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PubMed2006

Nonoverlapping functions of DNA polymerases mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo.

DNA polymerases mu (pol mu), lambda (pol lambda), and terminal deoxynucleotidyltransferase (TdT) are enzymes of the pol X family that share homology in sequence and functional domain organization. We showed previously that pol mu participates in light chain but surprisingly not heavy chain gene rearrangement. We show here that immunoglobulin heavy chain junctions from pol lambda-deficient animals have shorter length with normal N-additions, thus indicating that pol lambda is recruited during heavy chain rearrangement at a step that precedes the action of TdT. In contrast to previous in vitro studies, analysis of animals with combined inactivation of these enzymes revealed no overlapping or compensatory activities for V(D)J recombination between pol mu, pol lambda, and TdT. This complex usage of polymerases with distinct catalytic specificities may correspond to the specific function that the third hypervariable region assumes for each immunoglobulin chain, with pol lambda maintaining a large heavy chain junctional heterogeneity and pol mu ensuring a restricted light chain junctional variability.

Animals↗
PubMed2006

Some guidelines for the analysis of genomic DNA by PCR-LC-ESI-MS.

Ion-pair reversed-phase high-performance liquid chromatography online hyphenated to electrospray ionization mass spectrometry (ICEMS) represents an efficient method for the characterization of nucleic acids amplified by polymerase chain reaction (PCR). Since sample preparation is limited to PCR, the optimization of its solution conditions is of utmost importance for efficient mass spectrometric detection. The compatibility of a number of different commercially available PCR components including DNA polymerases, deoxynucleotide triphosphates, bovine serum albumin, enhancer, and ionic buffers was evaluated. These experiments revealed that higher concentration of enhancer and detergents such as Tween-20 or Nonidet P-40 impairs the mass spectrometric detection of nucleic acids and should be avoided within the PCR mixture. The optimized analytical platform was applied to the characterization of PCR products covering parts of the first hypervariable region of the noncoding mitochondrial control region. Truncated amplicons were detected attributable to the use of low quality primers. Furthermore, due to the proofreading activity of the applied polymerase system, mismatches between the primer and the target sequence located at the last or the second last base at the 3'-end of primers were corrected and detected within the corresponding amplicons.

Chromatography, High Pressure Liquid↗
PubMed2006

Prophylactic anti-tumor effects in a B cell lymphoma model with DNA vaccines delivered on polyethylenimine (PEI) functionalized PLGA microparticles.

Idiotypic sequences, specific to the hypervariable regions of immunoglobulins expressed by malignant B cells offer a therapeutic target in B cell lymphoma. Efficient approaches have been described to clone a single chain fragment of the tumor immunoglobulin (Ig) comprising of heavy and light Ig chains (sFv) fused with proinflammatory chemokines. Tumor associated, poorly immunogenic self antigens encoded by plasmid DNA (pDNA) have been rendered immunogenic by chemokine fusion, thereby targeting to antigen presenting cells (APCs) which differentially express chemokine receptors. Here we present an injectable (parenteral) approach using synthetic polymer based cationic microparticle formulations for enhancing the potency of such chemokine/self antigen expressing plasmid construct. Branched and linear polyethyleneimine (PEI) were conjugated on poly (D, L lactide-co-glycolide) (PLGA) microparticles using carbodiimide chemistry followed by efficient loading of plasmid DNA. In addition to imparting significant buffering ability to these cationic microparticles, flow cytometry studies indicate that these DNA loaded microparticles significantly up regulate CD80 and MHC class II markers in phagocytic RAW264.7 cells, indicating intrinsic adjuvant effects. Intradermal injections in Balb/c mice with these formulations induced significant protection upon tumor challenge with 2.5 times the minimal lethal dose. Long term survival rates were significant (p < 0.05) in comparison with saline injected controls or blank microparticles. Further studies indicated that intramuscular delivery might provide better protection compared to intradermal injections and perform similar to gene gun mediated administration. We conclude, based on these promising in vivo results, that such surface-functionalized microparticles offer an attractive strategy to improve the potency of self antigen-based cancer DNA vaccines.

Animals↗
PubMed2005

Genotypic and phenotypic diversity of a baculovirus population within an individual insect host.

