Further research in urban slums is contemplated to enhance the present effort to extricate facts that may lend a hand in COVID-19 prevention tomorrow.

Identification of a suitable promoter for the sigma factor of Mycobacterium tuberculosis

Promoter binding specificity is one of the important characteristics of transcription by Mycobacterium tuberculosis (Mtb) sigma (σ) factors, which remains unexplored due to limited structural evidence. Our previous study on the structural features of Mtb-SigH, consisting of three alpha helices, and its interaction with core RNA polymerase has been extended herein to determine the little known DNA sequence recognition pattern involving its cognate promoters. Herein, high resolution X-ray crystallographic structures of the protein-DNA complexes were inspected to determine the tentative DNA-binding helix of the σ factor. The binding interface in the available crystal structures is found to be populated mainly with specific residues such as Arg, Asn, Lys, Gln, and Ser. We uncovered the helix 3 of Mtb-SigH containing most of these amino acids, which ranged from Arg 64 to Arg 75, forming the predicted active site. The complex of Mtb-SigH:DNA is modelled with 20 promoter sequences. The binding affinity is predicted by scoring these protein-DNA complexes through proximity and interaction parameters obtained by molecular dynamics simulations. The promoters are ranked considering hydrogen bonding, energy of interaction, buried surface area, and distance between centers of masses in interaction with the protein. The ranking is validated through in vitro transcription assays. The trends of these selected promoter interactions have shown variations parallel to the experimental evaluation, emphasizing the success of the active site determination along with screening of the promoter strength. The promoter interaction of Mtb-SigH can be highly beneficial for understanding the regulation of gene expression of a pathogen and also extends a solid platform to predict promoters for other bacterial σ factors.

Lupus cystitis: An unusual presentation of systemic lupus erythematosus

Lupus cystitis is a rare complication of systemic lupus erythematosus (SLE) and occurs in association with gastrointestinal symptoms. This rare disorder has been reported mainly from Japan. We report a 20 year old female who diagnosed as having SLE associated with paralytic ileus and chronic interstitial cystitis. Treatment with intravenous methylprednisolone, cyclophosphamide pulse therapy followed by oral prednisolone and azathioprine led to amelioration of manifestations. Later she developed lupus nephritis which was treated with mycophenolate mofetil.

Abstract PD07-01: Phase 2 Study of Ixabepilone Versus Paclitaxel as Neoadjuvant Therapy for Early Stage Breast Cancer with Comparative Biomarker Analysis

Background: Anthracyclines (A) and taxanes (T) are standard neoadjuvant treatments for breast cancer (BC), achieving pathologic complete response (pCR) rates of 20-30% in unselected patient (pt) populations. Ixabepilone (ixa) is approved for treatment of metastatic BC: plus capecitabine (Cap) in pts progressing after A and T or as monotherapy after progression on A, T and Cap. Prior data suggest that overexpression of βIII tubulin is associated with resistance to paclitaxel (P) while activity of ixa was unaffected. We present the first randomized comparison of neoadjuvant ixa and P in early stage BC. Primary objectives were to estimate pathologic complete response rate (pCR) in the overall population and in biomarker-defined populations. Methods Pts with early stage BC were biopsied for immunohistochemical (IHC) and mRNA biomarker analyses prior to chemotherapy. Following 4 cycles of doxorubicin/cyclophosphamide (AC), pts were randomized to either every 3 week ixa (40mg/m2:4 cycles) or weekly P (80mg/m2:12 doses). Post-therapy surgery and pathological reports were used to assess pCR. Baseline βIII expression was assessed via a standardized IHC assay (Dako, CA) and predefined single gene mRNA markers (including TUBB3, CAPG, TACC3) were assessed via Affymetrix gene expression profilling. The pCR rate and cutoff for biomarker positivity were estimated using a cross-validation method. Secondary endpoints in the study included clinical objective response rate and safety. Results Pts (N=384) were enrolled in 15 countries: 313 pts were treated with AC. 295 pts were randomized; 289 were treated with either ixa or P. Of these, 247 (123, ixa; 124, P) had βIII IHC data and 231 (114, ixa; 117, P) had both pathologic and βIII IHC data. Baseline characteristics were balanced between arms, including triple negative pts (TN, 49%). The pCR rate in all randomized pts was 24.3% (90% CI: 18.6-30.8) with ixa and 25.2% (90% CI: 19.4-31.7) with P. pCR rates were similar regardless of sub-group.

