Algal and bacterial non-symbiotic nitrogen fixation in paddy soils

Summary The nitrogen fixing activity of three Ivory Coast soils was tested in the laboratory by the acetylene reduction assay and the Kjeldahl method. Nitrogen fixation due to algae was estimated to be of the order of 4 to 8 (acetylene method) and 7 μg N per g soil per day (Kjeldahl method). Nitrogen fixation due to bacterial activity in the rice rhizosphere was estimated to be of the order of 2 to 5 (acetylene method) and 1 to 3 μg N per g soil per day (Kjeldahl method). These results emphasize the importance of the bacterial nitrogen fixation in the rhizosphere which had been hitherto overlooked. Comparison of acetylene method and Kjeldahl method results shows discrepancies the origin of which has been discussed. Time course of acetylene reduction by rhizosphere soils exhibits a lag phase which may be attributed to Postgate's switch off — switch on process.     

Neophobia and Dietary Conservatism:Two Distinct Processes?

Birds show distinct hesitation when approaching novel food and this has been termed ‘neophobia’. In laboratory-held birds like domestic chicks this effect lasts for a matter of a few minutes at most, but hesitant attack of novel foods can last for weeks or even months in wild birds. This effect, called ‘dietary conservatism’, seems to be a different type of learning process from neophobia as first described and has hitherto been largely overlooked. This paper presents some evidence for the view that the processes may be fundamentally different. We outline results from laboratory chicks that show neophobia to be easily deactivated by experience, which renders it unlikely to be an important force in wild birds. We also report evidence that the process of incorporation of novel food into the diet is not a simple one-stage process but includes at least four steps of assessment. The paper concludes with an outline of the importance of dietary conservatism in our understanding of the evolution of aposematism and the workings of mimicry. This revised version was published online in July 2006 with corrections to the Cover Date.     

The timing of mating influences reproductive success in Drosophila melanogaster: implications for sexual conflict

Despite its potential importance, the role of the timing of mating(s) as a source of variation in female lifetime reproductive success has been largely overlooked. Here, using a laboratory‐adapted population of the model species Drosophila melanogaster, we explore how temporal variation in the patterns of single and multiple matings influences female fecundity. We find that the boost to fecundity known to occur after a virgin female’s initial mating also extends to subsequent matings as nonvirgins, but only for a short duration. This fecundity boost at least partially offsets the direct costs of multiple matings to females in this population of D. melanogaster. The implications of these results for our understanding of the evolution and maintenance of polyandry in this species are discussed in the context of sexual conflict.     

Enhanced technique to measure proteins in single segments of human skeletal muscle fibers: fiber-type dependence of AMPK-alpha1 and -beta1

Human physiological studies typically use skeletal muscle biopsies from the heterogeneous vastus lateralis muscle comprised of both fast-twitch and slow-twitch fiber types. It is likely that potential changes of physiological importance are overlooked because fiber-type specific responses may not be apparent in the whole muscle preparation. A technological advance in Western blotting is presented where proteins are analyzed in just one small segment (<2 mm) of individual fibers dissected from freeze-dried muscle samples using standard laboratory equipment. A significant advance is being able to classify every fiber at the level of both contractile (myosin heavy chain and tropomyosin) and sarcoplasmic reticulum [sarco(endo)plasmic reticulum Ca(2+)-ATPase type 1] properties and then being able to measure specific proteins in the very same segments. This removes the need to fiber type segments before further analyses and, as such, dramatically reduces the time required for sample collection. Compared with slow-twitch fibers, there was less AMP-activated protein kinase (AMPK)-α(1) (～25%) and AMPK-β(1) (～60%) in fast-twitch fibers from human skeletal muscle biopsies.     

