Evaluation of swimming performance for fish passage of longnose dace Rhinichthys cataractae using an experimental flume

The swimming performance of longnose dace Rhinichthys cataractae, the most widely distributed minnow (Cyprinidae) in North America, was assessed in relation to potential passage barriers. The study estimated passage success, maximum ascent distances and maximum sprint speed in an open‐channel flume over a range of water velocities and temperatures (10·7, 15·3 and 19·3° C). Rhinichthys cataractae had high passage success (95%) in a 9·2 m flume section at mean test velocities of 39 and 64 cm s^–1, but success rate dropped to 66% at 78 cm s^–1. Only 20% of fish were able to ascend a 2·7 m section with a mean velocity of 122 cm s^–1. Rhinichthys cataractae actively selected low‐velocity pathways located along the bottom and corners of the flume at all test velocities and adopted position‐holding behaviour at higher water velocities. Mean volitional sprint speed was 174 cm s^–1 when fish volitionally sprinted in areas of high water velocities. Swimming performance generally increased with water temperature and fish length. Based on these results, fishways with mean velocities <64 cm s^–1 should allow passage of most R. cataractae. Water velocities >100 cm s^–1 within structures should be limited to short distance (<1 m) and structures with velocities ≥158 cm s^–1 would probably represent movement barriers. Study results highlighted the advantages of evaluating a multitude of swimming performance metrics in an open‐channel flume, which can simulate the hydraulic features of fishways and allow for behavioural observations that can facilitate the design of effective passage structures.     

Environmental flow allocations in monsoonal Hong Kong

1. Hong Kong streams are subject to aggressive water extractions but the downstream water needs of ecosystems – i.e. environmental flow (e‐flow) requirements – have not yet been addressed. This study investigated hydro‐ecological relationships that could be used to establish e‐flow allocations for streams in monsoonal Hong Kong. 2. Data were collected during the wet and dry seasons from 10 unpolluted streams experiencing a gradient of flow reductions (c. 0–98%). Relationships between flow conditions (percentage discharge reduction and absolute discharge volume) and responses of macroinvertebrate composition and periphyton condition were established for each season. 3. Declines in richness of Ephemeroptera and abundance of hydropsychid caddisflies, as well as increases in the proportion of predators, were linearly related to percentage discharge reduction during both seasons. Relationships were also recorded for eight other macroinvertebrate richness or compositional metrics during the dry season only. Relationships between macroinvertebrate assemblage attributes and absolute discharge volume across downstream reaches were also evident. Periphyton was relatively insensitive to flow reductions and did not provide useful hydro‐ecological relationships, although declines in autotrophic index were related to percentage discharge reduction during the dry season. 4. Using hydro‐ecological relationships established for macroinvertebrates, two levels of e‐flow were proposed: a ‘threshold’ intended to maintain near‐natural conditions and a ‘degradation limit’ that allowed no more than 25% of the maximum indicator response to flow reduction. Calculated threshold e‐flows required downstream allocation of ≥74% of natural flows; degradation limit e‐flows were ≥12% (wet) and ≥27% (dry). The discharge needed to maintain threshold conditions was 30–105 L s^?1 (wet) and 5–14 L s^?1 (dry), with degradation limit e‐flows of 19–57 L s^?1 (wet) and 3–6 L s^?1 (dry), relative to natural mean discharges of 77–303 L s^?1 (wet) and 3–18 L s^?1 (dry). 5. The proposed e‐flow allocations are indicative only, and significant obstacles to implementation have yet to be surmounted. Any such implementation requires monitoring of outcomes in order to refine the allocations and inform adaptive flow management for Hong Kong streams.     

Effect of turbulence on feeding intensity and survival of Japanese flounder Paralichthys olivaceus pelagic larvae

