Migration in Dictyostelium polycephalum

By comparing two species of cellular slime molds that have stalkless migration stages it is possible to gain interesting insights into how the cells move. In contrast to the familiar behavior of Dictyostelium discoideum, Dictyostelium polycephalum slugs can travel greater distances through soil and even can migrate through agar. In addition to the interest in the differences, these differences shed light on the mechanism of slug movement. Unlike D. discoideum, D. polycephalum does not have prestalk and prespore zones and severed sections of any part of these slugs move at a rate proportional to their length. This leads to the hypothesis that longer slugs move faster because the amoebae aligned along the inside of the slime sheath each contribute a forward push and the more extended the amoebae line is the faster the slug moves.     

Morphological Aspects of Ciliary Motility

In Elliptio complanatus lateral cilia, two distinct patterns of filament termination can be discerned. In one case, all nine filaments are present and all are single; in the second, at least one filament is missing but doublets are still present. These probably represent different configurations within one cilium in different stroke positions; to get from one to the other, some peripheral filaments must move with respect to others. The data are consistent with the hypothesis that the filaments themselves do not change length, but rather slide past one another to accommodate increasing curvature. The bent regions of the cilium are in the form of circular arcs. In a few cases, apparent displacement of filaments at the tip (Δl) can be shown to be accounted for if we assume that all differences are generated within these arcs. The displacement per degree of bend is 35 A. Regions of bent arc are initially confined to the base of the cilium but move up the shaft as straight regions appear below them. From the relationship between arc length and radius of curvature, a shaft length that is the unit that initially bends and slides may be defined. Quantal displacements of the length of one 14S dynein may perhaps occur at sites between filaments at opposite sides of such a unit as sliding occurs.     

Understanding co-loading of doxorubicin and camptothecin on graphene and folic acid-conjugated graphene for targeting drug delivery: classical MD simulation and DFT calculation

Abstract

The surface modification ability is one of the remarkable characters of graphene (G) nanosheet. Based on this strategy, G surface is modified with folic acid (FA) to improve the targeting delivery of chemotherapy agents. The dual delivery strategy for the transport of doxorubicin (DOX) and camptothecin (CPT) by using G and folic acid functionalized G nanocarriers is examined. The density functional theory (DFT) and molecular dynamics (MD) simulation are employed to gain a deep insight into the nature of the drug and the carrier interactions. The obtained results indicate that the drug molecules spontaneously move toward the carriers and form stable complexes. In the graphene-based systems, the drug molecules form strong π-π interactions with the carrier surface. It is found that the FA functionalization of G (FA-G) not only improves targeting effect but also reinforces drug-carrier interaction. Furthermore, the MD and DFT results show that interaction of DOX molecules with G and FA-G is stronger than CPT. We believe that the results obtained from this study can be helpful to improve the drug effectiveness in cancer treatment.

Communicated by Ramaswamy H. Sarma     

Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization

The availability of bacterial genome sequences raises an important new problem - how can one move from completely sequenced microorganisms as a reference to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An efficient way to approach this task is the comparison of genomes by subtractive hybridization. Recently we developed a sensitive and reproducible subtraction procedure for comparison of bacterial genomes, based on the method of suppression subtractive hybridization (SSH). In this work we demonstrate the applicability of subtractive hybridization to the comparison of the related but markedly divergent bacterial species Escherichia coli and Salmonella typhimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences were directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and absent from the other. Additional differences in most cases represent sequences that have diverged considerably in the course of evolution. Such an approach to comparative bacterial genomics can be applied both to studies of interspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.     

Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases

HIV undergoes rapid genetic variation; this variation is caused primarily by the enormous number of viruses produced daily in an infected individual. Because of this variation, HIV presents a moving target for drug and vaccine development. The variation within individuals has led to the generation of diverse HIV-1 subtypes, which further complicates the development of effective drugs and vaccines. In general, it is more difficult to hit a moving target than a stationary target. Two broad strategies for hitting a moving target (in this case, HIV replication) are to understand the movement and to aim at the portions that move the least. In the case of anti-HIV drug development, the first option can be addressed by understanding the mechanism(s) of drug resistance and developing drugs that effectively inhibit mutant viruses. The second can be addressed by designing drugs that interact with portions of the viral machinery that are evolutionarily conserved, such as enzyme active sites.     

Universal and unique features of kinesin motors: insights from a comparison of fungal and animal conventional kinesins.

