Program review. The Interdisciplinary Biophysics Graduate Program at the University of Michigan

The Michigan Biophysics Graduate Program (MBGP) was established in 1949, making it one of the first such programs in the world. The intellectual base of the program was significantly broadened in the 1980 when faculty members from a number of other units on campus were invited to join. Currently over forty faculty members from a variety of disciplines participate as mentors for the Ph.D. students enrolled in the MBGP providing our students with rich opportunities for academic learning and research. The MBGP has two main objectives: 1) to provide graduate students with both the intellectual and technical training in modern biophysics, 2) to sensitize our students to the power and unique opportunities of interdisciplinary work and thinking so as to train them to conduct research that crosses the boundaries between the biological and physical sciences. The program offers students opportunities to conduct research in a variety of areas of contemporary biophysics including structural biology, single molecule spectroscopy, spectroscopy and its applications, computational biology, membrane biophysics, neurobiophysics and enzymology. The MBGP offers a balanced curriculum that aims to provide our students with a strong academic base and, at the same time, accommodate their different academic backgrounds. Judging its past performance through the success of its former students, the MBGP has been highly successful, and there is every reason to believe that strong training in the biophysical sciences, as provided by the MBGP, will become even more valuable in the future both in the academic and the industrial settings. in the academic and the industrial settings.     

Alteration in the action of cholinergic and anti cholinergic drugs after chronic haloperidol: indirect evidence for cholinergic hyposensitivity.

Following repeated treatment with haloperidol, spontaneous locomotor activity and the locomotor stimulation produced by amphetamine and the anti-cholinergic, dexetimide was enhanced compared with normal rats. The reduction in locomotor activity produced by the cholinergic agonist, pilocarpine, was retarded following this treatment. These results suggest that a dopaminergic supersensitivity and a cholinergic hyposensitivity develop as a result of chronic neuroleptic treatment.     

Frog lysozyme. II. Isozymes of lysozyme during the larval development of the leopard frog, Rana pipiens.

Eight isozymes of lysozyme were found differentially distributed among six developmental stages of Rana pipiens. Qualitative changes during early development involved a progressive loss of the more basic isozymes which then reappeared between metamorphosis and maturity. Though the egg contained five isozymes, only two were present by early metamorphosis including one not found in the egg. By metamorphic climax, the four isozymes in the egg were regained and one additional form appeared. By maturity, two less basic forms appeared giving a total of eight isozymes.From hatching to early metamorphosis, lysozyme units per animal increased, but lysozyme units/mg dry weight remained unchanged. Both lysozyme units per animal and units/mg dry weight increased sharply towards the end of metamorphosis.     

Mathematical modelling of dynamics and control in metabolic networks. II. Simple dimeric enzymes

The dynamics of enzyme cooperativity are examined by studying a homotropic dimeric enzyme with identical reaction sites, both of which follow irreversible Michaelis-Menten kinetics. The problem is approached via scaling and linearization of the governing mass action kinetic equations. Homotropic interaction between the two sites are found to depend on three dimensionless groups, two for the substrate binding step and one for the chemical transformation. The interaction between the two reaction sites is shown capable of producing dynamic behavior qualitatively different from that of a simple Michaelis-Menten system; when the two sites interact to increase enzymatic activity over that of two independent monomeric enzymes (positive cooperativity) damped oscillatory behavior is possible, and for negative cooperativity in the chemical transformation step a multiplicity of steady states can occur, with one state unstable and leading to runaway behavior. Linear analysis gives significant insight into system dynamics, and their parametric sensitivity, and a way to identify regions of the parameter space where the approximate quasi-stationary and quasi-equilibrium analyses are appropriate.     