Table 1. pCR rates

No significant interaction was observed between βIII expression and treatment arms (logistic regression analysis). Secondary efficacy measures were consistent with the pCR results. No clinically meaningful differences in efficacy endpoints were noted between ixa and P with mRNA markers (TUBB3, CAPG and TACC3; analyses are ongoing with others). The safety profiles of ixa and P were similar, including incidence of peripheral neuropathy (Grade 3/4: ixa 4.1% vs P 3.5%). An exception was greater neutropenia with ixa (Grade 3/4; 41.3% versus 8.4% with P) although there was no difference in the rate of febrile neutropenia (0.7%). Summary Overall, the results indicated that ixa had similar efficacy to P when measured by pCR in the neoadjuvant BC setting. No clinically meaningful differences were noted in the efficacy profile of ixa compared to P across the subsets analyzed. Ixa or P following AC was well tolerated with similar safety profiles.

Changes in vagal tone with posture in asthma are related to changes in ventilatory pattern

BACKGROUND

Posturally induced changes in minute ventilation in patients may be autonomically driven. This study aimed to test whether changes in autonomic tone with posture differed between normal and asthmatic subjects and whether this related to changes in indices of ventilation.

METHODS

Ten patients with type 1 brittle asthma (BA), 10 with non-brittle, severe asthma (SA), 10 with mild asthma (MA) and 10 normal individuals were studied lying flat, at 60 degrees head up tilt and flat again each for 30min, assessing end-tidal CO(2) (ETCO(2)), respiratory rate and autonomic tone by heart rate variability.

RESULTS

Parasympathetic tone (as high-frequency [HF] power) fell on tilt in all four groups, all showing increases in LF (low frequency)/HF ratio (sympatho-vagal balance) on tilt (BA, 2.03-4.9; SA, 3.3-8.2; MA, 1.5-4.9; normals, 2.3-6.6). ETCO(2) on tilt fell significantly in all 3 asthma groups (BA, DeltaETCO(2) -0.4, 95% CIs -0.18 to -0.75, P=0.005; SA, -0.7, 95% CIs -0.27 to -1.16, P=0.004; MA, -0.5, 95% CIs -0.14 to -0.78, P=0.01) but not in normals (-0.1, 95% CIs +0.23 to -0.49). The fall in ETCO(2) on tilt correlated with the fall in HF power in all three asthma groups but not in normal subjects.

CONCLUSION

Changes in vagal tone posture are seen on tilt in both normal and asthmatic subjects which relate to changes in ETCO(2) only in asthmatic subjects. This provides support for the hypothesis that hyper-ventilatory response to postural change in asthma is autonomically influenced.

Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA

Using fluorescence resonance energy transfer, we show that, in the majority of transcription complexes, sigma(70) is not released from RNA polymerase upon transition from initiation to elongation, but, instead, remains associated with RNA polymerase and translocates with RNA polymerase. The results argue against the presumption that there are necessary subunit-composition differences, and corresponding necessary mechanistic differences, in initiation and elongation. The methods of this report should be generalizable to monitor movement of any molecule relative to any nucleic acid.

Micropropagation of Paulownia fortuneii through in vitro axillary shoot proliferation

Primary cultures were established with nodal segments from juvenile shoots of two- year-old Paulownia fortuneii trees from a clonal plantation in Andhra Pradesh. A medium containing half-strength MS salts + RAP (1 mg/L) + sucrose (2%) produced optimum bud break in nodal explants. The same basal medium with reduced hormone level (0.5 mg/L) supported maximum multiplication of secondary cultures of P. fortuneii (1:6 in 6 weeks). Specific treatments were tested to enhance this rate of multiplication. In one approach, five to six week old in vitro grown shoots were ratooned (cutting the main shoot at the bottom leaving one node). The stumps (ratooned basal node) produced 2 to 3 axillary shoots, which grew into 4 to 5 nodes by 3 weeks; thus, providing additional shoots from the same explant. This provided 30% additional shoots in 4 cycles. Secondly, reducing the light intensity to 1200 lux resulted in higher shoot elongation, i.e, formation of 8 nodes in 5 weeks with healthier shoots than the normal intensity of 3000 lux under which only 6 nodes were produced in 6 weeks. In vitro-grown shoots could be successfully rooted ex vitro in vermiculite + cocopeat mixture (1:1 v/v) under 90% humidity, transferred to soil in polybags for hardening in the green house for 2 weeks and shifted to shade net for further hardening. After one month, the plants could be successfully transplanted to field with 95% survival. Micropropagated plants showed an excellent growth in the field attaining a height of 1.5 m and a collar diameter of 2.8 cm in 3 months.

