Establishment of Regional Herbarium Leads to More Than 200 New Flora Atlas Records for New York State

Loss of small herbaria is an unfortunate global trend, and initiation of new collections at small academic institutions is an increasingly rare occurrence. In 2006, a new herbarium was established at the State University of New York College at Plattsburgh. The PLAT herbarium has since grown to more than 7,000 specimens, many of them representative of the flora of northeastern New York (especially Clinton County). Previous to 2006, this region was without a recognized herbarium, the nearest in-state collections being more than 150 miles away. Although botanists have previously worked in the region, relatively few plant species were recorded for Clinton County by the New York Flora Atlas – a resource providing species distribution records based on specimens accessioned in herbarium collections. Given the dearth of available distribution data for Clinton County (including the eastern Adirondack Mountains and the western Lake Champlain valley), this project sought to provide records of previously unreported species by comparing NY Flora Atlas maps with current holdings. 203 species will now be added to the NY Flora Atlas for Clinton County, roughly half of those considered exotic. This exercise has amplified the importance of supporting and maintaining small regional herbaria as repositories of valuable biodiversity information. Likewise, this project also highlights the enduring value of training in floristics and taxonomy.

Metacommunity Dynamics Of Benthic Macroinvertebrates In A Large River

Metacommunity ecology focuses on the interaction between local communities and is inherently linked to dispersal as a result. Within this framework, communities are structured by a combination of in-site responses to the immediate environment (species sorting), stochasticity (patch dynamics), and connections to other communities via distance between communities and dispersal (neutrality), and source-sink dynamics (mass effects; see Chapter 1 for a detailed description of metacommunity theory, the study site, and macroinvertebrate communities found). In Chapter 2 I describe spatial scale of study and dispersal ability as both have the ability to influence the degree to which communities interact. However, little is known about how these factors influence the importance of all metacommunity dynamics. I compared dispersal mode of immature aquatic insects and dispersal ability of winged adults across multiple spatial scales in a large river. The strongest drivers of river communities were patch dynamics, followed by species sorting, then neutrality. Active dispersers during aquatic lifestages on average exhibited lower patch dynamics, higher species sorting, and significant mass effects compared to passive dispersers. Active and strong dispersers also had a scale-independent influence of neutrality, while neutrality was stronger at broader spatial scale for passive and weak dispersers. These results indicate as dispersal ability increases patch dynamics decreases, species sorting increases, and neutrality should decrease. The perceived influence of neutrality may also be dependent on spatial scale and dispersal ability. In Chapter 3 I describe how river benthic macroinvertebrate communities may influence tributary invertebrate communities via adult flight and tributaries may influence mainstem communities via immature drift. This relationship may also depend on relative mainstem and tributary size, as well as abiotic tributary influence on mainstem habitat. To investigate the interaction between a larger river and tributary I sampled mainstem benthic invertebrate communities and quantified habitat of a 7th order river (West Branch Susquehanna River) above and below a 5th order tributary confluence, as well as 0.95-3.2 km upstream in the tributary. Non-metric multidimensional scaling showed similar patterns of clustering between sampling locations for both habitat characteristics and invertebrate communities. In addition, mainstem river communities and habitat directly downstream of the tributary confluence cluster tightly together, intermediate between tributary and mid-channel river samples. In Bray-Curtis dissimilarity comparisons between tributary and mainstem river communities the furthest upstream tributary communities were least similar to river communities. Middle tributary samples were also closest by Euclidean distance to the upstream mainstem riffle and exhibited higher similarity to mid-channel samples than the furthest downstream tributary communities. My results indicate river and tributary benthic invertebrate communities may interact and likely result in direct and indirect mass effects of a tributary on the downstream mainstem community by invertebrate drift and habitat restructuring via material delivery from the tributary. I also showed likely direct effects of adult dispersal from the river and oviposition in proximal tributary locations where Euclidian, rather than river, distance may be more important in determining river-tributary interactions.

