Horizontal transfer of domains in ssrA gene among Enterobacteriaceae.

The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3' end than 5' end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.

Novel approaches on identification of conserved miRNAs for broad-spectrum Potyvirus control measures.

Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, tomato, yam, etc. Cumulatively, potyvirids cause a substantial economic loss. The major bottleneck in developing an efficient antiviral strategy is that viruses quickly evade host immunity owing to their higher mutation and recombination rates. Due to this reason, the emergence of newer and improved broad-spectrum approaches to combat viral infections is essential. The use of microRNA's (miRNA) to circumvent viral infection against animal viruses has been successfully employed. Fewer studies reported the development of efficient miRNA-based antivirus resistant strategies against plant viruses and none focused on multiple virus resistance. We focused on potyviruses since studies are limited and identification of conserved miRNAs among various host plants would be an initiative to design broad-spectrum antivirus strategies. In this study, we predicted evolutionarily conserved miRNAs by BLAST searching of reported miRNAs from 15 plants against the GSS and EST sequences of banana. A total of nine miRNAs were predicted and screened in nine diverse potyvirids' hosts (Banana, Tomato, Green gram, Jasmine, Chilli, Coriander, Onion, Rose and Colocasia) belonging to eight different orders (Zingiberales, Solanales, Fabales, Lamiales, Apiales, Asperagales, Rosales and Alismatales). Results suggested that miR168 and miR162 are conserved among all the selected plants. This comprehensive study laid the foundations to design broad-spectrum antivirus resistance using miRNAs. To conclude miR168 and miR162 are conserved among many plants and play a crucial role in evading virus infection which could be used as a potential candidate for developing antiviral strategies against potyvirid infections.

Soluble and membrane-bound interleukin (IL)-15 Rα/IL-15 complexes mediate proliferation of high-avidity central memory CD8+ T cells for adoptive immunotherapy of cancer and infections.

The lack of persistence of infused T cells is a principal limitation of adoptive immunotherapy in man. Interleukin (IL)-15 can sustain memory T cell expansion when presented in complex with IL-15Rα (15Rα/15). We developed a novel in-vitro system for generation of stable 15Rα/15 complexes. Immunologically quantifiable amounts of IL-15 were obtained when both IL-15Rα and IL-15 genes were co-transduced in NIH 3T3 fibroblast-based artificial antigen-presenting cells expressing human leucocyte antigen (HLA) A:0201, ß2 microglobulin, CD80, CD58 and CD54 [A2-artificial antigen presenting cell (AAPC)] and a murine pro-B cell line (Baf-3) (A2-AAPC15Rα/15 and Baf-315Rα/15 ). Transduction of cells with IL-15 alone resulted in only transient expression of IL-15, with minimal amounts of immunologically detectable IL-15. In comparison, cells transduced with IL-15Rα alone (A2-AAPCRα ) demonstrated stable expression of IL-15Rα; however, when loaded with soluble IL-15 (sIL-15), these cells sequestered 15Rα/15 intracellularly and also demonstrated minimal amounts of IL-15. Human T cells stimulated in vitro against a viral antigen (CMVpp65) in the presence of 15Rα/15 generated superior yields of high-avidity CMVpp65 epitope-specific T cells [cytomegalovirus-cytotoxic T lymphocytes (CMV-CTLs)] responding to ≤ 10- 13 M peptide concentrations, and lysing targets cells at lower effector : target ratios (1 : 10 and 1 : 100), where sIL-15, sIL-2 or sIL-7 CMV-CTLs demonstrated minimal or no activity. Both soluble and surface presented 15Rα/15, but not sIL-15, sustained in-vitro expansion of CD62L+ and CCR7+ central memory phenotype CMV-CTLs (TCM ). 15Rα/15 complexes represent a potent adjuvant for augmenting the efficacy of adoptive immunotherapy. Such cell-bound or soluble 15Rα/15 complexes could be developed for use in combination immunotherapy approaches.

Correlation of Histopathology and Radiological Findings Among the Diverse Breast Lesions in a Tertiary Care Centre.

