Complexity of avian evolution revealed by family-level genomes

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

A region of suppressed recombination misleads neoavian phylogenomics

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data

Recent dynamic lineage tracing technologies combine CRISPR-based genome editing with single-cell sequencing to track cell divisions during development. A key computational problem in dynamic lineage tracing is to infer a cell lineage tree from the measured CRISPR-induced mutations. Three features of dynamic lineage tracing data distinguish this problem from standard phylogenetic tree inference. First, the CRISPR-editing process modifies a genomic location exactly once. This non-modifiable property is not well described by the time-reversible models commonly used in phylogenetics. Second, as a consequence of non-modifiability, the number of mutations per time unit decreases over time. Third, CRISPR-based genome-editing and single-cell sequencing results in high rates of both heritable and non-heritable (dropout) missing data. To model these features, we introduce the Probabilistic Mixed-type Missing (PMM) model. We describe an algorithm, LAML (Lineage Analysis via Maximum Likelihood), to search for the maximum likelihood (ML) tree under the PMM model. LAML combines an Expectation Maximization (EM) algorithm with a heuristic tree search to jointly estimate tree topology, branch lengths and missing data parameters. We derive a closed-form solution for the M-step in the case of no heritable missing data, and a block coordinate ascent approach in the general case which is more efficient than the standard General Time Reversible (GTR) phylogenetic model. On simulated data, LAML infers more accurate tree topologies and branch lengths than existing methods, with greater advantages on datasets with higher ratios of heritable to non-heritable missing data. We show that LAML provides unbiased time-scaled estimates of branch lengths. In contrast, we demonstrate that maximum parsimony methods for lineage tracing data not only underestimate branch lengths, but also yield branch lengths which are not proportional to time, due to the nonlinear decay in the number of mutations on branches further from the root. On lineage tracing data from a mouse model of lung adenocarcinoma, we show that LAML infers phylogenetic distances that are more concordant with gene expression data compared to distances derived from maximum parsimony. The LAML tree topology is more plausible than existing published trees, with fewer total cell migrations between distant metastases and fewer reseeding events where cells migrate back to the primary tumor. Crucially, we identify three distinct time epochs of metastasis progression, which includes a burst of metastasis events to various anatomical sites during a single month.

Barriers and Facilitators of Surgical Prehabilitation Adherence from the Patient Perspective: a Mixed Method Study

BACKGROUND

Adherence to prehabilitation is crucial for optimal benefit, but reasons for low adherence to home-based programs remain unexplored. Our aim was to identify and explore barriers and facilitators to prehabilitation adherence among patients undergoing abdominal surgery.

METHODS

Nested in a single-center randomized controlled trial on prehabilitation (Perioperative Optimization With Enhanced Recovery (POWER)), this study had an explanatory sequential design with a connect integration. Patients randomized to the intervention arm were included in the quantitative analysis, and a subset of them was invited for a semi-structured interview. The exposure was the frequency of barriers to physical activity and healthy eating, and the outcome was adherence to those components of prehabilitation. Logistic or linear regression was used as appropriate.

RESULTS

Among 133 participants in the intervention arm, 116 (87.2%) completed the initial survey ((56.9% women, median age 61 years old (IQR 49.0; 69.4)). The most frequent barriers to exercise and healthy eating were medical issues (59%) and lack of motivation (31%), respectively. There was no significant association between the barriers to physical activity score and adherence to this component of the program (OR 0.89, 95% CI 0.78-1.02, p=0.09). Higher barriers to healthy eating scores were associated with lower Mediterranean diet scores pre- and post-intervention (coef.: -0.32, 95% CI: -0.49; -0.15, p<0.001; and coef.: -0.27, 95% CI: -0.47; -0.07, p=0.01, respectively). Interviews with 15 participants revealed that participating in prehabilitation was a motivator for healthy eating and exercising through goal setting, time-efficient workouts, and promoting self-efficacy.

CONCLUSIONS

We identified key barriers to be addressed and facilitators to be leveraged in future prehabilitation programs.

TRIAL REGISTRATION

NCT04504266.

