Joint analysis of single-cell and bulk tissue sequencing data to infer intratumor heterogeneity

Many computational methods have been developed to discern intratumor heterogeneity (ITH) using DNA sequence data from bulk tumor samples. These methods share an assumption that two mutations arise from the same subclone if they have similar mutant allele-frequencies (MAFs), and thus it is difficult or impossible to distinguish two subclones with similar MAFs. Single-cell DNA sequencing (scDNA-seq) data can be very informative for ITH inference. However, due to the difficulty of DNA amplification, scDNA-seq data are often very noisy. A promising new study design is to collect both bulk and single-cell DNA-seq data and jointly analyze them to mitigate the limitations of each data type. To address the analytic challenges of this new study design, we propose a computational method named BaSiC (B ulk tumor a nd Si ngle C ell), to discern ITH by jointly analyzing DNA-seq data from bulk tumor and single cells. We demonstrate that BaSiC has comparable or better performance than the methods using either data type. We further evaluate BaSiC using bulk tumor and single-cell DNA-seq data from a breast cancer patient and several leukemia patients.     

Acoustical Aspects of the Propagation of Long Calls of Wild <Emphasis Type="Italic">Leontopithecus rosalia</Emphasis>

Golden lion tamarins emit conspicuous and complex long calls. Little is known about the propagation distance of the calls, and the knowledge is important to understand the function of long calls. The high-frequency spectrum of the calls renders them susceptible to substantial degradation inside forest habitats. We investigated 1) the propagation distance of the long call and if the height from the ground affects the degree of degradation and 2) whether long-call acoustic variation affects the propagation distance. We conducted a playback study of 7 2-phrase long calls recorded at different distances (20, 40, 80, 120 m) and heights above ground (2 m and 7.5 m) in 3 transects of Brazilian Atlantic Forest. We quantified the degradation by measuring differences in the number of syllables and frequency measures of the calls at each distance. Degradation became significant at 80 m; the calls degraded below background noise at 120 m. The degradation of syllables was lower for recordings at 7.5 m above ground. The frequency spectra of the calls influenced significantly the propagation distance of the call. Because of the short propagation distance of long calls relative to territory size, we hypothesize that long calls may be adapted to avoiding ambient noise and that they evolved first for intragroup communication and then for territorial defense.     

Echolocation of Multiple Targets in 3-D Space from a Single Emission

Using frequency-modulated echolocation sound, bat can capture a moving target in real three-dimensional (3-D) space. It is impossible to locate multiple targets in 3-D space by using only the delay time between an emission and the resultingechoes received at two points (i.e., two ears). To locate multiple targets in 3-D space requires directional information for each target. The spectrum of the echoes from nearly equidistant targets includes spectral components of both the interference between the echoes and the interference resulting from the physical process of reception at the external ear. The frequency of the spectral notch, which is the frequency corresponding to the minimum of the external ear's transfer function (EEDNF), provides a crucial cue for directional localization. In the model we present, a computational model todiscriminate multiple close targets in 3-D space utilizing echoes evoked by a single emission by distinguishing the interference of echoes from each object and the EEDNF corresponding to each target.     

Confirmation of right whales near a nineteenth-century whaling ground east of southern Greenland

North Atlantic right whales (Eubalaena glacialis) were found in an important nineteenth century whaling area east of southern Greenland, from which they were once thought to have been extirpated. In 2007-2008, a 1-year passive acoustic survey was conducted at five sites in and near the 'Cape Farewell Ground', the former whaling ground. Over 2000 right whale calls were recorded at these sites, primarily during July-November. Most calls were northwest of the historic ground, suggesting a broader range in this region than previously known. Geographical and temporal separation of calls confirms use of this area by multiple animals.     

Postnatal handling reverses social anxiety in serotonin receptor 1A knockout mice

Mice lacking the serotonin receptor 1A (Htr1a knockout, Htr1a ^KO ) show increased innate and conditioned anxiety. This phenotype depends on functional receptor activity during the third through fifth weeks of life and thus appears to be the result of long-term changes in brain function as a consequence of an early deficit in serotonin signaling. To evaluate whether this phenotype can be influenced by early environmental factors, we subjected Htr1a knockout mice to postnatal handling, a procedure known to reduce anxiety-like behavior and stress responses in adulthood. Offspring of heterozygous Htr1a knockout mice were separated from their mother and exposed 15 min each day from postnatal day 1 (PD1) to PD14 to clean bedding. Control animals were left undisturbed. Maternal behavior was observed during the first 13 days of life. Adult male offspring were tested in the open field, social approach and resident–intruder tests and assessed for corticosterone response to restraint stress. Knockout mice showed increased anxiety in the open field and in the social approach test as well as an enhanced corticosterone response to stress. However, while no effect of postnatal handling was seen in wild-type mice, handling reduced anxiety-like behavior in the social interaction test and the corticosterone response to stress in knockout mice. These findings extend the anxiety phenotype of Htr1a ^KO mice to include social anxiety and demonstrate that this phenotype can be moderated by early environmental factors.     

