Ultrastructure of the "dark" hepatocytes under physiologically normal conditions and in toxic lesion of the liver (a morphometric study)]

Quanity and structural organization of the "dark" hepatocytes are different depending on the functional state of the liver. Therefore, functional estimation of the liver state with a changed number of "dark" hepatocytes demands detection of factors determining the changes in their organization and quantity in the organ.     

The interhemispheric brain asymmetry of the rabbit in a state of "animal hypnosis"]

By the method of forced immobilization the rabbits were brought into the state of "animal hypnosis" (immobilization reflex), and their ECoG was recorded, which was further processed on the computer. It was found that during hypnosis a functional interhemispheric brain asymmetry was developed in rabbits with activity predominance in the right hemisphere. The "animal hypnosis" is a phasic process: in the ECoG of the rabbit under hypnosis a regular alternation of delta and theta activity takes place. Electrophysiological reconstructions in the rabbit brain during the change of its functional state correlate with the brain thermal reactions, revealed earlier.     

Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H

Human cytosolic NADP-IDH (IDH1) has recently been found to be involved in tumorigenesis. Notably, the tumor-derived IDH1 mutations identified so far mainly occur at Arg132, and mutation R132H is the most prevalent one. This mutation impairs the oxidative IDH activity of the enzyme, but renders a new reduction function of converting α-ketoglutarate (αKG) to 2-hydroxyglutarate. Here, we report the structures of the R132H mutant IDH1 with and without isocitrate (ICT) bound. The structural data together with mutagenesis and biochemical data reveal a previously undefined initial ICT-binding state and demonstrate that IDH activity requires a conformational change to a closed pre-transition state. Arg132 plays multiple functional roles in the catalytic reaction; in particular, the R132H mutation hinders the conformational changes from the initial ICT-binding state to the pre-transition state, leading to the impairment of the IDH activity. Our results describe for the first time that there is an intermediate conformation that corresponds to an initial ICT-binding state and that the R132H mutation can trap the enzyme in this conformation, therefore shedding light on the molecular mechanism of the "off switch" of the potentially tumor-suppressive IDH activity. Furthermore, we proved the necessity of Tyr139 for the gained αKG reduction activity and propose that Tyr139 may play a vital role by compensating the increased negative charge on the C2 atom of αKG during the transfer of a hydride anion from NADPH to αKG, which provides new insights into the mechanism of the "on switch" of the hypothetically oncogenic reduction activity of IDH1 by this mutation.     

Non-stationarity in the "resting brain's" modular architecture

Task-free functional magnetic resonance imaging (TF-fMRI) has great potential for advancing the understanding and treatment of neurologic illness. However, as with all measures of neural activity, variability is a hallmark of intrinsic connectivity networks (ICNs) identified by TF-fMRI. This variability has hampered efforts to define a robust metric of connectivity suitable as a biomarker for neurologic illness. We hypothesized that some of this variability rather than representing noise in the measurement process, is related to a fundamental feature of connectivity within ICNs, which is their non-stationary nature. To test this hypothesis, we used a large (n = 892) population-based sample of older subjects to construct a well characterized atlas of 68 functional regions, which were categorized based on independent component analysis network of origin, anatomical locations, and a functional meta-analysis. These regions were then used to construct dynamic graphical representations of brain connectivity within a sliding time window for each subject. This allowed us to demonstrate the non-stationary nature of the brain's modular organization and assign each region to a "meta-modular" group. Using this grouping, we then compared dwell time in strong sub-network configurations of the default mode network (DMN) between 28 subjects with Alzheimer's dementia and 56 cognitively normal elderly subjects matched 1:2 on age, gender, and education. We found that differences in connectivity we and others have previously observed in Alzheimer's disease can be explained by differences in dwell time in DMN sub-network configurations, rather than steady state connectivity magnitude. DMN dwell time in specific modular configurations may also underlie the TF-fMRI findings that have been described in mild cognitive impairment and cognitively normal subjects who are at risk for Alzheimer's dementia.     

