Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests - the case of sympatric and parapatric Marantaceae species.

Gene flow within and between species is a fundamental process shaping the evolutionary history of taxa. However, the extent of hybridization and reinforcement is little documented in the tropics. Here we explore the pattern of gene flow between three sister species from the herbaceous genus Marantochloa (Marantaceae), sympatrically distributed in the understorey of the African rainforest, using data from the chloroplast and nuclear genomes (DNA sequences and AFLP). We found highly contrasting patterns: while there was no evidence of gene flow between M. congensis and M. monophylla, species identity between M. monophylla and M. incertifolia was maintained despite considerable gene flow. We hypothesize that M. incertifolia originated from an ancient hybridization event between M. congensis and M. monophylla, considering the current absence of hybridization between the two assumed parent species, the rare presence of shared haplotypes between all three species and the high percentage of haplotypes shared by M. incertifolia with each of the two parent species. This example is contrasted with two parapatrically distributed species from the same family in the genus Haumania forming a hybrid zone restricted to the area of overlap. This work illustrates the diversity of speciation/introgression patterns that can potentially occur in the flora of tropical Africa.

Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences.

Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding.

Novel frameworks as a source of high-affinity ligands.

The past year has seen further maturation of the techniques used to display populations of proteins and peptides and to select members with desired properties. Many protein domains have now been displayed on genetic packages, diverse populations have been made, and binders with specific useful properties have been selected. Affinity maturation has been demonstrated so that binding in the low nanomolar to subnanomolar range by non-antibodies is now achievable.

Inflammation and infection imaging with a 99mTc-neutrophil elastase inhibitor in monkeys.

UNLABELLED: A radiolabeled human neutrophil elastase inhibitor (EPI-HNE-2) may represent an improved nuclear medicine imaging agent for inflammation and infection. This peptide displays rapid pharmacokinetics due to its low molecular weight and localizes specifically on neutrophil elastase released in inflammatory sites by activated neutrophils. METHODS: In this investigation, the peptide was radiolabeled with 99mTc using N-hydroxysuccinimidyl S-acetylmercaptoacetyltriglycline (NHS-MAG3) as a bifunctional chelator and was administered on 18 occasions to 5 rhesus monkeys with inflammation/infection. RESULTS: Plasma clearance was rapid, with liver and kidneys representing the major organs of accumulation. No evidence of toxicity, dosage effects, or circulating antiMAG3-EPI-HNE-2 antibodies was observed. Specificity of localization was established using radiolabeled bovine pancreatic trypsin inhibitor (a non-hNE-binding peptide of similar size) as a nonspecific negative control peptide and by predosing with unlabeled EPI-HNE-2 to block receptor sites before the administration of radiolabeled EPI-HNE-2. The ability of radiolabeled EPI-HNE-2 to image inflammation/infection was evaluated in 12 studies in monkeys receiving only radiolabeled EPI-HNE-2 and with lesions in the arm, shoulder, or lower back. Positive images were obtained in all studies, uptake was apparent almost immediately, and images were still positive 24 h later. As a positive control, animals also received nonspecific IgG antibody radiolabeled with 99mTc either directly or by NHS-MAG3. Compared with labeled antibody, plasma clearance of 99mTc was faster with labeled EPI-HNE-2 and accumulation in liver and heart was lower. Uptake of radioactivity in the inflammation was higher during the first hour with EPI-HNE-2 versus antibody but lower thereafter. CONCLUSION: When radiolabeled with 99mTc, EPI-HNE-2 localized specifically in inflammations in a monkey model and provided early images of diagnostic quality.

Labeling peptides with technetium-99m using a bifunctional chelator of a N-hydroxysuccinimide ester of mercaptoacetyltriglycine.