16S rRNA terminal restriction fragment length polymorphism for the characterization of the nasopharyngeal microbiota

A novel non-culture based 16S rRNA Terminal Restriction Fragment Length Polymorphism (T-RFLP) method using the restriction enzymes Tsp509I and Hpy166II was developed for the characterization of the nasopharyngeal microbiota and validated using recently published 454 pyrosequencing data. 16S rRNA gene T-RFLP for 153 clinical nasopharyngeal samples from infants with acute otitis media (AOM) revealed 5 Tsp509I and 6 Hpy166II terminal fragments (TFs) with a prevalence of >10%. Cloning and sequencing identified all TFs with a prevalence >6% allowing a sufficient description of bacterial community changes for the most important bacterial taxa. The conjugated 7-valent pneumococcal polysaccharide vaccine (PCV-7) and prior antibiotic exposure had significant effects on the bacterial composition in an additive main effects and multiplicative interaction model (AMMI) in concordance with the 16S rRNA 454 pyrosequencing data. In addition, the presented T-RFLP method is able to discriminate S. pneumoniae from other members of the Mitis group of streptococci, which therefore allows the identification of one of the most important human respiratory tract pathogens. This is usually not achieved by current high throughput sequencing protocols. In conclusion, the presented 16S rRNA gene T-RFLP method is a highly robust, easy to handle and a cheap alternative to the computationally demanding next-generation sequencing analysis. In case a lot of nasopharyngeal samples have to be characterized, it is suggested to first perform 16S rRNA T-RFLP and only use next generation sequencing if the T-RFLP nasopharyngeal patterns differ or show unknown TFs.

Epidemiology of candidemia in Swiss tertiary care hospitals: secular trends, 1991-2000

Candida species are among the most common bloodstream pathogens in the United States, where the emergence of azole-resistant Candida glabrata and Candida krusei are major concerns. Recent comprehensive longitudinal data from Europe are lacking. We conducted a nationwide survey of candidemia during 1991-2000 in 17 university and university-affiliated hospitals representing 79% of all tertiary care hospital beds in Switzerland. The number of transplantations and bloodstream infections increased significantly (P<.001). A total of 1137 episodes of candidemia were observed: Candida species ranked seventh among etiologic agents (2.9% of all bloodstream isolates). The incidence of candidemia was stable over a 10-year period. C. albicans remained the predominant Candida species recovered (66%), followed by C. glabrata (15%). Candida tropicalis emerged (9%), the incidence of Candida parapsilosis decreased (1%), and recovery of C. krusei remained rare (2%). Fluconazole consumption increased significantly (P<.001). Despite increasing high-risk activities, the incidence of candidemia remained unchanged, and no shift to resistant species occurred.

INSTANTANEOUS PHOTOSYNTHETIC RESPONSE TO TEMPERATURE OF MATURE FOREST CANOPIES AND EXPERIMENTALLY WARMED SEEDLINGS

Tropical trees have been shown to be more susceptible to warming compared to temperate species, and have shown growth and photosynthetic declines at elevated temperatures as little as 3oC above ambient. However, regional and global vegetation models lack the data needed to accurately represent physiological response to increased temperatures in tropical forests. We compared the instantaneous photosynthetic responses to elevated temperatures of four mature tropical rainforest tree species in Puerto Rico and the temperate broadleaf species sugar maple (Acer saccharum) in Michigan. Contrary to expectations, leaves in the upper canopy of both temperate and tropical forests had temperature optima that are already exceeded by mean daily leaf temperatures. This indicates that tropical and temperate forests are already seeing photosynthesis decline at mid-day temperature. This decline may worsen as air temperatures rise with climate change if trees are unable to acclimate, increasing the likelihood that forests may shift from carbon sinks to sources. A secondary study was conducted on experimentally warmed sugar maple seedlings to determine if photosynthesis had been able to acclimate to +5oC air temperature over four years. Species abundance models had predicted a decline of sugar maple within the Upper Peninsula of Michigan over the next 100 years, due to elevated temperature and altered precipitation. Instantaneous photosynthetic temperature response curves on both control and heated seedlings showed that the differences between treatments were not statistically significant, though there was a 16% increase in temperature optima and a 3% increase in maximum rates of photosynthesis in warmed plots. Though evidence of acclimation was not significant, the seedlings did not fare poorly as the models suggest.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04-0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9-2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification.

Contribution of APOBEC3G/F Activity to the Development of Low-Abundance Drug-Resistant HIV-1 variants.

Plasma drug-resistant minority HIV-1 variants (DRMV) increase the risk of virological failure to first-line NNRTI antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from APOBEC3G/F activity. Out of 236 ART-naïve evaluated subjects, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I, or V108I were significantly associated with APOBEC3G/F activity (Fisher's p<0.005), defined as presence of >0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a reanalysis of the parent case-control study, presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of NNRTI ART.

