Nonlinear Analysis of the Dynamics of DNA Breathing

The base pairs that encode the genetic information in DNA show large amplitude localized excitations called DNA breathing. We discuss the experimental observations of this phenomenon and its theoretical analysis. Starting from a model introduced to study the thermal denaturation of DNA, we show that it can qualitatively describe DNA breathing but is quantitatively not satisfactory. We show how the model can be modified to be quantitatively correct. This defines a nonlinear lattice model, which is interesting in itself because it has nonlinear localized excitations, forming a new class of discrete breather.     

Changes in Mammal Fauna of the Northern Palearctic and Living Range Dynamics of the Component Species

Changes in the distribution of game animals that have living ranges with northern and southern boundaries in the northwestern regions of Russia have been analyzed and compared to horological materials published by a group of researchers almost 50 years ago. An anthropogenic impact has been identified as the major factor for the changes named above.     

Impact Loading and Locomotor-Respiratory Coordination Significantly Influence Breathing Dynamics in Running Humans

Locomotor-respiratory coupling (LRC), phase-locking between breathing and stepping rhythms, occurs in many vertebrates. When quadrupedal mammals gallop, 1∶1 stride per breath coupling is necessitated by pronounced mechanical interactions between locomotion and ventilation. Humans show more flexibility in breathing patterns during locomotion, using LRC ratios of 2∶1, 2.5∶1, 3∶1, or 4∶1 and sometimes no coupling. Previous studies provide conflicting evidence on the mechanical significance of LRC in running humans. Some studies suggest LRC improves breathing efficiency, but others suggest LRC is mechanically insignificant because ‘step-driven flows’ (ventilatory flows attributable to step-induced forces) contribute a negligible fraction of tidal volume. Yet, although step-driven flows are brief, they cause large fluctuations in ventilatory flow. Here we test the hypothesis that running humans use LRC to minimize antagonistic effects of step-driven flows on breathing. We measured locomotor-ventilatory dynamics in 14 subjects running at a self-selected speed (2.6±0.1 ms⁻¹) and compared breathing dynamics in their naturally ‘preferred’ and ‘avoided’ entrainment patterns. Step-driven flows occurred at 1-2X step frequency with peak magnitudes of 0.97±0.45 Ls⁻¹ (mean ±S.D). Step-driven flows varied depending on ventilatory state (high versus low lung volume), suggesting state-dependent changes in compliance and damping of thoraco-abdominal tissues. Subjects naturally preferred LRC patterns that minimized antagonistic interactions and aligned ventilatory transitions with assistive phases of the step. Ventilatory transitions initiated in ‘preferred’ phases within the step cycle occurred 2x faster than those in ‘avoided’ phases. We hypothesize that humans coordinate breathing and locomotion to minimize antagonistic loading of respiratory muscles, reduce work of breathing and minimize rate of fatigue. Future work could address the potential consequences of locomotor-ventilatory interactions for elite endurance athletes and individuals who are overweight or obese, populations in which respiratory muscle fatigue can be limiting.     

The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.     

Airflow Dynamics of Human Jets: Sneezing and Breathing - Potential Sources of Infectious Aerosols

Natural human exhalation flows such as coughing, sneezing and breathing can be considered as ‘jet-like’ airflows in the sense that they are produced from a single source in a single exhalation effort, with a relatively symmetrical, conical geometry. Although coughing and sneezing have garnered much attention as potential, explosive sources of infectious aerosols, these are relatively rare events during daily life, whereas breathing is necessary for life and is performed continuously. Real-time shadowgraph imaging was used to visualise and capture high-speed images of healthy volunteers sneezing and breathing (through the nose – nasally, and through the mouth - orally). Six volunteers, who were able to respond to the pepper sneeze stimulus, were recruited for the sneezing experiments (2 women: 27.5±6.36 years; 4 men: 29.25±10.53 years). The maximum visible distance over which the sneeze plumes (or puffs) travelled was 0.6 m, the maximum sneeze velocity derived from these measured distances was 4.5 m/s. The maximum 2-dimensional (2-D) area of dissemination of these sneezes was 0.2 m². The corresponding derived parameter, the maximum 2-D area expansion rate of these sneezes was 2 m²/s. For nasal breathing, the maximum propagation distance and derived velocity were 0.6 m and 1.4 m/s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.11 m² and 0.16 m²/s, respectively. Similarly, for mouth breathing, the maximum propagation distance and derived velocity were 0.8 m and 1.3 m/s, respectively. The maximum 2-D area of dissemination and derived expansion rate were 0.18 m² and 0.17 m²/s, respectively. Surprisingly, a comparison of the maximum exit velocities of sneezing reported here with those obtained from coughing (published previously) demonstrated that they are relatively similar, and not extremely high. This is in contrast with some earlier estimates of sneeze velocities, and some reasons for this difference are discussed.     

哺乳动物胚胎发生发育与表观遗传修饰

哺乳动物受精过程中染色体构象发生剧烈的变化.来自精子高度凝缩的染色质在卵母细胞胞质环境中解凝缩,与雌性染色质融合,发生基因组重编程共同构建合子基因组,激活胚胎基因组转录,获得发育的全能性,并进一步发育成完整的胚胎.表观遗传调节机制在这一过程中起重要作用,其中主要包括DNA甲基化、组蛋白甲基化、组蛋白乙酰化及组蛋白替代,这些修饰形式改变了染色体的空间构象以及与转录调节因子的结合模式,调控染色体的活性,进而调节胚胎的发生发育.     

