Development of the ciliature of Tetrahymena thermophila: II. Spatial subdivision prior to cytokinesis

The cell surface of Tetrahymena thermophila is made up of an anterior region in which virtually all basal bodies of ciliary rows are ciliated, and the remainder in which ciliated and unciliated basal bodies are fairly irregularly interspersed. This pattern persists through interfission development until the stage of appearance of the equatorial ring of gaps in the ciliary rows that marks the fission zone. The ciliation pattern then becomes subdivided, in large part through the rapid ciliation of contiguous basal bodies located posterior to the fission zone. We interpret this process as a wave of ciliation of preexisting basal bodies that propagates posteriorly from the site of the fission zone. The location, extent, and timing of the ciliation process are the same in inverted as in normally oriented ciliary rows, in spite of the fact that in inverted rows the visible fission zone gap is tardily formed and the local configuration of ciliature around this gap is abnormal. The putative ciliation wave thus does not depend directly upon the local manifestations of the fission zone. However, in a cell-division-arrest mutant, cdaA1, analyzed under conditions in which formation of fission-zone gaps is permanently prevented in some ciliary rows but not in all, it is found that the ciliation pattern becomes subdivided in those ciliary rows that express fission-zone gaps and fails to become subdivided in neighboring rows that fail to manifest gaps. We interpret this combination of findings to indicate that a signal localized at the cell equator initiates a set of polarized developmental events that simultaneously create and demarcate two cellular fields within what was previously one. We further suggest that the characteristic tandem cell division pattern of ciliates is fundamentally a process of segmentation, which might involve mechanisms of gradient subdivision analogous to those taking place during segmentation of insects and other multicellular organisms.     

Investigating the Role of Gene-Gene Interactions in TB Susceptibility

Tuberculosis (TB) is the second leading cause of mortality from infectious disease worldwide. One of the factors involved in developing disease is the genetics of the host, yet the field of TB susceptibility genetics has not yielded the answers that were expected. A commonly posited explanation for the missing heritability of complex disease is gene-gene interactions, also referred to as epistasis. In this study we investigate the role of gene-gene interactions in genetic susceptibility to TB using a cohort recruited from a high TB incidence community from Cape Town, South Africa. Our discovery data set incorporates genotypes from a large a number of candidate gene studies as well as genome-wide data. After limiting our search space to pairs of putative TB susceptibility genes, as well as pairs of genes that have been curated in online databases as potential interactors, we use statistical modelling to identify pairs of interacting SNPs. We attempt to validate the top models identified in our discovery data set using an independent genome-wide TB case-control data set from The Gambia. A number of models were successfully validated, indicating that interplay between the NRG1 - NRG3, GRIK1 - GRIK3 and IL23R - ATG4C gene pairs may modify susceptibility to TB. Gene pairs involved in the NF-κB pathway were also identified in the discovery data set (SFTPD - NOD2, ISG15 - TLR8 and NLRC5 - IL12RB1), but could not be tested in the Gambian study group due to lack of overlapping data.     

Cumulative geoecological effects of 62 years of infrastructure and climate change in ice‐rich permafrost landscapes,Prudhoe Bay Oilfield,Alaska

Many areas of the Arctic are simultaneously affected by rapid climate change and rapid industrial development. These areas are likely to increase in number and size as sea ice melts and abundant Arctic natural resources become more accessible. Documenting the changes that have already occurred is essential to inform management approaches to minimize the impacts of future activities. Here, we determine the cumulative geoecological effects of 62 years (1949–2011) of infrastructure‐ and climate‐related changes in the Prudhoe Bay Oilfield, the oldest and most extensive industrial complex in the Arctic, and an area with extensive ice‐rich permafrost that is extraordinarily sensitive to climate change. We demonstrate that thermokarst has recently affected broad areas of the entire region, and that a sudden increase in the area affected began shortly after 1990 corresponding to a rapid rise in regional summer air temperatures and related permafrost temperatures. We also present a conceptual model that describes how infrastructure‐related factors, including road dust and roadside flooding are contributing to more extensive thermokarst in areas adjacent to roads and gravel pads. We mapped the historical infrastructure changes for the Alaska North Slope oilfields for 10 dates from the initial oil discovery in 1968–2011. By 2010, over 34% of the intensively mapped area was affected by oil development. In addition, between 1990 and 2001, coincident with strong atmospheric warming during the 1990s, 19% of the remaining natural landscapes (excluding areas covered by infrastructure, lakes and river floodplains) exhibited expansion of thermokarst features resulting in more abundant small ponds, greater microrelief, more active lakeshore erosion and increased landscape and habitat heterogeneity. This transition to a new geoecological regime will have impacts to wildlife habitat, local residents and industry.     

