Experimental and Theoretical Bases of Specific Affinity, a Cytoarchitecture-Based Formulation of Nutrient Collection Proposed To Supercede the Michaelis-Menten Paradigm of Microbial Kinetics

A theory for solute uptake by whole cells was derived with a focus on the ability of oligobacteria to sequester nutrients. It provided a general relationship that was used to obtain the kinetic constants for in situ marine populations in the presence of naturally occurring substrates. In situ affinities of 0.9 to 400 liters g of cells⁻¹ h⁻¹ found were up to 10³ times smaller than those from a “Marinobacter arcticus ” isolate, but springtime values were greatly increased by warming. Affinities of the isolate for usual polar substrates but not for hydrocarbons were diminished by ionophores. A kinetic curve or Monod plot was constructed from the best available data for cytoarchitectural components of the isolate by using the theory together with concepts and calculations from first principles. The order of effect of these components on specific affinity was membrane potential > cytoplasmic enzyme concentration > cytoplasmic enzyme affinity > permease concentration > area of the permease site > translation coefficient > porin concentration. Component balance was influential as well; a small increase in cytoplasmic enzyme concentration gave a large increase in the effect of permease concentration. The effect of permease concentration on specific affinity was large, while the effect on K_m was small. These results are in contrast to the Michaelis-Menten theory as applied by Monod that has uptake kinetics dependent on the quality of the permease molecules, with K_m as an independent measure of affinity. Calculations demonstrated that most oligobacteria in the environment must use multiple substrates simultaneously to attain sufficient energy and material for growth, a requirement consistent with communities largely comprising few species.     

Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K₂), G. arboreum (A₂), and G. raimondii (D₅), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K₂, 2.44 Gb; A₂, 1.62 Gb; D₅, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K₂ and A₂ relative to D₅. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.     

Naphthoquinone inhibitors of Periplaneta americana and Scolytus multistriatus feeding: ultraviolet difference spectra of reactions of juglone, menadione, and 1,4-naphthoquinone with amino acids and the indicated mechanism of feeding inhibition

The relative reactivity of 3 naphthoquinones, which are feeding inhibitors for Periplaneta americana and Scolytus multistriatus, with each of 7 amino acids was measured by ultraviolet difference spectroscopy. Juglone (5-hydroxy-1,4-naphthoquinone), menadione(2-methyl-1,4-naphthoquinone) or 1,4-naphthoquinone produced difference spectra immediately upon mixing with cysteine, but not with valine, serine, glutamic acid, arginine, tryptophan or proline in phosphate buffer (pH 7.0). The K_s values for the reactions indicated that the affinities of 1,4-naphthoquinone (K_s = 4.4 · 10⁻⁴M) and juglone (K_s = 8.3 · 10⁻⁴M) for cysteine were comparable, but were both approx. 10 times greater than that for menadione (K_s = 3.2 · 10⁻³M). The extinction coefficient of the complex formed by cysteine with juglone (A = 3.448 · 10⁻¹M) was approx. 2 times greater than that of 1,4-naphthoquinone (A = 1.290 · 10⁻¹M) or menadione (A = 1.176 · 10⁻¹ M). The importance of these results to explaining the mechanism of chemoreception in P. americana and S. multistriatus is discussed.     

Nutrient Uptake by Microorganisms according to Kinetic Parameters from Theory as Related to Cytoarchitecture

The abilities of organisms to sequester substrate are described by the two kinetic constants specific affinity, a°, and maximal velocity V_max. Specific affinity is derived from the frequency of substrate-molecule collisions with permease sites on the cell surface at subsaturating concentrations of substrates. V_max is derived from the number of permeases and the effective residence time, τ, of the transported molecule on the permease. The results may be analyzed with affinity plots (v/S versus v, where v is the rate of substrate uptake), which extrapolate to the specific affinity and are usually concave up. A third derived parameter, the affinity constant K_A, is similar to K_M but is compared to the specific affinity rather than V_max and is defined as the concentration of substrate necessary to reduce the specific affinity by half. It can be determined in the absence of a maximal velocity measurement and is equal to the Michaelis constant for a system with hyperbolic kinetics. Both are taken as a measure of τ, with departure of K_M from K_A being affected by permease/enzyme ratios. Compilation of kinetic data indicates a 10⁸-fold range in specific affinities and a smaller (10³-fold) range in V_max values. Data suggest that both specific affinities and maximal velocities can be underestimated by protocols which interrupt nutrient flow prior to kinetic analysis. A previously reported inverse relationship between specific affinity and saturation constants was confirmed. Comparisons of affinities with ambient concentrations of substrates indicated that only the largest a°_S values are compatible with growth in natural systems.     

