Changing the diagnostic paradigm for sugarcane: development of a mill-based diagnostic for ratoon stunting disease in crude cane juice

The availability of efficient diagnostic methods is crucial to monitor the incidence of crop diseases and implement effective management strategies. One of the most important elements in diagnostics, especially in large acreage crops, is the sampling strategy as hundreds of thousands of individual plants can grow in a single farm, making it difficult to assess disease incidence in field surveys. This problem is compounded when there are no external disease symptoms, as in the case for the ratoon stunting disease (RSD) in sugarcane. We have developed an alternative approach of disease surveillance by using the crude cane juice expressed at the sugar factory (mill). For this purpose, we optimized DNA extraction and amplification conditions for the bacterium Leifsonia xyli subsp xyli, the causal agent of RSD. The use of nucleic acid dipsticks and LAMP isothermal amplification allows to perform the assays at the mills, even in the absence of molecular biology laboratories. Our method has been validated using the qPCR industry standard and shows higher sensitivity. This approach circumvents sampling limitations, providing RSD incidence evaluation on commercial crops and facilitating disease mapping across growing regions. There is also potential is to extend the technology to other sugarcane diseases as well as other processed crops.

New Insights into the Diversity of the Genus Faecalibacterium

Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters—A, B, and C—composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.

An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease?

While it is now accepted that the gut microbiota contribute to the genotype-environment-lifestyle interactions triggering inflammatory bowel disease (IBD) episodes, efforts to identify the pathogen(s) that cause these diseases have met with limited success. The advent of culture-independent techniques for characterizing the structure and/or function of microbial communities (hereafter referred to as metagenomics) has provided new insights into the events associated with the onset, remission and recurrence of IBD. A large number of observational and/or case-control studies of IBD patients have confirmed substantive changes in gut bacterial profiles (dysbiosis) associated with disease. These types of studies have been augmented by new profiling approaches that support the identification of more 'colitogenic' bacteria from numerically predominant taxa. Evidence of alterations in lesser abundant taxa such as the methanogenic archaea, to favor types that are more immunogenic, has also been forthcoming. Several recent longitudinal studies of patients with Crohn's disease have produced additional insights, including evidence for the role of 'anti-inflammatory' microbiota in providing a protective effect and/or promoting remission. In summation, the implications of dysbiosis and restoration of a 'healthy microbiota' in IBD patients requires definition beyond a taxonomic assessment of the changes in the gut microbiota during disease course. The available evidence does suggest that specific members of the gut microbiota can contribute either pro- or anti-inflammatory effects, and their ecological fitness in the large bowel affects the onset and recurrence of IBD. While metagenomics and related approaches offer the potential to provide novel and important insights into these microbiota and thereby the pathophysiology of IBD, we also need to better understand factors affecting the ecological fitness of these microbes, if new treatment of IBD patients are to be delivered.

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating

Metagenomics has rapidly advanced our inventory and appreciation of the genetic potential inherent to the gut microbiome. However it is widely accepted that two key constraints to further genetic dissection of the gut microbiota and host-microbe interactions have been our inability to recover new isolates from the human gut, and the paucity of genetically tractable gut microbes. To address this challenge we developed a modular RP4 mobilisable recombinant vector system and an approach termed metaparental mating to support the rapid and directed isolation of genetically tractable fastidious gut bacteria. Using this approach we isolated transconjugants affiliated with Clostridium cluster IV (Faecalibacterium and Oscillibacter spp.), Clostridium cluster XI (Anaerococcus) and Clostridium XIVa (Blautia spp.) and group 2 ruminococci amongst others, and demonstrated that the recombinant vectors were stably maintained in their recipient hosts. By a similar approach we constructed fluorescently labelled bacterial transconjugants affiliated with Clostridium cluster IV (including Flavonifractor and Pseudoflavonifractor spp.), Clostridium XIVa (Blautia spp.) and Clostridium cluster XVIII (Clostridium ramosum) that expressed a flavin mononucleotide-based reporter gene (evoglow-C-Bs2). Our approach will advance the integration of bacterial genetics with metagenomics and realize new directions to support a more mechanistic dissection of host-microbe associations relevant to human health and disease.

A comparative field trial of cephalonium and cloxacillin for dry cow therapy for mastitis in Australian dairy cows

OBJECTIVE

To investigate and compare the therapeutic efficacy of dry cow agents containing either cephalonium or cloxacillin within Australian dairy herds.

DESIGN

A treatment-control trial.

