A comparison of three strategies for biopanning of phage-scFv library against diphtheria toxin

The biopanning process is a critical step in phage display for isolating peptides or proteins with specific binding properties. Conventional panning methods are sometimes not so effective and may result in nonspecific or low-yield positive results. In this study, three different strategies including soluble antibody-capturing, pH-stepwise elution, and conventional panning were used for enrichment of specific clones against diphtheria toxoid. The reactivity of the selected clones was evaluated using an indirect enzyme-linked immunosorbent assay. The positive clones were screened using Vero cell viability assay. The neutralizing clones were expressed in HB2151 strain of Escherichia coli and soluble single-chain fragment variable (scFv) fragments were purified by nickel-nitrilotriacetic acid affinity chromatography. Finally, the ability of scFv fragments for neutralizing diphtheria toxin (DT) were evaluated again using Vero cell viability assay. After four rounds of panning, the soluble antibody-capturing method yielded 15 positive phage-scFv clones against diphtheria toxoid. Conventional panning and pH-stepwise elution model resulted from nine and five positive phage-scFv clones, respectively. Among all positive clones, three clones were able to neutralize DT in Vero cell viability assay. Two of these clones belonged to a soluble antibody-capturing method and one of them came from conventional panning. Three neutralizing clones were used for soluble expression and purification of scFvs fragments. It was found that these soluble scFv fragments possessed neutralizing activity ranging from 0.15 to 0.6 µg against two-fold cytotoxic dose 99% of DT. In conclusion, the results of our study indicate that soluble antibody-capturing method is an efficient method for isolation of specific scFv fragments.     

Application of suppression subtractive hybridization (SSH) to cloning differentially expressed cDNA inDunaliella salina (chlorophyta) under hyperosmotic shock

Two subtracted cDNA libraries ofDunaliella salina (Volvocales, Chlorophyceae) under different hyperosmotic shock were constructed using the suppression subtractive hybridization (SSH) method. The mRNA isolated from algae grown without stress was used as a “driver”, and the mRNAs isolated from algae 16 h (short-term treatment) or 7 d (long-term treatment) after salt stress were used as “testers”. The differentially expressed cDNA fragments inD. salina under salt stress were identified by screening these 2 libraries. Two cDNA fragments,D27 andD114, were identified from clones pL27 and pL114 after the long-term treatment. Three cDNA fragments,D21, D39, andD88, were identified from clones pSh21, pSh39, and pSh88 after the short-term treatment. The homology analysis revealed that D27 was highly similar (91%) to the subunit V of PS I reaction center inChlamydomonas reinhardtii. D21 was similar to fructose-1,6-diphosphate aldolase (78.4%). After searching GenBank with the sequences ofD39, D88, andD114, no similar sequences were found. Northern analysis revealed that the expression levels of all 5 cDNAs were increased significantly after salt stress. This means that SSH can be used in cloning differentially expressed cDNAs inD. salina under salt stress. The expression ofD27, D21, andD88 wasde novo induced by salt stress, and the expression ofD114 andD39 was increased from a relatively lower level; this indicates that all 5 cDNAs might exert an influence on the alga under hyperosmotic shock.     

A family of serine protease genes expressed in adult buffalo fly (Haematobia irritans exigua)

Gene fragments encoding serine proteases expressed in adult buffalo fly (Haematobia irritans exigua) were amplified from cDNA using generic oligonucleotide PCR primers, based on conserved residues surrounding the active-site His and Ser amino acids found in all serine proteases. The PCR product consisted of a broad band extending from about 450 by to 520 bp, which suggested that the PCR product actually consisted of numerous DNA fragments of slightly variable sizes. Seventeen independent clones of these fragments, each with an insert of approximately 480 bp, were digested with HaeIII. Comparison of restriction fragment patterns indicated that 13 of these clones harboured different PCR products. This was confirmed by DNA sequence analysis of 9 clones. Each of the sequenced clones contained an open reading frame which included structurally conserved regions characteristic of the serine protease superfamily. This study reveals the expression of a large and highly variable repertoire of serine proteases in adult buffalo fly. Importantly, these data also demonstrate the utility of such an approach in obtaining DNA probes for use in further investigations of gene family organization and expression, as well as providing recombinant antigens in the form of fusion proteins which may be used as candidates for vaccine production.     

