The presence of magnetite crystal chains, considered missing
evidence for the biological origin of magnetite in ALH84001
[Thomas-Keprta, K. L., Bazylinski, D. A., Kirschvink,
J. L., Clemett, S. J., McKay, D. S., Wentworth, S.
J., Vali, H., Gibson, E. K., Jr., & Romanek, C. S. (2000)
Geochim. Cosmochim. Acta 64, 4049–4081], is
demonstrated by high-power stereo backscattered scanning electron
microscopy. Five characteristics of such chains (uniform crystal size
and shape within chains, gaps between crystals, orientation of
elongated crystals along the chain axis, flexibility of chains, and a
halo that is a possible remnant of a membrane around chains), observed
or inferred to be present in magnetotactic bacteria but incompatible
with a nonbiological origin, are shown to be present. Although it is
unlikely that magnetotactic bacteria were ever alive in ALH84001,
decomposed remains of such organisms could have been deposited in
cracks in the rock while it was still on the surface on Mars.
IL-18 can be considered a proinflammatory cytokine mediating
disease as well as an immunostimulatory cytokine that is important for
host defense against infection and cancer. The high-affinity,
constitutively expressed, and circulating IL-18 binding protein
(IL-18BP), which competes with cell surface receptors for IL-18 and
neutralizes IL-18 activity, may act as a natural antiinflammatory as
well as immunosuppressive molecule. In the present studies, the IL-18
precursor caspase-1 cleavage site was changed to a factor Xa site, and,
after expression in Escherichia coli, mature IL-18 was
generated by factor Xa cleavage. Mature IL-18 generated by factor Xa
cleavage was fully active. Single point mutations in the mature IL-18
peptide were made, and the biological activities of the wild-type (WT)
IL-18 were compared with those of the mutants. Mutants E42A and K89A
exhibited 2-fold increased activity compared with WT IL-18. A double
mutant, E42A plus K89A, exhibited 4-fold greater activity.
Unexpectedly, IL-18BP failed to neutralize the double mutant E42A plus
K89A compared with WT IL-18. The K89A mutant was intermediate in being
neutralized by IL-18BP, whereas neutralization of the E42A mutant was
comparable to that in the WT IL-18. The identification of E42 and K89
in the mature IL-18 peptide is consistent with previous modeling
studies of IL-18 binding to IL-18BP and explains the unusually high
affinity of IL-18BP for IL-18.
Light microscopy of thick biological samples, such as tissues, is
often limited by aberrations caused by refractive index variations
within the sample itself. This problem is particularly severe for live
imaging, a field of great current excitement due to the development of
inherently fluorescent proteins. We describe a method of removing such
aberrations computationally by mapping the refractive index of the
sample using differential interference contrast microscopy, modeling
the aberrations by ray tracing through this index map, and using
space-variant deconvolution to remove aberrations. This approach will
open possibilities to study weakly labeled molecules in
difficult-to-image live specimens.
The atomic force microscope (AFM) is a powerful tool for imaging individual biological molecules attached to a substrate and placed in aqueous solution. At present, however, it is limited by the speed at which it can successively record highly resolved images. We sought to increase markedly the scan speed of the AFM, so that in the future it can be used to study the dynamic behavior of biomolecules. For this purpose, we have developed a high-speed scanner, free of resonant vibrations up to 60 kHz, small cantilevers with high resonance frequencies (450–650 kHz) and small spring constants (150–280 pN/nm), an objective-lens type of deflection detection device, and several electronic devices of wide bandwidth. Integration of these various devices has produced an AFM that can capture a 100 × 100 pixel2 image within 80 ms and therefore can generate a movie consisting of many successive images (80-ms intervals) of a sample in aqueous solution. This is demonstrated by imaging myosin V molecules moving on mica (see http://www.s.kanazawa-u.ac.jp/phys/biophys/bmv_movie.htm).
Magnetic relaxation has been used extensively to study and characterize biological tissues. In particular, spin-lattice relaxation in the rotating frame (T1ρ) of water in protein solutions has been demonstrated to be sensitive to macromolecular weight and composition. However, the nature of the contribution from low frequency processes to water relaxation remains unclear. We have examined this problem by studying the water T1ρ dispersion in peptide solutions (14N- and 15N-labeled), glycosaminoglycan solutions, and samples of bovine articular cartilage before and after proteoglycan degradation. We find in model systems and tissue that hydrogen exchange from NH and OH groups to water dominates the low frequency water T1ρ dispersion, in the context of the model used to interpret the relaxation data. Further, low frequency dispersion changes are correlated with loss of proteoglycan from the extra-cellular matrix of articular cartilage. This finding has significance for the noninvasive detection of matrix degradation.
