Polysaccharides of the Genus Bacillus Cross-Reactive with the Capsular Polysaccharides of Diplococcus pneumoniae Type III, Haemophilus influenzae Type b, and Neisseria meningitidis Group A

We studied 174 strains of the genus Bacillus for cross-reacting antigens to the capsular polysaccharides of groups A and C meningococcus, types I and III pneumococcus, and Haemophilus influenzae type b. Cross-reactions were detected by immunodiffusion in agarose gel by using type-specific antisera and confirmed by absorption and inhibition experiments. Of 20 Bacillus pumilis strains, six had an antigen cross-reacting with group A meningococcal polysaccharide. Other cross-reactions included one strain of B. pumilis with H. influenzae type b, one of B. cereus var. mycoides with pneumococcus type III, and one of B. alvei with both type b and SIII polysaccharides. These cross-reacting antigens are polysaccharides of vegetative cells and may be extracellular in location. Because these bacilli have antigens cross-reacting with the virulence factors of pyogenic bacteria, they may, as normal flora, be an antigenic stimulus for "natural" serum anti-capsular antibodies to the type b Haemophilus and group A meningococcus polysaccharides.     

Antigenic heterogeneity of influenza virus B neuraminidases

Antigenic relationships among neuraminidases of influenza B viruses isolated in 1940-1980 were studied by means of the neuraminidase activity inhibition test using hypoimmune sera from rats and roosters. Cross-reactions between influenza B virus enzymes showed their antigenic heterogeneity. The results permit conclusion that among influenza B virus strains both the drift and shift variants may be distinguished by the antigenic composition of the neuraminidase component.     

On Human Disease‐Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns

Statistical analysis was carried out on large set of naturally occurring human amino acid variations, and it was demonstrated that there is a preference for some amino acid substitutions to be associated with diseases. At an amino acid sequence level, it was shown that the disease‐causing variants frequently involve drastic changes in amino acid physicochemical properties of proteins such as charge, hydrophobicity, and geometry. Structural analysis of variants involved in diseases and being frequently observed in human population showed similar trends: disease‐causing variants tend to cause more changes in hydrogen bond network and salt bridges as compared with harmless amino acid mutations. Analysis of thermodynamics data reported in the literature, both experimental and computational, indicated that disease‐causing variants tend to destabilize proteins and their interactions, which prompted us to investigate the effects of amino acid mutations on large databases of experimentally measured energy changes in unrelated proteins. Although the experimental datasets were linked neither to diseases nor exclusory to human proteins, the observed trends were the same: amino acid mutations tend to destabilize proteins and their interactions. Having in mind that structural and thermodynamics properties are interrelated, it is pointed out that any large change in any of them is anticipated to cause a disease.     

Impaired interaction of naturally occurring mutant NF2 protein with actin-based cytoskeleton and membrane

Although schwannomin, the product of the neurofibromatosis type 2 gene, shares homology with three cytoskeleton-to-membrane protein linkers defining the ERM family, the mechanism by which it exerts a tumor suppressive activity remains elusive. Based on the knowledge of naturally occurring mutations, a functional study of schwannomin was initiated. Constructs encoding the two wild-type isoforms and nine mutant forms were transfected into HeLa cells. Transiently expressed wild-type isoforms were both observed underneath the plasma membrane. At this location they were detergent insoluble and redistributed by a cytochalasin D treatment, suggesting interaction with actin-based cytoskeletal structures. Proteins with single amino acid substitutions at positions 219 and 220 demonstrated identical properties. Three different truncated schwannomins, that are prototypic for most naturally occurring NF2 mutations, were affected neither in their location nor in their cytochalasin D sensitivity. However, they were revealed to be detergent soluble, indicating a relaxed interaction with the actin-based structures. An increased solubility was also observed for a mutant with a single amino acid substitution at position 360 in the C-terminal half of the protein. Mutant proteins with either a single amino acid deletion at position 118 or an 83 amino acid deletion within the N-terminal domain had lost the submembraneous localization and tended to accumulate in perinuclear patches that were unaffected by cytochalasin D treatment. A similar behavior was observed when the N- terminal domain was entirely deleted. Taken together these observations suggest that the N-terminal domain is the main determinant that localizes the protein at the membrane where it interacts weakly with actin-based cytoskeletal structures. The C-terminal domain potentiates this interaction. With rare exceptions, most naturally occurring mutant schwannomins that have lost their tumor suppressive activity are impaired in an interaction involving actin-based structures and are no longer firmly maintained at the membrane.      

