The Importance of Small Fire Refugia in the Central Sierra Nevada, California, USA

Fire refugia – the unburned areas within fire perimeters – are important to the survival of many taxa through fire events and the revegetation of post-fire landscapes. Previous work has shown that species use and benefit from small-scale fire refugia (1 m2 to 1000 m2), but our understanding of where and how fire refugia form is largely limited to the scale of remotely sensed data (i.e., 900 m2 Landsat pixels). To examine the causes and consequences of small fire refugia, we field-mapped all unburned patches ≥1 m2 within a contiguous 25.6 ha forest plot that burned at generally low-to-moderate severity in the 2013 Yosemite Rim Fire, California, USA. Within the Yosemite Forest Dynamics Plot (YFDP), there were 685 unburned patches ≥1 m2, covering a total unburned area of 12,597 m2 (4.9%). Small refugia occurred in all fire severity classifications. Random forest models showed that the proportion of unburned area of 100 m2 grid cells corresponded to pre-fire density and basal area of trees, distance to the nearest stream, and immediate fire mortality, but the relationships were complex and model accuracy was variable. From a pre-fire population of 34,061 total trees ≥1 cm diameter at breast height (1.37 m; DBH) within the plot (1,330 trees ha-1), trees of all five of the most common species and those DBH \u3c30 cm had higher immediate survival rates if their boles were wholly or partially within an unburned patch (P ≤0.001). Trees 1 cm ≤ DBH \u3c10 that survived were located closer to the center of the unburned patch than the edge (mean 1.1 m versus 0.6 m; ANOVA; P ≤0.001). Four-year survival rates for trees 1 cm ≤ DBH \u3c10 cm were 58.8% within small refugia and 2.7% in burned areas (P ≤0.001). Species richness and the Shannon Diversity Index (SDI) were associated with unburned quadrats in NMDS ordinations 3 years post-fire. Burn heterogeneity in mixed-conifer forests likely exists at all scales and small refugia contribute to diversity of forest species and structures. Thus, managers may wish to consider scales from 1-m2 to the landscape when designing fuel reduction prescriptions. The partial predictability of refugia location suggests that further work may lead to predictive models of refugial presence that have considerable potential to preserve ecological function or human habitation in fire-frequent forests

Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation

Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories

Volatile Characterisation Instrumentation for ISRU applications

Key to the success of any future mission(s) aimed at prospecting and extracting lunar volatiles is the availability of miniaturised instruments to identify and characterise the volatile inventory on and below the lunar surface. We will discuss two instruments, which are in development under the EU funded Lunar Volatiles Mobile Instrumentation (LUVMI) for this purpose and primarily aim at rover platforms: 1) The LUVMI Volatiles Analyser (VA), a TRL5 ion trap mass spectrometer based upon the Ptolemy flight-proven instrument. This is a low mass, compact and mechanically simple device capable of rapid detection of masses in the range of 10 to 200 m/z, enabling the rapid detection of volatiles, including water that may be released during regolith heating or during ISRU processing. 2) The LUVMI MMS, a TRL3 Miniature Magnetic Sector mass spectrometer with improved sensitivity over the ion trap mass spectrometer. The MMS will also address the limitations of on trap mass spectrometer by allowing direct measurement of H and 2H, allowing D/H ratio measurements to be done simultaneously with measurement of H2O during regolith heating or during ISRU processing

Shrub Communities, Spatial Patterns, and Shrub-Mediated Tree Mortality following Reintroduced Fire in Yosemite National Park, California, USA

Shrubs contribute to the forest fuel load; their distribution is important to tree mortality and regeneration, and vertebrate occupancy. We used a method new to fire ecology—extensive continuous mapping of trees and shrub patches within a single large (25.6 ha) study site—to identify changes in shrub area, biomass, and spatial pattern due to fire reintroduction by a backfire following a century of fire exclusion in lower montane forests of the Sierra Nevada, California, USA. We examined whether trees in close proximity to shrubs prior to fire experienced higher mortality rates than trees in areas without shrubs. We calculated shrub biomass using demography subplots and existing allometric equations, and we developed new equations for beaked hazel (Corylus cornuta ssp. californica [A. de Candolle] E. Murray) from full dissection of 50 stems. Fire decreased shrub patch area from 15.1 % to 0.9 %, reduced live shrub biomass from 3.49 Mg ha−1 to 0.27 Mg ha−1, and consumed 4.41 Mg ha−1 of living and dead shrubs. Distinct (non-overlapping) shrub patches decreased from 47 ha−1 to 6 ha−1. The mean distance between shrub patches increased 135 %. Distances between montane chaparral patches increased 285 %, compared to a 54 % increase in distances between riparian shrub patches and an increase of 267 % between generalist shrub patches. Fire-related tree mortality within shrub patches was marginally lower (67.6 % versus 71.8 %), showing a contrasting effect of shrubs on tree mortality between this forest ecosystem and chaparral-dominated ecosystems in which most trees are killed by fire