It is becoming increasingly apparent that many pathogen populations, including those of insects, show high levels of genotypic variation. Baculoviruses are known to be highly variable, with isolates collected from the same species in different geographical locations frequently showing genetic variation and differences in their biology. More recent studies at smaller scales have also shown that virus DNA profiles from individual larvae can show polymorphisms within and between populations of the same species. Here, we investigate the genotypic and phenotypic variation of an insect baculovirus infection within a single insect host. Twenty four genotypically distinct nucleopolyhedrovirus (NPV) variants were isolated from an individual pine beauty moth, Panolis flammea, caterpillar by in vivo cloning techniques. No variant appeared to be dominant in the population. The PaflNPV variants have been mapped using three restriction endonucleases and shown to contain three hypervariable regions containing insertions of 70-750 bp. Comparison of seven of these variants in an alternative host, Mamestra brassicae, demonstrated that the variants differed significantly in both pathogenicity and speed of kill. The generation and maintenance of pathogen heterogeneity are discussed.

Animals↗
PubMed2004

NMR characterization of full-length farnesylated and non-farnesylated H-Ras and its implications for Raf activation.

The C terminus, also known as the hypervariable region (residues 166-189), of H-, N-, and K-Ras proteins has sequence determinants necessary for full activation of downstream effectors such as Raf kinase and PI-3 kinase as well as for the correct targeting of Ras proteins to lipid rafts and non-raft membranes. There is considerable interest in understanding how residues in the extreme C terminus of the different Ras proteins and farnesylation of the CaaX box cysteine affect Ras membrane localization and allosteric activation of Raf kinase. To provide insights into the structural and dynamic changes that occur in Ras upon farnesylation, we have used NMR spectroscopy to compare the properties of truncated H-Ras (1-166), to non-processed full-length H-Ras (residues 1-185) and full-length (1-189) farnesylated H-Ras. We report that the C-terminal helix alpha-5 extends to residue N172, and the remaining 17 amino acid residues in the C terminus are conformationally averaged in solution. Removal of either 23 or 18 amino acid residues from the C terminus of full length H-Ras generates truncated H-Ras (1-166) and H-Ras (1-171) proteins, respectively, that have been structurally characterized and are biochemical active. Here we report that C-terminal truncation of H-Ras results in minor structural and dynamic perturbations that are propagated throughout the H-Ras protein including increased flexibility of the central beta-sheet and the C-terminal helix alpha-5. Ordering of residues in loop-2, which is involved in Raf CRD binding is also observed. Farnesylation of full-length H-Ras at C186 does not result in detectable conformational changes in H-Ras. Chemical shift mapping studies of farnesylated and non-farnesylated forms of H-Ras with the Raf-CRD show that the farnesyl moiety, the extreme H-Ras C terminus and residues 23-30, contribute to H-Ras:Raf-CRD interactions, thereby increasing the affinity of H-Ras for the Raf-CRD.

Cell Membrane↗
PubMed2005

CryoEM structure at 9A resolution of an adenovirus vector targeted to hematopoietic cells.

We report a sub-nanometer resolution cryo-electron microscopy (cryoEM) structural analysis of an adenoviral vector, Ad35F, comprised of an adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber. This vector transduces human hematopoietic cells via association of its fiber protein with CD46, a member of the complement regulatory protein family. Major advances in data acquisition and image processing allowed a significant improvement in resolution compared to earlier structures. Analysis of the cryoEM density was enhanced by docking the crystal structures of both the hexon and penton base capsid proteins. CryoEM density was observed for hexon residues missing from the crystal structure that include hypervariable regions and the epitope of a neutralizing monoclonal antibody. Within the penton base, density was observed for the integrin-binding RGD loop missing from the crystal structure and for the flexible beta ribbon of the variable loop on the side of the penton base. The Ad35 fiber is flexible, consistent with the sequence insert in the third beta-spiral repeat. On the inner capsid surface density is revealed at the base of the hexons and below the penton base. A revised model is presented for protein IX within the virion. Well-defined density was assigned to a conserved domain in the N terminus of protein IX required for incorporation into the virion. For the C-terminal domain of protein IX two alternate conformations are proposed, either binding on the capsid surface or extending away from the capsid. This model is consistent with the tolerance of the C terminus for inserted ligands and its potential use in vector retargeting. This structural study increases our knowledge of Ad capsid assembly, antibody neutralization mechanisms, and may aid further improvements in gene delivery to important human cell types.