Three‐day rearing experiments were conducted to study the effect of turbulence on the feeding intensity and survival of pelagic larvae of Japanese flounder Paralichthys olivaceus. Four levels of turbulence as control (10^?7·2 m² s^?3), low (10^?6·2 m² s^?3), mid (10^?5·6 m² s^?3) and high (10^?5·0 m² s^?3) were set by changing the flow rate of water pumped through pipes set on the bottom of the tanks. In B‐stage larvae, defined as having buds of elongated dorsal fin rays, the feeding intensity and growth were higher in the low and mid turbulence levels, while survival was highest in the control level. Most of the larvae surviving in the control level, however, were judged to be in a seriously starved condition leading to subsequent high mortality. Because the three‐day span of the rearing experiments was thought to be a little shorter than the periods before starvation‐induced, high mortality occurs. In contrast, for D‐stage larvae, their feeding and growth were optimal in the control and low levels. Feeding was more adversely affected in the high level for D‐stage larvae compared with B‐stage larvae. This is probably due to the compressed body shape and elongated dorsal fin rays of D‐stage larvae, which may be more strongly affected by turbulence and, as a consequence, the larval feeding behaviour such as pursuit and capture of prey organisms becomes less efficient than in lower turbulence. Considering the vertical distribution of B and D‐stage larvae in the oceanic water column, the optimum turbulence level range found in the present study corresponded to a wind speed of 7–10 m s^?1. Therefore, moderate weather conditions of this wind speed range are considered to potentially enhance survival of early larval stages of P. olivaceus.     

Effects of light history on primary productivity in a phytoplankton community dominated by the toxic cyanobacterium Cylindrospermopsis raciborskii

1. The effects of instantaneous irradiance and short‐term light history on primary production were determined for samples from a subtropical water reservoir dominated by the toxic cyanobacterium Cylindrospermopsis raciborskii. ¹⁴C‐bicarbonate uptake incubations were conducted on water samples from the reservoir, for irradiance (photosynthetically active radiation) ranging from 0 to 1654 μmol quanta m⁻² s⁻¹. Prior to the ¹⁴C incubations, cells were pre‐treated at irradiance levels ranging from 0 to 1006 μmol quanta m⁻² s⁻¹. 2. The average irradiance experienced by cells during the 2–2.5 h pre‐treatment incubations affected the productivity–irradiance (P–I) parameters: exposure to high light in pre‐treatment conditions caused a substantial decrease in maximum rate of primary production P_max and the photoinhibition parameter β when compared to cells pre‐treated in the dark. 3. While the data collected in this study were not sufficient to develop a full dynamic model of C. raciborskii productivity, P_max and β were modelled as a function of pre‐treatment irradiance, and these models were applied to predict the rate of primary production as a function of both instantaneous and historical irradiance. The results indicated that while cells with a history of exposure to high irradiance will be the most productive in high irradiance, production rates will be highest overall for dark‐acclimated cells in moderate irradiance. 4. Our results may explain why optically‐deep mixing favours C. raciborskii. If the mixing depth z_m exceeds the euphotic depth z_eu, cells will be dark‐acclimated, which will increase their rate of production when they are circulated through the euphotic zone. These results also predict that production rates will be higher during morning hours than for the same irradiance in the afternoon, which is consistent with other phytoplankton studies. 5. Since the rate of production of C. raciborskii‐dominated systems cannot be described by a single P–I curve, accurate estimates of production rates will require measurements over the daily light cycle.     

Variation in the significant environmental factors affecting larval abundance of four major Chinese carp species: fish spawning response to the Three Gorges Dam

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Quantitative measures of gastrovascular flow in octocorals and hydroids: toward a comparative biology of transport systems in cnidarians

Using microscopy, the gastrovascular systems of four hydroids (Eirene viridula, Cordylophora lacustris, Hydractinia symbiolongicarpus, and Podocoryna carnea) and two distantly related alcyonacean octocorals (Acrossota amboinensis and Sarcothelia sp.) were examined and compared within a phylogenetic framework. Despite a range of stolon widths (means 53–160 μm), the hydroid species exhibited similar patterns of gastrovascular flow: sequentially bidirectional flow in the stolons, driven by myoepithelial contractions emanating from the center of the colony. Unlike the hydroids, the gastrovascular system of A. amboinensis (mean stolon widths for 5 colonies, 0.57–1.21 mm) exhibited simultaneously bidirectional flow with incomplete, medial baffles (width 4–20 μm) separating the flow. Baffles visualized with transmission electron microscopy consisted of endoderm, mesoglea, and occasionally another layer of tissue. Mean flow rates of the gastrovascular fluid for seven stolons ranged from 125 to 275 μm s^?1, with maximum rates of 225–700 μm s^?1. In Sarcothelia sp., stolons were of comparable width (means for 13 colonies 0.55–1.4 mm) to those of A. amboinensis. These stolons, however, were divided by several partitions (width 8–25 μm), both complete and incomplete, which were spaced every 100.5±5.1 μm (mean±SE; range 27.1–283.7 μm) and appeared structurally similar to baffles. In lanes defined by these partitions, ciliary motion was visible in image sequences, and flow was unidirectional. Within a single stolon, flow moved in different directions in different lanes and changed direction by moving from lane to lane via occasional spaces between the partitions. Mean flow rates for 30 stolons ranged from 75 to 475 μm s^?1, with maximum rates of 85–775 μm s^?1. For both octocorals, flow rates of the gastrovascular fluid were not correlated with the width of the stolon lumen. While octocoral gastrovascular systems probably exhibit differences based on phylogenetic affinities, in all species studied thus far, gastrovascular flow is entirely driven by cilia, in contrast to the hydroid taxa.     