Using Raman spectroscopy to monitor the solvent-exposed and "buried" forms of flavin in p-hydroxybenzoate hydroxylase

X-ray crystallographic studies of several complexes involving FAD bound to p-hydroxybenzoate hydroxylase (PHBH) have revealed that the isoalloxazine ring system of FAD is capable of adopting in two positions on the protein. In one, the "in" form, the ring is surrounded by protein groups and has little contact with solvent; in the second, "out" form, the ring is largely solvent exposed. Using Raman difference spectroscopy, it has been possible to obtain Raman spectra for the flavin ring in both conformational states for different complexes in solution. The spectra consist of a rich assortment of isoalloxazine ring modes whose normal mode origin can be assigned by using density functional theory and ab initio calculations. Further insight into the sensitivity of these modes to changes in environment is provided by the Raman spectra of lumiflavin in the solid state, in DMSO and in aqueous solution. For the protein complexes, the Raman difference spectra of flavin bound to wt PHBH and wt PHBH plus substrate, p-hydroxybenzoate, provided examples of the "in" conformation. These data are compared to those for flavin bound to wt PHBH plus 2,4-dihydroxybenzoate, where X-ray analysis show that the flavin is "out". There are several spectral regions where characteristic differences exist for flavin in the "in" or "out" conformation, these occur near 1700, 1500, 1410, 1350, 1235, and 1145 cm(-)(1). These spectral features can be used as empirical marker bands to determine the populations of "in" and "out" for any complex of PHBH and to monitor changes in those populations with perturbations to the system, e.g., by changing temperature or pH. Thus, it will now be possible to determine the conformational state of the flavin in PHBH for those complexes that have resisted X-ray crystallographic analysis. Raman difference data are also presented for the Tyr222Phe mutant. The Raman data show that the isoalloxazine ring is predominantly "out" for Tyr222Phe. However, in the presence of the substrate p-hydroxybenzoate there is clear evidence from the Raman marker bands that a mixed population of "in" and "out" exists with the majority being in the "out" state. This is consistent with the conclusions drawn from crystallographic studies on this complex (Gatti, D. L., Palfey, B. A., Lah, M. S., Entsch, B., Massey, V., Ballou, D. P., and Ludwig, M. L. (1994) Science, 266, 110-114).     

Balinese "Water Temples" and the Management of Irrigation

Bali has figured prominently in debates on the question of whether irrigation centralizes state power. New evidence shows that irrigation is actually organized by networks of "water temples" that constitute an institutional system separate from the state. Earlier attempts to identify a discrete system of irrigation management misconceived the problem. For most crops, irrigation simply provides water for the plant's roots. But in a Balinese rice terrace, water is used to construct a complex, pulsed artificial ecosystem. Water temples manipulate the states of the system, at ascending levels in regional hierarchies. The permanence of water temple networks contrasts sharply with the instability of the traditional Balinese states. Since the water temples are real, perhaps it is the Balinese "state" that is chimerical.     

The receptor-bound "empty pocket" state of the heterotrimeric G-protein alpha-subunit is conformationally dynamic

Heterotrimeric G-protein activation by a G-protein-coupled receptor (GPCR) requires the propagation of structural signals from the receptor-interacting surfaces to the guanine nucleotide-binding pocket. To probe conformational changes in the G-protein alpha-subunit (G(alpha)) associated with activated GPCR (R*) interactions and guanine nucleotide exchange, high-resolution solution NMR methods are being applied in studying signaling of the G-protein, transducin, by light-activated rhodopsin. Using these methods, we recently demonstrated that an isotope-labeled G(alpha) reconstituted heterotrimer forms functional complexes under NMR experimental conditions with light-activated, detergent-solubilized rhodopsin and a soluble mimic of R*, both of which trigger guanine nucleotide exchange [Ridge, K. D., et al. (2006) J. Biol. Chem. 281, 7635-7648]. Here, it is shown that both light-activated rhodopsin and the soluble mimic of R form trapped intermediate complexes with a GDP-released "empty pocket" state of the heterotrimer in the absence of GTP (or GTPgammaS). In contrast to guanine nucleotide-bound forms of G(alpha), the NMR spectra of the GDP-released, R-bound empty pocket state of G(alpha) display severe line broadening suggestive of a dynamic intermediate state. Interestingly, the conformation of a GDP-depleted, Mg(2+)-bound state of G(alpha) generated in a manner independent of R* does not exhibit a similar degree of line broadening but rather appears structurally similar to the GDP/Mg(2+)-bound form of the protein. Taken together, these results suggest that R*-mediated changes in the receptor-interacting regions of G(alpha), and not the absence of bound guanine nucleotide, are the predominant factors which dictate G(alpha) conformation and dynamics in this R*-bound state of the heterotrimer.     