Identification of MADS genes from a brown alga,Sargassum fulvellum

The conserved region of numerous MADS genes in gulfweed (Sargassum fulvellum) was cloned by PCR with degenerate primers. Analysis of seventy individual clones resulted in the identification of nineteen types of nucleotide sequences. There sequences encode portions of the MADS domain in four distinctive groups. Six clones belong to the AGAMOUS subfamily, ten to AGL2, and two to AGL12. The remaining one clone is distinctive and appears to be diverged from an ancestor of the AGL2 and AP1 groups. There were no A or B class MADS genes. These results suggest that, as found in land plants, MADS genes also play major roles in controlling the development of algae.     

A false aciculariacean alga and its origin: an example from the Late Jurassic of the Northern Calcareous Alps,Austria

Slightly curved calcitic plates with marginal pores recalling an aciculariacean alga are common in Late Tithonian reefal platform margin deposits of the Plassen Carbonate Platform of the Northern Calcareous Alps of Austria. Illustrated also from the Western Carpathians, these forms were assigned to the genus Acicularia, e.g., Acicularia elongata Carozzi. It is demonstrated that these algal parts are not reproductive caps of polyphysacean algae (formerly known as acetabulariaceans), but represent sections through scattered articles fragments of the dasycladalean alga Neoteutloporella socialis (Praturlon), more precisely the proximal parts of the laterals. This alga formed reefal bushes at the platform margin near-by to coral-stromatoporoid patches. The characteristic aciculariacean algae recalling fragments occur in bioclastic packstones, a facies adjacent to these dasycladalean algal microreefs.     

Organization of mitochondrial DNA in normal and texas male sterile cytoplasms of maize

Recombinant DNA and hybridization techniques have been used to compare the organization of mitochondrial DNA (mtDNA) from normal (N) and Texas male sterile (T) cytoplasms of maize. Bam H1 restriction fragments of normal mtDNA were cloned and used in molecular hybridizations against Southern blots of Bam H1 digested N and T mtDNA. Fifteen of the 35 fragments were conserved in both N and T as indicated by hybridization to comigrating bands in their restriction patterns. Only three fragments produced autoradiographs whose differences could reasonably be attributed to single changes in the cleavage site of the enzyme while approximately half (17/35) of the clones resulted in more complicated differences between N and T. The autoradiographs produced by these 17 clones indicated multiple cleavage site changes and/or sequence rearrangements of the mtDNA. Patterns of six of these 17 clones indicated partial duplication of the sequence and two showed variation in the intensity of hybridization between N and T, which may be related to the molecular heterogeneity phenomenon found in maize mitochondrial genomes. The large proportion of changes observed between N and T mtDNA indicates that rearrangements may have played an important role in the evolution of the maize mitochondrial genome.     

Construction,characterization, and screening of a transformation-competent artificial chromosome library of peach

As a genome model of fruit trees, peach (Prunus persica [L.] Batch) has advantages for studying structural and functional genomics. Okubo, a traditional peach variety used as a parent in Asian peach breeding, displays economically valuable agronomic traits. To develop an efficient platform for peach gene cloning and genomic research, a large-insert genomic DNA library of Okubo was constructed in a transformation-competent artificial chromosome (TAC) vector, pYLTAC7, which can accept and stably maintain large genomic DNA fragments in bothEscherichia coli andAgrobacterium tumefaciens. The TAC library contains 41,472 recombinant clones with an average insert size of approximately 42 kb, and it is equivalent to 6 haploid peach genomes. The TAC library was stored in 2 ways: one copy as frozen cultures in 108 pieces of 384-well plates and another copy as bulked pools in 36 pieces of 96-well plates, each well containing 12 individual clones. The lack of hybridization signal to chloroplast and mitochondrial genes indicated that the TAC library had no significant cytoplast organelle DNA contamination. TAC clones were stable inE. coli cells until generation 100 and stable in bothE. coli andA. tumefaciens. Twenty-one clones containing the polygalacturonase-inhibiting protein (PGIP) gene were detected by using pooled PCR in the TAC library. Positive clones can be used for peach PGIP gene cloning and functional analysis. The library is well suited for gene cloning and genetic engineering in peach.     

