Evidence for enhanced convection of North Pacific Intermediate Water to the low-latitude Pacific under glacial conditions

We provide high-resolution foraminiferal stable carbon isotope (δ13C) records from the subarctic Pacific and Eastern Equatorial Pacific (EEP) to investigate circulation dynamics between the extra-tropical and tropical North Pacific during the past 60 kyr. We measured the δ13C composition of the epibenthic foraminiferal species Cibicides lobatulus from a shallow sediment core recovered from the western Bering Sea (SO201-2-101KL; 58°52.52’N, 170°41.45’E; 630 m water depth) to reconstruct past ventilation changes close to the source region of Glacial North Pacific Intermediate Water (GNPIW). Information regarding glacial changes in the δ13C of sub-thermocline water masses in the EEP is derived from the deep-dwelling planktonic foraminifera Globorotaloides hexagonus at ODP Site 1240 (00°01.31’N, 82°27.76’W; 2921 m water depth). Apparent similarities in the long-term evolution of δ13C between GNPIW, intermediate waters in the eastern tropical North Pacific and sub-thermocline water masses in the EEP suggest the expansion of relatively 13C-depleted, nutrient-enriched, and northern-sourced intermediate waters to the equatorial Pacific under glacial conditions. Further, it appears that additional influence of GNPIW to the tropical Pacific is consistent with changes in nutrient distribution and biological productivity in surface-waters of the glacial EEP. Our findings highlight potential links between North Pacific mid-depth circulation changes, nutrient cycling, and biological productivity in the equatorial Pacific under glacial boundary conditions

A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants

<p>Abstract</p> <p>Background</p> <p>The numerous diverse metabolic pathways by which plant compounds can be produced make it difficult to predict how colour pigmentation is lost for different tissues and plants. This study employs mathematical and <it>in silico </it>methods to identify correlated gene targets for the loss of colour pigmentation in plants from a whole cell perspective based on the full metabolic network of <it>Arabidopsis</it>. This involves extracting a self-contained flavonoid subnetwork from the AraCyc database and calculating feasible metabolic routes or elementary modes (EMs) for it. Those EMs leading to anthocyanin compounds are taken to constitute the anthocyanin biosynthetic pathway (ABP) and their interplay with the rest of the EMs is used to study the minimal cut sets (MCSs), which are different combinations of reactions to block for eliminating colour pigmentation. By relating the reactions to their corresponding genes, the MCSs are used to explore the phenotypic roles of the ABP genes, their relevance to the ABP and the impact their eliminations would have on other processes in the cell.</p> <p>Results</p> <p>Simulation and prediction results of the effect of different MCSs for eliminating colour pigmentation correspond with existing experimental observations. Two examples are: i) two MCSs which require the simultaneous suppression of genes DFR and ANS to eliminate colour pigmentation, correspond to observational results of the same genes being co-regulated for eliminating floral pigmentation in <it>Aquilegia </it>and; ii) the impact of another MCS requiring CHS suppression, corresponds to findings where the suppression of the early gene CHS eliminated nearly all flavonoids but did not affect the production of volatile benzenoids responsible for floral scent.</p> <p>Conclusions</p> <p>From the various MCSs identified for eliminating colour pigmentation, several correlate to existing experimental observations, indicating that different MCSs are suitable for different plants, different cells, and different conditions and could also be related to regulatory genes. Being able to correlate the predictions with experimental results gives credence to the use of these mathematical and <it>in silico </it>analyses methods in the design of experiments. The methods could be used to prioritize target enzymes for different objectives to achieve desired outcomes, especially for less understood pathways.</p

Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya

Early identification of causal genetic variants underlying antimalarial drug resistance could provide robust epidemiological tools for timely public health interventions. Using a novel natural genetics strategy for mapping novel candidate genes we analyzed &gt;75,000 high quality single nucleotide polymorphisms selected from high-resolution whole-genome sequencing data in 27 isolates of Plasmodium falciparum. We identified genetic variants associated with susceptibility to dihydroartemisinin that implicate one region on chromosome 13, a candidate gene on chromosome 1 (PFA0220w, a UBP1 ortholog) and others (PFB0560w, PFB0630c, PFF0445w) with putative roles in protein homeostasis and stress response. There was a strong signal for positive selection on PFA0220w, but not the other candidate loci. Our results demonstrate the power of full-genome sequencing-based association studies for uncovering candidate genes that determine parasite sensitivity to artemisinins. Our study provides a unique reference for the interpretation of results from resistant infections