Comparison of adult stem cells derived from multiple stem cell niches

Objectives

Adult stem cells (ASCs) have great potential for tissue regeneration; however, comparative studies of ASCs from different niches are required to understand the characteristics of each population for their potential therapeutic uses.

Results

We compared the proliferation, stem cell marker expression, and differentiation potential of ASCs from bone marrow, skin dermis, and adipose tissue. ASCs from bone marrow and skin dermis showed 50–100 % increased proliferation in comparison to the ASCs from adipose tissues. Furthermore, ASCs from each stem cell niche showed differential expression of stem cell marker genes, and preferentially differentiated into cell types of their tissue of origin.

Conclusion

Different characters of each ASC might be major factors for their effective use for therapeutics and tissue regeneration.

     

Investigation of the relationship between cell surface hydrophobicity and demulsifying capability of biodemulsifier-producing bacteria

Background

Cell surface hydrophobicity (CSH) is one of the key physicochemical features of biodemulsifier-producing bacteria that influence their demulsification capability maintenance in petroleum contaminated environments.

Methods

In present study, biodemulsifier-producing bacteria were isolated from petroleum contaminated environments using different isolation media and the correlation between their CSH and demulsifying ability was investigated. The demulsifying ability of isolates was measured through demulsification tests on water in kerosene emulsions. The microbial adhesion to the hydrocarbon (MATH) assay was used to denote their CSH.

Results

The evaluation of CSH showed that majority of biodemulsifier producing bacteria have high CSH which indicating a positive correlation between CSH and demulsifying capability.

Conclusions

According to these results it can be concluded that CSH can be used as an indicator for assessment of biodemulsifier-producing bacteria and screening of new isolates for their biodemulsifier production.

     

Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

Background

Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology.

Methods

We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching.

Results

We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix.

Conclusions

The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

     

Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy

Background

Metabolomics has been recognized as a powerful approach for disease screening. In order to highlight potential health issues in subjects, a key factor is the possibility to compare quantitatively the metabolome of their biofluids with reference values from healthy individuals. Such efforts towards the systematic characterization of the metabolome of biofluids in perfect health conditions, far from concluded for humans, have barely begun on horses.

Objectives

The present work attempts, for the first time, to give reference quantitative values for the molecules mostly represented in the urine metabolome of horses at rest and under light training, as observable by ¹H-NMR.

Methods

The metabolome of ten trotter horses, four male and six female, ranging from 3 to 8 years of age, has been observed by ¹H-NMR spectroscopy before and after three training sessions.

Results

We could characterize and quantify 54 molecules in trotter horse urine, originated from diet, protein digestion, energy generation or gut-microbial co-metabolism.

Conclusion

We were able to describe how gender, age and exercise affected their concentration, by means of a two steps protocol based on univariate and robust principal component analysis.

     

SNP‐based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen‐free rhesus macaque (Macaca mulatta) populations

Background

The rhesus macaque is an important biomedical model organism, and the Tulane National Primate Research Center (TNPRC) has one of the largest rhesus macaque breeding colonies in the United States.

Methods

SNP profiles from 3266 rhesus macaques were used to examine the TNPRC colony genetic composition over time and across conventional or SPF animals of Chinese and Indian ancestry.

Results

Chinese origin animals were the least genetically diverse and the most inbred; however, since their derivation from their conventional forebearers, neither the Chinese nor the Indian SPF animals exhibit any significant loss of genetic diversity or differentiation.

Conclusions

The TNPRC colony managers have successfully minimized loss in genetic variation across generations. Although founder effects and bottlenecks among the Indian animals have been successfully curtailed, the Chinese subpopulation still show some influences from these events.     

Are Neoclassical Canons Valid for Southern Chinese Faces?

Background

Proportions derived from neoclassical canons, initially described by Renaissance sculptors and painters, are still being employed as aesthetic guidelines during the clinical assessment of the facial morphology.

