Large-scale identification of polymorphic microsatellites using an <Emphasis Type="Italic">in silico</Emphasis> approach

Background  

Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs.     

Land use and dispersal influence mortality in white-tailed deer

Restoring male age structure in white-tailed deer populations has become an important objective for many state agencies aimed at improving herd dynamics. Limiting mortality in the yearling (1–2 yr old) age class is a primary consideration, and regional differences in climate, habitat characteristics, hunting regulations, and hunter behavior complicate the understanding of how specific factors influence the risk of mortality. We used Cox proportional hazard modeling to determine the effects of body size, mean distance to road, dispersal behaviors, use of forested land, and use of land open to public hunting on the risk of mortality for a population of radio-collared, yearling males (n = 76) in Sussex County, Delaware, USA. Annual survival averaged 0.55 (95% CI = 0.45–0.68), with harvest accounting for 79% (26/33) of all mortalities. Measurements of body size (chest girth, shoulder height, and total length; cm) influenced dispersal probability but not dispersal distance. The best approximating model for mortality risk included a covariate for landownership, whereby mortality risk increased on public land. Among males who dispersed, longer-distance dispersal was associated with reduced mortality, which contradicts previous research describing dispersal as a high-risk behavior. The effect of landownership on mortality risk has not been previously identified, especially when regulations regarding harvest of yearling males are similar between landownership types. We observed annual survival rates of 0.69 (95% CI = 0.57–0.82) for deer apparently using private land exclusively during the hunting season, and 0.20 (95% CI = 0.11–0.48) for deer that used public land during the hunting season. Survival rates on private land were comparable to those of other regions actively managing male age structure. These results suggest survival of yearling males in the region is influenced by hunter harvest and the risks associated with dispersal may be minimal in areas where harvest pressure is low, although hunter harvest on public land may limit male age structure on a localized scale. © The Wildlife Society, 2019     

Comparison of the effects of cationic porphyrins on DNA properties: influence of GC content of native and synthetic polymers

Interactions of meso-tetra(4-N-methylpyridyl)porphyrin [TMpyP(4)], meso-tetra(2-N-methylpyridyl)porphyrin [TMpyP(2)], and meso-tetra(para-N-trimethylanilinium)porphyrin (TMAP) with several native and synthetic DNAs were studied by a variety of physical techniques: nmr (³¹P and ¹H), absorption spectroscopy, viscosity, and flow dichroism (FD). Of the three porphyrins studied, only the interaction of TMpyP(4) with poly [d(G-C)₂] was fully consistent with intercalation. In particular, a large increase in viscosity, a downfield ³¹P-nmr signal (ca. -1 ppm), and upfield imino proton signals (11 to 12 ppm range) were observed. Comparison of the effects of TMpyP(4) on DNAs of different GC contents revealed larger changes in solution viscosity with increased GC content. However, the characteristic changes in ³¹P- and ¹H-nmr spectra were not observed. The viscosity increases observed in studies with poly[d(A-C)(G-T)] and C. Perf. DNA were much lower than with poly[d(G-C)₂], M. Lys. DNA, and calf thymus DNA. Thus, GC sequence and content are clearly important. The principal change in the ³¹P-nmr signal of native DNA is the appearance of a very broad shoulder centered at ca. -2.0 ppm, which is larger in M. Lys. DNA than in C. Perf. DNA. FD studies indicate highly ordered TMpyP(4) cations arranged perpendicular to the DNA axis of calf thymus DNA. Together, these results suggest the major effects of TMpyP(4) on DNA properties are due to strong GC-binding interactions that influence DNA structure. The data are consistent with combined intercalative and outside binding interactions of TMpyP(4) with GC regions of DNA. In contrast, similar studies with TMAP suggest that it influences AT regions of DNA by an outside binding mode. On the other hand, TMpyP(2) effects on DNA properties are consistent with nonselective outside binding.     

