Some personal and historical notes on the utility of “deep-etch” electron microscopy for making cell structure/function correlations

This brief essay talks up the advantages of metal replicas for electron microscopy and explains why they are still the best way to image frozen cells in the electron microscope. Then it explains our approach to freezing, namely the Van Harreveld trick of “slamming” living cells onto a supercold block of metal sprayed with liquid helium at −269ºC, and further talks up this slamming over the alternative of high-pressure freezing, which is much trickier but enjoys greater favor at the moment. This leads me to bemoan the fact that there are not more young investigators today who want to get their hands on electron microscopes and use our approach to get the most “true to life” views of cells out of them with a minimum of hassle. Finally, it ends with a few perspectives on my own career and concludes that, personally, I''m permanently stuck with the view of the “founding fathers” that cell ultrastructure will ultimately display and explain all of cell function, or as Palade said in his Nobel lecture,electron micrographs are “irresistible and half transparent … their meaning buried under only a few years of work,” and “reasonable working hypotheses are already suggested by the ultrastructural organization itself.”     

Diversity of “Candidatus Liberibacter asiaticus,” Based on the omp Gene Sequence

Huanglongbing (yellow dragon disease) is a destructive disease of citrus. The etiological agent is a noncultured, phloem-restricted alpha-proteobacterium, “Candidatus Liberibacter africanus” in Africa and “Candidatus Liberibacter asiaticus” in Asia. In this study, we used an omp-based PCR-restriction fragment length polymorphism (RFLP) approach to analyze the genetic variability of “Ca. Liberibacter asiaticus” isolates. By using five different enzymes, each the 10 isolates tested could be associated with a specific combination of restriction profiles. The results indicate that the species “Ca. Liberibacter asiaticus,” even within a given region, may comprise several different variants. Thus, omp-based PCR-RFLP analysis is a simple method for detecting and differentiating “Ca. Liberibacter asiaticus” isolates.     

“Candidatus Accumulibacter” Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes

We investigated the fine-scale population structure of the “Candidatus Accumulibacter” lineage in enhanced biological phosphorus removal (EBPR) systems using the polyphosphate kinase 1 gene (ppk1) as a genetic marker. We retrieved fragments of “Candidatus Accumulibacter” 16S rRNA and ppk1 genes from one laboratory-scale and several full-scale EBPR systems. Phylogenies reconstructed using 16S rRNA genes and ppk1 were largely congruent, with ppk1 granting higher phylogenetic resolution and clearer tree topology and thus serving as a better genetic marker than 16S rRNA for revealing population structure within the “Candidatus Accumulibacter” lineage. Sequences from at least five clades of “Candidatus Accumulibacter” were recovered by ppk1-targeted PCR, and subsequently, specific primer sets were designed to target the ppk1 gene for each clade. Quantitative real-time PCR (qPCR) assays using “Candidatus Accumulibacter”-specific 16S rRNA and “Candidatus Accumulibacter” clade-specific ppk1 primers were developed and conducted on three laboratory-scale and nine full-scale EBPR samples and two full-scale non-EBPR samples to determine the abundance of the total “Candidatus Accumulibacter” lineage and the relative distributions and abundances of the five “Candidatus Accumulibacter” clades. The qPCR-based estimation of the total “Candidatus Accumulibacter” fraction as a proportion of the bacterial community as measured using 16S rRNA genes was not significantly different from the estimation measured using ppk1, demonstrating the power of ppk1 as a genetic marker for detection of all currently defined “Candidatus Accumulibacter” clades. The relative distributions of “Candidatus Accumulibacter” clades varied among different EBPR systems and also temporally within a system. Our results suggest that the “Candidatus Accumulibacter” lineage is more diverse than previously realized and that different clades within the lineage are ecologically distinct.     

Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats

This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped “pink” (8.0%) or “pink neck” (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary “pink” and “pink neck” phenotype, estimated from 103,443 females was 0.26 for “pink” and 0.21 for “pink neck”. Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the “pink neck” phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the “pink” phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the “pink” and “pink neck” phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.     

Basis for Cumulative Cultural Evolution in Chimpanzees: Social Learning of a More Efficient Tool-Use Technique

Background

The evidence for culture in non-human animals has been growing incrementally over the past two decades. However, the ability for cumulative cultural evolution, with successive generations building on earlier achievements, in non-human animals remains debated. Faithful social learning of incremental improvements in technique is considered to be a defining feature of human culture, differentiating human from non-human cultures. This study presents the first experimental evidence for chimpanzees'' social transmission of a more efficient tool-use technique invented by a conspecific group member.

