Modeling the effect of an associated single-nucleotide polymorphism in linkage studies

For linkage analysis in affected sibling pairs, we propose a regression model to incorporate information from a disease-associated single-nucleotide polymorphism located under the linkage peak. This model can be used to study if the associated single-nucleotide polymorphism marker partly explains the original linkage peak. Two sources of information are used for performing this task, namely the genotypes of the parents and the genotypes of the siblings. We applied the methods to three significantly disease-associated single-nucleotide polymorphisms and five microsatellite markers at the end of chromosome 3 of replicate 1 of Aipotu population. Two out of five of the microsatellite markers showed a LOD score higher than 3. The question to be answered was whether one of the single-nucleotide polymorphisms partly explains these high LOD scores. We did not have the answers when we analyzed the data.     

Extracellular regulated kinase/mitogen activated protein kinase is up-regulated in pulmonary emphysema and mediates matrix metalloproteinase-1 induction by cigarette smoke

The interstitial collagenase matrix metalloprotein-ase-1 (MMP-1) is up-regulated in the lung during pulmonary emphysema. The mechanisms underlying this aberrant expression are poorly understood. Although cigarette smoking is the predominant cause of emphysema, only 15-20% of smokers develop the disease. To define the signaling pathways activated by smoke and to identify molecules responsible for emphysema-associated MMP-1 expression, we performed several in vitro and in vivo experiments. In this study, we showed that cigarette smoke directly induced MMP-1 mRNA and protein expression and increased the collagenolytic activity of human airway cells. Treatment with various chemical kinase inhibitors revealed that this response was dependent on the extracellular regulated kinase-1/2 (ERK) mitogen activated protein kinase pathway. Cigarette smoke increased phosphorylation of residues Thr-202 and Tyr-204 of ERK in airway lining cells and alveolar macrophages in mice at 10 days and 6 months of exposure. Moreover, analysis of lung tissues from emphysema patients revealed significantly increased ERK activity compared with lungs of control subjects. This ERK activity was evident in airway lining and alveolar cells. The identification of active ERK in the lungs of emphysema patients and the finding that induction of MMP-1 by cigarette smoke in pulmonary epithelial cells is ERK-dependent reveal a molecular mechanism and potential therapeutic target for excessive matrix remodeling in smokers who develop emphysema.     

Single chain variable fragment antibodies selected by phage display against the sporozoite surface antigen S16 of Cryptosporidium parvum

Two human single chain variable fragment (scFv) libraries were used to select clones that bound to the surface glycoprotein S16 of Cryptosporidium parvum. Panning of the Tomlinson libraries I and J resulted in the isolation of nine distinct clones. Of the four clones which had full-length scFv, three contained stop codons. The remaining five clones were truncated, with four missing the heavy chain, and one missing most of the light chain. The full-length clones exhibited better binding to native C. parvum proteins and recombinant S16 than the truncated clones, with the exception of one truncated clone. None of the selected clones cross-reacted with Giardia lamblia, Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus or another immunogenic target of C. parvum, P23. Clones expressed as the soluble scFv-gIIIp construct were able to detect C. parvum native proteins and sporozoites. Panning from naïve libraries was an useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.     

Bigger is better: age class-specific survival rates in long-lived turtles increase with size

Vital rates for small, non-breeding individuals are important components of population dynamics for many species, but often individuals of these sizes are difficult to locate, capture, and track. As such, biologists frequently lack reliable estimates of juvenile survival because sample sizes and recapture rates for this life stage are low. Long-lived animals often take many years to reach sexual maturity and spend much of this time in the smaller size classes, making them sensitive to changes in survival rates. We estimated the survival rates of all size classes for the northern map turtle (Graptemys geographica) using a mark-recapture dataset with >3,500 captures from 2019–2021 and 210 nests from 2018–2021. As turtle size increased, annual survival probability increased regardless of sex. Estimated annual survival probability for turtles >18 cm long (i.e., adult females >15 years) was about 0.95, over 4 times higher than turtles that were 3 cm long (i.e., hatchlings <1 year; 0.22 annual survival probability). Although we did not observe a difference in survival probability between sexes of any size class, adult females are nearly twice the size of adult males, leading to an increased annual survival probability for females of 0.95, compared to 0.80 for males. Changes in adult survival had the greatest influence on population estimates over time, with temporary decreases, such as those due to poaching or an environmental disaster, potentially leading to unrecoverable decreases in the overall population size. Our study provides detailed survival rates for all size classes in a long-lived turtle, which are necessary to assess population stability and can be used to determine the most effective conservation or management practices.     