GLIMPSE: I. A SIRTF Legacy Project to Map the Inner Galaxy

GLIMPSE (Galactic Legacy Infrared Mid-Plane Survey Extraordinaire), a SIRTF Legacy Science Program, will be a fully sampled, confusion-limited infrared survey of the inner two-thirds of the Galactic disk with a pixel resolution of \~1.2" using the Infrared Array Camera (IRAC) at 3.6, 4.5, 5.8, and 8.0 microns. The survey will cover Galactic latitudes |b| <1 degree and longitudes |l|=10 to 65 degrees (both sides of the Galactic center). The survey area contains the outer ends of the Galactic bar, the Galactic molecular ring, and the inner spiral arms. The GLIMPSE team will process these data to produce a point source catalog, a point source data archive, and a set of mosaicked images. We summarize our observing strategy, give details of our data products, and summarize some of the principal science questions that will be addressed using GLIMPSE data. Up-to-date documentation, survey progress, and information on complementary datasets are available on the GLIMPSE web site: www.astro.wisc.edu/glimpse.Comment: Description of GLIMPSE, a SIRTF Legacy project (Aug 2003 PASP, in press). Paper with full res.color figures at http://www.astro.wisc.edu/glimpse/glimpsepubs.htm

Root and crown rot pathogens found on dry beans grown in Mozambique

Dry edible beans are a vital food source in Mozambique, East Africa—one that alleviates hunger and malnutrition and adds value to the economy. In recent years, root/crown rot (RCR) pathogens have emerged as limiting constraints in dry bean production. Not much has been characterized concerning the causal agents of RCR in Mozambique. The purpose of this study was to identify the primary pathogen(s) associated with RCR dry bean samples collected at breeder nursery sites and farmer fields in Mozambique using molecular sequencing and culture-based methods. Sequencing revealed, not surprisingly, an increased diversity of fungal/oomycete operational taxonomic units when compared to culture-based methods of diversity. Species of Fusarium, mainly F. oxysporum, were the dominant taxa detected in RCR dry beans through sequencing the ITS rDNA region and partial EF-1α gene. Collectively, 333 fungi and/or Oomycetes were isolated in culture during the 2014–2015 growing seasons and tested for pathogenicity on healthy bean seedlings. Fusarium species were identified by both morphological and molecular characters. At least 60% of the isolates inoculated on common bean were recognized as potentially pathogenic. From both isolation frequency and pathogenicity testing, F. oxysporum and related species play an important role in the bean RCR complex. We found similar results from dry beans grown in the two main bean-growing regions of Mozambique. These findings will allow breeders to screen for resistance to F. oxysporum in greenhouse grown bean plants as well as within field grown bean cultivars

Species Diversity Associated with Foundation Species in Temperate and Tropical Forests

Foundation species define and structure ecological communities but are difficult to identify before they are declining. Yet, their defining role in ecosystems suggests they should be a high priority for protection and management while they are still common and abundant. We used comparative analyses of six large forest dynamics plots spanning a temperate-to-tropical gradient in the Western Hemisphere to identify statistical “fingerprints” of potential foundation species based on their size-frequency and abundance-diameter distributions, and their spatial association with five measures of diversity of associated woody plant species. Potential foundation species are outliers from the common “reverse-J” size-frequency distribution, and have negative effects on alpha diversity and positive effects on beta diversity at most spatial lags and directions. Potential foundation species also are more likely in temperate forests, but foundational species groups may occur in tropical forests. As foundation species (or species groups) decline, associated landscape-scale (beta) diversity is likely to decline along with them. Preservation of this component of biodiversity may be the most important consequence of protecting foundation species while they are still common