A novel RNA polymerase binding site upstream of the galactose promoter in Escherichia coli exhibits promoter-like activity

RNA polymerase is known to bind and utilize the overlapping promoters P1 and P2 in Escherichia coli galactose operon. We have identified an additional specific site upstream of P2, where RNA polymerase binds in a heparin-resistant manner. Binding of polymerase to this site, termed P3, occurs simultaneous to its binding at P1/P2. We have located this P3 site by DNase I footprinting. A 63 base pair region centered around position - 100 with respect to galP1 is protected by polymerase. Interestingly, a Pribnow box TATAAT is present within this protected region (-103 to -108). We have shown that transcription occurs from P3 in vitro. Primer extension analysis provides direct evidence that P3 is transcribed in vivo. The start site of transcription has been mapped at -96 position relative to galP1. beta-galactosidase assays with different gal promoter constructs reveal that while P3 alone functions as a weak in vivo promoter, it has a synergistic effect on transcription from the gal operon, since deletion of P3 or specifically mutating its -10 region result in a substantial reduction in the gal promoter activity.

Distribution of phlebotomine sand fly genotypes (Lutzomyia shannoni, Diptera: Psychodidae) across a highly heterogeneous landscape

Genetic variability of eight Colombian field populations and two laboratory colonies of a tropical forest sand fly, Lutzomyia shannoni Dyar, was assessed by comparing allozyme frequencies at 20 enzyme loci. Substantial genetic variability was noted in all strains, with mean heterozygosities of 13-21% and alleles per locus of 2.0-2.8. Four loci were monomorphic. Six populations in north and central Colombia showed close genetic similarity (Nei's distances, 0.01-0.09), despite mountainous environment, discontinuous forest habitat, and elevation differences from 125 to 1,220 m. Two samples representing the Orinoco (near Villavicencio) and Amazon (near Leticia) river basins were similar (Nei's distance, 0.08) but diverged substantially from the central six samples (Nei's distances, 0.26-0.40). Although the range of L. shannoni extends from the southeastern United States to northern Argentina, three genetically distinct, geographically discrete, groups were discerned by the current analysis: Orinoco-Amazon river basins, north-central Colombia, and eastern United States.

Identification of cutaneous Leishmaniasis vectors, Phlebotomus papatasi and P. duboscqi using random amplified polymorphic DNA

Phlebotomus papatasi and P. duboscqi are two closely related, morphologically similar sandfly species that are established vectors of zoonotic cutaneous leishmaniasis in the Old World. We have developed a Random Amplified Polymorphic DNA (RAPD) method to find species-specific DNA profiles of these two species. It was found that using a single 10-mer primer a 'species specific' amplification band of about 0.49 kb was produced in all specimens of P. duboscqi while it was absent in P. papatasi. The 0.49 kb diagnostic band was consistently present in both males and females of P. duboscqi. The suitability of this primer for Phlebotomus species identification will help to find the true vector-parasite relationship in the epidemiology of leishmaniasis, particularly in the African countries where both species are prevalent.

Morphology of larval antennae and mouthparts of four Indian sand flies (Diptera: Psychodidae) by scanning electron microscopy

The mouthparts and antennae of the fourth-instar larvae of four sand fly species were studied using scanning electron microscopy. The morphology of the clypeus, labrum, mandible, maxilla, mentum, and antennae were compared for Phlebotomus argentipes Annandale & Brunetti, P. papatasin (Scopoli), Sergentomyia babu babu (Annandale), and S. bailyi (Sinton). Most of structures exhibited species-specific features, particularly the characteristics of the antennae. P. papatasin larvae had heart-shaped antennae, a long mandible, stout maxilla, and a heavy mentum with large teeth. In contrast, P. argentipes larvae had dumbbell-shaped antennae and a singular club-shaped labrum. The antennae of S. b. babu were ovoid, whereas those of S. bailyi were elliptical. The labrum of S. b. babu was lanceolate, whereas that of S. bailyi was rounded and exhibited a small, thick projection with several folds. The teeth of the mentum of both Sergentomyia species were shorter than those of the Phlebotomus species. Species-specific differences in the morphology of larval mouthparts and antennae indicate that it may not always be necessary to rely on adult morphology to identify sympatric phlebotomines.

