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Time is a limited resource and how well it is allocated to competing behaviours can profoundly affect Darwinian fitness. Life history theory predicts that the amount of time allocated to vital behaviours will change with life history stage, resulting in trade-offs between competing behaviours. Moreover, a range of environmental factors can also affect activity budgets. We studied diurnal time allocation by migratory plains zebras (Equus quagga) in the Serengeti ecosystem, Tanzania, and investigated the effect of life history stage, social environment, habitat structure, and day time on time allocation to five behavioural categories (grazing, resting, vigilance, movement, other). We expected (1) increased vulnerability to predation and impeded predator detection to increase vigilance and decrease resting and grazing; (2) energetically costly life stages to increase grazing and decrease resting; and (3) increasing age in young to result in increased vigilance and grazing and decreased resting. Our findings revealed that in young zebras, resting decreased and grazing increased from the youngest to the oldest age class. Band stallions spent more time grazing and less time resting and moving than bachelors. Lactating mares devoted more time to grazing but less to resting and vigilance than other mares. Mares spent most time vigilant in the last third and stallions in the first third of the day. Adult zebras moved more, and mares were more vigilant in the woodland boundary than on short grass plains. Taken together, our study identifies intrinsic and extrinsic factors shaping time allocation decisions and trade-offs between competing behaviours in plains zebra.

The new edition of this introductory graduate textbook provides a concise but accessible introduction to the Standard Model. It has been updated to account for the successes of the theory of strong interactions, and the observations on matter-antimatter asymmetry. It has become clear that neutrinos are not mass-less, and this book gives a coherent presentation of the phenomena and the theory that describes them. It includes an account of progress in the theory of strong interactions and of advances in neutrino physics. The book clearly develops the theoretical concepts from the electromagnetic and weak interactions of leptons and quarks to the strong interactions of quarks. Each chapter ends with problems, and hints to selected problems are provided at the end of the book. The mathematical treatments are suitable for graduates in physics, and more sophisticated mathematical ideas are developed in the text and appendices.

Knut the polar bear of the Berlin Zoological Garden drowned in 2011 following seizures and was diagnosed as having suffered encephalitis of unknown etiology after exhaustive pathogen screening. Using the diagnostic criteria applied to human patients, we demonstrate that Knut’s encephalitis is almost identical to anti-NMDA receptor encephalitis which is a severe autoimmune disease representing the most common non-infectious encephalitis in humans. High concentrations of antibodies specific against the NR1 subunit of the NMDA receptor were detected in Knut’s cerebrospinal fluid. Histological examination demonstrated very similar patterns of plasma cell infiltration and minimal neuronal loss in affected brain areas. We conclude that Knut suffered anti-NMDA receptor encephalitis making his the first reported non-human case of this treatable disease. The results suggest that anti-NMDA receptor encephalitis may be a disease of broad relevance to mammals that until now has remained undiagnosed.

We report the retrieval and characterization of multi- and single-copy nuclear DNA sequences from Alaskan and Siberian mammoths (Mammuthus primigenius). In addition, a nuclear copy of a mitochondrial gene was recovered. Furthermore, a 13,000-year-old ground sloth and a 33,000-year-old cave bear yielded multicopy nuclear DNA sequences. Thus, multicopy and single-copy genes can be analyzed from Pleistocene faunal remains. The results also show that under some circumstances, nucleotide sequence differences between alleles found within one individual can be distinguished from DNA sequence variation caused by postmortem DNA damage. The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants.

Non-LTR retrotransposons are a diverse and taxonomically widely dispersed group of retroelements that can be divided into at least 14 distinguishable clades. Basal metazoans have not been examined in great detail for their retrotransposon content. In order to screen for the presence of reverse transcriptase (RT) related sequences in Cnidaria and Ctenophora, basal phyla of metazoans, PCR with highly degenerate oligonucleotides was performed and an RT-like sequence was identified from the sea anemone species Anemonia sulcata. Further screening identified a related element in another anemone species Actinia equina. Significant homology to non-LTR retrotransposon RTs was observed, particularly to L2-like elements of fish such as Maui. The sequence was not detected among other cnidarians and we have designated the A. sulcata and A. equina elements Abyss1 and Abyss2 respectively. Phylogenetic analysis of Abyss1 compared with members of 14 known non-LTR retroelement clades suggests that the sequence represents a novel L2 element.    

Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.

The prion protein (PrP) when misfolded into the pathogenic conformer PrP Sc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene ( PRNP ) and doppel gene ( PRND ) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2.

Caffeine at concentrations between 0.1% and 1% caused the condensation of phenolics inside the vacuoles of phenolic-storing cells prepared for electron microscopy. Caffeine added to the glutaraldehyde and washing buffer during fixation prevented the leaching of the phenolics into the cytoplasm. Phenolic-storing cells so treated had a cytoplasm similar in appearance to that of cells not storing phenolics. In contrast, mature phenolic-storing cells fixed without caffeine had a dense, osmiophilic cytoplasm. The appearance of the cytoplasm in these cells thus appears to represent an artefact of fixation.

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine → guanine and thymine → cytosine) and type 2 transitions (cytosine → thymine and guanine → adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.