Dietary essential amino acids affect the reproduction of the keystone herbivore Daphnia pulex

Recent studies have indicated that nitrogen availability can be an important determinant of primary production in freshwater lakes and that herbivore growth can be limited by low dietary nitrogen availability. Furthermore, a lack of specific essential nitrogenous biochemicals (such as essential amino acids) might be another important constraint on the fitness of consumers. This might be of particular importance for cladoceran zooplankton, which can switch between two alternative reproductive strategies--the production of subitaneously developing and resting eggs. Here, we hypothesize that both the somatic growth and the type of reproduction of the aquatic keystone herbivore Daphnia is limited by the availability of specific essential amino acids in the diet. In laboratory experiments, we investigated this hypothesis by feeding a high quality phytoplankton organism (Cryptomonas) and a green alga of moderate nutritional quality (Chlamydomonas) to a clone of Daphnia pulex with and without the addition of essential amino acids. The somatic growth of D. pulex differed between the algae of different nutritional quality, but not dependent on the addition of dissolved amino acids. However, in reproduction experiments, where moderate crowding conditions at saturating food quantities were applied, addition of the essential amino acids arginine and histidine (but not lysine and threonine) increased the total number and the developmental stage of subitaneous eggs. While D. pulex did not produce resting eggs on Cryptomonas, relatively high numbers of resting eggs were released on Chlamydomonas. When arginine and histidine were added to the green algal diet, the production of resting eggs was effectively suppressed. This demonstrates the high, but previously overlooked importance of single essential amino acids for the reproductive strategy of the aquatic keystone herbivore Daphnia.     

Environmental and genetic factors affecting the response of laboratory animals to drugs.

Only some of the diverse factors that can affect drug disposition and response in laboratory animals have been identified at the present time. These numerous factors contribute to large day-to-day variations that have become a major problem impeding investigation of drug disposition and response in laboratory animals. Although these variations render many experiments difficult to interpret and produce large discrepancies in the literature, few published investigations using laboratory animals provide sufficient details to permit replication of the studies under similar conditions with respect to these variables. Thus, the importance of these variables in affecting results is apparently insufficiently recognized at present. Two commonly overlooked variables affecting the activity of hepatic microsomal enzymes (HME) in rodents and hence the rate at which rodents eliminate from their bodies many foreign compounds are the bedding under the wire mesh cage and the relative cleanliness of the environment. Numerous chemicals present in relatively low concentrations in the environment of the animal room can significantly alter HME activity. Representative of these chemicals are aromatic hydrocarbons in cedarwood bedding, eucalyptol from aerosol sprays, and chlorinated hydrocarbon insecticides, each of which induces HME activity, whereas ammonia generated from feces and urine accumulated in unchanged pans under cages may inhibit HME activity. Chloroform, identified as an environmental contaminant of the water and air of certain cities, exhibits sex and strain differences with respect to toxicity (LD50) in mice. After intraperitoneal injection, twice as much chloroform accumulated in the kidneys of males from the sensitive strain (DBA/2J) as from the resistant (C57BL/6J) strain. First generation offspring were midway between parental strains both with respect to LD50 and renal accumulation of chloroform.     

Analysis of a fermentation recycle loop for on-line measurements

Summary Recycle lines have been widely used in on-line analysis of fermentation processes. However, like most tools, many practical considerations can remain overlooked. Upon reflecting on this technique, some of these overlooked considerations have been studied. Because of the importance of a debubbler to a recycle line, an improved design was made and tested which can produce a bubble free high flow rate stream to reduce residence times. The effect of the recycle line on the culture growth, and DO was also investigated and found to be negligible.     

Imine Reductases: A Comparison of Glutamate Dehydrogenase to Ketimine Reductases in the Brain

A key intermediate in the glutamate dehydrogenase (GDH)-catalyzed reaction is an imine. Mechanistically, therefore, GDH exhibits similarities to the ketimine reductases. In the current review, we briefly discuss (a) the metabolic importance of the GDH reaction in liver and brain, (b) the mechanistic similarities between GDH and the ketimine reductases, (c) the metabolic importance of the brain ketimine reductases, and (d) the neurochemical consequences of defective ketimine reductases. Our review contains many historical references to the early work on amino acid metabolism. This work tends to be overlooked nowadays, but is crucial for a contemporary understanding of the central importance of ketimines in nitrogen and intermediary metabolism. The ketimine reductases are important enzymes linking nitrogen flow among several key amino acids, yet have been little studied. The cerebral importance of the ketimine reductases is an area of biomedical research that deserves far more attention.     

