Ecology of Sleeping: The Microbial and Arthropod Associates of Chimpanzee Beds

The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment (n = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment

An automated segmentation approach to calibrating infantile nystagmus waveforms

Infantile nystagmus (IN) describes a regular, repetitive movement of the eyes. A characteristic feature of each cycle of the IN eye movement waveform is a period in which the eyes are moving at minimal velocity. This so-called “foveation” period has long been considered the basis for the best vision in individuals with IN. In recent years, the technology for measuring eye movements has improved considerably, but there remains the challenge of calibrating the direction of gaze in tracking systems when the eyes are continuously moving. Identifying portions of the nystagmus waveform suitable for calibration typically involves time-consuming manual selection of the foveation periods from the eye trace. Without an accurate calibration, the exact parameters of the waveform cannot be determined. In this study, we present an automated method for segmenting IN waveforms with the purpose of determining the foveation positions to be used for calibration of an eye tracker. On average, the “point of regard” was found to be within 0.21° of that determined by hand-marking by an expert observer. This method enables rapid clinical quantification of waveforms and the possibility of gaze-contingent research paradigms being performed with this patient group

A Multicellular Model of Intestinal Crypt Buckling and Fission

Crypt fission is an in vivo tissue deformation process that is involved in both intestinal homeostasis and colorectal tumourigenesis. Despite its importance, the mechanics underlying crypt fission are currently poorly understood. Recent experimental development of organoids, organ-like buds cultured from crypt stem cells in vitro, has shown promise in shedding light on crypt fission. Drawing inspiration from observations of organoid growth and fission in vivo, we develop a computational model of a deformable epithelial tissue layer. Results from in silico experiments show the stiffness of cells and the proportions of cell subpopulations affect the nature of deformation in the epithelial layer. In particular, we find that increasing the proportion of stiffer cells in the layer increases the likelihood of crypt fission occurring. This is in agreement with and helps explain recent experimental work

Combined changes in Wnt signalling response and contact inhibition induce altered proliferation in radiation treated intestinal crypts

Curative intervention is possible if colorectal cancer is identified early, underscoring the need to detect the earliest stages of malignant transformation. A candidate biomarker is the expanded proliferative zone observed in crypts before adenoma formation, also found in irradiated crypts. However, the underlying driving mechanism for this is not known. Wnt signaling is a key regulator of proliferation, and elevated Wnt signaling is implicated in cancer. Nonetheless, how cells differentiate Wnt signals of varying strengths is not understood. We use computational modeling to compare alternative hypotheses about how Wnt signaling and contact inhibition affect proliferation. Direct comparison of simulations with published experimental data revealed that the model that best reproduces proliferation patterns in normal crypts stipulates that proliferative fate and cell cycle duration are set by the Wnt stimulus experienced at birth. The model also showed that the broadened proliferation zone induced by tumorigenic radiation can be attributed to cells responding to lower Wnt concentrations and dividing at smaller volumes. Application of the model to data from irradiated crypts after an extended recovery period permitted deductions about the extent of the initial insult. Application of computational modeling to experimental data revealed how mechanisms that control cell dynamics are altered at the earliest stages of carcinogenesis

Characteristics and risk factors for typhoid fever after the tsunami, earthquake and under normal conditions in Indonesia

<p>Abstract</p> <p>Background</p> <p>Although typhoid transmitted by food and water is a common problem in daily life, its characteristics and risk factors may differ in disaster-affected areas, which reinforces the need for rapid public health intervention. Surveys were carried out post-tsunami in Banda Aceh, post-earthquake in Yogyakarta, and under normal conditions in Bandung, Indonesia. Logistic regression analysis was used to assess the risk factors with the dependent variable of typhoid fever, with or without complications.</p> <p>Findings</p> <p>Characteristic typhoid fever with complications was found in 5 patients (11.9%) affected by the tsunami in Aceh, 8 (20.5%) after the earthquake in Yogyakarta, and 13 (18.6%) in Bandung. After the tsunami in Aceh, clean water (OR = 0.05; 95%CI: 0.01-0.47) and drug availability (OR = 0.23; 95%CI: 0.02-2.43) are significant independent risk factors, while for the earthquake in Yogyakarta, contact with other typhoid patients (OR = 20.30; 95%CI: 1.93-213.02) and education (OR = 0.08; 95%CI: 0.01-0.98) were significant risk factors. Under normal conditions in Bandung, hand washing (OR = 0.07; 95%CI: 0.01-0.50) and education (OR = 0.08; 95%CI: 0.01-0.64) emerged as significant risk factors.</p> <p>Conclusion</p> <p>The change in risk factors for typhoid complication after the tsunami in Aceh and the earthquake in Yogyakarta emphasizes the need for rapid public health intervention in natural disasters in Indonesia.</p

