The size of the nucleosome

The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle is dictated by the fulfillment of two criteria: One is optimizing the volume fraction of the DNA double helix; this requirement for close-packing has its root in optimizing atomic and molecular interactions. The other criterion being that of having a zero strain-twist coupling; being a zero-twist structure is a necessity when allowing for transient tensile stresses during the reorganization of DNA, e.g., during the reposition, or sliding, of a nucleosome along the DNA double helix. The mathematical model we apply is based on a tubular description of double helices assuming hard walls. When the base-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix.Comment: 11 pages, 5 figures; v2: minor modification

Detection of HC11N in the Cold Dust Cloud TMC-1

Two consecutive rotational transitions of the long cyanopolyyne HC11N, J=39-38, and J=38-37, have been detected in the cold dust cloud TMC-1 at the frequencies expected from recent laboratory measurements by Travers et al. (1996), and at about the expected intensities. The astronomical lines have a mean radial velocity of 5.8(1) km/s, in good agreement with the shorter cyanopolyynes HC7N and HC9N observed in this very sharp-lined source [5.82(5) and 5.83(5) km/s, respectively]. The column density of HC11N is calculated to be 2.8x10^(11) cm^(-2). The abundance of the cyanopolyynes decreases smoothly with length to HC11N, the decrement from one to the next being about 6 for the longer carbon chains.Comment: plain tex 10 pages plus 3 ps fig file

Base sequence dependent sliding of proteins on DNA

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.Comment: 12 pages, 3 figure

Disordered, stretched, and semiflexible biopolymers in two dimensions

We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system". Moreover, under a strong stretching force and for a long biopolymer, the sequence-disorder is immaterial for elasticity. Finally, the effect of sequence-disorder may depend upon the quantity considered

Eccentric loading of triceps surae modulates stretch shortening cycle behaviour - a possible therapeutic mechanism

Context: Eccentric exercises are increasingly being used to treat lower limb musculoskeletal conditions such as Achilles tendinopathy. Despite widespread clinical application and documented efficacy, mechanisms underpinning clinical benefit remain unclear. Positive adaptations in motor performance are one potential mechanism. Objective: To investigate how an eccentric loading intervention influences measures of stretch-shortening cycle (SSC) behaviour during a hopping task. Design: Within subjects repeated measures observational study. Setting: University motion analysis laboratory. Participants: Healthy adults. Interventions: A single intervention of 5 sets of 10 eccentric plantarflexion contractions at 6 RM using a commercial seated calf raise machine. Main outcome measures: Lower limb stiffness, sagittal plane ankle kinematics, and temporal muscle activity of the agonist (soleus) and antagonist (tibialis anterior) muscles, measured during sub-maximal hopping on a custom-built sledge-jump system. Results: Eccentric loading altered ankle kinematics during sub-maximal hopping; peak ankle angle shifted to a less dorsiflexed position by 2.9° and ankle angle pre-contact shifted by 4.4° (p\u3c0.001). Lower limb stiffness increased from 5.9 to 6.8 Nm-1 (p\u3c0.001), whilst surface EMG measures of soleus occurred 14 to 44% earlier (p\u3c0.001) following the loading intervention. Conclusions: These findings suggest that eccentric loading alters SSC behaviour in a manner reflective of improved motor performance. Decreased ankle excursion, increased lower limb stiffness and alterations in motor control may represent a positive adaptive response to eccentric loading. These findings support the theory that mechanisms underpinning eccentric loading for tendinopathy may in part be due to improved ‘buffering’ of the tendon by the neuromuscular system

Checklist and new records of Christmas Island fishes: the influence of isolation, biogeography and habitat availability on species abundance and community composition

