An alternate statistical method for dealing outliers in perennial crop experiment

A statistical method based on Robust ANOVA to handle outliers induced high coefficient of variation (CV) in pooled (2011-2018) analysis of long-term Mango cv. Totapuri rootstock trail was suggested. Based on the results, it was concluded that the rootstock treatment T3: Olour (average yield over the period 2011 to 2018 as 57.21 kg/tree) as the best. Precision gained as estimated by reduction in CV (%) was in the range of 11.01 % to 78.9 %. SAS IML codes were built-in for analysis. Hence, this study calls for employing robust ANOVA approach in testing the significance of evaluated treatments in a designed perennial crop experiment with high CV that would have reduced the sensitivity of testing the significance of treatment differences otherwise

Comparison of leaf volatile aroma constituents and phenolic acid profiles of the seedling originated polyembryonic mango (Mangifera indica L.) genotypes

In mango, leaf and fruit volatile aroma profiles are variety specific which can be used as fingerprint of a variety. Such biochemical markers can also discriminate the nucellar and zygotic seedlings in polyembryonic mango varieties. In order to validate the applicability of volatile as well as phenolic acid profiles as biomarkers, the open pollinated seedlings of three polyembryonic varieties of mango were compared with their mother trees. Leaf volatile and phenol acid profiling were done using Gas Chromatography/Mass Spectrometry (GCMS) and Liquid Chromatography/Mass Spectrometry (LCMS) methods respectively. The sesquiterpene hydrocarbons were the most abundant in all the genotypes studied. Monoterpenoids were the major compounds in cultivars Vellaikolumban and Olour, while the sesquiterpenoids were the major compounds in cv. Turpentine. While terpinolene was the major monoterpenoid compound in Vellaikolumban and limonene in cv. Olour, the sesquiterpene á-gurjunene was the major compound in cv. Turpentine. Volatile profiling showed clear differences between the varieties but was similar within a variety. Among the 15 phenolic acids quantified in the leaves, P-coumaric acid, gallic acid, and ferulic acids were predominant whereas, vanillic acid, syringic acid, gentisic acid, benzoic acid, and sinapic acids were low in quantity. Phenolic acid profile did not show significant diversity among the varieties and therefore cannot be used for identification of varieties. The volatile profiling can be used for the identification and differentiation of polyembryonic mango genotypes

Effect of plasma lysozyme on live Mycobacterium tuberculosis

The role of plasma lysozyme of normal healthy subjects (NHS, n = 12) and active pulmonary tuberculosis (ATB) patients (n = 15) on the innate immune mechanism was studied by the binding activity of lysozyme on live Mycobacterium tuberculosis. Plasma samples of NHS and ATB patients treated with live M. tuberculosis for 4 h and 24 h time points showed a significant decrease in the plasma lysozyme level when compared to the untreated samples (4 h, P < 0.001; 24 h, P < 0.001). Pretreatment of live M. tuberculosis with plasma of NHS and ATB patients showed a trend in the reduction of viability of live M. tuberculosis. Moreover, M. tuberculosis pretreated plasma of NHS showed a trend towards an increased spontaneous as well as antigen-induced lymphocyte response when compared to ATB plasma. The enzymatic action of the lysozyme and other enzymes on the cell wall may induce M. tuberculosis to release some antigenic components which may be immunogenic and induce lymphocyte proliferation. The present study suggests that lysozyme and other enzymes may play an important role in the first line defence, i.e. the innate immunity, against M. tuberculosis infection

HLA-DR2 subtypes & immune responses in pulmonary tuberculosis

Background & objectives: HLA-DR2 has been shown to be associated with the susceptibility to pulmonary tuberculosis and altered antibody and lymphocyte response in pulmonary tuberculosis. In the present study, the influence of DR2 subtypes on antibody titre and lymphocyte response ,to Mycobacterium tuberculosis culture filtrate antigens (10 μg/ml) was studied in 22 patients with active pulmonary TB (ATB), 50 inactive (cured) TB (ITB) patients and 36 healthy control subjects. Methods. HLA-DR2 gene was amplified by polymerase chain reaction (PCR) and dot-blotted. Genotyping of DRBl*1501, *1502, *1503, *1601 and *1602 was carried out using sequence specific oligonucleotide probes (SSOPs) and detected by chemiluminescence method. Antibody titre as well as lymphocyte response to M.tuberculosis antigens were measured by enzyme linked immunosorbent assay (ELISA) and lymphocyte transformation test (LTT) respectively. Results: The allele frequency of DRB1*15Ol was significantly increased in pulmonary tuberculosis patients as compared to controls (P<0.05). No marked difference in the antibody titre and lymphocyte response to M. tuberculosis antigens was observed between the DRBl *1501, *1502 and *1503 positive or negative controls, ATB and ITB patients. DRBl *1501 and *1502 positive as well as negative ATB patients showed a higher antibody titre as compared to controls and ITB patients. ITB patients with *1502 showed a higher lymphocyte response as compared to *1502 positive controls (P<0.001) and ATB patients (P<0.05). Similarly, an increased lymphocyte response was observed in *1501, and *I503 negative ITB patients compared to *1501 and *1503 negative controls and ATB patients. Interpretation & conclusion: The present study revealed that DRBl *1501 may be associated either alone or with other DR2 alleles, with the susceptibility to pulmonary tuberculosis. None of the DR2 alleles influenced the antibody and lymphocyte response to M tuberculosis culture filtrate antigens. This suggested that HLA-DR2 gene/gene products as a whole may influence the immune response in pulmonary tuberculosis