Introduction Breast lumps in any age group are addressed cautiously to exclude the possibility of breast cancer. The clinical approach to breast lumps involves the "triple test" for cancer screening. The triple test includes clinical examination, imaging (mammogram or ultrasonogram), and tissue sampling (fine needle aspiration cytology (FNAC) and core needle biopsy). These tests happen in a sequential process, and it is important that their findings support the final diagnosis for accurate management of the patient. Aims and objectives This study aims to determine the correlation between the histopathological and radiological findings among the various breast lesions and describe the spectrum of breast lesions received in our center. Methods This is a retrospective observational study for a period of three years, from January 2020 to December 2022. The study included 400 patients who had undergone ultrasonography or mammograms for breast lumps, FNAC, core needle biopsy, or surgical resection. The data collected was analyzed for concordance and discordance status. Results A total of 400 cases were reviewed. There were 238 (59.5%) histologically confirmed benign breast lesions and 162 (40.5%) malignant lesions with their corresponding BI-RADS (Breast Imaging Reporting and Data System) scores. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy for the imaging modalities (ultrasonogram and mammogram) in diagnosing breast lesions were 95.06%, 94.96%, 92.77%, 96.58%, and 95%, respectively, which were comparable with other similar studies. The biological and immunohistochemical factors of all the invasive carcinomas were studied in detail. Conclusions Imaging modalities (ultrasonogram or mammogram) have good sensitivity and specificity in diagnosing breast lesions and can be reliably used as a preliminary test in breast lump evaluation. The BI-RADS score is a reliable indicator and can be considered for the effective follow-up or intervention of the breast lesion. In discordant cases, a repeated core needle biopsy or excision has to be recommended, as pathological diagnosis is the cornerstone of effective management. A good rapport between the surgeon, radiologist, and pathologist aids in effective feedback and learning for achieving diagnostic accuracy.

Biosorption of Rhodamine B onto novel biosorbents from Kappaphycus alvarezii, Gracilaria salicornia and Gracilaria edulis.

In the present investigation seaweeds of macroalgae like Kappaphycus alvarezii, Gracilaria salicornia and Gracilaria edulis used as novel biosorbent in native (KA, GS, GE) and ethanol modified (EKA, EGS, EGE) for Rhodamine B (RB) removal from aqueous solution in batch process. Effect of various biosorption parameters such as pH, initial concentration of RB, biosorbent dosage and contact time were studied. The maximum biosorption capacity determined as 9.84 (KA), 11.03 (GS), 8.96 (GE), 112.35 (EKA), 105.26 (EGS) and 97.08 mg/g (EGE), respectively towards the removal of RB from aqueous solutions. Better removal of RB was observed using EKA, EGS, and EGE biosorbents at 2.0 pH. The characterizations of the biosorbents were performed using Scanning Electron microscope and Fourier Transform Infrared Spectroscopy. Biosorption equilibrium data evaluated using Langmuir, Freundlich, Temkin, Dubinin-Radushkevich and Jovanovic isotherm model. The Langmuir isotherm model best suited the equilibrium data for all the biosorbents studied. The rate of RB removal subjected to kinetic analysis using pseudo-first-order, pseudo-second-order, intra-particle diffusion and Elovich models. Pseudo-second-order kinetic model better described the experimental data of the RB biosorption. Desorption studies performed using 0.1 M sodium hydroxide as eluting agents for regeneration and recycle analysis. The recyclability of the six biosorbents showed consistent biosorption capacity towards RB removal up to the entire three cycles. The studied biosorbents sourced from large volume and easily available, further biosorption performance indicated that the KA, GS, GE, EKA, EGS and EGE could be used as efficient, alternative and eco-friendly biosorbents for the removal of harmful dyes in the environment.

Artificial Antigen Presenting Cells: An Off the Shelf Approach for Generation of Desirable T-Cell Populations for Broad Application of Adoptive Immunotherapy.

Adoptive transfer of antigen specific T-cells can lead to eradication of cancer and viral infections. The broad application of this approach has further been hampered by the limited availability of adequate numbers of T-cells for treatment in a timely manner. This has led to efforts for the development of efficient methods to generate large numbers of T-cells with specificity for tumor or viral antigens that can be harnessed for use in cancer therapy. Recent studies have demonstrated that during encounter with tumor antigen, the signals delivered to T-cells by professional antigen-presenting cells can affect T-cell programming and their subsequent therapeutic efficacy. This has stimulated efforts to develop artificial antigen-presenting cells that allow optimal control over the signals provided to T-cells. In this review, we will discuss the cellular artificial antigen-presenting cell systems and their use in T-cell adoptive immunotherapy for cancer and infections.

Skin to serosa: scar endometrioma.

Extra pelvic endometriosis, an underappreciated and misdiagnosed gynaecological problem has been reported here for its rare location. Patient presented with swelling and cyclical pain over vertical scar (caesarean). Diagnosis was made on high index of clinical suspicion which was complimented by Magnetic Resonance Imaging (MRI). Scar endometrioma extended from the skin upto the uterine serosa which is extremely rare. Wide excision of endometrioma followed by mesh repair was done. Histopathology confirmed the diagnosis.

