《生物信息学》本科教学初探

针对生物信息学本科教学中的教学方法、实验教学、考核办法以及如何与现代教育技术相结合进行了初步的探索,并对如何提高教学效果培养跨学科的生物信息学人才做了深入思考。     

Is human longevity a consequence of cultural change or modern biology?

Increased longevity, expressed as the number of individuals surviving to older adulthood, represents a key way that Upper Paleolithic Europeans differ from earlier European (Neandertal) populations. Here, we address whether longevity increased as a result of cultural/adaptive change in Upper Paleolithic Europe, or whether it was introduced to Europe as a part of modern human biology. We compare the ratio of older to younger adults (OY ratio) in an early modern human sample associated with the Middle Paleolithic from Western Asia with OY ratios of European Upper Paleolithic moderns and penecontemporary Neandertals from the same region. We also compare these Neandertals to European Neandertals. The difference between the OY ratios of modern humans of the Middle and Upper Paleolithic is large and significant, but there is no significant difference between the Neandertals and early modern humans of Western Asia. Longevity for the West Asian Neandertals is significantly more common than for the European Neandertals. We conclude that the increase in adult survivorship associated with the Upper Paleolithic is not a biological attribute of modern humans, but reflects important cultural adaptations promoting the demographic and material representations of modernity.     

Role of Fish in Structuring Invertebrates on Stromatolites in Cuatro Ciénegas, México

Stromatolites, the dominant Precambrian life form, declined in the Phanerozoic to occur today in only a few sites. This decline has been attributed to evolution of metazoan grazers, but stromatolites in our study site, Cuatro Ciénegas, Coahuila, México, harbor diverse macroinvertebrates. Drawing on food chain theory, we hypothesized that fish predation on invertebrates controls invertebrate populations, allowing stromatolites to flourish in Cuatro Ciénegas. Our experiment used small mesh (1 mm) cages to exclude all but larval fishes, and larger (6.5 mm) cages to exclude all larger fishes (including the molluscivorous and omnivorous endemic polymorphic cichlid, Herichthys minckleyi), but allow access to all sizes of the abundant endemic pupfish, Cyprinodon bifasciatus. No effects of treatments on invertebrate densities were noted at 6 week, but significant effects were observed on specific taxonomic groups after 3 month. In absence of fishes, hydrobiidae snails and ceratopogonids increased 3- and 5-fold, respectively, and invertebrate assemblage composition varied among treatments. Algal biomass was not affected by treatments, but algal species composition appeared to change. Overall results suggest that fish assemblages structure invertebrate assemblages, and that fishes may also be factors in determining algal communities.     

Bilateral matching of frequency tuning in neural cross-correlators of the owl

Sound localization requires comparison between the inputs to the left and right ears. One important aspect of this comparison is the differences in arrival time to each side, also called interaural time difference (ITD). A prevalent model of ITD detection, consisting of delay lines and coincidence-detector neurons, was proposed by Jeffress (J Comp Physiol Psychol 41:35–39, 1948). As an extension of the Jeffress model, the process of detecting and encoding ITD has been compared to an effective cross-correlation between the input signals to the two ears. Because the cochlea performs a spectrotemporal decomposition of the input signal, this cross-correlation takes place over narrow frequency bands. Since the cochlear tonotopy is arranged in series, sounds of different frequencies will trigger neural activity with different temporal delays. Thus, the matching of the frequency tuning of the left and right inputs to the cross-correlator units becomes a ‘timing’ issue. These properties of auditory transduction gave theoretical support to an alternative model of ITD-detection based on a bilateral mismatch in frequency tuning, called the ‘stereausis’ model. Here we first review the current literature on the owl’s nucleus laminaris, the equivalent to the medial superior olive of mammals, which is the site where ITD is detected. Subsequently, we use reverse correlation analysis and stimulation with uncorrelated sounds to extract the effective monaural inputs to the cross-correlator neurons. We show that when the left and right inputs to the cross-correlators are defined in this manner, the computation performed by coincidence-detector neurons satisfies conditions of cross-correlation theory. We also show that the spectra of left and right inputs are matched, which is consistent with predictions made by the classic model put forth by Jeffress. This article is part of a special issue on Neuronal Dynamics of Sensory Coding.     

Dehydrolutein: a metabolically derived carotenoid never observed in raptors

Carotenoids are fat-soluble pigments synthesised by photosynthetic organisms(Brush,1990).Conversely,animals are incapable of synthesizing carotenoids de novo,and they must obtain them through their diet.However,some animal species are able to make some alterations to the basic chemical structure,converting ingested carotenoids into more oxidized and differently coloured forms(Schiedt,1998).     

White-tailed deer (Odocoileus virginianus) fecal pellet decomposition is accelerated by the invasive earthworm Lumbricus terrestris

Exotic European earthworms have expanded into worm-free forests of the United States. Concurrently, populations of the white-tailed deer, Odocoileus virginianus, have also increased. During winter, deer use hemlock stands for cover while browsing elsewhere, creating a net organic matter flux into these stands. Deer fecal pellets can provide annual inputs of 48.1 kg C, 1.4 kg N, and 1.3 kg Ca per hectare. We tested the hypothesis that these pellets were readily consumed by invading earthworms. The litter-feeding anecic earthworm Lumbricus terrestris redistributed fecal pellets and accelerated mass and nutrient loss rates. These losses are likely due to the combination of enhanced fragmentation and decomposition as earthworms drag pellets into their burrows for consumption. This nutrient subsidy may be an important source of high quality “litter” input to hemlock stands, which may in turn facilitate the invasion of these stands by earthworms under high deer densities.     