Adenoviridae↗
PubMed2006

Serotype-specific detection of adeno-associated virus during laboratory preparation.

Adeno-associated virus (AAV) is a small single-stranded DNA member of the family Parvoviradae with at least eight recognized human serotypes, several of which are being studied as candidate vectors for gene therapy. When multiple serotypes are handled in the same laboratory, it is critical to know the serotype of a sample with certainty. Here, a rapid and reliable PCR-based method is presented for the identification of serotypes 2, 3B or 6 and for screening for cross contamination. The PCR assay is based on the use of differentially annealing, serotype-specific primer pairs targeted to the hypervariable regions of the capsid coding region of the AAV genome. Identity is determined by the presence of a PCR product of size specific to each serotype. Multiplexing the reaction allows all serotypes to be queried in a single reaction tube and greatly diminishes the presence of false positives. The method is capable of detecting as little as 25 fg of a contaminating serotype and is potentially extensible to other AAV serotypes.

Base Sequence↗
PubMed2007

Separation of near full-length hepatitis C virus quasispecies variants from a complex population.

A long RT-PCR (LRP) protocol was developed recently for robust amplification of a near full-length HCV genomic sequence from clinical samples, followed by efficient cloning [Fan, X., Xu, Y., Di Biceglie, A.M., 2006. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem. Biophys. Res. Commun. 346, 1163-1172]. In the present study, the LRP protocol has been estimated for its error rate and the validation by sequencing fully the near full-length HCV inserts from six recombinant clones derived from a patient sample with complex viral diversity. These sequences were compared with the near full-length HCV sequence that was generated by direct sequencing of multiple overlapped PCR products from the same sample, referred to as the population sequence. Comparative analysis confirmed the artificial nature of the PCR-assembled population sequence and identified potential domains for linked viral mutations. The data also suggested that the hypervariable region 1 (HVR1) may be a biological marker for the phenotype at the quasispecies level. These observations emphasize the significance of the use of near full-length genomic sequences for HCV genetic studies and for reverse genetic analysis using authentic quasispecies variants.

Cloning, Molecular↗
PubMed2005

DNA typing of bone specimens--the potential use of the profiler test as a tool for bone identification.

Twenty-six bone DNA identification cases are described. The postmortem periods of the studied remains ranged from three days to over 30 years, and the locations where the remains were found varied resulting in a variety of postmortem conditions. Nuclear DNA typing using an AmpFLSTR Profiler kit and mitochondrial DNA (mtDNA) typing of hypervariable regions 1 and 2 (HV1 and HV2) in a control region were performed both with decalcified and non-treated bone powder samples. Decalcification was shown to improve the success of DNA typing. The nucleotide sequences of the HV1 and HV2 regions were successfully determined in all cases examined. Nuclear DNA typing was very successful, more than half of the loci were typed during multiple amplifications (10 loci in one reaction) in 23 cases. Polymerase chain reaction (PCR) inhibition was observed in five cases including three samples that were found buried in soil. This inhibitory effect was identified as the result of unbalanced multiple PCR during the profiler test. These results revealed that DNA typing targeting nuclear DNA is a potentially powerful tool for bone identification.

Adult↗
PubMed2004

Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns.