Kinesins are microtubule motors that use the energy derived from the hydrolysis of ATP to move unidirectionally along microtubules. The founding member of this still growing superfamily is conventional kinesin, a dimeric motor that moves processively towards the plus end of microtubules. Within the family of conventional kinesins, two groups can be distinguished to date, one derived from animal species, and one originating from filamentous fungi. So far no conventional kinesin has been reported from plant cells. Fungal and animal conventional kinesins differ in several respects, both in terms of their primary sequence and their physiological properties. Thus all fungal conventional kinesins move at velocities that are 4-5 times higher than those of animal conventional kinesins, and all of them appear to lack associated light chains. Both groups of motors are characterized by a number of group-specific sequence features which are considered here with respect to their functional importance. Animal and fungal conventional kinesins also share a number of sequence characteristics which point to common principles of motor function. The overall domain organization is remarkably similar. A C-terminal sequence motif common to all kinesins, which constitutes the only region of high homology outside the motor domain, suggests common principles of cargo association in both groups of motors. Consideration of the differences of, and similarities between, fungal and animal kinesins offers novel possibilities for experimentation (e. g., by constructing chimeras) that can be expected to contribute to our understanding of motor function.     

A stomach road or "Magenstrasse" for gastric emptying

Gastric muscle contractions grind and mix solid/liquid meal within the stomach, and move it into the bowels at a controlled rate. Contractions are of two types: slow volume-reducing contractions of the proximal stomach (the fundus), and peristaltic contraction waves in the distal stomach (the antrum). Fundic squeeze maintains gastro-duodenal pressure difference to drive gastric emptying. Emptying is generally assumed to proceed from the antrum to the fundus, so that ingested drugs can take hours to enter the small intestines and activate. Antral contraction waves (ACW), in contrast, generate fluid motions that break down and mix gastric content. Using a computer model of the human stomach, we discover a new function of these contraction waves apart from grinding and mixing. In coordination with fundic contraction, antral contraction waves move liquid content from the fundus along a very narrow path to the duodenum through the center of the antrum. Using physiological data, we show that this gastric emptying "Magenstrasse" (stomach road) can funnel liquid gastric content from the farthest reaches of the fundus directly to the intestines within 10 min. Consequently, whereas drugs (tablets, capsules, liquid) released off the Magenstrasse may require hours to enter the duodenum, at low concentration, when released on the Magenstrasse the drug can enter the duodenum and activate within 10 min-at high concentration. This discovery might explain observed high variability in drug initiation time, and may have important implications to both drug delivery and digestion, as well as to other wall-driven emptying of elastic containers.     

Locomotion in elongate fishes: A contact sport

Despite the physical differences between water and air, a number of fish lineages are known to make terrestrial excursions on land. Many of these fishes exhibit an elongate body plan. Elongation of the body can occur in several ways, the most common of which is increasing the number of vertebrae in one or both regions of the axial skeleton – precaudal and/or caudal. Elongate species are often found in three-dimensionally complex habitats. It has been hypothesized that elongate fishes use this structure to their locomotor advantage. In this study, we consider how elongation and differences in vertebral regionalization correspond with the use of wooden pegs, which are provided as analogs to vertically oriented substrate, structures that protrude above the ground. We compare aquatic and terrestrial locomotor behaviors of Polypterus senegalus, Erpetoichthys calabaricus, and Gymnallabes typus as they move through a peg array. When considering axial elongation we find that the highly elongate species, E. calabaricus and G. typus, contact more pegs but on average move slower in both environments than P. senegalus. When considering axial regionalization, we find that the precaudally elongate species, P. senegalus and E. calabaricus, differ in the patterns of peg contact between the two environments whereas the caudally elongate species, G. typus, exhibits similar peg contact between the two environments. Our study highlights the importance of incorporating body shape and vertebral regionalization to understand how elongate fishes move in water and on land.     

Molecular tools for companion diagnostics

The heterogeneous nature of cancer results in highly variable therapeutic responses even among patients with identical stages and grades of a malignancy. The move towards personalised medicine in cancer therapy has therefore been motivated by a need to customise therapy according to molecular features of individual tumours. Companion diagnostics serves to support early drug development, it can provide surrogate markers in clinical trials, and also guide selection of individual therapies and monitoring of responses in routine clinical care. The era of companion diagnostics can be said to have begun with the introduction of the HercepTest - a first-of-a-kind diagnostic tool developed by DakoCytomation in 1998 to select patients for therapy with the anticancer drug Herceptin (trastuzumab). Herceptin and the paired test proved that companion diagnostics can help guide patient-tailored therapies. We will discuss herein technologies to analyse companion diagnostics markers at the level of DNA, RNA or protein, focusing on a series of methods developed in our laboratory that can facilitate drug development and help stratify patients for therapy.     