Reproductive interference in laboratory experiments of interspecific competition

Many studies that have researched interspecific competition in Callosobruchus (bean beetles), Drosophila (fruit flies), and Tribolium (flour beetles) have considered the major drivers of interspecific competition to be interspecific resource competition and intraguild cannibalism. These competition drivers have a density-dependent effect on the population dynamics. However, some studies have also detected a relative-frequency-dependent effect in the observed population dynamics. The most likely causal mechanism of this relative frequency dependence is reproductive interference, defined as any interspecific sexual interaction that damages female reproductive success. Reproductive interference has been overlooked by most laboratory studies in spite of the critical effect on the competition outcome. In this paper, I review laboratory studies of these insect genera from the perspective of reproductive interference and show that the reported results can be more reasonably interpreted by the joint action of reproductive interference and resource competition, including intraguild cannibalism. In addition, on the basis of results reported by a small number of related studies, I discuss the behavioral and evolutionary changes induced in those genera by reproductive interference.     

Autophagy: An overlooked mechanism of HIV-1 pathogenesis and NeuroAIDS?

Human immunodeficiency virus type 1 (HIV-1) establishes a persistent infection characterized by progressive depletion of CD4⁺ lymphocytes and immunosuppression. Although extensive research has examined the importance of apoptosis as a cause of cell death associated with HIV-1 infection, the role of autophagy has been largely ignored. Our laboratory has examined the autophagic process in HIV-1-infected cells. Following infection of human peripheral blood CD4+ T-cells or U937 cells with HIV-1 for 48 hours, the autophagy proteins Beclin 1 and LC3-II were found to be markedly decreased. Beclin 1 mRNA expression and autophagosomes were also reduced in HIV-1 infected cells. Thus, our data indicate that HIV-1 infection inhibits autophagy in infected cells in contrast to the previously described induction of autophagy by gp120 in uninfected bystander cells. It is likely that HIV-1 has evolved this mechanism as part of an elaborate attempt to evade the immune system while promoting its own replication. We believe that autophagy is an overlooked mechanism in HIV-1 pathogenesis and plays a particularly important role in the early cognitive impairment and dementia often associated with advanced AIDS. A model is presented that describes the potential role of autophagy in NeuroAIDS.

Addendum to: Zhou D, Spector SA. Human immunodeficiency virus type-1 infection inhibits autophagy. Aids 2008;22:695-9.     

Tallow and the time capsule: Claude Bernard's discovery of the pancreatic digestion of fat

In 1848, Claude Bernard discovered that pancreatic secretion could emulsify and saponify fatty substances. He would eventually attribute these reactions to an enzyme that was later named 'pancreatic lipase'. This essay has three goals: 1) to examine Bernard's previously overlooked research on the pancreas; 2) to explore the equally ignored history of lipid digestion and metabolism; 3) to reconstruct Bernard's discovery of pancreatic lipase through a parallel analysis of his laboratory notebooks and his publications. This method reveals a discrepancy between the sequence and motivation of events as they were reported by Bernard in his publications and as they appear in his laboratory notebooks.     

Effects of extreme,fluctuating temperature events on life history traits of the grain aphid,Sitobion avenae

Altered temperatures affect insects’ life history traits, such as development period and fecundity, which ultimately determine population growth rates. Understanding insects’ thermal biology is therefore integral to population forecasting and pest management decision‐making such as when to utilise crop spraying or biological control. Aphids are important crop pests in temperate regions, causing considerable yield losses. The aphid thermal‐biology literature is, however, heavily biased towards the effects of rising mean temperatures, whereas the effects of fluctuating, extreme climatic events (e.g., heat waves and sub‐zero cold periods) are largely overlooked. This study assessed the effects of laboratory‐simulated heat waves and sub‐zero cold periods on the survival, development period, and fecundity of the grain aphid, Sitobion avenae (Fabricius) (Hemiptera: Aphididae: Microsiphini), in addition to assessing maternal effects on the birth weight and development period of the offspring of exposed individuals. Exposure to heat stress periods (total of 16 h at 30 °C) significantly reduced aphid fecundity and increased physiological development period (in day‐degrees) resulting in a reduced population growth rate. Cold exposure (total of 1.33 h at ?15 °C) reduced population growth rate due to an elongated development period (in days), but did not affect fecundity or physiological development period (in day‐degrees). Both cold and heat stress significantly reduced aphid survival. Maternal experience of heat stress reduced nymphal birth weight although nymphal development period was not affected by either cold or heat stress. The results suggest that including the effects of fluctuating, extreme temperature events on aphid life history in population forecast models is likely to be of great importance to pest management decision‐making. The demonstration of maternal effects on birth weight also suggests that cross‐generational effects of heat waves on population growth rates could occur.     

