Revisiting historical Khoe-San skeletal remains in European collections: A search for identity through craniometric analysis

As the identity of a large number of Khoe-San skeletal material in European collections recently came into question during its documentation, a re-evaluation of the remains by employing a non-invasive method such as craniometrics was done to investigate the biological affinity. For this purpose, gene flow and population diversity present within the group, as well as between the study sample (N = 63) and other modern and historic population groups from southern, central and east Africa were explored. Available comparative groups included the historic Khoe-San from Riet River (N = 31), the Sotho-Tswana from southern Africa (N = 61), the Basuku from central Africa (N = 66) and the Bahutu (N = 53) and Teita (N = 24) from east Africa. Ten craniometric variables were selected and used to perform population structure analysis based on model bound quantitative genetics and multiple discriminant function analysis (MDA). Quantitative genetic distances revealed that the Khoe-San sample was closest to the Riet River group. Residual variance analysis performed on two-sample subsets of the Khoe-San group (Cape KS and Various KS) showed a higher level of heterogeneity in the Cape KS than seen in the Khoe-San from various other areas in southern Africa. MDA revealed that Khoe-San intra-sample variance is relatively high, with 44% of the sample (sexes pooled) classified into the Riet River group. The remaining individuals were classified (in decreasing order) into Bahutu (24%), Basuku (24%) and Sotho-Tswana (8%). Although the Khoe-San specimens are closest to the Riet River group, they are clearly not homogenous. Their high level of phenotypic diversity most likely originated from a complex population history involving many group interactions driven by social and political marginalization.     

FT-IR microspectroscopy: a promising method for the rapid identification of Listeria species

This work presents a pilot study to investigate the potential of fourier transform infrared (FT-IR) microspectroscopy for rapid identification of Listeria at the species level. Using this technique, FT-IR spectra were acquired from 30 strains from five Listeria species. The FT-IR spectra were analysed using stepwise canonical discriminant analysis and partial least-squares regression in a stepwise identification scheme. The results showed that 93% of all the samples were assigned to the correct species, and that 80% of the Listeria monocytogenes strains were correctly identified. In comparison, 100% of the samples, including the L. monocytogenes samples, were correctly identified using spectra acquired by FT-IR macrospectroscopy. The results show that FT-IR microspectroscopy has potential as a rapid screening method for Listeria, which is especially valuable for the food industry.     

离散增量结合二次判别分析预测人类DNA甲基化位点

DNA甲基化作为直接作用于DNA序列的一种表观遗传修饰,能够在不改变DNA分子一级结构的情况下影响基因表达,在生命活动中扮演着重要的角色.在哺乳动物中,DNA甲基化主要发生在C_pG二核苷酸的胞嘧啶上,并且在基因组中呈现不均匀分布.准确预测DNA甲基化位点有助于阐明DNA甲基化对基因表达的调控作用,并为肿瘤的早期诊断及治疗提供新的依据.本文应用离散增量结合二次判别分析的方法,对人类的C_pG二核苷酸甲基化状态进行了识别.5折交叉检验的整体准确率超过了80%,受试者操作特性曲线面积也达到了0.86.与现有方法相比,预测成功率显著提高.这说明离散增量结合二次判别分析方法适用于甲基化位点的预测;基因组序列中甲基化位点具有序列依赖性.     

Assessment of a dry and a wet route for the production of biofuels from microalgae: energy balance analysis

In this study, the energy balance of two microalgae-to-biofuel concepts, one via a so called “dry route” (oil extraction from dried algae) and one via a “wet route” (oil extraction in the water phase), are assessed. Both routes are intended to convert the chemical energy contained in the microalgae into high-value biofuels with minimal fossil energy consumption. The analysis shows that the drying process in the dry route and the oil extraction process in the wet route consume a significant amount of energy. By coupling waste heat from a nearby power plant to the process, the energy balance can be improved and a potential fossil energy ratio (FER) up to 2.38 and 1.82 can be reached for the dry and wet route, respectively. The results indicate that based on current available technologies, the dry route has higher FER and the wet route has more potential in producing high valuable biofuels.     

Argyrophilic nucleolar organizer region (AgNOR) technique: a helpful tool for differential diagnosis in urinary cytology

The aim of this study was to investigate whether the AgNOR technique could be helpful for the cytologic diagnosis of neoplastic and non-neoplastic urinary tract lesions. We analysed the AgNOR pattern in urinary cytology in samples from 70 patients. In every case the average number of silver precipitations per nucleus was counted and the range between the minimum and maximum AgNOR value calculated. Furthermore we noted whether the AgNOR precipitations had a homogeneous or heterogeneous distribution. The diseases were classified in three groups: non-neoplastic lesions, low grade and high grade carcinoma. Linear discriminant analysis (with jack-knife procedure) was performed with the AgNOR parameters as independent variables. The final diagnosis of each patient had been established by histological analysis of bladder biopsies. We obtained a correct classification in 84.3% of the cases. All patients with normal or reactive lesions were correctly classified and only two cases of low grade malignancy were erroneously diagnosed as non-malignant. Five high grade neoplasms had been classified as low grade and four low grade carcinomas had been over-diagnosed as high grade neoplasms. We conclude that a combined qualitative and quantitative AgNOR analysis can be useful in the differential diagnosis of urinary cytology.     

Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment

K. Yamashiro, M. Tagami, K. Azuma, A. Nakamura, O. Kato, K. Taira, M. Azuma, H. Takeda and H. Suzuki Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment Objective: This study examined whether cytological diagnosis through the use of a video, which shows the changing depth of focus in the microscopic field, described as a z‐axis video, is useful compared with a still image. Methods: From 17 cytology preparations of fine needle aspiration of the breast, we made six z‐axis videos per case. A frame exhibiting the characteristic features was then extracted from each video and saved as a representative still image. One hundred and twenty‐eight volunteer cytotechnologists were randomly divided into two groups of video observers and still image observers. The participants were asked to make a diagnosis of benign, indeterminate, suspicious or malignant without having any clinical information other than the age of the patient. Diagnoses were categorized as ‘recommended’ or ‘unacceptable’ according to degree of correlation with histology. Results: The number of definitive diagnoses of ‘benign’ or ‘malignant’ were increased in video observers, and indeterminate or suspicious categories were decreased (P = 0.013). The distribution of diagnostic categories in three of the 17 cases was significantly different; the distribution in the remaining cases was similar between the two groups. The z‐axis video observers may have selected the definite diagnoses with confidence because they observed valuable microscopic findings by ‘focusing through observation’. The average number of ‘recommended’ diagnoses by individual observers was significantly higher in the video observer group than in the still image observer group (P = 0.016). In contrast, the average number of ‘unacceptable’ diagnoses was significantly lower (P = 0.019). Conclusions: A z‐axis video is easy to obtain and is therefore expected to become a powerful diagnostic modality for the external quality assessment of clinical cytology and even in the field of primary cytodiagnosis.     

Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering

Rational metabolic engineering requires powerful theoretical methods such as pathway analysis, in which the topology of metabolic networks is considered. All metabolic capabilities in steady states are composed of elementary flux modes, which are minimal sets of enzymes that can each generate valid steady states. The modes of the fructose-2,6-bisphosphate cycle, the combined tricarboxylic-acid-glyoxylate-shunt system and tryptophan synthesis are used here for illustration. This approach can be used for many biotechnological applications such as increasing the yield of a product, channelling a product into desired pathways and in functional reconstruction from genomic data.     

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Background

Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.

Results

We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

Conclusions

InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net.     

Maintenance of polygenic variation through mutation-selection balance: bifurcation analysis of a biallelic model

Biallelic models which ignore linkage disequilibrium have been used to study variability maintained by mutation in the presence of Gaussian stabilizing selection. Recent work of Barton (1986) showed that these models have stable equilibria at which the mean phenotype differed from the optimum, and that the variability maintained at such equilibria would be higher than at the symmetric equilibria calculated by Bulmer (1980) and others. Here I determine the bifurcation structure of this model, and confirm and extend Barton's results. The form of the bifurcations gives information about the domains of attraction of various equilibria, and shows why the nonsymmetric equilibria may not be observed. The techniques may prove useful in the analysis of other population genetic models.     

Photosensitivity in Smith-Lemli-Opitz syndrome: a flux balance analysis of altered metabolism

Ultraviolet A photosensitivity is a debilitating symptom associated with the metabolic disorder Smith-Lemli-Opitz syndrome (SLOS). SLOS is a manifestation of the deficiency of 7-dehydrocholesterol reductase, an enzyme involved in the cholesterol biosynthesis. As a result several abnormal intermediary compounds are formed among which Cholesta 5, 7, 9(11)-trien-3beta-ol is the most likely cause of photosensitivity. The effect of various drugs acting on cholesterol biosynthetic pathway on SLOS is not clear as clinical trials are not available for this rare disorder. A Flux Balance Analysis (FBA) has been carried out using the software CellNetAnalyzer or FluxAnalyzer to gain insight into the probable effects of various drugs acting on cholesterol biosynthetic pathway on photosensitivity in SLOS. The model consisted of 44 metabolites and 40 reactions. The formation flux of Cholesta 5, 7, 9(11)-trien-3beta-ol increased in SLOS and remained unchanged on simulation of the effect of miconazole and SR31747. However zaragozic acid can potentially reduce the flux through the entire pathway. FBA predicts zaragozic acid along with cholesterol supplementation as an effective treatment for photosensitivity in SLOS.     

