Graphs, random sums, and sojourn time distributions, with application to ion-channel modeling.

This paper considers the distribution of a sojourn time in a class of states of a stochastic process having finite discrete state space where sojourn times in any individual state are independent and identically distributed, and transitions between states follow a Markov chain. The state space and possible transitions of the process are represented by a graph. Class sojourn time distributions are derived by modifying this graph using 'composition' of states, defining a new Markov chain on the modified graph, and expressing the sojourn time in a composition state as a random sum. Appropriate compositions are chosen according to the possible "cores" of sojourns in the particular class, where a core describes the structure of a sojourn in terms of a single state or a chain in the original graph. Graph methods provide an algorithmic basis for the derivation, which can be simplified by using symmetry results. Models of ion-channel kinetics are used throughout for illustration; class sojourn time distributions are important in such models because individual states are often indistinguishable experimentally. Markov processes are the special case where sojourn times in individual states are exponentially distributed. In this case kinetic parameter estimation based on the observed class sojourn time distribution is briefly discussed; explicit estimating equations applicable to sequential models of nicotinic receptor kinetics are given.     

Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.     

高迁移率族蛋白成员HMG20a/b的研究进展

高迁移率族(HMG)蛋白是一类广泛存在的非组蛋白型染色体蛋白,能通过诱导染色质结构的变化影响DNA表达。HMG20a和HMG20b是一对高度同源的HMG家族蛋白,均含有一个结构保守的HMG-box结构域和一个coiled-coil结构域,在生物体内广泛表达。HMG20a/b在细胞核内参与组蛋白去甲基酶复合物LSD1-Co REST的形成及一系列与细胞分裂分化相关的生理进程,如神经细胞核红细胞的分化、细胞质分裂以及EMT过程。研究发现,HMG20a/b一些功能的发挥是通过LSD1-Co REST复合物来实现的;在神经分化过程中,HMG20a、HMG20b具有相互拮抗的作用;而HMG20a促进EMT过程反映它很可能是一个促癌因子。本文对HMG20a/b的结构和体内分布及生物学功能进行综述。     

Coding of visual objects in the ventral stream

How are objects represented in the brain? Two facets of this question are currently under investigation. First, are objects represented by activity in a relatively small number of neurons that are each selective for the shape or identity of a specific object (a 'sparse code'), or are they represented by a pattern of activity across a large number of less selective neurons (a 'population code')? Second, how are the neurons that code for an object distributed across the cortex: are they clustered together in patches, or are they scattered widely across the cortex? The results from neurophysiology and functional magnetic resonance imaging studies are beginning to provide preliminary answers to both questions.     

Ultrastructural and biochemical studies of the swelling of developing chick telencephalic slices

Summary An ultrastructural and biochemical study of the importance and localization of tissue swelling was performed on telencephalic slices of 1- and 30-day-old chicks incubated in an oxygenated or a non-oxygenated physiological medium. The swelling of slices is greater for 30-day-old chick material than for that from 1-day-old chicks. It also reaches higher values in the non-oxygenated than in the oxygenated medium. When the 30-day-old chick telencephalic slices are incubated in an oxygenated medium, swelling mainly affects astrocytes, and especially the astrocytic endfeet. When they are incubated in a non-oxygenated medium, the astrocytes and astrocytic endfeet are very swollen and in addition the swelling also affects the neurons and their organelles. Extracellular space is increased. When 1-day-old chick telencephalic slices are incubated in a non-oxygenated medium, the tissue structures are well preserved. Swelling predominantly affects astrocytes and astrocytic endfeet. Neurons are not affected and the extracellular space is reduced. However, when they are incubated in an oxygenated medium, tissue structures are greatly affected showing a high degree of disorganization. Extracellular space is greatly increased. This study thus indicates that the best incubation conditions are an oxygenated medium for 30-day-old chick telencephalic slices which are characterized by an aerobic metabolism, and a non-oxygenated medium for 1-day-old chick telencephalic slices which have a predominantly anaerobic metabolism.     