METHODS

Milk from infected quarters of cows with high somatic cell counts in milk on eight Australian dairy farms was cultured to identify bacterial pathogens. Cows were randomly assigned to treatment groups and one group was treated with cephalonium at drying off and the other group was treated with cloxacillin at drying off. Milk samples from infected quarters were collected immediately after calving and were cultured for pathogens. The effect of treatment on bacteriological cure was examined and somatic cell counts from infected cows from the first two herd tests after calving were examined for a treatment effect. On four farms, milk samples were collected for culture from all cases of clinical mastitis identified within the first 7 days after calving. The effect of treatment upon incidence of clinical mastitis after calving was examined.

RESULTS

There was no significant difference between treatments on quarter cure rates for new infections, for chronic infections and for infections with Staphylococcus aureus, Streptococcus agalactiae and Streptococcus uberis. Infected quarters treated with cephalonium had a significantly higher cure rate than quarters treated with cloxacillin when Corynebacterium bovis and Staphylococcus epidermids were included as pathogens combined (80.3% versus 70.7%). There was no significant difference between the treatments on somatic cell counts of infected cows at the first two herd tests after calving. There was no difference between treatments on the incidence of clinical mastitis in the first 7 days after calving.

Statistical validation of reproducibility of HPLC peptide mapping for the identity of an investigational drug compound based on principal component analysis

Peptide mapping is a key analytical method for studying the primary structure of proteins. The sensitivity of the peptide map to even the smallest change in the covalent structure of the protein makes it a valuable "fingerprint" for identity testing and process monitoring. We recently conducted a full method validation study of an optimized reverse-phase high-performance liquid chromatography (RP-HPLC) tryptic map of a therapeutic anti-CD4 monoclonal antibody. We have used this method routinely for over a year to test production lots for clinical trials and to support bioprocess development. One of the difficulties in the validation of the peptide mapping method is the lack of proper quantitative measures of its reproducibility. A reproducibility study may include method and system precision study, ruggedness study, and robustness study. In this paper, we discuss the use of principal component analysis (PCA) to quantitate peptide maps properly using its projected scores on the reduced dimensions. This approach allowed us not only to summarize the reproducibility study properly, but also to use the method as a diagnostic tool to investigate any troubles in the reproducibility validation process.

Ruggedness study of HPLC peptide mapping for the identity of a drug compound: a chemometrics approach

A statistically more reliable approach than the traditional visual inspection of peptide maps to identify a drug compound is to generate a set of reference standards from a designed experiment that incorporates many possible factors that affect variation of peptide mapping. In fact, the experiment can be done for a ruggedness study as part of a high-performance liquid chromatography (HPLC) method validation. Once the ruggedness is proved with the study, those articles in the experiment may form a set of reference standards, and future articles can be compared to the set later to prove identity. A quantitative analysis of the ruggedness study can be done using a chemometrics approach, principal component analysis (PCA). The analysis is used to reduce the many channels of peptide maps to a few manageable dimensions. The scores projected onto the reduced dimensions are used to test factor effects of the ruggedness study. As a by-product, the analysis provides visual inspection of the set of articles in the experiment for any outliers and anomalies.

Validation of a peptide mapping method for a therapeutic monoclonal antibody: what could we possibly learn about a method we have run 100 times?

Peptide mapping is a key analytical method for studying the primary structure of proteins. The sensitivity of the peptide map to even the smallest change in the covalent structure of the protein makes it a valuable 'finger-print' for identity testing and process monitoring. We recently conducted a full method validation study of an optimised reverse-phase high-performance liquid chromatography (RP-HPLC) tryptic map of a therapeutic anti-CD4 IgG1 monoclonal antibody. We have used this method routinely for over 1 year to support bioprocess development and test production lots for clinical trials. Herein we summarize the precision and ruggedness of the testing procedure and the main findings with respect to 'coverage of amino acid sequence' and limits-of-detection for various hypothetical structural variants. We also describe, in more detail, two unanticipated insights into the method gained from the validation study. The first of these is a potentially troublesome side-product arising during the reduction/alkylation step. Once the cause of this side-product was identified, it was easily prevented. We also report on subtle changes to the peptide map upon extended storage of the digest in the autosampler. These findings helped us to develop a 'robust' method for implementation in a quality control laboratory.

