Carbonic anhydrase IX

Cell migration can be principally viewed as a chain of well-orchestrated morphological events that lead to dynamic reshaping of the cell body. However, behind the scene of such a “morphological theater” there are very complex, interrelated molecular and physiological processes that drive the cell movement. Among them, ion transport and pH regulation play a key role, with carbonic anhydrase IX (CA IX) emerging as one of the important “molecular actors.” CA IX is a highly active cell surface enzyme expressed in a broad range of solid tumors in response to hypoxia and explored as a clinically useful biomarker of hypoxia and as a therapeutic target. Its biological role is to protect tumor cells from hypoxia and acidosis in the tumor microenvironment. The study published recently by our group showed that CA IX actively contributes to cell migration and invasion. For the first time, we demonstrated CA IX accumulation in lamellipodia of migrating cells and its direct in situ interaction with bicarbonate transporters. Our findings indicate that tumor cells need CA IX not only as a pro-survival factor in hypoxia and acidosis, but also as a pro-migratory component of the cellular apparatus driving epithelial-mesenchymal transition.     

B chromosomes in plants

Abstract

B chromosomes (Bs) can be described as “selfish chromosomes”, a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. They can accumulate in number by various processes of mitotic or meiotic drive, especially in the gametophyte phase of the life cycle of flowering plants. This parasitic property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. B chromosomes are inhabitants of the nucleus and they are subject to control by “genes” in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a Bs. In this review, we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology.     

Reduction of lactic acid secreted from SV3T3 cells by a serum factor and biotin and its relationship to cell growth

Supplementation of media containing a low concentration (0.15–0.30% $\text{v}\text{>v}$) of calf serum with biotin or a low molecular weight serum growth factor (Peak III) reduces the amount of lactic acid secreted by simian virus 40-transformed 3T3 cells. While biotin and Peak III (which has been tentatively identified as biotin) can stimulate “stationary phase” cells to resume viable cell division, this growth promotion is not due to an alleviation of lactic acid toxicity per se. This conclusion is based on the finding that, although higher concentrations of lactic acid are cytotoxic, lactic acid added at concentrations found during “stationary phase” to cells plated in fresh medium is not growth inhibitory. These results suggest, instead, a possible major role for biotin and Peak III in energy production.     

Pendular activity of human upper limbs during slow and normal walking

When walking at normal and fast speeds, humans swing their upper limbs in alternation, each upper limb swinging in phase with the contralateral lower limb. However, at slow and very slow speeds, the upper limbs swing forward and back in unison, at twice the stride frequency of the lower limbs. The change from “single swinging” (in alternation) to “double swinging” (in unison) occurs consistently at a certain stride frequency for agiven individual, though different individuals may change at different stride frequencies. To explain this change in the way we use our upper limbs and individual variations in the occurrence of the change, the upper limb is modelled as a compound pendulum. Based on the kinematic properties of pendulums, we hypothesize that the stride frequency at which the change from “single swinging” to “double swinging” occurs will be at or slightly below the natural pendular frequency (NPF) of the upper limbs. Twenty-seven subjects were measured and then filmed while walking at various speeds. The mathematically derived NPF of each subject's upper limbs was compared to the stride frequency at which the subject changed from “single swinging” to “double swinging.” The results of the study conform very closely to the hypothesis, even when the NPF is artificially altered by adding weights to the subjects' hands. These results indicate that the pendulum model of the upper limb will be useful in further investigations of the function of the upper limbs in human walking. © 1994 Wiley-Liss, Inc.     