Instream habitat use by blue duck (Hymenolaimus malacorhynchos) in a New Zealand river

1. The feeding habitat of a river specialist, blue duck (Hymenolaimus malacorhynchos (Gmelin 1789): Anatidae), was characterized in terms of water depth and velocity on eight occasions over a 13-month period in a river in the central North Island of New Zealand using video to record activity and relocate feeding sites. 2. Of the five feeding activities identified (‘pecking’, ‘grazing’, ‘head-dipping’, up-ending’ and ‘diving’), adult blue duck used mostly head-dipping (> 60% of feeding events on all dates), although diving or grazing from submerged surfaces of exposed boulders comprised major proportions of feeding behaviour (up to 33%) on occasions. Variations in feeding behaviour between dates partly reflected changes in antecedent flow conditions and the annual cycle of the birds. 3. Grazing and diving occurred in significantly faster water (mostly 0.3–0.45 m s^–1) and at significantly different depths (mean = 0.10 and 0.55 m, respectively) than head-dipping (0.20 m depth and 0.28 m s^–1 velocity). Adult feeding depths and velocities at four sites on different dates averaged 0.20 m and 0.31 m s^–1, respectively. Most feeding by 3–4-week-old ducklings occurred over a similar distribution of water velocities to adults but over a wider range of depths. 4. Adult birds fed in significantly shallower and lower velocity water than was available on the two dates that comparisons could be made. Ducklings also fed over a slower range of water velocities but were not selective in terms of water depth. 5. Energetically more expensive search methods were employed at times of high apparent energy demand to access flow microhabitats where larger bodied prey were more likely to be encountered. 6. These data indicate that, like other aquatic organisms, river birds can be influenced by basic hydraulic elements of river flow, but show at the same time that adult blue duck can accommodate variable lotic environments efficiently.     

Short‐term survival and movements of Atlantic sharpnose sharks captured by hook‐and‐line in the north‐east Gulf of Mexico

Ultrasonic telemetry was used to compare post‐release survival and movements of Atlantic sharpnose sharks Rhizoprionodon terraenovae in a coastal area of the north‐east Gulf of Mexico. Ten fish were caught with standardized hook‐and‐line gear during June to October 1999. Atlantic sharpnose sharks were continuously tracked after release for periods of 0·75 to 5·90 h and their positions recorded at a median interval of 9 min. Individual rate of movement was the mean of all distance and time measurements for each fish. Mean ± s.e . individual rate of movement was 0·45 ± 0·06 total lengths per second (L_T s^?1) and ranged from 0·28 to 0·92 L_T s^?1 over all fish. Movement patterns did not differ between jaw and internally hooked Atlantic sharpnose sharks. Individual rate of movement was inversely correlated with bottom water temperature at capture (r² = 0·52, P ≤ 0·05). No consistent direction in movement was detected for Atlantic sharpnose sharks after release, except that they avoided movement towards shallower areas. Capture‐release survival was high (90%), with only one fish not surviving, i.e. this particular fish stopped movement for a period of 10 min. Total rate of movement was total distance over total time (m min^?1) for each Atlantic sharpnose shark. Mean total rate of movement was significantly higher immediately after release at 21·5 m min^?1 over the first 1·5 h of tracking, then decreased to 11·2 m min^?1 over 1·5–6 h, and 7·7 m min^?1 over 3–6 h (P ≤ 0·002), which suggested initial post‐release stress but quick recovery from capture. Thus, high survival (90%) and quick recovery indicate that the practice of catch‐and‐release would be a viable method to reduce capture mortality for R. terraenovae.     

