IMMUNOHISTOCHEMICAL LOCALIZATION OF CONTRACTILE PROTEINS IN LIMULUS STRIATED MUSCLE

Limulus paramyosin and myosin were localized in the A bands of glycerinated Limulus striated muscle by the indirect horseradish peroxidase-labeled antibody and direct and indirect fluorescent antibody techniques. Localization of each protein in the A band varied with sarcomere length. Antiparamyosin was bound at the lateral margins of the A bands in long (~ 10.0 µ) and intermediate (~ 7.0 µ) length sarcomeres, and also in a thin line in the central A bands of sarcomeres, 7.0–~6.0 µ. Antiparamyosin stained the entire A bands of short sarcomeres (<6.0). Conversely, antimyosin stained the entire A bands of long sarcomeres, showed decreased intensity of central A band staining except for a thin medial line in intermediate length sarcomeres, and was bound only in the lateral A bands of short sarcomeres. These results are consistent with a model in which paramyosin comprises the core of the thick filament and myosin forms a cortex. Differential staining observed using antiparamyosin and antimyosin at various sarcomere lengths and changes in A band lengths reflect the extent of thick-thin filament interaction and conformational change in the thick filament during sarcomeric shortening.     

Mechanism of length determination in bacteriophage lambda tails

The mechanism of length determination in bacteriophage λ tails is discussed as a model for regulation in protein assembly systems.The λ tail is a long flexible tube ending in a conical part and a single tail fiber. Its length is exactly determined in the sense that the number of major tail protein (gpV) molecules, which comprise more than 80% of the mass of the tail, is exactly the same in all tails. Assembly of gpV is regulated by the initiator complex, which contains the tail fiber and the conical part,and by the terminator protein gpU. There are two key points in the assembly of gpV with respect to length determination. (1) Assembly of gpV on the initiator pauses at the correct tail length. Binding of gpU to the tail only fixes the pause firmly. (2) When the tail length is too short, binding of gpU to tails is inhibited.Deletions and a duplication (both in frame) in gene H, which codes for one of the proteins in the initiator, result in production of phage particles with altered tail length. Moreover, the tail length is roughly proportional to the length of the mutated versions of gene H. This shows that the tail length is measured by the length of gene H protein (gpH), which seems to be approximately as long as the tail tube, if extended like a thread, according to secondary structure prediction (α-helices connected by other structures). Various pieces of evidence show that about six molecules of gpH are attached to the remaining portion of the initiator by the C-terminal part and folded into a somewhat compact form, while they are elongated as they are enclosed in the tail tube during assembly of gpV. Unlike interaction between the length-measuring genome RNA and the coat protein of tobacco mosaic virus, the major tail protein gpV does not bind specifically to the ruler protein gpH. Rather, gpH determines the tail length by inhibiting the binding of gpU to short tails and by signalling the pause when the correct tail length is attained.     

The initiation factor 3 (IF3) residues interacting with initiator tRNA elbow modulate the fidelity of translation initiation and growth fitness in Escherichia coli

Initiation factor 3 (IF3) regulates the fidelity of bacterial translation initiation by debarring the use of non-canonical start codons or non-initiator tRNAs and prevents premature docking of the 50S ribosomal subunit to the 30S pre-initiation complex (PIC). The C-terminal domain (CTD) of IF3 can carry out most of the known functions of IF3 and sustain Escherichia coli growth. However, the roles of the N-terminal domain (NTD) have remained unclear. We hypothesized that the interaction between NTD and initiator tRNA^fMet (i-tRNA) is essential to coordinate the movement of the two domains during the initiation pathway to ensure fidelity of the process. Here, using atomistic molecular dynamics (MD) simulation, we show that R25A/Q33A/R66A mutations do not impact NTD structure but disrupt its interaction with i-tRNA. These NTD residues modulate the fidelity of translation initiation and are crucial for bacterial growth. Our observations also implicate the role of these interactions in the subunit dissociation activity of CTD of IF3. Overall, the study shows that the interactions between NTD of IF3 and i-tRNA are crucial for coupling the movements of NTD and CTD of IF3 during the initiation pathway and in imparting growth fitness to E. coli.     

Molecular dynamics simulations of the interaction of phospholipid bilayers with polycaprolactone

The molecular interaction between common polymer chains and the cell membrane is unknown. Molecular dynamics simulations offer an emerging tool to characterise the nature of the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. Herein we characterise with all-atomistic and coarse-grained molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a phospholipid membrane. We find that the length of the polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilise advanced sampling techniques in molecular dynamics to characterise the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. Finally, we perform coarse-grained molecular dynamics simulations of slightly larger membranes with polymers of the same length and characterise the results as compared with all-atomistic molecular dynamics simulations. These results can be used to design polymer chain lengths and chemistries to optimise their interaction with cell membranes at the molecular level.     

