Energy flux controls tetraether lipid cyclization in Sulfolobus acidocaldarius

Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain the fluidity and permeability of their membranes by adjusting the number of cyclic moieties within the cores of their glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing and stability, which has been shown to help cells survive shifts in temperature and pH. However, the extent of this cyclization also varies with growth phase and electron acceptor or donor limitation. These observations indicate a relationship between energy metabolism and membrane composition. Here we show that the average degree of GDGT cyclization increases with doubling time in continuous cultures of the thermoacidophile Sulfolobus acidocaldarius (DSM 639). This is consistent with the behavior of a mesoneutrophile, Nitrosopumilus maritimus SCM1. Together, these results demonstrate that archaeal GDGT distributions can shift in response to electron donor flux and energy availability, independent of pH or temperature. Paleoenvironmental reconstructions based on GDGTs thus capture the energy available to microbes, which encompasses fluctuations in temperature and pH, as well as electron donor and acceptor availability. The ability of Archaea to adjust membrane composition and packing may be an important strategy that enables survival during episodes of energy stress.     

Untargeted Lipidomics Highlight the Depletion of Deoxyceramides during Therapy‐Induced Senescence

Therapy‐induced senescence is a state of cell cycle arrest that occurs as a response to various chemotherapeutic reagents, especially ones that cause DNA damage. Senescent cells display resistance to cell death and can impair the efficacy of chemotherapeutic strategies. Since lipids can exhibit pro‐survival activity, it is envisioned in this article that probing the lipidome could provide insights into novel lipids that are involved in senescence. Therefore, a tissue culture model system is established and the cellular lipidomes of senescent and proliferating cells are comparatively analyzed. Out of thousands of features detected, 17 species are identified that show significant changes in senescent cells. The majority of these species (11 out of 17) are atypical sphingolipids, 1‐deoxyceramides/dihydroceramides, which are produced as a result of the utilization of alanine, instead of serine during sphingolipid biosynthesis. These lipids are depleted in senescent cells. Elevating the levels of deoxyceramides by supplementing the growth medium with metabolic precursors or by directly adding deoxyceramide result in decreased senescence, suggesting that these species might play a key role in this process.     

Near-Infrared 808 nm Light Boosts Complex IV-Dependent Respiration and Rescues a Parkinson-Related pink1 Model

Mitochondrial electron transport chain (ETC) defects are observed in Parkinson’s disease (PD) patients and in PD fly- and mouse-models; however it remains to be tested if acute improvement of ETC function alleviates PD-relevant defects. We tested the hypothesis that 808 nm infrared light that effectively penetrates tissues rescues pink1 mutants. We show that irradiating isolated fly or mouse mitochondria with 808 nm light that is absorbed by ETC-Complex IV acutely improves Complex IV-dependent oxygen consumption and ATP production, a feature that is wavelength-specific. Irradiating Drosophila pink1 mutants using a single dose of 808 nm light results in a rescue of major systemic and mitochondrial defects. Time-course experiments indicate mitochondrial membrane potential defects are rescued prior to mitochondrial morphological defects, also in dopaminergic neurons, suggesting mitochondrial functional defects precede mitochondrial swelling. Thus, our data indicate that improvement of mitochondrial function using infrared light stimulation is a viable strategy to alleviate pink1-related defects.     

The 5' guanosine tracts of human telomerase RNA are recognized by the G-quadruplex binding domain of the RNA helicase DHX36 and function to increase RNA accumulation

Telomerase promotes telomere maintenance by copying a template within its integral RNA subunit to elongate chromosome ends with new telomeric repeats. Motifs have been defined within the telomerase RNA that contribute to mature RNA accumulation, holoenzyme catalytic activity, or enzyme recruitment to telomeres. Here, we describe a motif of human telomerase RNA (hTR), not previously characterized in a cellular context, comprised of several guanosine tracts near the RNA 5' end. These guanosine tracts together are recognized by the DEXH box RNA helicase DHX36. The helicase domain of DHX36 does not mediate hTR binding; instead, hTR interacts with the N-terminal accessory domain of DHX36 known to bind specifically to the parallel-strand G-quadruplex substrates resolved by the helicase domain. The steady-state level of DHX36-hTR interaction is low, but hTR guanosine tract substitutions substantially reduce mature hTR accumulation and thereby reduce telomere maintenance. These findings suggest that G-quadruplex formation in the hTR precursor improves the escape of immature RNP from degradation, but subsequently the G-quadruplex may be resolved in favor of a longer terminal stem. We conclude that G-quadruplex formation within hTR can stimulate telomerase-mediated telomere maintenance.     