Mathematical modelling of dynamics and control in metabolic networks. I. On Michaelis-Menten kinetics

As a starting point for modeling of metabolic networks this paper considers the simple Michaelis-Menten reaction mechanism. After the elimination of diffusional effects a mathematically intractable mass action kinetic model is obtained. The properties of this model are explored via scaling and linearization. The scaling is carried out such that kinetic properties, concentration parameters and external influences are clearly separated. We then try to obtain reasonable estimates for values of the dimensionless groups and examine the dynamic properties of the model over this part of the parameter space. Linear analysis is found to give excellent insight into reaction dynamics and it also gives a forum for understanding and justifying the two commonly used quasi-stationary and quasi-equilibrium analyses. The first finding is that there are two separate time scales inherent in the model existing over most of the parameter space, and in particular over the regions of importance here. Full modal analysis gives a new interpretation of quasi-stationary analysis, and its extension via singular perturbation theory, and a rationalization of the quasi-equilibrium approximation. The new interpretation of the quasi-steady state assumption is that the applicability is intimately related to dynamic interactions between the concentration variables rather than the traditional notion that a quasi-stationary state is reached, after a short transient period, where the rates of formation and decomposition of the enzyme intermediate are approximately equal. The modal analysis reveals that the generally used criterion for the applicability of quasi-stationary analysis that total enzyme concentration must be much less than total substrate concentration, et much less than St, is incomplete and that the criterion et much less than Km much less than St (Km is the well known Michaelis constant) is the appropriate one. The first inequality (et much less than Km) guarantees agreement over the longer time scale leading to quasi-stationary behavior or the applicability of the zeroth order outer singular perturbation solution but the second half of the criterion (Km much less than St) justifies zeroth order inner singular perturbation solution where the substrate concentration is assumed to be invariant. Furthermore linear analysis shows that when a fast mode representing the binding of substrate to the enzyme is fast it can be relaxed leading to the quasi-equilibrium assumption. The influence of the dimensionless groups is ascertained by integrating the equations numerically, and the predictions made by the linear analysis are found to be accurate.(ABSTRACT TRUNCATED AT 400 WORDS)     

Effects of cyclic adenosine 3': 5'-monophosphate on phosphoprotein kinase and phosphatase fractions prepared from rat liver nuclei.

A soluble rat liver nuclear extract containing total RNA polymerase activities also exhibits appreciable amounts of protein kinase activity. This unfractionated protein kinase catalyzes the phosphorylation of both endogenous proteins and exogenous lysine-rich histone in the presence of [γ-³²P]ATP and Mg²⁺. The optimal concentration of Mg²⁺ is 5 mm for histone phosphorylation and 25 mm for the phosphorylation of endogenous proteins. Cyclic AMP has no effect on the phosphorylation of lysine-rich histone by this unfractionated nuclear protein kinase. However, addition of cyclic AMP causes a reduction in the ³²P-labeling of an endogenous protein (CAI) which can be characterized by its mobility during SDS-acrylamide gel electrophoresis and elution in the unbound fraction of a DEAESephadex column. If CAI is first labeled with ³²P and then incubated with 10^?6m cyclic AMP under conditions where protein kinase activity is inhibited, the presence of the cyclic nucleotide causes a loss of the ³²P-labeling of this protein, implying the activation of a substrate-specific protein phosphatase. When rat liver RNA polymerases are purified by DEAE-Sephadex chromatography, protein kinase activity is found in the unbound fraction and in those column fractions containing RNA polymerase I and II. The fractionated protein kinases exhibit different responses to cyclic AMP, the unbound protein kinase being stimulated and the RNA polymerase-associated protein kinases being dramatically inhibited. A second protein (CAII) whose phosphorylated state is modified by cyclic AMP is found within the DEAE-Sephadex column fractions containing RNA polymerase II. The cyclic nucleotide in this case appears to reduce labeling of CAII by inhibition of the protein kinase activity which co-chromatographs with both CAII and RNA polymerase II. Based on molecular weight estimates, neither CAI nor CAII appears to be an RNA polymerase subunit. The identity of CAI as a protein factor whose phosphorylated state influences nuclear RNA synthesis is suggested by the fact that addition of fractions containing CAI to purified RNA polymerase II inhibits the activity of this enzyme, but only if CAI has been previously incubated in the presence of cyclic AMP.     

The suppressive effect of a supernate from concanavalin A-activated human lymphocytes: effects of concanavalin A-activated lymphocytes and their supernates on cytotoxic and mixed lymphocyte reactions.