Objective

1. to determine the applicability of neoclassical canons for Southern Chinese faces and 2. to explore gender differences in relation to the applicability of the neoclassical canons and their variants.

Methodology

3-D photographs acquired from 103 young adults (51 males and 52 females) without facial dysmorphology were used to test applicability of four neoclassical canons. Standard anthropometric measurements that determine the facial canons were made on these 3-D images. The validity of the canons as well as their different variants were quantified.

Principal Findings

The neoclassical cannons seldom applied to these individuals, and facial three-section and orbital canons did not apply at all. The orbitonasal canon was most frequently applicable, with a frequency of 19%. Significant sexual dimorphism was found relative to the prevalence of the variants of facial three-section and orbitonasal canons.

Conclusion

The neoclassical canons did not appear to apply to our sample when rigorous quantitative measurements were employed. Thus, they should not be used as esthetic goals for craniofacial surgical interventions.     

Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study

Background

Phylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed.

Question

Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets?

Data

I conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002–2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117.

Analysis Method

I used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared.

Conclusions

For phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data.     

Warming drives poleward range contractions of Beringian endemic plant species at high latitudes

Aim

Species are expected to disperse poleward in response to climate change. For species that are endemic to the high latitudes, this implies that many in the future would face a “no-where-to-go” situation as they are currently occupying the northernmost portion of the continent. Further, because endemism may arise from a combination of physical barriers, climate and geological history, the persistence of many species may require spatial matching of multiple environmental factors within a limited dispersal space. Thus, it is not clear how endemic species might spatially adjust their distributions in response to climate change and whether there are future climate change refugia for these species.

Location

Northwest North America.

Taxa

Plants.

Time Period

Current and the future (2040).

Methods

We used ensemble bioclimatic models to evaluate drivers and directional patterns of future change in the distributions of 66 North American Beringian and amphi-Beringian species currently occurring in Alaska and the Yukon. We explored the spatial pattern of species richness, losses and climate change refugia across the region.

Results

More than 80% of the species showed northward shifts in their latitudinal centroids under intermediate warming and are expected to shift their range northward by more than 140 km on average by 2040. Additionally, more than 60% were projected to experience range contractions and up to 20% of the species would have the potential to expand their ranges by more than 100%.

Main Conclusions

Suitable habitat for endemic species in northwest North America is expected to decline significantly, especially for species occupying the Arctic tundra. Although the models identified several potential refugia from future climate change, especially at high latitude and elevation, whether the species would be able to colonize new habitats on their own and/or capitalize sufficiently on in situ refugia remains a pertinent conservation question.     

Applying the scientific method when assessing the influence of migratory birds on the dispersal of H5N1

Background

The epidemiology of viral hepatitis during pregnancy is essential for health planners and programme managers. While much data exist concerning viral hepatitis during pregnancy in many African countries, no proper published data are available in Sudan.

Aim

The study aimed to investigate the sero-prevalance and the possible risk factors for hepatitis B virus (HBV) and hepatitis C virus (HCV) among antenatal care attendants in central Sudan.

Methods

During 3 months from March–June 2006, sera were collected from pregnant women at Umdurman Maternity Hospital in Sudan, and they were tested for markers of hepatitis B virus (HBVsAg) and HCV.

Results

HBVsAg was detected in 41 (5.6%) out 728 women, Anti-HCV was detected in 3 (0.6%) out of 423 women, all of them were not aware of their condition. Age, parity, gestational age, residence, history of blood transfusion, dental manipulations, tattooing and circumcision did not contribute significantly to increased HBVsAg sero-positivity.

Conclusion

Thus 5.6% of pregnant women were positive for HBVsAg irrespective of their age, parity and socio-demographic characteristics. There was low prevalence of Anti-HCV.     