基于遥感数据对中国表土花粉进行植被覆盖度定量估算的研究

本文主要探讨利用现代类比法将表土花粉数据定量转换为植被覆盖度的方法,以及该方法在中国复杂地貌和气候环境中应用的可行性和可信度.陆地植被覆盖使用了卫星遥感MODIS 500×500m分辨率的栅格数据,覆盖度分类为乔木、草地和裸地三种.使用的表土花粉数据共1 127个样点,其地理分布基本能够覆盖中国的各种植被类型.用于现代类比法定量计算的化粉变量类型共64个.研究结果表明,计算获得的每个样点的植被覆盖度与MODIS实际观测值具有很好的对应性,基于花粉的覆盖度估算值与遥感实际观测值之间的相关性很高,其中裸地达到0.99,乔木达到0.97,草地为0.95.从空间分布看,利用花粉定量转换的植被覆盖样点可以清楚地识别从裸地向草地和乔木的变化区间,并且与植被分布的实际情况吻合.本研究证明,基于中国表土花粉数据对植被覆盖度的定量恢复足可行的.此外,研究发现乔木覆盖度较高的对应特征花粉较多,主要是松属、栲属、栎属(含青冈栎)、桦属、桤木属、杨梅属、冷杉属,云杉属等,而草地的对应特征花粉类型有莎草科、禾本科、蒿属、蔷薇科、豆科等,裸地主要为麻黄属和藜科等.     

Comparative study of the fluid dynamics of bottom spray fluid bed coaters

Fluid dynamics of pellets processed in bottom spray traditional Wurster coating and swirl accelerated air (precision) coating were compared with the intent to understand and facilitate improvements in the coating processes. Fluid dynamics was described by pellet mass flow rate (MFR) obtained using a pellet collection system and images captured using high speed photography. Pellet flow within the partition column was found to be denser and slower in Wurster coating than in precision coating, suggesting a higher tendency of agglomeration during the coating process. The influence of partition gap and load on the MFR indicated that the mechanism of transport of pellets into the coating zone in precision coating depended on a strong suction, whereas in Wurster coating, pellets were transported by a combination of peripheral fluidization, gravity, and weak suction pressure. In precision coating, MFR was found to increase uniformly with air flow rate and atomizing pressure, whereas MFR in Wurster coating did not correlate as well with air flow rate and atomizing pressure. This demonstration showed that transport in precision coating was air dominated. In conclusion, fluid dynamics in precision coating was found to be air dominated and dependent on pressure differential, thus it is more responsive to changes in operational variables than Wurster coating.     

Phytogeographical data and modern pollen rain of the puna belt in southern Peru (Nevado Coropuna, Western Cordillera)

Aim To improve knowledge of the distribution of species and modern pollen dispersal in the puna vegetation belt (central Andes) for palaeoenvironmental analysis and reconstructions. Location Puna belt, Nevado Coropuna, Western Cordillera, Peru. Methods The vegetation facies and belts of the area were mapped by remote sensing using a March 1998 SPOT4 image. This was complemented by the interpretation of aerial photographs, by field sampling, and by the identification of plants. Data from 1940 to 1994 from the Peruvian meteorological station network were modelled to characterize the relationship between climate and vegetation. Twenty‐four soil‐surface samples were collected in the various vegetation facies identified on the map, and standard palynological techniques were applied to analyse these samples. A principal components analysis was performed on the pollen data set. Results The map shows three bioclimatic belts and seven facies in the puna sensu lato, and identifies the main plants that are characteristic of each bioclimatic area. The pollen results fit the vegetation facies and belts, including the plant species of the distinct facies that are well represented in the pollen assemblages. The mesotropical belt is characterized by the predominance of Asteraceae‐type Ambrosia; the supratropical belt shows significant frequencies of Asteraceae‐type Senecio; the orotropical belt is characterized by high frequencies of Apiaceae and includes Polylepis woodland and peat bogs; and the cryorotropical belt shows significant frequencies of Asteraceae‐type Senecio and Apiaceae. Main conclusions The pollen grains of the plants that grow on the puna sensu lato are generally entomophilous and are therefore not transported far from their plant source. The distinct bioclimatic facies and belts identified by the cartography can thus be well distinguished by their pollen production and deposition. We were therefore able to characterize the relationship between pollen, vegetation and climate that can be used for palaeoenvironmental reconstructions. An altitudinal pollen gradient on the western slopes of the central Andes was revealed by the pollen study, with the succession of Asteraceae‐type Ambrosia (1800–2200 m), Malvaceae (2700–3300 m), Asteraceae‐type Senecio (3500–4100 m) and Apiaceae (above 4600 m).     

U-Series dating of Liujiang hominid site in Guangxi,Southern China

It has been established that modern humans were living in the Levant and Africa ca. 100ka ago. Hitherto, this has contrasted with the situation in China where no unequivocal specimens of this species have been securely dated to more than 30ka. Here we present the results of stratigraphic studies and U-series dating of the Tongtianyan Cave, the discovery site of the Liujiang hominid, which represents one of the few well-preserved fossils of modern Homo sapiens in China. The human fossils are inferred to come from either a refilling breccia or a primarily deposited gravel-bearing sandy clay layer. In the former case, which is better supported, the fossils would date to at least approximately 68ka, but more likely to approximately 111-139ka. Alternatively, they would be older than approximately 153ka. Both scenarios would make the Liujiang hominid one of the earliest modern humans in East Asia, possibly contemporaneous with the earliest known representatives from the Levant and Africa. Parallel studies on other Chinese localities have provided supporting evidence for the redating of Liujiang, which may have important implications for the origin of modern humans.