HETEROTROPHY OF FOUR MARINE PHYTOPLANKTERS AT LOW SUBSTRATE CONCENTRATIONS1

Three pelagic marine phytoplankters, Coccolithus huxleyi, Skeletonema costatum, and Thalassiosira rotula, and a facultative heterotroph, Cyclotella cryptica, have been exposed to three organic substrates, viz, glucose, acetate, and glutamate, at low concentrations (organic carbon 0.25 mg/liter). Experiments were performed in the dark and light and the net assimilation of substrate was measured by using radiocarbon. The dark uptake of carbon dioxide was also determined, together with photosynthesis at near optimum light intensity. The expected heterotrophy was detected with Cyclotella cryptica. Thalassiosira rotula was found to assimilate glutamate at an appreciable rate. In all cases, however, the short-term uptake of carbon dioxide in the dark was the greatest assimilation rate measured. Values are discussed in relation to their ecological significance and it is concluded that heterotrophic survival of these and probably most other algae in the open ocean would be impossible unless they were in contact with a high concentration of substrate in the form of particulate matter.     

A laser-based method for measuring thermal nociception of cattle

We describe a method for measuring nociception in cattle using a CO(2) laser aimed at the caudal aspect of the metatarsi. In Experiment 1, infrared thermography showed that calves responded by lifting their legs when skin temperatures reached 45-55 degrees C. In Experiment 2a, the validity of the method was tested by comparing the response latencies of 14 calves to two power settings (2.25 W vs. 4.5 W) with each setting being applied six times. We found that both leg-lift latencies and tail-flick latencies were lower at the higher power setting, and the calves were more likely to respond by kicking than by simply moving the leg. The standard deviations between and within calves were smaller at the higher power setting, and the large within-calf variation means that at least three tests were required to obtain reliable measures that could differentiate between calves. In Experiment 2b, application of the laser at a range of power settings (2.0, 3.0, 4.0, 4.5, 5.0 and 5.5 W) on 16 calves showed that response latencies decreased as power increased up to 4.5 W, after which no further change occurred. In Experiment 3, the repeatability of the method was evaluated on nine measures with the high power setting (4.5 W). The coefficient of variation associated with repetition of the measures was 36%. In general, we found little change in response latencies with repeated use of the laser, except that responses on the second test tended to be shorter. Experiment 4 showed that ambient temperatures between 16 degrees C and 27 degrees C did not affect response latencies, but these were longer at temperatures of 7 degrees C. We suggest that the method is a useful way of measuring cattle's sensitivity to nociception as the animals need not be restrained and the distance to the animal need not be closely controlled. However, to obtain accurate, valid and reliable measures it is necessary to use a high power setting (4.5 W) and take at least three consecutive measures of the response latency.     

Application of the automated spatial surveillance program to birth defects surveillance data

BACKGROUND: Although many birth defects surveillance programs incorporate georeferenced records into their databases, practical methods for routine spatial surveillance are lacking. We present a macroprogram written for the software package R designed for routine exploratory spatial analysis of birth defects data, the Automated Spatial Surveillance Program (ASSP), and present an application of this program using spina bifida prevalence data for metropolitan Atlanta. METHODS: Birth defects surveillance data were collected by the Metropolitan Atlanta Congenital Defects Program. We generated ASSP maps for two groups of years that correspond roughly to the periods before (1994-1998) and after (1999-2002) folic acid fortification of flour. ASSP maps display census tract-specific spina bifida prevalence, smoothed prevalence contours, and locations of statistically elevated prevalence. We used these maps to identify areas of elevated prevalence for spina bifida. RESULTS: We identified a large area of potential concern in the years following fortification of grains and cereals with folic acid. This area overlapped census tracts containing large numbers of Hispanic residents. CONCLUSIONS: The potential utility of ASSP for spatial disease monitoring was demonstrated by the identification of areas of high prevalence of spina bifida and may warrant further study and monitoring. We intend to further develop ASSP so that it becomes practical for routine spatial monitoring of birth defects.     

HETEROTROPHY OF FOUR MARINE PHYTOPLANKTERS AT LOW SUBSTRATE CONCENTRATIONS1

Three pelagic marine phytoplankters, Coccolithus huxleyi, Skeletonema costatum, and Thalassiosira ro-tula, and a facultative heterotroph, Cyclotella cryp-tica, have been exposed to three organic substrates, viz, glucose, acetate, and glutamate, at low concentrations (organic carbon 0.25 mg/liter). Experiments were performed in the dark and light and the net assimilation of substrate was measured by using radiocarbon. The dark uptake of carbon dioxide was also determined, together with photosynthesis at near optimum light intensity. The expected heterotrophy was detected with Cyclotella cryptica. Thalassiosira rotula was found to assimilate glutamate at an appreciable rate. In all cases, however, the short-term uptake of carbon dioxide in the dark was the greatest assimilation rate measured. Values are discussed in relation to their ecological significance and it is concluded that heterotrophic survival of these and probably most other algae in the open ocean xuould be impossible unless they were in contact with a high concentration of substrate in the form of particulate matter.     