Vancomycin-resistant Enterococci may obtain nutritional support by scavenging carbohydrate fragments generated during mucin degradation by the anaerobic microbiota of the colon

Vancomycin-resistant Enterococcus (VRE) is an important nosocomial pathogen that colonizes the intestinal tract. The substrates that provide nutritional support for VRE in the colon are not known. We tested the hypothesis that enzymatic breakdown of complex polysaccharides and glycoconjugates by other members of the indigenous microbiota could provide a source of nutrients for VRE. Nine vancomycin-resistant E. faecium strains were unable to ferment complex plant polysaccharides or hog gastric or bovine submaxillary mucin; however, each of the strains was able to ferment monosaccharides that are components of mucins and plant polysaccharides. Preincubation of hog gastric mucin with partially purified enzyme mixtures obtained from supernatants of Ruminococcus torques or a human stool specimen resulted in release of monosaccharides that supported growth of VRE. These results suggest that enzymatic breakdown of complex polysaccharides such as mucin by members of the indigenous microbiota may provide a source of nutritional support for VRE.     

Cellular and molecular mechanisms of neuronal degeneration: Amyotrophic lateral sclerosis,parkinsonism-demantia,and Alzheimer disease

Hyperendemic Pacific foci of amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia (PD) represent naturally occurring models of late-onset chronic degenerative diseases that occur in different cultures, in different ecological zones, and among genetically divergent populations. These diseases occur among the Chamorros of the Mariana Islands, among the Auyu and Jakai of southern West New Guinea, and among the Japanese from the Kill Peninsula of Honshu Island. Accumulating evidence supports the hypothesis that a defect in mineral metabolism may be etiologically involved. Toxic and essential elements, such as calcium aluminum, and silicon cross the blood-brain barrier, deposit in affected neurons, and disrupt the axonal transport system, resulting in the abnormal copolymerization of cytoskeletal and amyloid β-proteins in neurons. The pathological accumulation of these and other proteins into neurofibrillary tangles (the hallmark neuropathological lesion) causes neuronal dysfunction and death. Recent immunocytochemical and biochemical studies indicate that the amyloid β-protein in Guamanian PD has an identical amino acid sequence, a similar N-terminus heterogeneity (variation in polypeptide length), and a similar immunoreactivity to those found in Alzheimer disease, suggesting a common mechanism of pathogenesis. Investigations are now underway to determine whether the abnormal accumulation of amyloid β-protein in neurons of Guamanian patients with ALS and PD is the result of an aberrant post-translational modification of a larger precursor protein, an additional copy of the amyloid gene, or an impairment of amyloid catabolism all of which may be mediated by metal-enzyme or metal-gene interactions. The abnormal copolymerization of other proteins such as neurofilament, microtubule-associated protein tau, and ubiquitin in affected neurons suggests their interrelationship in the disease process.     

Immunochemical cross-reactions between pentraxins of different species.

Monospecific antisera were raised by immunization with pentraxins, C-reactive protein (CRP) or serum amyloid P component (SAP), that had been isolated from man and a number of different vertebrate species. These antisera were used to test sera or serous fluids from a range of other vertebrate species and also some invertebrates. Cross-reactions between species were comparatively rare but were seen among primates and among ruminants. There was also cross-reactivity between these two groups. Antisera to plaice pentraxins did not react with sera from higher vertebrates but did recognize antigens in sera from other flat fish. No cross-reactivity was observed between CRP and SAP either within or between species despite the known homologies of amino acid sequence and similarities of structure within the family. Several reactions occurred with sera in which either CRP or SAP had previously not been sought or in which only preliminary investigations had been performed. The proteins detected were: CRP in goat, cow, sheep, cat and lemon sole; SAP in monkey and dab. These findings significantly extend the range of species in which pentraxins are known to be present.     

Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6

The SLC6 family is a diverse set of transporters that mediate solute translocation across cell plasma membranes by coupling solute transport to the cotransport of sodium and chloride down their electrochemical gradients. These transporters probably have 12 transmembrane domains, with cytoplasmic N- and C-terminal tails, and at least some may function as homo-oligomers. Family members include the transporters for the inhibitory neurotransmitters GABA and glycine, the aminergic transmitters norepinephrine, serotonin, and dopamine, the osmolytes betaine and taurine, the amino acid proline, and the metabolic compound creatine. In addition, this family includes a system B(0+) cationic and neutral amino acid transporter, and two transporters for which the solutes are unknown. In general, SLC6 transporters act to regulate the level of extracellular solute concentrations. In the central and the peripheral nervous system, these transporters can regulate signaling among neurons, are the sites of action of various drugs of abuse, and naturally occurring mutations in several of these proteins are associated with a variety of neurological disorders. For example, transgenic animals lacking specific aminergic transporters show profoundly disturbed behavioral phenotypes and probably represent excellent systems for investigating psychiatric disease. SLC6 transporters are also found in many non-neural tissues, including kidney, intestine, and testis, consistent with their diverse physiological roles. Transporters in this family represent attractive therapeutic targets because they are subject to multiple forms of regulation by many different signaling cascades, and because a number of pharmacological agents have been identified that act specifically on these proteins.     

Cycloleucine fluxes during rat vasa recta and loop microinfusions in vivo and loop microperfusions in vitro

Amino acids are apparently recycled between loops of Henle and vasa recta in rat papilla in vivo. To examine this process in the absence of metabolism, we performed continuous microinfusions of rat renal papillary ascending thin limbs (ATLs) and vasa recta in vivo, and microperflusions of isolated rat renal papillary descending thin limbs (DTLs) and ATLs in vitro using the nonmetabolizable, synthetic, neutral amino acid cycloleucine. Like naturally occurring amino acids, approximately = 25% of radiolabeled cycloleucine microinfused into ATLs in vivo was reabsorbed by a process that was not saturable or inhibitable. Also, like naturally occurring amino acids, approximately = 47% (relative to inulin) of radiolabeled cycloleucine microinfused into ascending vasa recta in vivo was transferred directly into ipsilateral tubular structures (probably DTLs) by a saturable and inhibitable process. In DTLs perfused in vitro, unidirectional bath-to-lumen fluxes (Jbl) tended to exceed unidirectional lumen-to-bath fluxes (Jlb), whereas in ATLs perfused in vitro Jlb tended to exceed Jbl, but the differences were not statistically significant. Moreover, none of the unidirectional fluxes was saturable or inhibitable, an observation compatible with apparent reabsorption from ATLs in vivo but incompatible with apparent movement from vasa recta to DTLs in vivo. These in vitro observations are like those made previously for the naturally occurring neutral amino acid L-alanine. The lack of saturation and inhibition, like the previous data on L-alanine, suggest that transepithelial movement of amino acids in thin limbs of Henle's loop may occur via a paracellular route and that regulation of amino acid movement in vivo may involve vasa recta, not DTLs. They also suggest that cycloleucine is a good nonmetabolizable surrogate for the study of neutral amino acid transport in the kidney.     

Pathogenic and physiological autoantibodies in the central nervous system

In this article, we review the current knowledge on pathological and physiological autoantibodies directed toward structures in the central nervous system (CNS) with an emphasis on their regulation and origin. Pathological autoantibodies in the CNS that are associated with autoimmunity often lead to severe neurological deficits via inflammatory processes such as encephalitis. In some instances, however, autoantibodies function as a marker for diagnostic purposes without contributing to the pathological process and/or disease progression. The existence of naturally occurring physiological autoantibodies has been known for a long time, and their role in maintaining homeostasis is well established. Within the brain, naturally occurring autoantibodies targeting aggregated proteins have been detected and might be promising candidates for new therapeutic approaches for neurodegenerative disorders. Further evidence has demonstrated the existence of naturally occurring antibodies targeting antigens on neurons and oligodendrocytes that promote axonal outgrowth and remyelination. The numerous actions of physiological autoantibodies as well as their regulation and origin are summarized in this review.     

