Why and how to use the SeqCode.

The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections.

An optimized RNA extraction method for diverse leaves of Hawaiian , a hypervariable tree species complex.

Premise: The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites.

Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms.

Premise: In dioicous mosses, sex is determined by a single U (female, ♀) or V (male, ♂) chromosome. Although a 1 : 1 sex ratio is expected following meiosis, phenotypic sex ratios based on the production of gametangia are often female-biased. The dryland moss (Pottiaceae) is notable for its low frequency of sex expression and strong phenotypic female bias.

Comparative genomic analysis of provides insights into the evolutionary history of an incomplete denitrification pathway.

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle, and has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments. However, neither the denitrification potential nor the evolutionary history of denitrification genes in the genus or phylum is well understood. Here, we performed a comparative analysis of 23 genomes and identified denitrification genes in 15  strains.

Post-eclosion temperature effects on insect cuticular hydrocarbon profiles.

The insect cuticle is the interface between internal homeostasis and the often harsh external environment. Cuticular hydrocarbons (CHCs) are key constituents of this hard cuticle and are associated with a variety of functions including stress response and communication. CHC production and deposition on the insect cuticle vary among natural populations and are affected by developmental temperature; however, little is known about CHC plasticity in response to the environment experienced following eclosion, during which time the insect cuticle undergoes several crucial changes.

Incipient ecological speciation between successional varieties of a dominant tree involves intrinsic postzygotic isolating barriers.

Whereas disruptive selection imposed by heterogeneous environments can lead to the evolution of extrinsic isolating barriers between diverging populations, the evolution of intrinsic postzygotic barriers through divergent selection is less certain. Long-lived species such as trees may be especially slow to evolve intrinsic isolating barriers. We examined postpollination reproductive isolating barriers below the species boundary, in an ephemeral hybrid zone between two successional varieties of the landscape-dominant Hawaiian tree, , on volcanically active Hawai'i Island.

Effects of temperature on transcriptome and cuticular hydrocarbon expression in ecologically differentiated populations of desert .

We assessed the effects of temperature differences on gene expression using whole-transcriptome microarrays and cuticular hydrocarbon variation in populations of cactophilic . Four populations from Baja California and mainland Mexico and Arizona were each reared on two different host cacti, reared to sexual maturity on laboratory media, and adults were exposed for 12 hr to 15, 25, or 35°C. Temperature differences influenced the expression of 3,294 genes, while population differences and host plants affected >2,400 each in adult flies.

Temporal and temperature effects on the maximum rate of rewarming from hibernation.

During hibernation animals oscillate from near ambient (T(a)) to euthermic body temperatures (T(b)). As animals arouse, the rate of rewarming (RRW) might be expected to simply increase as a function of time. We monitored the T(b) of golden-mantled ground squirrels (Spermophilus lateralis) housed at 4, 8, 12, and 16 degrees C during natural arousals.