Views from the trenches: California family physicians' challenges and resilience factors while providing patient care during the initial wave of COVID-19

This study examined challenges and factors promoting resilience among 20 California family physicians (FPs) during the first six months of the COVID-19 pandemic. A subset of academic, community, and resident FPs who responded to an online survey also participated in a semi-structured interview that explored concerns, moral distress, burnout, resource needs, support systems, coping strategies, and motivation to continue caring for patients. Thematic analysis was used to identify common themes in participant interviews. Interviewees demonstrated adaptability, resilience, and grit (i.e., commitment to completing a valued goal in the face of setbacks and adversity) despite challenges disrupting patient care, fears for family and self, and frustration due to the politicization of the pandemic. Factors promoting well-being and perseverance included professional and personal support, strong coping skills, and focusing on the meaning derived from practicing medicine. A service orientation that permeates family medicine philosophy and values motivated practitioners to continue to provide patient care while dealing with overwhelming personal and structural challenges. FPs drew strength from their internal coping skills, core family medicine values, and external support, notwithstanding demoralizing effects of mixed messages and politicization of the pandemic. FPs demonstrated resilience and grit in the face of challenges created by the COVID-19 pandemic. Ensuring adequate resources to promote a physically and psychologically healthy workforce while increasing access to care for all patients is crucial to prepare for the next healthcare crisis.

Completing gene trees without species trees in sub-quadratic time

MOTIVATION

As genome-wide reconstruction of phylogenetic trees becomes more widespread, limitations of available data are being appreciated more than ever before. One issue is that phylogenomic datasets are riddled with missing data, and gene trees, in particular, almost always lack representatives from some species otherwise available in the dataset. Since many downstream applications of gene trees require or can benefit from access to complete gene trees, it will be beneficial to algorithmically complete gene trees. Also, gene trees are often unrooted, and rooting them is useful for downstream applications. While completing and rooting a gene tree with respect to a given species tree has been studied, those problems are not studied in depth when we lack such a reference species tree.

RESULTS

We study completion of gene trees without a need for a reference species tree. We formulate an optimization problem to complete the gene trees while minimizing their quartet distance to the given set of gene trees. We extend a seminal algorithm by Brodal et al. to solve this problem in quasi-linear time. In simulated studies and on a large empirical data, we show that completion of gene trees using other gene trees is relatively accurate and, unlike the case where a species tree is available, is unbiased.

AVAILABILITY AND IMPLEMENTATION

Our method, tripVote, is available at https://github.com/uym2/tripVote.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Log Transformation Improves Dating of Phylogenies

Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.

Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants

Lung macrophages mature after birth, placing newborn infants, particularly those born preterm, within a unique window of susceptibility to disease. We hypothesized that in preterm infants, lung macrophage immaturity contributes to the development of bronchopulmonary dysplasia (BPD), the most common serious complication of prematurity. By measuring changes in lung macrophage gene expression in preterm patients at risk of BPD, we show here that patients eventually developing BPD had higher inflammatory mediator expression even on the first day of life. Surprisingly, the ex vivo response to LPS was similar across all samples. Our analysis did however uncover macrophage signature genes whose expression increased in the first week of life specifically in patients resilient to disease. We propose that these changes describe the dynamics of human lung macrophage differentiation. Our study therefore provides new mechanistic insight into both neonatal lung disease and human developmental immunology.

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

TreeCluster: Clustering biological sequences using phylogenetic trees

Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is ultimately the result of their phylogenetic relationships. Despite this observation and the natural ways in which a tree can define clusters, most applications of sequence clustering do not use a phylogenetic tree and instead operate on pairwise sequence distances. Due to advances in large-scale phylogenetic inference, we argue that tree-based clustering is under-utilized. We define a family of optimization problems that, given an arbitrary tree, return the minimum number of clusters such that all clusters adhere to constraints on their heterogeneity. We study three specific constraints, limiting (1) the diameter of each cluster, (2) the sum of its branch lengths, or (3) chains of pairwise distances. These three problems can be solved in time that increases linearly with the size of the tree, and for two of the three criteria, the algorithms have been known in the theoretical computer scientist literature. We implement these algorithms in a tool called TreeCluster, which we test on three applications: OTU clustering for microbiome data, HIV transmission clustering, and divide-and-conquer multiple sequence alignment. We show that, by using tree-based distances, TreeCluster generates more internally consistent clusters than alternatives and improves the effectiveness of downstream applications. TreeCluster is available at https://github.com/niemasd/TreeCluster.

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

BACKGROUND

Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny.

RESULTS

We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled.

CONCLUSIONS

TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

Isolation of alpha-toxin-producing Staphylococcus aureus from the skin of highly sensitized adult patients with severe atopic dermatitis

BACKGROUND

Staphylococcus aureus (S. aureus) is a well-known trigger factor of atopic dermatitis (AD). Besides staphylococcal superantigens, alpha-toxin may influence cutaneous inflammation via induction of T-cell proliferation and cytokine secretion.

OBJECTIVES

To investigate the association between sensitization to inhalant allergens and skin colonization with alpha-toxin-producing S. aureus in AD.

