Informative and misinformative interactions in a school of fish

Quantifying distributed information processing is crucial to understanding collective motion in animal groups. Recent studies have begun to apply rigorous methods based on information theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e., U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) from fish that have already turned to fish that are turning, and a misinformative flow (negative transfer entropy) from fish that have not turned yet to fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general.     

An outbreak of adenovirus type 7 infection in children in Montreal

Thirteen infants and children with adenovirus type 7 infection proved by virus isolation are described. High fever, cough and dyspnea were the most frequent findings; in infants under 1 year of age wheezing was common. Four patients required artificial ventilation. Lobar collapse, consolidation and hyperinflation were frequent radiologic findings. None of the symptoms responded to antibiotic therapy or bronchodilator drugs. Three patients died (mortality rate of 23%). Pathologic findings were compatible with adenovirus type 7 pneumonia, and were characterized by a necrotizing bronchitis and bronchiolitis, patchy alveolar fibrinopurulent exudate and hyaline membrane formation. Some intra-alveolar epithelial cells showed strikingly abnormal nuclei and rare typical halo-outlined intranuclear inclusions were seen. Only one of eight survivors had evidence of significant chronic chest disease.     

Proliferative capacity and DNA content of aging human diploid cells in culture: A cytophotometric and autoradiographic analysis

Using a combination of DNA-cytophotometry and tritiated thymidine-autoradiography, we have shown that the majority of nondividing cells in serially propagated human diploid cell populations have the 2C DNA content consistent with their being arrested in the G₁ phase of the diploid cell cycle. Unlabeled 4C cells appear increasingly with time in culture. These may be arrested G₂ diploids or they may be G₁ tetraploids, since there is an associated increase in polyploidy in older cultures as evidenced by the appearance of labeled 8C cells.     

“Stepping-sticks” and “seat-sticks”: New types of tools used by wild chimpanzees (Pan troglodytes) in Sierra Leone

In Tenkere, Sierra Leone, a community of wild chimpanzees (Pan troglodytes verus) spent long hours eating the fruits and flowers of the Kapok (Ceiba pentandra) tree. The branches of this species are covered in sharp thorns which make movement in their high canopies problematic for the chimpanzees. In an apparent attempt to increase their mobility and to ease the discomfort of lengthy bouts of eating in these trees, some of the Tenkere chimpanzees have been observed using stick tools as foot (“stepping-sticks”) and body (“seat-sticks”) protection against the painful thorns. This form of tool-using is culturally unique to the Tenkere chimpanzees, as at other sites where these apes have been observed eating parts of kapok trees, there are no published records of this tool technology. In three of the stepping-stick tool use incidents, the chimpanzee used the tool(s), held between their greater and lesser toes, in locomotion. This form of tool use is the first recorded case of habitually used tools that can be justifiably categorized as being “worn” by any known wild population of Pan troglodytes. Am J Primatol 41:45–52, 1997. © 1997 Wiley-Liss, Inc.     

Detecting invertebrate species in archived collections using next‐generation sequencing

Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next‐generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill ‘gaps’ in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.     

Neuroscience, evolution and the sapient paradox: the factuality of value and of the sacred

The human genome, and hence the human brain at birth, may not have changed greatly over the past 60000 years. Yet many of the major behavioural changes that we associate with most human societies are very much more recent, some appearing with the sedentary revolution of some 10000 years ago. Among these are activities implying the emergence of powerful concepts of value and of the sacred. What then are the neuronal mechanisms that may underlie these consistent, significant (and emergent) patterns of behaviour?     

Olfactory Behavioral Testing in the Adult Mouse

The rodent olfactory system is of increasing interest to scientists, studied, in part, in systems biology because of its stereotyped, yet accessible circuitry. In addition, this area''s unique ability to generate new neurons throughout an organism''s lifetime makes it an attractive system for developmental and regenerative biologists alike. Such interest necessitates a means for a quick, yet reliable assessment of olfactory function. Many tests of olfactory ability are complex, variable or not specifically designed for mice. Also, some tests are sensitive to memory deficits as well as defects in olfactory abilities, confounding obtained results.Here, we describe a simple battery of tests designed to identify defects in olfactory sensitivity and preference. First, an initial general health assessment allows for the identification of animals suitable for further testing. Second, mice are exposed to various dilutions of scents to ascertain whether there is a threshold difference. Third, mice are presented with various scents, both attractive and aversive, that allow for the assessment of olfactory preference. These simple studies should make the initial characterization of olfactory behavior accessible for labs of varied resources and expertise.Download video file.^{(52M, flv)}     

Molecular diversity and catalytic activity of Thermus DNA polymerases

Thermus aquaticus DNA polymerase (Taq polymerase) made the polymerase chain reaction feasible and led to a paradigm shift in genomic analysis. Other Thermus polymerases were reported to have comparable performance in PCR and there was an analysis of their properties in the 1990s. We re-evaluated our earlier phylogeny of Thermus species on the basis of 16S rDNA sequences and concluded that the genus could be divided into eight clades. We examined 22 representative isolates and isolated their DNA polymerase I genes. The eight most diverse polymerase genes were selected to represent the eight clades and cloned into an expression vector coding for a His-tag. Six of the eight polymerases were expressed so that there was sufficient protein for purification. The proteins were purified to homogeneity and examination of the biochemical characteristics showed that although they were competent to perform PCR, none was as thermostable as commercially available Taq polymerase; all had similar error-frequencies to Taq polymerase and all showed the expected 5′–3′ exonuclease activity. We conclude that the initial selection of T. aquaticus for DNA polymerase purification was a far-reaching and fortuitous choice but simple mutagenesis procedures on other Thermus-derived polymerases should provide comparable thermostability for the PCR reaction.     

Oligo(N-alkoxy glycines): trans substantiating peptoid conformations

Peptoid oligomers possess many desirable attributes bioactive peptidomimetic agents, including their ease of synthesis, chemical diversity, and capability for molecular recognition. Ongoing efforts to develop functional peptoids will necessitate improved capability for control of peptoid structure, particularly of the backbone amide conformation. We introduce alkoxyamines as a new reagent for solid phase peptoid synthesis. Herein, we describe the synthesis of N-alkoxy peptoids, and present NMR data indicating that the oligomers adopt a single stable conformation featuring trans amide bonds. These findings, combined with results from computational modeling, suggest that N-alkoxy peptoid oligomers have a strong propensity to adopt a polyproline II type secondary structure.