Utility of a multiple serum biomarker test to monitor remission status and relapse in dogs with lymphoma undergoing treatment with chemotherapy.

A blinded retrospective study was conducted to investigate remission and recurrence of lymphoma in dogs receiving chemotherapy. The objective was to compare clinicians' assessment using palpation and cytology to the results of serum biochemical tests for haptoglobin (Hapt) and C-reactive protein (C-RP). These biochemical test results were combined using a diagnostic algorithm developed using data from 344 individual dogs. This multivariate approach, termed the canine lymphoma blood test (cLBT), was used to follow 57 dogs during and after treatment. cLBT of remission and recurrence compared well with clinicians' assessment and differentiated dogs in remission and those with recurring disease before appearance of lymphadenopathy (P < 0.001). The cLBT demonstrated prognostic potential based on pre-treatment values on dogs with shorter survival times and on those achieving the lowest cLBT score during treatment that showed longer survival times. The test, therefore, demonstrates potential to assist in monitoring treatment of canine lymphoma.

Computational diagnosis and risk evaluation for canine lymphoma.

The canine lymphoma blood test detects the levels of two biomarkers, the acute phase proteins (C-Reactive Protein and Haptoglobin). This test can be used for diagnostics, for screening, and for remission monitoring as well. We analyze clinical data, test various machine learning methods and select the best approach to these oblems. Three families of methods, decision trees, kNN (including advanced and adaptive kNN) and probability density evaluation with radial basis functions, are used for classification and risk estimation. Several pre-processing approaches were implemented and compared. The best of them are used to create the diagnostic system. For the differential diagnosis the best solution gives the sensitivity and specificity of 83.5% and 77%, respectively (using three input features, CRP, Haptoglobin and standard clinical symptom). For the screening task, the decision tree method provides the best result, with sensitivity and specificity of 81.4% and >99%, respectively (using the same input features). If the clinical symptoms (Lymphadenopathy) are considered as unknown then a decision tree with CRP and Hapt only provides sensitivity 69% and specificity 83.5%. The lymphoma risk evaluation problem is formulated and solved. The best models are selected as the system for computational lymphoma diagnosis and evaluation of the risk of lymphoma as well. These methods are implemented into a special web-accessed software and are applied to the problem of monitoring dogs with lymphoma after treatment. It detects recurrence of lymphoma up to two months prior to the appearance of clinical signs. The risk map visualization provides a friendly tool for exploratory data analysis.

Arsenate exposure affects amino acids, mineral nutrient status and antioxidants in rice (Oryza sativa L.) genotypes.

Simulated pot experiments were conducted on four rice (Oryza sativa L.) genotypes (Triguna, IR-36, PNR-519, and IET-4786) to examine the effects of As(V) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. Rice genotypes responded differentially to As(V) exposure in terms of amino acids and antioxidant profiles. Total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. While, most of the essential amino acids increased in all cultivars except IR-36, glutamic acid and glycine increased in IET-4786 and PNR-519. The level of nonprotein thiols (NPTs) and the activities of superoxide dismutase (SOD; EC 1.15.1.1), glutathione reductase (GR; EC 1.6.4.2) and ascorbate peroxidase (APX; EC 1.11.1.11) increased in all rice cultivars except IET-4786. A significant genotypic variation was also observed in specific arsenic uptake (SAU; mg kg(-1)dw), which was in the order of Triguna (134) > IR-36 (71) > PNR-519 (53) > IET-4786 (29). Further, application of As(V) at lower doses (4 and 8 mg L(-1) As) enhanced the accumulation of selenium (Se) and other nutrients (Fe, P, Zn, and S), however, higher dose (12 mg L(-1) As) limits the nutrient uptake in rice. In conclusion, low As accumulating genotype, IET-4786, which also had significantly induced level of essential amino acids, seems suitable for cultivation in moderately As contaminated soil and would be safe for human consumption.

Differential transcriptional expression following thidiazuron-induced callus differentiation developmental shifts in rice.

Very little is known about molecular events associated with callus differentiation in indica rice. The genes expressed differentially during shoot meristem initiation were identified on genomic arrays applied to efficiently regenerating rice calli. A thidiazuron (TDZ; N-phenyl-N-thiadiazol-1,2,3-5,ylurea)-dependent regeneration protocol was developed for efficient embryogenesis in indica rice. The regenerating embryogenic calli induced by TDZ for 10 days showed transcriptional modulation of a number of genes associated with photosynthesis, hormone metabolism, plant development, signal transduction, light response, and plant defense. Eighteen candidate miRNAs were predicted to target the genes expressed differentially in the embryogenic calli grown in TDZ-containing medium. The majority of the photosynthesis-related genes up-regulated in differentiating calli were not expressed or were down-regulated in developing seeds and inflorescences. Most of the genes down-regulated in differentiating calli were up-regulated in developing seeds. The transcriptome of differentiating callus most closely resembled that of the germinating whole seed.

