Modeling in the museum: On the role of remnant models in the work of Joseph Grinnell

Accounts of the relation between theories and models in biology concentrate on mathematical models. In this paper I consider the dual role of models as representations of natural systems and as a material basis for theorizing. In order to explicate the dual role, I develop the concept of a remnant model, a material entity made from parts of the natural system(s) under study. I present a case study of an important but neglected naturalist, Joseph Grinnell, to illustrate the extent to which mundane practices in a museum setting constitute theorizing. I speculate that historical and sociological analyses of institutions can play a specific role in the philosophical analysis of model-building strategies.     

Production and composition of phenylpyrrole metabolites prodcued by Pseudomonas cepacia

Summary In shaken cultures, a strain of Pseudomonas cepacia isolated from apple leaves produced pyrrolnitrin and four other phenylpyrrole antibiotics. The concentrations of these metabolites were determined at intervals for 7 days in three different media at two initial pH levels. Optical density measurements revealed maximum cell concentrations after 24 h in nutrient broth, after 48 h in King's B medium, and after 96 h in minimum salts solution. The effects caused by initiating fermentations at pH 5.8 rather than 7.0 were in most cases not dramatic, although in some instances, especially in minimum salts broth, higher concentrations of metabolites were produced with the lower initial pH. Concentrations of the phenylpyrrole antibiotics were greatly affected by choice of culture medium and incubation time. Concentrations of the two nitrophenyl metabolites, pyrrolnitrin and 2-chloropyrrolnitrin, rose throughout the 7-day incubation and were more than 20 times greater in minimum salts medium than in either King's B medium or nutrient broth. The maximum concentrations of each of the three aminophenyl metabolites (dichloroamino, trichloroamino and monochloroamino) occurred in different media, the monochloro compound in nutrient broth, the dichloro compound in Kings B medium and the trichloro compound in minimum salts medium. The time dependence of the concentrations of the five metabolites supports the proposed biosynthesis of these pyrroles from tryptophan by successive chlorinations followed by oxidation of the amino group at the end of the pathway.     

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: The effect of mononucleotide structure,phosphate activation and montmorillonite composition on phosphodiester bond formation

2-d-5-GMP and 2-d-5-AMP bind 2 times more strongly to montmorillonite 22A than do 2-d-5-CMP and 5-TMP. The dinucleotide d(pG)₂ forms in 9.2% yield and the cyclic dinucleotide c(dpG)₂ in 5.4% yield in the reaction of 2-d-5-GMP with EDAC in the presence of montmorillonite 22A. The yield of d(pC)₂ (2.0%) is significantly lower but comparable to that obtained from 5-TMP. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl₂. A low yield of d(pA)₂ was observed in the condensation reaction of 5-ImdpA on montmorillonite 22A. The cyclic nucleotide (3,5-cdAMP) was obtained in 14% yield from 3-ImdpA. The yield of d(pA)₂ obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na⁺-montmorillonite used as catalyst. Evidence is presented which shows that the acidity of the Na⁺-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.     

Positive and negative control of translation by the leader sequence of cauliflower mosaic virus pregenomic 35S RNA.

We have studied the influence of the 600 nt long leader sequence of cauliflower mosaic virus 35S RNA on downstream translation. Plant protoplasts were transfected with plasmids expressing a CAT reporter gene from a mRNA, containing wild-type or mutant forms of the 35S RNA leader. Deletion analysis revealed the presence of three separate stimulatory sequence regions, S1, S2 and S3. The latter two interact with each other to enhance downstream translation 5- to 10-fold. This enhancement was not observed in protoplasts from a non-host plant. In the absence of either S2 or S3, the region I2, located in between, exerts an inhibitory effect on downstream translation, probably due to the presence of short open reading frames. Expression of a reporter gene inserted into I2 increases 2-fold upon deletion of either S2 or S3. We propose that mRNA regions S2 and S3 form a complex with cellular factors that allows scanning ribosomes to bypass region I2.     

Isolation and characterization of acetonitrile utilizing bacteria

Summary Bacteria utilizing high concentrations of acetonitrile as the sole carbon source were isolated and identified asChromobacterium sp. andPseudomonas aeruginosa. Maximum growth was attained after 96 h of incubation andP. aeruginosa grew slightly faster thanChromobacterium sp. The strains were able to grow and oxidize acetonitrile at concentrations as high as 600 mM. However, higher concentrations inhibited growth and oxygen uptake. Degradation studies with (¹⁴C)acetonitrile indicated 57% of acetonitrile was degraded byPseudomonas aeruginosa as compared to 43% byChromobacterium. The isolates utilized different nitrile compounds as carbon substrates.     