The reduction of chromosome number in meiosis is determined by properties built into the chromosomes

In meiosis I, two chromatids move to each spindle pole. Then, in meiosis II, the two are distributed, one to each future gamete. This requires that meiosis I chromosomes attach to the spindle differently than meiosis II chromosomes and that they regulate chromosome cohesion differently. We investigated whether the information that dictates the division type of the chromosome comes from the whole cell, the spindle, or the chromosome itself. Also, we determined when chromosomes can switch from meiosis I behavior to meiosis II behavior. We used a micromanipulation needle to fuse grasshopper spermatocytes in meiosis I to spermatocytes in meiosis II, and to move chromosomes from one spindle to the other. Chromosomes placed on spindles of a different meiotic division always behaved as they would have on their native spindle; e.g., a meiosis I chromosome attached to a meiosis II spindle in its normal fashion and sister chromatids moved together to the same spindle pole. We also showed that meiosis I chromosomes become competent meiosis II chromosomes in anaphase of meiosis I, but not before. The patterns for attachment to the spindle and regulation of cohesion are built into the chromosome itself. These results suggest that regulation of chromosome cohesion may be linked to differences in the arrangement of kinetochores in the two meiotic divisions.     

Art pieces that 'move' in our minds--an explanation of illusory motion based on depth reversal

Certain art forms, such as Patrick Hughes's 'reverspectives', Dick Termes's 'Termespheres', intaglios, and hollow masks, appear to move vividly as viewers move in front of them, even though they are stationary. This illusory motion is accompanied by a perceived reversal of depth, where physical convex and concave surfaces are falsely seen as concave and convex, respectively. A geometric explanation is presented that considers this illusory motion as a result of the perceived depth reversal. The main argument is that the visual system constructs a three-dimensional representation of the surfaces, and that this representation is one of the sources that contribute to the illusory motion, together with vestibular signals of self-motion and signals of eye movements. This explanation is extended to stereograms that are also known to appear to move as viewers move in front of them. A quantitative model can be developed around this geometric explanation to examine the extent to which the visual system tolerates large distortions in size and shape and still maintains the illusion.     

Species diversity and structure of phytophagous beetle assemblages along a latitudinal gradient: predicting the potential impacts of climate change

Abstract.  1. Assemblages of phytophagous beetles on Acacia were examined along a 1150 km latitudinal gradient in eastern Australia to investigate the potential effects of climate change on insect communities. The latitudinal gradient was used as a surrogate for differences in temperature. Several possible confounding variables were held constant by selecting comparable sites and emphasising a single host-plant species.
2. Total species richness increased towards the tropics, but there were no significant differences among latitudes for average species density, species richness, Fisher's α , or average Chao-1 index.
3. Beetles sampled along the gradient were classified into four climate change response groups, depending on their latitudinal range and apparent host specificity: cosmopolitan species, generalist feeders , climate generalists , and specialists . These four groups might respond differently to shifting climate zones. Cosmopolitan species (22% of community, found at more than one latitude and on more than one host plant) may be resilient to climate change. Generalist feeders (16%, found only at one latitude but found on more than one Acacia species) may well feed on several species but will have to move with their climatic envelope. Climate generalists (6%, found only on Acacia falcata but found at more than one latitude) may be constrained by the host species' ability to either cope with the changing climate or move with it. Finally, specialists (55%, found only on A. falcata and at only one latitude) may be forced to move poleward concurrently with their host species, or go extinct.
4. The analyses indicate that community structure may be fairly resilient to temperature change. The displacement or local extinction of species, especially the species that are found at only one latitude and on only one host plant, however, may lead to significant changes in community composition.     

Excipient exchange in the comparison of preparations of the same biologic made by different manufacturing processes: An exploratory study with recombinant human growth hormone (rhGH)

Demonstrations of bio-similarity between subsequent entry (follow-on) biologics and innovator’s formulated drug products may depend upon methods that either remove excipients completely or allow the exchange of excipients to give equivalent formulations. Excipient exchange through dialysis is perhaps the simplest of such methods but its use has been hotly debated. This debate, in the absence of published data, has relied largely on theoretical considerations. This study presents data that indicate that excipient exchange can allow comparisons of different formulations of the same therapeutic protein. The use of excipient exchange to and from one concentration of mannitol to another or to a mixture of glycine and mannitol was reproducibly demonstrated for recombinant human growth hormone (rhGH). We show that marketed rhGH products from several different manufacturers exhibit differences in conformational stability when compared directly. These differences, however, are shown to be the result of differences in formulation rather than in the drug substance itself and were removed through excipient exchange. The data presented, therefore, also indicate that failure to assure a common excipient background can lead to erroneous conclusions about the similarities and differences in the physico-chemical properties of two preparations of the same therapeutic protein made by different manufacturing processes.     