Methodology/Principal Findings

The chimpanzees were provided with a straw-tube, and spontaneously demonstrated two different techniques in obtaining juice through a small hole: “dipping” and “straw-sucking”. Both the “dipping” and “straw-sucking” techniques depended on the use of the same tool (straw-tube) for the same target (juice) accessible from exactly the same location (small hole 1 cm in diameter). Therefore the difference between “dipping” and “straw-sucking” was only in “technique”. Although the two techniques differed significantly in their efficiency, their cognitive and perceptuo-motor complexity were comparable. All five chimpanzees who initially performed the “dipping” technique switched to using the more efficient “straw-sucking” technique upon observing a conspecific or human demonstrate the more proficient alternate “straw-sucking” technique.

Conclusions/Significance

The social learning mechanism involved here was clearly not local or stimulus enhancement, but imitation or emulation of a tool-use technique. When there is no biologically relevant difference in cognitive or perceptuo-motor complexity between two techniques, and when chimpanzees are dissatisfied with their own technique, chimpanzees may socially learn an improved technique upon close observation of a proficient demonstrator. This study provides important insights into the cognitive basis for cumulative culture in chimpanzees, and also suggests possible conditions in which cumulative cultural evolution could arise even in non-human animals.     

Nitrous Oxide Inhalation as a Fad—Dangers in Uncontrolled Sniffing for Psychedelic Effect

“LAUGHING GAS is the newest thing for kids seeking kicks,” the Stanford Daily reports. “They sniff it.”So begins a news story in the Los Angeles Times of 26 January 1967. The story continues:“It''s the latest way to travel, or so say a growing group of devotees on the campus,” the university student paper said. “It can produce much the same effects as psychedelic drugs, they claim, and it''s cheaper to obtain.”“One student said he buys the gas, nitrous oxide, from a medical supply house. `They think I am anesthetizing rats,'' he explained.“Campus medical authorities said the gas, sniffed `in sufficient amounts... could produce all the states of anesthesia, including the final stage—death.''”     

Commentary: Personal Renewal

After John Gardner''s presentation on “Self-Renewal” to THE WESTERN JOURNAL OF MEDICINE Editors'' Meeting, ^* Joseph Murphy, MD, Special Editor for Wyoming, asked the former Secretary of Health, Education, and Welfare, “Where are you in your life''s cycle?” Dr Gardner, who is 80 years old, answered, “When Chief Justice Oliver Wendell Holmes, Jr, was in his 90s, he was asked a similar question and said, `I''m like a race horse cantering along after the race is over, cooling down.'' Well, I''m nowhere near cantering! I''m still in the race, pushing the world.” race, pushing the world.”John Gardner, who received his undergraduate degree from Stanford and PhD from the University of California, Berkeley, taught at the college level for several years before he joined the Carnegie Foundation. As president of Carnegie Corporation and Carnegie Foundation for the Advancement of Teaching, he began to “push the world” toward education and in 1964 received the country''s highest civilian honor, the Presidential Medal of Freedom. He has also pushed it toward political reform by founding Common Cause, toward grass-roots political action by founding the Urban Coalition, toward leadership training by founding the White House Fellows program, and toward volunteerism by founding the Independent Sector (a coalition of for-profit and not-for-profit organizations and foundations). His books, including Excellence, Self-Renewal, No Easy Victories, and On Leadership, have pushed readers to new understanding of themselves and of organizations to higher levels of creativity and energy to get important work done. His current research focuses on discovering and defining the characteristics of healthy, vital communities. His call to “keep on keeping on,” indeed, to push the world, leads to constructive change. Active people become effective people, infused with the energy and optimism that good hard work inspires. I think you will find this paper as invigorating to read as it was to hear.     

The Novel New Jersey Eyewitness Instruction Induces Skepticism but Not Sensitivity

In recent decades, social scientists have shown that the reliability of eyewitness identifications is much worse than laypersons tend to believe. Although courts have only recently begun to react to this evidence, the New Jersey judiciary has reformed its jury instructions to notify jurors about the frailties of human memory, the potential for lineup administrators to nudge witnesses towards suspects that they police have already identified, and the advantages of alternative lineup procedures, including blinding of the administrator. This experiment tested the efficacy of New Jersey’s jury instruction. In a 2×2 between-subjects design, mock jurors (N = 335) watched a 35-minute murder trial, wherein identification quality was either “weak” or “strong” and either the New Jersey or a “standard” instruction was delivered. Jurors were more than twice as likely to convict when the standard instruction was used (OR = 2.55; 95% CI = 1.37–4.89, p < 0.001). The New Jersey instruction, however, did not improve juror''s ability to discern quality; rather, jurors receiving those instructions indiscriminatingly discounted “weak” and “strong” testimony in equal measure.     