Population ecology of Phlebotomus argentipes (Diptera: Psychodidae) in West Bengal, India

The population abundance of Phlebotomus argentipes Annandale & Brunetti was studied between January 1986 and December 1987 at 2 sites in West Bengal, India, in relation to 8 ecological parameters (air temperature, rainfall, windspeed, relative humidity, soil moisture, soil temperature, soil pH, and soil organic carbon). Sand flies were present throughout the year with minimum abundance in winter months and maximum during monsoon and postmonsoon months. Correlation analysis examined pairwise relationships among the 8 ecological parameters and P. argentipes abundance. Multiple linear regression of sand fly abundance on the 8 parameters showed that average soil temperature and soil moisture, both recorded 1 mo earlier, were associated positively with sand fly abundance. These findings have important implications for Indian kala-azar disease control and prevention. Effective vector management programs are needed most when weather conditions favor increased sand fly abundance, given that greater sand fly abundance increases the likelihood of host-vector contact and the transmission of Leishmania.

Functional roles of the two cyclic AMP-dependent forms of cyclic AMP receptor protein from Escherichia coli

The cyclic AMP receptor protein activates transcription in Escherichia coli, only when complexed with cyclic AMP. The cyclic AMP receptor protein-cyclic AMP complex formed at low concentrations of cyclic AMP has a different conformation from either cyclic AMP receptor protein alone or its complex with cyclic AMP formed at high cyclic AMP concentrations. Various biophysical data suggest that the latter complex resembles free cyclic AMP receptor protein. We have examined the conformational and biological properties of cyclic AMP receptor protein as a function of cyclic AMP concentrations, using the gal operon of E. coli. A biphasic behavior is observed. It is shown that only the complex formed at lower concentrations of cyclic AMP is the transcriptionally active form. This difference between the complexes at different levels of cyclic AMP arises from a decreased ability of the cyclic AMP receptor protein-cyclic AMP complex at high cyclic AMP concentrations to bind to DNA at specific sites.

Vector potential of Phlebotomus duboscqi and P. papatasi: a comparison of feeding behaviour, reproductive capacity and experimental infection with Leishmania major

Phlebotomus duboscqi and P. papatasi are the incriminated vectors of Leishmania major, the causative agent of zoonotic cutaneous leishmaniasis (ZCL) in various parts of the world. Factors contributing to the vector potential of these two species were investigated in the laboratory. It was found that 90.1% of the P. duboscqi females tested completed feeding in 1 h and they could complete up to eight gonotrophic cycles in their maximum adult life-span in the laboratory of almost 2 months. In contrast, only 70.3% of the female P. papatasi took bloodmeals within 1 h and they could only complete a maximum of four gonotrophic cycles in the maximum adult life-span of just 1 month. Biting habit (proportion feeding/day of the gonotrophic cycle), survival (proportion surviving first oviposition), gonotrophic discordance (proportion refeeding on blood before first oviposition) and experimental infection (proportion of flies offered a bloodmeal containing L. major which became infected) were all higher for P. duboscqi (0.18, 0.91, 0.50 and 0.65, respectively) than for P. papatasi (0.14, 0.71, 0.12 and 0.56, respectively). It therefore seems likely that P. duboscqi is a much more effective vector of L. major than P. papatasi in several endemic foci of ZCL.

Genetic variability in biochemical characters of Brazilian field populations of the Leishmania vector, Lutzomyia longipalpis (Diptera: Psychodidae)

The phlebotomine sand fly Lutzomyia longipalpis is the insect vector of visceral leishmaniasis, a protozoan disease of increasing incidence and distribution in Central and South America. Electrophoretic allele frequencies of 15 enzyme loci were compared among the L. longipalpis populations selected across its distribution range in Brazil. The mean heterozygosity of two colonized geographic strains (one each from Colombia and Brazil) were 6% and 13% respectively, with 1.6-1.9 alleles detected per locus. In contrast, among the seven widely separated field populations, the mean heterozygosity ranged from 11% to 16% with 2.1-2.9 alleles per locus. No locus was recovered that was diagnostic for any of the field populations. Allelic frequency differences among five field strains from the Amazon basin and eastern coastal Brazil were very low, with Nei's genetic distances of less than 0.01 separating them. The two inland and southerly samples from Minas Gerais (Lapinha) and Bahia (Jacobina) states were more distinctive with genetic distances of 0.024-0.038 and 0.038-0.059, respectively, when compared with the five other samples. These differences were the consequence of several high frequency alleles (glycerol-3-phosphate dehydrogenase [Gpd1.69] and phosphoglucomutase [Pgm1.69]) relatively uncommon in other strains. The low genetic distances, absence of diagnostic loci, and the distribution of genes in geographic space indicate L. longipalpis of Brazil to be a single, but genetically heterogeneous, polymorphic species.

