Biological Databases for Human Research

The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases.With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of humanrelated biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation.     

The role of behavior in tern conservation

Behavioral research has long had an important role in the conservation of terns （Ayes： Stemidae）. Habitat management and restoration of breeding colony sites depends on knowledge of the cues used to select colony and nest sites. For example, conspecific attraction with playback and decoys is commonly used to bring terns to suitable colony sites and habitat modification is often used to increase the availability of suitable nest sites. Tern colonies are interconnected by dispersal, and a metapopulation approach is needed for effective management. Population dynamics are therefore affected by behaviors that influence the frequency of movement among colony sites： site fidelity, natal and breeding dispersal, and group adherence. The monogamous breeding system of terns should keep effective population size similar to census population size, but variation in sex ratios （likely resulting from sex differences in behavior） and in parental quality can result in a smaller than expected effective population size. In addition to the behavior of terns, knowledge of the behavior of predators on terns contributes to management plans, because predator behavior can sometimes be manipulated and predation is often performed by only a few specialized individuals. Other examples of links between tern behavior and conservation are also briefly reviewed, such as behavioral toxicology research and studies of behavioral responses to human disturbance and manmade structures. More work is needed on the behavior of migratory terns at staging sites, stopover sites and wintering grounds, and on the behavior of less well-studied species and species in less well-studied geographic regions [Current Zoology 60 （4）： 500-514, 2014].     

Survival of transplanted nests of the red wood ant Formica aquilonia （Hymenoptera： Formicidae）： The effects of intraspecific competition and forest clear-cutting

The fitness and survival of ant colonies depend on the resources near their nests. These resources may be limited due to poor habitat quality or by intra- and interspecific competitions, which in extreme cases may cause the ant colony to perish. We tested the effect of intraspecific competition and habitat degradation （forest clear-cutting） on colony survival by transplanting 26 nests of the red wood ant （Formica aquilonia Yarrow, 1955） in 26 different forest areas that contained 0-11 conspecific alien nests per hectare. F. aquilonia is highly dependent on canopy-dwelling aphids, thus the removal of trees should cause food limitation. During the course of the 4-year experiment, 9 of the forests were partially clear- cut. We found that while forest clear-cutting significantly decreased the colonies＇ survival, intraspecific competition did not. As a highly polygynous and polydomous species, E aquilonia seems to tolerate the presence of alien conspecific colonies to a certain extent.     

Toxoplasma,testosterone, and behavior manipulation: the role of parasite strain,host variations,and intensity of infection

Toxoplasma gondii is an intracellular parasite involved in the etiology of various behavioral and hormonal alterations in humans and rodents. Various mechanisms, including induction changes of testosterone production, have been proposed in the etiology of behavioral alterations during T. gondii infection. However, controversy remains about the effects of T. gondii infection on testosterone production; in some studies, increased levels of testosterone were reported, whereas other studies reported decreased levels. This is a significant point, because testosterone has been shown to play important roles in various processes, from reproduction to fear and behavior. This contradiction seems to indicate that different factors--primarily parasite strains and host variations--have diverse effects on the intensity of T. gondii infection, which consequently has diverse effects on testosterone production and behavioral alterations. This paper reviews the role of parasite strains, host variations, and intensity of T. gondii infection on behavioral alterations and testosterone production, as well as the role of testosterone in the etiology of these alterations during toxoplasmosis.     

The magic of four： induction of pluripotent stem cells from somatic cells by Oct4, Sox2, Myc and Klf4

The developmental process from a fertilized egg to agrown adult is programmed with remarkable accuracy.While the genetic information of the fertilized egg and itsdescendent somatic cells are the same, it is the selectiveexpressions of the same genome that give rise to the 200or so different cell types in an adult. The differentiatedstates of these adult cells are maintained epigenetically,presumably through the modification of chromatins and theassociated histones. In higher mammals, it was thought thatthe differentiation process is irreversible until the successfulcloning of Dolly [1]. By transferring a nucleus from a fullydifferentiated cell in the mammary gland, Wilmut and col-leagues were able to generate an exact replica of a highermammal, the Doily [1]. This work not only demonstratedthat the genome of differentiated cells can be reprogrammedinto an embryonic state and then to resume a full-fledgeddevelopmental process to generate a normal adult, but alsorejuvenated the field of animal cloning. The prospect thata somatic cell from a patient may be reprogrammed to the     