UNLABELLED: A modified mercaptoacetyltriglycine (MAG3) chelator, which has acetyl S-protection and which is derivitized with N-hydroxysuccinimide (NHS) ester for conjugation, has been used to radiolabel four small (approximately 6- to 7-kDa) peptides, bovine pancreatic trypsin inhibitor, epidermal growth factor, human neutrophil elastase inhibitor and plasmin inhibitor, with 99mTc. METHODS: Each peptide was specifically labeled at the MAG3 chelation sites at ambient temperature and neutral pH. Specific activities of 100-150 mCi/mg were achieved at labeling efficiencies of about 50%, but specific activities of 3500 mCi/micromol could be attained. RESULTS: By a variety of assays, protein activity was unimpaired by the conjugation and labeling for two of the four peptides. The activities for plasmin of the plasmin inhibitor and bovine pancreatic trypsin inhibitor were reduced by conjugation, presumably because of a sensitive lysine residue in the structure of each of these two peptides. Multiple peaks were present in the high-performance liquid chromatography radiochromatograms, especially of human neutrophil elastase inhibitor; however, most peaks could be shown to be labeled active peptide. Stability during cysteine challenge at modest cysteine-to-peptide molar ratios and during incubation in serum was observed in each case. Large differences among the labeled peptides were apparent in the 3-hr biodistributions of 99mTc in normal mice. CONCLUSION: The use of NHS-S-acetyl-MAG3 may be a convenient method of radiolabeling peptides with 99mTc.

Obtaining a family of high-affinity, high-specificity protein inhibitors of plasmin and plasma kallikrein.

Human lipoprotein-associated coagulation inhibitor (LACI) is a serum protein containing three Kunitz domains. We displayed the first domain (LACI-D1) on the III protein of phage M13 and made libraries of this domain. We iteratively varied 13 residues in the region corresponding to the BPTI-trypsin interface and selected for binding to human plasmin (PLA) and human plasma kallikrein (pKAL). For PLA, our first-round best binder, EPI-P211, had KD = 2 nM. Using information from the first selection, we made a PLA-biased library containing approximately 500,000 proteins and selected from these a protein, EPI-P302, having a KD for PLA of 87 pM. EPI-P302 inhibits pKAL with KD approximately 250 nM (approximately 2800-fold higher than for PLA) and KD values for other proteases are higher yet. From the same initial LACI-D1 library, we selected an inhibitor of pKAL, EPI-K401, with a KD for pKAL of 287 pM. We used information from this selection to construct a pKAL-biased library from which we selected EPI-K502, which has a KD for pKAL of 40 pM. EPI-K502 inhibits PLA with KD approximately 20 nM (500-fold higher than for pKAL); KD values for other proteases are much higher. For both targets and for both selections, there are families of proteins having a few differences and a range of affinities for their targets. These proteins are candidate drugs and imaging agents for indications involving excess PLA or pKAL. Structure-activity relationships of PLA and pKAL binders will allow design of small molecules that are specific for these targets.

Iterative optimization of high-affinity proteases inhibitors using phage display. 1. Plasmin.

We generated a series of libraries having variants of the first Kunitz domain of human lipoprotein-associated coagulation inhibitor (LACI-D1, also known as tissue-factor pathway inhibitor-I) displayed on bacteriophage M13 as pIII-fusions. We varied LACI-DI iteratively in two regions: the P1 region (positions 10-21) and the "second loop", (positions 31-39), which together form one end of the domain. Display-phage library Lib#1 allows 31 200 amino-acid sequences in P1 region (residues 13, 16-19). Preliminary, we screened Lib#1 against human plasmin (PLA, EC 3.4.21.7) immobolized on agarose to enrich for phage displaying variants with PLA affinity. We introduced a 1600-fold increase in second-loop diversity (residues 31, 32, 34, 39) into the population of selectants from Lib#1, yielding Lib#2. Lib#2 (allowing approximately 50 million amino-acid sequences) was screened against PLA-agarose to isolate highest affinity binders. Protein EPI-P211, derived from the best isolate of Lib#2, inhibits PLA with Ki = 2 nM (at least 500-fold better than LACI-D1) and with high specificity. We used amino-acid sequences of PLA-binding selectants to design a PLA-biased library (Lib#3) which we screened against PLA. The protein EPI-P302 (derived from the best binder obtained from Lib#3) has Ki for PLA inhibition of 87 pM, which is 25-fold better than the first-round best binder and > or = 12 500-fold better than LACI-D1. EPI-P302 also shows very high specificity for PLA vs other human proteases and is resistant to inactivation by oxidants and extremes of temperature or pH. Thus, one can use selectants from one library to design target-tailored combinatorial libraries and obtain quite stable, highly specific, very high-affinity binding molecules while maintaining an essentially human framework.

Iterative optimization of high-affinity protease inhibitors using phage display. 2. Plasma kallikrein and thrombin.