Culture and taxonomic status of Chlorochytrium lemnae a green algal endophyte

Pure (axenic) strains of an intercellular endophyte identified as Chlorochytrium lemnae Cohn (= Chlorosphaeropsis lemnae Moewus) were isolated from infected duckweed (Lemna spp.). Pure cultures of the host were also obtained. Both grew well in mineral media, requiring no organic growth factors. In suitably dilute media, the algae could be induced to infect dead leaves of several different Lemna clones. Since its cells divide vegetatively by the formation of common cross walls (“desmoschisis”), Chlorochytrium lemnae should be transferred from the Chlorococcales to the Chaetophorales. The taxonomic status of other algae identified as Chlorochytrium—some of them demonstrated to be stages in the life-cycle of filamentous algae—should be re-evaluated.     

Construction and Characterization of a cDNA Library from the Pulp of Cara Cara Navel Orange （Citrus sinensis Osbeck）

A cDNA library was constructed end characterized from the pulp of Cera Care navel orange （Citrus sinensis Osbeck） at different stages of ripening. Tittering results revealed that approximately 5.086×10^5 independent clones were included in this library. Electrophoresls gel results of 15 randomly selected clones revealed that the size of the insertion fragments ranged from 400 bp to 2 kb, with an average size of 900 bp. Sequencing results of 150 randomly picked clones showed that the recombination rate was 94%. During subsequent sequence analysis, 41 of 139 clones failed to be identified end the amino sequence of 71 clones shared less than 30% identity with related plants in GenBank. Of 27 clones whose amino sequences shared more than 60% identity with other related plants in GenBenk, 17 clones showed an 80% identity with the corresponding candidate genes of citrus. The clone recognized as the type Ⅲ metallothlonein-llke （MT） gene was observed to occur 13 tlmes, Indlcatlng that the protein may play an important role In frult development and rlpenlng.     

Construction and characterization of a rice YAC library for physical mapping

Genomic libraries of rice,Oryza sativa L. cv. Nipponbare, in yeast artificial chromosomes were prepared for construction of a rice physical map. High-molecular-weight genomic DNA was extracted from cultured suspension cells embedded in agarose plugs. After size fractionation of theEco RI- andNot I-digested DNA fragments, they were ligated with pYAC4 and pYAC55, respectively, and used to transformSaccharomyces cerevisiae AB1380. A total of 6932 clones were obtained containing on average ca. 350 kb DNA. The YAC library was estimated to contain six haploid genome equivalents. The YACs were examined for their chimerism by mapping both ends on an RFLP linkage map. Most YACs withEco RI fragments below 400 kb were intact colinear clones. About 40% of clones were chimeric. Genetic mapping of end clones from large size YACs revealed that the physical distance corresponding to 1 cM genetic distance varies from 120 to 1000 kb, depending on the chromosome region. To select and order YAC clones for making contig maps, high-density colony hybridization using ECL was applied. With several probes, at least one and at most ten YAC clones could be selected in this library. The library size and clone insert size indicate that this YAC library is suitable for physical map construction and map-based cloning.     

Obtaining plantlets from apical meristem of the red alga Gelidium sp.

For the first time, plantlets were obtained from fragments and cell aggregates (CA) of apical meristem of the red alga Gelidium sp. After two months of cultivation, an initial weight of 100 mg of fragments and CA from fresh meristem produced 3 g of plantlets without rhizoids. During the same period of cultivation, 100 mg of meristem fragments and CA isolated from thalli by the freezing-thawing procedure produced more than 20 g of plantlets with rhizoids. It is assumed that our methods for obtaining plantlets from fragments and CA of fresh and frozen-thawed meristem could be used to generate mass planting material for cultivation of algae (plantlets with rhizoids) in the sea and for tank-bubbling cultivation (plantlets without rhizoids). We speculate that meristem cells of frozen-thawed algae might be natural “seedstock” in the Arctic and Antarctic seas.     

Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75–100 kilobase pairs

A multiple-hit bacteriophage P1 library containing DNA fragments from Drosophila melanogaster in the size range 75–100 kb was created and subjected to a preliminary evaluation for completeness, randomness, fidelity, and clone stability. This P1 library presently contains 3840 individual clones, or approximately two genome equivalents. The library was screened with a small set of unique-sequence test probes, and clones containing the sequences have been recovered. In situ hybridization with salivary gland chromosomes indicates that the clones originate from the site of the probe sequences in the genome, and filter hybridization of restriction digests suggests that the clones are not rearranged in comparison with the genomic sequences. Approximately 1.7% of the clones contain sequences that hybridize with ribosomal DNA. A small subset of these clones was tested for stability by examination of restriction fragments produced after repeated subculturing, and no evidence for instability was found. The P1 cloning system has general utility in molecular genetics and may provide an important intermediate level of resolution in physical mapping of the Drosophila genome.by W. Hennig     