Arsenic affects mineral nutrients in grains of various Indian rice (Oryza sativa L.) genotypes grown on arsenic-contaminated soils of West Bengal.

The exposure of paddy fields to arsenic (As) through groundwater irrigation is a serious concern that may not only lead to As accumulation to unacceptable levels but also interfere with mineral nutrients in rice grains. In the present field study, profiling of the mineral nutrients (iron (Fe), phosphorous, zinc, and selenium (Se)) was done in various rice genotypes with respect to As accumulation. A significant genotypic variation was observed in elemental retention on root Fe plaque and their accumulation in various plant parts including grains, specific As uptake (29-167 mg kg(-1) dw), as well as As transfer factor (4-45%). Grains retained the least level of As (0.7-3%) with inorganic As species being the dominant forms, while organic As species, viz., dimethylarsinic acid and monomethylarsonic acid, were non-detectable. In all tested varieties, the level of Se was low (0.05-0.12 mg kg(-1) dw), whereas that of As was high (0.4-1.68 mg kg(-1) dw), considering their safe/recommended daily intake limits, which may not warrant their human consumption. Hence, their utilization may increase the risk of arsenicosis, when grown in As-contaminated areas.

Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba.

Monopartite begomoviruses comprise DNA-A as the main genome and associated satellite DNAs. Viral DNA extracted from guar (Cyamopsis tetragonoloba) showing leaf curl symptoms exhibited positive amplification of coat protein (CP) gene of DNA-A component, suggesting the presence of begomovirus. Full length DNA-A was amplified by primer pair re-designed from CP gene nucleotide sequence. The associated alphasatellite and betasatellite DNA molecules were amplified and sequenced, confirming the presence of monopartite begomovirus. Sequence comparisons showed 89% identity with other begomoviruses. The Neighbor-Joining tree based on full length DNA-A nucleotide sequence showed that the guar infecting begomovirus clustered separately from other known begomoviruses. The betasatellite shared a high (96%) nucleotide identity to Cotton leaf curl Multan betasatellites. The alphasatellite showed 91% nucleotide identity to alphasatellite associated with begomovirus infecting Okra. Recombination analyses showed three recombinant fragments in DNA-A, two in betasatellite, and four in alphasatellite. The results suggest that the begomovirus identified in this study was a new recombinant virus. Its name was proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).

p38 MAP kinase regulation of AP-2 binding in TGF-beta1-stimulated chondrogenesis of human trabecular bone-derived cells.

Collagenase-treated, explanted human trabecular-bone chips are an excellent source of osteoblast-like cells. We have recently shown the multiple differentiation potential of these cells; in addition to osteogenesis and adipogenesis, these cells also undergo chondrogenesis when maintained as high-density pellet cultures (250,000 cells/pellet) in a serum-free, chemically defined medium stimulated with TGF-beta1 (10 ng/mL). In this investigation, we have analyzed how transactivating nuclear transcription factors, specifically AP-2 and SP-1, may interact with common cis-acting elements found in the regulatory region of cartilage-specific genes as part of the signal transduction mechanism of TGF-beta1 and p38 during chondrogenesis of human trabecular bone-derived multipotential cells. Both TGF-beta1 stimulation and p38 MAP kinase activation affect the binding of AP-2 as well as SP-1 to oligonucleotides with sequence similarity to the overlapping AP-2/SP-1 sites found in the putative 52-bp immediate upstream regulatory region and the 5'-untranslated region of the human aggrecan gene. Electrophoretic mobility shift assays show that TGF-beta1 treatment of the bone-derived cells inhibits AP-2 DNA binding but enhances the DNA binding ability of SP-1. Additionally, treatment of these TGF-beta1-stimulated cells with p38 MAP kinase inhibitor, SB203580, rescued the AP-2 DNA binding but did not affect SP-1 DNA binding. These findings indicate that AP-2 DNA binding is the target of both TGF-beta1 and p38 MAP kinase signaling pathways and suggest a possible signal transduction cascade whereby TGF-beta1 induction of chondrogenesis involves the activation of p38 MAP kinase and the subsequent inhibition of DNA binding by AP-2, thereby preventing the transcriptional repression of the aggrecan gene.

Sequence architecture downstream of the initiator codon enhances gene expression and protein stability in plants.