Evidence from Liposome Encapsulation for Transport-Limited Microbial Metabolism of Solid Alkanes

The recalcitrance of xenobiotics may be caused by an absence of transforming enzymes or by their inability to enter microbial cells. A nondestructive method for differentiating between these two possibilities is described. The solid n-alkanes octadecane (C₁₈) and hexatriacontane (C₃₆) were encapsulated into phosphatidylcholine bilayers (liposomes). The uptake and metabolism rates of encapsulated and unencapsulated substrates were then compared. During 1 h at 25°C, a Pseudomonas isolate took up 1.3% of radiolabeled and unencapsulated C₁₈ (solid state) versus 23.5% of labeled and encapsulated C₁₈. Growth at 25°C occurred with an apparent k_s of 2453 ± 148 mg/liter. Liposome encapsulation decreased this K_s to 60 ± 12 mg/liter. At 34°C, growth on C₁₈ (liquid state) occurred with an apparent K_s of 819 ± 83 mg/liter and on the readily available carbon source succinate, K_s values were 80 ± 10 and 13 ± 7 mg/liter at 25 and 34°C, respectively. At 25°C, the isolate grew on C₃₆ with an apparent K_s of 2,698 ± 831 mg/liter. Liposome encapsulation decreased the K_s more than 60-fold to 41 ± 7 mg/liter, resulting in the complete utilization of 400 mg of C₃₆ per liter in 16 h. Since controls excluded the metabolic utilization of phosphatidylcholine, the results clearly identify transport limitation as the cause for C₃₆ recalcitrance.     

Transport Parameters in a Porous Cellulose Acetate Membrane

The transport parameters of a cellulose acetate membrane prepared from a mixture of cellulose acetate, formamide, and acetone, 25:25:50 by weight, were studied. The membrane consists of a thin, porous layer, the skin, in series with a thick, highly porous layer, the coarse support. In the skin the diffusional permeability coefficient, ω, of a number of small amides and alcohols depends critically upon the partition coefficient, K_s, the size of the molecule, and the apparent hydrogen-bonding ability, N_s, of the solute. These observations are in general agreement with our earlier conclusions on the properties of nonporous membranes. On the other hand, the corrected reflection coefficient, σ', is not a very sensitive function of either N_s or K_s taken separately. The correlation between σ' and molecular diameter is reasonably good; however, it is much improved when both N_s and K_s are taken into consideration. Isotope interaction was also studied in the present preparation and was found to provide only a small (5–8%) contribution to the diffusional permeability coefficient of ethylene glycol. The contribution of solute-water friction was found to be less than 24% of the total solute friction.     

Discovery of 2,4-thiazolidinedione-tethered coumarins as novel selective inhibitors for carbonic anhydrase IX and XII isoforms

Different 2,4-thiazolidinedione-tethered coumarins 5a–b, 10a–n and 11a–d were synthesised and evaluated for their inhibitory action against the cancer-associated hCAs IX and XII, as well as the physiologically dominant hCAs I and II to explore their selectivity. Un-substituted phenyl-bearing coumarins 10a, 10 h, and 2-thienyl/furyl-bearing coumarins 11a–c exhibited the best hCA IX (K_Is between 0.48 and 0.93 µM) and hCA XII (K_Is between 0.44 and 1.1 µM) inhibitory actions. Interestingly, none of the coumarins had any inhibitory effect on the off-target hCA I and II isoforms. The sub-micromolar compounds from the biochemical assay, coumarins 10a, 10 h and 11a–c, were assessed in an in vitro antiproliferative assay, and then the most potent antiproliferative agent 11a was tested to explore its impact on the cell cycle phases and apoptosis in MCF-7 breast cancer cells to provide more insights into the anticancer activity of these compounds.     

Synthesis and antidepressant-like activity of novel alkoxy-piperidine derivatives targeting SSRI/5-HT1A/5-HT7

A series of novel alkoxy-piperidine derivatives were synthesized and evaluated for their serotonin reuptake inhibitory and binding affinities for 5-HT_1A/5-HT₇ receptors. In vivo antidepressant activities of the selective compounds were explored using the forced swimming test (FST) and tail suspension test (TST) in mice. The results showed that compounds 7a (reuptake inhibition (RUI), IC₅₀ = 177 nM; 5-HT_1A, K_i = 12 nM; 5-HT₇, K_i = 25 nM) and 15g (RUI, IC₅₀ = 85 nM; 5-HT_1A, K_i = 17 nM; 5-HT₇, K_i = 35 nM) were potential antidepressant agents in animal behavioral models with high 5-HT_1A/5-HT₇ receptor affinities and moderate serotonin reuptake inhibition, and good metabolic stability in vitro.     

