Assessment of homozygosity in transgenic plants using selectable markers

Production of homozygous transgenic plants is a prerequisite for the phenotypic analysis and/or for the commercial release of transgenic plants for cultivation. Here we present a simple protocol for the selection of homozygous transgenics using antibiotics as a selectable marker. The protocol has been used to select homozygous rice transgenic plants using hygromycin antibiotic. However, the described protocol can be used for selction of homozygous in any transgenic plants using a appropriate selectable marker. For complete details on the use and execution of this protocol, please refer to Passricha et al. (2016).1.

An exopolysaccharide-producing novel Agrobacterium pusense strain JAS1 isolated from snake plant enhances plant growth and soil water retention

A peculiar bacterial growth was very often noticed in leaf-initiated tissue cultures of Sansevieria trifasciata, a succulent belonging to the Asparagaceae family. The isolate left trails of some highly viscous material on the walls of the suspension vessels or developed a thick overlay on semisolid media without adversities in plant growth. FTIR identified this substance to be an extracellular polysaccharide. Various morphological, biochemical tests, and molecular analyses using 16S rRNA, atpD, and recA genes characterized this isolate JAS1 as a novel strain of Agrobacterium pusense. Its mucoidal growth over Murashige and Skoog media yielded enormous exopolysaccharide (7252 mg l^-1), while in nutrient agar it only developed fast-growing swarms. As a qualifying plant growth-promoting bacteria, it produces significant indole-3-acetic acid (86.95 mg l^-1), gibberellic acid (172.98 mg l^-1), ammonia (42.66 µmol ml^-1). Besides, it produces siderophores, 1-aminocyclopropane-1-carboxylic acid deaminase, fixes nitrogen, forms biofilms, and productively solubilizes soil inorganic phosphates, and zinc. Under various treatments with JAS1, wheat and chickpea resulted in significantly enhanced shoot and root growth parameters. PGP effects of JAS1 positively enhanced plants' physiological growth parameters reflecting significant increments in overall chlorophyll, carotenoids, proline, phenols, flavonoids, and sugar contents. In addition, the isolated strain maintained both plant and soil health under an intermittent soil drying regime, probably by both its PGP and EPS production attributes, respectively.

Arsenite provides a selective signal that coordinates arsenate uptake and detoxification through the regulation of PHR1 stability in Arabidopsis

In nature, plants acquire nutrients from soils to sustain growth, and at the same time, they need to avoid the uptake of toxic compounds and/or possess tolerance systems to cope with them. This is particularly challenging when the toxic compound and the nutrient are chemically similar, as in the case of phosphate and arsenate. In this study, we demonstrated that regulatory elements of the phosphate starvation response (PSR) coordinate the arsenate detoxification machinery in the cell. We showed that arsenate repression of the phosphate transporter PHT1;1 is associated with the degradation of the PSR master regulator PHR1. Once arsenic is sequestered into the vacuole, PHR1 stability is restored and PHT1;1 expression is recovered. Furthermore, we identified an arsenite responsive SKP1-like protein and a PHR1 interactor F-box (PHIF1) as constituents of the SCF complex responsible for PHR1 degradation.We found that arsenite, the form to which arsenate is reduced for compartmentalization in vacuoles, represses PHT1;1 expression, providing a highly selective signal versus phosphate to control PHT1;1 expression in response to arsenate. Collectively, our results provide molecular insights into a sensing mechanism that regulates arsenate/phosphate uptake depending on the plant's detoxification capacity.