Automated multi-level pathology identification techniques for abnormal retinal images using artificial neural networks.

AIM: To automatically classify abnormal retinal images from four different categories using artificial neural networks with a high degree of accuracy in minimal time to assist the ophthalmologist in subsequent treatment planning. METHODS: We used 420 abnormal retinal images from four different categories (non-proliferative diabetic retinopathy, central retinal vein occlusion, central serous retinopathy and central neo-vascularisation membrane). Green channel extraction, histogram equalisation and median filtering were used as image pre-processing techniques, followed by texture-based feature extraction. The application of Kohonen neural networks for pathology identification was also explored. RESULTS: The approach described yielded an average classification accuracy of 97.7% with ±0.8% deviation for individual categories. The average sensitivity and the specificity values are 96% and 98%, respectively. The time taken by the Kohonen neural network to achieve these accurate results was 300±40 s for the 420 images. CONCLUSION: This study suggests that the approach described can act as a diagnostic tool for retinal disease identification. Simultaneous multi-level classification of abnormal images is possible with high accuracy using artificial neural networks. The results also suggest that the approach is time-efficient, which is essential for ophthalmologic applications.

Knowledge, beliefs, and health care practices relating to treatment of HIV in Vellore, India.

In India, little is known about health care-seeking behavior among HIV-infected individuals. Similarly, little is known about how HIV is being treated in the community, in particular by Indian Systems of Medicine (ISM) providers. Therefore, while ART implementation programs continue to expand, it is important to determine whether the knowledge, attitudes, and treatment practices of HIV-infected individuals and their health care providers are aligned with current treatment recommendations. We conducted in-depth qualitative interviews with persons with HIV (n = 9 men and 17 women), family members of persons with HIV (n = 14 men and 3 women), and ISM providers (n = 7). Many of the patients we studied turned at some point to ISM providers because they believed that such practitioners offer a cure for HIV. ISM treatments sometimes had negative impacts including side effects, unchecked progression of an underlying illness, and financial depletion. Indian women tended to be less knowledgeable about HIV and HIV treatments, and had less access to financial and other resources, than men. Finally, most of the ISM providers reported dangerous misconceptions about HIV transmission, diagnosis, and treatment. While the existence of ART in India is potentially of great benefit to those with HIV infection, this study shows that a variety of social, cultural and governmental barriers may interfere with the effective use of these therapies. Partnerships between the allopathic and traditional/complementary health sectors in research, policy, and practice are essential in building comprehensive HIV/AIDS treatment strategies.

Detection of in-vivo chloroquine resistance in Plasmodium falciparum from Rameswaram Island, a pilgrim centre in southern India.

Resistance to chloroquine (CQ) in Plasmodium falciparum is one of the main causes of the wide-spread resurgence of malaria in India and a challenge to the effective control of the disease. In the pilgrim centre of Rameswaram Island, malaria has persisted despite the various control measures undertaken over the years. When CQ resistance in Rameswaram was investigated in vivo, recrudescent parasitaemias were observed in 25 (58%) of the 43 study subjects who were given CQ and completed follow-up, all occurring between days 10 and 28 (late treatment failures). The results of the msp(1), msp(2) and glurp genotyping of paired samples of P. falciparum, collected on day 0 and the day of recrudescence from 23 of the apparent treatment failures, indicated that 21 (91%) of the 23 were probably true treatment failures. All of the paired samples harboured parasites with the K76T mutation in their pfcrt genes, and subsequent sequencing of nine day-0 samples revealed the SVMNT haplotype in all nine. This is the first report of in-vivo drug resistance in P. falciparum from Rameswaram Island. Such resistance, which is probably the result of the indiscriminate use of CQ and/or the import of malaria from mainland India, warrants a change in the drug regimen used locally for the first-line treatment of uncomplicated, P. falciparum malaria, to make treatment more effective and slow the development and spread of more foci of CQ resistance.

Polymorphism and domain variability of human killer cell inhibitory receptors.