Genomic patterns of homozygosity in worldwide human populations

Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes—short, intermediate, and long—with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.     

Wave propagation in bone media

The composite nature of bone dictates the use of a model for bone which is transversely isotropic. We solve the associated sets of partial differential equations governing the dynamic elastic behavoor of a two-layered cylindrical-shaped bone. The solution is analyzed for long, short, and intermediate length waves. The special case of compact bone is treated for long and short wave lengths and a numerical example is worked out to determine the wave speeds (for short wave lengths) given a set of elastic constants, determined by ultrasonic methods, and the bone density, wave frequency, and radius.     

Information transfer during shell exchange in the hermit crab Clibanarius antillensis

The shell exchange behaviour of the hermit crab Clibanarius antillensis was examined for evidence that the non-initiating crab used information about the initiator's shell. Manipulation of the internal volume of the initiator's shell altered the outcome of exchanges in a manner consistent with the negotiations model of resource exchange. It is suggested that the fundamental frequency of shells is detected by crabs during rapping behaviour when the initiator raps its shell against that of the non-initiator.     

Grass silage particle size when fed with or without maize silage alters performance,reticular pH and metabolism of Holstein-Friesian dairy cows

The particle size of the forage has been proposed as a key factor to ensure a healthy rumen function and maintain dairy cow performance, but little work has been conducted on ryegrass silage (GS). To determine the effect of chop length of GS and GS:maize silage (MS) ratio on the performance, reticular pH, metabolism and eating behaviour of dairy cows, 16 multiparous Holstein-Friesian cows were used in a 4×4 Latin square design with four periods each of 28-days duration. Ryegrass was harvested and ensiled at two mean chop lengths (short and long) and included at two ratios of GS:MS (100:0 or 40:60 dry matter (DM) basis). The forages were fed in mixed rations to produce four isonitrogenous and isoenergetic diets: long chop GS, short chop GS, long chop GS and MS and short chop GS and MS. The DM intake (DMI) was 3.2 kg/day higher (P<0.001) when cows were fed the MS than the GS-based diets. The short chop length GS also resulted in a 0.9 kg/day DM higher (P<0.05) DMI compared with the long chop length. When fed the GS:MS-based diets, cows produced 2.4 kg/day more (P<0.001) milk than when fed diets containing GS only. There was an interaction (P<0.05) between chop length and forage ratio for milk yield, with a short chop length GS increasing yield in cows fed GS but not MS-based diets. An interaction for DM and organic matter digestibility was also observed (P<0.05), where a short chop length GS increased digestibility in cows when fed the GS-based diets but had little effect when fed the MS-based diet. When fed the MS-based diets, cows spent longer at reticular pH levels below pH 6.2 and pH 6.5 (P<0.01), but chop length had little effect. Cows when fed the MS-based diets had a higher (P<0.05) milk fat concentration of C18 : 2n-6 and total polyunsaturated fatty acids compared with when fed the GS only diets. In conclusion, GS chop length had little effect on reticular pH, but a longer chop length reduced DMI and milk yield but had little effect on milk fat yield. Including MS reduced reticular pH, but increased DMI and milk performance irrespective of the GS chop length.     

Free kinetosomes in Austrialian flagellates. I. Types and spatial arrangement

An electron microscope study was made of Deltotrichonympha and Koruga, two closely-related hypermastigote flagellates that live in the hindgut of the Australian termite, Mastotermes darwiniensis These symbiotic protozoans have a typical flagellated rostrum and long body flagella. Their "giant centrioles" (centriolar apparatus) are large, fibrillar, and granular bodies which do not resemble typical centrioles in structure. The unique feature of interphase cells is the presence of more than half a million free kinetosomes in the anterior cytoplasm. Two classes of free kinetosomes, differing in length and spatial arrangement, were found. 500,000–750,000 short free kinetosomes are concentrated in a dense column which extends from the centriolar apparatus in the rostrum to the anterior side of the nucleus Most of the short free kinetosomes in the column are arranged end-to-end in chains of varying lengths. Within a kinetosomal chain, all of the individual kinetosomes face in the same direction with respect to their cartwheel ends In most flagellates, the short free kinetosomes are 0 07–0.13 µ long, and are remarkably similar in length within any cell Occasionally, cells with uniformly "longer" short free kinetosomes are found. 70,000–120,000 long free kinetosomes are scattered singly throughout the cytoplasm between the column of short free kinetosomes and the cell surface These long free kinetosomes are 0 4–0 7 µ long, similar in length to the kinetosomes of the body flagella, and are oriented parallel to the anterior-posterior axis of the cell. The significance of this remarkable accumulation of free kinetosomes is discussed.     

Genetic Architecture of Natural Variation of Telomere Length in Arabidopsis thaliana

Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.     

Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast

In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (<150 bp), whereas American isolates had telomeres approximately three times as long (>400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres.     

Exogenous T3 mimics long day lengths in Siberian hamsters

Siberian hamsters (Phodopus sungorus) exhibit seasonal cycles of reproduction driven by changes in day length. Day length is encoded endogenously by the duration of nocturnal melatonin (Mel) secretion from the pineal gland. Short-duration Mel signals stimulate reproduction and long-duration signals inhibit reproduction. The mechanism by which Mel signals are decoded at the level of neural target tissues remains uncharacterized. In Siberian hamsters, exposure to short day lengths or injections of Mel in long days results in a decrease in hypothalamic expression of type 2 iodothyronine deiodinase (Dio2) mRNA. Dio2 catalyzes the conversion of the thyroid hormone thyroxine to triiodothyronine (T3). Thus exposure to short and long day lengths should decrease and increase hypothalamic T3 concentrations, respectively. We tested the hypothesis that exogenous T3 administered to short-day hamsters would mimic exposure to long day lengths with respect to gonadal stimulation. Hamsters gestated and raised in short day lengths that exhibited photoinhibition of the testes were given daily subutaneous injections of T3 or saline vehicle for 4 wk beginning at week 12 of life. The results indicate that exogenous T3 induced gonadal growth in short-day hamsters and delayed spontaneous gonadal development by an interval equal to the number of weeks during which T3 was administered. T3 injections delayed gonadal regression if given coincident with the transfer of hamsters from long to short day lengths. These results suggest that T3 mimics long day exposure in Siberian hamsters and may serve as an intermediate step between the Mel rhythm and the reproductive response.     

Length regulation and dynamics of individual telomere tracts in wild-type Arabidopsis

Although length of the telomeric DNA tract varies widely across evolution, a species-specific set point is established and maintained by unknown mechanisms. To investigate how telomere length is controlled in Arabidopsis thaliana, we analyzed bulk telomere length in 14 wild-type accessions. We found that telomere tracts in Arabidopsis are fairly uniformly distributed throughout a size range of 2 to 9 kb. Unexpectedly, telomeres in plants of the Wassilewskija ecotype displayed a bimodal size distribution, with some individuals harboring telomeres of 2 to 5 kb and others telomeres of 4 to 9 kb. F1 and F2 progeny of a cross between long and short telomere parents had intermediate telomeres, implying that telomere length in Arabidopsis is not controlled by a single genetic factor. We provide evidence that although global telomere length is strictly regulated within an ecotype-specific range, telomere tracts on individual chromosome ends do not occupy a predetermined length territory. We also demonstrate that individual telomere tracts on homologous chromosomes are coordinately regulated throughout development and that telomerase acts preferentially on the shortest telomeres. We propose that an optimal size for telomere tracts is established and maintained for each Arabidopsis ecotype.     

Individual recognition, dominance hierarchies and winner and loser effects

Winner and loser effects are defined as an increased probability of winning an aggressive interaction at time T, based on victories at time T-1, T-2, etc., and an increased probability of losing at time T, based on losses at time T-1, T-2, etc., respectively. Prior theoretical work on dominance hierarchy formation has demonstrated that when players are not capable of individual recognition, loser effects always produce a clear top-ranked (alpha) individual, but all other ranks in a group remain unclear; whereas winner effects always produce strict linear hierarchies in which the rank of each individual is clear. Paradoxically, however, when individual recognition--a phenomenon long thought to stabilize hierarchies--is possible, winner and loser effects have no impact on the probability of forming strict linear hierarchies.     

Polarized light observations on striated muscle contraction in a mite

Contraction of individual sarcomeres within the living mite Tarsonemus sp. was observed by polarized light microscopy. In unflattened animals the usual range of contraction was such that the minimum sarcomere length approximated the length of the A region, and the maximum sarcomere length was about twice the length of the A region. The central sarcomeres of the dorsal metapodosomal muscles were observed in detail. The A band length increased slightly with increasing sarcomere length since the regression of I region length on sarcomere length had an average slope of 0.91. When the A band length in a sarcomere which was shortening was compared with the length when the same sarcomere lengthened, no significant difference was seen. The A band of each sarcomere seemed to act as a not too rigid limit to further shortening; this agreed with the reversible shortening of a muscle in which the A band had been experimentally shortened. An H region was visible at long sarcomere lengths and was not visible at short sarcomere lengths, even when the muscle was actively shortening. The rate of change of H region length with sarcomere length suggested that I filament length may increase as sarcomere length increases. Despite this effect and the small increase in A length with sarcomere length, the results are considered to be consistent with a model in which shortening occurs by the relative movement of A and I filaments, with little or no change in length of either set of filaments. Sarcomere shortening was clearly associated with an increase in the retardation of the A region.     

