Thermococcus kodakarensis provides a versatile hyperthermophilic archaeal platform for protein expression.

Hyperthermophiles, typically defined as organisms with growth optima ≥80°C, are dominated by the Archaea. Proteins that support life at the extremes of temperatures often retain substantial biotechnological and commercial value, but the recombinant expression of individual hyperthermophilic proteins is commonly complicated in non-native mesophilic hosts due to differences in codon bias, intracellular solutes and the requirement for accessory factors that aid in folding or deposition of metal centers within archaeal proteins. The development of versatile protein expression and facilitated protein purification systems in the model, genetically tractable, hyperthermophilic marine archaeon Thermococcus kodakarensis provides an attractive platform for protein expression within the hyperthermophiles. The assortment of T. kodakarensis genetic backgrounds and compatible selection markers allow iterative genetic manipulations that facilitate protein overexpression and expedite protein purifications. Expression vectors that stably replicate both in T. kodakarensis and Escherichia coli have been validated and permit high-level ectopic gene expression from a variety of controlled and constitutive promoters. Biologically relevant protein associations can be maintained during protein purifications to identify native protein partnerships and define protein interaction networks. T. kodakarensis thus provides a versatile platform for the expression and purification of thermostable proteins.

How ecologists define drought, and why we should do better.

Drought, widely studied as an important driver of ecosystem dynamics, is predicted to increase in frequency and severity globally. To study drought, ecologists must define or at least operationalize what constitutes a drought. How this is accomplished in practice is unclear, particularly given that climatologists have long struggled to agree on definitions of drought, beyond general variants of "an abnormal deficiency of water." We conducted a literature review of ecological drought studies (564 papers) to assess how ecologists describe and study drought. We found that ecologists characterize drought in a wide variety of ways (reduced precipitation, low soil moisture, reduced streamflow, etc.), but relatively few publications (~32%) explicitly define what are, and are not, drought conditions. More troubling, a surprising number of papers (~30%) simply equated "dry conditions" with "drought" and provided little characterization of the drought conditions studied. For a subset of these, we calculated Standardized Precipitation Evapotranspiration Index values for the reported drought periods. We found that while almost 90% of the studies were conducted under conditions quantifiable as slightly to extremely drier than average, ~50% were within the range of normal climatic variability. We conclude that the current state of the ecological drought literature hinders synthesis and our ability to draw broad ecological inferences because drought is often declared but is not explicitly defined or well characterized. We suggest that future drought publications provide at least one of the following: (a) the climatic context of the drought period based on long-term records; (b) standardized climatic index values; (c) published metrics from drought-monitoring organizations; (d) a quantitative definition of what the authors consider to be drought conditions for their system. With more detailed and consistent quantification of drought conditions, comparisons among studies can be more rigorous, increasing our understanding of the ecological effects of drought.

Determinants of histone H4 N-terminal domain function during nucleosomal array oligomerization: roles of amino acid sequence, domain length, and charge density.

Mg(2+)-dependent oligomerization of nucleosomal arrays is correlated with higher order folding transitions that stabilize chromosome structure beyond the 30-nm diameter fiber. In the present studies, we have employed a novel mutagenesis-based approach to identify the macromolecular determinants that control H4 N-terminal domain (NTD) function during oligomerization. Core histones were engineered in which 1) the H2A, H2B, and H3 NTDs were swapped onto the H4 histone fold; 2) the length of the H4 NTD and the H2A NTD on the H4 histone fold, were increased; 3) the charge density of the NTDs on the H4 histone fold was increased or decreased; and 4) the H4 NTD was placed on the H2B histone fold. Model nucleosomal arrays were assembled from wild type and mutant core histone octamers, and Mg(2+)-dependent oligomerization was characterized. The results demonstrated that the H2B and H3 NTDs could replace the H4 NTD, as could the H2A NTD if it was duplicated to the length of the native H4 NTD. Arrays oligomerized at lower salt concentrations as the length of the NTD on the H4 histone fold was increased. Mutations that decreased the NTD charge density required more Mg(2+) to oligomerize, whereas mutants that increased the charge density required less salt. Finally, the H4 NTD functioned differently when attached to the H2B histone fold than the H4 histone fold. These studies have revealed new insights into the biochemical basis for H4 NTD effects on genome architecture as well as the protein chemistry that underlies the function of the intrinsically disordered H4 NTD.