Diversity and taxonomic distribution of bacterial biosynthetic gene clusters predicted to produce compounds with therapeutically relevant bioactivities

Bacteria have long been a source of natural products with diverse bioactivities that have been developed into therapeutics to treat human disease. Historically, researchers have focused on a few taxa of bacteria, mainly Streptomyces and other actinomycetes. This strategy was initially highly successful and resulted in the golden era of antibiotic discovery. The golden era ended when the most common antibiotics from Streptomyces had been discovered. Rediscovery of known compounds has plagued natural product discovery ever since. Recently, there has been increasing interest in identifying other taxa that produce bioactive natural products. Several bioinformatics studies have identified promising taxa with high biosynthetic capacity. However, these studies do not address the question of whether any of the products produced by these taxa are likely to have activities that will make them useful as human therapeutics. We address this gap by applying a recently developed machine learning tool that predicts natural product activity from biosynthetic gene cluster (BGC) sequences to determine which taxa are likely to produce compounds that are not only novel but also bioactive. This machine learning tool is trained on a dataset of BGC-natural product activity pairs and relies on counts of different protein domains and resistance genes in the BGC to make its predictions. We find that rare and understudied actinomycetes are the most promising sources for novel active compounds. There are also several taxa outside of actinomycetes that are likely to produce novel active compounds. We also find that most strains of Streptomyces likely produce both characterized and uncharacterized bioactive natural products. The results of this study provide guidelines to increase the efficiency of future bioprospecting efforts.

ONE-SENTENCE SUMMARY

This paper combines several bioinformatics workflows to identify which genera of bacteria are most likely to produce novel natural products with useful bioactivities such as antibacterial, antitumor, or antifungal activity.

Temporal and Spatial Genetic Variability in White-tailed Deer (Odocoileus virginianus)

Starch-gel electrophoresis was used to assess temporal and spatial genetic variation in populations of white-tailed deer (Odocoileus virginianus) in western Tennessee. Samples of liver and kidney obtained from animals at five localities during 1985-1992 were analyzed at 11 loci known to be polymorphic in white-tailed deer. There were minimal significant differences in allelic frequencies between sexes and among age groups for each year at each locality and among years at each locality with ages and sexes combined. No significant difference occurred among mean values of heterozygosity. A heterozygote deficiency was detected in white-tailed deer populations from western Tennessee and could reflect limited inbreeding but was more likely due to Wahlund effects. Limited temporal variation occurred among years within a locality and indicated a stasis in terms of minimal genetic drift and harvest effects on genetic structure of the populations. Herd origin, stocking history of populations, and gene flow were probable causes of spatial heterogeneity in deer populations in western Tennessee.

Karyotypic analysis of the cotton boll weevil, Anthonomus grandis Boheman

The diploid chromosome number of the cotton boll weevil, Anthonomus grandis Boheman, is 44. Both C- and N-banding techniques of mitotic cells demonstrated constitutive heterochromatin in the p arm of the eight largest chromosomes, the p arm of the X chromosome, and the centromeric region of autosomal groups A-D. Neither the y nor the group E autosomes appeared to contain constitutive heterochromatin. Supernumerary chromosomes were not found in the boll weevil. Restriction endonuclease banding of primary spermatocytes revealed a rod-shaped Xy tetrad in which the X and y were terminally associated. The p arm of the large, submetacentric X was C-band positive. While two of the autosomal tetrads were typically ring-shaped in primary spermatocytes, the remaining 19 autosomal tetrads were rod-shaped.

Red blood cell polyagglutination: clinical aspects

Polyagglutination is the term applied to red blood cells (RBCs) that are agglutinated by almost all samples of human sera from adults but not by autologous serum or sera of newborns. The polyagglutinable state may be transient or persistent. Transient polyagglutinability results from the exposure of normally cryptic antigens by bacterial enzymatic activity during the course of an infectious process. RBCs are polyagglutinable because most sera from adults contain agglutinins for the exposed antigens. This type of polyagglutination can often be reproduced in vitro with bacterial culture fluids or isolated enzymes. Persistent polyagglutination may be a consequence of somatic mutation leading to a cellular lineage characterized by an enzyme deficiency that results in exposure of a normally cryptic antigen, Tn. Most human sera contain anti-Tn. Tn polyagglutination is regularly accompanied by leukopenia and thrombocytopenia and has been associated with leukemia. Other forms of persistent polyagglutination are due to the inheritance of rare blood groups or are associated with a hematologic dyscrasia.

