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The high resolution solution structure of the insulin monomer determined by NMR.

Studies of naturally occurring and chemically modified insulins indicate that relatively few of the 51 amino acid residues may be assigned specific roles in insulin-receptor interactions. Most of the insulin X-ray structural information is derived from aggregated species (notably hexamers). Because insulin exerts its physiological effect as a 5808 Dalton monomeric species, it is necessary to consider whether crystal-packing forces have modified the structure from that required for biological action. Insulin aggregation in solution complicates high resolution NMR studies of the monomer. However, site-directed mutagenesis can be used to generate biologically active mutants (e.g., B16-Tyr--> His) that remain monomeric at millimolar concentrations in aqueous solution at low pH. The resulting homogeneous and monomeric samples are suitable for structure determination by NMR methods. The high resolution solution structure of B16--Tyr--> His insulin resembles crystal structures, notably molecule 1 of T6 insulin. Side-chain conformation in some biologically important motifs, however, shows subtle differences between solution and crystal structures.

Amino Acid Sequence↗

Iraq's biological weapons. The past as future?

Between 1985 and April 1991, Iraq developed anthrax, botulinum toxin, and aflatoxin for biological warfare; 200 bombs and 25 ballistic missiles laden with biological agents were deployed by the time Operation Desert Storm occurred. Although cause for concern, if used during the Persian Gulf War, Iraq's biological warfare arsenal probably would have been militarily ineffective for 3 reasons: (1) it was small; (2) payload dispersal mechanisms were inefficient; and (3) coalition forces dominated the theater of war (ie, they had overwhelming air superiority and had crippled Iraq's command and control capability). Despite the Gulf War defeat, the Iraqi biological warfare threat has not been extinguished. Saddam Hussein remains in power, and his desire to acquire weapons of mass destruction continues unabated. In this context, the international community must be firm in its enforcement of United Nations resolutions designed to deter Iraq from reacquiring biological warfare capability and must take steps to develop a multidisciplinary approach to limiting future development of weapons of mass destruction.

Aflatoxins↗

Multicolor deconvolution microscopy of thick biological specimens.

One limitation in understanding disease at the cellular level has been the inability to efficiently analyze DNA on a cell-to-cell basis within the natural tissue context. However, DNA analyses at a single-cell resolution should be instrumental for the understanding of cancer cell biology, cancer evolution, for chromosomal mosaic analysis and rare cell events, and should provide otherwise inaccessible information on essential biological processes. Here we present a fluorescence in situ hybridization-based multicolor deconvolution technique for three-dimensional microscopy. We use up to seven different color channels for probe detection, which allows the simultaneous high-resolution localization of multiple point-like sources within a biological specimen with a thickness of up to 30 micro m. In addition, a DNA counterstain is used for volume labeling of the nuclei offering the opportunity for a simultaneous segmentation of nuclei. Furthermore, as the instrumentation consists of a standard fluorescence microscope it represents a low-cost method as compared to confocal microscopy.

Centromere↗

Resolution in electron microscope autoradiography. III. Iodine-125, the effect of heavy metal staining, and a reassessment of critical parameters.

Resolution for 125I-labeled specimens under electron microscope (EM) autoradiographic conditions was assessed experimentally. With this isotope the size of the silver halide crystal was the most important resolution-limiting factor. Heavy metal staining such as is routinely used in preparing animal tissues for EM autoradiography produced an improvement in resolution of approximately 15-20%. For a 500-1,000-A biological tissue section fixed with OsO4 and stained with uranyl acetate, we obtained resolution (half distance, HD) values of approximately 800 +/- 120 A using Ilford L4 emulsion and 500 +/- 70 A using a Kodak NTE-type emulsion. General aspects of resolution-limiting factors and comparison with 3H and 14C values are discussed.

Animals↗

Identification of transformation products arising from bacterial oxidation of codeine by Streptomyces griseus.