X-Ray Solution Scattering of Squid Heavy Meromyosin: Strengthening the Evidence for an Ancient Compact off State

The overall conformations of regulated myosins or heavy meromyosins from chicken/turkey, scallop, tarantula, limulus, and scorpion sources have been studied by a number of techniques, including electron microscopy, sedimentation, and pulsed electron paramagnetic resonance. These studies have indicated that the binding of regulatory ions changes the conformation of the molecule from a compact shape found in the “off” state of the muscle to extended relationships between the tail and independently mobile heads that predominate in the “on” state. Here we strengthen the argument for the generality of this conformational change by using small angle X-ray scattering on heavy meromyosin from squid. Small angle X-ray scattering allows the protein to be visualized in solution under mild and relatively physiological conditions, and squid differs from the other species studied by at least 500 million years of evolution. Analysis of the data indicates that upon addition of Ca²⁺ the radius of gyration increases. Differences in the squid “on” and “off” states are clearly distinguishable as bimodal and unimodal pair distance distribution functions respectively. These observations are consistent with a Ca²⁺-free squid heavy meromyosin that is compact, but which becomes extended when Ca²⁺ is bound. Further, the scattering profile derived from the current model of tarantula heavy meromyosin in the “off” state is in excellent agreement with the measured “off” state scattering profile for squid heavy meromyosin. The previous and current studies together provide significant evidence that regulated myosin''s compact off-state conformation is an ancient trait, inherited from a common ancestor during divergent evolution.     

Health Hazard Appraisal Counseling—Continuing Evaluation

A program of annual health examinations was expanded to include counseling based on a computerized appraisal of individual patients'' specific health risk factors. Data obtained from a specially designed questionnaire, laboratory tests and a physical examination yielded a health hazard appraisal showing a number of weighted risk factors and their relation to ten leading causes of death as determined for that patient. From all of this information, a “risk age” was developed which could then be compared with the patient''s “true age.” The results were reviewed with each patient, and methods of correcting health hazards were stressed. The first annual retesting of a group of 107 examinees showed a net risk age reduction of 1.4 years (formerly reported in this journal). The longer term follow-up reported in this paper showed a net risk reduction of 2.38 years in a group of 26 examinees. The net risk age reduction in the two groups represented 32 and 40 percent, respectively, of the achievable risk age reduction when patients comply with suggestions made during risk reduction counseling. These findings indicate that health hazard appraisal counseling is an effective method of altering priorities of health practices.     

Foetal Blood Sampling. Practical Approach to Management of Foetal Distress

The practical application of foetal blood sampling in the routine management of patients in labour has been reviewed in a six-month survey, during which time 1,668 patients were delivered at Queen Charlotte''s Hospital.Foetal acidaemia (pH 7·25 or less) occurred in 45 of the 295 patients who showed clinical signs of foetal distress. Foetal tachycardia was the presenting sign in 33 of these 45 patients, underlining the importance of this physical sign. Foetal acidaemia in association with clinical foetal distress occurred twice as often in patients who had complications of pregnancy and who were therefore regarded as obstetrically “at risk” as it did in patients who were obstetrically “normal” No cases of acidaemia were detected in any of the foetal blood samples performed routinely on “at-risk” patients in the absence of clinical foetal distress.     

Characterization of Chlorinated Aliphatic Hydrocarbons and Environmental Variables in a Shallow Groundwater in Shanghai Using Kriging Interpolation and Multifactorial Analysis

CAHs, as a cleaning solvent, widely contaminated shallow groundwater with the development of manufacturing in China''s Yangtze River Delta. This study focused on the distribution of CAHs, and correlations between CAHs and environmental variables in a shallow groundwater in Shanghai, using kriging interpolation and multifactorial analysis. The results showed that the overall CAHs plume area (above DIV) was approximately 9,000 m² and located in the 2–4 m underground, DNAPL was accumulated at an area of approximately 1,400 m² and located in the 6-8m sandy silt layer on the top of the muddy silty clay. Heatmap of PPC for CAHs and environmental variables showed that the correlation between “Fe²⁺” and most CAHs such as “1,1,1-TCA”, “1,1-DCA”, “1,1-DCE” and “%TCA” were significantly positive (p<0.001), but “%CA” and/or “%VC” was not, and “Cl^-” was significantly positive correlated with “1,1-DCA” and “1,1-DCE” (p<0.001). The PCA demonstrated that the relative proportions of CAHs in groundwater were mostly controlled by the sources and the natural attenuation. In conclusion, the combination of geographical and chemometrics was helpful to establishing an aerial perspective of CAHs and identifying reasons for the accumulation of toxic dechlorination intermediates, and could become a useful tool for characterizing contaminated sites in general.     