Telomere-homologous sequences occur near the centromeres of many tomato chromosomes

Several bacteriophage lambda clones containinginterstitialtelomererepeats (ITR) were isolated from a library of tomato genomic DNA by plaque hybridization with the clonedArabidopsis thaliana telomere repeat. Restriction fragments lacking highly repetitive DNA were identified and used as probes to map 14 of the 20 lambda clones. All of these markers mapped near the centromere on eight of the twelve tomato chromosomes. The exact centromere location of chromosomes 7 and 9 has recently been determined, and all ITR clones that localize to these two chromosomes map to the marker clusters known to contain the centromere. High-resolution mapping of one of these markers showed cosegregation of the telomere repeat with the marker cluster closest to the centromere in over 9000 meiotic products. We propose that the map location of interstitial telomere clones may reflect specific sequence interchanges between telomeric and centromeric regions and may provide an expedient means of localizing centromere positions.     

Evaluating Methods for Transplanting Endangered Elkhorn Corals in the Virgin Islands

Restoration of rare corals is desirable and restoration projects are fairly common, but scientific evaluation of this approach is limited. We tested several techniques for transplant and restabilization of Acropora palmata (the elkhorn coral), an ecologically important Caribbean coral whose populations have suffered severe declines. In rough weather, fragments break‐off colonies of branching corals like A. palmata as a normal form of asexual reproduction. We transplanted naturally produced coral fragments from remnant populations to nearby restoration sites. Untouched control fragments at the donor site died faster and grew slower than fragments attached to the reef, so attaching fragments to the reef is beneficial. Transplanted fragments grew and died at a rate similar to fragments left at the donor site (both groups were attached to the reef), so there were no effects of moving fragments or differences in habitat quality between donor and restoration sites. Growth and survival were similar using four methods of attaching fragments to the reef: cable ties, two types of epoxy resin, and hydrostatic cement. Corals sometimes compete with the macroalgae that dominate degraded reefs, and clearing surrounding algae improved the growth of fragments. After 4 years, transplanted fragments grew to 1,450 cm² in area and so were potentially sexually active. Because the methods tested are simple and cheap, they could be used by volunteer recreational divers to restore locally extirpated A. palmata populations or to enhance reefs where natural recovery is slow.     

DNA analysis methods for recognizing species invasion: the example of Codium,and generally applicable methods for algae

Analysis of DNA can help to distinguish those morphological characters indicative of species difference from those representing retained traits or parallel evolution. This can be of great value in detecting recent invaders. The choice of which DNA characters to examine not only dictates the methodology to be used but must also be appropriate for the detection level sought. Restriction endonuclease fragment comparisons of plastid DNA have been used to assess Codium species; the results show C. fragile subsp. tomentosoides from east and west coast North America to be identical while sympatric endemic Codium species each display their own unique set of fragments. For species of other algae, plastid DNA fragment patterns are not necessarily identical across a morphological species, e.g. Pandorina morum. Such repetitive element probes as M13 and the use of RAPDs are more appropriate for analysis of populations within species. DNA base sequence comparisons of nuclear rDNA genes often yield too few variant bases between closely related species for reliable identifications. Analysis of the more variable Internal Transcribed Spacer (ITS) region, lying between the small and large ribosomal subunit genes in nuclear DNA, yields more extensive base pair variation between species and relatively little within species; it may be an alternative choice for endonuclease restriction fragment analysis or for sequencing.     

Assessment of gene copy number in the homosporous fernsCeratopteris thalictroides andC. richardii (Parkeriaceae) by restriction fragment length polymorphisms

Homosporous ferns are generally considered polyploid due to high chromosome numbers, but genetically diploid since the expression of isozymes is generally controlled by a single locus. Gene silencing over evolutionary time is one means by which this apparent contradiction can be explained. A prediction of this hypothesis is that silenced gene sequences still reside in the genomes of homosporous ferns. We examined the genomes ofCeratopteris richardii andC. thalictroides for sequences which are similar to expressed gene sequences. Genomic DNA blots hybridized withC. richardii cDNA clones showed that the majority of these clones detected multiple fragments, suggesting that most gene-like sequences are duplicated inCeratopteris. Hybridization signal intensity often varied between fragments of the same size between accessions, sometimes dramatically, which indicates that not all sequences are equivalent, and may represent the products of silenced genes. Observed reciprocal differences in intensity could be due to reciprocally silenced genes. In addition, an unusual segregation pattern for one locus followed by one probe may indicate homeologous chromosome pairing and segregation.     

