Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Justice at Sea: Fishers’ politics and marine conservation in coastal Odisha, India

This is a paper about the politics of fishing rights in and around the Gahirmatha marine sanctuary in coastal Odisha, in eastern India. Claims to the resources of this sanctuary are politicised through the creation of a particularly damaging narrative by influential Odiya environmental actors about Bengalis, as illegal immigrants who have hurt the ecosystem through their fishing practices. Anchored within a theoretical framework of justice as recognition, the paper considers the making of a regional Odiya environmentalism that is, potentially, deeply exclusionary. It details how an argument about ‘illegal Bengalis’ depriving ‘indigenous Odiyas’ of their legitimate ‘traditional fishing rights’ derives from particular notions of indigeneity and territory. But the paper also shows that such environmentalism is tenuous, and fits uneasily with the everyday social landscape of fishing in coastal Odisha. It concludes that a wider class conflict between small fishers and the state over a sanctuary sets the context in which questions about legitimate resource rights are raised, sometimes with important effects, like when out at sea

Differential patterns of PMN-elastase and type III procollagen peptide in knee joint effusions due to acute and chronic sports injuries

In 38 traumatic knee joint effusions the proteolytic enzyme PMN-elastase (PMN-E) and the repair marker procollagen III aminoterminal peptide (PIIINP) were determined. According to the period between trauma and first aspiration of the effusion, the patients were divided into 3 groups. Group I (17 patients; period between trauma and first aspiration not longer than 72 hours) showed high concentrations of PMN-E (up to 5400 ng/ml) and low concentrations of PIIINP (<13 U/ml). Group II (11 patients; aspiration within 4 to 14 days) had mean PMN-E and PIIINP concentrations of 125.6 ng/ml and 52.1 U/ ml, respectively. In group III (10 patients, aspiration after 14 days) mean PMN-E concentration was 123.8 ng/ml and mean PIIINP concentration was 63.4 U/ml. Graphic depiction of PMN-E and PIIINP levels in each individual sample as a function of time between trauma and fluid collection revealed highly increasing PMN-E levels during the first 24 posttraumatic hours, followed by rapidly decreasing levels within 72 hours post trauma, and no change after the 4th posttraumatic day. In contrast, PIIINP increased continuously up to the first posttraumatic week and stayed at high levels up to 90 days (end of the observation period). The differential patterns of PMN-E and PIIINP concentration in knee joint effusions may be useful in estimating the period between trauma and first treatment (aspiration of effusion) and should, therefore, be helpful in detecting degenerative lesions, which seem to be characterized by low PMN-E concomitantly with high PIIINP levels

Layered material platform for surface plasmon resonance biosensing

Plasmonic biosensing has emerged as the most sensitive label-free technique to detect various molecular species in solutions and has already proved crucial in drug discovery, food safety and studies of bio-reactions. This technique relies on surface plasmon resonances in ~50 nm metallic films and the possibility to functionalize the surface of the metal in order to achieve selectivity. At the same time, most metals corrode in bio-solutions, which reduces the quality factor and darkness of plasmonic resonances and thus the sensitivity. Furthermore, functionalization itself might have a detrimental effect on the quality of the surface, also reducing sensitivity. Here we demonstrate that the use of graphene and other layered materials for passivation and functionalization broadens the range of metals which can be used for plasmonic biosensing and increases the sensitivity by 3-4 orders of magnitude, as it guarantees stability of a metal in liquid and preserves the plasmonic resonances under biofunctionalization. We use this approach to detect low molecular weight HT-2 toxins (crucial for food safety), achieving phase sensitivity~0.5 fg/mL, three orders of magnitude higher than previously reported. This proves that layered materials provide a new platform for surface plasmon resonance biosensing, paving the way for compact biosensors for point of care testing

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Heat conduction from the exceedingly hot fiber tip contributes to the endovenous laser ablation of varicose veins

Lower-extremity venous insufficiency is a common condition, associated with considerable health care costs. Endovenous laser ablation is increasingly used as therapy, but its mechanism of action is insufficiently understood. Here, direct absorption of the laser light, collapsing steam bubbles and direct fiber-wall contact have all been mentioned as contributing mechanisms. Because fiber tips have reported temperatures of 800-1,300°C during endovenous laser ablation, we sought to assess whether heat conduction from the hot tip could cause irreversible thermal injury to the venous wall. We approximated the hot fiber tip as a sphere with diameter equal to the fiber diameter, having a steady state temperature of 800°C or 1,000°C. We computed venous wall temperatures due to heat conduction from this hot sphere, varying the pullback velocity of the fiber and the diameter of the vein. Venous wall temperatures corresponding to irreversible injury resulted for a 3 mm diameter vein and pullback velocities <3 mm/s but not for 5 mm and 1 mm/s. The highest wall temperature corresponded to the position on the wall closest to the fiber tip, hence it moves longitudinally in parallel with the moving fiber tip. We concluded that heat conduction from the hot fiber tip is a contributing mechanism in endovenous laser ablation

Paneth cell - rich regions separated by a cluster of Lgr5+ cells initiate crypt fission in the intestinal stem cell niche

The crypts of the intestinal epithelium house the stem cells that ensure the continual renewal of the epithelial cells that line the intestinal tract. Crypt number increases by a process called crypt fission, the division of a single crypt into two daughter crypts. Fission drives normal tissue growth and maintenance. Correspondingly, it becomes less frequent in adulthood. Importantly, fission is reactivated to drive adenoma growth. The mechanisms governing fission are poorly understood. However, only by knowing how normal fission operates can cancer-associated changes be elucidated. We studied normal fission in tissue in three dimensions using high-resolution imaging and used intestinal organoids to identify underlying mechanisms. We discovered that both the number and relative position of Paneth cells and Lgr5+ cells are important for fission. Furthermore, the higher stiffness and increased adhesion of Paneth cells are involved in determining the site of fission. Formation of a cluster of Lgr5+ cells between at least two Paneth-cell-rich domains establishes the site for the upward invagination that initiates fission

The Repetitive Landscape of the Barley Genome

While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially, in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. The barley genome with its vast repetitive fraction is an ideal system to study chromosomal organization and evolution of TEs. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low-copy numbers. The barley genome is highly compartmentalized with different types of TEs occupying different chromosomal “niches”, such as distal, interstitial or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Some TE families also show a strong preference to insert in specific sequence motifs which may, in part, explain their distribution. The family-specific distribution patterns result in distinct TE compositions of different chromosomal compartments.Peer reviewe

Group Decisions in Biodiversity Conservation: Implications from Game Theory

. This paper shows how game theory may be used to inform group decisions in biodiversity conservation scenarios by modeling conflicts between stakeholders to identify Pareto–inefficient Nash equilibria. These are cases in which each agent pursuing individual self–interest leads to a worse outcome for all, relative to other feasible outcomes. Three case studies from biodiversity conservation contexts showing this feature are modeled to demonstrate how game–theoretical representation can inform group decision-making.–agent fish and coral conservation scenario from the Philippines. In each case there is reason to believe that traditional mechanism–design solutions that appeal to material incentives may be inadequate, and the game–theoretical analysis recommends a resumption of further deliberation between agents and the initiation of trust—and confidence—building measures. that formal mechanism–design solutions may backfire in certain cases. Such scenarios demand a return to group deliberation and the creation of reciprocal relationships of trust