Tobacco Mesophyll Protoplasts Synthesize 1,3-beta-Glucanase, Chitinases, and "Osmotins" during in Vitro Culture

Tobacco (Nicotiana tabacum) mesophyll protoplasts synthesize six basic proteins (a, a′, a₁, b, b′, and c) which are undetectable in the leaf and whose synthesis is reduced by auxin (Y Meyer, L Aspart, Y Chartier [1984] Plant Physiol 75: 1027-1033). Polypeptides a, a′, and a₁ were shown to have similar mobilities on two-dimensional electrophoresis as one 1,3-β-glucanase and two chitinases from tobacco mosaic virus-infected leaves. In immunoblotting experiments, polypeptide a was recognized by specific antibodies raised against the 1,3-β-glucanase and a′ and a₁ reacted with anti-chitinase antibodies. Similarly, b and b′ comigrated with osmotin and its neutral counterpart, two proteins characteristic of salt-adapted tobacco cells, and reacted with anti-osmotin antibodies. In addition it has been shown that 1,3-β-glucanase and chitinase activities increased at the same time as a, a′, and a₁ accumulated in cultivated protoplasts. Finally, polypeptide c was also detected in tobacco mosaic virus-infected leaves but could not be identified as any of the pathogenesis-related proteins characterized so far in tobacco. Thus, cultivated tobacco protoplasts synthesize and accumulate typical stress proteins.     

Purification, characterization, and immunological properties for two isoforms of glutathione reductase from eastern white pine needles

Glutathione reductase (EC 1.6.4.2) was purified from Eastern white pine (Pinus strobus L.) needles. The purification steps included affinity chromatography using 2′, 5′-ADP-Sepharose, FPLC-anion-exchange, FPLC-hydrophobic interaction, and FPLC-gel filtration. Separation of proteins by FPLC-anion-exchange resulted in the recovery of two distinct isoforms of glutathione reductase (GR_A and GR_B). Purified GR_A had a specific activity of 1.81 microkatals per milligram of protein and GR_B had a specific activity of 6.08 microkatals per milligram of protein. GR_A accounted for 17% of the total units of glutathione reductase recovered after anion-exchange separation and GR_B accounted for 83%. The native molecular mass for GR_A was 103 to 104 kilodaltons and for GR_B was 88 to 95 kilodaltons. Both isoforms of glutathione reductase were dimers composed of identical subunit molecular masses which were 53 to 54 kilodaltons for GR_A and 57 kilodaltons for GR_B. The pH optimum for GR_A was 7.25 to 7.75 and for GR_B was 7.25. At 25°C the K_m for GSSG was 15.3 and 39.8 micromolar for GR_A and GR_B, respectively. For NADPH, the K_m was 3.7 and 8.8 micromolar for GR_A and GR_B, respectively. Antibody produced from purified GR_B was reactive with both native and denatured GR_B, but was cross-reactive with only native GR_A.     

Synthesis and biological evaluation of a series of benzoxazole/benzothiazole-containing 2,3-dihydrobenzo[b][1,4]dioxine derivatives as potential antidepressants

A series of benzoxazole/benzothiazole-2,3-dihydrobenzo[b][1,4]dioxine derivatives (5a–5d and 8a–8j) was synthesized. Compounds were evaluated for binding affinities at the 5-HT_1A and 5-HT_2A receptors. Antidepressant activities of the compounds were screened using the forced swimming test (FST) and the tail suspension test (TST). The results indicated that the compounds exhibited high affinities for the 5-HT_1A and 5-HT_2A receptors and showed a marked antidepressant-like activity. Compound 8g exhibited high affinities for the 5-HT_1A (K_i = 17 nM) and 5-HT_2A (K_i = 0.71 nM) receptors; it also produced a decrease of the immobility time and exhibited potent antidepressant-like effects in the FST and TST in mice.     