Allelic Negative Complementation at the Abruptex Locus of DROSOPHILA MELANOGASTER

The mutations of the Abruptex locus in Drosophila melanogaster fall into three categories. There are recessive lethal alleles and viable alleles. The latter can be divided into suppressors and nonsuppressors of Notch mutations. The recessive lethals are lethal in heterozygous combination with Notch. As a rule the recessive lethals are lethal also in heterozygous combination with the viable alleles. Heterozygous combinations of certain viable alleles are also lethal. In such heterozygotes, one heteroallele is a suppressor of Notch and the other is a nonsuppressor. Other heterozygous combinations of viable alleles are viable and have an Abruptex phenotype. The insertion of the wild allele of the Abruptex locus as an extra dose (carried by a duplication) into the chromosomal complement of the fly fully restores the viability of the otherwise lethal heterozygotes if two viable alleles are involved. The extra wild allele also restores the viability of heterozygotes in which a lethal and a suppressor allele are present. If, however, a lethal and a nonsuppressor are involved, the wild allele only partly restores the viability, and the effect of the wild allele is weakest if two lethal alleles are involved. It seems likely that of the viable alleles the suppressors of Notch are hypermorphic and the nonsuppressors are hypomorphic. The lethal alleles share properties of both types, and are possibly antimorphic mutations. It is suggested that the locus is responsible for a single function which, however, consists of two components. The hypermorphic mutations are defects of the one component and the hypomorphic mutations of the other. In heterozygotes their cumulative action leads to decreased viability. The lethal alleles are supposed to be defects of the function as a whole. The function controlled by the locus might be a regulative function.     

SOLDIER-REPRODUCTIVE INTERCASTES IN A SPECIES OF TUMULITERMES (ISOPTERA: TERMITIDAE)

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Two aberrant specimens in a collection of a species of Tumulitermes are described. These specimens are basically soldier like in appearance, but show a number of reproductive caste characters in such structures as the antennae, head capsule and mandibles, and in the presence of wing rudiments. They are evidently soldier-reproductive intercastes, which are quite uncommon in the higher termites.     

Italian palaeolithic and mesolithic burials

More than 50 skeletons have been found in Italy in Upper Palaeolithic and Mesolithic burials, most of them being of Pleistocene age. As for as Upper Palaeolithic is concerned, two distinct phases are recognized, with a gap in records between them of several millennia: 1) a first phase, in which rich burials, generally of adult or adolescent males, are found. Associated industries are of Gravettian — Early Epigravettian type. Strict rules are followed in funerary practices. Sites of this period are only a few in Italy, but most of them yelded burials; 2) a second phase, of late Würm IV age, with burials found in several sites all over Italy, associated with Final Epigravettian industries. Women as well as children are now buried in single graves, but men still outnumber women. Grave goods are scarce or lacking, except at Arene Candide, where very rich burials, customarily attributed to Mesolithic, but actually of Dryas III age, were found. Truly Mesolithic sepultures are only a few, and burial goods are scarce or lacking.     

Frequency clustering in spontaneous otoacoustic emissions from a lizard's ear

Spontaneous otoacoustic emissions (SOAEs) are indicators of an active process in the inner ear that enhances the sensitivity and frequency selectivity of hearing. They are particularly regular and robust in certain lizards, so these animals are good model organisms for studying how SOAEs are generated. We show that the published properties of SOAEs in the bobtail lizard are wholly consistent with a mathematical model in which active oscillators, with exponentially varying characteristic frequencies, are coupled together in a chain by visco-elastic elements. Physically, each oscillator corresponds to a small group of hair cells, covered by a tectorial sallet, so our theoretical analysis directly links SOAEs to the micromechanics of active hair bundles.     