Osmium-Based Pyrimidine Contrast Tags for Enhanced Nanopore-Based DNA Base Discrimination

Nanopores are a promising platform in next generation DNA sequencing. In this platform, an individual DNA strand is threaded into nanopore using an electric field, and enzyme-based ratcheting is used to move the strand through the detector. During this process the residual ion current through the pore is measured, which exhibits unique levels for different base combinations inside the pore. While this approach has shown great promise, accuracy is not optimal because the four bases are chemically comparable to one another, leading to small differences in current obstruction. Nucleobase-specific chemical tagging can be a viable approach to enhancing the contrast between different bases in the sequence. Herein we show that covalent modification of one or both of the pyrimidine bases by an osmium bipyridine complex leads to measureable differences in the blockade amplitudes of DNA molecules. We qualitatively determine the degree of osmylation of a DNA strand by passing it through a solid-state nanopore, and are thus able to gauge T and C base content. In addition, we show that osmium bipyridine reacts with dsDNA, leading to substantially different current blockade levels than exhibited for bare dsDNA. This work serves as a proof of principle for nanopore sequencing and mapping via base-specific DNA osmylation.     

Competition between microorganisms for a single limiting resource with cell quota structure and spatial variation

Microbial populations compete for nutrient resources, and the simplest mathematical models of competition neglect differences in the nutrient content of individuals. The simplest models also assume a spatially uniform habitat. Here both of these assumptions are relaxed. Nutrient content of individuals is assumed proportional to cell size, which varies for populations that reproduce by division, and the habitat is taken to be an unstirred chemostat where organisms and nutrients move by simple diffusion. In a spatially uniform habitat, the size-structured model predicts competitive exclusion, such that only the species with lowest break-even concentration persists. In the unstirred chemostat, coexistence of two competitors is possible, if one has a lower break-even concentration and the other can grow more rapidly. In all habitats, the calculation of competitive outcomes depends on a principal eigenvalue that summarizes relationships among cell growth, cell division, and cell size.     

BioGPS: Navigating biological space to predict polypharmacology,off‐targeting,and selectivity

The structural comparison of protein binding sites is increasingly important in drug design; identifying structurally similar sites can be useful for techniques such as drug repurposing, and also in a polypharmacological approach to deliberately affect multiple targets in a disease pathway, or to explain unwanted off‐target effects. Once similar sites are identified, identifying local differences can aid in the design of selectivity. Such an approach moves away from the classical “one target one drug” approach and toward a wider systems biology paradigm. Here, we report a semiautomated approach, called BioGPS, that is based on the software FLAP which combines GRID Molecular Interactions Fields (MIFs) and pharmacophoric fingerprints. BioGPS comprises the automatic preparation of protein structure data, identification of binding sites, and subsequent comparison by aligning the sites and directly comparing the MIFs. Chemometric approaches are included to reduce the complexity of the resulting data on large datasets, enabling focus on the most relevant information. Individual site similarities can be analyzed in terms of their Pharmacophoric Interaction Field (PIF) similarity, and importantly the differences in their PIFs can be extracted. Here we describe the BioGPS approach, and demonstrate its applicability to rationalize off‐target effects (ERα and SERCA), to classify protein families and explain polypharmacology (ABL1 kinase and NQO2), and to rationalize selectivity between subfamilies (MAP kinases p38α/ERK2 and PPARδ/PPARγ). The examples shown demonstrate a significant validation of the method and illustrate the effectiveness of the approach. Proteins 2015; 83:517–532. © 2015 Wiley Periodicals, Inc.     

Neuroblastoma cells recapitulate their detailed neurite morphologies after reversible microtubule disassembly

The detailed neurite morphologies of neuroblastoma cells can be specified by heritable information. This paper reports an investigation into how that information is stored. Cells with neurites are incubated with the microtubule-depolymerizing drug Nocodazole. The neurites retract and the cell bodies round up. The neurites reextend when the drug is removed. 58% of all cells recapitulate their original neurite morphology in detail. The same percentage of recapitulation is observed among a subset of the cells, about half the population, which move across the substratum during retraction and reextension. The results suggest that the storage of morphological determinants survives an interruption in their expression. In addition, reexpression of specific morphology does not require external cues or maintenance of the overall geometry of the cytoskeleton.