Characterization of binding kinetics of A2AR to Gαs protein by surface plasmon resonance

Because of their surface localization, G protein-coupled receptors (GPCRs) are often pharmaceutical targets as they respond to a variety of extracellular stimuli (e.g., light, hormones, small molecules) that may activate or inhibit a downstream signaling response. The adenosine A_2A receptor (A_2AR) is a well-characterized GPCR that is expressed widely throughout the human body, with over 10 crystal structures determined. Truncation of the A_2AR C-terminus is necessary for crystallization as this portion of the receptor is long and unstructured; however, previous work suggests shortening of the A_2AR C-terminus from 412 to 316 amino acids (A_2AΔ316R) ablates downstream signaling, as measured by cAMP production, to below that of constitutive full-length A_2AR levels. As cAMP production is downstream of the first activation event—coupling of G protein to its receptor—investigating that first step in activation is important in understanding how the truncation effects native GPCR function. Here, using purified receptor and Gα_s proteins, we characterize the association of A_2AR and A_2AΔ316R to Gα_s with and without GDP or GTPγs using surface plasmon resonance (SPR). Gα_s affinity for A_2AR was greatest for apo-Gα_s, moderately affected in the presence of GDP and nearly completely ablated by the addition of GTPγs. Truncation of the A_2AR C-terminus (A_2AΔ316R) decreased the affinity of the unliganded receptor for Gα_s by ～20%, suggesting small changes to binding can greatly impact downstream signaling.     

Synthesis and antidepressant effect of novel aralkyl piperazine and piperidine derivatives targeting SSRI/5-HT1A/5-HT7

A series of novel aralkyl piperazine and piperidine derivatives were synthesized, and evaluated for their serotonin reuptake inhibitory and 5-HT_1A/5-HT₇ receptors affinities activity. Antidepressant activities in vivo of the selective compound were screened using the forced swimming test (FST) and tail suspension test (TST). The results indicated that compound 19a exhibited high affinities for the 5-HT_1A/5-HT₇ receptors (5-HT_1A, K_i = 12 nM; 5-HT₇, K_i = 3.2 nM) coupled with potent serotonin reuptake inhibition (IC₅₀ = 14 nM) and showed a marked antidepressant-like effect in the FST and TST models.     

Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions

Marine bacteria in Resurrection Bay near Seward, Alaska, and in the central North Sea off the Dutch coast were cultured in filtered autoclaved seawater following dilution to extinction. The populations present before dilution varied from 0.11 × 10⁹ to 1.07 × 10⁹ cells per liter. The mean cell volume varied between 0.042 and 0.074 μm³, and the mean apparent DNA content of the cells ranged from 2.5 to 4.7 fg of DNA per cell. All three parameters were determined by high-resolution flow cytometry. All 37 strains that were obtained from very high dilutions of Resurrection Bay and North Sea samples represented facultatively oligotrophic bacteria. However, 15 of these isolates were eventually obtained from dilution cultures that could initially be cultured only on very low-nutrient media and that could initially not form visible colonies on any of the agar media tested, indicating that these cultures contained obligately oligotrophic bacteria. It was concluded that the cells in these 15 dilution cultures had adapted to growth under laboratory conditions after several months of nutrient deprivation prior to isolation. From the North Sea experiment, it was concluded that the contribution of facultative oligotrophs and eutrophs to the total population was less than 1% and that while more than half of the population behaved as obligately oligotrophic bacteria upon first cultivation in the dilution culture media, around 50% could not be cultured at all. During one of the Resurrection Bay experiments, 53% of the dilution cultures obtained from samples diluted more than 2.5 × 10⁵ times consisted of such obligate oligotrophs. These cultures invariably harbored a small rod-shaped bacterium with a mean cell volume of 0.05 to 0.06 μm³ and an apparent DNA content of 1 to 1.5 fg per cell. This cell type had the dimensions of ultramicrobacteria. Isolates of these ultramicrobacterial cultures that were eventually obtained on relatively high-nutrient agar plates were, with respect to cell volume and apparent DNA content, identical to the cells in the initially obligately oligotrophic bacterial dilution culture. Determination of kinetic parameters from one of these small rod-shaped strains revealed a high specific affinity for the uptake of mixed amino acids (a°_A, 1,860 liters/g of cells per h), but not for glucose or alanine as the sole source of carbon and energy (a°_A, ± 200 liters/g of cells per h). The ultramicrobial strains obtained are potentially a very important part of picoplankton biomass in the areas investigated.     