Transplantation rate of the blood group B waiting list is increased by using A2 and A2B kidneys

BACKGROUND

We have increased the transplantation rate for blood group B cadaveric waiting list candidates by transplanting them with A2 and A2B kidneys.

METHODS

Since 1991, five of the seven renal transplant programs in our organ procurement organization service area have preferentially transplanted blood group A2 and A2B cadaveric kidneys to B blood group waiting list candidates with histories of low anti-A isoagglutinin titers.

RESULTS

Between 1991 and 1997, these five centers performed transplantations on 71 patients from the B cadaveric waiting list. Of those 71 patients, 29% (21 of 71) underwent transplantation with either A2 (n=18) or A2B (n=3) cadaveric kidneys. In 1997 alone, 48% (11 of 23) of the B patient transplant recipients received A2 or A2B kidneys.

CONCLUSIONS

Transplantation of A2 and A2B kidneys into B waiting list patients has successfully increased access of B patients to kidneys. Such an allocation algorithm implemented nationally may similarly increase the transplantation rate of B waiting list candidates.

Differential reactivity of cardiac and skeletal muscle from various species in two generations of cardiac troponin-T immunoassays

Cardiac troponin T (cTnT) is being increasingly used as a blood marker of acute or ongoing cardiac injury in various laboratory animals although the range of species in which it is applicable and its tissue selectivity has not been demonstrated. To address this concern, cardiac and skeletal muscle biopsy specimens from various species were homogenised and diluted, and their reactivity was then determined in the first- and second-generation immunoassays for cTnT. Cardiac tissue reactivity was found for all species studies, being highest for rats and several-fold lower for chickens and fish, and intermediate for dogs, pigs, goats, cows, sheep, horses, rabbits, and turkeys. Skeletal muscle had 10 per cent of the reactivity of cardiac muscle in the first-generation assay and 1 per cent of the reactivity of cardiac muscle in the second-generation assay. In the absence of moderate to marked skeletal muscle injury, the second-generation cTnT immunoassay has sufficient reactivity and tissue-selectivity to serve as a blood test for the discrimination between cardiac and skeletal muscle injury in a wide range of species.

Ten-year experience in transplantation of A2 kidneys into B and O recipients

BACKGROUND

This article summarizes our 10-year multicenter experience with transplantation of 50 blood group A2 and A2B kidneys into B and O patients.

METHODS

Since 1986, we have transplanted kidneys from 46 cadaver donors and 4 living donors who were blood group A2 (47 donors) or A2B (3 donors) into 19 B and 31 O patients. In 1991, we began allocating these kidneys preferentially to B and O recipients who were selected based on a history of low (< or =4) anti-A IgG isoagglutinin titers. Immunosuppression was no different from that used in ABO-compatible grafts.

RESULTS

The 1-month function rate before thus selecting the patients was 68% (19/28), but is now 94% (17/18). Two-year cadaver-donor graft survival with this selection method is 94%, compared with 88% for 640 concurrent and consecutive ABO-compatible transplants (log-rank, 0.15). All four living-related transplants are still functioning, with a mean follow-up of 71 months. Since we began allocating A2 kidneys preferentially to B and O recipients, the percentage of the B patients who received A2 or A2B kidneys has increased from 29% (8/28) to 55% (10/18).

CONCLUSIONS

Transplantation of A2 or A2B kidneys into B and O patients is clinically equivalent to that of ABO-compatible transplantation when recipients are selected by low pretransplant anti-A titer histories. This approach increases access of blood group B recipients to kidneys.