Transfer of stabilising mutations between different secondary active transporter families

Integral membrane transporters play essential roles in the movement of substrates across biological membranes. One approach to produce transporters suitable for structural studies is to introduce mutations that reduce conformational flexibility and increase stability. However, it can be difficult to predict which mutations will result in a more stable protein. Previously, we stabilised the uric acid‐xanthine transporter, UapA, a member of the SLC23 family, through introduction of a single‐point mutation, G411V, trapping the protein in the inward‐facing conformation. Here, we attempted to stabilise the structurally related BOR1 transporter from Arabidopsis thaliana, a member of the SLC4 family, by introducing the equivalent substitution. We identified possible residues, P362 and M363, in AtBOR1, likely to be equivalent to the G411 of UapA, and generated four mutants, P362V or L and M363F or Y. Stability analysis using heated Fluorescent Size Exclusion Chromatography indicated that the M363F/Y mutants were more stable than the WT AtBOR1 and P362V/L mutants. Furthermore, functional complementation analysis revealed that the M363F/Y mutants exhibited reduced transport activity compared to the P362V/L and WT proteins. Purification and crystallisation of the M363F/Y proteins yielded crystals that diffracted better than WT (5.5 vs 7 Å). We hypothesise that the increased bulk of the F and Y substitutions limits the ability of the protein to undergo the conformational rearrangements associated with transport. These proteins represent a basis for future studies on AtBOR1.

Determination of Boron Content Using a Simple and Rapid Miniaturized Curcumin Assay

To determine boron quantity in soil, water and biological samples, several protocols are available. Colorimetric assays are the simplest and cheapest methods which can be used to determine boron concentration. However, published protocols do not give straightforward guidance for beginners to adopt these protocols for routine use in the laboratory. Based on a previously published available procedure, we present a detailed and modified version of a curcumin based colorimetric protocol to determine boron concentration extracted from any sample. Our modified protocol is able to determine up to 0.2 nmole of Boron in a sample volume of 300 μl.

Cytokinin Determines Thiol-Mediated Arsenic Tolerance and Accumulation

The presence of arsenic in soil and water is a constant threat to plant growth in many regions of the world. Phytohormones act in the integration of growth control and stress response, but their role in plant responses to arsenic remains to be elucidated. Here, we show that arsenate [As(V)], the most prevalent arsenic chemical species in nature, causes severe depletion of endogenous cytokinins (CKs) in the model plant Arabidopsis (Arabidopsis thaliana). We found that CK signaling mutants and transgenic plants with reduced endogenous CK levels showed an As(V)-tolerant phenotype. Our data indicate that in CK-depleted plants exposed to As(V), transcript levels of As(V)/phosphate-transporters were similar or even higher than in wild-type plants. In contrast, CK depletion provoked the coordinated activation of As(V) tolerance mechanisms, leading to the accumulation of thiol compounds such as phytochelatins and glutathione, which are essential for arsenic sequestration. Transgenic CK-deficient Arabidopsis and tobacco lines show a marked increase in arsenic accumulation. Our findings indicate that CK is an important regulatory factor in plant adaptation to arsenic stress.

Functional genomics of fuzzless-lintless mutant of Gossypium hirsutum L. cv. MCU5 reveal key genes and pathways involved in cotton fibre initiation and elongation

Background

Fuzzless-lintless cotton mutants are considered to be the ideal material to understand the molecular mechanisms involved in fibre cell development. Although there are few reports on transcriptome and proteome analyses in cotton at fibre initiation and elongation stages, there is no comprehensive comparative transcriptome analysis of fibre-bearing and fuzzless-lintless cotton ovules covering fibre initiation to secondary cell wall (SCW) synthesis stages. In the present study, a comparative transcriptome analysis was carried out using G. hirsutum L. cv. MCU5 wild-type (WT) and it’s near isogenic fuzzless-lintless (fl) mutant at fibre initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and SCW synthesis (20 dpa) stages.