Different size limitations for increased transepithelial paracellular solute flux across phorbol ester and tumor necrosis factor-treated epithelial cell sheets

By observing increases in the transepithelial paracellular permeability of a range of radiolabeled solutes and electron dense dyes, changes in molecular sieving caused by the cytokine, TNF (tumor necrosis factor), and the phorbol ester, TPA (12-0-tetra-decanoylphorbol-13-acetate), were characterized. Using ¹⁴C-labeled mannitol (mw 182), raffinose (mw 504), PEG (polyethylene glycol; mw 4000), and dextran (mw 10,000, 70,000 and 2,000,000), the transepithelial flux rates of these compounds were determined at the peak of the transepithelial electrical resistance (TER) changes caused by these two agents. TNF treatment resulted in increased permeability across LLC-PK₁ epithelial cell sheets only to relatively small solutes, with an upper limit of approximately 4,000 mw. The low molecular weight “ceiling” for the TNF-treated epithelium is further evidence against TNF increasing transepithelial permeability by means of inducing nonspecific, microscopic “holes” in the epithelium, for which a “ceiling” would not exist. TPA treatment increases transepithelial paracellular permeability to a much broader range of solutes, extending well beyond 2 million mw. Transmission electron micrographs provide evidence that even the electron-dense dye complex, ruthenium red, can cross tight junctions of TPA-treated cell sheets. However, cationic ferritin cannot cross tight junctions of TPA-treated cell sheets. This shows that there is an upper limit to solutes able to cross TPA-treated cell sheets, but that this upper limit will include most proteins, which would then be able to cross tumor promoter-exposed (protein kinase C-activated) epithelial layers at accelerated rates. The biomedical implications for a high molecular weight cutoff in tumor promoter action in epithelial carcinogenesis, and for a low molecular weight cutoff in cytokine-induced epithelial apoptosis in inflammation, are discussed. J. Cell. Physiol. 171:226–233, 1997. © 1997 Wiley-Liss, Inc.     

Beyond the GTP-cap: Elucidating the molecular mechanisms of microtubule catastrophe

Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The “standard model” of microtubule dynamics implicates a “cap” of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule “catastrophe,” a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end – which may or may not be directly linked to the nucleotide content at the microtubule end – ultimately drive microtubule catastrophe.     

Fallenbewegungen fleischfressender Pflanzen

How carnivorous plants outsmart their prey The non‐muscular movements of plants, especially the fast traps of carnivorous plants, might appear as natural “wonders”, but they are all evoked by the interplay of functional morphological structures developed during evolution with well‐described biophysical and chemical processes. Hydraulic “motors”, which are based on water displacement in the respective cells and tissues, entail rather slow motions. Large and fast structures, as e.g., the snap‐traps of the carnivorous Venus flytrap, often depend on the release of stored elastic energy (relaxation) which acts as a speed boost and significantly speeds up the motion. The fast traps presented here and the deformation principles involved, including some mechanical “tricks”, can be rebuild in simple and low‐cost physical models which are especially useful for an application in teaching.     

Thermal variations, between 1 and 3000 degrees K, of the specific heat of L-alanine, tri(L-alanine) and poly(L-alanine) for the alpha and beta forms]

The heat capacities of L -Alanine, tri(L -alanine), and poly (L -alanine) (α helicoidal form and β pleated sheet structure) have been measured between 1.5 and 300°K with a standard adiabatic calorimeter. In the solid state, the heat capacity is in general dut to three parts which are additive in first-order approximation. (1) The lattice vibrations or “acoustical modes” which are the largest at low temperatures. The low-temperature lattice specific heat is proportional to T, T², or T³ for an ideal one-, two- or three-dimensional solid, respectively. (2) The so-called group vibrations or “optical modes” which, due to their high frequencies, usually take effect only at higher temperatures. (3) The defects and unharmonic effects. The α-amino acid and its trimer present a specific heat thermal variation characteristic of molecular solids which is correctly fitted with an empirical law proposed by Kitaigorodskii. This author assumes that, for such solids, the molecular lattice point has six degrees of freedom (three of translation and three of rotation). Thus the lattice contribution of the specific heat satisfies the Debye approximation in agreement with the doubling of the number of degrees of freedom per molecule (compared with atomic crystals). The polypeptide behavior is, however, different. The specific heat for each form exhibits a thermal dependence connected with a strong vibrational anisotropy. The model proposed earlier by Tarasov accounts well for these results. In the case of the β form, we have observed the predicted three- and two-dimensional behavior due to the intermolecular H bondings responsible for the sheet structure. For the α form we observed a one-dimensional pattern at higher temperature, since each peptidic chain vibrates separately. The comparison with other spectroscopic and theoretical investigations shows a large discrepancy. However, we have attemped to account for the “optical contribution” to the specific heat of poly(L -alanine) by using a continuum of mean frequencies as suggested by Wunderlich. Vibrational frequency spectra are proposed to explain our results, but the overlapping of acoustical and optical branches in the case of the α form outlines the limits of macroscopic models. It is quite likely that the acoustical spectrum is greatly affected by the intramolecular H bonding. At low temperature the specific heat is a physical property sensitive to the long-range order of the macromolecule, and therefore further spectroscopic and theoretical investigations are necessary to explain correctly these experimental results.     