Nucleotide positions conserved on the 3' side of the initiator codon ATG and the corresponding N-terminal amino acid residues in a number of highly abundant plant proteins were identified by computational analysis of a dataset of highly expressed plant genes. The reporter genes uidA and gfp were modified to introduce these features. Insertion of GCT TCC TCC after the initiator codon ATG augmented expression for both the reporter genes. The insertion of each successive codon improved the expression of beta-glucuronidase (GUS) in an incremental fashion in transient transformation of tobacco (Nicotiana tabacum) leaves. The insertion of alanine-serine (Ser)-Ser resulted in about a 2-fold increase in the stability of GUS. However, this did not account for the 30- to 40-fold increase in GUS activity between the constructs coding for methionine-alanine-Ser-Ser-GUS and the native enzyme. Substitution of the codon for Ser at the third amino acid residue with synonymous codons reduced GUS expression. The results suggest a role for the conserved nucleotides in the +4 to +11 region in augmenting posttranscriptional events in the expression of genes in plants.

The delta-endotoxin proteins accumulate in Escherichia coli as a protein-DNA complex that can be dissociated by hydrophobic interaction chromatography.

The insecticidal protein CryIAc accumulated to form inclusion bodies in Escherichia coli upon overexpression of the cloned gene. The solubilized inclusion bodies contained the delta-endotoxin in association with DNA fragments of about 25 kb. The protein-DNA complex could be dissociated and the delta-endotoxin purified by hydrophobic interaction chromatography on phenyl-Sepharose. The DNA was washed out in the high-salt buffer while the delta-endotoxin was bound to the matrix and was eluted at 4 degrees C by a stepwise decreasing potassium chloride gradient. The DNA-protein complex also contained plasmids harbored by the host strain. The plasmid DNA associated with the complex became competent to transform E. coli only after it was dissociated from the delta-endotoxin. The hydrophobic interaction chromatography provides an efficient method for the purification of DNA-free activated toxin.

The effect of heparin, caffeine and calcium ionophore A23187 on in vitro induction of the acrosome reaction in frozen-thawed bovine and caprine spermatozoa.

The effect of heparin (5 IU), caffeine (5 mM) and calcium-ionophore A23187 (0.1 mM) on motility and in vitro induction of the acrosome reaction in glass wool filtered frozen-thawed bull and goat semen was studied. The motile spermatozoa fraction was obtained after glass wool filtration of frozen-thawed semen. The seminal plasma was removed from filtered semen by centrifugation, and the sperm pellet was resuspended in Sperm-TALP medium. Samples of treated and untreated control semen of both species were incubated at 37 degrees C. At 1, 15 and 30 min of incubation the proportions of progressively motile and acrosome-reacted spermatozoa were assessed. Trypan blue and Giemsa stain was used to differentiate live and dead spermatozoa having undergone acrosome reaction. Glass wool filtration enhanced the proportion of motile spermatozoa from 43% to 62% in the bovine and from 41% to 60% in the caprine. Whereas the effect of incubation with caffeine, heparin and calcium-ionophore on spermatozoan motility was negligible, the treatment of semen with calcium-ionophore resulted in a significantly improved percentage of live spermatozoa with true acrosome reaction at all stages of incubation, both in the bovine and the caprine.

Differential expression of photosynthesis and nitrogen fixation genes in the cyanobacterium Plectonema boryanum.

The filamentous non-heterocystous cyanobacterium Plectonema boryanum fixes dinitrogen at a high rate during microaerobic growth in continuous illumination by temporal separation of oxygen-evolving photosynthesis and oxygen-sensitive dinitrogen fixation. The onset of nitrogen fixation is preceded by a depression in photosynthesis that establishes a sufficiently low level of dissolved oxygen in the growth medium. A several-fold reduction in the level of transcripts coding for phycocyanin (cpcBA) and the chlorophyll a binding protein of photosystem II (psbC) and psbA accompanied the depression in photosynthetic oxygen evolution. Unlike most of the other organisms examined to date, in P. boryanum, psbC and psbD do not appear to be co-transcribed. The psbC transcripts were down-regulated several fold, while the psbD transcript declined marginally during the nitrogen fixation phase. A decrease in dissolved oxygen and a dramatic increase in the level of nifH transcripts and the enzyme activity of nitrogenase were characteristic of the nitrogen fixation phase. The level of transcript for glnA, which encodes glutamine synthetase, was not altered. Reciprocal regulation of gene expression was well orchestrated with the alternating cycles of photosynthesis and nitrogen fixation in P. boryanum.

Diurnal regulation of plastid genes in Populus deltoides.

