Molecular characterization of vermicompost-derived IAA-releasing bacterial isolates and assessment of their impact on the root improvement of banana during primary hardening

The hardening step of micropropagation is crucial to make the in vitro raised plants mature and further enhancing their survivability in the external environment. Auxin regulates various root physiological parameters in plant systems. Therefore, the present study aimed to assess the impact of three vermicompost-derived IAA-releasing microbial strains, designated S1, S2, and S3, as biofertilizers on in vitro raised banana plantlets during primary hardening. The High-Performance Thin-Layer Chromatography (HPTLC) analysis of these strains revealed a higher IAA content for S1 and S2 than that of S3 after 144 h of incubation. In total, seven different treatments were applied to banana plantlets, and significant variations were observed in all plant growth parameters for all treatments except autoclaved cocopeat (100%) mixed with autoclaved vermicompost (100%) at a 1:1 ratio. Among these treatments, the application of S3 biofertilizer: autoclaved cocopeat (1:1), followed by S2 biofertlizer: autoclaved cocopeat (1:1), was found to be better than other treatments for root numbers per plant, root length per plant, root volume, and chlorophyll content. These findings have confirmed the beneficial effects of microbial strains on plant systems and propose a link between root improvement and bacterial auxin. Further, these strains were identified at the molecular level as Bacillus sp. As per our knowledge, this is the first report of Bacillus strains isolated from vermicompost and applied as biofertilizer along with cocopeat for the primary hardening of banana. This unique approach may be adopted to improve the quality of plants during hardening, which increases their survival under abiotic stresses.

Exploring the Charge Density Wave Phase of 1T-TaSe_{2}: Mott or Charge-Transfer Gap?

1T-TaSe_{2} is widely believed to host a Mott metal-insulator transition in the charge density wave (CDW) phase according to the spectroscopic observation of a band gap that extends across all momentum space. Previous investigations inferred that the occurrence of the Mott phase is limited to the surface only of bulk specimens, but recent analysis on thin samples revealed that the Mott-like behavior, observed in the monolayer, is rapidly suppressed with increasing thickness. Here, we report combined time- and angle-resolved photoemission spectroscopy and theoretical investigations of the electronic structure of 1T-TaSe_{2}. Our experimental results confirm the existence of a state above E_{F}, previously ascribed to the upper Hubbard band, and an overall band gap of ∼0.7  eV at Γ[over ¯]. However, supported by density functional theory calculations, we demonstrate that the origin of this state and the gap rests on band structure modifications induced by the CDW phase alone, without the need for Mott correlation effects.

Revisiting the oldest manure of India, Kunapajala: Assessment of its animal waste recycling potential as a source of plant biostimulant

India's oldest documented manure, most commonly referred to as Kunapajala, has a long history of over 1,000 years in crop cultivation. Kunapajala is primarily an in-situ decomposition technology of animal waste and can potentially provide an eco-friendly pipeline for recycling bio-waste into essential plant nutrients. This traditional animal manure, in addition, also contains dairy excreta (e.g., feces and urine), dairy products (e.g., milk and ghee), natural resources (e.g., honey), broken seeds or grains, and their non-edible by-product waste. Here, we aimed to assess the waste recycling and plant biostimulant potential of Kunapajala prepared from livestock (e.g., Black Bengal goats) or fish (e.g., Bombay duck) post-processed wastes over different decomposition periods, e.g., (0, 30, 60, and 90-days). In this study, an in-situ quantification of livestock- (lKPJ) and fish-based Kunapajala (fKPJ) reveals a dynamic landscape of essential plant primary nutrients, e.g., (0.70 > NH4-N < 3.40 g•L−1), (100.00 > P2O5 < 620.00 mg•L−1), and (175.00 > K2O < 340.00 mg•L−1), including other physico-chemical attributes of Kunapajala. Using correlation statistics, we find that the plant-available nutrient content of Kunapajala depicts a significant (p < 0.0001) transformation over decomposition along with microbial dynamics, abundance, and diversities, delineating a microbial interface to animal waste decomposition and plant growth promotion. Importantly, this study also reports the indole 3-acetic acid (IAA) content (40.00 > IAA < 135.00 mg•L−1) in Kunapajala. Furthermore, the bacterial screening based on plant growth-promoting traits and their functional analyses elucidate the mechanism of the plant biostimulant potential of Kunapajala. This assay finally reports two best-performing plant growth-promoting bacteria (e.g., Pseudomonas chlororaphis and Bacillus subtilis) by the 16S ribotyping method. In support, in-planta experiments have demonstrated, in detail, the bio-stimulative effects of Kunapajala, including these two bacterial isolates alone or in combination, on seed germination, root-shoot length, and other important agronomic, physio-biochemical traits in rice. Together, our findings establish that Kunapajala can be recommended as a source of plant biostimulant to improve crop quality traits in rice. Overall, this work highlights Kunapajala, for the first time, as a promising low-cost microbial technology that can serve a dual function of animal waste recycling and plant nutrient recovery to promote sustainable intensification in agroecosystems.