RP-HPLC tryptic mapping of IgG1 proteins with post-column fluorescence derivatization

Peptide mapping is an important analytical technique widely used to study the primary structure of proteins. In quality control settings, it is employed as an identity test to probe for small changes in protein primary structure. A great challenge in peptide mapping is to minimize the detection limit for peptides due to the low detectability of smaller peptides based on their ultraviolet absorbance. The detection of peptide fragments can be enhanced by pre-or post-column derivatization with fluorescent tags. The use of post-column o-pthalaldehyde (OPA) and fluorescamine chemistries for on-line derivatization of peptide fragments from the RP-HPLC tryptic maps of several IgG1 monoclonal antibodies was explored. This paper describes the simple and sensitive peptide mapping technique for structural confirmation of proteins using picomoles of samples by post-column fluorescence derivatization. A comparison of UV and fluorescence detection of a peptide map is also presented. The method includes post column OPA derivatization of tryptic peptides from RP-HPLC tryptic maps with fluorescence detection. The conclusion reached that fluorescence detection gave relative detectability for tryptic peptides that range from 10- to 100-fold better than those observed with UV detection. The sensitivity of the peptide map increased by about 200-500 fold, i.e. peptide maps could be obtained using 2-5 pmol of digest instead of 1 nmol of digest. A roughly equal fluorescence response for all peptides (equal peak areas) was generally observed.

The challenge of sobriety: natural recovery without treatment and self-help groups

Natural recovery is a phenomenon that is not understood and largely challenged by self-help group members and professionals working in the field of substance abuse. So strong is the supposition of the process of recovering as a life-long condition that requires treatment and/or a self-help group for on-going support and rehabilitation that recovery on one's own is given little credence. Yet there is growing empirical evidence that natural recovery not only exists, but may be more prominent than is currently recognized. This article presents a study of natural recoverers from alcoholism and problem drinking, reporting their subjective motivating factors and strategies of recovery, while examining an issue of which there is still limited data--the perceived changes since abstaining, i.e., how their lives have been altered by pursuing abstinence on their own. It concentrates on rich narrative data to explore the meaning of the change experience that can be applied to various addictions, for the purpose of illuminating novel approaches that have the potential for expanding practice techniques and forums, thereby enhancing its effectiveness.

Randomized trial of vinorelbine compared with fluorouracil plus leucovorin in patients with stage IV non-small-cell lung cancer

PURPOSE

This prospective randomized trial was performed to compare the effectiveness of intravenous vinorelbine tartrate with intravenous fluorouracil and leucovorin (5-FU/LV) on the primary end points of survival, quality of life (QOL), and relief of cancer-related symptoms in patients with advanced non-small-cell lung cancer (NSCLC). Secondary end points included tumor response rates and time to treatment failure. In addition, the safety of both treatment regimens was evaluated in this multicenter study.

PATIENTS AND METHODS

Two hundred sixteen patients with stage IV NSCLC were enrolled onto this study from 18 centers. Vinorelbine was administered at a dose of 30 mg/m2/wk. 5-FU/LV was administered at a dose of 425 mg/m2 and 20 mg/m2, respectively, for 5 consecutive days every 4 weeks. Patients with progressive disease or toxicity were removed from study while responding and stable patients were continued on therapy.

RESULTS

The median survival time of patients who received vinorelbine was 30 weeks, with 25% of patients alive at 1 year, compared with a median survival time of 22 weeks and 16% of patients alive at 1 year for those treated with 5-FU/LV (P = .03, log-rank test). This improvement in survival was associated with a higher objective response rate (12% v 3%) and time to treatment failure (10 weeks v 8 weeks) for vinorelbine versus 5-FU/LV. The dose-limiting toxicity of vinorelbine was granulocytopenia, with 54% of patients experiencing grade 3/4 granulocytopenia. Nonhematologic toxicity of vinorelbine was generally grade 1 or 2. The most common grade 3 toxicities were related to injection-site reactions.

CONCLUSION

This trial confirms the efficacy of vinorelbine in patients with advanced NSCLC. The clinical activity and relatively favorable toxicity profile of this agent make it a reasonable and useful treatment option in the management of patients with this disease.

An integrated strategy for structural characterization of the protein and carbohydrate components of monoclonal antibodies: application to anti-respiratory syncytial virus MAb