39-kDa protein modulates binding of ligands to low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor.

A 39-kDa protein of unknown function has previously been reported to copurify with the low density lipoprotein receptor-related protein (LRP)/alpha 2-macroglobulin receptor. In this study we demonstrate that a recombinant 39-kDa fusion protein can reversibly bind to the 515-kDa subunit of the LRP/alpha 2-macroglobulin receptor. This interaction inhibits the binding and uptake of the receptor's two known ligands: 1) beta-migrating very low density lipoproteins activated by enrichment with apoprotein E and 2) alpha 2-macroglobulin activated by incubation with plasma proteases or methylamine. A potential in vivo role of the 39-kDa protein is to modulate the uptake of apoE-enriched lipoproteins and activated alpha 2-macroglobulin in hepatic and extrahepatic tissues.     

Phage display of ScFv peptides recognizing the thymidine(6-4)thymidine photoproduct

Solar ultraviolet (UV) radiation induces DNA photoproducts in skin cells and is the predominant cause of human skin cancers. To understand human susceptibility to skin cancer and to facilitate the development of prevention measures, highly specific reagents to detect and quantitate UV-induced DNA adducts in human skin will be needed. One approach towards this end is the use of monoclonal antibody-based molecular dosimetry methods. To facilitate the development of photoproduct-specific antibody reagents we have: (i) cloned and sequenced a single chain variable fragment (ScFv) gene coding for one such high affinity monoclonal antibody, [alpha]UVssDNA-1 (mAb C3B6), recognizing the thymidine(6-4)thymidine photoproduct; (ii) expressed and displayed the cloned ScFv gene on the surface of phage; (iii) selected functional recombinant phage by panning; (iv) purified the ScFv peptide; (v) shown that the purified ScFv peptide binds to UV-irradiated polythymidylic acid but not unirradiated polythymidylic acid. This is the first demonstration of the use of phage display to select a ScFv recognizing DNA damage. In addition, this is the initial step towards immortalizing the antibody gene for genetic manipulation, structure-function studies and application to human investigations.     

Effects of double ligation of Stensen's duct on the rabbit parotid gland

Salivary gland duct ligation is an alternative to gland excision for treating sialorrhea or reducing salivary gland size prior to tumor excision. Duct ligation also is used as an approach to study salivary gland aging, regeneration, radiotherapy, sialolithiasis and sialadenitis. Reports conflict about the contribution of each salivary cell population to gland size reduction after ductal ligation. Certain cell populations, especially acini, reportedly undergo atrophy, apoptosis and proliferation during reduction of gland size. Acini also have been reported to de-differentiate into ducts. These contradictory results have been attributed to different animal or salivary gland models, or to methods of ligation. We report here a bilateral double ligature technique for rabbit parotid glands with histologic observations at 1, 7, 14, 30, 60 days after ligation. A large battery of special stains and immunohistochemical procedures was employed to define the cell populations. Four stages with overlapping features were observed that led to progressive shutdown of gland activities: 1) marked atrophy of the acinar cells occurred by 14 days, 2) response to and removal of the secretory material trapped in the acinar and ductal lumens mainly between 30 and 60 days, 3) reduction in the number of parenchymal (mostly acinar) cells by apoptosis that occurred mainly between 14–30 days, and 4) maintenance of steady-state at 60 days with a low rate of fluid, protein, and glycoprotein secretion, which greatly decreased the number of leukocytes engaged in the removal of the luminal contents. The main post- ligation characteristics were dilation of ductal and acinar lumens, massive transient infiltration of mostly heterophils (rabbit polymorphonuclear leukocytes), acinar atrophy, and apoptosis of both acinar and ductal cells. Proliferation was uncommon except in the larger ducts. By 30 days, the distribution of myoepithelial cells had spread from exclusively investing the intercalated ducts pre-ligation to surrounding a majority of the residual duct-like structures, many of which clearly were atrophic acini. Thus, both atrophy and apoptosis made major contributions to the post-ligation reduction in gland size. Structures also occurred with both ductal and acinar markers that suggested acini differentiating into ducts. Overall, the reaction to duct ligation proceeded at a considerably slower pace in the rabbit parotid glands than has been reported for the salivary glands of the rat.