A New Method to Quantify and Compare the Multiple Components of Fitness—A Study Case with Kelp Niche Partition by Divergent Microstage Adaptations to Temperature

Point 1

Management of crops, commercialized or protected species, plagues or life-cycle evolution are subjects requiring comparisons among different demographic strategies. The simpler methods fail in relating changes in vital rates with changes in population viability whereas more complex methods lack accuracy by neglecting interactions among vital rates.

Point 2

The difference between the fitness (evaluated by the population growth rate λ) of two alternative demographies is decomposed into the contributions of the differences between the pair-wised vital rates and their interactions. This is achieved through a full Taylor expansion (i.e. remainder = 0) of the demographic model. The significance of each term is determined by permutation tests under the null hypothesis that all demographies come from the same pool.

Point 3

An example is given with periodic demographic matrices of the microscopic haploid phase of two kelp cryptic species observed to partition their niche occupation along the Chilean coast. The method provided clear and synthetic results showing conditional differentiation of reproduction is an important driver for their differences in fitness along the latitudinal temperature gradient. But it also demonstrated that interactions among vital rates cannot be neglected as they compose a significant part of the differences between demographies.

Point 4

This method allows researchers to access the effects of multiple effective changes in a life-cycle from only two experiments. Evolutionists can determine with confidence the effective causes for changes in fitness whereas population managers can determine best strategies from simpler experimental designs.     

LitMiner: integration of library services within a bio-informatics application

Background

This paper examines how the adoption of a subject-specific library service has changed the way in which its users interact with a digital library. The LitMiner text-analysis application was developed to enable biologists to explore gene relationships in the published literature. The application features a suite of interfaces that enable users to search PubMed as well as local databases, to view document abstracts, to filter terms, to select gene name aliases, and to visualize the co-occurrences of genes in the literature. At each of these stages, LitMiner offers the functionality of a digital library. Documents that are accessible online are identified by an icon. Users can also order documents from their institution's library collection from within the application. In so doing, LitMiner aims to integrate digital library services into the research process of its users.

Methods

Case study

Results

This integration of digital library services into the research process of biologists results in increased access to the published literature.

Conclusion

In order to make better use of their collections, digital libraries should customize their services to suit the research needs of their patrons.

     

An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data

Background

Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address the missing data crudely by ignoring such atoms from their structures.

Results

In this paper, we propose an effective method for superpositioning pairwise and multiple structures without sequence alignment. It is a two-stage procedure including data reduction and data registration.

Conclusions

Numerical experiments demonstrated that our method is effective and efficient. The code package of protein structure superposition method for addressing the cases with missing data is implemented by MATLAB, and it is freely available from: http://sourceforge.net/projects/pssm123/files/?source=navbar

     

Human-induced behavioural changes of global threatened terrestrial mammals

Aim

Understanding changes in the behaviour of threatened species responding to rapidly increasing human disturbances is critical for biodiversity conservation. Here, we synthesize a meta-analysis of the cumulative effect of human disturbances on the behaviour of global threatened terrestrial mammals.

Location

Global terrestrial ecosystem.

Time Period

Data collected from 1993 to 2021.

Major Taxa Studied

Terrestrial mammals.

Results

There were significant differences in behavioural changes among categories of human disturbances (i.e. biological invasion, climate change, grazing, habitat degradation, protection management, road traffic and tourism). The effect size of road traffic on behavioural change was the largest and particularly led habitat selection to be more specialized. The effect size for habitat degradation on foraging behaviour was the largest, and the effect mainly led to a shorter time spent in foraging and a change in food selection. Changes to behaviour increased with human disturbance intensity and varied among species according to their functional traits including body mass, food habits, migration and group type. Climate change, grazing, road traffic and tourism had a greater effect on larger species. The effect size for habitat degradation on omnivorous species was the largest, while carnivorous and solitary species were more sensitive to tourism, and migratory species were especially vulnerable to climate changes.

Main Conclusions

The diverse human disturbances interact with disturbance intensity, and some species' functional traits significantly affected the behavioural change in threatened terrestrial mammals. Such behavioural changes away from predisturbance patterns may have consequences for their fitness and community interactions. The management and conservation of threatened species should incorporate knowledge of their behavioural responses to human disturbance and take into account the potential ecological consequences for biodiversity conservation.     