CANCER DETECTION CENTERS—The Experience to Date in California

Cancer “detection centers” (that is, centers for the examination of presumably well or asymptomatic persons) have been tried out in four different California communities during the last three years. In all instances—as in most other such centers throughout the United States—they have not been successful in restricting examination to well persons.The detection centers in California may therefore be described more accurately as “cancer examination and detection clinics.”Three of the four centers have been closed owing to the small yield of cancer cases discovered, plus the fact that the cost of operation exceeded the total available funds of the local branch of the Cancer Society. In addition, it was extremely difficult to obtain and maintain competence on the part of the professional staff in such centers.A more practical approach to the problem of earlier tumor detection would appear to be emphasis on making “every physician''s office a detection center,” and stressing the annual examination of persons over 40 years of age for tumors in the five common accessible sites. These are the tumors most readily curable today.     

Determining the Variability of Lesion Size Measurements from CT Patient Data Sets Acquired under “No Change” Conditions

PURPOSE: To determine the variability of lesion size measurements in computed tomography data sets of patients imaged under a “no change” (“coffee break”) condition and to determine the impact of two reading paradigms on measurement variability. METHOD AND MATERIALS: Using data sets from 32 non-small cell lung cancer patients scanned twice within 15 minutes (“no change”), measurements were performed by five radiologists in two phases: (1) independent reading of each computed tomography dataset (timepoint): (2) a locked, sequential reading of datasets. Readers performed measurements using several sizing methods, including one-dimensional (1D) longest in-slice dimension and 3D semi-automated segmented volume. Change in size was estimated by comparing measurements performed on both timepoints for the same lesion, for each reader and each measurement method. For each reading paradigm, results were pooled across lesions, across readers, and across both readers and lesions, for each measurement method. RESULTS: The mean percent difference (± SD) when pooled across both readers and lesions for 1D and 3D measurements extracted from contours was 2.8 ± 22.2% and 23.4 ± 105.0%, respectively, for the independent reads. For the locked, sequential reads, the mean percent differences (± SD) reduced to 2.52 ± 14.2% and 7.4 ± 44.2% for the 1D and 3D measurements, respectively. CONCLUSION: Even under a “no change” condition between scans, there is variation in lesion size measurements due to repeat scans and variations in reader, lesion, and measurement method. This variation is reduced when using a locked, sequential reading paradigm compared to an independent reading paradigm.     

A Novel Attempt to Standardize Results of CFD Simulations Basing on Spatial Configuration of Aortic Stent-Grafts

Currently, studies connected with Computational Fluid Dynamic (CFD) techniques focus on assessing hemodynamic of blood flow in vessels in different conditions e.g. after stent-graft’s placement. The paper propose a novel method of standardization of results obtained from calculations of stent-grafts'' “pushing forces” (cumulative WSS—Wall Shear Stress), and describes its usefulness in diagnostic process. AngioCT data from 27 patients were used to reconstruct 3D geometries of stent-grafts which next were used to create respective reference cylinders. We made an assumption that both the side surface and the height of a stent-graft and a reference cylinder were equal. The proposed algorithm in conjunction with a stent-graft “pushing forces” on an implant wall, allowed us to determine which spatial configuration of a stent-graft predispose to the higher risk of its migration. For stent-grafts close to cylindrical shape (shape factor φ close to 1) WSS value was about 267Pa, while for stent-grafts different from cylindrical shape (φ close to 2) WSS value was about 635Pa. It was also noticed that deformation in the stent-graft’s bifurcation part impaired blood flow hemodynamic. Concluding the proposed algorithm of standardization proved its usefulness in estimating the WSS values that may be useful in diagnostic process. Angular bends or tortuosity in bifurcations of an aortic implant should be considered in further studies of estimation of the risk of implantation failure.     

Plant intelligence: Why,why not or where?