"The avoidance" of the direct current application to the sensorimotor cortex (a computer-controlled experiment in rabbits)

In a computer controlled experiment the electric activity of rabbits right sensorimotor cortex was recorded in the area of the excitation focus produced by the direct current (2 mcA) application. The current was switched on at the 5th, 10th and 15th minutes of experiment only in cases when the mean amplitude of the delta waves exceeded the baseline. The current was switched off at the mean amplitude of the delta waves exceeding the baseline level by 50%. After training some experiments (2-4), rabbits learned to change their functional state in such way that they "avoided" the action of the direct current.     

Motor polarization dominance and "animal hypnosis"

Two kinds of dominanta were simultaneously formed under conditions of chronic experiments in rabbits. The motor polarization dominanta was formed under exposure of the right sensorimotor cortex of an animal to direct anodic current, and the state of "animal hypnosis" (the second dominanta) was induced. Animal behavior and electrophysiological characteristics were recorded. It was shown that the "animal hypnosis" induced at the optimum of the right motor polarization dominanta inhibited the motor reaction of the "dominant" extremity to testing stimuli. After the "animal hypnosis session, exposure of the right sensorimotor cortex to anodic current produced the latent excitation focus, which did not reach the level of summation. Two days later, exposure to testing stimuli developed the latent foci at first in the right cortex and then in subcortical structures. In the course of recovery of the motor polarization dominanta and its further change for the state characteristic of the "animal hypnosis", the patterns of cortical EEG coherence in the delta range typical of each kind of dominanta alternated in parallel with the time course of state changes.     

“反向免疫学”与免疫功能基因的发现

人类基因组测序的结束为生命科学领域展开了全新的一章.尽管已经得到了人类基因组的序列,但是隐藏在DNA序列中的功能基因,它们之间的相互作用以及对整个机体的意义大部分有待发掘.近些年来形成的“反向生物学”为免疫功能基因的发现、功能的研究及其应用价值提供了一套全新的技术与思路.     

Formation and development of photosynthetic units in repigmenting Rhodopseudomonas sphaeroides wild type and "Phofil" mutant strain.

The formation of the photosynthetic apparatus in the wild type Rhodopseudomonas sphaeroides and in the "Phofil" mutant was investigated by analyzing absorption and fluorescence parameters and the kinetics of fluorescence induction. Repigmentation was induced by transfer of bleached cells to semi-aerobic culture conditions. 1. In the "Phofil" mutant, functional photosynthetic units appear at pigment cellular contents which depend on the physiological state of the inoculum. The unadapted mutant can reach the functional units stage at a cellular pigment level 20 times lower than that of the wild type, although the size and composition of the units are identical in both strains. This rules out the hypothesis of photosynthetic units forming by random integration of pigments into the membrane. Moreover, the fact that units are separate at this stage (as shown by the exponential shape of fluorescence induction kinetics) suggests that the units' formation proceeds from discrete predetermined membrane sites. 2. In repigmentng wild type cells, the multistep assembly of bacteriochlorophyll complexes appears correlated to their organization in photosynthetic units as follows: (i) During a first stage, B-875 is mostly synthesized, while the efficiency of transfer increases, suggesting that the pigments are initially interpersed at comparatively large average distances from each other in the bleached membrane. (ii) After 1.5 h of repigmentation, the transfer and trapping efficiencies reach a maximum. The units (26 B-875 + 11 B-850 per center) are still separate, as shown by exponential fluorescence kinetics. (iii) The increase in the units' size then essentially proceeds through B-850 incorporation. Energy transfer between units occurs at a comparatively late stage, i.e., 5 h repigmentation.     