Do plants adjust their sex allocation and secondary sexual morphology in response to their neighbours?

Background and aims

Changes in the sex allocation (i.e. in pollen versus seed production) of hermaphroditic plants often occur in response to the environment. In some homosporous ferns, gametophytes choose their gender in response to chemical cues sent by neighbours, such that spores develop as male gametophytes if they perceive a female or hermaphrodite nearby. Here it is considered whether a similar process might occur in the androdioecious angiosperm species Mercurialis annua, in which males co-occur with hermaphrodites; previous work on a Spanish population of M. annua found that individuals were more likely to develop as males at high density.

Methods

Using a novel approach to treat plants with leachate from pots containing males or hermaphrodites of M. annua, the hypothesis that individuals assess their mating opportunities, and adjust their sex expression accordingly, was tested through an exchange of chemical cues through the soil.

Key Results

For the population under study, from Morocco, no evidence was found for soil-signal-dependent sex expression: neither sex ratios nor sex allocation differed among experimental treatments.

Conclusions

The results imply either that the Moroccan population under study behaves differently from that previously studied in Spain (pointing to potential geographical variation in plasticity for sex expression), or that our method failed to capture the signals used by M. annua for adjustment of sex expression.     

Use of Powered Prosthesis for Children with Upper Limb Deficiency at Hyogo Rehabilitation Center

Background

There has been no research investigating the use of powered prosthetic for children in Japan.

Objective

To gain better insight into the state of powered prosthesis usage and identify a ratio of rejection among children.

Methods

Subjects were 37 unilateral below elbow amputees between the ages of 0 and 16 at the time of their first experienced fitting with a powered prosthesis at our Center. The information was collected from medical records and through face-to-face interviews, and we examined rejection rate and the factors affecting the use of powered prosthesis.

Results

The rate of discontinuation was 21.6% as 8 of the 37 children stopped using powered prosthesis. All of them were fitted their prosthesis after 2 years of age, and they rejected prosthesis between 5 to 19 years. We found that the level of amputation had no influence on the use of a powered prosthesis.

Conclusions

Children fitted before 2 years of age tend to accept their powered prosthesis than those fitted after 2 years. Multidisciprinary team approach, adequate rehabilitation, detailed follow-up and involvement of parents are quite important for introducing powered prosthesis for children.     

The role of refuges in biological invasions: A systematic review

Aim

Ecological refuges buffer organisms against stressors and mediate a range of species interactions. However, their role in the context of biological invasions has yet to be synthesized, despite the increasing prevalence and impact of non-native species. To address this, we conducted a systematic review aiming to determine the extent to which refuges are considered explicitly in the invasion literature and to synthesize their function.

Location

Global.

Time period

Present day.

Major taxa studied

All.

Methods

Our search of the literature was conducted using the SCOPUS and Web of Science databases and followed the preferred reporting items for systematic reviews and meta-analyses (PRISMA) protocol. We obtained 315 records of refuge use in biological invasions from 300 studies. From each record, we extracted information relating to the experimental design, species characteristics and refuge type, where available.

Results

Refuges and refuge-mediated processes are widely reported in the invasion literature. Native species commonly use refuges to avoid non-native predation and competition, with spatial complexity and habitat heterogeneity key factors in facilitating their coexistence. Records show that artificial structures safeguard non-natives in their introduced range. However, there were key differences in the use of such structures in marine and terrestrial environments. Moreover, the enhanced structural complexity created by non-native plants and bivalves is often reported to act as a predation refuge for other species.

Main conclusions

The ubiquity of refuge-based processes suggests that refuges can play an important role in affecting the persistence, spread and impacts of non-native species, either through previously described mechanisms (i.e. refuge-mediated apparent competition and the persistent pressure scenario) or through a mechanism we describe (i.e. when non-native species use existing refuges), or both.     

