Bifurcating spatially heterogeneous solutions in a chemotaxis model for biological pattern generation

We consider a simple cell-chemotaxis model for spatial pattern formation on two-dimensional domains proposed by Oster and Murray (1989,J. exp. Zool. 251, 186–202). We determine finite-amplitude, steady-state, spatially heterogeneous solutions and study the effect of domain growth on the resulting patterns. We also investigate in-depth bifurcating solutions as the chemotactic parameter varies. This numerical study shows that this deceptively simple-chemotaxis model can produce a surprisingly rich spectrum of complex spatial patterns.     

On multipole representation of current generators

In Yeh, Martinek, and de Beaumont (Bull. Math. Biophysics,20, 203–216, 1958), multipole representations of current generators in a volume conductor are used, based upon the Taylor series expansion of the potential function. In Yeh, (Bull. Math. Biophysics,23, 263–276, 1961) multipole representations of current generators in a spherical volume conductor are used, based upon the spherical harmonic expansion. This paper correlates these two systems of multipole representations so that formulations in terms of one system of the representations may be readily transformed into formulations in terms of the other system. Since the Taylor series representation is more graphic, whereas the spherical harmonic representation is more compact, such a transformation between these two systems of formulations can serve useful purposes in the application of the theory of electrocardiography. This investigation was supported by the National Heart Institute under Research Grant H-2263 (c-4).     

Comparison of surface potentials due to several singularity representations of the human heart

In electrocardiography the electrical potentials due to the heart actions can be analyzed by assuming the human body to be a conductor of homogeneous medium and the heart to be a combination of singularities within it. For a spherical conductor the “interior sphere theorem” of G. Ludford, J. Martinek, and G. Yeh (Proc. Cambridge Phil. Soc.,51, 389–93, 1955) renders potential expressions due to any singularity. For a conductor of prolate spheroidal shape the potential expressions due to a source-sink pair and a general dipole have been given by J. R. Wait (Jour. App. Physics,24, 496–97, 1953) and the authors (paper at the Conference on the Electrophysiology of the Heart, Feb. 16–17, 1956, in New York, to appear in theAnn. N. Y. Acad. Sciences) respectively. (A theorem which applies to any singularity inside a prolate or oblate spheroid will be published by the authors soon). This paper presents numerical and graphical results of potentials on the surfaces of a prolate spheroid and a sphere due to source-sink pairs and dipoles of several locations and directions and compares the various representations. A discussion on the judicious choice of heart models concludes the paper. This investigation was supported by The National Heart Institute under a research grant H-2263.     

On the stall force for growing microtubules

The assembly of microtubules generates forces that play a role in cellular motility processes such as the motion of chromosomes during mitosis. Recently, Mogilner and Oster proposed a model for the growth of microtubules that agrees quantitatively with the force-velocity relation measured for individual microtubules. In addition, the authors predicted that the stall force for any polymer consisting of N independently growing protofilaments should increase as the square root of N. We simulated this model and found that the stall force increases linearly with N, and is in fact consistent with the maximum force predicted by thermodynamic arguments. We show that this discrepancy can be explained by a more careful treatment of the “off-term” in the Mogilner-Oster model. Received: 27 September 1999 / Revised version: 12 December 1999 / Accepted: 20 December 1999     

Grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.): Old Varieties are Reflected in Works of Art

Grapevine (Vitis vinifera L.): Old Varieties Are Reflected in Works of Art. The northwest of the Iberian Peninsula is home to a number of ancient grapevine varieties now in danger of extinction, regarding which the literature contains only a few references, dating from the 19th century. In this region, baroque religious art, which is commonly ornamented with grapevine motifs, achieved great importance. This work reports the ampelographic comparison of the leaves of 19 old grapevine varieties from this region with those represented on 42 baroque altarpieces. Many of the latter were found to be ampelographically correct representations of grapevine leaves; in some cases they showed such similarity to these old varieties that their cultivation at the time when the corresponding sculptures were made can be confirmed. A larger study may therefore help determine when other varieties were cultivated in the past.     

Bill morphology and biometrics of three sibling woodpecker species from sympatric populations

ABSTRACT

Capsule Different methods of comparing bill morphology between woodpecker species show different, but not contradictory results.

Aims Differences among similar, closely related species which co-occur are still highly debated. In such a scenario, species should diverge morphologically to reduce competition. We studied this phenomenon, in three closely related woodpecker species that co-occur in eastern Slovakia: Great Spotted Woodpecker Dendrocopos major, Syrian Woodpecker Dendrocopos syriacus and White-backed Woodpecker Dendrocopos leucotos. The Great Spotted Woodpecker has the widest niche and lives sympatrically with both Syrian and White-backed Woodpeckers, while the distributions of the latter two species do not overlap because of their use of different habitats. We predicted that Great Spotted Woodpeckers should differ morphologically from both sympatric species: Syrian and White-backed Woodpeckers.

Methods Comparisons were made between species, based on dorsal and lateral views of maxilla using both geometric morphometric techniques and traditional measurements.