14-Hydroxycodeine and norcodeine were rigorously identified as products arising from codeine oxidation by Streptomyces griseus ATCC 10137. Both products were routinely detected in extracted culture filtrates after growth of cells in the presence of codeine for 1 week. Under these conditions, about 4 mol% of the codeine starting material was consumed, with norcodeine and 14-hydroxycodeine representing the only identifiable transformation products (molar ratio, 4:1, respectively). Extraction of a series of culture filtrates and purification of the pooled metabolites by thin-layer and high-pressure liquid chromatography led to the isolation of both biological products, the structures of which were verified by high-resolution mass spectrometry and proton nuclear magnetic resonance spectroscopy. The identities of both biological products were further confirmed by comparison of their spectral properties with those of authentic standards. This is the first report providing structural evidence for the biological formation of 14-hydroxycodeine from codeine and of codeine oxidation by S. griseus.

Biotransformation↗

The Caenorhabditis elegans gonad: a test tube for cell and developmental biology.

Sexual reproduction of multicellular organisms depends critically on the coordinate development of the germ line and somatic gonad, a process known as gonadogenesis. Together these tissues ensure the formation of functional gametes and, in the female of many species, create a context for production and further development of the zygote. Since the future of the species hangs in the balance, it is not surprising that gonadogenesis is a complex process involving conserved and multi-faceted developmental mechanisms. Genetic, anatomical, cell biological, and molecular experiments have established the nematode Caenorhabditis elegans as a paradigm for studying gonadogenesis. Furthermore, these studies demonstrate the utility of C. elegans gonadogenesis for exploring broad issues in cell and developmental biology, such as cell fate specification, morphogenesis, cell signaling, cell cycle control, and programmed cell death. The synergy of molecular genetics and cell biology conducted at single-cell resolution in real time permits an extraordinary depth of analysis in this organism. In this review, we first describe the embryonic and post-embryonic development and morphology of the C. elegans gonad. Next we recount seminal experiments that established the field, highlight recent results that provide insight into conserved developmental mechanisms, and present future prospects for the field.

Animals↗

Capillary isoelectric focusing-mass spectrometry: analysis of protein mixtures from human body fluids.

Isoelectric focusing within a fused silica capillary (cIEF) has proved to be a powerful and practical method for high-resolution separation of analytes from complex biological mixtures. This technique overcomes many of the problems of isoelectric focusing within slab gel media. However current cIEF systems commonly utilize UV detection which limits the detail of analyte structural information that is obtained during analysis. The use of mass spectrometry (MS) as the detection system provides much greater structural information about the detected analytes allowing accurate relative molecular mass (M(r)) determination for proteins and polypeptides. We have constructed a cIEF-MS interface and compared the separation of standard proteins analyzed by cIEF-UV with cIEF-MS. This allowed rapid optimization of the cIEF-MS system performance. Further we have demonstrated the use of MS as a detection system provides accurate M(r) information and can provide analyte modification details. These factors increase the likelihood of absolute identification for physiological proteins within complex in vivo-derived mixtures. To demonstrate the value of cIEF-MS in such analyses we have undertaken an examination of cerebrospinal fluid (CSF), and tentatively identified a number of constituent proteins. We have also analyzed whole blood from control and diabetic patients. We show that glycated alpha- and beta- chains of hemoglobin are found in almost equal abundance in diabetic patient blood. From these results we suggest cIEF-MS is an efficient and useful tool for the separation and examination of in vivo-derived analytes within physiological fluids.

Adult↗

Chemical extraction of the cytosol using osmium tetroxide for high resolution scanning electron microscopy.