Ecophysiology of the hypotonic response in the salt-tolerant charophyte alga Lamprothamnium papulosum

The ecophysiology of the hypotonic response was studied in the charophyte alga, Lamprothamnium papulosum, which was grown in a marine (SW; 1072 mosmol kg^–1) and a brackish (1/2 SW; 536 mosmol kg^–1) environment. The cells produced an extracellular mucilage identified by histochemical staining as a mixture of sulphated and carboxylated polysaccharides. The thickness and chemical composition of the mucilage layer was a function of environmental salinity and cell age. Mucilage progressively increased in thickness from the apex (9 SW cells: 12·6 ± 1·8 μm; 15 1/2 SW cells: 4·8 ± 0·7 μm) to the base of the plants (15 SW cells: 44·8 ± 3·3 μm; nine 1/2 SW cells: 23·8 ± 2·5 μm); with a corresponding increase in the sulphated proportion. The mucilage was significantly thicker in SW plants. Hydraulic conductivity (Lp) at the apex of SW plants, measured by transcellular osmosis, was 8·3 × 10^–13 m s^–1 Pa^–1. This was close to Lp of freshwater Chara (8·5 × 10^–13 m s^–1 Pa^–1) which lacked mucilage. Basal SW cells with thicker mucilage had a smaller apparent Lp of 3·5 × 10^–13 m s^–1 Pa^–1. The electrophysiology of the resting state and hypotonic response was compared in cells from the two environments based on current/voltage (I/V) analysis. The resting potential difference (PD) and conductance differed (11 SW cells: – 102·4 ± 10·1 mV, eight SW cells: 18·6 ± 2·4 S m^–2; 19 1/2 SW cells: –125·7 ± 5·9 mV, 8·3 ± 0·8 S m^–2). The type of cellular response to a hypotonic shock (decrease of 268 mosmol kg^–1) also differed. In 1/2 SW plants, only the apical cells with thin mucilage responded classically with depolarization, conductance increase, Ca²⁺ influx, cessation of cytoplasmic streaming, and K⁺ and Cl^– effluxes. Older cells making up the bulk of the plants responded with depolarization, but continued cytoplasmic streaming, and had only a small increase in conductance; or depolarized transiently without altering the I/V profile, conductance or streaming speed. Most cells remained depolarized and in the K⁺ state 1 h post-shock. Cells treated with the K⁺ channel blocker tetraethylammonium chloride also depolarized and remained depolarized. The SW cells depolarized but otherwise responded minimally to a 268 mosmol kg^–1 drop in osmolarity and required a further 268 mosmol kg^–1 down-step to elicit a change in the conductance. A spectrum of responses was measured in successively older and more mucilaginous cells from the same marine plant. We discuss the ecophysiological significance of the mucilage layer which modulates the cellular response to osmotic shock and which can be secreted to different degrees by plants inhabiting environments of different salinity.     

Structure and on-site formation of biofilms in paper machine water flow

Paper machine biofilms formed in situ on stainless steel surfaces were studied. A robust flow cell was fitted to side stream (1.8 m s⁻¹) of the spray water circuit of a paper machine. This on-site tool allowed for assessing the efficacy of antifoulants and the adequacy of steel polishing under mill conditions. A rapid fluorescence-based assay was developed to quantify the biomass of shallow biofilms on machine steel. The fluorescence matched the ATP content measured for the same biofilms. Electrolytic polishing reduced the tendency of biofouling of 500 grit surface steel. Biofilm grew under machine conditions as clusters on the steels, showing uniformly coccoid, filaments or short rods; only one cell type in each cluster. The biofilm clusters excluded latex beads of 0.02 μm with hydrophilic or with hydrophobic surfaces from penetrating more than three to four layers of cells. Under the high hydraulic flow at the machine (1.8 m s⁻¹), the biofilm grew in 7 days 6–10 μm thick. The high flow rate guided the shape of the biofilm clusters emerging after the primary attachment of cells. Adhered individual bacteria were the platform on steel to which solids such as paper machine fines then accumulated. Journal of Industrial Microbiology & Biotechnology (2002) 28, 268–279 DOI: 10.1038/sj/jim/7000242 Received 04 October 2001/ Accepted in revised form 14 January 2002     

Seasonal variation in energy fluxes and carbon dioxide exchange for a broad-leaved semi-arid savanna (Mopane woodland) in Southern Africa