Results

Scanning electron microscopy study revealed the delay in the initiation of fibre cells and lack of any further development after 2 dpa in the fl mutant. Transcriptome analysis showed major down regulation of transcripts (90%) at fibre initiation and early elongation (5 dpa) stages in the fl mutant. Majority of the down regulated transcripts at fibre initiation stage in the fl mutant represent calcium and phytohormone mediated signal transduction pathways, biosynthesis of auxin and ethylene and stress responsive transcription factors (TFs). Further, transcripts involved in carbohydrate and lipid metabolisms, mitochondrial electron transport system (mETS) and cell wall loosening and elongation were highly down-regulated at fibre elongation stage (5–15 dpa) in the fl mutant. In addition, cellulose synthases and sucrose synthase C were down-regulated at SCW biosynthesis stage (15–20 dpa). Interestingly, some of the transcripts (~50%) involved in phytohormone signalling and stress responsive transcription factors that were up-regulated at fibre initiation stage in the WT were found to be up-regulated at much later stage (15 dpa) in fl mutant.

Conclusions

Comparative transcriptome analysis of WT and its near isogenic fl mutant revealed key genes and pathways involved at various stages of fibre development. Our data implicated the significant role of mitochondria mediated energy metabolism during fibre elongation process. The delayed expression of genes involved in phytohormone signalling and stress responsive TFs in the fl mutant suggests the need for a coordinated expression of regulatory mechanisms in fibre cell initiation and differentiation.

Anti-toxoplasma serotitres in uveitis and ocular toxoplasmosis

This study was based on anti-toxoplasma serotitres obtained from 80 normal healthy adults and 103 consecutive patients with anterior, posterior and panuveitis over a 42 month period. Twelve out of 80 (15%) normal healthy sera were found to have low titres (1:64 to 1:256), while 3 (3.8%) had high titres (1:1024 or higher). The distribution of serotitres in patients with clinical toxoplasmosis was significantly different from the population sample (p less than 0.001, chi-squared test). Similarly, the distribution of serotitres in patients with posterior uveitis (of which 28 out of 54 were clinically ocular toxoplasmosis) having serotitres of 1:1024 or greater, was found to be significantly different from the normal population (p less than 0.001, Chi-squared test), but not statistically different from those with clinical ocular toxoplasmosis. Hence, anti-toxoplasma serotitre is useful as a diagnostic screening tool only in patients with posterior uveitis. It is also useful in confirming cases of suspected clinically positive ocular toxoplasmosis in our local population.

Anti-toxoplasma antibodies in healthy adults and in different patient categories

This study analyzes the anti-toxoplasma sero-titres and prevalence rates in normal healthy adults and in patients presenting with different symptom-complexes. The study was based on sera from 80 normal healthy adults and 2,185 patient sera samples from 2,032 patients (from various clinics and hospitals in Singapore) being investigated for the diagnosis or exclusion of toxoplasmosis, over a 42-month study period. About 15% of the healthy adults were found to have low IgG antibody titres (1:64 to 1:256), while 3.8% had high IgG titres (1:1024 or higher). Interestingly, among the patients investigated for toxoplasmosis: i) more than 20% of those presenting with lymphadenopathy (usually cervical) had antibody titres more than or equal to 1:1024; ii) more than half of all patients with an antibody titre of 1:4096, and more than three-quarters of all patients with a titre exceeding 1:4096 had presented with lymphadenopathy; iii) about 20% of those presenting with ocular symptoms had low antibody titres of 1:64 or 1:256, whereas 7% had higher titres. Malay (p less than 0.01) and Indian (p less than 0.05) patients had significantly higher seropositive rates than the Chinese. In particular, the Malays (p less than 0.00001) and Indians (p less than 0.01) had significantly higher incidence of low-positive titres (1:64, 1:256); conversely the Chinese patients had a significantly higher (p less than 0.01) incidence of high-positive titres (1:4096 or higher). Finally, the epidemiology and clinical profiles of patients presenting with acute toxoplasmic lymphadenitis are contrasted with that of patients presenting with ocular manifestations of congenital toxoplasmosis.

Four patients in Singapore with anti-Golgi antibodies

Serum specimens for anti-nuclear fluorescence tests are routinely received in our laboratory. Four specimens were spotted to be negative for anti-nuclear fluorescence but positive for fluorescence characteristic of that caused by anti-golgi antibodies. (a) Patient A had acute glomerulonephritis; (b) Patient B had acute viral hepatitis; (c) Patient C had deep vein thrombosis; and (d) Patient D had non-Hodgkin's lymphoma. The relevance and possible aetiology of anti-golgi antibodies are also discussed.

