Psychrophilic prokaryote structural-functional relationships, biogeography and evolution within marine sediment.

Prokaryote diversity has been found to be surprisingly high in cold marine sediments with numerous clades detected spread throughout many phyla. Marine benthic sediment clades are largely ecotypically distinct and autochthonous. Since almost all marine sediment prokaryotic taxa have yet to be cultivated, functionality is currently overwhelmingly cryptic for most benthic prokaryotic taxa except those falling into specific lineages for which there is cultivation or detailed biogeochemical data. Multivariate statistical comparisons of 16S rRNA gene sequence and denaturing gradient gel electrophoresis (DGGE) data show distinct distribution patterns of prokaryotic communities in sediment layers. By comparison geographical differences and differences related to the physical texture and organic content seem to result in generally smaller differences.     

The interdependence of fire, grass, kangaroos and Australian Aborigines: a case study from central Arnhem Land, northern Australia

Aim To describe the nexus between Aboriginal landscape burning and patterns of habitat use by kangaroos in a tropical savanna habitat mosaic, and to provide evidence to evaluate the claim that Aboriginal landscape burning is a game management tool. Location Central Arnhem Land, a stronghold of traditional Aboriginal culture, in the monsoon tropics of northern Australia. Methods The abundance of kangaroo scats was recorded throughout a landscape burnt by Aboriginal people, and used as a proxy for the intensity of habitat use by kangaroos. Scat abundance was assessed along field traverses totalling 112 km, at three time periods: (1) 1–4 weeks following mid‐dry season burning (July 2003); (2) in the late dry season (November 2003); and (3) in the following mid‐dry season (July 2004). We compared the intensity with which kangaroos used burnt vs. unburnt areas in various habitat types, with time since mid‐dry season burning. Scats were collected from areas that had been burnt to a varying extent and the abundance of carbon and nitrogen stable isotopes (δ¹³C and δ¹⁵N) and carbon to nitrogen ratios (C : N) determined. Results There was clear evidence of an interaction between burning and habitat type on the abundance of kangaroo scats. Scats were much more abundant in burnt vs. unburnt areas in the moist habitats, but the opposite effect was observed in the dry rocky habitats, with higher scat abundance in unburnt areas. This interactive effect of burning and habitat type on scat abundance was observed immediately (< 4 weeks) following fire, and was still present one year later. High concentrations of nitrogen in resprouting grasses indicate that burnt areas may provide kangaroos with greater access to nutrients. The isotopic composition of scats indicates that kangaroos feeding in extensively burnt areas were consuming more grasses, and possibly sedges, than kangaroos feeding in unburnt areas. Main conclusions The fine‐scale mosaic of burnt and unburnt areas created by mid‐dry season Aboriginal landscape burning has clear effects on the distribution of kangaroos. Kangaroos move into burnt moist habitats and away from burnt dry, rocky habitats. Isotopic analysis of scats suggests that the mechanism driving this effect is the increased abundance of nitrogen rich grasses in burnt moist habitats.     

HLA Typing for the Next Generation

Allele-level resolution data at primary HLA typing is the ideal for most histocompatibility testing laboratories. Many high-throughput molecular HLA typing approaches are unable to determine the phase of observed DNA sequence polymorphisms, leading to ambiguous results. The use of higher resolution methods is often restricted due to cost and time limitations. Here we report on the feasibility of using Pacific Biosciences’ Single Molecule Real-Time (SMRT) DNA sequencing technology for high-resolution and high-throughput HLA typing. Seven DNA samples were typed for HLA-A, -B and -C. The results showed that SMRT DNA sequencing technology was able to generate sequences that spanned entire HLA Class I genes that allowed for accurate allele calling. Eight novel genomic HLA class I sequences were identified, four were novel alleles, three were confirmed as genomic sequence extensions and one corrected an existing genomic reference sequence. This method has the potential to revolutionize the field of HLA typing. The clinical impact of achieving this level of resolution HLA typing data is likely to considerable, particularly in applications such as organ and blood stem cell transplantation where matching donors and recipients for their HLA is of utmost importance.     

Comparative Analysis of the Conserved Functions of Arabidopsis DRL1 and Yeast KTI12

Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.     

Auxin Produced by the Indole-3-Pyruvic Acid Pathway Regulates Development and Gemmae Dormancy in the Liverwort Marchantia polymorpha

The plant hormone auxin (indole-3-acetic acid [IAA]) has previously been suggested to regulate diverse forms of dormancy in both seed plants and liverworts. Here, we use loss- and gain-of-function alleles for auxin synthesis- and signaling-related genes, as well as pharmacological approaches, to study how auxin regulates development and dormancy in the gametophyte generation of the liverwort Marchantia polymorpha. We found that M. polymorpha possess the smallest known toolkit for the indole-3-pyruvic acid (IPyA) pathway in any land plant and that this auxin synthesis pathway mainly is active in meristematic regions of the thallus. Previously a Trp-independent auxin synthesis pathway has been suggested to produce a majority of IAA in bryophytes. Our results indicate that the Trp-dependent IPyA pathway produces IAA that is essential for proper development of the gametophyte thallus of M. polymorpha. Furthermore, we show that dormancy of gemmae is positively regulated by auxin synthesized by the IPyA pathway in the apex of the thallus. Our results indicate that auxin synthesis, transport, and signaling, in addition to its role in growth and development, have a critical role in regulation of gemmae dormancy in M. polymorpha.     

A BLOC-1–AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers

Membrane transport carriers fuse with target membranes through engagement of cognate vSNAREs and tSNAREs on each membrane. How vSNAREs are sorted into transport carriers is incompletely understood. Here we show that VAMP7, the vSNARE for fusing endosome-derived tubular transport carriers with maturing melanosomes in melanocytes, is sorted into transport carriers in complex with the tSNARE component STX13. Sorting requires either recognition of VAMP7 by the AP-3δ subunit of AP-3 or of STX13 by the pallidin subunit of BLOC-1, but not both. Consequently, melanocytes expressing both AP-3δ and pallidin variants that cannot bind their respective SNARE proteins are hypopigmented and fail to sort BLOC-1–dependent cargo, STX13, or VAMP7 into transport carriers. However, SNARE binding does not influence BLOC-1 function in generating tubular transport carriers. These data reveal a novel mechanism of vSNARE sorting by recognition of redundant sorting determinants on a SNARE complex by an AP-3–BLOC-1 super-complex.