Mechanical vibration in “double-wound” magnetic field exposure coils

It has been suggested that “double-wound” (bifilar) exposure coils are capable of producing a sham environment in which hum and vibration will be “similar” to the field-exposed condition. We found by direct measurements in a bifilar coil system that vibration amplitude in sham and exposed conditions differed by a factor of 50 when our test system was driven at B = 10 mT. We also found that the normal laboratory environment can include vibrations of an intensity similar to that produced by the exposure system, although not necessarily of similar spectral distribution. © 1996 Wiley-Liss, Inc.     

Droplet organelles?

Cells contain numerous, molecularly distinct cellular compartments that are not enclosed by lipid bilayers. These compartments are implicated in a wide range of cellular activities, and they have been variously described as bodies, granules, or organelles. Recent evidence suggests that a liquid–liquid phase separation (LLPS) process may drive their formation, possibly justifying the unifying term “droplet organelle”. A veritable deluge of recent publications points to the importance of low‐complexity proteins and RNA in determining the physical properties of phase‐separated structures. Many of the proteins linked to such structures are implicated in human diseases, such as amyotrophic lateral sclerosis (ALS). We provide an overview of the organizational principles that characterize putative “droplet organelles” in healthy and diseased cells, connecting protein biochemistry with cell physiology.     

Dysfunction of thymocytes of C3H/HeJ mice in blastogenic response to anti-thymocyte serum in vitro and its repair with lipopolysaccharide induced mediator.

In vitro mitogenic responses of thymocytes to rabbit anti-mouse thymocyte serum (ATS) have been compared in several mouse strains. The response of thymocytes of C3H/HeJ mice is about one-third of those of thymocytes of C3H/He, ATL or ATH strains. Phenol-extracted bacterial lipopolysaccharide (LPS) does not induce mitogenic response in cultured C3H/HeJ spleen cells, but the spleen cells of all other strains used are capable of responding to LPS. The low response of C3H/HeJ thymocytes to ATS is restored by adding “endotoxin soup” prepared from spleen cell cultures of LPS-responder mice in the presence of LPS. Neither soup prepared from C3H/HeJ spleen cell cultures without the addition of LPS nor soup prepared from cell cultures with LPS show such restoration of the response of C3H/HeJ thymocytes to ATS. The molecular size of the active factor in “endotoxin soup” was estimated on a Sepharose CL-4B column and determined to be about 20,000 daltons. The activity of “endotoxin soup” is destroyed by heating at 70 C for 30 min or 80 C for 10 min and diminished by digestion with trypsin. The mechanisms of restoration of low response of C3H/HeJ thymocytes to ATS by “endotoxin soup” are discussed.     