Results We confirmed our hypothesis, and found significant differences in bill shape between Great Spotted Woodpecker and both congeners. This is in contrast to the observed higher similarity of Great Spotted Woodpecker and Syrian Woodpecker in traditional body measurements. However, surprisingly, Syrian Woodpecker and White-backed Woodpecker do not differ significantly in bill shape.

Conclusions This work indicates that geometric morphometry appears to be a promising tool for the investigation of how interspecific competition influences the shape of the bill between co-occurring species.     

Taenidium and Associated Ichnofossils in Fluvial Deposits,Cretaceous Tuscaloosa Formation,Eastern Alabama,Southeastern U.S.A

Casts of the foraging tunnels of eastern American moles ( Scalopus aquaticus ) show impressions from the moles' mani along the lateral walls. The number of discernable impressions ranges from one to five, each showing two or three long, flat, blunt-ended claws. The size and shape of the impressions matches the claws on the paddle-like manus of S. aquaticus . The impressions are spaced at regular intervals of about two cm, and probably represent points at which the mole pushed off from the tunnel wall with alternating laterad digging strokes. Tunnel width generally exceeds height by about 15%, reflecting the laterally compressed body of the mole. These tunnel casts help show that clear, recognizable traces can be preserved in loose, humic soils, and demonstrate the type of traces left by a “lateral-thrust” digger with fully sprawled stance, such as S. aquaticus . Identification of traces on the tunnels of living moles may be applied to the fossil record, in which fossilized burrows with similar marks could be attributed to extinct burrowing moles or mole-like locomotion.     

Children with Avoidant or Disorganized Attachment Relate Differently to a Dog and to Humans During a Socially Stressful Situation

ABSTRACT

Human attachment representations are shaped in interaction with the primary caregiver and are generally transferred to further bonding/ social partners later in life. According to previous evidence, primary attachment representations acquired with humans do not seem to be transferred to companion animals. This was held as a major factor why such animals would effectively provide social support also to persons with insecure attachment. The aim of this study in 19 male children, 7–11 years of age and with insecure-avoidant or disorganized attachment, was to investigate differences in their social behavior and in physiological responses when socially supported by an unfamiliar therapy dog in a socially stressful situation. The Trier Social Stress Test for Children (TSST-C) was conducted to elicit stress in the children when in the presence of the dog and a female human investigator. We found that boys with disorganized attachment (n=11) communicated more intensely than avoidantly attached boys (n=8) with both the dog and humans present. Boys with a disorganized attachment had more physical contact with the dog during the TSST-C and talked more to the dog during and after the TSST-C than did boys with an insecure-avoidant attachment. While the prevailing wisdom holds that attachment representations acquired with the primary human caregiver would not transfer to companion animals, our data indicate otherwise. At least components of attachment-related interaction styles, such as degree of contact seeking in verbal and tactile interactions are also displayed in interaction with animal partners.     

Some state space models of HIV pathogenesis under treatment by anti-viral drugs in HIV-infected individuals

In this paper we have extended the model of HIV pathogenesis under treatment by anti-viral drugs given by Perelson et al. [A.S. Perelson et al., Science 271 (1999) 1582] to a stochastic model. By using this stochastic model as the stochastic system model, we have developed a state space model for the HIV pathogenesis under treatment by anti-viral drugs. In this state space model, the observation model is a statistical model based on the observed numbers of RNA virus copies over different times. For this model we have developed procedures for estimating and predicting the numbers of infectious free HIV and non-infectious free HIV as well as the numbers of different types of T cells through extended Kalman filter method. As an illustration, we have applied the method of this paper to the data of patient Nos. 104, 105 and 107 given by Perelson et al. [A.S. Perelson et al., Science 271 (1999) 1582] under treatment by Ritonavir. For these individuals, it is shown that within two weeks since treatment, most of the free HIV are non-infectious, indicating the usefulness of the treatment. Furthermore, the Kalman filter method revealed a much stronger effect of the treatment within the first 10 to 20 h than that predicted by the deterministic model.     

Proacrosome and acrosome of the spermatozoon in Acanthobdella peledina (Annelida: Clitellata)

Summary

Proacrosome and acrosome of the primitive leech Acanthobdella peledina are described by means of transmission electron microscopy. The proacrosome develops in early spermatids and has the shape of a pot-bellied urn with an opening towards the nucleus. Its wall is formed by a thin vesicle. In its interior, many sections of tubular structures are visible. This urn is seated atop a short, electron-dense tube. The resultant acrosome is unusually elongated, with a helically coiled acrosomal tube forming its base. Above the tube the thin acrosomal vesicle encloses a central space, within which is the acrosomal rod. The acrosomal structures clearly indicate a sister-group relationship to the Euhirudinea, but do not corroborate the notion of close kinship with the Branchiobdellidae.     