A familiar stranger:CD34 expression and putative functions in SVF cells of adipose tissue

Human adipose tissue obtained by liposuction is easily accessible and an abundant potential source of autologous cells for regenerative medicine applications. After digestion of the tissue and removal of differentiated adipocytes, the so-called stromal vascular fraction (SVF) of adipose, a mix of various cell types, is obtained. SVF contains mesenchymal fibroblastic cells, able to adhere to culture plastic and to generate large colonies in vitro , that closely resemble bone marrow-derived colony forming units-fibroblastic, and whose expanded progeny, adipose mesenchymal stem/stromal cells (ASC), show strong similarities with bone marrow mesenchymal stem cells. The sialomucin CD34, which is well known as a hematopoietic stem cell marker, is also expressed by ASC in native adipose tissue but its expression is gradually lost upon standard ASC expansion in vitro . Surprisingly little is known about the functional role of CD34 in the biology and tissue forming capacity of SVF cells and ASC. The present editorial provides a short introduction to the CD34 family of sialomucins and reviews the data from the literature concerning ex- pression and function of these proteins in SVF cells and their in vitro expanded progeny.     

Soil Organic Matter Dynamics Along a Vertical Vegetation Gradient in the Gongga Mountain on the Tibetan Plateau

Our knowledge about soil organic matter (SOM) dynamics is limited although this is an important issue in the study of responses of ecosystems to global climate changes. Twelve sampling plots were set up every 200 m from 1 700 to 3 900 m along the vertical vegetation gradient along the east slope of Gongga Mountain. Samples were taken from all 12 plots for SOM content measurement, although only 5 of the 12 plots were subjected to radiocarbon measurements. A radiocarbon isotope method and a time-dependent model were used to quantify the SOM dynamics and SOM turnover rates along the vertical vegetation gradient. The results showed that the SOM turnover rate decreased and turnover time increased with soil depth for all vegetation types. The litter layer turnover rates presented a clear trend along the gradient. The litter layer turnover rates decreased with an increase in elevation, except that the litter layer turnover rate of mixed forest was higher than that of evergreen forest. Climatic factors, such as temperature and precipitation, were the main factors influencing the surface soil carbon dynamics. The turnover rates of the subsoil (including the A, B, and C horizons in the soil profiles) along the vertical gradient had no clear trends. The SOM of subalpine shrub and meadow turned over more slowly than that of the forest types in almost all soil horizons. The characteristic of short roots distributing in the upper part of the soil profile leads to different SOM dynamics of shrub and meadow compared with the forest types. Coniferous and mixed forests were susceptible to carbon loss from the young carbon pool, but their long and big roots resulted in high △^14C values of the deep soil profiles and increased the input of young carbon to the deep soil. In evergreen forest, the carbon cumulative ability from the B horizon to the C horizon was weak. The different vegetation types, together with their different modes of nutrient and carbon intake, may be the mechanism conditioning the subsoil organic matter dynamics.     

Aphid populations showing differential levels of virulence on Capsicum accessions

The green peach aphid,Myzus persicae,is one of the most threatening pests in pepper cultivation and growers would benefit from resistant varietices.Previously,we identified two Capsicum acessions as susceptible and three as resistant to M.persicae using an aphid population originating from the Netherlands(NL).Later on we identified an aphid population originating from a diferent gcographical region(Switserland,SW)that was virulent on all tested Capsicum acessions.The objeetive of the current work is to describe in detail diferent aspects of the interaction between two aphid populations and two sclected Capsicum acessions(one that was susceptible[PB2013046]and one that was resistant[PB2013071]to population NL),including biochemical processes involved.Electrical penetration graph(EPG)recordings showed similar feeding activities for both aphid populations on PB2013046.On acession PB2013071 the aphid population sw was able to devote significantly more time to phloem ingestion than population NL.We also studied plant defense response and found that plants of acession PB2013046 could not induce an accumulation of reactive oxygen species and callose formation after infestation with either aphid population.However,plants of PB2013071 induced a stronger defense response after infestation by population NL than after infestation by population SW.Based on these results,population SW of M.persicae seems to have overcome the resistance of PB2013071 that prevented feeding of aphids from NL population.The potential mechanism by which SW population overcomes the resistance is discussed.     