Cytologic characteristics of "dark" and "light" cells in the brain amygdaloid complex

This paper reports data on cytological peculiarities of neurons of two main zones of sexual dimorphism in brain amygdala (dorsomedial nucleus and anterior cortical nucleus). The main attention was paid to some characteristics of "dark" and "pale" cells found in the amygdaloid complex for the first time. It is supposed that the dark and pale cells are targets for gonadal steroids, whose cyclic changes in concentration in the blood difined their functional states. Though the ultrastructure of dark and pale cells of the amygdaloid complex is similar to that of neurosecretory cells of hypothalamus, there are necessary electron microscopic and cytochemical evidences.     

Functional properties of hemoglobin in the goldfish <Emphasis Type="Italic">Carassius auratus</Emphasis> before death

The effect of the prelethal state on functional properties of hemoglobin has been studied in the goldfish Carassius auratus. A considerable decrease in hemoglobin affinity for oxygen and the Bohr effect values and the change in the shape of the curve of oxygen equilibrium have been detected. Such state may be compared to the effect of strong short-term stress.     

"Dark" and "pale" cells of the amygdala complex in dynamics of the estrous cycle

Data on cytological peculiarities of dorsomedial nucleus neurones of the amygdala complex, one of the main zones of sexual dimorphism, in dynamics of estrous cycle are reported. We show that structural and functional characteristics of "dark" and "pale" cells may change depending on the concentrations of gonadal steroids in estrous and metaestrous stages. This specifies the previous hypothesis about mutual reorganization of these cells.     

Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases

Although some members of Ras family small GTPases, including M-Ras, share the primary structure of their effector regions with Ras, they exhibit vastly different binding properties to Ras effectors such as c-Raf-1. We have solved the crystal structure of M-Ras in the GDP-bound and guanosine 5'-(beta,gamma-imido)triphosphate (Gpp(NH)p)-bound forms. The overall structure of M-Ras resembles those of H-Ras and Rap2A, except that M-Ras-Gpp(NH)p exhibits a distinctive switch I conformation, which is caused by impaired intramolecular interactions between Thr-45 (corresponding to Thr-35 of H-Ras) of the effector region and the gamma-phosphate of Gpp(NH)p. Previous 31P NMR studies showed that H-Ras-Gpp(NH)p exists in two interconverting conformations, states 1 and 2. Whereas state 2 is a predominant form of H-Ras and corresponds to the "on" conformation found in the complex with effectors, state 1 is thought to represent the "off" conformation, whose tertiary structure remains unknown. 31P NMR analysis shows that free M-Ras-Gpp(NH)p predominantly assumes the state 1 conformation, which undergoes conformational transition to state 2 upon association with c-Raf-1. These results indicate that the solved structure of M-Ras-Gp-p(NH)p corresponds to the state 1 conformation. The predominance of state 1 in M-Ras is likely to account for its weak binding ability to the Ras effectors, suggesting the importance of the tertiary structure factor in small GTPase-effector interaction. Further, the first determination of the state 1 structure provides a molecular basis for developing novel anti-cancer drugs as compounds that hold Ras in the state 1 "off" conformation.     