A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling

Background

In conditions of nitrogen limitation, Saccharomyces cerevisiae strains differ in their fermentation capacities, due to differences in their nitrogen requirements. The mechanisms ensuring the maintenance of glycolytic flux in these conditions are unknown. We investigated the genetic basis of these differences, by studying quantitative trait loci (QTL) in a population of 133 individuals from the F2 segregant population generated from a cross between two strains with different nitrogen requirements for efficient fermentation.

Results

By comparing two bulks of segregants with low and high nitrogen requirements, we detected four regions making a quantitative contribution to these traits. We identified four polymorphic genes, in three of these four regions, for which involvement in the phenotype was validated by hemizygote comparison. The functions of the four validated genes, GCN1, MDS3, ARG81 and BIO3, relate to key roles in nitrogen metabolism and signaling, helping to maintain fermentation performance.

Conclusions

This study reveals that differences in nitrogen requirement between yeast strains results from a complex allelic combination. The identification of three genes involved in sensing and signaling nitrogen and specially one from the TOR pathway as affecting nitrogen requirements suggests a role for this pathway in regulating the fermentation rate in starvation through unknown mechanisms linking nitrogen signaling to glycolytic flux.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-495) contains supplementary material, which is available to authorized users.     

The Development of a Preference for Cocaine over Food Identifies Individual Rats with Addiction-Like Behaviors

Rationale

Cocaine dependence is characterized by compulsive drug taking that supercedes other recreational, occupational or social pursuits. We hypothesized that rats vulnerable to addiction could be identified within the larger population based on their preference for cocaine over palatable food rewards.

Objectives

To validate the choice self-administration paradigm as a preclinical model of addiction, we examined changes in motivation for cocaine and recidivism to drug seeking in cocaine-preferring and pellet-preferring rats. We also examined behavior in males and females to identify sex differences in this “addicted” phenotype.

Methods

Preferences were identified during self-administration on a fixed-ratio schedule with cocaine-only, pellet-only and choice sessions. Motivation for each reward was probed early and late during self-administration using a progressive-ratio schedule. Reinstatement of cocaine- and pellet-seeking was examined following exposure to their cues and non-contingent delivery of each reward.

Results

Cocaine preferring rats increased their drug intake at the expense of pellets, displayed increased motivation for cocaine, attenuated motivation for pellets and greater cocaine and cue-induced reinstatement of drug seeking. Females were more likely to develop cocaine preferences and recidivism of cocaine- and pellet-seeking was sexually dimorphic.

Conclusions

The choice self-administration paradigm is a valid preclinical model of addiction. The unbiased selection criteria also revealed sex-specific vulnerability factors that could be differentiated from generalized sex differences in behavior, which has implications for the neurobiology of addiction and effective treatments in each sex.     

Biases and distribution patterns in hard-bodied microscopic animals (Acari: Halacaridae): Size does not matter,but generalism and sampling effort do

Aim

The interplay between distribution ranges, species traits and sampling and taxonomic biases remains elusive amongst microscopic animals. This ignorance obscures our understanding of the diversity patterns of a major component of biodiversity. Here, we used marine Halacaridae to explore whether differences between marine provinces can explain their distribution patterns or if differential sampling efforts across regions prevent any macroecological inference. Furthermore, we test if certain functional traits influence their distribution patterns.

Location

Europe.

Results

Whereas geographical variables provided a better explanation for differences in species composition, sampling effort and distance from marine biological stations accounted for the majority of differences in European Halacaridae richness. Species occurring in more habitats showed broader geographical ranges and accumulated more records. Species traits like generalism affected the distribution of halacarid species.

Main Conclusions

We propose that the sampling effort of halacarid mites in Europe might be explained by two different cognitive biases: the convenience of selecting certain sampling localities compared to others and the tendency of zoologists to scrutinise habitats where their target organisms are more common.