EVOLUTION AND COEXISTENCE OF POLLINATION ECOTYPES IN AN AFRICAN GLADIOLUS (IRIDACEAE)

Pollinator‐mediated selection has been suggested as a key driver of speciation in plants. We examined the potential role of hawkmoth pollinators in driving allopatric divergence and maintaining sympatric coexistence of morphotypes in the African iris Gladiolus longicollis. Floral tube length in this species varies from 35 mm to 130 mm across its geographic range and reflects the prevailing tongue lengths of local hawkmoth assemblages. The distribution of floral tube lengths is bimodal with two relatively discrete categories—long (about 90 mm) or short (about 50 mm)—that match the bimodal distribution of hawkmoth tongue lengths in eastern South Africa. At a contact site between these two floral morphs, we found few individuals of intermediate length, suggesting limited gene flow between morphs despite their interfertility. A difference in flowering phenology appears to be the main isolating barrier between morphs at this site. Long‐ and short‐tubed morphs differed markedly in the chemical composition of their floral fragrance, a trait that could be used as a cue for morph‐specific foraging by hawkmoths. Positive directional selection on tube length was found to occur in both morphs.     

The Wzz (Cld) Protein in Escherichia coli: Amino Acid Sequence Variation Determines O-Antigen Chain Length Specificity

The O antigen is a polymer with a repeated unit. The chain length in most Escherichia coli strains has a modal value of 10 to 18 O units, but other strains have higher or lower modal values. wzz (cld/rol) mutants have a random chain length distribution, showing that the modal distribution is determined by the Wzz protein. Cloned wzz genes from E. coli strains with short (7 to 16), intermediate (10 to 18), and long (16 to 25) modal chain lengths were transferred to a model system, and their effects on O111 antigen were studied. The O111 chain length closely resembled that of the parent strains. We present data based on the construction of chimeric wzz genes and site-directed mutagenesis of the wzz gene to show that the modal value of O-antigen chain length of E. coli O1, O2, O7, and O157 strains can be changed by specific amino acid substitutions in wzz. It is concluded that the O-antigen chain length heterogeneity in E. coli strains is the result of amino acid sequence variation of the Wzz protein.     

VARIATION IN VESSEL LENGTH AND DIAMETER IN STEMS OF SIX TROPICAL AND SUBTROPICAL LIANAS

Within-species and within-stem variation in vessel diameter and total vessel length were examined using the latex paint method on six species of tropical and subtropical lianas (woody vines). Narrow vessels were almost always rather short, but wide vessels ranged from short to long. Within Pithecoctenium crucigerum, larger diameter stems tended to have longer as well as wider vessels, with a maximum vessel length and width of 6.25 m and 366 μm, respectively. Within stems of Saritaea magnifica, P. crucigerum, Hippocratea volubilis, and Vitis rotundifolia, narrow vessels had lower mean, median, and maximum vessel lengths than wide vessels. Vessels with intermediate diameters tended to have intermediate lengths. In Stigmaphyllon ellipticum and Bauhinia fassoglensis the outer system of secondary xylem tended to have longer as well as wider vessels than the inner system. Those narrow vessels (<50 μm) that did occur in the outer system were short (<0.20 m), and were similar in length and diameter to those of the inner system.     

Bursty Communication Patterns Facilitate Spreading in a Threshold-Based Epidemic Dynamics

Records of social interactions provide us with new sources of data for understanding how interaction patterns affect collective dynamics. Such human activity patterns are often bursty, i.e., they consist of short periods of intense activity followed by long periods of silence. This burstiness has been shown to affect spreading phenomena; it accelerates epidemic spreading in some cases and slows it down in other cases. We investigate a model of history-dependent contagion. In our model, repeated interactions between susceptible and infected individuals in a short period of time is needed for a susceptible individual to contract infection. We carry out numerical simulations on real temporal network data to find that bursty activity patterns facilitate epidemic spreading in our model.     

Scaling of the equilibrium sedimentation distribution in dense DNA solutions

DNA molecules, several persistence lengths long in sedimentation equilibrium at speeds high enough to maintain fairly close packing, show a dense, sharply-bounded turbid phase and an isotropic phase (as with shorter fragments) and also an intermediate, somewhat turbid region. The concentration distribution in the isotropic phase is in satisfactory agreement with a simple extension of scaled particle theory in which semiflexible chains are equivalent to straight rods of the same length. The net intermolecular interactions, as inferred from the Zimm cluster integral, are purely repulsive. As in our previous study with short fragments, the results are compatible with a hard-core electrostatic radius, decreasing with increasing salt concentration. However, for the longer fragments it is necessary to infer either a slightly greater mass per unit length or a slightly smaller electrostatic radius for closest agreement with scaled particle theory. The properties of the solution at the boundary with the turbid, presumably strongly ordered phase are consistent with those found for shorter fragments and with theoretical scaling expectation for a hard, asymmetric particle.