How the mirror-image pattern specified by a janus mutation of Tetrahymena thermophila comes to expression

The initial changes of cell-surface organization that occurred as the recessive janAl (janus) mutation of Tetrahymena thermophila first became expressed were elucidated in a special mating scheme in which old macronuclei homozygous for janA⁺ were synchronously replaced by new macronuclei homozygous for janAl. During this period of onset of expression, the number, regularity, and asymmetry of the ciliary rows remained unchanged. New normal (primary) oral apparatuses (OAs) continued to be formed posterior to old OAs, as in normal cells. At about four fissions after conjugation, abnormal (secondary) OAs with a partial reversal of asymmetry began to appear nearly opposite to the primary OAs, close to but not at the eventual circumferential position of janAl secondary OAs. The array of contractile vacuole pores (CVPs), normally located adjacent to two ciliary rows centered near 22% of the cell circumference to the righ of the primary oral meridian, underwent a two-step transformation: first, the number of adjacent ciliary rows bearing CVPs increased to 3, 4, and sometimes 5, then “skipped” rows appeared within this broadened CVP-arc to split the single set of CVPs into two separated subsets. The CVP transformations occurred gradually and progressively. They began prior to the expression of secondary OAs but accelerated as secondary OAs appeared. As the CVP are became broader, its midpoint shifted somewhat to the right, away from the primary oral meridian, but ended up close to halfway between the primary and secondary oral meridians. The data provide a better fit to an intercalation model than to an alternative double gradient model, suggesting that the janAl mutation alters the large-scale organization of positional values by preventing the expression of a subset of these values and thus provoking reverse-intercalation of the remainder.     

A new tool for prioritization of sequence variants from whole exome sequencing data

Background

Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them.

Results

We designed a novel method for the filtration of WES data called TAPER? (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants).

Conclusions

TAPER? implements a set of logical steps by which to prioritize candidate variants that could be associated with disease and this is aimed for implementation in biomedical laboratories with limited bioinformatics capacity. TAPER? is free, can be setup on a Windows operating system (from Windows 7 and above) and does not require any programming knowledge. In summary, we have developed a freely available tool that simplifies variant prioritization from WES data in order to facilitate discovery of disease-causing genes.

     

REGULATION OF MICROTUBULES IN TETRAHYMENA : II. Relation Between Turnover of Microtubule Proteins and Microtubule Dissociation and Assembly during Oral Replacement

Experiments are reported which were designed to test for induced synthesis of microtubule proteins associated with the rapid proliferation of basal bodies and associated intracytoplasmic microtubules which occurs during oral replacement in Tetrahymena. None was found. Instead, it is shown that these structures can be formed with de novo synthesis of as little as 6% of their microtubule proteins. It is suggested that basal body proliferation may be controlled by synthesis of morphogenetic regulator proteins.     

Development of the ciliature of Tetrahymena thermophila: I. Temporal coordination with oral development

The number of basal bodies and cilia along pole-to-pole ciliary rows was enumerated in Tetrahymena thermophila cells sampled during the rapid-exponential phase of culture growth in three different media that supported generation times ranging from 2 to 4 hr. The time required for oral development was nearly constant in the three media, and thus most of the differences in generation time were accounted for by differences in the interval prior to the onset of oral development (stage 0), which ranged from 50% of the generation time in the “poorest” medium to 20% in the “richest.” There was very little increase in number of basal bodies and of cilia along ciliary rows during stage 0, irrespective of the duration of this stage. The bulk of the increase took place during oral development, following a time course suggestive of coordination wth oral development. The same temporal pattern of increase was found in several ciliary rows, although the proportion of basal bodies that were ciliated differed among rows. There is no simple relationship between the number of basal bodies along ciliary rows and cell length, surface area, or volume. However, a large and constant proportion of the total division-to-division cell growth took place during the interval prior to the onset of oral development, suggesting that an ensemble of developmental events, including oral development and an associated activation of the remainder of the cell surface, may be triggered by attainment of a threshold cell size.     

Past, present and future directions in human genetic susceptibility to tuberculosis

The historical impression that tuberculosis was an inherited disorder has come full circle and substantial evidence now exists of the human genetic contribution to susceptibility to tuberculosis. This evidence has come from several whole-genome linkage scans, and numerous case-control association studies where the candidate genes were derived from the genome screens, animal models and hypotheses pertaining to the disease pathways. Although many of the associated genes have not been validated in all studies, the list of those that have been is growing, and includes NRAMP1, IFNG, NOS2A, MBL, VDR and some TLR . Certain of these genes have consistently been associated with tuberculosis in diverse populations. The future investigation of susceptibility to tuberculosis is almost certain to include genome-wide association studies, admixture mapping and the search for rare variants and epigenetic mechanisms. The genetic identification of more vulnerable individuals is expected to inform personalized treatment and perhaps vaccination strategies.     

The relative mass-energy-economic (RMEE) method for system boundary selection Part 1: A means to systematically and quantitatively select LCA boundaries

Life-cycle assessment (LCA) is being used more and more as a decision making tool to compare alternative systems of providing a given product or service. Each system is theoretically made up of a near infinite number of elements or unit processes to produce the product or service. In practice, time and resources to complete an LCA are limited, hence the need to draw practical boundaries on the systems being analyzed. However, how does the LCA practitioner draw fair boundaries on two or more different systems being compared? In other words, how does one decide which unit processes to include in each system? A consistent quantitative method of selecting boundaries is essential for comparative LCA studies. This paper first outlines the requirements for a system boundary selection methodology and then demonstrates the shortfalls of existing methods. The primary objective is to present the Relative Mass-Energy-Economic (RMEE) method for system boundary selection. This concise, repeatable and quantitative method for selecting system boundaries for LCA is demonstrated on a life-cycle system for ethanol fuel. Unlike many other methods of selecting system boundaries, the RMEE method is practical to use and quantitatively ensures different systems have similar system boundaries to ensure a fair comparison between options. The RMEE method has been designed specifically for LCA studies of energy systems