The concept of plant intelligence, as proposed by Anthony Trewavas, has raised considerable discussion. However, plant intelligence remains loosely defined; often it is either perceived as practically synonymous to Darwinian fitness, or reduced to a mere decorative metaphor. A more strict view can be taken, emphasizing necessary prerequisites such as memory and learning, which requires clarifying the definition of memory itself. To qualify as memories, traces of past events have to be not only stored, but also actively accessed. We propose a criterion for eliminating false candidates of possible plant intelligence phenomena in this stricter sense: an “intelligent” behavior must involve a component that can be approximated by a plausible algorithmic model involving recourse to stored information about past states of the individual or its environment. Re-evaluation of previously presented examples of plant intelligence shows that only some of them pass our test.

“You were hurt?” Kumiko said, looking at the scar.Sally looked down. “Yeah.”“Why didn''t you have it removed?”“Sometimes it''s good to remember.”“Being hurt?”“Being stupid.”—(W. Gibson: Mona Lisa Overdrive)

Key words: intelligence, memory, learning, plant development, mathematical models, plant neurobiology, definition of terms     

Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating,Iron-Oxidizing,Acidophilic Bacterium “Ferrovum myxofaciens”

A betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of “acid streamer” growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified “overlay” solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine (“Ferrovum myxofaciens” strain P3G) have been elucidated. “F. myxofaciens” is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO₂ and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growth in vitro) and to different solid surfaces. “F. myxofaciens” can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. “F. myxofaciens” and related clone sequences form a monophyletic group within the Betaproteobacteria distantly related to classified orders, with genera of the family Nitrosomonadaceae (lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of “F. myxofaciens” and other Betaproteobacteria, a new family, “Ferrovaceae,” and order, “Ferrovales,” within the class Betaproteobacteria are proposed. “F. myxofaciens” is the first extreme acidophile to be described in the class Betaproteobacteria.     

Cloning of the spoT Gene of “Candidatus Phlomobacter fragariae” and Development of a PCR-Restriction Fragment Length Polymorphism Assay for Detection of the Bacterium in Insects

Marginal chlorosis is a new disease of strawberry in which the uncultured phloem-restricted proteobacterium “Candidatus Phlomobacter fragariae” is involved. In order to identify the insect(s) vector(s) of this bacterium, homopteran insects have been captured. Because a PCR test based on the 16S rRNA gene (rDNA) applied to these insects was unable to discriminate between “P. fragariae” and other insect-associated proteobacteria, isolation of “P. fragariae” genes other than 16S rDNA was undertaken. Using comparative randomly amplified polymorphic DNAs, an amplicon was specifically amplified from “P. fragariae”-infected strawberry plants. It encodes part of a “P. fragariae” open reading frame sharing appreciable homology with the spoT gene from other proteobacteria. A spoT-based PCR test combined with restriction fragment length polymorphisms was developed and was able to distinguish “P. fragariae” from other insect bacteria. None of the many leafhoppers and psyllids captured during several years in and around infected strawberry fields was found to carry “P. fragariae.” Interestingly however, the “P. fragariae” spoT sequence could be easily detected in whiteflies proliferating on “P. fragariae”-infected strawberry plants under confined greenhouse conditions but not on control whiteflies, indicating that these insects can become infected with the bacterium.     

Intention Understanding in Autism

When we observe a motor act (e.g. grasping a cup) done by another individual, we extract, according to how the motor act is performed and its context, two types of information: the goal (grasping) and the intention underlying it (e.g. grasping for drinking). Here we examined whether children with autistic spectrum disorder (ASD) are able to understand these two aspects of motor acts. Two experiments were carried out. In the first, one group of high-functioning children with ASD and one of typically developing (TD) children were presented with pictures showing hand-object interactions and asked what the individual was doing and why. In half of the “why” trials the observed grip was congruent with the function of the object (“why-use” trials), in the other half it corresponded to the grip typically used to move that object (“why-place” trials). The results showed that children with ASD have no difficulties in reporting the goals of individual motor acts. In contrast they made several errors in the why task with all errors occurring in the “why-place” trials. In the second experiment the same two groups of children saw pictures showing a hand-grip congruent with the object use, but within a context suggesting either the use of the object or its placement into a container. Here children with ASD performed as TD children, correctly indicating the agent''s intention. In conclusion, our data show that understanding others'' intentions can occur in two ways: by relying on motor information derived from the hand-object interaction, and by using functional information derived from the object''s standard use. Children with ASD have no deficit in the second type of understanding, while they have difficulties in understanding others'' intentions when they have to rely exclusively on motor cues.