PATIENTS AND METHODS

We investigated 127 patients with AD, aged 14-65 years, who were on standard anti-inflammatory and antiseptic treatment before investigation. We evaluated skin colonization, medical history, severity of AD and sensitization to inhalant allergens.

RESULTS

Forty-eight of 127 patients were colonized with S. aureus, suffered from more severe AD, had asthma more often and showed higher sensitization levels to inhalant allergens. Thirty of 48 patients with S. aureus skin-colonizing strains produced alpha-toxin and had higher total IgE and specific IgE to birch pollen and timothy grass pollen.

CONCLUSIONS

Under topical treatment with antiseptic and anti-inflammatory agents the colonization of lesional skin with S. aureus was clearly lower than commonly found in untreated patients with AD. Colonization with S. aureus was associated with a higher severity of AD, higher degree of sensitization, and a higher frequency of asthma. The proportion of patients whose skin was colonized with alpha-toxin-producing S. aureus was higher than expected from a former study. Cutaneous colonization with alpha-toxin-producing S. aureus was associated with a higher sensitization level to birch pollen allergen in AD. This may point to a higher susceptibility of patients with higher T-helper 2 polarization towards alpha-toxin-producing S. aureus.

Alpha-toxin is produced by skin colonizing Staphylococcus aureus and induces a T helper type 1 response in atopic dermatitis

BACKGROUND

Staphylococcus aureus is a well known trigger factor of atopic dermatitis (AD). Besides the superantigens, further exotoxins are produced by S. aureus and may have an influence on the eczema.

OBJECTIVE

To explore the impact of staphylococcal alpha-toxin on human T cells, as those represent the majority of skin infiltrating cells in AD.

METHODS

Adult patients with AD were screened for cutaneous colonization with alpha-toxin producing S. aureus. As alpha-toxin may induce necrosis, CD4(+) T cells were incubated with sublytic alpha-toxin concentrations. Proliferation and up-regulation of IFN-gamma on the mRNA and the protein level were assessed. The induction of t-bet translocation in CD4(+) T cells was detected with the Electrophoretic Mobility Shift Assay.

RESULTS

Thirty-four percent of the patients were colonized with alpha-toxin producing S. aureus and alpha-toxin was detected in lesional skin of these patients by immunohistochemistry. Sublytic alpha-toxin concentrations induced a marked proliferation of isolated CD4(+) T cells. Microarray analysis indicated that alpha-toxin induced particularly high amounts of IFN-gamma transcripts. Up-regulation of IFN-gamma was confirmed both on the mRNA and the protein level. Stimulation of CD4(+) T cells with alpha-toxin resulted in DNA binding of t-bet, known as a key transcription factor involved into primary T helper type 1 (Th1) commitment.

CONCLUSION

alpha-toxin is produced by S. aureus isolated from patients with AD. We show here for the first time that sublytic alpha-toxin concentrations activate T cells in the absence of antigen-presenting cells. Our results indicate that alpha-toxin is relevant for the induction of a Th1 like cytokine response. In AD, this facilitates the development of Th1 cell dominated chronic eczema.

Use of autoradiography to assess viability of Helicobacter pylori in water

Autoradiographic methods have been developed to detect metabolic activity of viable but nonculturable cells of Helicobacter pylori in water. Four strains of H. pylori were studied by using microcosms containing suspensions of 72-h cultures in water. The suspensions of aged, nonculturable cells of H. pylori were incubated with [3H]thymidine for 24 to 72 h, after which the cell suspensions were exposed to Kodak NTB2 emulsion for 3 to 28 days. Each sample was processed with three separate controls to rule out false-positive reactions. The organism remains viable and culturable under these conditions for up to 48 h and, in some cases, 20 to 30 days, depending on physical conditions of the environment. We found that temperature was a significant (P < or equal to 0.01) environmental factor associated with the viability of H. pylori cells in water. Autoradiographs of tritium-labeled cells of H. pylori revealed aggregations of silver grains associated with uptake by H. pylori of radiolabelled substrate. Findings based on the autoradiographic approach give strong evidence supporting the hypothesis that there is a waterborne route of infection for H. pylori. The possibility that H. pylori may persist in water in a metabolically active stage but not actively growing and dividing is intriguing and relevant to public health concerns.