Detailed examination of subcellular structures in three dimensions (3D) by high resolution scanning electron microscopy (HRSEM) is now possible due to improvements in the design of the scanning electron microscope and the introduction of methods of specimen preparation using chemical removal of the cytosol and cytoskeleton by dilute osmium tetroxide. Cells which have been fixed, frozen, cleaved, thawed, and subjected to cytosol extraction display intact intracellular structures in 3D including nuclear chromatin, endoplasmic reticulum, mitochondria, and the Golgi complex at a resolution close to that of conventional biological transmission electron microscopy (TEM). Small changes in the 3D structure of subcellular components can be conveniently examined in this way in development, in a variety of physiological processes and in disease. Broad areas of the specimen can be quickly surveyed by HRSEM since sectioning is not required and specimens of comparatively large size (up to 5 mm3) can be placed in the microscope. Extraction of the cytosol with dilute osmium tetroxide (OsO4) exposes subcellular structures in relief, permitting their examination in 3D from several aspects. However, the OsO4 extraction technique is limited, since significant intracellular structures, such as the cytoskeleton, vesicles, and antibody binding sites can be removed or inactivated during the cytosol removal steps.

Animals↗

Quantitation of arachidonic acid metabolites in small tissue biopsies by reversed-phase high-performance liquid chromatography.

Arachidonic acid metabolites exert a variety of distinct biological effects on the initiation and resolution of inflammatory diseases and their measurements in tissue can be critical to evaluate their regulatory function during the course of inflammation and to supplement in vitro experiments. The aim of this study was the detection and quantitative analysis of four arachidonic acid metabolites in small-sized biopsies of human periodontal tissues. The biopsies were homogenized and injected directly into a single analytical column of a RP-HPLC system. Detection was performed by a photodiode array detector. Calibration was established by dilutions of authentic standards of prostaglandin E2 (PGE2), leukotriene B4 (LTB4), 12(R)-hydroxy-5,8,10,14-eicosatetraenoic acid (12-HETE), and 15(S)-hydroxy-5,8,11,13-eicosatetraenoic acid (15-HETE). A total of 38 specimens weighing between 19 and 191 mg (wet tissue) were analyzed (mean = 59.9 +/- 30.2 mg). The detection limits were 1 pg for LTB4 and 12-HETE, 0.5 pg for 15-HETE, and 10 ng for PGE2. The concentrations of PGE2 and LTB4 were significantly higher in inflamed than in healthy periodontal tissues (P = 0.0079; P = 0. 0114). 12-HETE was detected in one biopsy (30 pg/g); 15-HETE was not detected. This method of homogenization, extraction, and analysis of arachidonic acid metabolites by RP-HPLC appears to be well suited for studies of human oral biopsies. Only small tissue samples and minimal laboratory equipment were required for a sensitive analysis.

12-Hydroxy-5,8,10,14-eicosatetraenoic Acid↗

Phyllotaxis: the status of the field.

In the last decade important progress has been made regarding pattern recognition and generation of the phenomenon of phyllotaxis. Phyllotaxis, a central area in plant morphogenesis, proposes a challenge that reaches beyond the field of botany and whose resolution must be sought through evolutionary biology and general comparative morphology. This review summarizes the contributions in the area, redefines the challenge, and proposes an adequate framework for the study of the phenomenon.

Mathematics↗

An optimized differential heat conduction solution microcalorimeter for thermal kinetic measurements.

Heat conduction calorimeters are widely used in the biological sciences, but baseline instability, low resolution, electrical noise and motion artifacts have limited their utility. Two main sources of noise, baseline fluctuation or drift and a motion artifact, were traced to amplifier drift, a small (0.015 degrees C) gradient within the constant temperature cylinder, and the method of installing the thermopiles. The addition of heaters to the top and bottom of the cylinder reduced the gradient to approximately 0.003 degrees C and greatly reduced the slow component of the motion artifact. The drift error was reduced by proper mounting of the amplifier and its external components and the enclosure of the calorimeter in a temperature-controlled box. An R-C model of the heat flow in the calorimeter was developed which was employed to discover several means of increasing sensitivity without increasing the rise-time of the calorimeter. Analysis, also based on the model, showed that variations in the air gap between the cell and cell holder can be a major source of error when the calorimeter is used to investigate the kinetics of a chemical reaction. This analysis also showed that the time for the heat to flow through the solution in the cell can be the dominant factor in determining the rise-time of the instrument. The heat conduction calorimeter described here has improved characteristics: a baseline stability of 200 nJ x s-1 (peak-to-peak) over a 48 h period; a resolution of 200 nJ x s-1; a sensitivity of 6.504 +/- 0.045 J x V-1 x s-1 referred to the sensor output; and a rise-time of 122 s for the 10-90% response.