Cardiac troponin T is a sensitive, specific biomarker of cardiac injury in laboratory animals

A reliable serum assay that can discriminate between cardiac and skeletal muscle injury is not available for diagnostic use in laboratory animals. We tested and supported the hypotheses that serum cardiac troponin T (cTnT) was widely applicable in laboratory animals as a biomarker of cardiac injury arising from various causes; that it increased in proportion to severity of cardiac injury; and that it was more cardiospecific than creatine kinase (CK) or lactate dehydrogenase (LD) isozyme activities. In canine and rat models of myocardial infarction, cTnT concentration increased 1,000- to 10,000-fold and was highly correlated with infarct size within 3 h of injury. Serum CK and LD isozymes were substantially less effective biomarkers and, in contrast to cTnT, were ineffective markers in the presence of moderate skeletal muscle injury, with resulting serum CK activity > 5,000 U/L. Using these animal models, and mouse and ferret models, we also showed cTnT to be an effective biomarker in doxorubicin cardiotoxicosis, traumatic injury, ischemia, and cardiac puncture. Reference range serum concentrations for all species were at the detection limit of the assay, except those for mice, in which they were slightly increased, possibly because mice were used to generate assay monoclonal antibodies. We conclude that cTnT is a powerful biomarker in laboratory animals for the sensitive and specific detection of cardiac injury arising from various causes.

Chromosomal variation in the southern short-tailed shrew (Blarina carolinensis)

Chromosomal polymorphism was assessed in the southern short-tailed shrew (Blarina carolinensis) using standard metaphase chromosome and G-banding techniques. Twenty-one animals (11 males, 10 females) from the Meeman Biological Station in Shelby Co., Tennessee, were examined for diploid number. Results showed diploid numbers of 35, 36, 37, 38, 39, 40 and 41 and fundamental numbers of 41, 42, 43, 44 and 45. No diploid numbers or fundamental numbers were unique to a specific collecting locality. The first G-banded karyotypes are reported for the species. These results indicate that Robertsonian polymorphisms, inversions, and possibly other events are responsible for chromosomal variation in B. carolinensis.

Evaluation of an autotutorial-simulator program for instruction of hollow organ closure

Forty students were randomly assigned into two study groups (traditional, T; and simulator, S) of 20 students each for a core operative practice laboratory. Students were randomly paired and their group assignment and identity remained anonymous to the evaluators throughout the study. Questionnaires were distributed to students to evaluate prior surgical experience and obtain learning resource use information. Before the evaluation sessions, both groups were given identical learning resource opportunities except students in Group S received hollow organ simulators and practice materials for gastrotomy closure. All students were forewarned that surgical instruction would not be available during the evaluation sessions. In the first live animal evaluation session, all student pairs were videotaped after which stomachs were harvested for gross evaluation of the surgical site. Group T performed an additional gastrotomy for video and gross evaluation 2 weeks later. Questionnaire, and gross and video evaluation results were compared statistically between groups and sessions. The hollow organ model did not suitably simulate live stomach tissue; the material was more fragile and stiff and suture cut-out was a problem even with appropriate suture tension and technique. The model was effective for teaching needle placement, instrument usage, creating proper tissue inversion, and methods to minimize instrument handling of tissue during gastrotomy closure. Prior practice with models did not boost student confidence during their live gastrotomy session. The autotutorials (ATs) were well received by students but did not sufficiently address how to manage mucosal eversion, suture tension, and bleeding encountered during live gastrotomy. AT viewing time positively correlated with mean total video score for Group T during both sessions. None of the students had prior experience performing hollow organ closure and no significant difference in experience level was evident between groups. Mean closure time was not significantly different between groups for session one (Group T, mean, 31.5 minutes, range, 18.4 to 53.4; Group S, mean, 28.2 minutes, range, 16.8 to 36), but was significantly reduced for session two (Group T, mean, 21.3 minutes, range, 13.9 to 31). This AT/simulator program does not significantly influence students' overall gastrotomy closure technique; gross and video evaluation scores were not significantly different between groups. Without instructor supervision, an additional gastrotomy experience did not improve surgical technique appreciably for Group T; however, these students performed the second procedure with more confidence and speed.(ABSTRACT TRUNCATED AT 400 WORDS)

Microcomputer software simulating problems in Rh immune globulin prophylaxis and hemolytic disease of the newborn

Our purpose was to develop educational software that would simulate laboratory investigation of problems in Rh immune globulin prophylaxis and hemolytic disease of the newborn. An interactive, branching style program was developed using a 256K Penonal Computer (International Business Machines, Boca Raton, FL). The software has been used in over 125 institutions for preprofessional and continuing professional education.