THE MAINTENANCE OF GYNODIOECY AND ANDRODIOECY IN A METAPOPULATION

Males and females are at a selective disadvantage relative to hermaphrodites (cosexuals) in species with a colonizing habit, as only cosexuals are able to establish new colonies on their own. The implications of this disadvantage are assessed by means of a computer model of metapopulation dynamics, in which individual colonies are established through different rates of immigration and suffer different rates of local extinction. Results are given for simulations of an island model, a stepping-stone model, and for a partial analysis of the island model with simplifying assumptions. It is shown that: (1) unisexual frequencies in a metapopulation can be reasonably approximated by a linear function of the logarithm of the ratio of the immigration rate to the colony extinction rate; (2) metapopulation dynamics favor the maintenance of females (gynodioecy) over males (androdioecy) with cosexuals when they would otherwise be equally likely in a panmictic situation; (3) the way in which extinction and immigration rates affect unisexual frequencies at metapopulation equilibrium interacts with whether sterility is determined by a dominant or a recessive allele; and (4) unisexual frequencies are affected in a qualitatively similar way by the dynamics of a metapopulation when cosexuals are self-incompatible to when they are self-compatible, although only in the former case are high frequencies of unisexuals maintained when extinction and colonization rates approach the threshold at which the metapopulation goes extinct. These results are discussed with reference to existing data from species with nuclear male or female sterility.     

Nonlinear theory of ion-acoustic waves in an ideal plasma with degenerate electrons

A nonlinear theory is constructed that describes steady-state ion-acoustic waves in an ideal plasma in which the electron component is a degenerate Fermi gas and the ion component is a classical gas. The parameter ranges in which such a plasma can exist are determined, and dispersion relations for ion-acoustic waves are obtained that make it possible to find the linear ion-acoustic velocity. Analytic gas-dynamic models of ion sound are developed for a plasma with the ion component as a cold, an isothermal, or an adiabatic gas, and moreover, the solutions to the equations of all the models are brought to a quadrature form. Profiles of a subsonic periodic and a supersonic solitary wave are calculated, and the upper critical Mach numbers of a solitary wave are determined. For a plasma with cold ions, the critical Mach number is expressed by an explicit exact formula.     

Cytology of pyelitis glandularis cystica. A case report.

Cytologic findings that occur in association with proliferative lesions involving von Brunn's nests in the urinary tract are rare. Such lesions are probably far more common than recognized and are probably considered in the clinicoradiologic differential diagnosis when space-occupying lesions are found, particularly in the upper urinary tract. Reported here are the cytologic findings in a case of pyelitis glandularis cystica that presented as a renal pelvic lesion.     

Biological functions of amyloids: Facts and hypotheses

Amyloids are fibrous protein aggregates that arise via polymerization of proteins with their concurrent conformational rearrangement and the formation of a specific cross-β structure. Amyloids are of particular interest as a cause of a vast group of human and animal diseases called amyloidoses. Some of these diseases are caused by prions, a specific type of amyloids, and are transmissible. Apart from mammals, prion amyloids are described in lower eukaryotes, where they act as nonchromosomal genetic determinants. Although amyloids are usually associated with pathologies in humans and animals, the increasing number of findings suggests that the acquisition of an amyloid or prion form by a protein is of biological significance in some cases. The review summarizes the data on the biological significance of prion and nonprion amyloids in a wide range of species from bacteria to mammals.     

Electron microscopical studies on the thyroid of a cyclostome,Lampetra japonica,during its upstream migration

Summary Electron microscopical studies were made of the thyroid gland of an adult lamprey, Lampetra japonica, in the upstream migration period.The thyroid consists of many usual follicles containing the colloid in their lumina, and a large parafollicle without colloid. The paper concerns only the usual follicle.The follicle cells found in the usual follicle wall are classified into three types; 1. a non-ciliated taller cell, 2. a ciliated taller one, and 3. a non-ciliated cuboidal one. From their cytoplasmic fine structure, it is considered that all these cells are essentially identical and differences among them are due to their functional state.All these type cells are characterized by irregularly developed interdigitations and aggregates of tonofilaments throughout the cytoplasm, especially in the perinuclear region. Although the rough-surfaced endoplasmic reticulum and the Golgi apparatus are fairly well developed in the first and second type cells, the cisternae are not so large-vacuolated but flattened, and the cytoplasm is more compact as compared with that of the higher vertebrate. In the third type cell, the cytomembranes are poorly developed.Large dense inclusion-bodies consisting of heterogeneously dense materials, of lamellar structures, and of less dense vacuoles, which are found often in taller follicle cells, are also characteristic for the lamprey thyroid. The body which might be intimately related to the Golgi apparatus is considered to be a kind of lysosomes and it perhaps corresponds to the yellow pigment observed by light microscopy.In the apical part of the cytoplasm in taller cells, there are three kinds of granules or vesicles; numerous small vesicles considered to be derived from the Golgi apparatus, a few small dense granules which seem to originate from the Golgi region, and a few large less-dense granules.In the third type cell, the cytomembranes are not so well developed as those of the first and second type cells. The large heterogeneously dense bodies and the cytoplasmic granules are very few in number.Around the follicle of the lamprey thyroid, there are a dense basement membrane and a relatively compact connective tissue with few blood capillaries. Characteristic fat cells are found in the connective tissue.     