Inhibition of the Fermentation of Propionate to Methane by Hydrogen, Acetate, and Propionate

Inhibition of the fermentation of propionate to methane and carbon dioxide by hydrogen, acetate, and propionate was analyzed with a mesophilic propionate-acclimatized sludge that consisted of numerous flocs (size, 150 to 300 μm). The acclimatized sludge could convert propionate to methane and carbon dioxide stoichiometrically without accumulating hydrogen and acetate in a propionate-minimal medium. Inhibition of propionate utilization by propionate could be analyzed by a second-order substrate inhibition model (shown below) given that the substrate saturation constant, K_s, was 15.9 μM; the substrate inhibition constant, K_i, was 0.79 mM; and the maximum specific rate of propionate utilization, q_m, was 2.15 mmol/g of mixed-liquor volatile suspended solids (MLVSS) per day: q_s = q_mS/[K_s + S + (S²/K_i)], where q_s is the specific rate of propionate utilization and S is the initial concentration of undissociated propionic acid. For inhibition by hydrogen and acetate to propionate utilization, a noncompetitive product inhibition model was used: q_s = q_m/[1 + (P/K_p)ⁿ], where P is the initial concentration of hydrogen or undissociated acetic acid and K_p is the inhibition constant. Kinetic analysis gave, for hydrogen inhibition, K_p(H2) = 0.11 atm (= 11.1 kPa, 71.5 μM), q_m = 2.40 mmol/g of MLVSS per day, and n = 1.51 and, for acetate inhibition, K_p(HAc) = 48.6 μM, q_m = 1.85 mmol/g of MLVSS per day, and n = 0.96. It could be concluded that the increase in undissociated propionic acid concentration was a key factor in inhibition of propionate utilization and that hydrogen and acetate cooperatively inhibited propionate degradation, suggesting that hydrogenotrophic and acetoclastic methanogens might play an important role in enhancing propionate degradation to methane and carbon dioxide.     

Effects of Water-Deficit Stress on Photosynthesis, Its Components and Component Limitations, and on Water Use Efficiency in Wheat (Triticum aestivum L.)

It is of theoretical as well as practical interest to identify the components of the photosynthetic machinery that govern variability in photosynthesis rate (A) and water-use efficiency (WUE), and to define the extent by which the component processes limit A and WUE during developing water-deficit stress. For that purpose, leaf exchange of CO₂ and H₂O was determined in two growth-chamber-grown wheat cultivars (Triticum aestivum L. cv TAM W-101 and cv Sturdy), and the capacity of A was determined and broken down into carboxylation efficiency (c.e.), light- and CO₂-saturated A, and stomatal conductance (g_s) components. The limitations on A measured at ambient CO₂ concentration (A₃₅₀) were estimated. No cultivar difference was observed when A₃₅₀ was plotted versus leaf water potential (Ψ_w). Light- and CO₂-saturated A, c.e., and g_s decreased with decreasing leaf Ψ_w, but of the corresponding photosynthesis limitations only those caused by insufficient c.e. and g_s increased. Thus, reduced stomatal aperture and Calvin cycle activity, but not electron transport/photophosphorylation, appeared to be major reasons for drought stress-induced inhibition of A₃₅₀. WUE measured as A₃₅₀/g_s first increased with stomatal closure down to a g_s of about 0.25 mol H₂O m⁻² s⁻¹ (Ψ_w = −1.6 MPa). However, it was predicted that A₃₅₀/g_s would decrease with more severe stress due to inhibition of c.e.     

Seawater exposure causes hydraulic damage in dying Sitka-spruce trees

Sea-level rise is one of the most critical challenges facing coastal ecosystems under climate change. Observations of elevated tree mortality in global coastal forests are increasing, but important knowledge gaps persist concerning the mechanism of salinity stress-induced nonhalophytic tree mortality. We monitored progressive mortality and associated gas exchange and hydraulic shifts in Sitka-spruce (Picea sitchensis) trees located within a salinity gradient under an ecosystem-scale change of seawater exposure in Washington State, USA. Percentage of live foliated crown (PLFC) decreased and tree mortality increased with increasing soil salinity during the study period. A strong reduction in gas exchange and xylem hydraulic conductivity (K_s) occurred during tree death, with an increase in the percentage loss of conductivity (PLC) and turgor loss point (π_tlp). Hydraulic and osmotic shifts reflected that hydraulic function declined from seawater exposure, and dying trees were unable to support osmotic adjustment. Constrained gas exchange was strongly related to hydraulic damage at both stem and leaf levels. Significant correlations between foliar sodium (Na⁺) concentration and gas exchange and key hydraulic parameters (K_s, PLC, and π_tlp) suggest that cellular injury related to the toxic effects of ion accumulation impacted the physiology of these dying trees. This study provides evidence of toxic effects on the cellular function that manifests in all aspects of plant functioning, leading to unfavourable osmotic and hydraulic conditions.