[Serodiagnosis of Campylobacter pylori]

The colonization of gastric mucosa with Campylobacter pylori can be detected by serological methods. ELISA and immunoblot methods are currently being employed for detection of antibodies against Campylobacter pylori. In general, both tests will differentiate between Campylobacter pylori positive and Campylobacter pylori negative patients. However, 5-10% of persons with negative cultures for Campylobacter pylori have positive serological tests, but only very few patients with Campylobacter pylori associated with chronic gastritis have negative serological tests. This is true for tests detecting IgG and IgA antibodies. Tests for IgM antibodies have not been found to be useful. Immunoblot analyses have shown that detection of antibodies against a 100-120 KD antigen has a high specificity for Campylobacter pylori infection. In a small study we evaluated the possible use of serological testing for follow-up studies on patients after Campylobacter pylori therapy. We found that patients who became Campylobacter pylori negative after therapy showed a significant decline of serum IgG titers against Campylobacter pylori.

[Campylobacter pylori: clinical correlations and prospective comparative studies of various diagnostic techniques]

The diagnostic performance of two different urease tests and of histologic search after modified Giemsa staining to detect Campylobacter pylori (CP) colonization of the upper gastrointestinal tract was prospectively investigated in 215 esophagogastroduodenoscopies, by using a sensitive culture technique as reference. Single antral urease tests had a high specificity of 95-96%, but a limited sensitivity of 78-83%, which increased to 91-94%, when one antral and one additional body biopsy were submitted to the biochemical tests. Giemsa stains were very sensitive, but less specific. The rate of colonization was similar in antrum and body biopsies, and increased with age. There was a close association of Campylobacter pylori colonization with duodenal and to a lower degree with gastric ulcer disease, but especially with gastritic mucosal changes. CP was never detected in patients without gastritis. Therefore, submitting one antral and one body biopsy specimen to validated urease tests represents a sensitive (91-94%) and specific (93%) method to detect Campylobacter pylori colonization, which appears to be a diffuse phenomenon affecting antral and body mucosae with similar frequency.

Ultrastructure and chemical analysis of Campylobacter pylori flagella

Flagella of Campylobacter pylori were analyzed by electron microscopy and purified, and the molecular weight of the flagellin was determined. Isolation of flagella was performed by mechanical shearing from the cell surface, sucrose density gradient centrifugation, and Sepharose CL-4B gel chromatography. The flagella of C. pylori differ from those of other Campylobacter species and of most other bacteria by the presence of a flagellar sheath. The sheath narrows at the end and is linked to a club-shaped terminal structure. The molecular weight of C. pylori flagellin was 51,000.

Are dyspeptic symptoms in patients with Campylobacter pylori-associated type B gastritis linked to delayed gastric emptying?

In this paper, the association of gastric Campylobacter pylori (CP) colonization with histologic findings and gastric emptying of a mixed solid-liquid meal was prospectively investigated in 43 consecutive patients with essential non-ulcer dyspepsia (ENUD). Gastric emptying was also measured in 30 symptom-free control subjects. The frequency of CP infection in patients with ENUD was 44.2%. We found a strong association between gastric CP colonization and chronic antral type B gastritis. Although gastric emptying was significantly prolonged in patients with ENUD, compared with the control group (p less than 0.05), we could not detect significant differences of gastric emptying between CP-negative and CP-positive ENUD patients, both groups disclosing a similar proportion of patients with significantly delayed gastric emptying (29.2% vs 31.6%). We therefore conclude that delayed gastric emptying of a mixed solid-liquid meal is not correlated with CP-positive chronic antral type B gastritis, and does not help to explain dyspeptic symptoms, which may possibly arise in relation to gastric CP colonization.

[Microbiology of Campylobacter pylori]

Campylobacter pylori is a hitherto unknown spiral bacterium. It is implicated in the pathogenesis of chronic antral type B gastritis and also of duodenal and gastric ulcer disease. However, its causal role has not yet been unequivocally established. Taxonomically, C.pylori appears to belong to a genus different from genuine campylobacters, but a precise classification is likewise lacking. The in vitro sensitivity analyses of various antibiotics are complicated by a number of technical difficulties. This is one of the reasons, that results of in vivo eradication trials have to be interpreted with considerable caution.

Monotherapy or polychemotherapy in the treatment of Campylobacter pylori-related gastroduodenal disease

Three pilot studies were performed to evaluate the efficacy of bismuth subsalicylate (BSS) and nitrofurantoin to eradicate Campylobacter pylori colonization in man. Nitrofurantoin 3 x 100 mg capsules for 10 days did not clear C. pylori in any of 13 patients, and neither did the combination of BSS and nitrofurantoin suspension (0/6 patients). Immediately after high dose BSS therapy 3 x 900 mg for 28 days, 8/17 patients (47%) had negative cultures and rapid urease tests. There was recrudescence in 5 out of 6 patients so far submitted to follow-up investigations, giving a best possible outcome estimate of 18% and a worst possible eradication rate of 6% in this study. Preliminary data indicate that triple therapy may be a more effective option, but doubts remain as to whether the puristic therapeutic goal of complete bacterial eradication can be safely and effectively achieved with presently available drugs.