Analysis of heat shock protein 65 (hsp65) gene restriction fragment length polymorphism (RFLP) is done frequently to identify non-tuberculous mycobacteria (NTM) on a genetic basis. Here we report the results of analysing the hsp65 patterns of some rarely isolated NTM for which patterns have not been published before (Mycobacterium bohemicum, Mycobacterium hassiacum, Mycobacterium heckeshornense, Mycobacterium monacense, and Mycobacterium triplex). Furthermore new hsp65-variants for Mycobacterium interjectum (type II), Mycobacterium mucogenicum (type V), Mycobacterium gordonae (type VIII) and Mycobacterium paraffinicum (perhaps synonymous to Mycobacterium scrofulaceum) are described. All species were characterised by hsp65-RFLP, sequencing a 441-bp fragment of the hsp65 gene and sequencing the hypervariable region of the 16S rDNA. Additional data for less frequently isolated mycobacteria are provided and the hitherto described data for the Mycobacterium gordonae complex are summarised. Although the hsp65-RFLP analysis turned out to be a useful method a number of restraints (lack of standardisation, slight variability in fragment length) limits its broader use. Reliable identification of NTM needs, however, more than one molecular method. Identification results obtained by applying different methods yielded conflicting results. Confusion may be caused by older data base entries which are not updated and not longer reflect the actual systematic and taxonomy of the genus Mycobacterium.

Bacterial Proteins↗
PubMed2006

Nucleotide substitution at the highly polymorphic K1 locus of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus).

The K1 locus is a highly polymorphic locus in the genome of human herpesvirus 8, the causative agent of Kaposi's sarcoma. Analysis of the pattern of nucleotide substitution among alleles at this locus supported the hypothesis that natural selection has acted to enhance amino acid diversity in the two hypervariable regions (VR1 and VR2) of the extracellular portion of the K1 protein. A phylogenetic analysis of 125 complete K1 sequences revealed two major clades, designated A/C and B. There was strong evidence against recombination between VR1 and VR2 among alleles belonging to different clades, and little support for frequent recombination within clades. The pattern of diversification of VR1 and VR2 within clades was similar to that between clades, but the immunoreceptor tyrosine-based activation motif (ITAM)-like sequence in the cytoplasmic region of K1 showed strong divergence between clades despite conservation within clades. The latter finding suggests that, while being subject to similar selection favoring diversity in the extracellular region, the two major clades of K1 alleles may be adapted for different types of interaction with host intracellular signal transduction mechanisms.

Amino Acid Substitution↗
PubMed2006

Identification and sizing of GAA trinucleotide repeat expansion, investigation for D-loop variations and mitochondrial deletions in Iranian patients with Friedreich's ataxia.

Friedreich's Ataxia (FA) is the commonest genetic cause of ataxia and is associated with the expansion of a GAA repeat in intron 1 of the frataxin gene. Iron accumulation in the mitochondria of patients with FA would result in hypersensitivity to oxidative stress. Mitochondrial DNA (mtDNA) could be considered a candidate modifier factor for FA disease, since mitochondrial oxidative stress is thought to be involved in the pathogenesis of this disease. We studied 25 Iranian patients (16 females and 9 males) from 12 unrelated families. DNA from each patient was extracted and frequency and length of (GAA)(n) repeat was analyzed using a long-range polymerase chain reaction (PCR) test. Also we investigated impact of GAA size on neurological findings, age of onset and disease development. In order to identify polymorphic sites and genetic background, the sequence of two hypervariable regions (HVR-I and HVR-II) of mtDNA was obtained from FA patients harbouring GAA trinucletide expansions. Alignment was made with the revised cambridge reference sequence (rCRS) and any differences recorded as single base substitution (SBS), insertions and deletions. Homozygous GAA expansion was found in 21 (84%) of all cases. In four cases (16%), no expansion was observed, ruling out the diagnosis of Friedreich's ataxia. In cases with GAA expansions, ataxia, scoliosis and pes cavus, cardiac abnormalities and some neurological findings occurred more frequently than in our patients without GAA expansion. Molecular analysis was imperative for diagnosis of Friedreich's ataxia, not only for typical cases, but also for atypical ones. Diagnosis bases only on clinical findings is limited, however, it aids in better screening for suspected cases that should be tested. Our results showed that the rate of D-loop variations was higher in FA patients than control (P<0.05). mtDNA deletions were present in 76% of our patients representing mtDNA damage, which may be due to iron accumulation in mitochondria.

Adolescent↗
PubMed2006

Signal sequences modulate the immunogenic performance of human hepatitis C virus E2 gene.