Hydraulic and osmotic shifts during tree death under seawater exposure are related to the toxic effects of ion accumulation on the maintenance of cellular function.     

Design,synthesis and evaluation of benzo[a]thieno[3,2-g]quinolizines as novel l-SPD derivatives possessing dopamine D1, D2 and serotonin 5-HT1A multiple action profiles

A novel scaffold derived from l-SPD with a substituted thiophene group in the D ring were designed, synthesized, and evaluated for their binding affinities at dopamine (D₁, D₂ and D₃) and serotonin (5-HT_1A and 5-HT_2A) receptors. Most of the tetracyclic compounds exhibited higher affinities for D₂ and 5-HT_1A receptors than l-SPD, while compound 23e showed the highest K_i value of 7.54 nM at D₂ receptor which was 14 times more potent than l-SPD. Additionally, compounds 23d and 23e were more potent than l-SPD at D₃ receptor. According to the functional assays, 23d and 23e were demonstrated as full antagonists at D₁ and D₂ receptors and full agonists at 5-HT_1A receptor. Since the combination of D₂ antagonism and 5-HT_1A agonism is considered effective in treating both the positive and negative symptoms of schizophrenia, these novel compounds are implicated as potential therapeutic agents.     

Respiratory Kinetics of Marine Bacteria Exposed to Decreasing Oxygen Concentrations

During aerobic respiration, microorganisms consume oxygen (O₂) through the use of different types of terminal oxidases which have a wide range of affinities for O₂. The K_m values for O₂ of these enzymes have been determined to be in the range of 3 to 200 nmol liter⁻¹. In this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (Dinoroseobacter shibae, Roseobacter denitrificans, Idiomarina loihiensis, and Marinobacter daepoensis) during exposure to decreasing O₂ concentrations. The genomes of all four species have genes for both high-affinity and low-affinity terminal oxidases. The respiration rate of the bacteria was measured by the use of extremely sensitive optical trace O₂ sensors (range, 1 to 1,000 nmol liter⁻¹). Three of the four isolates exhibited apparent K_m values of 30 to 60 nmol liter⁻¹ when exposed to submicromolar O₂ concentrations, but a decrease to values below 10 nmol liter⁻¹ was observed when the respiration rate per cell was lowered and the cell size was decreased due to starvation. The fourth isolate did not reach a low respiration rate per cell during starvation and exhibited apparent K_m values of about 20 nmol liter⁻¹ throughout the experiment. The results clearly demonstrate not only that enzyme kinetics may limit O₂ uptake but also that even individual cells may be diffusion limited and that this diffusion limitation is the most pronounced at high respiration rates. A decrease in cell size by starvation, due to limiting organic carbon, and thereby more efficient diffusion uptake may also contribute to lower apparent K_m values.     

Evolution of Hypervariable Region 1 of Hepatitis C Virus in Primary Infection

The hypervariable region 1 (HVR-1) of the putative envelope encoding E2 region of hepatitis C virus (HCV) RNA was analyzed in sequential samples from three patients with acute type C hepatitis infected from different sources to address (i) the dynamics of intrahost HCV variability during the primary infection and (ii) the role of host selective pressure in driving viral genetic evolution. HVR-1 sequences from 20 clones per each point in time were analyzed after amplification, cloning, and purification of plasmid DNA from single colonies of transformed cells. The intrasample evolutionary analysis (nonsynonymous mutations per nonsynonymous site [K_a], synonymous mutations per synonymous site [K_s], K_a/K_s ratio, and genetic distances [gd]) documented low gd in early samples (ranging from 2.11 to 7.79%) and a further decrease after seroconversion (from 0 to 4.80%), suggesting that primary HCV infection is an oligoclonal event, and found different levels and dynamics of host pressure in the three cases. The intersample analysis (pairwise comparisons of intrapatient sequences; rK_a, rK_s, rK_a/rK_s ratio, and gd) confirmed the individual features of HCV genetic evolution in the three subjects and pointed to the relative contribution of either neutral evolution or selective forces in driving viral variability, documenting that adaptation of HCV for persistence in vivo follows different routes, probably representing the molecular counterpart of the viral fitness for individual environments.