As discussed in the accompanying paper [Markland, W., Ley, A. C., & Ladner, R. C. (1996) Biochemistry 35, 8045-8057], we generated libraries from the first Kunitz domain of human lipoprotein-associated coagulation inhibitor (LACI-D1) using multivalent M13 III display and derived potent inhibitors of human plasmin (PLA) by iterative variegation and selection. Here, we show that high-affinity, high-specificity binders to human plasma kallikrein (pKAL) and human thrombin (THBN) can be obtained starting from the identical library and employing the same iterative variegation procedures used to obtain PLA inhibitors. Lib#1 (allowing 31 200 variants involving five positions near the P1 residue of LACI-D1) and its pKAL-biased derivative, Lib#4 (allowing an additional 1600 variants at residues 31, 32, 34, and 39), were screened against pKAL, yielding potent inhibitors. One of these, EPI-K401, has Ki = 284 pM, very high specificity, and excellent stability. We used information from Lib#4 selectants to design Lib#5 (allowing 1.5 x 10(6) amino-acid sequences involving nine varied positions) from which we obtained an inhibitor (EPI-K503) having high affinity for pKAL (Ki = 40 pM) and retaining the high specificity of EPI-K401. When we screened Lib#1 and its THBN-tailored derivative, Lib#6, against THBN, we obtained a different and very homogeneous population of selected molecules. The purified proteins derived from Lib#6 selectants bound to THBN-agarose beads but did not inhibit proteolytic activity of THBN, suggesting that these selectants bind to a site on THBN other than the catalytic site. Thus, a single large combinatorial library can serve as a source to obtain highly specific, high-affinity binding molecules for each of several targets. Furthermore, the results with THBN show that the binding of Kunitz domains to other proteins is not limited to the catalytic sites of trypsin-homologous proteases.

Perinatal 'TORCH' infections identified by serology: correlation with abnormalities in the children through 7 years of age.

A matched case-control methodology was used to assess the risk for a wide range of abnormalities in children associated with serological evidence for 'TORCH' infections in the mothers. Specimens were selected from the large bank of sera from the approximately 54,000 pregnant women who participated in the Collaborative Perinatal Project. There was no clear association between any of the antigens studied and any specific damage to the child. These 'negative' findings are consistent with the absence of frequent significant effects due to these agents in the second and third trimesters of pregnancy.

Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage.

Inhibitors of human neutrophil elastase were engineered by designing and producing a library of phage-displayed protease inhibitory domains derived from wild-type bovine pancreatic trypsin inhibitor and fractionating the library for binding to the target protease. The affinity of one of the engineered variants for human neutrophil elastase (Kd = 1.0 pM) is 3.6 x 10(6)-fold higher than that of the parental protein and exceeds the highest affinity reported for any reversible human neutrophil elastase inhibitor by 50-fold. Thus the display phage method has allowed us to obtain protein derivatives that exhibit greatly increased affinity for a predetermined target. The technology can be applied to design high-affinity proteins for a wide variety of target molecules.

Characterization of the ndhC-psbG-ORF157/159 operon of maize plastid DNA and of the cyanobacterium Synechocystis sp. PCC6803.

The ndhC and ORF159 genes of the maize plastid DNA (ptDNA) were sequenced and maize ORF159 was used to screen a library of genomic DNA of the blue-green alga Synechocystis sp. PCC 6803. The cyanobacterial gene homologous to ORF159 (ORF157) was isolated and sequenced. In sequencing the region upstream of ORF157, reading frames with homology to the ndhC and psbG genes of maize ptDNA were identified. The ndhC and psbG genes overlap in the ptDNAs of maize, tobacco and Marchantia polymorpha, but are separated by a noncoding spacer in Synechocystis. Northern blot analysis showed that the ndhC, psbG and ORF157/159 genes are cotranscribed in maize and Synechocystis. The three genes occur in the same order in ptDNA of maize, tobacco, and M. polymorpha as in Synechocystis 6803. The amino acid sequences of the NDH-C, PSII-G and the ORF157/159 proteins deduced from the maize genes are 65%, 52% and 53% homologous to those of Synechocystis. However, the cyanobacterial and higher plant NDH-C protein sequences are only 23% homologous to the mitochondrial NDH-3 protein. Protein products of in vitro transcription/translation of the Synechocystis transcription unit had apparent molecular masses of 6 kDa (NDH-C), 25 kDa (PSII-G) and 22 kDa (ORF157) on lithium dodecyl sulfate (LDS) polyacrylamide gel electrophoresis. If these are components of an NADH dehydrogenase, cyanobacteria appear to resemble mitochondria more than they do Escherichia coli and Rhodopseudomonas capsulata with regard to this enzyme complex.