Rationale, study design and methodology of the LANDMARC trial: a 3-year, pan-India, prospective, longitudinal study to assess management and real-world outcomes of diabetes mellitus

AIM

India contributes towards a large part of the worldwide epidemic of diabetes and its associated complications. However, there are limited longitudinal studies available in India to understand the occurrence of diabetes complications over time. This pan-India longitudinal study was initiated to assess the real-world outcomes of diabetes across the country.

METHODS

The LANDMARC study is the first prospective, multicentre, longitudinal, observational study investigating a large cohort of people with type 2 diabetes mellitus across India over a period of 3 years. The primary objective of this ongoing study is to determine the proportion of people developing macrovascular diabetes complications over the duration of the study (36 months ± 45 days) distributed over seven visits; the secondary objective is to evaluate microvascular diabetes complications, glycaemic control and time-to-treatment adaptation or intensification. Overall, 6300 participants (aged 25-60 years) diagnosed with type 2 diabetes for at least 2 years will be included from 450 centres across India. Data will be recorded for baseline demographics, comorbidities, glycaemic measurements, use of anti-hyperglycaemic medications and any cardiovascular or other diabetes-related events occurring during the observational study period.

CONCLUSIONS

The LANDMARC study is expected to reveal the trends in complications associated with diabetes, treatment strategies used by physicians, and correlation among treatment, control and complications of diabetes within the Indian context. The findings of this study will help to identify the disease burden, emergence of early-onset complications and dose titration patterns, and eventually develop person-centred care and facilitate public health agencies to invest appropriate resources in the management of diabetes. (Trial Registration No: CTRI/2017/05/008452).

Acquired Lymphangiectasia of the Scrotum

A 56-year-old man presented with multiple, skin-colored, raised eruptions of the scrotum that had been present for 2 years. Their onset had been gradual, and they had been increasing in size, resulting in cosmetic disfigurement. A year previously, he had been operated on for a bilateral vaginal hydrocele with partial excision and eversion of the sac (Jabouley method).¹ There had been no extramarital or unprotected sexual contact, other hospitalizations, or major surgery, swelling of the legs, or long periods of incumbency. Cutaneous examination revealed multiple, discrete and/or coalescing verrucous papules distributed on the upper portion of the scrotum and associated with edema of the penis (Figure 1). The inguinal lymph nodes were not enlarged. Complete blood counts and ultrasonography of the abdomen were normal. Tissue sections stained with hematoxylin and eosin showed hyperkeratosis and multiple ectatic vessels, primarily confined to the papillary dermis, abutting the overlying epidermis, and demarcated by a single endothelial lining. The dilated vessels contained homogenous eosinophillic material (Figure 2).

Assessing the impact of a program for late surgical intervention in early-blind children

OBJECTIVE

Many blind children in the developing world are unable to obtain timely treatment due to lack of financial and medical resources. Can public health programs that identify and treat such children several years after the onset of blindness enhance their quality of life? The notion that visual development is subject to an early 'critical period' argues against this possibility. However, there are inadequate empirical data from humans on this issue. To address this need, we examined the quality of life of children living in India and who were treated for early-onset blindness (before one year of age), due to cataracts or corneal opacities.