Degeneracy, the ability of elements that are structurally different to perform the same function or yield the same output, is a well known characteristic of the genetic code and immune systems. Here, we point out that degeneracy is a ubiquitous biological property and argue that it is a feature of complexity at genetic, cellular, system, and population levels. Furthermore, it is both necessary for, and an inevitable outcome of, natural selection.
The Hawaiian honeycreepers (Drepanidae) represent a superb illustration of evolutionary radiation, with a single colonization event giving rise to 19 extant and at least 10 extinct species [Curnutt, J. & Pimm, S. (2001) Stud. Avian Biol. 22, 15–30]. They also represent a dramatic example of anthropogenic extinction. Crop and pasture land has replaced their forest habitat, and human introductions of predators and diseases, particularly of mosquitoes and avian malaria, has eliminated them from the remaining low- and mid-elevation forests. Landscape analyses of three high-elevation forest refuges show that anthropogenic climate change is likely to combine with past land-use changes and biological invasions to drive several of the remaining species to extinction, especially on the islands of Kauai and Hawaii.
A general relationship between fluctuation and response in a biological system is presented. The fluctuation is given by the variance of some quantity, whereas the response is given as the average change of that quantity for a given parameter change. We propose a relationship where the two are proportional, in a similar way to the fluctuation–dissipation theorem in physics. By studying an evolution experiment where fluorescence of protein in bacteria increases, we confirm our relation by observing a positive correlation between the speed of fluorescence evolution and the phenotypic fluctuation of the fluorescence over clone bacteria. The generality of the relationship as well as its relevance to evolution is discussed.
Endothelial cells in most vascular beds release a factor that hyperpolarizes the underlying smooth muscle, produces vasodilatation, and plays a fundamental role in the regulation of local blood flow and systemic blood pressure. The identity of this endothelium-derived hyperpolarizing factor (EDHF), which is neither NO nor prostacyclin, remains obscure. Herein, we demonstrate that in mesenteric resistance arteries, release of C-type natriuretic peptide (CNP) accounts for the biological activity of EDHF. Both produce identical smooth muscle hyperpolarizations that are attenuated in the presence of high [K+], the Gi G protein (Gi) inhibitor pertussis toxin, the G protein-gated inwardly rectifying K+ channel inhibitor tertiapin, and a combination of Ba2+ (inwardly rectifying K+ channel blocker) plus ouabain (Na+/K+-ATPase inhibitor). Responses to EDHF and CNP are unaffected by the natriuretic peptide receptor (NPR)-A/B antagonist HS-142-1, but mimicked by the selective NPR-C agonist, cANF4–23. EDHF-dependent relaxation is concomitant with liberation of endothelial CNP; in the presence of the myoendothelial gap-junction inhibitor 18α-glycyrrhetinic acid or after endothelial denudation, CNP release and EDHF responses are profoundly suppressed. These data demonstrate that acetylcholine-evoked release of endothelial CNP activates NPR-C on vascular smooth muscle that via a Gi coupling promotes Ba2+/ouabain-sensitive hyperpolarization. Thus...
It is becoming increasingly clear that bistability (or, more generally, multistability) is an important recurring theme in cell signaling. Bistability may be of particular relevance to biological systems that switch between discrete states, generate oscillatory responses, or “remember” transitory stimuli. Standard mathematical methods allow the detection of bistability in some very simple feedback systems (systems with one or two proteins or genes that either activate each other or inhibit each other), but realistic depictions of signal transduction networks are invariably much more complex. Here, we show that for a class of feedback systems of arbitrary order the stability properties of the system can be deduced mathematically from how the system behaves when feedback is blocked. Provided that this open-loop, feedback-blocked system is monotone and possesses a sigmoidal characteristic, the system is guaranteed to be bistable for some range of feedback strengths. We present a simple graphical method for deducing the stability behavior and bifurcation diagrams for such systems and illustrate the method with two examples taken from recent experimental studies of bistable systems: a two-variable Cdc2/Wee1 system and a more complicated five-variable mitogen-activated protein kinase cascade.