Thirty-two different full-length cDNA clones for human killer cell inhibitory receptors (KIR) have been identified. They all belong to the immunoglobulin superfamily and encode mature proteins with one, two or three extracellular Ig domains. The inhibitory receptors have nearly identical transmembrane domains and cytoplasmic domains ranging in length from 76 to 95 amino-acid residues. The activating receptors have a characteristic transmembrane domain with a charged lysine residue and a short cytoplasmic tail without the protein tyrosine phosphatase binding motif I/VXYXXL present in the inhibitory receptors. Sequence analysis demonstrates that three clusters correspond to the inhibitory receptors of 58 kDa, while two clusters encode activating receptors of 50 kDa. Two other clusters correspond to the inhibitory receptors of 70 kDa and one cluster encodes genes with sequence homology to one of the two p70 clusters but contains the transmembrane and cytoplasmic domains characteristic of activating receptors. The data are consistent with a genomic organization of the KIR genetic region containing at least three KIR genes encoding receptors for each of the gene products of the HLA class I loci. Alternative mRNA splicing could be responsible for generation of activating or inhibitory receptors with the same extracellular domains. Separate genes encoding receptors with opposite function is, however, an equally likely possibility.

The killer cell inhibitory receptor genomic region on human chromosome 19q13.4.

Multiple genes encoding type I transmembrane molecules and belonging to the immunoglobulin superfamily have recently been localized to human chromosome 19q13.4. These include a family of genes encoding killer cell inhibitory receptors (KIR) expressed on natural killer (NK) cells and subsets of T-lymphocytes, immunoglobulin-like transcripts (ILT-1, -2 and 3) expressed on myeloid cells and subsets of lymphoid cells, the gp49 family of receptors expressed on mast cells and NK cells and the gene encoding human myeloid immunoglobulin A Fc receptor (CD89). The receptors have one to four extracellular immunoglobulin domains, and the ligands are known for some of these molecules. This includes the Fc alpha R and KIRs of the p58/p50 and p70/p70 delta, but the ligands for many others are unknown. Except for CD89, each subfamily of receptors exist, in two forms, of which one has a long cytoplasmic domain containing one to four immunoreceptor tyrosine-based inhibitory motifs (ITIM) and another form with a short cytoplasmic tail without ITIMs. ITIM-containing receptors can recruit cytoplasmic tyrosine phosphatases and provide inhibitory signals for cell activation, whereas receptors with a "short" tail induce activating signals. The 19q13.4 chromosomal region is therefore now emerging as the immunoglobulin superfamily linkage group of genes differentially expressed on hematopoietic cell lineages and encoding pairs of receptors with opposing effects on signal transduction pathways and effector functions in hematopoietic cells.

NK cell receptor gene of the KIR family with two IG domains but highest homology to KIR receptors with three IG domains.

The killer cell inhibitory receptors (KIRs) are surface glycoproteins expressed by natural killer (NK) cells and some T cells. They recognize polymorphic human HLA class I molecules. Two families of KIRs have been identified and named p58 and p70. The p58 family of genes encode type I membrane proteins with two extracellular immunoglobulin (Ig) domains, while the p70 genes have three Ig domains. We here report the cloning and characterization of a novel KIR cDNA obtained from tumor cell lines with NK reactivity (YT and NK-92). This gene is also expressed in the normal cell line NK 3.3 and in NK cells obtained from some but not all normal donors. The clone, KIR103AS, has an open reading frame consistent with a KIR with two extracellular Ig domains, a transmembrane region and a 114 amino acid long cytoplasmic domain containing a single src homology 2 (SH2) binding motif. The membrane distal Ig domain of KIR103AS has highest homology with the first Ig domain of p70 KIRs and differs significantly from the first Ig domain of p58 KIRs. The second, membrane proximal Ig domain of KIR103AS has similar and high homology with the membrane proximal Ig domains of both p70 and p58 KIRs. The extracellular domains of KIR103AS therefore share characteristic features with both p70 and p58 genes: the domain structure is identical to p58 KIRs but the sequence homology matches closely with p70 KIRs. The putative transmembrane and cytoplasmic domains are distinctly different from all previously reported KIR cDNAs.

Distribution of HLA antigens in the native South Indian Tamil Hindus.

Blood samples from 240 unrelated healthy Tamil-speaking South Indian Hindus residing in Madras (capital city of Tamil Nadu, India) were screened for HLA-A and -B antigen profiles. Antigen, gene and haplotype frequencies were calculated and compared with the literature. Tamil Hindus lack A31, A32, Aw33, B16, B21 and Bw41. However, except for minor differences (low occurrence of Aw19 antigen), the South Indians show similarity to North Indian and other Indian groups. The data confirm once more that the haplotype A1-B17 is characteristic of Indians.

Nucleotide and amino acid sequence alignment for human killer cell inhibitory receptors (KIR), 1998.