The effects of Concanavalin A-treated human peripheral blood lymphocytes and their supernatants were evaluated on the MLC reaction and on the generation of cytotoxic lymphocytes assessed by cell-mediated lympholysis (CML). Experiments were performed with both allogeneic and xenogenic sensitization. It was found that Con A-activated cells suppressed the MLC and CML reactions in allogeneic and xenogeneic systems. On the other hand, the SIRS-like supernate was able to suppress the MLC reaction and blastogenesis, but had no suppressive effect on the generation of cytotoxic lymphocytes. We found no difference in the magnitude of suppression, whether or not Con A-activated lymphocytes were syngeneic to the responder cells. This finding suggests that there is no requirement for allogeneic restriction in the interaction between suppressor and suppressed cells, and demonstrates a soluble human suppressor substance capable of suppressing some cell-mediated reactions.     

Forest distribution and site quality in southern Lower Michigan, USA

Aim The primary objectives of this research were to determine whether current forest patches in southern Lower Michigan are a proportionate sample of forest types present in the pre‐settlement cover and, if not, to establish the degree to which certain types are over‐ or under‐represented in the contemporary landscape. This determination is useful not only because any conservation policy designed to restore the present forest to pre‐settlement biodiversity through preservation of existing stands requires an accurate understanding of the degree to which these stands in sum mirror past forest diversity, but also because it fills a gap in the existing ecological literature. Location The research was conducted within four counties in southern Lower Michigan, USA (Ionia, Livingston, Tuscola and Van Buren). Methods Soil survey data were used to characterize the range of site quality across the study area and the areal extent of each quality category. The geographic locations of all current forest patches in each county were then determined from land use maps and were overlaid on the site quality classification. This procedure yielded the observed distribution of forest relative to site quality. The expected areal extent of forest within each category of site quality on the landscape was determined by assuming a random distribution and multiplying the total area of forestland by the proportion of landscape within each category of site quality. This procedure calculated the expected distribution of forest in terms of site quality by dividing the total forestland among the landscape types, relative to how well represented the landscape types were. The observed and expected distributions were then compared both in terms of absolute difference and normalized difference. Results Overall results indicate that categories of site quality that support a large proportion of the present‐day forest patches are generally composed of agriculturally inferior soil and are over‐represented with forest. Surviving or reforested tracts are concentrated on inferior types of habitat. Main conclusions Results suggest that the present‐day forest patches may not be a proportionate sample of the primeval forest. Rather, they are concentrated on agriculturally‐inferior (coarse‐textured, steeply‐sloped, or poorly‐drained) types of habitat. Unless these stands are for some unknown reason compositionally richer than their pre‐settlement counterparts, these results suggest that the existing forest resource in southern Lower Michigan is an inferior (biased) sample of the primeval cover. Furthermore, because forest types associated with the most heavily‐developed agricultural sites have apparently suffered the most loss of habitat, species more characteristic of these types may have experienced a greater decline in overall importance across the landscape. This study suggests that policy aimed at increasing the potential biodiversity of the area should include provisions that encourage the redevelopment of forest habitat on those sites no longer supporting their equal share of forest.     

Multiyear Population Dynamics of Ditylenchus dipsaci Associated with Phlox subulata

Field population densities of Ditylenchus dipsaci associated with shoot tissue of Phlox subulata were monitored during two consecutive growing seasons and intervening periods of overwintering and plant storage. The population density increased significantly through four peaks during the first growing season, and decreased significantly during storage at 5-7 C or overwintering in the field. During the second growing season, there was only a single increase to a moderate population density, followed by a severe population decline associated with the poor physiological condition of the host. A simple model is proposed to explain the population dynamics of D. dipsaci during the first growing season.     

A New Ichnospecies of Arthrophycus from the Late Carboniferous (Pennsylvanian) of Michigan,USA

A unique ichnofossil assemblage from Pennsylvanian-age sandstones near Eaton Rapids, Michigan, USA, comprises straight-to-curved traces preserved in convex hyporelief, with the transverse ridges and median grove associated with the ichnogenus Arthrophycus. The Michigan traces show some branching or pseudo-branching (also known from other Arthrophycus specimens) and are among the smallest structures (millimeters in diameter) attributed to this ichnogenus. The orientation of the Michigan Arthrophycus burrows is distinct from other ichnospecies of this taxon in the pronounced co-planar alignment of the burrows, as opposed to the multiplanar, interweaving, “bundled” nature typical of the ichnogenus. On this basis we assign the Michigan specimens to a new ichnospecies of Arthrophycus. The “paralleling behavior” of the new taxon may reflect a strategy of the tracemaker to avoid previous burrows and reflect differences in resource availability or current energy. This new taxon supports previous records of the occurrence of this ichnogenus in Upper Carboniferous strata.     