Chemical deception among ant social parasites

Deception is widespread throughout the animal kingdom and various deceptive strategies are exemplified by social parasites. These are species of ants, bees and wasps that have evolved to invade, survive and reproduce within a host colony of another social species. This is achieved principally by chemical deception that tricks the host workers into treating the invading parasite as their own kin. Achieving levels of acceptance into typically hostile host colonies requires an amazing level of decep- tion as social insects have evolved complex species- and colony-specific recognition systems. This allows the detection of for- eigners, both hetero- and con-specific. Therefore, social parasitic ants not only have to overcome the unique species recognition profiles that each ant species produces, but also the subtle variations in theses profiles which generate the colony-specific profiles We present data on the level of chemical similarity between social parasites and their hosts in four different systems and then discuss these data in the wider context with previous studies, especially in respect to using multivariate statistical methods when looking for differences in these systems.     

Up-regulation of Bcl-2 is required for the progression of prostate cancer cells from an androgen-dependent to an androgen-independent growth stage

Bcl-2 is an anti-apoptotic oncoprotein and its protein levels are inversely correlated with prognosis in many cancers.However, the role of Bcl-2 in the progression of prostate cancer is not clear. Here we report that Bcl-2 is required for theprogression of LNCaP prostate cancer cells from an androgen-dependent to an androgen-independent growth stage. ThemRNA and protein levels of Bcl-2 are significantly increased in androgen-independent prostate cancer cells. shRNA-medi-ated gene silencing of Bcl-2 in androgen-independent prostate cancer cells promotes UV-induced apoptosis and suppressesthe growth of prostate tumors in vivo. Growing androgen-dependent cells under androgen-deprivation conditions resultsin formation of androgen-independent colonies; and the transition from androgen-dependent to androgen-independentgrowth is blocked by ectopic expression of the Bcl-2 antagonist Bax or Bcl-2 shRNA. Thus, our results demonstratethat Bcl-2 is not only critical for the survival of androgen-independent prostate cancer cells, but is also required for theprogression of prostate cancer cells from an androgen-dependent to an androgen-independent growth stage.     

Spatial distribution of Vespa velutina individuals hunting at domestic honeybee hives： heterogeneity at a local scale

Since its recent introduction into Europe, the yellow-legged hornet, Vespa velutina, has become a major predator of the domestic honeybee, Apis mellifera, but little is known about its hunting behavior. We studied V. velutina hunting behavior by a capture- mark-recapture procedure in an experimental apiary. A total of 360 hornets were captured and tagged, and we determined： （i） the number of hornets visiting the apiary and the changes in time, （ii） the average number of individual visits per half-day and the time elapsed between consecutive recaptures, and （iii） the individual and global distribution of the hornets in the apiary. More than 50% of the marked hornets were recaptured at least once, this increased to 74% in considering the first marked individuals. We estimated 350 hornets visiting the patch daily with at least 1 visit per half-day. The number of marked hornets decreased over time while the number of unmarked ones increased, suggesting a turnover of individuals. The reduction of the delay between consecutive visits indicates that hornets became more efficient over time. Most of the hornets （88%） were recaptured in front of different hives but, overall, the global distribution was aggregative. Hornets were mainly recaptured in front of 1 hive which was neither the smallest nor the biggest colony, suggesting that the major cue used by hornets is not the amount of food. We hypothesize that the defensive behavior of the honeybee colony could explain our results which may be promising to further studies.     