Flight speed of seabirds in relation to wind speed and direction

We studied flight speed among all major seabird taxa. Our objectives were to provide further insight into dynamics of seabird flight and to develop allometric equations relating ground speed to wind speed and direction for use in adjusting seabird density estimates (calculated from surveys at sea) for the effect of bird movement. We used triangulation at sea to estimate ground speeds of 1562 individuals of 98 species. Species sorted into 25 “groups” based on similarity in ground speeds and taxonomy. After they were controlled for differences inground speed, the 25 groups sorted into eight major “types” on the basis of response to wind speed and wind direction. Wind speed and direction explained 1664% of the variation in ground speed among seabird types. For analyses on air speed (ground speed minus apparent wind speed), we divided the 25 groups according to four flight styles: gliding, flap-gliding, glide-flapping and flapping. Tailwind speed had little effect on air speed of gliders (albatrosses and large gadfly petrels), but species that more often used flapping decreased air speed with increase in tailwinds. All species increased air speeds significantly with increased headwinds. Gliders showed the greatest increase relative to increase in headwind speed and flappers the least. With tailwind flight, air speeds were greatest among species with highest wing loading for each flight style except gliders, which showed no relationship. For headwind flight, species with higher wing loading had higher air speeds; however, the relation was weaker in flappers compared with species using some amount of gliding. In contrast, analyses for air speed ratio (i.e. difference between air speed in acrosswinds [with no apparent wind] and speed flown into headwinds, or with tailwinds, divided by speed acrosswind) revealed that among species using some flapping, and with lower wing loading (surface-feeding shearwaters, small gadfly petrels, storm petrels, phalaropes, gulls and terns), adjusted air speeds more than those with higher wing loading (alcids, “diving shearwaters”, “Manx-type shearwaters”, pelicans, boobies and cormorants). As a result, most flappers of low wing loading flew much faster than V_mr (the most energy efficient air speed per distance flown) when flying into headwinds. We suggest that better-than-predicted gliding performance with acrosswinds and tailwinds of large gadfly petrels, compared with albatrosses, resulted from a different type of “soaring” not previously described in seabirds.     

Mechanical energy oscillations of two brachiation gaits: measurement and simulation

How do arm‐swinging apes locomote effectively over a variety of speeds? One way to reduce the metabolic energy cost of locomotion is to transfer energy between reversible mechanical modes. In terrestrial animals, at least two transfer mechanisms have been identified: 1) a pendulum‐like mechanism for walking, with exchange between gravitational potential energy and translational kinetic energy, and 2) a spring‐like mechanism for running, where the elastic strain energy of stretched muscle and tendon is largely returned to reaccelerate the animal. At slower speeds, a brachiator will always have at least one limb in contact with the support, similar to the overlap of foot contact in bipedal walking. At faster speeds, brachiators exhibit an aerial phase, similar to that seen in bipedal running. Are there two distinct brachiation gaits even though the animal appears to simply swing beneath its overhead support? If so, are different exchange mechanisms employed? Our kinetic analysis of brachiation in a white‐handed gibbon (Hylobates lar) indicates that brachiation is indeed comprised of two mechanically distinct gaits. At slower speeds in “continuous contact” brachiation, the gibbon utilizes a simple pendulum‐like transfer of mechanical energy within each stride. At faster speeds in “ricochetal” brachiation, translational and rotational kinetic energy are exchanged in a novel “whip‐like” transfer. We propose that brachiators utilize the transfer between translational and rotational kinetic energy to control the dynamics of their swing. This maneuver may allow muscle action at the shoulder to control the transfer and adjust the ballistic portion of the step to meet the requirements for the next hand contact. Am J Phys Anthropol 115:319–326, 2001. © 2001 Wiley‐Liss, Inc.     

Involvement of a low molecular weight component(s) in the mechanism of action of the glucocorticoid receptor.

[³H]Dexamethasone-receptor complexes from rat liver cytosol preincubated at 0° bind poorly to DNA-cellulose. However, if the steroid-receptor complex is subjected to gel filtration at 0–4° separating it from the low molecular weight components of cytosol, the steroid-receptor complex becomes “activated” enabling its binding to DNA-cellulose. This activation can be prevented if the gel filtration column is first equilibrated with the low molecular weight components of cytosol. In addition, if adrenalectomized rat liver cytosol, in the absence of exogeneous steroid, is subjected to gel filtration the macromolecular fractions separated from the “small molecules” of that cytosol have much reduced binding activity towards [³H]dexamethasone. These results suggest that rat liver cytosol contains a low molecular weight component(s) which maintains the glucocorticoid receptor in a conformational state that allows the binding of dexamethasone. Furthermore, this component must be removed from the steroid-receptor complex before binding to DNA can occur.     

