Incorporation of a high potential quinone reveals that electron transfer in Photosystem I becomes highly asymmetric at low temperature

Photosystem I (PS I) has two nearly identical branches of electron-transfer co-factors. Based on point mutation studies, there is general agreement that both branches are active at ambient temperature but that the majority of electron-transfer events occur in the A-branch. At low temperature, reversible electron transfer between P(700) and A(1A) occurs in the A-branch. However, it has been postulated that irreversible electron transfer from P(700) through A(1B) to the terminal iron-sulfur clusters F(A) and F(B) occurs via the B-branch. Thus, to study the directionality of electron transfer at low temperature, electron transfer to the iron-sulfur clusters must be blocked. Because the geometries of the donor-acceptor radical pairs formed by electron transfer in the A- and B-branch differ, they have different spin-polarized EPR spectra and echo-modulation decay curves. Hence, time-resolved, multiple-frequency EPR spectroscopy, both in the direct-detection and pulse mode, can be used to probe the use of the two branches if electron transfer to the iron-sulfur clusters is blocked. Here, we use the PS I variant from the menB deletion mutant strain of Synechocyctis sp. PCC 6803, which is unable to synthesize phylloquinone, to incorporate 2,3-dichloro-1,4-naphthoquinone (Cl(2)NQ) into the A(1A) and A(1B) binding sites. The reduction midpoint potential of Cl(2)NQ is approximately 400 mV more positive than that of phylloquinone and is unable to transfer electrons to the iron-sulfur clusters. In contrast to previous studies, in which the iron-sulfur clusters were chemically reduced and/or point mutations were used to prevent electron transfer past the quinones, we find no evidence for radical-pair formation in the B-branch. The implications of this result for the directionality of electron transfer in PS I are discussed.     

Phylogeographic analysis of invasive Asian earthworms (Amynthas) in the northeast United States

Phylogeographic studies are useful in reconstructing the history of species invasions, and in some instances can elucidate cryptic diversity of invading taxa. This can help in predicting or managing the spread of invasive species. Among terrestrial invasive species in North America, earthworms can have profound ecological effects. We are familiar with the centuries‐old invasions of European earthworms (Lumbricidae) and their impacts on nutrient cycling in soils. More recent invasions by Asian earthworms of the family Megascolecidae are less fully understood. We used data for two mitochondrial gene fragments, cytochrome oxidase I (COI) and 16S rRNA, to examine the relationships among populations of Asian earthworms in the megascolecid genus Amynthas in the northeast United States. Recent reports have indicated that one species in particular, Amynthas agrestis, is having detrimental effects in mixed forest ecosystems, and we were interested in understanding the invasion history for this species. We were surprised to discover three divergent mitochondrial lineages of Amynthas occurring sympatrically in upstate New York. Given the gap between intra‐ and inter‐lineage sequence divergences, we propose that these three lineages represent cryptic species of Amynthas, one of which is A. agrestis. For each of the three lineages of Amynthas, we observed shared haplotypes across broad geographic distances. This may reflect common origins for populations in each lineage, either by direct routes from native ranges or through post‐introduction spread by natural dispersal or human‐mediated transport within North America. Management efforts focused on horticultural imports from Asia, commercial nurseries within the USA, and on prohibition of bait disposal may help to reduce the further invasion success of Amynthas.     

Using Microwave and Macroscopic Samples of Dielectric Solids to Study the Photonic Properties of Disordered Photonic Bandgap Materials

Recently, disordered photonic materials have been suggested as an alternative to periodic crystals for the formation of a complete photonic bandgap (PBG). In this article we will describe the methods for constructing and characterizing macroscopic disordered photonic structures using microwaves. The microwave regime offers the most convenient experimental sample size to build and test PBG media. Easily manipulated dielectric lattice components extend flexibility in building various 2D structures on top of pre-printed plastic templates. Once built, the structures could be quickly modified with point and line defects to make freeform waveguides and filters. Testing is done using a widely available Vector Network Analyzer and pairs of microwave horn antennas. Due to the scale invariance property of electromagnetic fields, the results we obtained in the microwave region can be directly applied to infrared and optical regions. Our approach is simple but delivers exciting new insight into the nature of light and disordered matter interaction.Our representative results include the first experimental demonstration of the existence of a complete and isotropic PBG in a two-dimensional (2D) hyperuniform disordered dielectric structure. Additionally we demonstrate experimentally the ability of this novel photonic structure to guide electromagnetic waves (EM) through freeform waveguides of arbitrary shape.     

PATJ regulates tight junction formation and polarity in mammalian epithelial cells

Recent studies have revealed an important role for tight junction protein complexes in epithelial cell polarity. One of these complexes contains the apical transmembrane protein, Crumbs, and two PSD95/discs large/zonula occludens domain proteins, protein associated with Lin seven 1 (PALS1)/Stardust and PALS1-associated tight junction protein (PATJ). Although Crumbs and PALS1/Stardust are known to be important for cell polarization, recent studies have suggested that Drosophila PATJ is not essential and its function is unclear. Here, we find that PATJ is targeted to the apical region and tight junctions once cell polarization is initiated. We show using RNAi techniques that reduction in PATJ expression leads to delayed tight junction formation as well as defects in cell polarization. These effects are reversed by reintroduction of PATJ into these RNAi cells. This study provides new functional information on PATJ as a polarity protein and increases our understanding of the Crumbs-PALS1-PATJ complex function in epithelial polarity.     