Evaluation of video tape and a simulator for instruction of basic surgical skills

Twenty first-year veterinary students with no prior participatory experience in surgery were randomly paired and assigned into two study groups. Ten students (group V) viewed a hemostatic technique video tape until they thought they could competently perform and assist in performing a hand-tied ligature on a blood vessel in a live animal. Ten students (group VS) wer also given a simulator for technique practice. Paired students were video recorded and blindly evaluated on their ability to perform and assist proper ligation of a bleeding vessel. Inexpensive hemostasis models were very helpful for teaching students essential surgeon and assistant skills involved in hand-tied ligature placement. Students who practiced with simulators performed significantly better as surgeon and assistant, and in total psychomotor skill evaluation, then students watching the video only. Students using simulators performed ligation with significantly more accuracy and tended to be more expeditious at this task. Further training is needed for students to acquire skills necessary for efficient bleeding vessel exposure and isolation.

Identification of a subset of group B donors reactive with monoclonal anti-A reagent

Two red blood cell (RBC) units labeled group B were returned to the source blood center after they had been retyped as AB by a transfusion service. The discrepancy could be reproduced, but only with the use of the transfusion service's reagent, Ortho Diagnostic's anti-A Bioclone (a licensed, blended, murine monoclonal anti-A reagent). RBCs from 35 of 3,458 random group B donors (1%) reacted with the monoclonal anti-A after immediate centrifugation. Reactivity was associated with high serum levels of B-gene-specified transferase and was caused by the MH04 component, a potent anti-A capable of detecting some examples of Ax RBCs. It is probable that the potency of MH04 permitted detection of low levels of A determinants synthesized by the donors' unusually strong B-gene-specified transferase. Transfer of N-acetylgalactosamine by B-gene-specified transferases, reported in vitro, has not been detected previously in vivo. Use of highly sensitive monoclonal reagents may result in clinically ambiguous blood grouping results.

A simple alternative for Rh phenotyping red cells that have a persistently positive Rh control

Investigation of a patient's red cell sample with a persistently positive Rh control revealed that if the patient's red cells were treated with ZZAP, then incubated at 37 degrees C with commercial Rhtyping reagents, then washed four times with saline, the positive Rh control could be circumvented and the Rh phenotype readily determined. One hundred red cell samples of known Rh phenotype were treated with ZZAP and coated with autoantibody to resemble the cells of the index case. Accurate results were obtained when these modified cell samples were tested against Rh typing reagents from three manufacturers using a 37 degrees C incubation followed by four saline washes. The procedure, termed Z37W, appears to be a simple alternative that can assist in determination of Rh phenotypes when the Rh control is positive.

Investigation of transfusion reactions through microcomputer education software

The purpose of this study was to develop educational software to simulate laboratory investigation of transfusion reactions. An interactive, branching-style program was developed using a 256K Personal Computer (International Business Machines, Boca Raton, FL). Over 75 institutions in the United States and Canada are currently using the software in preprofessional and continuing professional education programs.