Information storing by biomagnetites

Since the discovery of the presence of biogenic magnetites in living organisms, there have been speculations on the role that these biomagnetites play in cellular processes. It seems that the formation of biomagnetite crystals is a universal phenomenon and not an exception in living cells. Many experimental facts show that features of organic and inorganic processes could be indistinguishable at nanoscale levels. Living cells are quantum "devices" rather than simple electronic devices utilizing only the charge of conduction electrons. In our opinion, due to their unusual biophysical properties, special biomagnetites must have a biological function in living cells in general and in the brain in particular. In this paper we advance a hypothesis that while biomagnetites are developed jointly with organic molecules and cellular electromagnetic fields in cells, they can record information about the Earth's magnetic vector potential of the entire flight in migratory birds.Comment: 17 pages, 3 figure

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Abstract The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system, which with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range allows exploration of genomic changes both within sponges and in early animal evolution

Information and Discriminability as Measures of Reliability of Sensory Coding

Response variability is a fundamental issue in neural coding because it limits all information processing. The reliability of neuronal coding is quantified by various approaches in different studies. In most cases it is largely unclear to what extent the conclusions depend on the applied reliability measure, making a comparison across studies almost impossible. We demonstrate that different reliability measures can lead to very different conclusions even if applied to the same set of data: in particular, we applied information theoretical measures (Shannon information capacity and Kullback-Leibler divergence) as well as a discrimination measure derived from signal-detection theory to the responses of blowfly photoreceptors which represent a well established model system for sensory information processing. We stimulated the photoreceptors with white noise modulated light intensity fluctuations of different contrasts. Surprisingly, the signal-detection approach leads to a safe discrimination of the photoreceptor response even when the response signal-to-noise ratio (SNR) is well below unity whereas Shannon information capacity and also Kullback-Leibler divergence indicate a very low performance. Applying different measures, can, therefore, lead to very different interpretations concerning the system's coding performance. As a consequence of the lower sensitivity compared to the signal-detection approach, the information theoretical measures overestimate internal noise sources and underestimate the importance of photon shot noise. We stress that none of the used measures and, most likely no other measure alone, allows for an unbiased estimation of a neuron's coding properties. Therefore the applied measure needs to be selected with respect to the scientific question and the analyzed neuron's functional context

Dynamic assembly of ribbon synapses and circuit maintenance in a vertebrate sensory system

Ribbon synapses transmit information in sensory systems, but their development is not well understood. To test the hypothesis that ribbon assembly stabilizes nascent synapses, we performed simultaneous time-lapse imaging of fluorescently-tagged ribbons in retinal cone bipolar cells (BCs) and postsynaptic densities (PSD95-FP) of retinal ganglion cells (RGCs). Ribbons and PSD95-FP clusters were more stable when these components colocalized at synapses. However, synapse density on ON-alpha RGCs was unchanged in mice lacking ribbons (ribeye knockout). Wildtype BCs make both ribbon-containing and ribbon-free synapses with these GCs even at maturity. Ribbon assembly and cone BC-RGC synapse maintenance are thus regulated independently. Despite the absence of synaptic ribbons, RGCs continued to respond robustly to light stimuli, although quantitative examination of the responses revealed reduced frequency and contrast sensitivity

Cruel to be kind but not cruel for cash : harm aversion in the dictator game

People regularly take prosocial actions, making individual sacrifices for the greater good. Similarly, people generally avoid causing harm to others. These twin desires to do good and avoid harm often align, but sometimes they can diverge, creating situations of moral conflict. Here, we examined this moral conflict using a modified dictator game. Participants chose how much money to allocate away from a recipient who was designated as an orphan, creating a sense of harm. This money was then reallocated to either the participant or a charity. People were strongly prosocial: they allocated more money away from the orphan for charity than for themselves. Furthermore, people left more money with the orphan when the harm was framed as a means (taking) than as a side effect (splitting). As is predicted by dual-process theories of moral decision making, response times were longer with the take action and were positively correlated with the amount taken from the orphan. We concluded that just as people take positive actions for the greater good, they are similarly more willing to cause harm when it benefits others rather than themselves