Laboratory Diagnosis and Characterization of Fungal Disease in Patients with Cystic Fibrosis (CF): A Survey of Current UK Practice in a Cohort of Clinical Microbiology Laboratories

There is much uncertainty as to how fungal disease is diagnosed and characterized in patients with cystic fibrosis (CF). A 19-question anonymous electronic questionnaire was developed and distributed to ascertain current practice in clinical microbiology laboratories providing a fungal laboratory service to CF centres in the UK. Analyses of responses identified the following: (1) current UK laboratory practice, in general, follows the current guidelines, but the scope and diversity of what is currently being delivered by laboratories far exceeds what is detailed in the guidelines; (2) there is a lack of standardization of fungal tests amongst laboratories, outside of the current guidelines; (3) both the UK CF Trust Laboratory Standards for Processing Microbiological Samples from People with Cystic Fibrosis and the US Cumulative Techniques and Procedures in Clinical Microbiology (Cumitech) Guidelines 43 Cystic Fibrosis Microbiology need to be updated to reflect both new methodological innovations, as well as better knowledge of fungal disease pathophysiology in CF; (4) there is a need for clinical medicine to decide upon a stratification strategy for the provision of new fungal assays that will add value to the physician in the optimal management of CF patients; (5) there is also a need to rationale what assays should be performed at local laboratory level and those which are best served at National Mycology Reference Laboratory level; and (6) further research is required in developing laboratory assays, which will help ascertain the clinical importance of ‘old’ fungal pathogens, as well as ‘emerging’ fungal pathogens.     

Ephemeral Sexual Dichromatism in Zebrafish (Danio rerio)

Secondary sexual displays may be overlooked in many species, especially when they are ephemerally expressed or imperceptible to human senses. Zebrafish (Danio rerio), like many schooling fish, do not appear sexually dichromatic, but previous anecdotal observations indicate that sexual colouration is expressed briefly during courtship (ephemeral nuptial colouration). Our goals were to compare colour estimates of male vs. female zebrafish using digital photography in situ, computer software and human observations. We found that both sexes changed their colour estimates during spawning (dark and light stripes) and that some sex differences (light stripes) were larger or only became apparent during this time. We also found that individual males that appeared more colourful and conspicuous to the human eye engaged in courtship more often than less conspicuous males. We detected differences in the colour estimates between wild‐derived vs. a laboratory strain of zebrafish and reduced individual variation in the laboratory strain. This is the first study to systematically and objectively quantify body colour in zebrafish by utilizing colour estimates, although further studies are needed to determine the underlying mechanisms and signalling functions of this sexual dichromatism.     

L-Glutamate production by lysozyme-sensitive Corynebacterium glutamicum ltsA mutant strains

Background  

Infections of bacterial cultures by bacteriophages are serious problems in biotechnological laboratories. Apart from such infections, prophage induction in the host cells may also be dangerous. Escherichia coli is a commonly used host in biotechnological production, and many laboratory strains of this bacterium harbour lambdoid prophages. These prophages may be induced under certain conditions leading to phage lytic development. This is fatal for further cultivations as relatively low, though still significant, numbers of phages may be overlooked. Thus, subsequent cultures of non-lysogenic strains may be infected and destroyed by such phage.     

Autophagy: an overlooked mechanism of HIV-1 pathogenesis and neuroAIDS?

Human immunodeficiency virus type 1 (HIV-1) establishes a persistent infection characterized by progressive depletion of CD4(+) lymphocytes and immunosuppression. Although extensive research has examined the importance of apoptosis as a cause of cell death associated with HIV-1 infection, the role of autophagy has been largely ignored. Our laboratory has examined the autophagic process in HIV-1-infected cells. Following infection of human peripheral blood CD4(+) T-cells or U937 cells with HIV-1 for 48 hours, the autophagy proteins Beclin 1 and LC3-II were found to be markedly decreased. Beclin 1 mRNA expression and autophagosomes were also reduced in HIV-1 infected cells. Thus, our data indicate that HIV-1 infection inhibits autophagy in infected cells in contrast to the previously described induction of autophagy by gp120 in uninfected bystander cells. It is likely that HIV-1 has evolved this mechanism as part of an elaborate attempt to evade the immune system while promoting its own replication. We believe that autophagy is an overlooked mechanism in HIV-1 pathogenesis and plays a particularly important role in the early cognitive impairment and dementia often associated with advanced AIDS. A model is presented that describes the potential role of autophagy in NeuroAIDS.     