STUDY DESIGN

Survey study.

METHODS

As part of an ongoing scientific effort named Project Prakash, we screened over 40,000 children in rural northern India to identify those suffering from early-onset blindness. They were provided eye surgeries in a tertiary care ophthalmic center in New Delhi. We subsequently surveyed 64 Prakash children, ranging in age from 5 to 22 years and obtained their responses on a multi-dimensional quality of life questionnaire.

RESULTS

Nearly all of the subjects indicated that their quality of life had improved after treatment. Children reported marked enhancement in their mobility, independence, and safety, and also in social integration. Surprisingly, we found no significant correlations between quality of life metrics and factors such as age at treatment, gender, time since treatment, and pre-surgery and post-surgery acuity.

CONCLUSIONS

A key question for public health policy makers is whether a program of surgical intervention for older blind children is likely to be beneficial, or if the resources are better spent on rehabilitation via vocational training and assistive devices. The marked improvements in quality of life we find in our data strongly argue for the provision of surgical care regardless of a child's age.

Elimination and molecular identification of endophytic bacterial contaminants during in vitro propagation of Bambusa balcooa

Bambusa balcooa is an economically important, multipurpose bamboo species, decidedly used in construction industry. Availability of natural bamboo is depleting very rapidly due to accelerated deforestation and its unrestrained use. The large number and timely supply of saplings are the need of the hour for the restoration of bamboo stands. Micropropagation, being the potent alternative for season independent rapid regeneration, is restricted in bamboo because of endophytic contamination. An in vitro attempt has been taken to overcome the endophytic contamination by using broad spectrum antibiotics as surface sterilant as well as a media component. Ampicillin sodium salt (5 mg/ml for 30 min) as a surface sterilant was found as the best treatment for high bud breaking (80%) coupled with high branching and low contamination (20%) but it was found ineffective to control the contamination during multiplication stage. Then, two endophytes were isolated and minimum inhibitory concentration was determined through antibiotic susceptibility test for successful eradication at multiplication stage. Finally, contamination free cultures were obtained when streptocycline (100 μg/ml) and gentamicin sulphate (75 μg/ml) were added into the medium. The two isolated endophytes, BB1 and BB2, were identified through 16S rDNA techniques and NCBI-BLAST algorithm with 99% sequence similarity with those of Janibacter sp. (KX423734) and Serratia marcescens strain (KX423735). To our knowledge, this is the first report for B. balcooa where antibiotics were used as surface sterilant as well as medium component, to control endophytic bacterial contaminants, followed by their identification.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species--Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast.

Chromatin Immunoprecipitation (ChIP) Assay in Candida albicans

Chromatin immunoprecipitation (ChIP) is a widely used technique which can determine the in vivo association of a specific protein on a particular DNA locus in the genome. In this method cross-linked chromatin is sheared and immunoprecipitated with antibodies raised against a target protein of interest. The end result of this process is the enrichment of DNA fragments associated with the desired protein. Thus, interactions between proteins and genomic loci in cellular context can be determined by this technique. Here, we are describing a ChIP protocol that is optimized for Candida albicans. The protocol requires 4-5 days for completion of the assay and has been used to produce robust ChIP results for diverse proteins in this organism and its related species including Candida dubliniensis and Candida tropicalis.

Clinicohematological profiles of hospitalized patients with dengue in kolkata in 2012 epidemic, west bengal