A Family of Cross-Reacting Proteins Secreted by Mycobacterium tuberculosis

Cross-reactions between five proteins actively secreted by Mycobacterium tuberculosis were studied by crossed immunoelectrophoresis, SDS-PAGE with immunoblotting, and ELISA using polyclonal rabbit antisera and mouse monoclonal antibodies to the purified proteins. The monoclonal antibody HBT4 was demonstrated to react with the MPT51 protein. The 85A, 85B and 85C constituents of the M. tuberculosis and Mycobacterium bovis BCG antigen 85 complex cross-react extensively, each of the components containing component-specific as well as cross-reacting epitopes. These components also cross-reacted with MPT51 and MPT64. N-terminal sequence studies revealed striking homology at the amino acid level between 85A, 85B, 85C and MPT51. MPT64 showed less homology. In addition, striking homology was demonstrated between two different stretches within the 85B sequence and indicated between three stretches within the MPT64 molecule. Thus, a family of at least four secreted proteins with common structural features has been demonstrated in mycobacteria. MPT64 may also belong to this family.     

Determination of the number of nonoverlapping antigenic areas on Hong Kong (H3N2) influenza virus hemagglutinin with monoclonal antibodies and the selection of variants with potential epidemiological significance

Monoclonal antibodies provided evidence for at least three nonoverlapping antigenic areas on the hemagglutinin molecule of A/Mem/V71 (H3N2) influenza virus. This was established by determining the reactivity patterns of 30 different monoclonal antibodies in hemagglutination-inhibition tests and by the failure to select antigenic variants of influenza virus when monoclonal antibodies from two nonoverlapping areas were used in combination. Antigenic analysis showed that most of the variants selected with monoclonal antibodies could not be distinguished from the parental virus with heterogeneous sera, suggesting that they are probably epidemiologically irrelevant. One variant, however, could be distinguished from the parental virus with heterogeneous sera and this variant had a change in sequence at residue 144 of the HAl polypeptide, from glycine in the parent to aspartic acid in the variant. A similar amino acid change has been found in naturally occurring variants at this residue. These studies suggest that some amino acid substitutions are more important than others for producing viruses with epidemiological potential. Antigenic analysis of naturally occurring H3N2 strains with monoclonal antibodies showed that antigenic variation occurs in each nonoverlapping antigenic area of the HA molecule and established that two distinct variants cocirculated in 1968, Hong Kong/1/68 being distinguishable from Aichi/2/68 in at least two antigenic areas. It appears that there may have been two separate lineages of H3N2 viruses, Hong Kong/1/68 giving rise to variants in England and Aichi/2/68 to variants in the USA and Australia.     

Isolation, structure, and immunogenicity of Pseudomonas aeruginosa immunotype 4 high-molecular-weight polysaccharide.

A high-molecular-weight, immunogenic form of the lipopolysaccharide O side chain of Pseudomonas aeruginosa Fisher immunotype 4 (type 4, International Antigenic Typing System 1, Lanyi O:6) was isolated and characterized. Analysis by nuclear magnetic resonance spectroscopy confirmed the structural similarity of this high-molecular-weight polysaccharide and the type 4 O side chain. The polysaccharide was immunogenic in rabbits and mice, eliciting opsonophagocytic killing antibodies. Immunization with the polysaccharide produced significant protection against homologous challenge in both burned and granulocytopenic mice. Naturally acquired opsonic killing antibodies to type 4 polysaccharide were present in sera from unimmunized normal adults at levels comparable to postimmunization levels achieved after immunization with other type-specific polysaccharides. The specificity of the naturally occurring antibodies for the O side chain was documented by immunoblot analysis and inhibition studies. Naturally occurring polysaccharide-specific antibodies were comparable in their protective activity against live challenge in neutropenic animals to immunization-induced murine antibodies with similar specificity. These data suggest that naturally occurring serum antibody to P. aeruginosa type 4 lipopolysaccharide O side chains in most adults is not distinguishable in quantity or quality from immunization-induced antibodies in mice; evaluation of type 4-specific vaccines in humans may be complicated by this finding.     