Isolation and genetic characterization of a relapsing fever spirochete isolated from Ornithodoros puertoricensis collected in central Panama

Tick-borne relapsing fever (TBRF) spirochetes are likely an overlooked cause of disease in Latin America. In Panama, the pathogens were first reported to cause human disease in the early 1900s. Recent collections of Ornithodoros puertoricensis from human dwellings in Panama prompted our interest to determine whether spirochetes still circulate in the country. Ornithodoros puertoricensis ticks were collected at field sites around the City of Panama. In the laboratory, the ticks were determined to be infected with TBRF spirochetes by transmission to mice, and we report the laboratory isolation and genetic characterization of a species of TBRF spirochete from Panama. Since this was the first isolation of a species of TBRF spirochete from Central America, we propose to designate the bacteria as Borrelia puertoricensis sp. nov. This is consistent with TBRF spirochete species nomenclature from North America that are designated after their tick vector. These findings warrant further investigations to assess the threat B. puertoricensis sp. nov. may impose on human health.     

Stabilization provided by neighboring strands is critical for the mechanical stability of proteins

Single-molecule force spectroscopy studies and steered molecular dynamics simulations have revealed that protein topology and pulling geometry play important roles in determining the mechanical stability of proteins. Most studies have focused on local interactions that are associated with the force-bearing β-strands. Interactions mediated by neighboring strands are often overlooked. Here we use Top7 and barstar as model systems to illustrate the critical importance of the stabilization effect provided by neighboring β-strands on the mechanical stability. Using single-molecule atomic force microscopy, we showed that Top7 and barstar, which have similar topology in their force-bearing region, exhibit vastly different mechanical-stability characteristics. Top7 is mechanically stable and unfolds at ∼150 pN, whereas barstar is mechanically labile and unfolds largely below 50 pN. Steered molecular dynamics simulations revealed that stretching force peels one force-bearing strand away from barstar to trigger unfolding, whereas Top7 unfolds via a substructure-sliding mechanism. This previously overlooked stabilization effect from neighboring β-strands is likely to be a general mechanism in protein mechanics and can serve as a guideline for the de novo design of proteins with significant mechanical stability and novel protein topology.     

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

In contrast to common meiotic gene conversion, mitotic gene conversion, because it is so rare, is often ignored as a process influencing allelic diversity. We show that if there is a large enough number of premeiotic cell divisions, as seen in many organisms without early germline sequestration, such as plants, this is an unsafe position. From examination of 1.1 million rice plants, we determined that the rate of mitotic gene conversion events, per mitosis, is 2 orders of magnitude lower than the meiotic rate. However, owing to the large number of mitoses between zygote and gamete and because of long mitotic tract lengths, meiotic and mitotic gene conversion can be of approximately equivalent importance in terms of numbers of markers converted from zygote to gamete. This holds even if we assume a low number of premeiotic cell divisions (approximately 40) as witnessed in Arabidopsis. A low mitotic rate associated with long tracts is also seen in yeast, suggesting generality of results. For species with many mitoses between each meiotic event, mitotic gene conversion should not be overlooked.

Gene conversion associated with meiosis has long been a focus of attention in population genomics, but mitotic conversion has been relatively overlooked as it was thought to be rare. Analysis in plants suggests that this could be a mistake; long tract lengths and multiple mitoses in species lacking germline sequestration suggest that mitotic conversion, although rare per mitosis, should not be ignored.     

Primary Isolation Of Mycobacterium chelonei Subspecies abscessus from Pus Inoculated into Peptone Broth

We have described the isolation of Mycobacterium chelonei subspecies abscessus which on two occasions grew out within 4 days in routine cultures after inoculation with purulent material from injection abscesses in a patient with diabetes mellitus. Media isolation and culture characteristics of this organism in comparison to others in the Mycobacterium fortuitum complex are described. Mycobacteria in routine laboratory media can be mistaken for diphtheroids or other "contaminants" or can be overlooked entirely. The possibility of clinical infection of mycobacterial species should be kept in mind when confronted with "sterile" abscesses at injection sites.