We studied the seasonal variation in carbon dioxide, water vapour and energy fluxes in a broad‐leafed semi‐arid savanna in Southern Africa using the eddy covariance technique. The open woodland studied consisted of an overstorey dominated by Colophospermum mopane with a sparse understorey of grasses and herbs. Measurements presented here cover a 19‐month period from the end of the rainy season in March 1999 to the end of the dry season September 2000. During the wet season, sensible and latent heat fluxes showed a linear dependence on incoming solar radiation (I) with a Bowen ratio (β) typically just below unity. Although β was typically around 1 at low incoming solar radiation (150 W m^?2) during the dry season, it increased dramatically with I, typically being as high as 4 or 5 around solar noon. Thus, under these water‐limited conditions, almost all available energy was dissipated as sensible, rather than latent heat. Marked spikes of CO₂ release occurred at the onset of the rainfall season after isolated rainfall events and respiration dominated the balance well into the rainfall season. During this time, the ecosystem was a constant source of CO₂ with an average flux of 3–5 μmol m^?2 s^?1 to the atmosphere during both day and night. But later in the wet season, for example, in March 2000 under optimal soil moisture conditions, with maximum leaf canopy development (leaf area index 0.9–1.3), the peak ecosystem CO₂ influx was as much as 10 μmol m^?2 s^?1. The net ecosystem maximum photosynthesis at this time was estimated at 14 μmol m^?2 s^?1, with the woodland ecosystem a significant sink for CO₂. During the dry season, just before leaf fall in August, maximum day‐ and night‐time net ecosystem fluxes were typically ?3 μmol m^?2 s^?1 and 1–2 μmol m^?2 s^?1, respectively, with the ecosystem still being a marginal sink. Over the course of 12 months (March 1999–March 2000), the woodland was more or less carbon neutral, with a net uptake estimated at only about 1 mol C m^?2 yr^?1. The annual net photosynthesis (gross primary production) was estimated at 32.2 mol m^?2 yr^?1.     

Abundance and production of bacteria, and relationship to phytoplankton production, in a large tropical lake (Lake Tanganyika)

1. Abundance and bacterial production (BP) of heterotrophic bacteria (HBact) were measured in the north and south basins of Lake Tanganyika, East Africa, during seasonal sampling series between 2002 and 2007. The major objective of the study was to assess whether BP can supplement phytoplankton particulate primary production (particulate PP) in the pelagic waters, and whether BP and particulate PP are related in this large lake. HBact were enumerated in the 0–100 m surface layer by epifluorescence microscopy and flow cytometry; BP was quantified using ³H‐thymidine incorporation, usually in three mixolimnion layers (0–40, 40–60 and 60–100 m). 2. Flow cytometry allowed three subpopulations to be distinguished: low nucleic acid content bacteria (LNA), high nucleic acid content bacteria (HNA) and Synechococcus‐like picocyanobacteria (PCya). The proportion of HNA was on average 67% of total bacterial abundance, and tended to increase with depth. HBact abundance was between 1.2 × 10⁵ and 4.8 × 10⁶ cells mL⁻¹, and was maximal in the 0–40 m layer (i.e. roughly, the euphotic layer). Using a single conversion factor of 15 fg C cell⁻¹, estimated from biovolume measurements, average HBact biomass (integrated over a 100‐m water column depth) was 1.89 ± 1.05 g C m⁻². 3. Significant differences in BP appeared between seasons, especially in the south basin. The range of BP integrated over the 0–100 m layer was 93–735 mg C m⁻² day⁻¹, and overlapped with the range of particulate PP (150–1687 mg C m⁻² day⁻¹) measured in the same period of time at the same sites. 4. Depth‐integrated BP was significantly correlated to particulate PP and chlorophyll‐a, and BP in the euphotic layer was on average 25% of PP. 5. These results suggest that HBact contribute substantially to the particulate organic carbon available to consumers in Lake Tanganyika, and that BP may be sustained by phytoplankton‐derived organic carbon in the pelagic waters.     