Toxoplasmosis: maternal and pediatric findings in 23,000 pregnancies.

An analysis of the antibody titers to toxoplasmosis for 22,845 pregnant women in the Collaborative Perinatal Project was conducted in relation to clinical and laboratory findings in the mothers and children through 7 years of age. More than 900 observations were considered for each mother and child. The major findings were in the children and included a predicted doubling in the frequency of deafness among children born to women with antibody to toxoplasmosis, a predicted 60% increase in microcephaly, and a 30% increase in low IQ (less than 70) in association with the presence of high maternal antibody titer (256 to 512) to toxoplasma. A serologically defined high-risk group of mothers was identified on the basis of high indirect hemagglutination antibody levels or seroconversions and increased IgM toxoplasma antibody levels (indirect fluorescent antibody greater than or equal to 32, enzyme-linked immunosorbent assay greater than or equal to 0.7). Of the 15 pregnancies in this group, two children had congenital toxoplasmosis and three were stillborn.

Use of a light-induced respiratory transient to measure the optical cross section of photosystem I in chlorella.

A method has been developed whereby the magnitude of a transient in O(2) uptake attributable to photosystem (PS) I activity, following single-turnover laser flashes of varying energy, can be used to measure the optical cross section of PSI. As measurements are made under the identical physiological conditions for which the cross section of PSII has previously been determined (AC Ley, DC Mauzerall 1982 Biochim Biophys Acta 680: 96-105), it is now possible to simultaneously measure the cross section of both photosystems in intact, photosynthetically competent cells, without the use of inhibitors or artificial mediators of electron transport. Plots of light-saturation behavior of the respiratory oscillation following pulses at 596 nanometers indicate a mean optical cross section similar to that of PSII at this wavelength, but suggest significant heterogeneity in the cross section of PSI. If this method measures only PSI activity, this result implies that there exist units with different numbers of identical chromophores, or units having populations of chromophores with different absorption spectra.

Relationships among cell chlorophyll content, photosystem II light-harvesting and the quantum yield for oxygen production in Chlorella.

Cells of the green alga Chlorella vulgaris were grown under conditions where total Chl/cell varied by a factor of almost 80; from 0.02 fmol/cell to nearly 1.6 fmol/cell. The change in Chl/cell was accomplished by an approximately 11-fold increase in RCII/cell along with a 7-fold increase in Chl/RCII. The effective absorption cross section per RCII at 596 nm varied by a factor of 6, increasing with Chl/cell from a minimum of 20 A(2) to a maximum of 116 A(2). In contrast, over the same range of Chl/cell, the quantum requirement for O2 production remained relatively constant at 10.4±1.8 quanta absorbed/O2 evolved. The results are well described by a simple model in which changes in Chl/cell are produced by coordinated changes in reaction center and light-harvesting complexes. The model predicts that between 20 and 40% of the light-harvesting chlorophyll-protein complexes commonly assigned to PSII, do not function as antenna for PSII.

Effective Absorption Cross-Sections in Porphyridium cruentum: Implications for Energy Transfer between Phycobilisomes and Photosystem II Reaction Centers.

Effective absorption cross-sections for O(2) production by Porphyridium cruentum were measured at 546 and 596 nanometers. Although all photosystem II reaction centers are energetically coupled to phycobilisomes, any single phycobilisome acts as antenna for several photosystem II reaction centers. The cross-section measured in state I was 50% larger than that measured in state II.

Effects of growth irradiance levels on the ratio of reaction centers in two species of marine phytoplankton.

Cells of two species of single-celled marine algae, the diatom Skeletonema costatum (Greve), Cleve, and the chlorophyte Dunaliella tertiolecta Butcher, were cultured in white light of high (500-600 microeinsteins per square meter per second) and low (30 microeinsteins per square meter per second) intensity. For both algal species, cells grown at low light levels contained more chlorophyll a and had a lower ratio of chlorophyll a to chlorophylls b or c than did cells grown at high light levels. When photosynthetic unit sizes were measured on the basis of either oxygen flash yields or P(700) photooxidation, different results were obtained with the different species. In the chlorophyte, the cellular content of photosystem I (PSI) and photosystem II (PSII) reaction centers increased in tandem as chlorophyll a content increased so that photosynthetic unit sizes changed only slightly and the ratio PSI:PSII reaction centers remained constant at about 1.1. In the diatom, as the chlorophyll content of the cells increased, the number of PSI reaction centers decreased and the number of PSII reaction centers increased so that the ratio of PSI:PSII reaction centers decreased from about unity to 0.44. In neither organism did photosynthetic capacity correlate with changes in cellular content of PSI or PSII reaction centers. The results are discussed in relationship to the physical and biological significance of the photosynthetic unit concept.