Envelope protein E2 of human hepatitis C virus (HCV) is an attractive component of a prototype HCV vaccine. Delivered by DNA immunogens, E2 evokes specific immune response of Th1-type, failing to induce either considerable antibody production, or T-helper cell proliferation. We aimed at modulating the immunogenic performance of E2 gene by changing the mode of protein expression in eukaryotic cells. Plasmids were constructed encoding full-length E2 and nonstructural protein 1 (p7) fused to either 13 or 38 C-terminal amino acids (aa) of HCV E1 that contain second hydrophobic segment of E1 stop-transfer signal, or a complete E1 stop-transfer signal with duplicated second hydrophobic segment. Injected into BALB/c mice, E2/p7 genes induced potent antibody and T-helper cell response targeted against hypervariable region 1, aa 472-586 of E2, and a novel epitope at aa 774-796 of p7. Profile of cytokines secreted by proliferating mouse splenocytes stimulated in vitro with E2- and p7-derived peptides, indicated mixed Th1/Th2 type of immune response. Thus, the full-length E2 and p7 genes supplied in one cassette were both immunogenic. E2/p7 containing a complete E1 stop-transfer signal with prolonged membrane spanning domain was superior to the shorter E2/p7 version in terms of both antibody and cellular immunogenicity. Optimal performance of HCV E2 could thus be achieved without the aid of external/heterologous signals by easing, through modification of the E2 signal sequence, the release of E2 from the rough ER while retaining full-length E2 and p7 sequences. This finding may help to improve the Th2 performance of HCV envelope genes as prototype vaccines.

Amino Acid Sequence↗
PubMed2005

GLYX-13: a monoclonal antibody-derived peptide that acts as an N-methyl-D-aspartate receptor modulator.

We previously created a monoclonal antibody (MAb), B6B21, that acts as a partial agonist at the glycine site of the N-methyl-d-aspartate (NMDA) receptor [Moskal, J.R., Schaffner, A.E., 1986. Monoclonal antibodies to the dentate gyrus: immunocytochemical characterization and flow cytometric analysis of hippocampal neurons bearing a unique cell-surface antigen. J. Neurosci. 6, 2045-2053.]. The hypervariable region of the light chain of B6B21 was cloned and sequenced. Peptides were then synthesized based on this sequence information and screened using rat hippocampal membrane preparations to measure [(3)H]MK-801 binding in the presence of 7-chlorokynurenic acid, a glycine site-specific competitive inhibitor of NMDA receptor [Moskal, J.R., Yamamoto, H., Colley, P.A., 2001. The use of antibody engineering to create novel drugs that target N-methyl-d-aspartate receptors. Curr. Drug Targets 2, 331-345.]. Peptides that were able to increase [(3)H]MK-801 binding in a dose-dependent manner under these conditions were named Glyxins. Here we report that GLYX-13, a tetrapeptide (TPPT-amide), was found to readily cross the blood-brain barrier and modulate the NMDA receptor in a glycine-like fashion when examined pharmacologically and electrophysiologically. When GLYX-13 was administered to rats at 0.5-1.0mg/kg i.v., a significant enhancement in learning was observed using a hippocampus-dependent trace eye blink conditioning paradigm. These data indicate that the Glyxins are a new class of NMDA receptor modulators that may have therapeutic potential. Based on the broad agonist range in vitro and the potent cognitive-enhancing properties in a valid in vivo model of learning, GLYX-13 is a new drug candidate with potential for the treatment of cognitive disorders.

Animals↗
PubMed2004

[High prevalence and incidence of hepatitis C virus infections among dialysis patients in the East-Centre of Tunisia].

Hemodialysed patients are recognised as a group at increased risk of infection with hepatitis C virus (HCV). The aim of this study was to determine the prevalence and incidence of HCV infection among dialysis patients of the east-centre part of Tunisia. Two hundred and seventy-six patients dialysed until 2001 were recruited within seven hemodialysis units located in the cities of Sousse, Monastir and Mahdia. The serum markers of HCV infection were tested over the period of March 2000-December 2002, by a 3rd generation ELISA test for antibodies and by qualitative RT-PCR technique for viral RNA. The prevalence of anti-HCV antibodies and of HCV RNA was 32.6% (90 patients) and 25.7% (71 patients), respectively. Between 1998 and 2002, 20 new infections were documented in five of the seven dialysis units corresponding to an incidence of 2.34% per year, with an average time of contamination after the beginning of dialysis of 4.6 years. If all the infections are assessed to have occurred during dialysis, the density of incidence of HCV contamination was 4.4% per year of dialysis. A high correlation was noticed between the presence of HCV markers in serum and the duration of dialysis (F = 34.15, P < 0.0001). In the absence of other risk factors (transfusion, drug-addiction), these results plead for the nosocomial transmission of the observed HCV infections. A phylogenetic analysis of the E2 hypervariable region of the viral genome is in progress to confirm this assumption.