Successful transplantation of blood group A2 kidneys into non-A recipients

The ABO subgroup A2 has been reported to be less reactive with the anti-A1 antibody naturally occurring in the serum of group O and B recipients and to occur in approximately 20% of group A individuals. Between March 1986 and February 1987, the Midwest Organ Bank (MOB) in Kansas City, screened all group A renal donors for the A2 subgroup. A total of 190 cadaverdonor kidneys were retrieved during this time, of which 68 were subgroup A1 and 16 were subgroup A2 (incidence of A2 = 19% of As and 8.5% of all donors). Of the subgroup A2 kidneys, 13 were transplanted into 9 group O and 4 group B recipients. One group O recipient received an HLA-identical A2 living-related graft. Recipients were not preselected or modified by splenectomy, plasmapheresis, or other means, and were treated with cyclosporine, steroids--and, in most cases, azathioprine, after transplantation. There was one hyperacute rejection and there were 5 acute cellular rejection episodes, 3 of which were reversed. One additional patient died at 2.5 months with a functioning graft. Including the successful living-related graft, 10 of 14 patients (71%) have functioning grafts, with a follow-up of 5 to 14 months, and a mean creatinine of 1.7 mg/dl. We find that the A2 subgroup represents a small but important minority of A donors, and that transplantation into non-A recipients can generally, but not universally, be safely accomplished. We recommend the screening of A donors for the A2 subgroup in both the cadaver-donor and living-related groups, and suggest that the utilization of A2 donors in non-A patients may contribute to the transplantation of group O and highly sensitized patients--and, in some cases, improve the degree of HLA matching.

Example of a thimerosal-dependent antibody without apparent blood group specificity

A third example of a thimerosal-dependent hemagglutinin is reported. The IgG antibody reacted by antiglobulin or ficin techniques with all cells incubated in the presence of thimerosal, including iadult cells and two examples of the Rhnull phenotype. Agglutination was inhibited by excess thimerosal (5 g/dl).

Solid-phase ABO grouping and Rh typing

A solid-phase adherence method (SPAM) for ABO grouping and Rh typing of red cells (RBCs) has been developed. Adherence reactions were read spectrophotometrically and interpreted by a computer. The SPAM had a 99.6 percent correlation with conventional microplate agglutination methods for ABO grouping and Rh typing. The increased sensitivity of the SPAM was demonstrated because it directly detected Du-positive RBCs and weak subgroups of A and B.

Solid-phase techniques in blood transfusion serology

For nearly a century, erythrocyte agglutination has persisted as the most widely used method for the demonstration of antigen-antibody reaction in immunohematology. So far, no other system has been developed which can match its simplicity, versatility, and general reliability. The major disadvantage of agglutination reactions is the lack of an objective endpoint, which has severely hindered attempts to automate routine pretransfusion tests. To overcome this problem, we have designed a series of solid-phase assays for ABO and Rh grouping, antibody screening, compatibility, and hepatitis tests. Each of these solid-phase assays shares a common endpoint of red cell adherence, which is easily interpreted visually or spectrophotometrically. Computer interface permits the automatic interpretation and recording of results. We believe this solid-phase system should finally bring the blood bank laboratory into the age of automation.

A solid-phase antiglobulin test

A solid-phase antiglobulin test was developed as an alternative to hemagglutination for compatibility testing. The solid-phase endpoint of red cell adherence allowed results to be read visually or spectrophotometrically. This method was easier to perform than a hemagglutination antiglobulin test and had increased sensitivity without loss of specificity.

A solid phase antibody screen

An automated solid phase antibody screen (SPAS) in microplates has been developed. Red blood cell (RBC) adherence was used as the end point instead of agglutination. Consequently, positive and negative reactions were readily distinguished by a microplate spectrophotometer. The SPAS performed as well as conventional antiglobulin methods for detecting IgG antibodies in donor sera and had increased sensitivity as determined by serial dilutions of antibodies.

Fatal intravascular immune hemolysis induced by hydrochlorothiazide

A patient receiving antihypertensive therapy developed acute intravascular hemolysis and died. Hemolysis was due to an immune process associated with antibody to thiazide. Only two other cases have been reported. Thiazide-induced hemolysis appears to be confined to those patients treated concommitantly with methyldopa.

Range forb lectins

In this study we tested the seeds of uncultivated plants for lectin activity. Extracts prepared from the seeds of 167 forb species were tested against human red cell samples. Extracts of 54 species agglutinated unmodified or enzyme-modified red cells. In nine species, the hemagglutinating lectin activity could be neutralized by N-acetyl-D-galactosamine, mannose, or glucose.