Evaluation of commercially available diagnostic test kits for rubella.

Three standard hemagglutination-inhibition (HAI) methods were compared with 11 commercially available diagnostic test kits for determination of immunity and serologic diagnosis of rubella using a panel of 100 sera. The three standard HAI methods involved removal of serum inhibitors with kaolin, heparin-MnCl2, or dextran sulfate-CaCl2. The HAI kaolin (Flow Laboratories, McLean, Virginia) and Rubelisa (Microbiological Associates Bioproducts, Walkersville, Maryland) kits gave the best specificity as judged by the absence of false-positive results. Rubacell (Abbott Laboratories, Chicago, Illinois), Rubindex (Ortho Diagnostics, Raritan, New Jersey), Fiax (International Diagnostic Technology, Santa Clara, California), and Rubesure (Calbiochem-Behring, La Jolla, California) gave the best sensitivity as judged by the absence of false-negative results. The kits with the highest degree of both specificity and sensitivity were HAI kaolin (Flow), HAI heparin-MnCl2 (Flow), Rubacell (Abbott), and Rubindex (Ortho). In paired sera from five patients with clinical rubella, seroconversions were shown by seven of the kits. One of the kits, Cordia R (Cordis Laboratories, Miami, Florida), showed no significant rise in antibody titer with one pair of sera. Antibody titers in the same serum varied widely between the different kits.

Energy distribution in the photochemical apparatus of Porphyridium cruentum in state I and state II.

Fluorescence of Porphyridium cruentum in state I (cells equilibrated in light absorbed predominantly by Photosystem I) and in state II (cells equilibrated in light absorbed appreciably by Photosystem II) was examined to determine how the distribution of excitation energy was altered in the transitions between state I and state II. Low temperature emission spectra of cells frozen state I and state II confirmed that a larger fraction of the excitation energy is delivered to Photosystem II in state I. Low temperature measurements showed that the yield of energy transfer from Photosystem II to Photosystem I was greater in state II and calculations indicated that the photochemical rate constant for such energy transfer was approximately twice as large in state II. Measurements at low temperature also showed that the cross sections and the spectral properties of the photosystems did not change in the transitions between state I and state II. In agreement with predictions made from the parameters measured at low temperature, the action spectra for oxygen evolution measured at room temperature were found to be the same in state I and state II.

Effects of Chromatic Adaptation on the Photochemical Apparatus of Photosynthesis in Porphyridium cruentum.

Cells of Porphyridium cruentum were grown in different colors of light which would be absorbed primarily by chlorophyll (Chl) (red and blue light) or by the phycobilisomes (green or two intensities of cool-white fluorescent light), and samples of these cells were frozen to -196 C for measurements of absorption and fluorescence emission spectra. Cells grown in the high intensity white light had least of all of the photosynthetic pigments, a higher ratio of carotenoid/Chl, but essentially the same ratio of phycobilin to Chl as cells grown in the low intensity white light. The ratio of photosystem II (PSII) to photosystem I (PSI) pigments was affected by light quality; the ratios of phycobilin to Chl and of short wavelength (PSII) Chl to long wavelength (PSI) Chl were both greater in the cells grown in red or blue light.Light quality also exerted a strong influence on the structural and functional organization of the photochemical apparatus. Data on the relative optical cross-sections of PSI and PSII as a function of excitation wavelength indicate that cells grown in light absorbed primarily by the phycobilisomes package a large fraction of their Chl into PSI (PSI Chl/PSII Chl approximately 20), whereas cells grown in light absorbed by Chl distribute their Chl much more equitably (PSI Chl/PSII Chl approximately 1.5). In both types of cells the phycobilisomes transfer their excitation energy predominantly to PSII Chl with little or no direct energy transfer to PSI, but the yield of energy transfer from PSII to PSI is approximately twice as large for cells grown in the phycobilin wavelengths of light. These differences in functional organization and energy distribution account for the physiological expressions of chromatic adaptation. The effects of chromatic adaptation on O(2) evolution can be predicted from our calculations of energy distribution between PSI and PSII for cells grown in the different colors of light.