Calorimetry↗

Scanning tunnelling microscopy in biotechnology.

The scanning tunnelling microscope (STM) is capable of atomic resolution of highly conductive materials. Whether biological molecules can be visualized to the same extent remains an open question, but remarkable progress in the past year confirms the possibility of seeing the fine structure of nucleic acids, proteins, membranes and viruses, and provides evidence that their dynamic interactions can be monitored under conditions approximating to those of the native environment.

Biotechnology↗

The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles.

Cryo-electron microscopy of single biological particles opens up new possibilities for structure analysis: the particle can be reconstructed in its native shape and internal features are preserved. To take advantage of these possibilities we have developed new methods of data collection and image processing and we have applied them to the 70S Escherichia coli ribosome. A method of orientation search is proposed, which makes it possible to relate random-conical data sets to one another even if they are collected from low-tilt micrographs. A technique for 3D alignment of projections is described and applied to the single-micrograph 3D reconstruction.

Escherichia coli↗

Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site.

PriB is not only an essential protein necessary for the replication restart on the collapsed and disintegrated replication fork, but also an important protein for assembling of primosome onto PhiX174 genomic DNA during replication initiation. Here we report a 2.0-A-resolution X-ray structure of a biologically functional form of PriB from Escherichia coli. The crystal structure revealed that despite a low level of primary sequence identity, the PriB monomer, as well as the dimeric form, are structurally identical to the N-terminal DNA-binding domain of the single-stranded DNA-binding protein (SSB) from Escherichia coli, which possesses an oligonucleotides-binding-fold. The oligonucleotide-PriB complex model based on the oligonucleotides-SSB complex structure suggested that PriB had a DNA-binding pocket conserved in SSB from Escherichia coli and might bind to single-stranded DNA in the manner of SSB. Furthermore, surface plasmon resonance analysis and fluorescence measurements demonstrated that PriB binds single-stranded DNA with high affinity, by involving tryptophan residue. The significance of these results with respect to the functional role of PriB in the assembly of primosome is discussed.

Amino Acid Sequence↗

Matching genomic evidence to claims about Mycobacterium avium subsp. paratuberculosis: Host association, host adaptation, mechanism, and virulence.

Whole-genome sequencing (WGS) permits high-resolution comparison of Mycobacterium avium subsp. paratuberculosis (MAP) isolates and pangenome analysis. Combined with animal-movement data, WGS can support transmission inference, but resolution alone does not establish the biological meaning of genomic variation. This focused narrative review applies a two-dimensional framework to purposively selected MAP studies, separating claim targets from support profiles. Claim targets include lineage identity, host-source or lineage characterization, host association, transmission, candidate genomic features, measured bacterial or host-cell phenotypes, natural-host infection fitness, disease or damage, shedding, and control outcomes. Depending on the claim, evidence operations may include characterization, context-aware comparative inference, direct endpoint ascertainment, and controlled feature perturbation; these are non-ordinal and may co-occur. On-target attribution, independent replication, and transportability are reported separately. The claim, not the study, is the unit of assessment. Typing markers support isolate or lineage discrimination, whereas phylogenomics supports evolutionary inference; neither alone establishes host adaptation. Pangenome comparisons and microbial genome-wide association studies nominate candidate features rather than establish adaptation. Cell-envelope and iron-associated studies support specified biochemical, transcriptional, or physiological phenotypes under defined conditions, while macrophage and calf models support only the endpoints measured. Annotated sequence variation alone nominates pathogenicity hypotheses. Across the illustrative studies selected here, MAP genomics most directly supported lineage classification, candidate discovery, measured bacterial phenotypes, bounded transmission inference, and natural-host infection-fitness claims. Claims about adaptation, mechanism, virulence, or control require endpoints and comparisons matched to the stated claim and model; feature-specific causal claims additionally require evidence linking the bacterial feature to the measured endpoint.