The relatively rapid and extensive characterization of the amino acid sequence and site-specific carbohydrate structures of a recombinant, reshaped human monoclonal antibody directed against respiratory syncytial virus (RSHZ19) is presented. The integrated strategy used a combination of mass spectrometric and conventional methodologies. Liquid chromatography/electrospray mass spectrometry was used for peptide mapping and selective identification of glycopeptides, and Edman degradation and tandem mass spectrometry were used to define the sequences of selected peptides. Matrix-assisted laser desorption/ionization mass spectrometry provided the M(r) of the intact protein and was used to characterize endo- and exoglycosidase digests of isolated glycopeptides to identify the glycosylation-site peptide and define the structures of the carbohydrates at that site. These experiments verified 99.1% of the light- and 99.3% of the heavy-chain amino acid sequences. The N and C termini of both chains were confirmed, and the nature and extent of heterogeneity at the N and C termini of the heavy chain were determined. Oxidation of a specific methionine residue to the sulfoxide was demonstrated by sequencing the N-terminally blocked peptide by tandem MS. Carbohydrate was found exclusively at Asn296 of the heavy chain. There was no evidence for a nonglycosylated form of the molecule or for the presence of O-linked carbohydrate. The qualitative distribution of glycoforms at this site was determined by MS of the isolated, tryptic glycopeptide and compared with results obtained by high-performance anion exchange chromatography and high-resolution gel permeation chromatography of oligosaccharides released by hydrazinolysis. The sequence and linkage of individual glycan species were determined using matrix-assisted laser desorption/ionization MS to monitor the results of a series of controlled digestions with specific exoglycosidases. The set of glycoforms consists predominantly of biantennary, core fucosylated carbohydrates lacking sialic acid. The present study is one of the first to directly evaluate the quantitative as well as qualitative consistency of the MS methods with conventional methods for carbohydrate analysis.

The disease concept of alcoholism: its impact on women's treatment

The disease concept of alcoholism has had a dynamic impact on attitudes, policies, and treatment orientations. Despite its demonstrable effects on changing behaviors and belief systems, it remains both an acceptable and controversial entity amongst researchers and treatment personnel alike. This report provides a current focus of the disease concept as its applies to the characteristics and experiences of women alcoholics and their treatment. It especially targets the need for empowerment in this population and questions whether this important trait can be developed by the disease concept's emphasis on illness and the sick role, which inadvertently validates the feelings of powerlessness and helplessness of these women who already have been intensively socialized in dependent and subordinate roles.

Neglected victims of murder: children's witness to parental homicide

Children who witness parental homicides are emotionally traumatized, stigmatized, and deeply scarred by a terrifying event. They often exhibit debilitating symptoms comparable to those of posttraumatic stress disorder. As attention is focused on the deceased and on the perpetrator of the crime, the child witnesses inadvertently become the neglected victims. A case report of two such children who observed their mother being murdered by their father is presented. Theories of psychosocial development and social learning guided the assessment and intervention phases. Behavioral and expressive therapeutic treatment strategies that helped the children work through the resultant anxiety and underlying grief are delineated, and family intervention practices that served to improve interaction and communication patterns are described. Further discussion focuses on the potential intergenerational cycle of violence and on a sociocultural perspective of family violence within an ecological framework.

Complete assignment of neurophysin disulfides indicates pairing in two separate domains

The pairing of the 14 half-cystine residues of bovine neurophysin was established by sequential proteolytic digestion. Purified released peptides and the residual disulfide-linked core were monitored at each step by use of amino acid analysis, gas-phase sequencing, and mass spectrometry. The approach included application of gas-phase sequencing to assign disulfide pairs in peptides containing multiple disulfides. The results demonstrate that neurophysin disulfides are paired in two distinct domains--an NH2 domain (residues 10-54) containing four disulfides and a COOH domain (residues 61-85) containing three disulfides. The specific disulfide bridges are Cys-10 to Cys-54, Cys-13 to Cys-27, Cys-21 to Cys-44, Cys-28 to Cys-34, Cys-61 to Cys-73, Cys-74 to Cys-79, and Cys-67 to Cys-85. The results place the internally duplicated segments of neurophysin (residues 12-31 and 60-77) in separate domains. Disulfide-pairing patterns within each domain are homologous with the exception of the Cys-10 to Cys-54 bond, which is unique to the NH2 domain and which links the two ends of this domain together. The potential role of the Cys-10 to Cys-54 bond in organizing the hormone-binding site is discussed.

Application of high-performance liquid chromatography in neurophysin disulfide assignment

The combined use of ion-exchange, and reversed-phase high-performance liquid chromatography (HPLC) for the isolation of cystine-containing peptides from highly heterogeneous products of the proteolytic digestion of bovine neurophysins is described. The protein was sequentially cleaved by enzymes of decreasing specificity; the peptides released were initially fractionated by gel chromatography and then purified by HPLC. The purified peptides were analyzed by determination of their amino acid composition and mass spectrometry, supported by sequencing techniques. Three of the seven disulfide pairs of neurophysin have now been assigned. The usefulness of the combined use of HPLC and mass spectrometry in assigning these and the other disulfide pairs is illustrated.

