An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia

BACKGROUND: Only one spliceosomal-type intron has previously been identified in the unicellular eukaryotic parasite, Giardia lamblia (a diplomonad). This intron is only 35 nucleotides in length and is unusual in possessing a non-canonical 5' intron boundary sequence, CT, instead of GT. RESULTS: We have identified a second spliceosomal-type intron in G. lamblia, in the ribosomal protein L7a gene (Rpl7a), that possesses a canonical GT 5' intron boundary sequence. A comparison of the two known Giardia intron sequences revealed extensive nucleotide identity at both the 5' and 3' intron boundaries, similar to the conserved sequence motifs recently identified at the boundaries of spliceosomal-type introns in Trichomonas vaginalis (a parabasalid). Based on these observations, we searched the partial G. lamblia genome sequence for these conserved features and identified a third spliceosomal intron, in an unassigned open reading frame. Our comprehensive analysis of the Rpl7a intron in other eukaryotic taxa demonstrates that it is evolutionarily conserved and is an ancient eukaryotic intron. CONCLUSION: An analysis of the phylogenetic distribution and properties of the Rpl7a intron suggests its utility as a phylogenetic marker to evaluate particular eukaryotic groupings. Additionally, analysis of the G. lamblia introns has provided further insight into some of the conserved and unique features possessed by the recently identified spliceosomal introns in related organisms such as T. vaginalis and Carpediemonas membranifera

Understory Vegetation in Old-Growth and Second-Growth Tsuga Canadensis Forests in Western Massachusetts

We compared the understory communities (herbs, shrubs, and tree seedlings and saplings) of old-growth and second-growth eastern hemlock forests (Tsuga canadensis) in western Massachusetts, USA. Second-growth hemlock forests originated following clear-cut logging in the late 1800s and were 108–136 years old at the time of sampling. Old-growth hemlock forests contained total ground cover of herbaceous and shrub species that was approximately 4 times greater than in second-growth forests (4.02 ± 0.41%/m^2 versus 1.06 ± 0.47%/m^2) and supported greater overall species richness and diversity. In addition, seedling and sapling densities were greater in old-growth stands compared to second-growth stands and the composition of these layers was positively correlated with overstory species composition (Mantel tests, r > 0.26, P < 0.05) highlighting the strong positive neighborhood effects in these systems. Ordination of study site understory species composition identified a strong gradient in community composition from second-growth to old-growth stands. Vector overlays of environmental and forest structural variables indicated that these gradients were related to differences in overstory tree density, nitrogen availability, and coarse woody debris characteristics among hemlock stands. These relationships suggest that differences in resource availability (e.g., light, moisture, and nutrients) and microhabitat heterogeneity between old-growth and second-growth stands were likely driving these compositional patterns. Interestingly, several common forest understory plants, including Aralia nudicaulis, Dryopteris intermedia, and Viburnum alnifolium, were significant indicator species for old-growth hemlock stands, highlighting the lasting legacy of past land use on the reestablishment and growth of these common species within second-growth areas. The return of old-growth understory conditions to these second-growth areas will largely be dependent on disturbance and self-thinning mediated changes in overstory structure, resource availability, and microhabitat heterogeneity.Organismic and Evolutionary BiologyOther Research Uni

Quantifying the Extent of North American Mammal Extinction Relative to the Pre-Anthropogenic Baseline

Earth has experienced five major extinction events in the past 450 million years. Many scientists suggest we are now witnessing a sixth, driven by human impacts. However, it has been difficult to quantify the real extent of the current extinction episode, either for a given taxonomic group at the continental scale or for the worldwide biota, largely because comparisons of pre-anthropogenic and anthropogenic biodiversity baselines have been unavailable. Here, we compute those baselines for mammals of temperate North America, using a sampling-standardized rich fossil record to reconstruct species-area relationships for a series of time slices ranging from 30 million to 500 years ago. We show that shortly after humans first arrived in North America, mammalian diversity dropped to become at least 15%–42% too low compared to the “normal” diversity baseline that had existed for millions of years. While the Holocene reduction in North American mammal diversity has long been recognized qualitatively, our results provide a quantitative measure that clarifies how significant the diversity reduction actually was. If mass extinctions are defined as loss of at least 75% of species on a global scale, our data suggest that North American mammals had already progressed one-fifth to more than halfway (depending on biogeographic province) towards that benchmark, even before industrialized society began to affect them. Data currently are not available to make similar quantitative estimates for other continents, but qualitative declines in Holocene mammal diversity are also widely recognized in South America, Eurasia, and Australia. Extending our methodology to mammals in these areas, as well as to other taxa where possible, would provide a reasonable way to assess the magnitude of global extinction, the biodiversity impact of extinctions of currently threatened species, and the efficacy of conservation efforts into the future

Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya

Box C/D ribonucleoprotein (RNP) particles mediate O(2′)-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts, containing four core protein components (Snu13p, Nop56p, Nop58p and fibrillarin) compared with three in Archaea. This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain. In protists, the primarily unicellular organisms comprising the bulk of eukaryotic diversity, the protein composition of box C/D RNPs has not yet been extensively explored. This study describes the complete gene, cDNA and protein sequences of the fibrillarin homolog from the protozoon Euglena gracilis, the first such information to be obtained for a nucleolus-localized protein in this organism. The E.gracilis fibrillarin gene contains a mixture of intron types exhibiting markedly different sizes. In contrast to most other E.gracilis mRNAs characterized to date, the fibrillarin mRNA lacks a spliced leader (SL) sequence. The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other eukaryotic fibrillarins. In an evolutionarily diverse collection of protists that includes E.gracilis, we have also identified putative homologs of the other core protein components of box C/D RNPs, thereby providing evidence that the protein composition seen in the higher eukaryotic complexes was established very early in eukaryotic cell evolution

Influenza Vaccine Effectiveness among US Military Basic Trainees, 2005–06 Season

Virtually all US military basic trainees receive seasonal influenza vaccine. Surveillance data collected from December 2005 through March 2006 were evaluated to estimate effectiveness of the influenza vaccine at 6 US military basic training centers. Vaccine effectiveness against laboratory-confirmed influenza was 92% (95% confidence interval 85%–96%)

Ophthalmic and clinical factors that predict four-year development and worsening of diabetic retinopathy in type 1 diabetes

To investigate the role of ophthalmic imaging markers - namely retinal thickness measures and corneal nerve morphology - in predicting four-year development and worsening of diabetic retinopathy (DR) in type 1 diabetes (T1DM).126 eyes of 126 participants with T1DM were examined at baseline and after four years. Diabetic retinopathy (DR) was graded using the Early Treatment Diabetic Retinopathy Study scale. HbA1c, nephropathy, neuropathy, cardiovascular factors, and retinal thickness using optical coherence tomography (OCT) and corneal nerve fiber length (CNFL) using corneal confocal microscopy at baseline were assessed by univariate and step-wise multiple logistic regression, and their diagnostic capabilities for single and combined measures.Four-year development of DR was 19% (13 of 68 without DR at baseline). Worsening of DR was seen in 43% (25 of 58 with DR at baseline). When adjusted for potential confounders, a lower CNFL (AUC=0.637, p=0.040, 64% sensitivity and 64% specificity at 14.9mm/mm(2) cut-off), higher triglycerides (AUC=0.669, p=0.012, 64% sensitivity, 62% specificity at 0.85mmol/L) and an elevated vibration threshold (AUC=0.708, p=0.002, 96% sensitivity, 40% specificity at 3.55Hz) were significant predictors for four-year worsening of DR.Reduced CNFL, elevated vibration perception threshold and higher triglycerides can predict future worsening of DR

Insulin-like growth factor-I prevents apoptosis in neurons after nerve growth factor withdrawal

Insulin-like growth factor-I (IGF-I) is emerging as an important growth factor able to modulate the programmed cell death (PCD) pathway mediated by the cysteine-dependent aspartate proteases (caspases); however, little is known about the effect of IGF-I after nerve growth factor (NGF) withdrawal in neurons. To begin to understand the neuronal death-sparing effect of IGF-I under NGF-free conditions, we tested whether embryonic sensory dorsal root ganglion neurons (DRG) were able to survive in defined serum-free medium in the presence of IGF-I. We further studied the role of IGF-I signaling and caspase inhibition after NGF withdrawal. NGF withdrawal produced histological changes of apoptosis including chromatin condensation, shrinkage of the perikaryon and nucleus, retention of the plasma membrane, and deletion of single cells. Both IGF-I and Boc-aspartyl (OMe)-fluoromethylketone (BAF), a caspase inhibitor, equally reduced apoptosis after NGF withdrawal. The antiapoptotic effect of IGF-I was completely blocked by LY294002, an inhibitor of PI 3-kinase signaling, but not by the mitogen-activated protein (MAP) kinase/extracellular signal-regulated protein kinase (ERK) activated protein kinase inhibitor PD98059. Functional IGF-I receptors were extensively expressed both in rat and human DRG neurons, although they were most abundant in the neuronal growth cone. Collectively, these findings indicate that IGF-I, signaling though the PI-3 kinase pathway, is important in modulating PCD in cultured DRG neurons after NGF withdrawal, and IGF-I may be important in DRG embryogenesis. © 1998 John Wiley & Sons, Inc. J Neurobiol 36: 455–467, 1998Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34477/1/1_ftp.pd