Complete genome sequence of Desulfomicrobium baculatum type strain (X)

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO(2). Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10)

Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in a genomically under-characterized region of the tree of life, and because of its origin from a multiply extreme environment; the Atlantis Deep brines of the Red Sea, where it had to struggle with high temperatures, high salinity, and a high concentrations of heavy metals. This is the fourth completed genome sequence to be published of a type strain of the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

A selenocysteine tRNA and SECIS element in Plasmodium falciparum

The molecular machinery for incorporating selenocysteine into proteins is present in both prokaryotes and eukaryotes. Although selenocysteine insertion has been reported in animals, plants, and protozoans, known eukaryotic selenocysteine tRNA sequences and selenocysteine insertion sequences are limited to animals and plants. Here we present clear indications of the presence of selenocysteine-tRNA and a selenocysteine insertion sequence in Plasmodium falciparum. To our knowledge, this is the first report of an identification of protozoan selenocysteine insertion machinery at the sequence level.     

When can refuges mediate the genetic effects of fire regimes? A simulation study of the effects of topography and weather on neutral and adaptive genetic diversity in fire‐prone landscapes

Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection‐driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which microrefuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically complex landscapes, with fire refuges and fire‐prone “hotspots” apparent. Interannual weather variability reduced the effect of topography on fire patterns, with refuges less apparent under high weather variability. Neutral genetic diversity was correlated with long‐term fire frequency under spatially heterogeneous fire regimes, being higher in fire refuges than fire‐prone areas, except under high dispersal or low fire severity (low mortality). This generated different spatial genetic structures in fire‐prone and fire‐refuge components of the landscape, despite similar dispersal. In contrast, genetic diversity was only associated with time since the most recent fire in flat landscapes without predictable refuges and hotspots. Genetic effects of selection driven by fire‐related conditions depended on selection pressure, migration distance and spatial heterogeneity in fire regimes. Allele frequencies at a locus conferring higher fitness under successional environmental conditions followed a pattern of “temporal adaptation” to contemporary conditions under strong selection pressure and high migration. However, selected allele frequencies were correlated with spatial variation in long‐term mean fire frequency (relating to environmental predictability) under weak dispersal, low selection pressure and strong spatial heterogeneity in fire regimes.     

Impacts of fever on locust life-history traits: costs or benefits?

Fever, like other mechanisms for defence against pathogens, may have positive and negative consequences for host fitness. In ectotherms, fever can be attained through modified behavioural thermoregulation. Here we examine potential costs of behavioural fever by holding adult, gregarious desert locusts at elevated temperatures simulating a range of fever intensities. We found no effect of fever temperatures on primary fitness correlates of survival and fecundity. However, flight capacity and mate competition were reduced, although there was no relation between time spent at fever temperatures and magnitude of the response. While these effects could indicate a direct cost of fever, they are also consistent with a shift towards the solitaria phase state that, in a field context, could be considered an adaptive life-history response to limit the impact of disease. These conflicting interpretations highlight the importance of considering complex defence mechanisms and trade-offs in an appropriate ecological context.     

Sustainable use of tropical forests by reduced-impact logging in Deramakot Forest Reserve,Sabah, Malaysia

In pursuance of economic growth and development, logging has exhausted the natural timber resource in the tropical rainforest of Sabah, Malaysia. Realizing the forest depletion, the Sabah Forestry Department, with technical support from the German Agency for Technical Cooperation, begun developing a management system with the intent of managing all commercial forest reserves in a way that mimics natural processes for sustainable production of low volume, high quality, and high priced timber products in 1989. As dictated by a forest management plan based on forest zoning, about 51,000 ha of the entire area is set aside for log production and 4,000 ha for conservation in Deramakot Forest Reserve, Sabah, Malaysia. This Forest Management Plan has served as the blueprint for operational work and biodiversity conservation in Deramakot to the present. A strict protection area is set aside for biodiversity conservation within the reserve. A reduced-impact logging system is being employed for harvesting with minimal impacts on the physical environment. Deramakot Forest Reserve was certified as “well managed” by an international certification body, the Forest Stewardship Council, in 1997 and is the first natural forest reserve in Southeast Asia managed in accordance with sustainable forestry principles. In addition to providing a "green premium," certification provides easier market access, evidence of legality, multi-stakeholder participation, conservation of biodiversity and best forest management practices, particularly reduced-impact logging techniques. Deramakot Forest Reserve is the flagship of the Sabah Forestry Department and serves as a symbol of what can be achieved with political support and institutional commitment.