Dynamics of morphofunctional organization and developmental potential of mouse embryos in the state of "two-cell block in vitro"

Vital observation in combination with electron microscopy and immunocytochemistry was used for studying structural organization and developmental potential of BALB/c mouse embryos after cleavage cessation at a two cell stage caused by the "two-cell block in vitro" phenomenon. Modification of structure and viability of embryos was followed for 2 days from the time of cleavage arrest. Several hours before cleavage arrest, changes in mitochondrian distribution were noticed in embryos, no other disturbances in structural organization of blastomeres being obvious. Embryos, whose development was arrested for 24 h, remained viable and demonstrated some morphological changes similar to those seen in normally developing embryos of the same age. Towards the end of a 48 h block period some embryos died, the surviving embryos remained morphologically intact and metabolically active. At the same time, the nuclei of the latter frequently displayed chromatin condensation near the nuclear membrane, which is similar to the pattern of chromatin reorganization in the nuclei of early apoptotic cells. Our results support a concept on the "two-cell block in vitro" phenomenon as a specific functional state of embryos, and well compare with data on a partial realization by blocked embryos of the developmental program.     

A chemical approach to the fine structure of biomolecular complexes: the amino terminal region of the 50S ribosomal "A" protein from Bacillus stearothermophilus.

An experimental approach and methodology are described for determining the reactive properties and ionization constants of individual functional groups of proteins within biomolecular complexes. The ionization constants and reactivities of the methionyl-l amino terminus and the lysyl-3 residue of the alanine rich 50S ribosomal "A" protein from Bacillus stearothermophilus have been determined by an extension of the competitive labeling technique used by H. Kaplan, K. J. Stevenson, and B. S. Hartley ((1971), Biochem. J. 124, 289-299). This approach employs (1-14C)- and (3H)acetic anhydride in a double-labeling procedure. In 0.1 M KCl-0.02 M Mg2+-0.05 M Veronal at 10 degrees the methionyl-l amino terminus has a pKa of 7.5 and is exposed on the surface of the ribosome. The lysyl-3 has a pKa of 10 and is also exposed to solvent at the surface of the 50S subunit. Based on a linear free energy relationship (Bronsted plot) obtained with a series of standard amines the methionyl amino terminus has a substantially higher reactivity than expected from its ionization constant. The lysyl epsilon-amino group has the expected reactivity. The abnormally high reactivity of the methionyl amino terminus can only be accounted for by a specific interaction with other functional groups in the ribosome. These data support the proposal that the charged state of this residue is important in the structure and function of the "A" protein at the surface of the ribosome.     

Breathing patterns peculiarities as the index of the "animal hypnosis" state in the rabbit

Breathing patterns were recorded during "animal hypnosis" in seven Chinchilla rabbits. The state of "animal hypnosis" was evoked by the hand pressure on the thorax and the waist of a rabbit. Breathing pattern was recorded by means of an elastic coal-powder element that was set round the rabbit's thorax. Distortions of the breathing patterns in the active state and in the course of hypnosis development were marked by numbers 0, 1, 2. In all rabbits, modifications of the breathing patterns depended on the features of the animal state: quiet state, tension, and "animal hypnosis".     

A Kv channel with an altered activation gate sequence displays both "fast" and "slow" activation kinetics

The Kv1-4 families of K+ channels contain a tandem proline motif (PXP) in the S6 helix that is crucial for channel gating. In human Kv1.5, replacing the first proline by an alanine resulted in a nonfunctional channel. This mutant was rescued by introducing another proline at a nearby position, changing the sequence into AVPP. This resulted in a channel that activated quickly (ms range) upon the first depolarization. However, thereafter, the channel became trapped in another gating mode that was characterized by slow activation kinetics (s range) with a shallow voltage dependence. The switch in gating mode was observed even with very short depolarization steps, but recovery to the initial "fast" mode was extremely slow. Computational modeling suggested that switching occurred during channel deactivation. To test the effect of the altered PXP sequence on the mobility of the S6 helix, we used molecular dynamics simulations of the isolated S6 domain of wild type (WT) and mutants starting from either a closed or open conformation. The WT S6 helix displayed movements around the PXP region with simulations starting from either state. However, the S6 with a AVPP sequence displayed flexibility only when started from the closed conformation and was rigid when started from the open state. These results indicate that the region around the PXP motif may serve as a "hinge" and that changing the sequence to AVPP results in channels that deactivate to a state with an alternate configuration that renders them "reluctant" to open subsequently.