Immunotherapy and naturally occurring autoantibodies in neurodegenerative disorders

Parkinson's disease, Alzheimer's disease and other neurodegenerative disorders share a common pathologic pathway with aggregation and deposition of misfolded proteins causing a disruption of particular neuronal networks. Several mechanisms have been implicated in the down-stream events following deposition of misfolded proteins including failure of cellular defenses among many others. Recently, naturally occurring autoantibodies against ss-amyloid and alpha-synuclein have been detected in healthy persons and altered levels in patients were associated with particular neurodegenerative disorders. In this review the current knowledge on the role of naturally occurring autoantibodies is discussed in respect to neurodegenerative disorders.     

Functional conservation of HIV-1 Vpr and variability in a mother-child pair of long-term non-progressors

Increasing evidence suggests that HIV-1 Vpr is required in vivo for viral pathogenesis. Since Vpr displays multiple activities, little is known about which Vpr-specific activities are conserved in naturally occurring viruses or how natural mutations in Vpr might modulate viral pathogenesis in HIV-infected individuals. The goals of this study were to evaluate the functional variability of Vpr in naturally occurring viruses. The Vpr-specific activities of nuclear localization, induction of cell cycle G2 arrest and cell death were compared between viruses isolated from the fast progressing AIDS patients and a mother-child pair of long-term non-progressors (LTNPs). Wild-type Vpr activities were found in all of the viruses that were isolated from the fast progressing AIDS patients except for the truncated Vpr(IIIB) which lacked these activities. In contrast, defective Vpr were readily detected in viral populations isolated, over an 11-year period, from the mother-child pair. Sequence analyses indicated that these Vpr carried unique amino acid substitutions that frequently interrupted a highly conserved domain containing an N-terminal alpha-helix-turn-alpha-helix. Thus, Vpr activities are generally conserved in naturally occurring viruses. The functionally defective Vpr identified in the mother-child pair of LTNPs are likely to be unique and may possibly contribute to the slow disease progression.     

Antibodies to synthetic peptides corresponding to variable-region first-framework segments of T cell receptors

Recent studies at the gene level have shown that T cells express rearranged genes for four types of T cell receptors that are strongly homologous to classical immunoglobulins in the joining region and in the framework 1 (Fr1) and 3 segments of the variable region. Based upon the homologies in gene sequence, it follows that the gene products would show similarities in amino acid sequence and in the folding of the proteins so that cross-reactivities in antigenic determinants would be expected between variable regions of the T cell receptors and classical immunoglobulins. We have synthesized peptides corresponding to predicted protein sequences of the Fr1 residues of T cell receptor alpha, beta- and gamma-chains and have produced antibodies in rabbits against these synthetic peptides. Use of antisera and affinity-purified antipeptide antibodies indicated that high-titer antibodies could be raised that were specific for individual Fr1 peptides. Cross-reactions among Fr1 peptides of T cell receptors and immunoglobulin light chains were observed. In addition, some rabbit antisera raised against classical polyclonal immunoglobulins or affinity-purified immunoglobulin-like T cell receptors were found to exhibit binding activity against Fr1 peptides of T cell receptor beta- and gamma-chains. The sequence homology, although real among the Fr1 of T cell receptors and immunoglobulin light chains, is moderate and the antigenic cross-reaction must reflect the configuration and types of amino acids present. The development of antipeptide antibodies holds promise for the characterization of T cell receptors of various T cell sources and also offers a new means for the identification of molecules related to rearranging immunoglobulins.     