Co-operation between different targeting pathways during integration of a membrane protein

Membrane protein assembly is a fundamental process in all cells. The membrane-bound Rieske iron-sulfur protein is an essential component of the cytochrome bc₁ and cytochrome b₆f complexes, and it is exported across the energy-coupling membranes of bacteria and plants in a folded conformation by the twin arginine protein transport pathway (Tat) transport pathway. Although the Rieske protein in most organisms is a monotopic membrane protein, in actinobacteria, it is a polytopic protein with three transmembrane domains. In this work, we show that the Rieske protein of Streptomyces coelicolor requires both the Sec and the Tat pathways for its assembly. Genetic and biochemical approaches revealed that the initial two transmembrane domains were integrated into the membrane in a Sec-dependent manner, whereas integration of the third transmembrane domain, and thus the correct orientation of the iron-sulfur domain, required the activity of the Tat translocase. This work reveals an unprecedented co-operation between the mechanistically distinct Sec and Tat systems in the assembly of a single integral membrane protein.     

Range-wide analysis of eastern massasauga survivorship

Decisions affecting wildlife management and conservation policy of imperiled species are often aided by population models. Reliable population models require accurate estimates of vital rates and an understanding of how vital rates vary geographically. The eastern massasauga (Sistrurus catenatus catenatus) is a rattlesnake species found in the Great Lakes region of North America. Populations of the eastern massasauga are fragmented and only a few areas harbor multiple, sizable populations. Eastern massasauga research has typically focused on single populations or local metapopulations but results suggest that demographic parameters vary geographically. We used 21 radiotelemetry datasets comprising 499 telemetered snakes from 16 distinct locations throughout the range of the eastern massasauga to characterize geographic patterns of adult survival using the known-fate model in Program MARK. Annual adult survival ranged from 0.35 to 0.95 (mean = 0.67) and increased along a southwest to northeast geographic axis. Further analysis of 6 datasets indicated no consistent difference in survival between males and females. Our results provide a better understanding of the relationship between survivorship and geography for the eastern massasauga and suggest that such variation should be incorporated into population models as well as local and regional management plans. © 2012 The Wildlife Society.     

Phenology constrains opportunistic growth response in <Emphasis Type="Italic">Bromus tectorum</Emphasis> L.

Seasonal resource availability may act as a constraint on plant phenology and thereby influence the range of growth responses observed among populations of annual species, especially those occupying a wide range of environments. We compared a mesic and a xeric population of the non-native, annual grass, Bromus tectorum, to examine phenology in response to interspecific competition and water availability. Using a target-neighborhood approach, we assessed how phenological patterns of the two populations affected morphological and growth responses to enhanced resource availability represented by late-season soil moisture. The xeric population exhibited a highly constrained phenology and was unable to extend the growing season despite available soil resources. Because of the low phenotypic variation, allocation to reproduction was similar across resource conditions. In contrast, the mesic population flowered later and showed a more opportunistic phenology in response to late-season water availability. The mesic population was not able to maintain consistent reproductive allocation at low resource levels. The responses of the two populations to late-season water availability were not affected by the density of neighboring plants. We suggest that post-introduction selection pressure on B. tectorum in the xeric habitat has resulted in a more fixed phenology which limits opportunistic response to unpredictable, particularly late-season resource availability. Opportunistic and fixed responses represent contrasting strategies for optimizing fitness in temporally varying environments and, while both play important roles for ensuring reproductive success, these results suggest that local adaptation to temporal resource variation may reflect a balance between flexible and inflexible phenology.     

The Pox in the North American Backyard: Volepox Virus Pathogenesis in California Mice (Peromyscus californicus)

Volepox virus (VPXV) was first isolated in 1985 from a hind foot scab of an otherwise healthy California vole (Microtus californicus). Subsequent surveys in San Mateo County, CA, revealed serological evidence suggesting that VPXV is endemic to this area, and a second viral isolate from a Pinyon mouse (Peromyscus truei) was collected in 1988. Since then, few studies have been conducted regarding the ecology, pathology, and pathogenicity of VPXV, and its prevalence and role as a potential zoonotic agent remain unknown. To increase our understanding of VPXV disease progression, we challenged 24 California mice (Peromyscus californicus) intranasally with 1.6×10(3) PFU of purified VPXV. By day five post infection (pi) we observed decreased activity level, conjunctivitis, ruffled hair, skin lesions, facial edema, and crusty noses. A mortality rate of 54% was noted by day eight pi. In addition, internal organ necrosis and hemorrhages were observed during necropsy of deceased or euthanized animals. Viral loads in tissues (brain, gonad, kidney, liver, lung, spleen, submandibular lymph node, and adrenal gland), bodily secretions (saliva, and tears), and excretions (urine, and/or feces) were evaluated and compared using real time-PCR and tissue culture. Viral loads measured as high as 2×10(9) PFU/mL in some organs. Our results suggest that VPXV can cause extreme morbidity and mortality within rodent populations sympatric with the known VPXV reservoirs.