B lymphocytes can be activated by many different stimuli. However, the mechanisms responsible for the signaling and functional specificities of individual stimuli remain to be elucidated. Here, we have compared the contribution of the type 1 (p50-dependent) and type 2 (p52-dependent) NF-κB activation pathways to cell survival, proliferation, homotypic aggregation, and specific gene regulation of murine primary B lymphocytes. Whereas lipopolysaccharide (LPS) and B cell activation factor (BAFF) mainly activate the type 1 or type 2 pathways, respectively, CD40 ligand (CD40L) strongly activates both. Rescue of spontaneous apoptosis is diminished in p52–/– B cells after BAFF stimulation and in p50–/–c-Rel–/– B cells after LPS stimulation. Interestingly, significant CD40-induced B cell survival is still observed even in p50–/–c-Rel–/–p65–/+ B cells, which is correlated with the ability of CD40L to up-regulate Bcl-xL expression in these cells. CD40L- and LPS-induced B cell proliferation, as well as up-regulation of proliferation-related genes, however, are greatly reduced in c-Rel–/– and p50–/–c-Rel–/– B cells but are normal in p52–/– B cells. We have further demonstrated that both c-Rel and p52 are required for CD40-mediated B cell homotypic aggregation...
Bacteria use small diffusible molecules to exchange information in a process called quorum sensing. An important class of autoinducers used by Gram-negative bacteria is the family of N-acylhomoserine lactones. Here, we report the discovery of a previously undescribed nonenzymatically formed product from N-(3-oxododecanoyl)-L-homoserine lactone; both the N-acylhomoserine and its novel tetramic acid degradation product, 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione, are potent antibacterial agents. Bactericidal activity was observed against all tested Gram-positive bacterial strains, whereas no toxicity was seen against Gram-negative bacteria. We propose that Pseudomonas aeruginosa utilizes this tetramic acid as an interference strategy to preclude encroachment by competing bacteria. Additionally, we have discovered that this tetramic acid binds iron with comparable affinity to known bacterial siderophores, possibly providing an unrecognized mechanism for iron solubilization. These findings merit new attention such that other previously identified autoinducers be reevaluated for additional biological functions.
Biological invasions are rapidly producing planet-wide changes in biodiversity and ecosystem function. In coastal waters of the U.S., >500 invaders have become established, and new introductions continue at an increasing rate. Although most species have little impact on native communities, some initially benign introductions may occasionally turn into damaging invasions, although such introductions are rarely documented. Here, I demonstrate that a recently introduced crab has resulted in the rapid spread and increase of an introduced bivalve that had been rare in the system for nearly 50 yr. This increase has occurred through the positive indirect effects of predation by the introduced crab on native bivalves. I used field and laboratory experiments to show that the mechanism is size-specific predation interacting with the different reproductive life histories of the native (protandrous hermaphrodite) and the introduced (dioecious) bivalves. These results suggest that positive interactions among the hundreds of introduced species that are accumulating in coastal systems could result in the rapid transformation of previously benign introductions into aggressively expanding invasions. Even if future management efforts reduce the number of new introductions...
We examine the process of expansion of a focal adhesion complex by which a biological membrane containing mobile binders adheres to a substrate with complementary binders. Attention is focused on the situation, common among living cells, in which the mean mobile binder density is insufficient to overcome generic resistance to close approach of the membrane to its substrate. For the membrane to adhere, binders must be recruited from adjacent regions to join an adhesion patch of density adequate for adhesion, thereby expanding the size of the patch. The specific configuration examined is the expansion of a circular adhesion zone for which diffusive binder transport driven by a chemical potential gradient is the mechanism of binder recruitment. An aspect of the process of particular interest is the stability of the circular shape of the expanding front. It is found that the adhesion front radius increases as √t, where t is the time elapsed since nucleation, and that the circular shape becomes unstable under sinusoidal perturbations for radii large compared with the nucleation size, as observed in recent experiments.