The development of silk fibroin scaffolds using an indirect rapid prototyping approach: Morphological analysis and cell growth monitoring by spectral-domain optical coherence tomography

To date, naturally derived biomaterials are rarely used in advanced tissue engineering (TE) methods despite their superior biocompatibility. This is because these native materials, which consist mainly of proteins and polysaccharides, do not possess the ability to withstand harsh processing conditions. Unlike synthetic polymers, natural materials degrade and decompose rapidly in the presence of chemical solvents and high temperature, respectively. Thus, the fabrication of tissue scaffolds using natural biomaterials is often carried out using conventional techniques, where the efficiency in mass transport of nutrients and removal of waste products within the construct is compromised. The present study identified silk fibroin (SF) protein as a suitable material for the application of rapid prototyping (RP) or additive manufacturing (AM) technology. Using the indirect RP method, via the use of a mould, SF tissue scaffolds with both macro- and micro-morphological features can be produced and qualitatively examined by spectral-domain optical coherence tomography (SD-OCT). The advanced imaging technique showed the ability to differentiate the cells and SF material by producing high contrasting images, therefore suggesting the method as a feasible alternative to the histological analysis of cell growth within tissue scaffolds.     

Serum resistance in Haemophilus ducreyi requires outer membrane protein DsrA

Haemophilus ducreyi is resistant to killing by normal serum antibody and complement. We discovered an H. ducreyi outer membrane protein required for expression of serum resistance and termed it DsrA (for "ducreyi serum resistance A"). The dsrA locus was cloned, sequenced, and mutagenized. An isogenic mutant (FX517) of parent strain 35000 was constructed and characterized, and it was found to no longer express dsrA. FX517 was at least 10-fold more serum susceptible than 35000. DsrA was expressed by all strains of H. ducreyi tested, except three naturally occurring, avirulent, serum-sensitive strains. FX517 and the three naturally occurring dsrA-nonexpressing strains were complemented in trans with a plasmid expressing dsrA. All four strains were converted to a serum-resistant phenotype, including two that contained truncated lipooligosaccharide (LOS). Therefore, serum resistance in H. ducreyi does not require expression of full-length LOS but does require expression of dsrA. The dsrA locus from eight additional H. ducreyi strains was sequenced, and the deduced amino acid sequences were more than 85% identical. The major difference between the DsrA proteins was due to the presence of one, two, or three copies of the heptameric amino acid repeat NTHNINK. These repeats account for the variability in apparent molecular mass of the monomeric form of DsrA (28 to 35 kDa) observed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Since DsrA is present in virulent strains, is highly conserved, and is required for serum resistance, we speculate that it may be a virulence factor and a potential vaccine candidate.     

Amino acid homologies between human biotinidase and bacterial aliphatic amidases: putative identification of the active site of biotinidase

A search of protein databases revealed amino acid homologies among human biotinidase, bacterial aliphatic amidases, and bacterial and plant nitrilases. Amino acids YRK(210-212) of biotinidase are conserved among the enzyme families. This homology and naturally occurring mutations that cause biotinidase deficiency suggest that this region is essential for enzyme activity and is conserved from bacteria. Cys(245) is likely the cysteine in the active site of biotinidase.     

Functional characterization of naturally occurring genetic variants in the human TLR1-2-6 gene family

Toll-like receptors (TLRs) are considered an essential component of the innate immune system, initiating inflammatory responses following infection of the host. Humans have 10 functional TLRs, differing in their subcellular distributions and the microbial agonists they sense. The phylogenetically conserved TLR1-2-6 family is unique in that TLR1 and TLR6 form heterodimers with TLR2 to mediate signalling in response to agonists. Epidemiological genetic studies have identified several TLR variants that appear to influence susceptibility to infectious diseases, but the functional consequences of which remain largely unknown. Here, we assessed the functional impact of the TLR1-2-6 variants with altered amino acid sequences segregating naturally in the human population. We used an NF-κB reporter assay in TLR-transfected human embryonic kidney 293T cells stimulated with the corresponding TLR agonists. We found that among the 41 naturally occurring variants with amino acid alterations identified in the TLR1-2-6 family, 14 of them (five TLR1, four TLR2, and five TLR6 variants) displayed marked impairment of NF-κB activation. Most of these variants are present at very low population frequencies and are population-specific. These observations suggest that rare, nonsynonymous TLR mutations are likely to have deleterious effects on immune responses and may therefore contribute to complex susceptibility to infection at the population level.