Implications of chirality and geometric isomerism in some psychoactive drugs and their metabolites

Many drugs contain a chiral centre, or such a centre is introduced during metabolism of the drug in man and in animals. If a single chiral centre is present, the drug will normally exist as a mixture of two enantiomers, of which one may have quite different pharmacologic and/or toxic effects than the other. Chiral drugs that are used in psychiatry, and some other pharmacologically related drugs are identified, and the implications of the presence of one or two chiral centres in these drugs are discussed. Differences in pharmacologic properties of drug and metabolite enantiomers are identified and discussed. Also reviewed are the properties of some drugs used in psychiatry that both are chiral and display geometric isomerism.     

How do potentials derived from structural databases relate to “true” potentials?

Knowledge-based potentials are used widely in protein folding and inverse folding algorithms. Two kinds of derivation methods are used. (1) The interactions in a database of known protein structures are assumed to obey a Boltzmann distribution. (2) The stability of the native folds relative to a manifold of misfolded structures is optimized. Here, a set of previously derived contact and secondary structure propensity potentials, taken as the "true" potentials, are employed to construct an artificial protein structural database from protein fragments. Then, new sets of potentials are derived to see how they are related to the true potentials. Using the Boltzmann distribution method, when the stability of the structures in the database lies within a certain range, both contact potentials and secondary structure propensities can be derived separately with remarkable accuracy. In general, the optimization method was found to be less accurate due to errors in the "excess energy" contribution. When the excess energy terms are kept as a constraint, the true potentials are recovered exactly.     

Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs

We have collected all aromatic pairs (3152) involving an N-phenyl partner in a dataset of 593 proteins of the PDB: 728 of these pairs involve a partner residue less than 6 apart in the sequence. These near-sequence Phe-X pairs correspond to specific conformations that stabilize secondary structures, mainly alpha-helices when the residues are 1, 3, and 4 apart, and beta-strands when they are 2 apart in the sequence. These conformations are not spatially random and have been examined in detail. The remaining phenylalanine pairs (2424) are between partners more than 5 apart in the sequence. Of these far-sequence pairs, 34% of occurrences are in sheets. Next in frequencies are pairs that bridge a beta-strand to a helix (24%), followed by pairs that bridge a beta-strand to a random coiled structure (15%). Helix to helix pairs only constitute 12% of these far-sequence pairs. Analysis of the pairing frequency supports the hypothesis that aromatic interactions are late events of protein folding.     

Vortical flow in the utricle and the ampulla: a computational study on the fluid dynamics of the vestibular system

We present a computational study of the fluid dynamics in healthy semicircular canals (SCCs) and the utricle. The SCCs are the primary sensors for angular velocity and are located in the vestibular part of the inner ear. The SCCs are connected to the utricle that hosts the utricular macula, a sensor for linear acceleration. The transduction of angular motion is triggered by the motion of a fluid called endolymph and by the interaction of this fluid with the sensory structures of the SCC. In our computations, we observe a vortical flow in the utricle and in the ampulla (the enlarged terminal part of the SCCs) which can lead to flow velocities in the utricle that are even higher than those in the SCCs. This is a fundamentally new result which is in contrast to the common belief that the fluid velocities in the utricle are negligible from a physiological point of view. Moreover, we show that the wall shear stresses in the utricle and the ampulla are maximized at the positions of the sensory epithelia. Possible physiological and clinical implications are discussed.