Baffinella frigidus gen. et sp. nov. (Baffinellaceae fam. nov., Cryptophyceae) from Baffin Bay: Morphology,pigment profile,phylogeny, and growth rate response to three abiotic factors

Twenty years ago an Arctic cryptophyte was isolated from Baffin Bay and given strain number CCMP 2045. Here, it was described using morphology, water‐ and non‐water soluble pigments and nuclear‐encoded SSU rDNA . The influence of temperature, salinity, and light intensity on growth rates was also examined. Microscopy revealed typical cryptophyte features but the chloroplast color was either green or red depending on the light intensity provided. Phycoerythrin (Cr‐PE 566) was only produced when cells were grown under low‐light conditions (5 μmol photons · m^?2 · s^?1). Non‐water‐soluble pigments included chlorophyll a , c ₂ and five major carotenoids. Cells measured 8.2 × 5.1 μm and a tail‐like appendage gave them a comma‐shape. The nucleus was located posteriorly and a horseshoe‐shaped chloroplast contained a single pyrenoid. Ejectosomes of two sizes and a nucleomorph anterior to the pyrenoid were discerned in TEM . SEM revealed a slightly elevated vestibular plate in the vestibulum. The inner periplast component consisted of slightly overlapping hexagonal plates arranged in 16–20 oblique rows. Antapical plates were smaller and their shape less profound. Temperature and salinity studies revealed CCMP 2045 as stenothermal and euryhaline and growth was saturated between 5 and 20 μmol photons · m^?2 · s^?1. The phylogeny based on SSU rDNA showed that CCMP 2045 formed a distinct clade with CCMP 2293 and Falcomonas sp. isolated from Spain. Combining pheno‐ and genotypic data, the Arctic cryptophyte could not be placed in an existing family and genus and therefore Baffinellaceae fam. nov. and Baffinella frigidus gen. et sp. nov. were proposed.     

The effect of turbulent flow and surface roughness on biofilm formation in drinking water

There is considerable interest in both Europe and the USA in the effects of microbiological fouling on stainless steels in potable water. However, little is known about the formation and effects of biofilms, on stainless steel in potable water environments, particularly in turbulent flow regimes. Results are presented on the development of biofilms on stainless steel grades 304 and 316 after exposure to potable water at velocities of 0.32, 0.96 and 1.75 m s⁻¹. Cell counts on slides of stainless steel grades 304 and 316 with both 2B (smooth) and 2D (rough) finishes showed viable and total cell counts were higher at the higher flow rates of 0.96 and 1.75 m s⁻¹, compared to a flow rate of 0.32 m s⁻¹. Extracellular polysaccharide levels were not significantly different (P< 0.05) between each flow rate on all stainless steel surfaces studied. higher levels were found at the higher water velocities. the biofilm attached to stainless steel was comprised of a mixed bacterial flora including Acinetobacter sp, Pseudomonas spp, Methylobacterium sp, and Corynebacterium/Arthrobacter spp. Epifluorescence microscopy provided evidence of rod-shaped bacteria and the formation of stands, possibly of extracellular material attached to stainless steel at high flow rates but not at low flow rates. Received 04 February 1998/ Accepted in revised form 12 February 1999     

Structure‐kinetic relationship of carbapenem antibacterials permeating through E. coli OmpC porin

The emergence of Gram‐negative “superbugs” exhibiting resistance to known antibacterials poses a major public health concern. Low molecular weight Gram‐negative antibacterials are believed to penetrate the outer bacterial membrane (OM) through porin channels. Therefore, intracellular exposure needed to drive antibacterial target occupancy should depend critically on the translocation rates through these proteins and avoidance of efflux pumps. We used electrophysiology to study the structure‐translocation kinetics relationships of a set of carbapenem antibacterials through purified porin OmpC reconstituted in phospholipid bilayers. We also studied the relative susceptibility of OmpC+ and OmpC‐ E. coli to these compounds as an orthogonal test of translocation. Carbapenems exhibit good efficacy in OmpC‐expressing E. coli cells compared with other known antibacterials. Ertapenem, which contains an additional acidic group compared to other analogs, exhibits the fastest entry into OmpC (k_on ≈ 2 × 10⁴ M^?1 s^?1). Zwitterionic compounds with highly polar groups attached to the penem‐2 ring, including panipenem, imipenem and doripenem exhibit faster k_on (>10⁴ M^?1 s^?1), while meropenem and biapenem with fewer exposed polar groups exhibit slower k_on (～5 × 10³ M^?1 s^?1). Tebipenem pivoxil and razupenem exhibit ～13‐fold slower k_on (～1.5 × 10³ M^?1 s^?1) than ertapenem. Overall, our results suggest that (a) OmpC serves as an important route of entry of these antibacterials into E. coli cells; and (b) that the structure‐kinetic relationships of carbapenem translocation are governed by H‐bond acceptor/donor composition (in accordance with our previous findings that the enthalpic cost of transferring water from the constriction zone to bulk solvent increases in the presence of exposed nonpolar groups). Proteins 2014; 82:2998–3012. © 2014 Wiley Periodicals, Inc.     