Incompatibility associated with the bite of a brown recluse spider (Loxosceles reclusa)

Red cell samples from a patient who was suffering from massive hemolysis due to a brown recluse spider (Loxosceles reclusa) bite were found to be reactive by indirect antiglobulin test with most ABO-compatible serum samples. Spider venom, enzymes related to those in spider venom, and antisera to plasma proteins and Rh antigens were used to investigate the unusual reactivity of the patient's cells. IgG was detected on the patient's cells by indirect antiglobulin tests. Cells treated with brown recluse spider venom or phosphatidylcholine phosphatidohydrolase reacted similarly. These findings suggest that sphingomyelinase D, which has been identified in brown recluse spider venom, may be related to the unusual reactivity of the patient's cells. Unexpected reactions were observed when venom-treated cells were tested with Rh antibodies: O negative cells absorbed and eluted anti-D from Rh immune globulin; E negative cells were reactive with a commercial anti-E reagent.

Anti-Wj: an autoantibody that defines a high-incidence antigen modified by the In(Lu) gene

An IgG autoantibody, named anti-Wj, reacts with all random and most selected red cell samples. It does not agglutinate cells of Lu(a-b-) type caused by the In(Lu) dominant inhibitor gene, but cells of recessive Lu(a-b-) type are reactive. These data establish that synthesis of the Wj antigen is suppressed by the In(Lu) gene, but it is not a part of the Lutheran blood group system. The Wj antigen is not well developed on fetal red cells. This example of auto anti-Wj is a non-complement-binding IgGl protein that did not appear to cause accelerated in vivo destruction of the patient's red cells.

Hematologic and enzymatic analysis of Ctenopharyngodon idella x Hypophthalmichthys nobilis F1 hybrids

1. Erythrocyte counts, hemoglobin concentrations and hematocrit values were determined for diploid and triploid Ctenopharyngodon idella X Hypophthalmichthys nobilis hybrids and the parental species. 2. Comparisons of diploid and triploid hybrids with the parental species revealed low erythrocyte counts for triploids, high mean corpuscular hemoglobin values for triploids, elevated hematocrits for diploids and triploids and similar hemoglobin concentrations for all fish. 3. Alkaline phosphatase, aldolase, and lactate dehydrogenase specific activities were determined spectrophotometrically. Levels of specific activity of these enzymes in the hybrids were consistently elevated above that of the parental species. These higher levels of enzyme activities in hybrids were probably the result of a breakdown in gene regulation.

Factors influencing monocyte recognition of human erythrocyte autoantibodies in vitro

Erythrocytes, serum, and blood monocytes from patients with erythrocyte autoantibodies were examined by in vitro serologic and cell culture procedures in order to evaluate factors modulating patient mononuclear phagocyte activity. Monocyte recognition of autoantibody-coated erythrocytes was influenced both by antibody titer score and by the monocyte source. The results suggest that patients with low serum autoantibody titer scores and normal monocyte behavior are less likely to destroy autologous or normal donor erythrocytes than are patients with high-serum antibody titer scores or enhanced monocyte activity. We conclude that patient, rather than normal donor monocytes, must be used in cellular assays designed to predict the fate of erythrocytes transfused into patients with erythrocyte autoantibodies.

SEM analysis of body hairs and whiskers of heterozygous tortoiseshell (Moto/+) female mice (Mus musculus)

Back hairs of +/+ and Moto/+ female Mus musculus generally exhibited identical form when examined by SEM. However, the hair shafts of Moto/+ female mice were beaded in appearance (monilethrix), twisted (pili torti) or exhibited a rough nodular appearance. Also, some hairs of Moto/+ female mice which were devoid of pigment appeared enlarged and bitubular. The whiskers of +/+ and Moto/+ female mice were identical in form. The hair abnormalities of Moto/+ female mice resulted from a copper deficiency and were similar to those hair anomalies observed in other mottled mice and in copper-deficient crinkled mice.