A review of 58 patients in Singapore with significantly high anti-Toxoplasma serotitres

Over a 42-month period, 58 patients presenting at the Singapore General Hospital were identified to have IgG anti-Toxoplasma serotitres of 1:1024 or higher by the indirect immunofluorescence test. This retrospective study examines the clinical presentation and management of these 58 patients. About 60% of these 58 patients had presented with lymphadenopathy, 20% with ocular symptoms and 14% with bad obstetric history. Almost all patients with IgG anti-Toxoplasma serotitres exceeding 1:1024 had presented with lymphadenopathy (with a modal titre of 1:4096). In contrast, most of the patients who presented with ocular symptoms or bad obstetric history had lower modal titres. The majority of patients who had presented with lymphadenopathy were Chinese, aged 21 to 35. Typically, they presented with a painless, mobile, solitary cervical node of three to four weeks duration as the only symptom, had biopsies where the histopathology was suggestive of toxoplasmosis, received no treatment and experienced no sequelae. The study concludes that: acute toxoplasmosis is common in Singapore and presents typically as asymptomatic cervical lymphadenopathy in a young Chinese; the incidence of congenital infection is also believed to be high, based on the number of cases presenting with fetal wastage and the prevalence of ocular toxoplasmosis; pigs in Singapore may constitute an important reservoir for the transmission of this disease to man.

The role of counterimmunoelectrophoresis in the identification of antibodies to extractable nuclear antigens

Antibodies to saline-extractable nuclear antigens are hallmarks of autoimmune diseases including systemic lupus erythematosus (SLE), mixed connective tissue disease, progressive systemic sclerosis and Sjogren's syndrome. In our laboratory, we use counterimmunoelectrophoresis as a screening test and immunodiffusion as a confirmatory test to identify these autoantibodies. This study examines the drawbacks of such an approach. Though 17 out of 19 sera that formed ribonuclease sensitive lines with rabbit thymus extract on counterimmunoelectrophoresis were confirmed to have anti-RNP by immunodiffusion, sera of several different autoantibody specificities were seen to form ribonuclease resistant precipitin lines with the thymus extract on counterimmunoelectrophoresis. Having screened sera to have autoantibodies by counterimmunoelectrophoresis, the identity of some of these autoantibodies were not confirmed because of the poor sensitivity of immunodiffusion or because inappropriate controls had been used for the confirmatory immunodiffusion test. To check these drawbacks and to obviate the need for a confirmatory test, a modification of the current approach is suggested.

A study of the P blood group system in the Singaporean population

The P blood-group system was discovered by Landsteiner and Levine in 1927. This study delineates: a) The ethnic group specific distribution patterns of the P1 blood group antigen in the population of Singapore. b) The occurrence rate of the anti-P1 antibody in the same population. In the blood donor population, the estimated incidence of the P1-negative phenotype was calculated to be 75%. Though the percentage of P1-negative individuals among the Chinese did not differ significantly from that for the Malays, it was significantly higher than that for the Indians (P less than 0.01). The weighted average incidence of anti-P1 in the blood-donor population over the period 1982-1987 was calculated to be 9.14 per 100,000. For the patients, the average incidence of the anti-P1 antibody was calculated to be about 13.9 per 100,000 patients. The Malays were noted to have the highest incidence of anti-P1 antibody despite the occurrence of a higher proportion of P1-negatives among the Chinese.