Dengue usually presents itself with subclinical or mild infection to full blown dengue fever (DF) to dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). In Kolkata, dengue started in 1824 followed by five epidemics that occurred in 1836, 1906, 1911, 1923 and 2005. The aim of this investigation is to study the clinicohematological correlation of all patients with respect to their gender that were admitted to "Kali Pada Chowdhury Medical College and Hospital" during 2012 epidemic. Amongst a total of 1237 dengue patients (either dengue Nonstructural protein1 antigen or dengue Immunoglobulin M positive) that were admitted to the hospital, 11 patients died within 48 hours of admission; hence they have been excluded from the study. DHF patients were divided into males and females. During admission, proper history, physical examinations with necessary hematological investigations were performed and repeated again after 24-48 hours. After collection of all the reports, correlations of the collected data were carried out. 170 and 1056 patients were diagnosed with DF and DHF respectively; significant symptoms and signs were headache, backache/myalgia, nausea/vomiting, loose motion and anorexia hepatomegaly. Hemoglobin level was low in females, leucopenia observed in 79.52% patients and thrombocytopenia seen in 57.58% and 86.13% patients during and 24-48 hours after admission respectively. 96 and 97 DHF patients showed evidences of ascites and plural effusion respectively. In 2012 epidemic, 86.13% patients suffered from DHF, headache, backache, nausea/vomiting, loose motion and anorexia were predominant symptoms. Significant number of patients had leucopenia; only few showed evidence of plasma leakage.

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Cryptococcus neoformans var. grubii is a major human pathogen responsible for deadly meningoencephalitis in immunocompromised patients. Here, we report the sequencing and annotation of its genome. Evidence for extensive intron splicing, antisense transcription, non-coding RNAs, and alternative polyadenylation indicates the potential for highly intricate regulation of gene expression in this opportunistic pathogen. In addition, detailed molecular, genetic, and genomic studies were performed to characterize structural features of the genome, including centromeres and origins of replication. Finally, the phenotypic and genome re-sequencing analysis of a collection of isolates of the reference H99 strain resulting from laboratory passage revealed that microevolutionary processes during in vitro culturing of pathogenic fungi can impact virulence.

Basal cell carcinoma, oculo-cutaneous albinism and actinic keratosis in a native Indian

The report highlights the occurrence of basal cell carcinoma in a native Indian with oculo-cutaneous albinism, an association not frequently encountered. The clinical and histopathological features, which assisted to form the diagnosis, are outlined. A high degree of suspicion and timely recognition of the potentially aggressive neoplasm, under this unusual circumstance, is the key to its diagnosis.

Origin and evolution of syphilis: drifting myth

The venereal form of treponematosis, caused by the spirochete Treponema pallidum, plagued every major city in the preantibiotic era. "Civilization means syphilization," was an idea touted by Richard von Krafft-Ebing in the late 19th, and early 20th centuries that the effects of modern life make men more susceptible to syphilis and other diseases. Christopher Columbus was thought of as an importer of syphilis to Europe. Because his serendipitous voyages to the New World initiated the process of Spanish colonization, which foreshadowed general European colonization of the New World, it is difficult to rule out the cultural and political animosity created by Columbus and his men. These recent revelations are intriguing and may create dialogue that may subsequently challenge the age-old theory of "East to West" spread of venereal syphilis. This contribution warrants the continuation of study in this direction, taking into account skeletal studies that utilized radiocarbon dating technique and the phylogenetic analysis of the bacterial strains, offering a possible consensus on the origin and evolution of syphilis.

Alopecia universalis in a case of systemic lupus erythematosus

We report a case of systemic lupus erythematosus (SLE) who presented with alopecia universalis. MR, a 23 years female patient was admitted with alopecia universalis and other features of SLE like peripheral arthritis, fever, nephritis, butterfly rash over the malar regions, positive ANA and anti-ds DNA antibodies. There was a gap of four years between the onset of alopecia universalis and other clinical features of SLE. The alopecia was of non-scarry variety and responded to systemic and topical steroids.

The interferon- and differentiation-inducible p202a protein inhibits the transcriptional activity of c-Myc by blocking its association with Max