Advancement on techniques for the separation and maintenance of the red imported fire ant colonies

Advancement has recently been made on the techniques for separating and maintaining colonies of red imported fire ants, Solenopsis invicta Buren. A new brood rescue method significantly improved the efficiency in separating colony from mound soil. Furthermore, a new method was developed to separate brood from the colony using fire ant repellants. Finally, a cost-effective method was developed to coat containers with diluted Fluon （AGC Chemicals America, Inc, Moorestown, NJ, USA）, an aqueous polytetrafluoroethylene, to prevent housed ants from escaping a container. Usually the original Fluon solution is directly applied to the wall of the containers. Reduced concentrations of Fhion were found to be equally effective in preventing ant escape. The use of diluted Fluon solutions to coat the containers was recommended because of environmental and cost-saving benefits. Application of these new techniques can significantly reduce labor, cost and environmental contamination. This review paper collates all the new techniques in one reference which readers can use as a manual.     

Daily number of bee louse （Braula coeca） in honey bee （Apis mellifera carnica and A. m. syriaca） colonies maintained under semi-arid conditions

Experimental work was conducted at two apiaries located in Irbid district and in Shuna North, Jordan, during the years 2004-2006. The aims of these investigations were to estimate the seasonal changes in the infestation rates of the bee louse （Braula sp.） and to develop an easy and rapid method of estimating the infestation rate on workers with bee Braula. Two major honey bee subspecies are reared in Jordan; Apis mellifera carnica and Apis mellifera syriaca were used in this study. The results showed that the infestation rate began to increase rapidly in May, reaching the season＇s maximum rate of 16.2%, 15.8% and 17.4% forA. m. carnica and 22.6%, 23.9% and 22.9% forA. m. syriaca in December of 2004, 2005 and 2006, respectively. The maximum adult numbers of bees were found in April and June, whereas the minimum for the year was in January in both honey bee subspecies colonies during the study period. The actual population of the bee louse could be estimated by counting the daily dropped lice and multiplying by a factor of 158. This factor is valid for the experimental colonies of both subspecies kept for 3 years under semi-arid Mediterranean conditions.     

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach （Prunus persica）

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.     

Influence of visual targets and landmarks on honey bee foraging and waggle dancing

Animals use diverse sensory stimuli to navigate their environment and to recognize rewarding food sources.Honey bees use visual atributes of the targeted food source,such as its color,shape,size,direction and distance from the hive,and the landmarks around it to navigate during foraging.They transmit the location information of the food source to other bees if it is highly rewarding.To investigate the relative importance of these attributes,we trained bees to feeders in two different experiments.In the first experiment,we asked whether bees prefer to land on(a)a similar feeder at a different distance on the same heading or on(b)a visually distinct feeder located at the exact same location.We found that,within a short foraging range,bees relied heavily on the color and the shape of the food source and to a lesser extent on its distance from the hive.In the second experiment,we asked if moving the main landmark or the feeder(visual target)influenced recruitment dancing for the feeder.We found that foragers took longer to land and danced fewer circuits when the location of the food source,or a major landmark associated with it,changed.These results demonstrate that prominent visual atributes of food sources and landmarks are evidently more reliable than distance information and that foraging bees heavily utilize these visual cues at the later stages of their journey.     

Asymmetry in genitalia is in sync with lateralized mating behavior but not with the lateralization of other behaviors

Asymmetries in bilateral organisms attract a lot of curiosity given that they are conspicuous departures from the norm.They allow the investigation of the integration at different levels of biological organization.Here we study whether and how behavioral and asymmetrical anatomical traits coevolved and work together.We ask if asymmetry is determined locally for each trait or at a whole individual level in a species bearing conspicuous asymmetrical genitalia.Asymmetric genitalia evolved in many species;however,in most cases the direction of asymmetry is fixed.Therefore,it has been rarely determined if there is an association between the direction of asymmetry in genitalia and other traits.In onesided livebearer fish of the genus Jenynsia(Cyprinodontiformes,Anablepidae),the anal fin of males is modified into a gonopodium,an intromittent organ that serves to inseminate females.The gonopodium shows a conspicuous asymmetry,with its tip bending either to the left or the right.By surveying 13 natural populations of Jenynsia lineata,we found that both genital morphs are equally common in wild populations.In a series of experiments in a laboratory population,we discovered asymmetry and lateralization for multiple other traits;yet,the degree of integration varied highly among them.Lateralization in exploratory behavior in response to different stimuli was not associated with genital morphology.Interestingly,the direction of genital asymmetry was positively correlated with sidedness of mating preference and the number of neuromasts in the lateral line.This suggests integration of functionally linked asymmetric traits;however,there is no evidence that asymmetry is determined at the whole individual level in our study species.     