We present alignments of nucleotide sequences and deduced amino acid sequences for all currently identified killer cell inhibitory receptors (KIR). The genes for these receptors have been localized to human chromosome 19q13.4 and constitute a large gene family. They all encode structures typical of type I transmembrane molecules belonging to the immunoglobulin superfamily (Ig-SF). Extensive polymorphism exists within the genes and many of the currently identified cDNA clones represent alternatively spliced forms of previously reported full-length clones. The sequence alignments have been posted on the World Wide Web and are accessible at the Tissue Antigens web site at: http://www.tissue-antigens.dk/kir-align.html. The alignments will be updated at intervals.

Multiple transcripts of the killer cell immunoglobulin-like receptor family, KIR3DL1 (NKB1), are expressed by natural killer cells of a single individual.

Natural killer (NK) cells express receptors that are ligands for HLA class I molecules. One family of such NK receptors are called killer cell immunoglobulin-like receptors (KIR). The KIR2DL (inhibiting) and KIR2DS (activating) molecules recognize HLA-Cw antigens, while the KIR3DL (inhibiting) and KIR3DS (activating) molecules interact with HLA-B antigens with the Bw4 epitope. No NK receptors have yet been identified for HLA-B antigens with the Bw6 epitope. We here report four novel full length cDNA transcripts encoding KIR3DL1-like proteins isolated from mRNA obtained from interleukin-2-activated peripheral blood mononuclear cells of a donor with two HLA-B antigens expressing the Bw6 epitope. These four transcripts belong to a group of closely related KIR3DL1-like molecules initially defined by the cDNA clone NKB1. They differ from NKB1 by only 2 to 7 nucleotides and have 2 to 4 codon changes within the 423 residues of the mature protein. All transcripts were detected by RT-PCR, together with the previously reported KIR3DL1 transcripts, NKB1 and KIR3DL1v, in mRNA from NK cells of 10 of 10 donors tested, and in seven of eight NK clones derived from one donor. Functionally, the KIR3DL1 receptors expressed by five DX9-positive NK clones were not inhibiting NK-mediated cytotoxicity when tested against the 721.221 B-lymphoblastoid cell line expressing a HLA-B antigen with Bw4 epitope. All NK clones were, however, inhibited by 721.221 cells transfected with a HLA-B antigen carrying the Bw6 epitope.

Characterization of a novel, human cytotoxic lymphocyte-specific serine protease cDNA clone (CSP-C).

A human cDNA clone encoding a novel serine protease, cytotoxic serine protease-C(CSP-C), has been isolated from a cDNA library prepared from recombinant interleukin-2 (IL-2)-activated lymphocytes of a patient with a large granular lymphoproliferative disorder. The clone has a 741-base pair open reading frame encoding a putative 246-amino acid protein. The protein sequence contains the catalytic charge relay system characteristic of a serine protease and the conserved N-terminal amino acid sequence of the mature cytotoxic lymphocyte serine proteases found in both mouse and human. The amino acid sequence of CSP-C has 71% identity with the previously reported cytotoxic serine protease-B(CSP-B)/human lymphocyte protease (HLP)/SECT and 57% identity with the granulocyte-specific serine protease cathepsin G. The homology with another lymphocyte-specific serine protease, human Hanukah factor (HF)/Granzyme A was 41%. The transcript is expressed in lymphocytes stimulated with IL-2 or IL-2 plus phytohemagglutinin (PHA). CSP-C is not expressed in B-lymphoblastoid cell lines or in the T-leukemia cell line MOLT4. The cDNA sequence suggests that the protein is expressed as a prepropeptide, as has been found in the other murine and human serine proteases of lymphocyte origin. It has recently been reported that human chromosome 14q11, in addition to containing the genes encoding cytotoxic serine protease B (CSP-B), cathepsin G, and the T-cell receptor alpha and delta genes, also includes an additional genomic DNA clone which cross-hybridized with CSP-B and cathepsin G, cathepsin-like gene-2 (CGL-2). It is likely that the CSP-C cDNA clone reported in this study corresponds to CGL-2.

Distribution of HLA antigens in Kotas and Badagas of the Nilgiri Hills, South India.

Blood samples from 103 Kotas and 58 Badagas residing in the Nilgiri Hills, South India, were examined for HLA-A and -B antigen profiles. The Kota group was characterized by fairly high frequencies of A2 and B7 antigens as well as the haplotype A2-B7. The frequencies of Aw19, A28, and Bw22 were found to be higher in Badagas than in Kotas. The results are compared with the literature available on other Indian populations.