Genetic polymorphism of morphological and biochemical characters in a Natal, Brazil, population of Lutzomyia longipalpis (Diptera: Psychodidae)

The phlebotomine sand fly, Lutzomyia longipalpis, is the vector of visceral leishmaniasis in the New World. Variability in its tergal spot morphology has led to conflicting interpretations of the species status of the various forms. An L. longipalpis field population from eastern Brazil was found with three co-occurring morphological variations--1-spot, 2-spot, and an intermediate form. Genetic profiles were established for each form. Fifteen isoenzyme loci provided the data matrix for comparison of genetic variation among the forms. Spot patterns and isoenzyme frequencies fit Hardy-Weinberg expectations, and no significant differences in isoenzyme frequencies were associated with morphological phenotype. The spot phenotype appears to be a polymorphic character not related to genetic isolation or differentiation at the species level.

The effect of anti-sandfly saliva antibodies on Phlebotomus argentipes and Leishmania donovani

A study was undertaken to find the effect of repeated bites of the sandfly, Phlebotomus argentipes, on its host as well as on the vector itself. The study also aimed to find the effect of the immune serum on the parasite, Leishmania donovani, naturally transmitted by the vector. The hamster which was exposed to sandfly feeding showed good antibody titre against the sandfly salivary-gland secretion, which indicates that the salivary-gland secretion is immunogenic in nature. The result also revealed that the feeding attraction of the females, which has been expressed as the percentage of engorgement, gradually decreased as the mortality rate increased during the subsequent bites. Similar mortality rate was observed when the flies were fed with the immune sera through an artificial membrane feeding method. When the sandflies were fed both with the immune sera and the blood-parasite (L. donovani) suspension, in addition to the major loss of the number of vectors, there was an inhibition of development in the gut and a concomitant reduction in the migration of the parasite in the surviving females. These results indicate that the anti-sandfly saliva immune sera probably bind with the respective antigen-presenting sites of the sandfly salivary gland and, thus, cause the sandfly death. The possible explanation of the inhibition of the forward movement of the parasites is that the attraction of the parasites to the oesophagus, mediated by the sandfly saliva, is inhibited by the anti-saliva antibodies. The importance of anti-sandfly saliva antibodies as a tool of vector control and also to block the transmission of leishmaniasis has been indicated.

Patterns of genetic variability in colonized strains of Lutzomyia longipalpis (Diptera: Psychodidae) and its consequences

The genetic qualities of laboratory colonies of phlebotomine sand flies have not been compared with field specimens despite 1) probable genetic shifts due to the colonization process and 2) the problems associated with the extrapolation of experimental data derived from colonized organisms to field populations. The present study compared the genetic profiles of five laboratory colonies of geographic strains of the New World sand fly Lutzomyia longipalpis, and contrasted them with field populations. The profiles were based on the variability exhibited with polyacrylamide gels at 14 enzyme loci. A general pattern of a loss of infrequent alleles and decreased heterozygosity emerged as an apparent consequence of colonization. The average number of alleles per locus ranged from 1.2 to 1.6, and the average heterozygosity ranged from 4% to 11%. The field collection from Lapinha Caves (near Belo Horizonte, Brazil) averaged 2.1 alleles with a heterozygosity of 16%. In contrast, the LAPINHA laboratory colony established from that site 24 years earlier showed very low values (1.2 alleles/locus and 4% heterozygosity) and fixation for alleles not present or rare in the field collection from the same site. The genetic differences between the other Brazilian colonies and the Lapinha Caves field samples were due to presence of both different alleles and highly diverged allelic frequencies. Biological inferences based on colonized sand flies must be tempered by recognizing that the colony may represent a highly skewed genetic subsample of the L. longipalpis field genome.