Enhancement and suppression of immunoglobulin G-producing B cells in the presence of immune T cells.

Mice were immunized one to three times with sheep red blood cells. Four to seven days after the last immunization, the spleens were removed and the cells were cultured in vitro in the absence of antigen. Removal of most T cells by anti-θ serum treatment prior to culture could increase the number of IgG-producing B cells without affecting the number of specific or nonspecific IgM-producing B cells detected after 2 days of culture. Addition of graded numbers of immune cells to pure immune B cells enhanced the number of IgG-producing B cells, whereas addition or higher number of immune cells caused suppression. Since removal of T cells could also enhance the proliferation of IgG-producing B cells induced by lipopolysaccharide (LPS), a polyclonal B-cell activator, it is suggested that the suppressive effects of high numbers of immune T cells are exerted directly on the B cells.     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.     

Properties of reticulum cell sarcomas in SJL/J mice. VII. Nature of normal lymphoid cells proliferating in response to tumor cells.

Treatment of SJL lymph node, spleen, and thymus cells with anti-Ly 1.2 serum and C caused a marked reduction in the usually observed T-cell proliferation in response to syngeneic X-irradiated transplantable reticulum cell sarcoma cells. By contrast, treatment of lymphoid cells with anti-Ly 2.2 serum and C either failed to affect or increased the proliferative response. It is concluded that the Ly 1 cell is the major T-cell subpopulation which proliferates in response to RCS.     

The possibility of predator avoidance by Lake Michigan zooplankton

Low densities of Diaptomus ashlandi, Diacyclops thomasi, and Daphnia galeata mendotae were measured at depths where Mysis relicta formed nighttime aggregations. Calculations suggest that mysid predation can not account for the rarity of prey animals at these depths, which further suggests that the prey avoided the mysids. Unlike D. galeata mendotae, Daphnia pulicaria was common in mysid aggregations. The somewhat larger size of D. pulicaria may reduce its vulnerability to mysid predation, and consequently may explain the vertical distribution differences between the two congeners. Vertical distributions of Limnocalanus macrurus and copepod nauplii showed no obvious relationships to the mysid distributions. These were the only two taxa with distributions that were correlated with chlorophyll a concentrations. All crustacean taxa were rare in the epilimnion at night when sonar recorded a dense fish school.     

Gape limitation and piscine prey size‐selection by yellow perch in the extreme southern area of Lake Michigan, with emphasis on two exotic prey items

The trophic linkage between yellow perch Perca flavescens and two exotic prey items, alewife Alosa pseudoharengus and round goby Neogobius melanostomus , was investigated in the extreme southern area of Lake Michigan during the summer of 2002. Yellow perch ≥100 mm total length, L _T( n  = 1293) exhibited size selective feeding, with 148 fish containing round gobies and 120 fish containing alewives. The mean round goby L _T, preyed on by yellow perch, was 23% of the predator L _T, with a range of 7 to 47%, and mean alewife L _T was 32% of yellow perch L _T, with a range of 18 to 46%. Although the selection of prey size by yellow perch increased proportionally with yellow perch L _T, prey consumed appeared smaller than theoretically possible based on gape size.     

Spatial and temporal variability of internal and external phosphorus loads in Mona Lake,Michigan

A study was conducted in Mona Lake, a small eutrophic lake located in western Michigan (USA) to address the temporal and spatial variability of external and internal phosphorus loading. External P load varied among subbasins, which was mostly related to discharge, but also to land use. Black Creek, which drains lands with natural cover and agriculture, accounted for the majority of flow, and total phosphorus (TP) and soluble reactive phosphorus (SRP) load, to Mona Lake. However, the relative contribution of SRP load was greater in Little Black Creek, which flows through a mostly urbanized subbasin, than in Black Creek. The relative importance of internal loading was strongly related to season, as internal TP loads contributed only ∼9% of the overall P load in April 2005, but ∼68–82% of the overall P load in the summer and early fall seasons. Internal TP and SRP loading was greater under anaerobic than aerobic conditions. Mean anaerobic TP release rates ranged from 0.80 to 15.56 mg P m⁻² d⁻¹, varying with site and season. Spatial variability in both internal phosphorus loading and sediment P concentration was also evident. By taking into account the spatial and temporal variability of different loading sources, management practices can be targeted to optimize nutrient source control strategies.     