Altered Redox Status in Erythrocytes From Hypertensive Subjects： Effect of （-）Epicatechin

Hypertension is a major problem worldwide. There is much evidence to suggest that reactive oxygen species (ROS) radical may play a role in the development of organ damage associated with cardiovascular disease and hypertension. ( － )Epicatechin, a member of tea catechins belonging to flavonoid group, is known to be a potent anti-oxidant. The study has been undertaken to evaluate the effect of ( － )epicatechin on markers of oxidative stress: reduced glutathione (GSH) and membrane sulfhydryl ( — SH) groups in erythrocytes from hypertensive patients. The effect of ( － )epicatechin was also compared with a known anti-oxidant L-ascorbic acid. The erythrocyte intracellular GSH content and membrane — SH group content were significantly (P<0.01) decreased in hypertensive subjects. In vitro incubation with ( － )epicatechin caused an increase in GSH and — SH content, the effect was more pronounced in hypertensive erythrocytes. Similar results were obtained with L-ascorbic acid. The observed decrease in the level of GSH and — SH groups in hypertension is an indicator of oxidative stress condition. Observation of an increase in red cell GSH content and the protection of membrane — SH group oxidation by ( － )epicatechin in hypertensive subjects is a convincing reason to suggest that high dietary intake of foods rich in catechins may help to reduce oxidative stress and concomitant free radical damage in hypertensive patients.     

Nitrogen released from different plant residues of the Loess Plateau and their additions on contents of microbial biomass carbon, nitrogen in soil

An incubation method was used to investigate the nitrogen release characteristics from the residue of ten plant species which commonly grow in the northern part of the Loess Plateau. The effect of the residue on soil microbial biomass carbon (SMBC) and soil microbial biomass nitrogen (SMBN) was also determined. There were significant differences in the total N content and the C/N ratios among the different types of plant residue. The total N content of the residues ranged from 6.61 to 32.78 g kg^?1. The C/N ratio of the residue ranged from 14 to 65. There was an immediate increase in soil N after alfalfa, erect milkvetch, and korshinsk peashrub residue was added to the soil. In contrast, soil N decreased after elm, sea buckthorn, and wild peach residue was added to the soil. The soil N content remained relatively low for 14–34 days and then increased. This indicated that N immobilization occurred during the early portion of the incubation period when elm, sea buckthorn and wild peach residue was added to the soil. Soil N levels were low during the entire incubation period when simon poplar, locust, Stipa bungeana, and old world bluestem residue were added to the soil. The addition of plant residue significantly increased SMBC and SMBN in all treatments. The SMBC and SMBN values were greatest in treatments containing plant residue with high total N content and low C/N ratios. The C/N ratios of korshinsk peashrub, sea buckthorn, and wild peach residues were similar, but the amount of N released from these residues and the effects of the residue on SMBC and SMBN in soil were significantly different. This indicates that not only the C/N ratio but also the chemical composition of the plant residue affected decomposition. It is important to consider C and N release characteristics from plant residue in order to adjust the C and N balance of soil when revegetating degraded ecosystems.     

Impacts of recreational trampling on sub-alpine vegetation and soils in Northwest Yunnan, China

Controlled trampling experiments were undertaken to assess impacts of recreation in a sub-alpine environment in an upper-Mekong mountainous protected area in China. Hiking and recreational horse-riding were applied at different trampling intensity to two typical, widespread vegetation types (Carex grassland and low Rhododendron shrubland) and trampling effects were assessed to study vegetation resistance and soil compaction. The results indicate: (1) low shrub vegetation is highly vulnerable to trampling damage while the graminoids-dominated grassland is more resistant; (2) dry soil with low organic matter, which often is found in the shrubland, is more susceptible to compaction than wet soil and (3) horses cause substantially more damage than hikers at equivalent trampling levels. These data are useful to develop a visitor’s management strategy that allows to minimize the impact from recreation on the vegetation.