Molecular patterns of differentiation in canyon treefrogs (Hyla arenicolor): evidence for introgressive hybridization with the Arizona treefrog (H. wrightorum) and correlations with advertisement call differences

Detection of genetic and behavioural diversity within morphologically similar species has led to the discovery of cryptic species complexes. We tested the hypothesis that US populations of the canyon treefrog (Hyla arenicolor) may consist of cryptic species by examining mate‐attraction signals among three divergent clades defined by mtDNA. Using a multi‐locus approach, we re‐analysed phylogenetic relationships among the three clades and a closely related, but morphologically and behaviourally dissimilar species, the Arizona treefrog (H. wrightorum). We found evidence for introgression of H. wrightorum’s mitochondrial genome into H. arenicolor. Additionally, the two‐clade topology based on nuclear data is more congruent with patterns of call variation than the three‐clade topology from the mitochondrial dataset. The magnitude of the call divergence is probably insufficient to promote isolation of the nuclear DNA‐defined clades should they become sympatric, but further divergence in call properties significant in species identification could promote speciation in the future.     

恒频-调频蝙蝠特化的听觉系统对回声定位的适应

在漫长的生物演化过程中,蝙蝠演化出了能飞行和高度适应生存环境的生物声纳系统和行为.蝙蝠属于哺乳动物纲的翼手目(Chiroptera),是唯一能真正飞行的哺乳动物,其种类超过1000种,位列哺乳类动物的第二大目.根据其体型大小和形态特征将其分成大蝙蝠亚目(Megachiroptera)和小蝙蝠亚目(Microchiroptera).对蝙蝠的研究具有重要的科学意义和实际应用价值,如在听感觉方面与人类共享听觉的某些基本原理,研究结果有助于认识人类听觉.它们发出的回声定位信号规整,便于模拟后用于研究听觉系统对声信号加工的机制,尤其是在听中枢对复杂声信号处理方面,认识其细胞和分子机制才刚开始,它们是极好的模型动物.另外,在仿生学方面也具有极其重要的价值,回声定位蝙蝠的生物声纳系统具有极高的时间和空间分辨率,是极具诱惑力的研究课题.有关恒频-调频蝙蝠听觉结构和功能的研究,已有相当的时日,获得了不少新的认识,窥探到敏锐的听觉与回声定位行为之间的某些适应性的机制,本文对这方面的研究进展做了简要介绍和评述.     

Calling louder and longer: how bats use biosonar under severe acoustic interference from other bats

Active-sensing systems such as echolocation provide animals with distinct advantages in dark environments. For social animals, however, like many bat species, active sensing can present problems as well: when many individuals emit bio-sonar calls simultaneously, detecting and recognizing the faint echoes generated by one''s own calls amid the general cacophony of the group becomes challenging. This problem is often termed ‘jamming’ and bats have been hypothesized to solve it by shifting the spectral content of their calls to decrease the overlap with the jamming signals. We tested bats’ response in situations of extreme interference, mimicking a high density of bats. We played-back bat echolocation calls from multiple speakers, to jam flying Pipistrellus kuhlii bats, simulating a naturally occurring situation of many bats flying in proximity. We examined behavioural and echolocation parameters during search phase and target approach. Under severe interference, bats emitted calls of higher intensity and longer duration, and called more often. Slight spectral shifts were observed but they did not decrease the spectral overlap with jamming signals. We also found that pre-existing inter-individual spectral differences could allow self-call recognition. Results suggest that the bats’ response aimed to increase the signal-to-noise ratio and not to avoid spectral overlap.     

南蝠海南岛分布新纪录、回声定位信号和ND1分析

2007年11月于海南省保亭黎族苗族自治县毛感乡网捕到5只蝙蝠标本.形态特征及线粒体DNAND1基因序列的研究证实其为蝙蝠科南蝠属南蝠(Ia io),该物种为海南岛翼手目新纪录.本文详述了海南岛南蝠的形态与回声定位信号特征,并与该物种已报道的数据进行了比较.     

Birds adjust acoustic directionality to beam their antipredator calls to predators and conspecifics

Animals in many vertebrate species vocalize in response to predators, but it is often unclear whether these antipredator calls function to communicate with predators, conspecifics or both. We evaluated the function of antipredator calls in 10 species of passerines by measuring the acoustic directionality of these calls in response to experimental presentations of a model predator. Acoustic directionality quantifies the radiation pattern of vocalizations and may provide evidence about the receiver of these calls. We predicted that antipredator calls would have a lower directionality if they function to communicate with surrounding conspecifics, and a higher directionality and aimed at the receiver if they function to communicate with the predator. Our results support both of these functions. Overall, the birds produce antipredator calls that have a relatively low directionality, suggesting that the calls radiate in many directions to alert conspecifics. However, birds in some species increase the directionality of their calls when facing the predator. They can even direct their calls towards the predator when facing lateral to it—effectively vocalizing sideways towards the predator. These results suggest that antipredator calls in some species are used to communicate both to conspecifics and to predators, and that birds adjust the directionality of their calls with remarkable sophistication according to the context in which they are used.