Vitamin D receptor and interleukin-1 receptor antagonist gene polymorphism in spinal tuberculosis

Our earlier studies revealed that both MHC (Major Histocomptibility Complex) and non-MHC genes are associated with the susceptibility to pulmonary tuberculosis (TB). To find out whether non-MHC genes such as vitamin D receptor (VDR) and interleukin-1 receptor antagonist (IL-1RA) genes are associated with the susceptibility to spinal TB (extrapulmonary form of TB), the present study was carried out in spinal TB patients (n=66) and spouses of TB patients (spinal-TB and pulmonary-TB) ( n = 80) (family contacts). A trend towards an increased per cent genotype frequency of IL-1RA genotype variant 22 (12.1%) was seen in spinal TB patients when compared to the controls (3.8%) (spouses of the patients) (P=0.057; odds ratio 3.5). No difference was observed in the frequency of VDR genotypes between the overall spinal TB patients and the family contacts. However, the VDR mutant genotype tt was seen at a higher frequency in female patients with TB spine (TBS) (12.8%) than female contacts (4.2%) ( P >0.05 not significant; odds ratio 3.5). Among the contacts, a significantly increased frequency of wild type genotype TT (wild homozygotes) was seen in female contacts (55.1%) than male contacts (16.1%) (P =0.0012). Similarly a significant decrease in tt genotype was seen in female contacts (4.1%) than male contacts (25.8%) (P=0.012). The present study suggests that IL-1RA genotype 22 may be associated with the susceptibility to spinal TB. Moreover, vitamin D receptor tt genotype may be associated with the susceptibility to spinal TB in female patients. The study reveals that multicandidate genes may be associated with the susceptibility to spinal TB

Influence of non-MHC genes on lymphocyte response to Mycobacterium tuberculosis antigens and tuberculin status in Pulmonary tuberculosis

Background & objectives : Major histocompatibility complex (MHC) genes are known to influence the immune functions. In the present study, the influence of non-MHC genes such as mannose binding protein (MBP), vitamin D receptor (VDR) and interleukin-1 receptor antagonist (IL-IRA) gene polymorphisms on lymphocyte response to Mycobacterium tuberculosis culture filtrate antigen (10 μg/ml) was studied in 44 patients with active pulmonary TB and the family contacts (35) and in 32 normal healthy subjects. The influence of these gene polymorphisms on tuberculin (1TU of PPD of M. tuberculosis) reactivity status in 146 pulmonary TB patients was also studied. Methods : The MBP and VDR genes were amplified using polymerase chain reaction (PCR) and genotyping was carried out using sequence specific oligonucleotide probes by dot blot and IL-1RA by agarose gel electrophoresis. Results : A significantly decreased lymphocyte response to M. tuberculosis antigen was seen in pulmonary TB patients positive for functional mutant homozygotes of MBP (00) compared to heterozygote carriers (AO; P<0.02) and wild homozygotes (AA; P<0.01). The variant mutant genotype (tt) of VDR gene was associated with an increased lymphocyte response in control subjects compared to active TB patients with tt genotype (P<0.05). Heterozygote carriers of MBP (AO) were associated with a significantly (P<0.001) decreased tuberculin reactivity compared to wild homozygotes (AA). The VDR genotype Tt (heterozygote carrier) was associated with an increased tuberculin reactivity in female TB patients as compared to male patients (P<0.001). Interpretation & conclusions : The present study suggested that MBP and VDR genes influence the cell mediated immune response in pulmonary TB patients. Non-MHC genes along with HLA-Class II genes/gene products may be playing an immunoregulatory role in the mechanism of susceptibility/resistance to tuberculosis

HLA-DR phenotypes and IgG, IgA and IgM antibody responses to Mycobacterium tuberculosis culture filtrate and 30 kDa antigens in pulmonary tuberculosis