Claim boundaries↗

A microchip electrophoresis device with on-line microdialysis sampling and on-chip sample derivatization by naphthalene 2,3-dicarboxaldehyde/2-mercaptoethanol for amino acid and peptide analysis.

The integration of rapid on-chip sample derivatization employing naphthalene 2,3-dicarboxaldehyde and 2-mercaptoethanol (NDA/2ME) with an easily assembled microdialysis/microchip electrophoresis device was carried out. The microchip device consisted of a glass layer with etched microfluidic channels that was sealed with a layer of poly(dimethylsiloxane) (PDMS) via plasma oxidation. This simple sealing procedure alleviated the need for glass thermal bonding and allowed the device to be re-sealed in the event of blockages within the channels. The device was used for analysis of a mixture of amino acids and peptides derivatized on-chip with NDA/2ME for laser-induced fluorescence (LIF) detection. A 0.6 mM NDA/1.2 mM 2ME mixture was simply added into the buffer reservoir for dynamic on-column derivatization of sample mixtures introduced at a flow rate of 1.0 microl/min. Using this scheme, sample injection plugs were derivatized and separated simultaneously. Injections of ca. 12 fmol of 5 mM amino acid and peptide samples were conducted using the system. Finally, a three-component mixture of Arg, Gly-Pro, and Asp was sampled from a vial using microdialysis, derivatized, separated and detected with the system. The ultimate goal of this effort is the creation of a micro-total analysis system for high-temporal resolution monitoring of primary amines in biological systems.

Amino Acids↗

Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy.

Cryo-electron microscopy of vitreous sections (CEMOVIS) has recently been shown to provide images of biological specimens with unprecedented quality and resolution. Cutting the sections remains however the major difficulty. Here, we examine the parameters influencing the quality of the sections and analyse the resulting artefacts. They are in particular: knife marks, compression, crevasses, and chatter. We propose a model taking into account the interplay between viscous flow and fracture. We confirm that crevasses are formed on only one side of the section, and define conditions by which they can be avoided. Chatter is an effect of irregular compression due to friction of the section of the knife edge and conditions to prevent this are also explored. In absence of crevasses and chatter, the bulk of the section is compressed approximately homogeneously. Within this approximation, it is possible to correct for compression by a simple linear transformation for the bulk of the section. A research program is proposed to test and refine our understanding of the sectioning process.

Artifacts↗

Can vision of the body ameliorate impaired somatosensory function?

Viewing the body is reported to improve tactile acuity [Kennett, S., Taylor-Clarke, M., & Haggard, P. (2001). Non-informative vision improves the spatial resolution of touch in humans. Current Biology, 11, 1188-1191]. The aim of the present study was to investigate whether this effect might be useful in improving somatosensory deficits of brain damaged patients. To support this proposal, we firstly tested the hypothesis that vision might modulate tactile performance when tactile information is limited. Thirty-two healthy subjects performed a two points discrimination task (2PDT) in three conditions: looking at their stimulated forearm, at a neutral object or at a rubber foot. The results showed that the effectiveness of visual enhancement of touch varies as a function of subjects' tactile acuity. Moreover, the accuracy in 2PDT was higher when viewing their arm only in subjects with lower tactile sensitivity. To directly demonstrate that viewing the body might ameliorate tactile deficits, the same experiment was conducted on 10 brain damaged patients suffering a reduced somatosensory sensitivity. An amelioration of the performance was found in viewing arm condition. These findings suggest that the interaction between different sensory modalities might be effective in ameliorating deficits in single modalities.

Adult↗