Germinación y crecimiento inicial de Habranthus gracilifolius y Rhodophiala bifida, amarilidáceas nativas con potencial ornamental

La azucena del campo (Az-del campo) (Habranthus gracilifolius) y la azucenita colorada (Az-colorada) (Rhodophiala bifida) son bulbosas nativas de Argentina de valor ornamental potencial, de las que se tiene escasa información sobre la germinación y el crecimiento. Para establecer la aptitud germinativa, el régimen de incubación más adecuado, y el crecimiento de las hojas y los bulbos, se realizó un ensayo de germinación y las plántulas se cultivaron en macetas durante un año. Se emplearon cuatro regímenes de incubación: temperatura constante de 20°C y alternadas de 20°/30°C y de 10°/20°C, todos con 8 horas de luz, y de 10°/20°C en oscuridad. Las semillas resultaron fotoblásticas neutras. A temperaturas de 20°C o de 10°/20°C, en ambas especies, la energía y el poder germinativo superaron el 75 y 92%, respectivamente, pero temperaturas de 20°/30°C demoraron la germinación. De otoño a fin de primavera las plantas presentaron hasta 4 hojas en Az-del campo y 2,5 hojas/ planta en Az-colorada, pero en verano no exhibieron hojas. Los bulbos presentaron crecimiento lineal, siendo mayores las tasas en Az-del campo (ancho = 0,022 y longitud = 0,049 mm.día-1) que en Az-colorada (ancho = 0,011 y longitud = 0,014 mm.día-1). La multiplicación por semillas es efectiva, pero en ambas especies se necesita más de un año para alcanzar el estadio reproductivo.

Trematomus bernacchii experimental data files

As a response to ocean warming, shifts in fish species distribution and changes in production have been reported that have been partly attributed to temperature effects on the physiology of animals. The Southern Ocean hosts some of the most rapidly warming regions on earth and Antarctic organisms are reported to be especially temperature sensitive. While cellular and molecular organismic levels appear, at least partially, to compensate for elevated temperatures, the consequences of acclimation to elevated temperature for the whole organism are often less clear. Growth and reproduction are the driving factors for population structure and abundance. The aim of this study was to assess the effect of long-term acclimation to elevated temperature on energy budget parameters in the high-Antarctic fish Trematomus bernacchii. Our results show a complete temperature compensation for routine metabolic costs after 9 weeks of acclimation to 4°C. However, an up to 84% reduction in mass growth was measured at 2 and 4°C compared with the control group at 0°C, which is best explained by reduced food assimilation rates at warmer temperatures. With regard to a predicted temperature increase of up to 1.4°C in the Ross Sea by 2200, such a significant reduction in growth is likely to affect population structures in nature, for example by delaying sexual maturity and reducing production, with severe impacts on Antarctic fish communities and ecosystems.

Diatom assamblage in samples from sediment traps across the Pacific Sector of the Southern Ocean

An array of four sediment trap moorings recorded the particulate flux across the Antarctic Circumpolar Current (ACC) at 170 °W, between November 1996 and January 1998, as part of the US JGOFS-Antarctic Environment and Southern Ocean Process Study (AESOPS) program. The trap locations represent sampling within the Polar Frontal Zone, the Antarctic Polar Front, the Antarctic Zone and the Southern Antarctic Zone. Here we report observations from 1000 m below the sea-surface compared to seafloor and surface water distributions. Sub-sample splits from each trap were obtained and total diatom flux and species composition were determined. The diatom fluxes were quantified using both a dilution and a 'spike' method to allow for the rapid repeatability of measurements. Diatom flux was found to be highly seasonal across the ACC particularly at higher latitudes. Marine snow aggregates of intact diatom cells and chains were the major components of the biogenic flux. Siliceous particle size was noted to decrease with increasing latitude, which could be aligned with a shift of the diatom assemblage to small-size species/sea-ice affiliated species. A 'double-structured' diatom flux was recorded at the location of the Antarctic Polar Front trap, with a shift in the diatom assemblage from larger to smaller diatoms in the second flux episode. The sediment trap assemblage shows deviations from the surface water assemblage, while surface sediment samples indicate that significant dissolution occurs after 1000 m and at the sediment-water interface. Estimation of diatom biovolumes across the ACC shows that large diatoms have the potential to greatly impact biogenic fluxes to the ocean interior despite their low fluxes. Small species of the genus Fragilariopsis could potentially export as much Corg as Fragilariopsis kerguelensis near the retreating ice edge. However, their low abundance in the surface sediments also suggests that these diatoms are a shallow export species.