The role of HLA-DR genetic make-up on the IgG, IgA and IgM antibody response to Mycobacterium tuberculosis culture filtrate and 30 kDa antigens was studied in pulmonary tuberculosis. The study was carried out in HLA-DR typed active pulmonary tuberculosis (ATB) patients (n = 37), inactive (cured) pulmonary tuberculosis (ITB) patients (n = 79) and normal healthy subjects (NHS; n = 46). In ATB and ITB (cured) patients, IgG antibody (optical density at 490 nm for 1 : 3200 dilution) as measured by enzyme-linked immunosorbent assay was the predominant one than IgA and IgM antibodies. Increased IgG antibody titre to culture filtrate (P = 0.03) and decreased titre to 30 kDa antigen were observed with HLA-DR1-positive ATB patients than non-DR1 (ATB) patients. Moreover, HLA-DR4- and HLA-DR6-positive ATB patients showed trends toward an increased IgG antibody response to 30 kDa antigen than HLA-DR4- and HLADR6- negative (ATB) patients respectively. Significantly increased IgA antibody to 30 kDa antigen was observed with HLA-DR1-positive ATB patients than non-DR1 patients (P = 0.03). The study suggests that multiple HLA-DR molecules may regulate the IgG and IgA antibody responses to various proteins of M. tuberculosis. Moreover, HLA-DR phenotypes and increased IgG and IgA antibody titres may be useful to differentiate M. tuberculosis-infected subjects from normal subjects and cured patients with the same HLA-DR phenotypes or genetic make-up

HLA antigen profile in pulmonary tuberculosis patients and their spouses

HLA-A, -B, -DR and -DQ antigen profile was studied in pulmonary tuberculosis patients (n=209) and their spouses (family contacts; n=50) and healthy volunteers (n=72). An increased frequency of HLAA- 10, B7, B15, DR2 and DQ1 was seen in the pulmonary-TB (PTB) patients when compared to the total control subjects (n=122). However, a significant increase was seen only with HLA-DR2 (P < 0.001; Pc < 0.01; Relative Risk 2.3) and -DQ1 (P < 0.005; Pc<0.015; Relative Risk 2.8). Among the spouses and the corresponding patients, a similar increase of HLA-DR2 was seen. A decreased frequency of HLA-A19, B8, B17, B35, DR5 and DR6 were seen in PTB as compared to control groups. The present study suggested that HLA-DR2 and DQ1 genes/gene products may be associated with the susceptibility to tuberculosis either alone or in combination with other HLA or non-HLA genes

HLA-DR phenotypes and lymphocyte response to M. tuberculosis antigens and in cured spinal tuberculosis patients and their contacts

Background: Our earlier studies on Human Leucocyte Antigens (HLA) in pulmonary tuberculosis patients revealed the association of HLA-DR2 antigen with susceptibility to pulmonary TB and DR2 antigen has been shown to influence the immunity to tuberculosis. Objectives: The present study was carried out to find out whether HLA-DR antigens are associated with susceptibility to spinal tuberculosis. Moreover, the role of HLA-DR antigens on lymphoproliferative response to Mycobacterium tuberculosis culture filtrate antigens was studied using Lymphocyte Transformation Test (LTT). Material and Methods: HLA-DR genotyping and lymphoproliferative response was carried out in 63 cured spinal TB patients and 63 control subjects (spouses of pulmonary and spinal TB patients). Results: A trend towards an increased frequency of HLA-DR9 antigen was observed in spinal TB patients compared to controls. A significantly decreased lymphocyte response to M. tuberculosis antigens was observed in HLA-DR9 antigen positive control subjects compared to HLA- DR9 antigen negative subjects (P=0.0009) whereas increased response was observed with DR9 positive cured spinal TB patients compared to HLA-DR9 antigen negative patients. Further, HLADR3 antigen positive patients showed a decreased lymphocyte response compared to HLA-DR3 antigen negative patients (P<0.05). Conclusion: The study suggests that HLA-DR9 antigen either alone or in combination with other HLA antigen as lhplotype and non-HLA genes may be associated with susceptibility to spinal TB and play a regulatory role on the immune response to M. tuberculosis in spinal tuberculosis patients

NRAMP1 gene polymorphism in pulmonary and spinal tuberculosis

NRAMP1 gene polymorphisms such as 823 C/T (exon 8), deletion of TGTG in the 3'-UTR (3¢ untranslated region) and D543N G/A (exon 15) were studied to find out whether the gene polymorphic variants are associated with the susceptibility or resistance to tuberculosis (TB). The study was carried out in pulmonary (n = 100) and spinal TB patients (n = 57) and control subjects (n = 112). No difference was observed in the variant genotype frequencies of NRAMP1 – 823 C/T, TGTG+/del and D543N G/A polymorphisms. However, a trend towards an increased frequency of the variant genotype 823 C/T (heterozygotes) was observed in pulmonary TB patients than control and spinal TB patients (odds ratio (OR) : 1.6; confidence interval (CI): 0.74–3.4). A trend towards an increased frequency of the variant genotype TGTG del/del of 3'-UTR was observed in control subjects than pulmonary and spinal TB patients (OR : 0.48; CI: 0.10–1.78; OR: 0.42; CI: 0.04– 2.12, respectively). The above trends were not significant. The study suggests that NRAMP1 gene may not be associated with the susceptibility to pulmonary and spinal TB in the Indian population. Major Histocompatibility Complex (MHC) and other non- MHC gene polymorphic variants may be associated