Light regulates leaf and chloroplast development, together with overall chloroplast gene expression at various levels. Plants respond to diurnal and seasonal changes in light by changing expression of photosynthesis genes and metabolism. In Populus deltoides, a deciduous tree species, leaf development begins in the month of March and leaf maturation is attained by summer, which is subsequently followed by autumnal senescence and fall. In the present study, diurnal changes in the steady state transcript levels of plastid genes were examined in the fully developed leaves during summer season. Our results show that steady state level of the psaA/B, psbA, psbEFLJ and petA transcripts showed differential accumulation during diurnal cycle in summer. However, there was no significant change in the pigment composition during the day/night cycle. Our studies suggest that the diurnal regulation of steady state mRNA accumulation may play a crucial role during daily adjustments in plants life with rapidly changing light irradiance and temperature.

Effect of light intensity on in vitro multiple shoot induction and regeneration of cotton (Gossypium hirsutum L. cv Khandawa-2).

Cotyledonary nodes taken alongwith shoot apex from seedlings of cotton (G. hirsutum) proliferated into shoots on nutrient agar medium supplemented with cytokinins. In the presence of optimal plant growth regulators, low light intensity enhanced the number of shoots initiated per explant in cotton. An average of 33.5 +/- 2.9 shoots were obtained from a single explant cultured for 8 weeks which is about four fold higher than the values reported in earlier protocols. The isolated shoots were rooted on nutrient agar medium supplemented with alpha-naphthalene acetic acid and transferred to soil after acclimatization. Regenerated plants were morphologically identical to the seed-germinated plants and were fertile.

Expression of chloroplastic genes during autumnal senescence in a deciduous tree Populus deltiodes.

In Populus deltoides, a deciduous tree, the development on new leaves starts in the month of March, the leaves reach maturity by October and fall by December. Changes in the composition and function of the photosynthetic apparatus were analysed during autumnal senescence. With the progress of senescence, there was an initial increase followed by a decrease in the steady state levels of psbA, psbD/C and psaA/B gene transcripts. Decrease in the steady state level of D1 protein was faster than that of Cytochrome f. The decline in LHCP level was seen only during late senescence. Although the leaves continue to look green and healthy till late November, the electron transport driven by individual photosystems started declining by October end suggesting the onset of senescence.

Bacterial endophthalmitis following extracapsular cataract extraction: recommendations for early detection.

OBJECTIVE: To determine the time between the onset of symptoms of endophthalmitis after cataract extraction and presentation to an ophthalmologist and to determine the spectrum of organisms responsible for postoperative endophthalmitis. DESIGN: Case series. SETTING: Tertiary care vitreoretinal service in Toronto. PATIENTS: Thirty-three patients with early (presentation within 2 weeks of surgery) endophthalmitis following extracapsular cataract extraction and intraocular lens implantation performed between January 1989 and December 1992. OUTCOME MEASURES: Time to presentation to an ophthalmologist, duration of symptoms, culture results. RESULTS: Twenty-two patients (66.7%) were documented to experience identifiable symptoms of endophthalmitis before presentation to their ophthalmologist; the mean time of onset of symptoms was 3.6 (standard deviation [SD] 1.7) days after surgery. Of the 22 patients 16 (72.7%) became symptomatic by the fourth postoperative day, and 21 (95.4%) experienced symptoms by the fifth postoperative day. The mean delay between onset of symptoms and presentation was 1.9 (SD 1.6) days. Bacteria were identified in 27 cases (81.8%), confirmed by culture in 23 cases (69.7%). The organisms were gram-positive in 25 (92.6%) of the 27 cases, and coagulase-negative Staphylococcus predominated. CONCLUSIONS: In our series a considerable delay existed between the development of symptoms of endophthalmitis following extracapsular cataract extraction and clinical diagnosis. This delay could be minimized by scheduling routine postoperative visits at 1 and 4 days following cataract surgery.

Comparison of quality and freezability of water buffalo semen after washing or Sephadex filtration.

Split aliquots of pooled buffalo semen samples were processed before freezing 1) by washing twice with Tris-citric acid buffer by centrifugation and re-suspension to the original volume in the same buffer, or 2) or by passage through a G-15 Sephadex column. The effect of these procedures on progressive motility, percentages of live spermatozoa, sperm abnormalities and intact acrosomes and release of glutamate oxatoacetate transaminase (GOT) into the medium were assessed after extension, after equilibration and after 18 to 24 h or 15 d of frozen storage. Prior to extension, gel filtration reduced sperm concentration and enhanced progressive motility, whereas washing produced little effect on these attributes. Except in the case of GOT release, which was significantly (P < 0.05) lower after the washing of semen (34.3 +/- 16.40) than the filtering of semen (45.7 +/- 12.35), the 2 procedures did not cause significant effects (P > 0.05). Damage to spermatozoa due to freeze-processing was also similar in the 2 treatments, and the extent of beneficial effect in improved motility and live spermatozoan numbers after thawing was also similar.