p202a is a murine protein that is induced during the fusion of myoblasts to myotubes and can also be induced by interferon. Even 2-3-fold overexpression of p202a in cells retards proliferation. p202a was shown to modulate transcription by binding, and inhibiting the activity of several transcription factors including c-Fos, c-Jun, AP-2, E2F1, E2F4, NF-kappaB, MyoD, and myogenin. Here we report that p202a also bound the c-Myc protein in vitro and in vivo; the C-terminal p202a b segment bound the C-terminal basic region helix-loop-helix-leucine zipper (bHLHLZ) region of c-Myc. The transfection of a p202a expression plasmid inhibited the c-Myc-dependent expression of reporter plasmids in transient assays; moreover, overexpression of p202a in stable cell lines decreased the endogenous levels of mRNAs whose expression is driven by c-Myc. These effects of p202a are consistent with our finding that the binding of p202a to c-Myc inhibited the binding of c-Myc to Max in vitro and in vivo. p202a also inhibited the c-Myc-induced anchorage-independent growth and apoptosis of Rat-1 cells. The inhibition of c-Myc-dependent transcription, proliferation, and apoptosis by p202a is in line with the involvement of p202a in differentiation.

MyoD-dependent induction during myoblast differentiation of p204, a protein also inducible by interferon

p204, an interferon-inducible p200 family protein, inhibits rRNA synthesis in fibroblasts by blocking the binding of the upstream binding factor transcription factor to DNA. Here we report that among 10 adult mouse tissues tested, the level of p204 was highest in heart and skeletal muscles. In cultured C2C12 skeletal muscle myoblasts, p204 was nucleoplasmic and its level was low. During myoblast fusion this level strongly increased, p204 became phosphorylated, and the bulk of p204 appeared in the cytoplasm of the myotubes. Leptomycin B, an inhibitor of nuclear export that blocked myoblast fusion, inhibited the nuclear export signal-dependent translocation of p204 to the cytoplasm. The increase in the p204 level during myoblast fusion was a consequence of MyoD transcription factor binding to several MyoD-specific sequences in the gene encoding p204, followed by transcription. Overexpression of p204 (in C2C12 myoblasts carrying an inducible p204 expression plasmid) accelerated the fusion of myoblasts to myotubes in differentiation medium and induced the fusion even in growth medium. The level of p204 in mouse heart muscle strongly increased during differentiation; it was barely detectable in 10. 5-day-old embryos, reached the peak level in 16.5-day-old embryos, and remained high thereafter. p204 is the second p200 family protein (after p202a) found to be involved in muscle differentiation. (p202a was formerly designated p202. The new designation is due to the identification of a highly similar protein-p202b [H. Wang, G. Chatterjee, J. J. Meyer, C. J. Liu, N. A. Manjunath, P. Bray-Ward, and P. Lengyel, Genomics 60:281-294, 1999].) These results reveal that p204 and p202a function in both muscle differentiation and interferon action.

Characteristics of three homologous 202 genes (Ifi202a, Ifi202b, and Ifi202c) from the murine interferon-activatable gene 200 cluster

The Ifi202 gene is part of the interferon-activatable murine gene 200 cluster on chromosome 1. Ifi202 encodes the p202 protein whose overexpression is growth inhibitory and which can bind and inhibit the activity of numerous transcription factors including c-Jun, c-Fos, NF-kappaB, E2F-1, E2F-4, MyoD, and myogenin. We report here the exon-intron structure of Ifi202 and the discovery of Ifi202b and Ifi202c, close homologs of Ifi202 (whose designation we now change to Ifi202a). Ifi202a, b, and c were colocalized to chromosome 1 bands H4-H5 by fluorescence in situ hybridization. Ifi202b encodes p202b, which is interferon-inducible and differs from p202a in only 7 of 445 amino acids. 202b mRNA is constitutively expressed in tissues in which 202a mRNA is expressed. Ifi202c is apparently an unexpressed pseudogene. In murine embryonic fibroblasts (MEFs) from 129 mice, the level of 202b mRNA is approximately half that of 202a mRNA. We knocked out the Ifi202a gene from 129 mice. The expression of 202b mRNA, but not 202a mRNA, persisted in the knockout mice and their MEFs at the same level as in wildtype mice. However, in MEFs from the knockout mice, the constitutive and interferon-induced levels of p202b were approximately as high as the constitutive and the interferon-induced levels of p202a plus p202b, respectively, in MEFs from wildtype mice. These findings suggest dosage compensation at the posttranscriptional level. This might account for the apparent lack of phenotype of the knockout mice.