Evaluation of surveillance methods for monitoring house fly abundance and activity on large commercial dairy operations

Relative house fly, Musca domestica L., activity at three large dairies in central California was monitored during the peak fly activity period from June to August 2005 by using spot cards, fly tapes, bait traps, and Alsynite traps. Counts for all monitoring methods were significantly related at two of three dairies; with spot card counts significantly related to fly tape counts recorded the same week, and both spot card counts and fly tape counts significantly related to bait trap counts 1-2 wk later. Mean fly counts differed significantly between dairies, but a significant interaction between dairies sampled and monitoring methods used demonstrates that between-dairy comparisons are unwise. Estimate precision was determined by the coefficient of variability (CV) (or SE/mean). Using a CV = 0.15 as a desired level of estimate precision and assuming an integrate pest management (IPM) action threshold near the peak house fly activity measured by each monitoring method, house fly monitoring at a large dairy would require 12 spot cards placed in midafternoon shaded fly resting sites near cattle or seven bait traps placed in open areas near cattle. Software (FlySpotter; http://ucanr.org/ sites/FlySpotter/download/) using computer vision technology was developed to count fly spots on a scanned image of a spot card to dramatically reduce time invested in monitoring house flies. Counts provided by the FlySpotter software were highly correlated to visual counts. The use of spot cards for monitoring house flies is recommended for dairy IPM programs.     

Otolith allometry informs age and growth of long-lived Quillback Carpiodes cyprinus

Environmental Biology of Fishes - The carpsuckers, which include Quillback Carpiodes cyprinus, river carpsucker Carpiodes carpio, and highfin carpsucker Carpiodes velifer, are ictiobine catostomids...     

An updated classification of Orchidaceae

Since the last classification of Orchidaceae in 2003, there has been major progress in the determination of relationships, and we present here a revised classification including a list of all 736 currently recognized genera. A number of generic changes have occurred in Orchideae (Orchidoideae), but the majority of changes have occurred in Epidendroideae. In the latter, almost all of the problematic placements recognized in the previous classification 11 years ago have now been resolved. In Epidendroideae, we have recognized three new tribes (relative to the last classification): Thaieae (monogeneric) for Thaia, which was previously considered to be the only taxon incertae sedis; Xerorchideae (monogeneric) for Xerorchis; and Wullschlaegelieae for achlorophyllous Wullschlaegelia, which had tentatively been placed in Calypsoeae. Another genus, Devogelia, takes the place of Thaia as incertae sedis in Epidendroideae. Gastrodieae are clearly placed among the tribes in the neottioid grade, with Neottieae sister to the remainder of Epidendroideae. Arethuseae are sister to the rest of the higher Epidendroideae, which is unsurprising given their mostly soft pollinia. Tribal relationships within Epidendroideae have been much clarified by analyses of multiple plastid DNA regions and the low‐copy nuclear gene Xdh. Four major clades within the remainder of Epidendroideae are recognized: Vandeae/Podochileae/Collabieae, Cymbidieae, Malaxideae and Epidendreae, the last now including Calypsoinae (previously recognized as a tribe on its own) and Agrostophyllinae s.s. Agrostophyllinae and Collabiinae were unplaced subtribes in the 2003 classification. The former are now split between two subtribes, Agrostophyllinae s.s. and Adrorhizinae, the first now included in Epidendreae and the second in Vandeae. Collabiinae, also probably related to Vandeae, are now elevated to a tribe along with Podochileae. Malaxis and relatives are placed in Malaxidinae and included with Dendrobiinae in Malaxideae. The increased resolution and content of larger clades, recognized here as tribes, do not support the ‘phylads’ in Epidendroideae proposed 22 years ago by Dressler. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 151–174.