Christmas Island (Indian Ocean) is an oceanic high island that is situated 300 km southwest of Java, Indonesia. From 2010 to 2014, the fish community of Christmas Island was surveyed using underwater visual surveys for shallow water (0–60 m) fishes, and line fishing (bottom fishing and trolling) for deepwater (60–300 m) and pelagic fishes. Forty-seven new records (from 22 families) were identified, thereby increasing the total number of fishes described from Christmas Island to 681 (from 91 families). Notable new records include the first records for the families Alopiidae, Anomalopidae, Muraenesocidae, Tetrarogidae and Trichonotidae, and the first reports of Pacific Ocean species Plectranthias yamakawai, and Polylepion russelli in the Indian Ocean. The ten most species-rich families accounted for 58% of the community and included: Labridae (13%), Pomacentridae (8%), Epinephelidae (6%), Acanthuridae (5%), Chaetodontidae (5%), Muraenidae (5%), Gobiidae (5%), Blenniidae (4%), Apogonidae (4%) and Scorpaenidae (3%). The majority (89%) of species inhabit shallow coral reefs, with deep reefs (60–300 m) and pelagic waters only accounting for 7% and 2% of fish community. Approximately 76% of thefishes are widespread Indo-Pacific species, 12% are Pacific Ocean species, 5% are circumtropical, 4% are Indian Ocean species and approximately 1% are endemic. Abundance surveys revealed that endemic species, and species at the edge of their geographic range, do not conform to terrestrial-based predictions of low abundance. The structure and composition of the Christmas Island fish community is influenced by three main factors. Firstly, the isolation of the island means that fishes with poor dispersal abilities (e.g., syngnathids) are underrepresented. Secondly, thebiogeographic position of the island results in a unique mixing of Indian and Pacific Ocean species. Thirdly, the lack of lagoonal habitats means that fishes that use these habitats (e.g., ophichthids, lethrinids, epinephelids) are underrepresented or have low abundance

Time walkers and spatial dynamics of ageing information

The distribution of information is essential for living system's ability to coordinate and adapt. Random walkers are often used to model this distribution process and, in doing so, one effectively assumes that information maintains its relevance over time. But the value of information in social and biological systems often decay and must continuously be updated. To capture the spatial dynamics of ageing information, we introduce time walkers. A time walker moves like a random walker, but interacts with traces left by other walkers, some representing older information, some newer. The traces forms a navigable information landscape. We quantify the dynamical properties of time walkers moving on a two-dimensional lattice and the quality of the information landscape generated by their movements. We visualise the self-similar landscape as a river network, and show that searching in this landscape is superior to random searching and scales as the length of loop-erased random walks

Ionization-induced asymmetric self-phase modulation and universal modulational instability in gas-filled hollow-core photonic crystal fibers

We study theoretically the propagation of relatively long pulses with ionizing intensities in a hollow-core photonic crystal fiber filled with a Raman-inactive gas. Due to photoionization, previously unknown types of asymmetric self-phase modulation and `universal' modulational instabilities existing in both normal and anomalous dispersion regions appear. We also show that it is possible to spontaneously generate a plasma-induced continuum of blueshifting solitons, opening up new possibilities for pushing supercontinuum generation towards shorter and shorter wavelengths.Comment: 5 pages, 4 figure

Eccentric fatigue modulates stretch-shortening cycle effectiveness - a possible role in lower limb overuse injuries

The role of fatigue in injury development is an important consideration for clinicians. In particular, the role of eccentric fatigue in stretch shortening cycle (SSC) activities may be linked to lower limb overuse conditions. The purpose of this study was to explore the influence of ankle plantarflexor eccentric fatigue on SSC effectiveness during a hopping task in healthy volunteers. 11 healthy volunteers (23.2 ± 6.7 years) performed a sub-maximal hopping task on a custom- built sledge system. 3D motion capture and surface EMG were utilised to measure lower limb stiffness, temporal kinematic measures and muscle timing measures at baseline and immediately following an eccentric fatigue protocol. A linear mixed model was used to test whether measures differed between conditions. Compared to baseline, eccentric fatigue induced increased stiffness during the hopping task (+ 15.3 %; P \u3c 0.001). Furthermore, ankle stretch amplitude decreased (– 9.1 %; P \u3c 0.001), whilst all other ankle kinematic measures remained unchanged. These changes were accompanied by a temporal shift in onset of activity in soleus and tibialis anterior muscles (– 4.6 to – 8.5 %; p \u3c 0.001). These findings indicate that eccentric fatigue alters SSC effectiveness in healthy volunteers. These findings may be applied to inform pathogenetic models of overuse injury development