Eccentric multipole representations of current generators in a spherical volume conductor

In Yeh, Martinek and de Beaumont (Bull. Math. Biophysics,20, 203–16, 1958), a method is presented for determining successively better central multipole representations of the current generators in a homogeneous conducting sphere by measuring surface potentials at a successively increasing number of points. This paper generalizes the method such that the multipoles may be located at any chosen point in the conductor. The spherical harmonic expansion is advantageously used and the “interior sphere theorem” of Ludford, Martinek and Yeh (Proc. Cambridge Philos. Soc.,51, 389–93, 1955) makes possible disturbance potential expressions in closed forms. A method for approximate determination of the eccentricity is also presented. In the theory of electrocardiography, the eccentric multipoles can more accurately represent the heart as a current generator with fewer surface potential measurements than the central multipoles. This investigation was supported by The National Heart Institute under Research Grant H-2263(c-4).     

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes.     

Euclidean sections of protein conformation space and their implications in dimensionality reduction

Dimensionality reduction is widely used in searching for the intrinsic reaction coordinates for protein conformational changes. We find the dimensionality?reduction methods using the pairwise root?mean?square deviation (RMSD) as the local distance metric face a challenge. We use Isomap as an example to illustrate the problem. We believe that there is an implied assumption for the dimensionality‐reduction approaches that aim to preserve the geometric relations between the objects: both the original space and the reduced space have the same kind of geometry, such as Euclidean geometry vs. Euclidean geometry or spherical geometry vs. spherical geometry. When the protein free energy landscape is mapped onto a 2D plane or 3D space, the reduced space is Euclidean, thus the original space should also be Euclidean. For a protein with N atoms, its conformation space is a subset of the 3N‐dimensional Euclidean space R^3N. We formally define the protein conformation space as the quotient space of R^3N by the equivalence relation of rigid motions. Whether the quotient space is Euclidean or not depends on how it is parameterized. When the pairwise RMSD is employed as the local distance metric, implicit representations are used for the protein conformation space, leading to no direct correspondence to a Euclidean set. We have demonstrated that an explicit Euclidean‐based representation of protein conformation space and the local distance metric associated to it improve the quality of dimensionality reduction in the tetra‐peptide and β‐hairpin systems. Proteins 2014; 82:2585–2596. © 2014 Wiley Periodicals, Inc.     

Relational forces and structures produced by them

After giving a brief review of the theory of organismic sets (Bull. Math. Biophysics,29, 139–152, 1967;31, 159–198, 1969), in which the concept of relational forces, introduced earlier (Bull. Math. Biophysics,28, 283–308, 1966a) plays a fundamental role, the author discusses examples of possible different structures produced by relational forces. For biological organisms the different structures found theoretically are in general agreement with observation. For societies, which are also organismic sets as discussed in the above references, the structures can be described only in an abstract space, the nature of which is discussed. Different isomorphisms between anatomical structures, as described in ordinary Euclidean space, and the sociological structures described in an abstract space are noted, as should be expected from the theory of organismic sets.     

Geometric morphometric study of populations of the social wasp,Polistes dominulus (Christ, 1791) from Zanjan province,north‐west Iran

Abstract

We analysed morphological variation among 17 forewing characters within five populations of the paper wasp, Polistes dominulus, in Iran. The raw planar coordinate data were aligned using geometric and mathematical calculations in Kendall's shape space. After transfer of the data to a linear Euclidean space, i.e., tangent space, multi‐variate analysis of 135 images of forewings were made using their geometric morphometric characters (30 in the forewings). We observed a direct correlation between morphological characters and the geographically easiest travel distance along river valleys and mountain ranges.     

Notes on gamete production in Lanice conchilega (Annelida,Polychaeta, Terebellidae)

Summary

Male and female gametogenesis in Lanice conchilega are described and illustrated as seen by light microscopy. There is no evidence for size-selectivity in the uptake of male gametes by the hypertrophied reproductive nephromixia, since undissociated motile sperm platelets as well as spermatozoa appear to be taken up by the genital funnels, and such funnels show no sexual dimorphism. Maturation of the coelomic oocytes is marked by a change in shape and the appearance of a surface reticulum of ridges.     

撕裂蜡孔菌(Emmia lacerata)SR5抑菌特性及生防潜力评价

【背景】撕裂蜡孔菌(Emmia lacerata)是一种在世界范围内广泛分布的白腐真菌,对植物病原真菌有较好的抑制作用,可作为生防真菌进行开发和利用。【目的】对撕裂蜡孔菌SR5的抑菌能力和胞外产铁载体能力进行测定,挖掘其生防潜力。【方法】采用平板对峙法检测SR5对9种植物病原真菌的抑菌能力,并通过不同浓度的发酵原液测定真菌胞外代谢物的抑菌效果;结合铬天青S(chrome azurol S, CAS)检测法测定真菌产铁载体能力,明确SR5抑菌特性。【结果】SR5以过度生长的方式快速竞争营养和生存空间,拮抗9种植物病原真菌,抑菌率为23.7%–62.7%,对可可毛色二孢(Lasiodiplodia theobromae)的拮抗等级为Ⅳ级,而对其余8种病原真菌的拮抗等级为Ⅲ级,其中对香港丽赤壳(Calonectria hongkongensis)和间座壳(Diaporthe sp.)抑菌效果最佳;CAS检测法表明SR5能产生分泌型铁载体,产铁载体能力中等,最高铁载体活性单位(siderophore unit, SU)为44.1%。【结论】SR5以过度生长方式快速竞争营养和生存空间,而且以分泌...