Sharp-tailed grouse lek attendance and fidelity in upper Michigan

To assess and improve existing monitoring protocols for sharp-tailed grouse (Tympanuchus phasianellus) in the eastern Upper Peninsula of Michigan, we used data from 58 radio-collared grouse (46 M, 12 F) monitored within 3 openland landscape types: a xeric, conifer-dominated site, a wetland-dominated site, and a site dominated by low-intensity agriculture. We used lek counts and radio telemetry to determine lek attendance rates, factors affecting lek attendance rates, lek fidelity, and inter-sexual variation in these parameters. Our analysis indicated lek attendance varied with respect to sex of bird, day of year, time after sunrise, and wind speed. Peak male lek attendance rates exceeded those of females by up to 40%, and peak lekking activity for both males and females occurred during the second and third weeks of April. Male lekking activity occurred earlier and was sustained longer than that of females. Lekking activity was negatively related to time of day and wind speed. We observed strong lek fidelity as radio-collared birds attended a primary lek 94% of the time, indicating a low probability of multiple counting of individual birds. We also proposed a method to adjust lek count data for the probability that birds are on a lek during lek counts. Our proposed method can be used by researchers and managers to improve estimates of the number of birds attending a lek by reducing the negative bias associated with observed counts. © 2011 The Wildlife Society.     

Evidence for a coordination position available to solute molecules on one of the metals at the active center of reduced bovine superoxide dismutase

We have measured the contribution of the reduced form of bovine $\text{Zn}\text{Cu}$ superoxide dismutase to the relaxation of the ³⁵Cl nucleus of chloride ion. The reduced protein has a molar relaxivity approximately 2.5 greater than the metal free protein, and addition of a small excess of cyanide lowers the relaxivity of the reduced protein to that of the apo-protein. We have interpreted these observations in terms of an open coordination position on one of the two metal ions, and we have proposed a mechanism for the reduction of superoxide by reduced superoxide dismutase which requires that $\text{O}{}_2{}^{\mathrm{?}}$ binds to Cu⁺ prior to electron transfer.     

Changes in adenosine 3',5'-monophosphate induced by parathyroid hormone and theophylline in the developing rat renal cortex

To test the biochemical responsiveness of developing rat renal cortex to parathyroid hormone (PTH), intracellular concentrations of adenosine 3′,5′-monophosphate (cyclic AMP) were measured. Renal cortical slices from 10-day-, 20-day-, and 12-week-old animals contained higher concentrations of cyclic AMP when incubated in the presence of theophylline than in its absence. In the absence of theophylline, tissue from all three age groups responded to PTH with dose-dependent increases in cyclic AMP. In the presence of theophylline the response of tissue from 10-day-old animals was greater than that of 12-week-old animals.It is suggested that the differential effect of theophylline with respect to age may be the result of higher turnover rates of cyclic AMP in the young animals.     

Miospore biostratigraphy of the Lower Mississippian clastics of the Michigan Basin, USA

Two moderately diverse, moderately abundant miospore assemblages are recorded from the Lower Mississippian Coldwater Shale and Marshall Sandstone of the Michigan Basin. The microfloral assemblage from the older Coldwater Shale is similar to assemblages of the Spelaeotriletes balteatus-Rugospora polyptycha Biozone of western Europe. This biozone is generally absent from North America. The overlying Marshall Sandstone has a miospore assemblage representative of the oldest Osagean Spelaeotriletes pretiosus-Raistrickia clavata Biozone of western Europe. Identification of these assemblages indicates the presence of the Kinderhookian-Osagean boundary within or between the two clastic units. The identification of this boundary has important stratigraphical and sedimentological implications for age relations with Lower Mississippian rocks in adjacent basins and also provides information on regional sedimentology and depositional patterns.