The Survival Attractor in the Sensory Functions: The Example of Hearing

High noise levels may have an adverse effect on the normal cochlea function and lead to significant hearing loss. Clinically, exposure to high intensity impulse noise produces a wide range of audiometric effects which may result in long term or even irreversible symptoms. Nevertheless, there is sometimes a spontaneous rebound recovery of the auditory function. This phenomenon was previously studied in the vision, another sensory function. It was called the visual survival attractor. In view of the importance that the sensory organs have for the brain, and in particular in its function of recognising and dealing with its environment, it was interesting to know whether this survival attractor concept already described for vision occurs more generally in all the sensory functions. With this in mind we present here the results of a new study, this time on hearing. This study was carried out on guinea pigs subjected to a pulsed acoustic trauma simulating the sound of a gun going off. Auditory function was explored using electrocochleography and two types of investigation were carried out. At first the change in hearing loss was studied in relation to frequencies varying between 2 and 24 kHz by calculating the difference, at each frequency, between the compound action potential thresholds measured before and then 20 mn, 24 h and 7 days after the acoustic trauma. On the other hand, the change in compound action potential amplitude was determined by varying the stimulating sound level from the auditory threshold up to 90 dB. This change was also recorded at the same time intervals as the investigation of hearing loss. In both the analysis of changes to hearing loss and in the investigation of variations in compound action potential, the results of the electrocochleographic investigations after acoustic trauma confirm the presence of a butterfly catastrophe type reaction process, that is positive evidence of a hearing survival attractor.     

Geographical Distribution of Adolescent Body Height with Respect to Effective Day Length in Japan: An Ecological Analysis

The height of Japanese youth raised in the northern region tends to be greater than that of youth raised in the southern region; therefore, a geographical gradient in youth body height exists. Although this gradient has existed for about 100 years, the reasons for it remain unclear. Consideration of the nutritional improvement, economic growth, and intense migration that has occurred in this period indicates that it is probably the result of environmental rather than nutritional or genetic factors. To identify possible environmental factors, ecological analysis of prefecture-level data on the body size of 8- to 17-year-old youth averaged over a 13-year period (1996 to 2008) and Japanese mesh climatic data on the climatic variables of temperature, solar radiation, and effective day length (duration of photoperiod exceeding the threshold of light intensity) was performed. The geographical distribution of the standardized height of Japanese adolescents was found to be inversely correlated to a great extent with the distribution of effective day length at a light intensity greater than 4000 lx. The results of multiple regression analysis of effective day length, temperature, and weight (as an index of food intake) indicated that a combination of effective day length and weight was statistically significant as predictors of height in early adolescence; however, only effective day length was statistically significant as a predictor of height in late adolescence. Day length may affect height by affecting the secretion of melatonin, a hormone that inhibits sexual and skeletal maturation, which in turn induces increases in height. By affecting melatonin production, regional differences in the duration of the photoperiod may lead to regional differences in height. Exposure to light intensity greater than 4000 lx appears to be the threshold at which light intensity begins to affect the melatonin secretion of humans who spend much of their time indoors.     

Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis

Sequence data arising from an increasing number of partial and complete genome projects is revealing the presence of the polyketide synthase (PKS) family of genes not only in microbes and fungi but also in plants and other eukaryotes. PKSs are huge multifunctional megasynthases that use a variety of biosynthetic paradigms to generate enormously diverse arrays of polyketide products that posses several pharmaceutically important properties. The remarkable conservation of these gene clusters across organisms offers abundant scope for obtaining novel insights into PKS biosynthetic code by computational analysis. We have carried out a comprehensive in silico analysis of modular and iterative gene clusters to test whether chemical structures of the secondary metabolites can be predicted from PKS protein sequences. Here, we report the success of our method and demonstrate the feasibility of deciphering the putative metabolic products of uncharacterized PKS clusters found in newly sequenced genomes. Profile Hidden Markov Model analysis has revealed distinct sequence features that can distinguish modular PKS proteins from their iterative counterparts. For iterative PKS proteins, structural models of iterative ketosynthase (KS) domains have revealed novel correlations between the size of the polyketide products and volume of the active site pocket. Furthermore, we have identified key residues in the substrate binding pocket that control the number of chain extensions in iterative PKSs. For modular PKS proteins, we describe for the first time an automated method based on crucial intermolecular contacts that can distinguish the correct biosynthetic order of substrate channeling from a large number of non-cognate combinatorial possibilities. Taken together, our in silico analysis provides valuable clues for formulating rules for predicting polyketide products of iterative as well as modular PKS clusters. These results have promising potential for discovery of novel natural products by genome mining and rational design of novel natural products.     