Rethinking the (im)possible in evolution

This paper will discuss the philosophical background to evolutionary theory and present multiple counterfactuals to each of the following seven empirically unsustainable but nonetheless widespread assumptions about genomic (DNA-based) evolution:1. “All heredity transmission occurs from parent to progeny”2. “Mutations are the result of inevitable replication errors”3. “Mutations occur at constant low probabilities over time” (= there are “mutation rates”)4. “Virus infection cannot induce genetic changes giving heritable resistance”5. “Mutations cannot be targeted within the genome”6. “Spontaneous hereditary changes are localized and limited to those of small effect”7. “Cells cannot integrate DNA change with biologically useful adaptive needs”.The summary take-home lesson is that we have to change from thinking of the genome as a read-only memory (ROM) that dictates the fate of the cell or organism to conceptualizing the genome as a read-write (RW) organelle modified transiently or permanently by the cell at different time scales.     

Synthesis of a Smart Gold Nano‐vehicle for Liver Specific Drug Delivery

Targeting drug formulations to specific tissues and releasing the bioactive content in response to a certain stimuli remains a significant challenge in the field of biomedical science. We have developed a nanovehicle that can be used to deliver “drugs” to “specific” tissues. For this, we have simultaneously modified the surface of the nanovehicle with “drugs” and “tissue-specific ligands”. The “tissue-specific ligands” will target the nanovehicle to the correct tissue and release the “drug” of interest in response to specific stimuli. We have synthesised a “lactose surface-modified gold nanovehicle” to target liver cells and release the model fluorescent drug (coumarin derivative) in response to the differential glutathione concentration (between blood plasma and liver cells). Lactose is used as the liver-specific targeting ligand given the abundance of l-galactose receptors in hepatic cells. The coumarin derivative is used as a fluorescent tag as well as a linker for the attachment of various biologically relevant molecules. The model delivery system is compatible with a host of different ligands and hence could be used to target other tissues as well in future. The synthesised nanovehicle was found to be non-toxic to cultured human cell lines even at elevated non-physiological concentrations as high as 100 μg/mL. We discover that the synthesised gold-based nanovehicle shows considerable stability at low extracellular glutathione concentrations; however coumarin is selectively released at high hepatic glutathione concentration.     

Functions and cellular signaling by ribosomal extracellular RNA (rexRNA): Facts and hypotheses on a non-typical DAMP

Upon microbial infections with the subsequent host response of innate immunity, a variety of fragmented RNA- and DNA-based “Pathogen-associated molecular patterns” (PAMPs) are recognized mainly by endosomal or cytoplasmic host cell “Pattern recognition receptors” (PRRs), particularly “Toll-like receptors” (TLRs). Concomitantly, various self-extracellular RNA species (exRNAs) are present in extracellular body fluids where they contribute to diverse physiological and homeostatic processes. In principle, such exRNAs, including the most abundant one, ribosomal exRNA (rexRNA), are designated as “Danger-associated molecular patterns” (DAMPs) and are prevented by e.g. natural modifications from uncontrolled signaling via TLRs to avoid hyper-inflammatory responses or autoimmunity. Upon cellular stress or tissue damage/necrosis, the levels and composition of released self-exRNA species, either in free form, in complex with proteins or in association with extracellular vesicles (EVs), can change considerably. Among the self-exRNAs, rexRNA is considered as a non-typical DAMP, since it may induce inflammatory responses by cell membrane receptors, both in the absence or presence of PAMPs. Yet, its mode of receptor activation to mount inflammatory responses remains obscure. RexRNA also serves as a universal damaging factor in cardiovascular and other diseases independent of PRRs. In general, RNase1 provides a profound antagonist in these pathologies and in rexRNA-mediated inflammatory cell responses. Based on the extrapolation of the here described aspects of rexRNA-biology, further activities of this molecular entity are hypothesized that may stimulate additional research in this area.