Evidence for a fungal affinity for Nematasketum,a close ally of Prototaxites

As part of a project investigating diversity in early terrestrial vegetation, new specimens of the enigmatic, non‐embryophyte Nematasketum diversiforme have been described from Lower Devonian strata in the Welsh Borderland to elucidate its affinities and role in the ecosystem. Charcoalified fragments were investigated using scanning electron microscopy. They show for the first time that at least part of the organism possessed an axial organization with a peripheral zone forming a rind. The specimens differ from the closely‐allied Prototaxites by the presence of unevenly thickened tubes, both in well‐defined areas (medullary spots), hypothesized as being the sites of hyphal generation, and in the matrix of wide, smooth‐walled and narrow hyphae. Two specimens that show branching but no unequivocal thickened tubes are best assigned to the prototaxalean complex. The fragments, with longitudinally aligned wide tubes in a matrix of much branched, narrower examples, resemble rhizomorphs and cords of extant basidiomycote fungi and are interpreted as exploratory and translocating organs. Postulated affinities of Prototaxites include algae, fungi and hepatics, with the latter interpreting the fossils as rolled‐up liverwort mats. Our studies on a close ally of Prototaxites show no evidence for hepatic affinity, although similarities with fungal linear mycelial structures. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 1–18.     

Factors that Control the Species Composition of Freshwater Phytoplankton,with Special Attention to Nutrient Concentrations

Variations of species composition and population size of planktonic algae were studied in relation to the different nutrient levels in a eutrophic pond and an oligotrophic lake. The results obtained were discussed in comparison with the changes in photosynthesis and chlorophyll of several algal populations cultured under different nutrient conditions. As based on unialgal culture experiments two types of algae (the Chlorella-type and the Melosira-type) could be distinguished with regard to variations of photosynthesis and chlorophyll in response to different nutrient levels. Distribution of the Chlorella-type algae may be confined to eutrophic waters, while the Melosira-type algae can be distributed widely in waters from oligotrophic to eutrophic.     

Transformation of 12 different plasmids into soybean via particle bombardment

Particle bombardment offers a simple method for the introduction of DNA into plant cells. Multiple DNA fragments may be introduced on a single plasmid or on separate plasmids (co-transformation). To investigate some of the properties and limits of co-transformation, 12 different plasmids were introduced into embryogenic suspension culture tissue of soybean [Glycine max (L.) Merrill] via particle bombardment. The DNAs used for co-transformation included 10 plasmids containing KFLP markers for maize and 2 plasmids separately encoding hygromycin-resistance and ß-glucuronidase. Two weeks following bombardment with the 12 different plasmids, suspension culture tissue was placed under hygromycin selection. Hygromycin-resistant clones were isolated after an additional 5 to 6 weeks. Southern hybridization analysis of 26 hygromycin-resistant embryogenic clones verified the presence of introduced plasmid DNAs. All of the co-transforming plasmids were present in most of the transgenic soybean clones and there was no preferential uptake and integration of any of the plasmids. The copy number of individual plasmids was approximately equal within clones but highly variable between clones. While some clones contained as few as zero to three copies of each plasmid, others clones contained as many as 10 to 15 copies of each of the 12 different plasmids.     

Isolation of ScFv antibodies of rP27Kip1 from phage display libraries constructed from immunized and non-immunized repertoires

Through mRNA extract, RT and a series of PCR, phage antibody libraries were constructed from rP27^{kip 1}-immunized and non-immunized mice. After only one round of selection with rP27^{kip 1}, clones from each library were chosen randomly and digested byTag I and Hinf I. 11 of 64 clones from the immunized animal had consistent restriction pattern, while none of the 64 clones from the non-immunized animal had, except that one had the same fragments pattern as that of the 11 clones. The 12 fragments were expressed inE. coli BL21(DE3)/pET-28b(+) system. ELISA showed that some of the fragments could bind to rP27^{kip 1} specifically. AU these results implied that specific antibody can be obtained by genetic engineering without hybridoma or many rounds of growth and panning selection.