Ecological and Geographical Analysis of the Distribution of the Mountain Tapir (Tapirus pinchaque) in Ecuador: Importance of Protected Areas in Future Scenarios of Global Warming

In Ecuador, Tapirus pinchaque is considered to be critically endangered. Although the species has been registered in several localities, its geographic distribution remains unclear, and the effects of climate change and current land uses on this species are largely unknown. We modeled the ecological niche of T. pinchaque using MaxEnt, in order to assess its potential adaptation to present and future climate change scenarios. We evaluated the effects of habitat loss due by current land use, the ecosystem availability and importance of Ecuadorian System of Protected Areas into the models. The model of environmental suitability estimated an extent of occurrence for species of 21,729 km² in all of Ecuador, mainly occurring along the corridor of the eastern Ecuadorian Andes. A total of 10 Andean ecosystems encompassed ~98% of the area defined by the model, with herbaceous paramo, northeastern Andean montane evergreen forest and northeastern Andes upper montane evergreen forest being the most representative. When considering the effect of habitat loss, a significant reduction in model area (~17%) occurred, and the effect of climate change represented a net reduction up to 37.86%. However, the synergistic effect of both climate change and habitat loss, given current land use practices, could represent a greater risk in the short-term, leading to a net reduction of 19.90 to 44.65% in T. pinchaque’s potential distribution. Even under such a scenarios, several Protected Areas harbor a portion (~36 to 48%) of the potential distribution defined by the models. However, the central and southern populations are highly threatened by habitat loss and climate change. Based on these results and due to the restricted home range of T. pinchaque, its preference for upland forests and paramos, and its small estimated population size in the Andes, we suggest to maintaining its current status as Critically Endangered in Ecuador.     

芜菁花青素合成酶基因的克隆、序列分析及表达

目的：克隆津田芜菁和赤丸芜菁花青素合成酶（ANS）基因并研究其表达特性。方法：用UV-A处理津田芜菁和赤丸芜菁块根24h后提取总RNA,通过RT-PCR方法克隆BrANS1和BrANS2基因并进行序列分析,通过Northern杂交检测BrANS1和BrANS2基因的表达。结果：BrANS1和BrANS2的开放读码框为1077bp,编码358个氨基酸残基;BRANS1和BRANS2与甘蓝ANS的同源性达97％,第211-307肽段具有20G-Fe（Ⅱ）加氧酶家族基因的结构域;BrANS1和BRANS2基因具有高度同源性,核苷酸序列在5个位置上存在差异,推导的氨基酸序列完全相同;uv-A可以诱导BrANS1和BrANS2表达,基因的表达量与处理时间相关。结论：克隆了津田芜菁和赤丸芜菁的BRANS1和BrANS2基因,这将为筛选依光型和非依光型花青素生物合成催化酶基因奠定研究基础。     

系谱分析中概率问题的贝叶斯分析一例

《生物学通报》2007年第2期“遗传概率的一个认识误区”一文,给出了一个家系概率问题的答案,但没有详尽的分析过程,不利于初学者的学习掌握,本文对此予以补充和完善。[第一段]     

Population and Settlement Area: An Example from Iran

It can be argued that observed variation in the relationship between settlement area and population, along with uncertainties introduced by the assumption that archeological site area is equal to settlement area, makes efforts to estimate population from site area an impossible task. Such an argument leads to the conclusion that only a relative measure is justified, using site area as a proxy for population, rather than an estimator. However, the requirement for actual population estimates in production, consumption, and land use analysis is more than sufficient justification for a continued effort to develop methods of estimating population from site area.     

Characterizing the Smell of Marijuana by Odor Impact of Volatile Compounds: An Application of Simultaneous Chemical and Sensory Analysis

Recent US legislation permitting recreational use of marijuana in certain states brings the use of marijuana odor as probable cause for search and seizure to the forefront of forensic science, once again. This study showed the use of solid-phase microextraction with multidimensional gas chromatography—mass spectrometry and simultaneous human olfaction to characterize the total aroma of marijuana. The application of odor activity analysis offers an explanation as to why high volatile chemical concentration does not equate to most potent odor impact of a certain compound. This suggests that more attention should be focused on highly odorous compounds typically present in low concentrations, such as nonanal, decanol, o-cymene, benzaldehyde, which have more potent odor impact than previously reported marijuana headspace volatiles.     

Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.     

Flexible and Adaptable Restoration: An Example from South Korea

Ecological restoration is set to play a key role in mitigating biodiversity loss. While many restorationists worry about what to do about and what to call rapidly changing ecosystems (no‐analog, novel, or other terms), ecologists and managers in some parts of the world have avoided these controversies and proceeded with developing and implementing innovative restoration projects. We discuss examples from South Korea, including the Cheonggyecheon river project in Seoul and the new National Institute of Ecology, which combines scientific research, planted reference systems for future restoration, and an Ecorium for outreach and education. South Korea faces a range of restoration challenges, including managing even‐aged planted forests, major land use changes (especially urbanization) affecting valuable tidal flats, and fragmented landscapes caused by intensive land use and the fenced Demilitarized Zone (DMZ). The examples from South Korea provide insights that might guide future actions more broadly. These include flexible targets for restoration not based on historical precedents, considering ecosystem functions and functional trait diversity as well as species composition, creating model restoration projects, and managing adaptively.     

Forest Loss in Protected Areas and Intact Forest Landscapes: A Global Analysis

In spite of the high importance of forests, global forest loss has remained alarmingly high during the last decades. Forest loss at a global scale has been unveiled with increasingly finer spatial resolution, but the forest extent and loss in protected areas (PAs) and in large intact forest landscapes (IFLs) have not so far been systematically assessed. Moreover, the impact of protection on preserving the IFLs is not well understood. In this study we conducted a consistent assessment of the global forest loss in PAs and IFLs over the period 2000–2012. We used recently published global remote sensing based spatial forest cover change data, being a uniform and consistent dataset over space and time, together with global datasets on PAs’ and IFLs’ locations. Our analyses revealed that on a global scale 3% of the protected forest, 2.5% of the intact forest, and 1.5% of the protected intact forest were lost during the study period. These forest loss rates are relatively high compared to global total forest loss of 5% for the same time period. The variation in forest losses and in protection effect was large among geographical regions and countries. In some regions the loss in protected forests exceeded 5% (e.g. in Australia and Oceania, and North America) and the relative forest loss was higher inside protected areas than outside those areas (e.g. in Mongolia and parts of Africa, Central Asia, and Europe). At the same time, protection was found to prevent forest loss in several countries (e.g. in South America and Southeast Asia). Globally, high area-weighted forest loss rates of protected and intact forests were associated with high gross domestic product and in the case of protected forests also with high proportions of agricultural land. Our findings reinforce the need for improved understanding of the reasons for the high forest losses in PAs and IFLs and strategies to prevent further losses.     

The Interdependence of Long- and Short-Term Components in Unmasked Repetition Priming: An Indication of Shared Resources

It has been suggested that unmasked repetition priming is composed of distinct long-and short-term priming components. The current study sought to clarify the relationship between these components by examining the relationship between them. A total of 60 people (45 females, 15 males) participated in a computer-based lexical decision task designed to measure levels of short-term priming across different levels of long-term priming. The results revealed an interdependent relationship between the two components, whereby an increase in long-term priming prompted a decrease in short-term priming. Both long-term and short-term priming were accurately captured by a single power function over seven minutes post repetition, suggesting the two components may draw on the same resources. This interdependence between long- and short-term priming may serve to improve fluency in reading.     

Measuring Dominance and Constructing Hierarchies: An Example Using Mule Deer

Important issues that are still unresolved in the study of animal social groups are how dominance is measured and how individuals are ranked. Based on observations of mule deer (Odocoileus hemionus hemionus), we constructed hierarchies for the same 26 bucks using five potential correlates of dominance and three measures based on the outcome of agonistic interactions. Data for each of six behavior measures were converted to ranks by six different numerical techniques. Different measures of behavior resulted in different hierarchies. This was especially so when the hierarchy based on sparring rates was compared to hierarchies based on other criteria. Although our results showed that dominance is not a unitary concept, several measures of dominance were highly correlated with one another. Thus, one measure, in some instances, may be a good but imperfect predictor of dominance defined by other criteria. For data sets based on index scores or rates of performing behavior, the mean difference and standard-error difference ranking methods had distinct advantages. Both produced equally weighted ranks that minimized the effects of sampling errors.