We used airborne imaging spectroscopy and photon transport modeling to determine how biological invasion altered the chemistry of forest canopies across a Hawaiian montane rain forest landscape. The nitrogen-fixing tree Myrica faya doubled canopy nitrogen concentrations and water content as it replaced native forest, whereas the understory herb Hedychium gardnerianum reduced nitrogen concentrations in the forest overstory and substantially increased aboveground water content. This remote sensing approach indicates the geographic extent, intensity, and biogeochemical impacts of two distinct invaders; its wider application could enhance the role of remote sensing in ecosystem analysis and management.
p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers (containing chains A, B, and C) were crystallized with the DNA-consensus element. Although the structure provides crucial data on the p53–DNA contacts, the active oligomeric state is unclear because the two dimeric (A–B and B–C) interfaces present in the crystal cannot both exist in the tetramer. Here, we address the question of which of these two dimeric interfaces may be more biologically relevant. We analyze the sequence and structural properties of the p53–p53 dimeric interfaces and carry out extensive molecular dynamics simulations of the crystal structures of the human and mouse p53 dimers. We find that the A–B interface residues are more conserved than those of the B–C. Molecular dynamics simulations show that the A–B interface can provide a stable DNA-binding motif in the dimeric state, unlike B–C. Our results indicate that the interface between chains A–B in the p53–DNA complex constitutes a better candidate for a stable biological interface, whereas the B–C interface is more likely to be due to crystal packing. Thus...
A central tenet in understanding the biological effects of ionizing radiation has been that the initially affected cells were directly damaged by the radiation. By contrast, evidence has emerged concerning “bystander” responses involving damage to nearby cells that were not themselves directly traversed by the radiation. These long-range effects are of interest both mechanistically and for assessing risks from low-dose exposures, where only a small proportion of cells are directly hit. Bystander effects have been observed largely by using single-cell in vitro systems that do not have realistic multicellular morphology; no studies have as yet been reported in three-dimensional, normal human tissue. Given that the bystander phenomenon must involve cell-to-cell interactions, the relevance of such single-cell in vitro studies is questionable, and thus the significance of bystander responses for human health has remained unclear. Here, we describe bystander responses in a three-dimensional, normal human-tissue system. Endpoints were induction of micronucleated and apoptotic cells. A charged-particle microbeam was used, allowing irradiation of cells in defined locations in the tissue yet guaranteeing that no cells located more than a few micrometers away receive any radiation exposure. Unirradiated cells up to 1 mm distant from irradiated cells showed a significant enhancement in effect over background...
Survival of living cells and organisms is largely based on highly reliable function of their regulatory networks. However, the elements of biological networks, e.g., regulatory genes in genetic networks or neurons in the nervous system, are far from being reliable dynamical elements. How can networks of unreliable elements perform reliably? We here address this question in networks of autonomous noisy elements with fluctuating timing and study the conditions for an overall system behavior being reproducible in the presence of such noise. We find a clear distinction between reliable and unreliable dynamical attractors. In the reliable case, synchrony is sustained in the network, whereas in the unreliable scenario, fluctuating timing of single elements can gradually desynchronize the system, leading to nonreproducible behavior. The likelihood of reliable dynamical attractors strongly depends on the underlying topology of a network. Comparing with the observed architectures of gene regulation networks, we find that those 3-node subgraphs that allow for reliable dynamics are also those that are more abundant in nature, suggesting that specific topologies of regulatory networks may provide a selective advantage in evolution through their resistance against noise.
Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of ≈22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For ≈1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60–80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume ≈40% of the known microRNA sequences...
Targeting tyrosine kinase receptors (RTKs) with specific Abs is a promising therapeutic approach for cancer treatment, although the molecular mechanism(s) responsible for the Abs’ biological activity are not completely known. We targeted the transmembrane RTK for hepatocyte growth factor (HGF) with a monoclonal Ab (DN30). In vitro, chronic treatment of carcinoma cell lines resulted in impairment of HGF-induced signal transduction, anchorage-independent growth, and invasiveness. In vivo, administration of DN30 inhibited growth and metastatic spread to the lung of neoplastic cells s.c. transplanted into immunodeficient nu/nu mice. This Ab efficiently down-regulates HGF receptor through a molecular mechanism involving a double proteolytic cleavage: (i) cleavage of the extracellular portion, resulting in “shedding” of the ectodomain, and (ii) cleavage of the intracellular domain, which is rapidly degraded by the proteasome. Interestingly, the “decoy effect” generated by the shed ectodomain, acting as a dominant negative molecule, enhanced the inhibitory effect of the Ab.