Identification of fragments of proximal and distal tubular cells in the urine of patients under cytostatic treatment by immunoelectron microscopy with monoclonal antibodies

In an attempt to identify the origin of cellular fragments released in the urine of patients treated with potentially nephrotoxic drugs such as cytostatics, two monoclonal antibodies were applied: monoclonal antibody PM II 9 C2, directed against an antigen in distal tubular cells; and monoclonal antibody PM II 39 H11 specific for an antigen in proximal tubular cells. The specificities of both monoclonal antibodies were elaborated in the indirect as well as in the direct immunofluorescence technique. Both antibodies were then used to identify cellular fragments obtained from the urine of patients treated with cytostatic drugs by ultracentrifugation. By application of the indirect immunogold method, it was shown that material of proximal as well as distal tubular origin was shed by the damaged cells. Whereas the proximal tubular antigenic epitope recognized by PM II 39 H11 was always found in large irregular complexes of debris-containing vesicles, the distal tubular antigenic epitope recognized by PM II 9 C2 was always found associated with filament-like regular structures. This is the first report in which excretion of components of distal tubular cells is demonstrated as a consequence of the nephrotoxic side effects of cytostatic treatment. With the help of monoclonal antibodies, it has now become possible to identify and to investigate the damage inflicted on the distal part of the tubule system in addition to the well-documented proximal tubular damage.

Kidney-derived urinary antigens assayed with monoclonal antibodies for the detection of renal damage

For the quantitation of kidney-derived Urinary Antigens (UA) monoclonal antibodies specific for antigens localized in cells of defined subunits of the nephron were applied in sandwich ELISA. Antigen excretion was measured in the urine of healthy individuals, patients suffering from various diseases, kidney transplant recipients, and healthy volunteers receiving therapeutic doses of antibiotic drugs. In healthy individuals, in patients with diseases primarily affecting the glomerulus, and in inactive phases of chronic diseases antigen excretion was low. Toxic drug effects enhanced antigenuria. Excretion of some or all of the antigens always indicated tubular alterations. The tests thus provide information on location and extent of acute primary tubular damage.

Urinary kidney-derived antigens determined by tests built on monoclonal antibodies: new markers for kidney damage

We have developed a series of sandwich ELISA for the quantitation of kidney derived urinary antigens (UA) utilizing monoclonal antibodies specific for antigens localized in cells of defined subunits of the nephron of human kidney. Antigens derived from the distal and proximal parts of the tubular system as well as antigens localized over its entire length can be detected and quantified in urine samples. Antigen excretion was measured in the urine of healthy individuals, patients with various diseases with and without kidney involvement, kidney transplant recipients, and healthy volunteers after receiving antibiotics. Low antigen excretion values were found in healthy individuals, patients with diseases primarily affecting the glomerulus, and inactive phases of chronic diseases. Toxic side effects of drugs were reflected by slightly (antibiotic drugs) or strongly (cytostatic drugs) enhanced antigenuria. Excretion of some or all of the antigens was always indicative of massive alteration of tubular structures, such as in acute phases of tubulointerstitial disease or during rejection episodes in kidney transplant recipients. The results obtained indicate that it is possible to obtain information on the location and extent of acute primary processes in the kidney with these tests.

Polyclonal and monoclonal antibodies as reagents in biochemical and in clinical-chemical analysis

Conventionally prepared polyclonal antibodies have been used for a long time in biomedical research and in clinical-chemical diagnosis. The hybridoma technology introduced by Köhler & Milstein [1975) Nature 256, 495-497), has opened the way to a new dimension in serology. It is now possible to prepare monoclonal antibodies to any determinant on any component of biological matter. Such monoclonal and thus specific antibodies can be obtained even against previously unknown antigens which had not been available in purified or enriched form. Thus the dreams of immunologists and clinical scientists who were searching for new disease-related markers, have become a reality. The present impact and the predictable future influence of these new developments on biomedical research and especially on clinical-chemical diagnosis, as well as their potential, limitations and problems, will be critically reviewed in this paper. As an example of the potential of the new technology, recent results of tests on the quantitation of urinary kidney-derived antigens with the help of monoclonal antibodies are presented. With these monoclonal antibodies, which are specific for antigens in defined regions of the nephron of the human kidney, recognition of the location and extent of primary damage at the cellular level will be possible without invasive techniques.