Plant community structure in an oligohaline tidal marsh

An oligohaline tidal marsh on the northern shore of Lake Pontchartrain, LA was characterized with respect to the distributions and abundances of plant species over spatial and temporal gradients using Detrended Correspondence Analysis (DCA). In addition, the species distributions were correlated to several physical environmental factors using Detrended Canonical Correspondence Analysis (DCCA). The distributions of species were best correlated with distance from Lake Pontchartrain, and to a lesser extent with elevation and substrate organic matter. They were least correlated with mean soil salinity (referred to here as background salinity). Of the three mid-seasonal dominant species, the perennial grass, Spartina patens, is the most salt tolerant and was found closest to the lake. Further inland the dominant perennial was Sagittaria lancifolia, which has a salt tolerance less than that of Spartina patens. The perennial sedge, Cladium jamaicense, which is the least salt tolerant of the three, was dominant furthest inland. Background salinity levels were generally low (<5 ppt.) and did not explain species distributions. We hypothesize that the distribution of species is regulated by occasional storm-generated salt pulses that generate strong, short-lived salinity gradients as a function of distance from the lake. Biotic interactions likely also play a role in structuring the plant community. The distributions of several annuals depended on the size and life history of the mid-seasonal dominant perennials. Most of the annuals frequently co-occurred with Sagittaria lancifolia, which was the shortest in stature and had the least persistent canopy of the three mid-seasonal dominant perennials.Abbreviations DCA Detrended Correspondence Analysis - DCCA Detrended Canonical Correspondence Analysis     

Contraction of smooth muscle of pig airway tissues from before birth to maturity

Two heavy chains of smooth muscle myosin (MHC1 and MHC2) were identified in pig airways and parenchyma. The ratio of MHC1 to MHC2 was the same along the bronchial tree in animals of the same age, but it changed with age (mature, young, suckling, and fetus), ranging from 0.8 in the mature to 2.2 in the fetus. Stress developed in airway (trachea, bronchus, and bronchiole) and parenchymal preparations in response to carbachol and histamine (mN/mm2) was normalized for myosin content (N/mm2 myosin). Airways from sucklings always developed the greatest stress to carbachol and histamine with the rank order of maximum force (Emax) suckling greater than fetus greater than young greater than mature for carbachol in large airways. Airway ranking to histamine was similar except that Emax of fetal bronchus and bronchiole were least. In parenchymal strips, mature animals gave strong responses to carbachol and histamine compared with other age groups. Sensitivity to carbachol was increased in the suckling trachea; otherwise it did not vary with age. Chemically skinned tracheal fibers exhibited three- to fourfold greater sensitivity to Ca2+ in fetal and suckling airways compared with the older animals. It is concluded that maturation of smooth muscle occurs in the expression of myosin, in the Ca2(+)-force relationships of the contractile machinery, and in the pharmacological responsiveness of the intact smooth muscle, with the latter greatest at or soon after birth.     

Sagebrush (Artemisia tridentata Nutt.) roots maintain nutrient uptake capacity under water stress

Phosphorus and nitrogen uptake capacities were assessed during36–58 d drying cycles to determine whether the abilityof sagebrush (Artemisia tridentata Nutt.) to absorb these nutrientschanged as the roots were subjected to increasing levels ofwater stress. Water was withheld from mature plants in large(6 I) containers and the uptake capacity of excised roots insolution was determined as soil water potentials decreased from–0.03 MPa to –5.0 MPa. Phosphorus uptake rates of excised roots at given substrateconcentrations increased as preharvest soil water potentialsdecreased to –5.0 MPa. V_max and K_m also increased as soilwater potentials declined. Declining soil water potentials depressednitrogen uptake at set substrate concentrations, but uptakecapacity, calculated as the sum V_max for both NH⁺₄+NO^–₃,did not change significantly with drying. The sum V_max correlatedwith root nitrogen concentration. Root uptake capacity for nitrogen and phosphorus was extremelystable under severe water stress in this aridland shrub. Maintenanceof uptake capacity, coupled with a previously demonstrated abilityto conduct hydraulic lift, may enable A. tridentata better tomaintain nitrogen and phosphorus uptake as soil water availabilitydeclines. These mechanisms may be important in the ability ofA. tridentata to maintain growth, complete reproduction, andgain an advantage against competitors late in the season whenthe soil layers with higher nutrient availability are dry. Key words: Kinetics, nitrogen, phosphorus, roots, water stress     

Validation of age readings from otoliths of juvenile roundnose grenadier, Coryphaenoides rupestris, a deep-water macrourid fish

Validation of the ageing of deep-water fish is difficult and there are only a few instances where the rings on the otoliths have been shown to be laid down annually. Roundnose grenadier have been fished commercially in the North Atlantic since the 1960s and the adult fish have frequently been aged by counting the rings in otoliths or scales. All the ageing was done on the assumption that the rings in the otoliths or scales were annual. Between 1975 and 1992, the Scottish Association for Marine Science carried out seasonal trawling surveys in the Rockall Trough using a fine-meshed trawl, and collected otoliths from a wide size range of roundnose grenadier. An examination of the growing edge of otoliths from juvenile fish from these collections suggests that the rings in the otoliths are laid down annually. The broader, opaque zones which represent the growth phase were dominant between September and March. The thinner, hyaline zones were dominant between April and July. The apparent delay in the growth phase compared with most shallow-water species is discussed in relation to the availability of mesopelagic prey.     

In Vivo Expression of Inducible Nitric Oxide Synthase in Cerebellar Neurons

Abstract: In the CNS, nitric oxide (NO) functions as both neuromodulator and neurotoxic agent. In vivo neuronal expression of NO synthase (NOS) has been attributed to constitutive NOS—both the neuronal and the endothelial types. The other class of NOS—the inducible NOS (iNOS)—is known to mediate toxic effects of NO in various tissues. In this study, we show for the first time that direct intracerebellar injection of endotoxin and cytokine (lipopolysaccharide and interferon-γ) induced in vivo neuronal expression of the iNOS gene, as demonstrated by fluorescent in situ hybridization and immunohistochemical staining analyzed by confocal laser-scanning microscopy. This raises the possibility that neuronal iNOS might contribute significantly to the vulnerability of the brain to various insults.