Female↗
PubMed2006

Preparation of hepatitis C virus structural and non-structural protein fragments and studies of their immunogenicity.

Plasmids pQE-60 and pQE-30 containing 6 x His-tag sequence were used for expression of fragments of HCV structural and non-structural proteins in Escherichia coli (E. coli). The following fragments were used: core (1-98 aa), NS3 (202-482 aa), and tetramer of hypervariable region 1 (HVR1) of E2 protein. The constructed plasmids directed high levels of expression of HCV proteins in E. coli JM109. After purification by the metal-affinity chromatography on nickel-nitrilotriacetic acid (Ni-NTA) agarose, the His-tagged HCV proteins were used for immunization of BALB/c mice. All three proteins were able to induce high levels of specific antibodies and, in the case of the NS3 and HVR1 tetramer, also to mount vigorous cell-proliferating responses. High immunogenicity of the tested fragments of HCV proteins shows them as good candidates for inclusion into the future HCV vaccine preparations.

Animals↗
PubMed2026

Molecular characteristics, phylodynamics, and evolutionary changes of avian infectious bronchitis virus detected from chickens in Yunnan Province, 2021-2024.

Avian infectious bronchitis virus (IBV) is endemic in poultry flocks worldwide, posing a significant threat to the global poultry industry. Frequent mixing of free-range local chickens with introduced chickens in Yunnan Province, China, facilitates the transmission, recombination, and mutation of avian IBV, thereby complicating disease prevention and control. In this study, we aimed to investigate the presence of IBV in poultry populations in Yunnan Province. Samples were collected from live poultry markets (LPMs) and breeding farms, comprising 725 randomly sampled cloacal/fecal swabs and 55 tissue samples. IBV-positive samples were confirmed via polymerase chain reaction (PCR), with an overall positivity rate of 0.89% (7/780) for all tested samples. The positivity rate was 0.35% (2/564) in Kunming, 3.7% (2/54) in Zhaotong, 20% (1/5) in Yuxi, and 12.5% (2/16) in Baoshan, while no IBV was detected in samples from Lanping, Xichou, or Ninglang. Six IBV strains, including five GI-19 strains and one GVI-1 strain, were successfully isolated. Phylogenetic analysis further showed that the Yunnan GI-19 strains predominantly clustered with strains originating from Sichuan Province. Sequencing of the S1 gene revealed several amino acids substitutions per isolate in hypervariable regions HVR1-HVR3. Notably, a valine (V) and glycine (G) insertion between amino acid positions 88 and 89 was identified exclusively in isolate F210, a feature rarely reported in IBV. Protein-protein docking analysis indicated that the unique 88-89 insertion in isolate F210 S1 may alter its binding interactions with the host receptor ANPEP. Whole-genome comparison revealed that isolate YX3 shared 97.05% nucleotide identity with strain CK/CH/GX/YL17/2017 from Guangxi, whereas isolates Q47, F13, and F210 shared 96.40%-97.27% identity with strain CK/Henan/H1036/2021 from Henan. Recombination analysis detected obvious recombination events in isolates F13, F210, Q47, and YX3, with GI-22 strains serving as the major parental donors. These genetic characteristics, recombination patterns, and structural insights demonstrate the complex evolutionary dynamics of circulating IBV strains in Yunnan. Continuous molecular epidemiological surveillance combined with functional protein analysis is essential to monitor emerging variants and formulating targeted, effective disease control strategies.

Avian infectious bronchitis virus↗
PubMed2005

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates.

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

Alphaproteobacteria↗