Photoautotrophic Cell and Tissue Culture in a Tubular Photobioreactor

An externally illuminated tubular photobioreactor was constructed from 3.4 m stainless steel tubes and 22.1 m glass tubes for the cultivation of photoautotrophic organisms. The 30‐L reactor can be equipped with helical static mixers in order to create a uniform radial exchange within the tubes, 40 mm in diameter. A flexible construction of the reactor allows scale‐down experiments to be carried out with axial velocities between 0.3–2.5 m/s, gassing‐in rates of 0–0.5 L/min, k_L a values of 0.002–0.006 s^–1 and six metal halide lamps inducing photon flux densities in the range of 70–300 μE/m²s. Two model organisms, the green microalgae Chlorella vulgaris and the bryophyte Physcomitrella patens, were chosen to characterize cell growth and physiology in submerse cultures. Comparative experiments with Chlorella vulgaris in two configurations of the reactor with inserted helical static mixers and plates resulted in maximum growth rates of 1.6 d^–1. No growth enhancement was obtained in the case of helical static mixers at a mean PFD of 150 μE/m²s and an axial velocity of 0.4 m/s. No homogenous flow could be obtained in the case of inserted plates. Physcomitrella patens was successfully cultivated in the reactor (μ = 0.36 d^–1), whereas average axial velocities of ca. 0.6 m/s guarantee favorable gas transport without contributing to cell damage. This makes tubular photobioreactors a promising production system for the production of glycosylated recombinant proteins derived from moss.     

Synthesis, 18F‐Radiolabelling and Biological Evaluations of C‐6 Alkylated Pyrimidine Nucleoside Analogues

Synthesis of pyrimidine derivatives with a side‐chain attached to the C‐6 of pyrimidine ring (6–14) is reported. Target compounds 8 and 12 were subjected to in vitro phosphorylation tests, determination of their binding affinities to herpes simplex virus (HSV‐1) thymidine kinase (TK) and catalytic turnover constants. Fluorinated pyrimidine derivative 12 (40 µM) exhibited better binding affinity for HSV‐1 TK than acyclovir (ACV, 170 µM) and ganciclovir (GCV, 48 µM). Catalytic turnover constant (k _cat) of 12 (0.08 s^? 1) was close to the k _cat values of ACV (0.10 s^? 1) and GCV (0.10 s^? 1). Furthermore, compounds 8 and 12 showed no cytotoxic effects in HSV‐1 TK‐transduced and non‐transduced cell lines. Besides, compounds 8 and 12 did not exhibit antiviral or cytostatic activities against several viruses and malignant tumor cell lines that were evaluated. The new fluorinated pyrimidine derivative 16 that is phosphorylated by HSV‐1 TK could be developed as non‐toxic PET‐tracer molecule. Thus, ¹⁸F labelling of the precursor 14 was performed by nucleophilic substitution using [¹⁸F] tetrabutylammonium fluoride as the fluorinating reagent.     

A single‐molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed

The replisome catalyses DNA synthesis at a DNA replication fork. The molecular behaviour of the individual replisomes, and therefore the dynamics of replication fork movements, in growing Escherichia coli cells remains unknown. DNA combing enables a single‐molecule approach to measuring the speed of replication fork progression in cells pulse‐labelled with thymidine analogues. We constructed a new thymidine‐requiring strain, eCOMB (E. coli for combing), that rapidly and sufficiently incorporates the analogues into newly synthesized DNA chains for the DNA‐combing method. In combing experiments with eCOMB, we found the speed of most replication forks in the cells to be within the narrow range of 550–750 nt s^?1 and the average speed to be 653 ± 9 nt s^?1 (± SEM). We also found the average speed of the replication fork to be only 264 ± 9 nt s^?1 in a dnaE173‐eCOMB strain producing a mutant‐type of the replicative DNA polymerase III (Pol III) with a chain elongation rate (300 nt s^?1) much lower than that of the wild‐type Pol III (900 nt s^?1). This indicates that the speed of chain elongation by Pol III is a major determinant of replication fork speed in E. coli cells.