Relating new information to a previous vegetation classification: a case of discriminant coordinates analysis

Discriminant coordinates analysis is an adequate technique for analyzing the linear relationships between a number of new variates (i.e. environmental or functional attributes) and a set of vegetational attributes already summarized in the form of a classification. It displays the principal differences among classes in relation to the new variates considered. The procedure and its rationale are equivalent to a special case of principal components analysis.A case study on radiometer satellite data is presented. Two discriminant coordinates displayed the main differences in the seasonal dynamics of the NDVI (an index of standing green biomass) among broad phytogeo-graphic units in the Patagonia region. The first coordinate can be interpreted as an index of height and convexity of the NDVI seasonal curve. It suggests that the principal difference among regions was the total seasonal growth. The second coordinate represents a contrast that discriminated between two already detected patterns of seasonal NDVI curve.Abbreviations DC Discriminant Coordinate - NDVI Normalized Difference Vegetation Index     

Correlation between soil characters and forest types: a study in multiple discriminant analysis

Multiple discriminant analysis is a useful multivariate technique in vegetation studies that can be employed for several purposes, even if the underlying statistical assumptions are not satisfied. An example of application of this method is discussed: multiple discriminant analysis was successfully used for evaluating the predictivity of forest types defined by numerical classification of vegetation data with respect to soil variables.Species nomenclature follows Pignatti (1982) for vascular plants and Augier (1966) for mosses.The research has been supported by the IDROSER (Bologna, Italy) and by the Italian C. N. R. (Grant no. 83.02548.04, resp. Prof. A. Pirola). We wish to thank Prof. E. Feoli, Prof. E. van der Maarel, Prof. L. Orlóci and Prof. A. Pirola for suggestions. We are also indebted to Dr N. Filippi who analyzed the soil samples.     

ACUA: a software tool for automated codon usage analysis

Currently available codon usage analysis tools lack intuitive graphical user interface and are limited to inbuilt calculations. ACUA (Automated Codon Usage Tool) has been developed to perform high throughput sequence analysis aiding statistical profiling of codon usage. The results of ACUA are presented in a spreadsheet with all perquisite codon usage data required for statistical analysis, displayed in a graphical interface. The package is also capable of on-click sequence retrieval from the results interface, and this feature is unique to ACUA. AVAILABILITY: The package is available for non-commercial purposes and can be downloaded from: http://www.bioinsilico.com/acua.     

Comparison and analysis of objective functions in flux balance analysis

Flux balance analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over them, assuming that cellular metabolism is in steady state. Therefore, the obtained flux distribution depends on the specific objective function used. Multiple studies have been aimed to compare distinct objective functions at given conditions, in order to determine which of those functions produces values of fluxes closer to real data when used as objective in the FBA; in other words, what is the best objective function for modeling cell metabolism at a determined environmental condition. However, these comparative studies have been designed in very dissimilar ways, and in general, several factors that can change the ideal objective function in a cellular condition have not been adequately considered. Additionally, most of them have used only one dataset for representing one condition of cell growth, and different measuring techniques have been used. For these reasons, a rigorous study on the effect of factors such as the quantity of used data, the number and type of fluxes utilized as input data, and the selected classification of growth conditions, are required in order to obtain useful conclusions for these comparative studies, allowing limiting clearly the application range on any of those results. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:985–991, 2014     

The genus Poa in Patagonia (Argentine): a phenetic analysis of species of Poa subgenus Poa

Fifty-eight quantitative and qualitative exomorphological characters were recorded on 48 herbarium specimens belonging to rhizomatous species belonging to the genus Poa. These were treated as OTUs and analysed, together with the data from caespitose species treated in a previous paper, using cluster analysis, principal component analyses and stepwise discriminant analyses. The following hypotheses are proposed and discussed. (1) There is no evidence supporting the hypothesis that growth habit characterizes supraspecific entities. (2) P. trivialis, P. secunda, P. subenervis and probably P. compressa seem to be well defined species; those remaining are not discriminated through phenetic analysis. (3) There are no phenetic gaps between the rhizomatous species included in the P. oligeria—P. yaganica-P. chrysantha complex and the caespitose P. hachadoensis it is not clear that this single character supports its segregation. (4) The obscurity of the pattern of the species related to P. pratensis-P. nemoralis is probably explained by the capability of P. pratensis to introgress with taxonomically distant species and by the possibility of seasonal intraindividual variation of some characters. (5) The geographical origin of some species postulated as introduced seems to be doubtful.     

Kiwi: a tool for integration and visualization of network topology and gene-set analysis

Background

The analysis of high-throughput data in biology is aided by integrative approaches such as gene-set analysis. Gene-sets can represent well-defined biological entities (e.g. metabolites) that interact in networks (e.g. metabolic networks), to exert their function within the cell. Data interpretation can benefit from incorporating the underlying network, but there are currently no optimal methods that link gene-set analysis and network structures.

Results

Here we present Kiwi, a new tool that processes output data from gene-set analysis and integrates them with a network structure such that the inherent connectivity between gene-sets, i.e. not simply the gene overlap, becomes apparent. In two case studies, we demonstrate that standard gene-set analysis points at metabolites regulated in the interrogated condition. Nevertheless, only the integration of the interactions between these metabolites provides an extra layer of information that highlights how they are tightly connected in the metabolic network.

Conclusions

Kiwi is a tool that enhances interpretability of high-throughput data. It allows the users not only to discover a list of significant entities or processes as in gene-set analysis, but also to visualize whether these entities or processes are isolated or connected by means of their biological interaction. Kiwi is available as a Python package at http://www.sysbio.se/kiwi and an online tool in the BioMet Toolbox at http://www.biomet-toolbox.org.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0408-9) contains supplementary material, which is available to authorized users.