哺乳动物中蛋白质折叠异常与朊病毒病

在过去的两年中 ,有关朊病毒 (ｐｒｉｏｎ)蛋白结构的最新ＮＭＲ数据不断扩展 ,这主要是在仓鼠和人体蛋白质中取得的。另外 ,两种朊病毒蛋白的折叠动力学机制亦被阐明。目前已经得到几种朊病毒的样品 ,它们可以在溶液中采取不同的构象。近来所做的有关朊病毒蛋白链分子基础的研究工作进一步巩固了蛋白质独自致病的假说。通过对最小蛋白质片断的辨认 ,疾病与结构的相互关系的研究也取得了重要进展。1 .引言在 2 5种被确证为由动物组织中变性蛋白质沉积而引起的病症中 ,只有传染性海绵状脑病 (ＴＳＥｓ)会产生传染性物质。可能朊病毒疾病最独…     

蛋白质组学在哺乳动物睾丸和精子发生中的应用

“蛋白质组学”一词由Wilkins在1994年提出,被称作后基因组时代一个新兴的研究手段.它从整体水平上对组织或者细胞的蛋白质表达、功能、相互作用进行研究,现在成为生命科学未来发展的主要分支之一.睾丸是哺乳动物雄性生殖系统中的一个重要的器官,由曲精小管和间质细胞组成.蛋白质组学在睾丸和精子发生研究上的应用及其技术手段的不断创新,对睾丸功能、生殖机理、生殖疾病的研究起到了极其重要的作用.所以,从蛋白质水平对睾丸和精子发生进行研究,为更好地理解雄性哺乳动物的生殖机理和疾病提供了一个新思路.     

Mammal survey in the southeastern Pantanal, Brazil

The Pantanal floodplain of southwestern Brazil, with its mosaic of marshes,seasonally flooded savannas, woodlands and forests, is known as one of thewildlife hotspots of South America. The region harbors a rich mammal fauna andis a stronghold for a number of mammal species; however, still very few thoroughmammal surveys have been conducted in the Pantanal. This is the first mammalsurvey from the southeastern part of the region. An intensive,three-month study of the medium to large, non-volant species wasconducted at a location in the upper Rio Negro Basin, Aquidauana region, MatoGrosso do Sul. Thirty species of mammals were recorded, including 5 xenarthrans,1 primate, 10 carnivores, 7 ungulates and 5 caviomorph rodents. It was possibleto analyze the field biology of many of the species to a level not previouslypublished for the Pantanal. Recommendations are given for camera trapping in thePantanal and the Amazon. Finally, the effects of intensive cattle ranching onconservation in the Pantanal are discussed.     

Recovery Trends in Marine Mammal Populations

Marine mammals have greatly benefitted from a shift from resource exploitation towards conservation. Often lauded as symbols of conservation success, some marine mammal populations have shown remarkable recoveries after severe depletions. Others have remained at low abundance levels, continued to decline, or become extinct or extirpated. Here we provide a quantitative assessment of (1) publicly available population-level abundance data for marine mammals worldwide, (2) abundance trends and recovery status, and (3) historic population decline and recent recovery. We compiled 182 population abundance time series for 47 species and identified major data gaps. In order to compare across the largest possible set of time series with varying data quality, quantity and frequency, we considered an increase in population abundance as evidence of recovery. Using robust log-linear regression over three generations, we were able to classify abundance trends for 92 spatially non-overlapping populations as Significantly Increasing (42%), Significantly Decreasing (10%), Non-Significant Change (28%) and Unknown (20%). Our results were comparable to IUCN classifications for equivalent species. Among different groupings, pinnipeds and other marine mammals (sirenians, polar bears and otters) showed the highest proportion of recovering populations, likely benefiting from relatively fast life histories and nearshore habitats that provided visibility and protective management measures. Recovery was less frequent among cetaceans, but more common in coastal than offshore populations. For marine mammals with available historical abundance estimates (n = 47), larger historical population declines were associated with low or variable recent recoveries so far. Overall, our results show that many formerly depleted marine mammal populations are recovering. However, data-deficient populations and those with decreasing and non-significant trends require attention. In particular, increased study of populations with major data gaps, including offshore small cetaceans, cryptic species, and marine mammals in low latitudes and developing nations, is needed to better understand the status of marine mammal populations worldwide.     

Properties of Respiratory Pigments in Bimodal Breathing Animals: Air and Water Breathing by Fish and Crustaceans

SYNOPSIS. Oxygen is nearly 30 times more available in air comparedwith water, whereas the carbon dioxide capacity of water is{small tilde}28.5-fold greater than for oxygen, presenting bimodalbreathing species with two very different respiratory milieus.The respiratory pigment plays a variable role in animals switchingbetween the two media. In vertebrates the transition to airbreathing involves two main strategies: a decrease in oxygenaffinity and changes in other haematological parameters suchas haematocrit. When appropriately analyzed, data reveal a decreasein blood oxygen affinity during transition to air. This mayarise via differences in the intrinsic affinity as occurs insome amphibians, or be due to increasesin the organic phosphate:haemoglobin ratio when acclimating to air breathing. Adoptingair breathing often promotes increased haematocrit. It is difficultto discern trends in haemocyanin functioning. Many but not allbimodal and air breathingspecies of crab contain haemocyaninwith high affinity for oxygen. As with haemoglobin there issome tendency for blood haemocyanin concentration to increasewith air breathing but bimodal species are quite variable inthis regard. Different strategies for breathing air are employedby various bimodal crustaceans, some of which involve modulationof haemocyanin oxygenaffinity. The exact mechanisms are oftenspecies dependent and in all bimodal breathing organisms therole of the pigment is best appreciated when the demands ofthe local environment and the behaviour of the species are considered.