Partial assignment of disulfide pairs in neurophysins

The original report assigning the pairing of neurophysin's 14 half-cystine residues (Schlesinger et al. (1972), Proc. Natl. Acad. Sci., U.S.A., 69,3350-3353) was based on an incorrect amino acid sequence. In the present study, re-investigation of the results of proteolytic fragmentation of bovine neurophysins indicates that the majority of the original assignments were incorrect. Three disulfide pairs are now assigned as Cys21-Cys44, Cys67-Cys85 and Cys74-Cys79. The pairing pattern indicates that neurophysin's variable carboxyl terminal region, separately encoded by the third gene exon, does not form a self-contained domain.

The interaction of phosphate with the purple acid phosphatase from beef spleen: evidence that phosphate binding is accompanied by oxidation of the iron chromophore

Reaction of the reduced (pink) form of the purple acid phosphatase from beef spleen with excess phosphate at pH 5.0, monitored by optical and low temperature EPR spectroscopy and by measurement of enzymatic activity, results in parallel loss of activity and oxidation of the iron chromophore. Colorimetric and radiochemical (32P) experiments indicate the presence of one mole of tightly bound phosphate in the oxidized (purple) form of the enzyme; this phosphate is released upon reduction. Acid hydrolysis of 32P-phosphate-containing enzyme, followed by high voltage paper electrophoresis, gave no evidence for significant amounts of acid-stable phosphoamino acids.

Non-adherent, low-density cells from human peripheral blood contain dendritic cells and monocytes, both with veiled morphology

Dendritic cells (DC) from human peripheral blood, known to adhere transiently and to become non-adherent by 16 hr, can be separated in the low-density interface on hypertonic Metrizamide gradients. Many more low-density cells (5.8% of the mononuclear cells separated on Ficoll) were obtained from the population that was non-adherent after only 90 min. Over 95% of these low-density cells had veiled morphology. A proportion were monocytes by phenotypic and phagocytic properties. One-third of the cells (on average) were DC on the basis of lack of monocyte phenotype and of potency as stimulators in the mixed lymphocyte reaction. Including both the 16 hr and 90 min non-adherent cells, over 2% of the mononuclear cells isolated from human peripheral blood may be DC.

Lymphocyte responses in juvenile chronic arthritis and Behçet's disease--cell number requirements and effects of glucocorticosteroid therapy

Peripheral blood mononuclear cells from patients with clinically active Behçet's disease or juvenile chronic arthritis (JCA) gave high responses to phytohaemagglutinin (PHA) in vitro prior to prednisolone therapy and low responses when taking prednisolone in comparison with cells from control individuals. Such effects were not significantly different at the six concentrations of cells or the four times in culture studied. Differences from controls were also seen with cells from clinically controlled, prednisolone treated Behçet's patients; the cells responded better than controls at low cell concentrations and early times in culture, the reverse occurring at higher concentrations and later times. This pattern of response suggests the presence of a higher than normal proportion of responsive cells in these patients. These studies suggest that not only is a still wider range of culture conditions required to assess fully the differences in lymphocyte function related to disease activity and prednisolone treatment in JCA or Behçet's, but also that the use of a narrow set of 'optimized' conditions may be misleading.

Cell number requirements for lymphocyte stimulation in vitro: changes during the course of multiple sclerosis and the effects of immunosuppression

Peripheral blood lymphocytes from 20 patients with clinically definite, relapsing and remitting multiple sclerosis (MS) were studied during their participation in a double-blind trial of immunosuppressive treatment. Proliferative responses occurring with different numbers of cells in culture and on different days of culture in the presence of phytohaemagglutinin (PHA) or with allogeneic cells from lymphoid cell lines (MLC) were assessed. Cells taken from patients before treatment showed similar responses to cells from laboratory personnel. However, when cells were taken from patients in relapse or from untreated patients as the disease progressed, there was an alteration in the pattern of response; higher number of cells were required in culture to produce responses. A change in the responsiveness to PHA or in MLC may therefore accompany the progression of the disease in MS (reflecting clinical relapses and possibly subclinical activity of the disease), perhaps resulting from a simple reduction in the proportion of cells able to respond. After intense immunosuppression followed by long-term maintenance on azathioprine, cells from patients gave similar responses to those found before treatment. Thus long-term immunosuppression prevented the progressive alteration in lymphocyte function. Shifts in the total cell number and time in culture required to allow proliferation with mitogens of cells from untreated MS patients could explain both the 'low' of PHA responses reported and the changes of in vitro 'suppressor' function of these cells.