Relation of antinuclear fluorescence patterns and titres to autoantibody prevalence

Different profiles of antinuclear antibodies (ANAs) have been found to be associated with different connective tissue diseases. Though several techniques have been developed to detect ANA, indirect antinuclear immunofluorescence (ANF) continues to be the most widely used and accepted. This study assesses the role of ANF as a screening test. The ANF patterns of 428 patients were studied. About 23% of patients with homogenous ANF patterns and 13% with speckled patterns were eventually shown to have raised anti-dsDNA titres. The percentage of patients harbouring raised titres of anti-dsDNA and the absolute titres were both seen to rise with the ANF titres. None of the patients with low ANF titres (1:40) harboured antibodies to extractable nuclea antigens (ENAs) whereas with increasing ANF titres the incidence of these autoantibodies was also seen to rise. Finally, it was noted that more than 80% of patients with high ANF titres demonstrated autoantibodies to ENA and/or dsDNA.

A study of the Lewis blood group system in the Singapore population

The purpose of this retrospective study is to delineate: a) The ethnic group specific distribution patterns of the various Lewis phenotypes in our population in Singapore. b) The occurrence rates of the various anti-Lewis antibodies in our population. The approximate frequencies of the Lewis A-B-, Lewis A-B+ and Lewis A + B- phenotypes in the blood-donor population were estimated to be about 10%, 48% and 42% respectively. It was evident that frequency of the Lewis A-B- phenotype was highest among the Malays, being almost 3 times more frequent than it was among the Chinese (P less than 0.01). The anti-Lewis antibodies were noted to be the commonest irregular antibodies seen in our blood donor population, with an occurrence rate of about 127 per 100,000. Likewise, from 1982 to 1987, the anti-Lewis antibodies were also noted to be the most frequently encountered antibodies in our patient population, accounting for nearly 60% of all cases. Although the Malays comprised only about 15% of the Singaporean population, they accounted for as much as 42.9% of all patients with anti-Lewis antibodies. Similarly, out of all 76 blood donors in 1987 with anti-Lewis antibodies, 50% were found to be Malays although they comprised only 14.28% of the donor population. It was also interesting to note that a sizeable proportion of all patients with anti-Lewis antibodies were pregnant women with or without obstetric complications.

Evaluation of an ELISA method for the measurement of antibodies to dsDNA

Anti-dsDNA is found in 60-70% of patients with active, untreated systemic lupus erythematosus (SLE) and its detection serves as an important tool in the diagnosis and monitoring of these patients. This study evaluates the use of an Enzyme Linked Immunosorbent Assay (Elisa) to detect these antibodies. Its performance is also compared to the older, but established, method of detecting anti-dsDNA using Crithidia luciliae. The sera of the 56 normal healthy blood donors revealed a mean anti-dsDNA titre of 0.93mg% with a standard deviation of 0.23mg%. All 14 patients found to be negative by the Elisa method and 10 of the 11 patients found to have borderline anti-dsDNA Elisa titres were negative by immunofluorescence. 35 patients were found to harbour raised titres of anti-dsDNA by the Elisa method. All patients found to have anti-dsDNA titres exceeding 2mg% by the Elisa test were also positive by immunofluorescence. In fact, those with very high titres by the Elisa test were also strongly (titre greater than 1:100) positive by immunofluorescence. As a measurement of the kit's accuracy, the percentage of recovery of the activity of known amounts of antibody in a specimen fell within the range of about 89-104%. As a measurement of the kit's reproducibility, the coefficient of variation in the assayed titres of sample replicates was found to be 7.5% for within-batch assays and 9.7% for between-batch assays. The Elisa assay compared favourably to the immunofluorescence test in terms of enhanced sensitivity, quantitative approach with an objective end-point and the large number of samples that may be assayed simultaneously.

The distribution of the ABO genotypes and phenotypes in Singapore in 1987

The aims of this study are to determine for the 3 main ethnic groups in Singapore: a) the ABO phenotype distribution in 1987 b) the A, B and O gene frequencies c) the proportion of A and B group individuals who are homozygous using (i) temporal studies (trial & error) (ii) the derived A and B gene frequencies This paper presents the method of study and the results obtained using a sample of 39,019 blood donors in 1987. The opportunity has also been taken to compare the data derived in this study with that quoted in 2 previous studies.