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International audience; Gallium ferrite, Ga2-xFexO3 (GFO), is a promising magnetoelectric material as it exhibits both magnetic and electric orders close to room temperature. Here, we report a temperature-dependent investigation of GFO thin films with x = 1.0 and 1.4 by using Raman scattering. Our investigation suggests the absence of a structural phase transition of both films in the investigated 90-500 K temperature range, which is similar to earlier observations on bulk samples. We note, however, the occurrence of weak anomalies in the temperature-dependent band position of some phonons, which we attribute to spin-phonon coupling as the anomalies occur close to the Neel temperature of the materials.

Invited for this month's cover are the collaborating groups of Dr. Loic J. Charbonniere at CNRS/Universite de Strasbourg, France and Dr. Ka-Leung Wong at Hong Kong Baptist University, Hong Kong. The cover picture shows terbium-doped LaF3 nanoparticles that are surface functionalized by photon-harvesting antenna ligands. Surface capping with antenna ligands leads to ultrabright nanoparticles, with the typical green luminescence signature of the Tb atoms and very long excited-state lifetimes. These lanthanide dots can be incorporated into living cells at nanomolar concentrations for luminescence microscopy imaging. Read the full text of the article at 10.1002/cplu.201600007.

Silicon carbide containing cobalt (30 wt.%) doped with 0.1 wt.% of ruthenium catalysts prepared by incipient wetness impregnation of cobalt nitrate with either ethanol or water were tested in the Fischer-Tropsch synthesis (FTS) in a fixed-bed configuration. The catalyst prepared with ethanol exhibits a higher FTS performance compared to the one prepared with water and especially at high reaction temperature, i.e. 230 degrees C. The FTS performance of the cobalt-based catalyst impregnated with ethanol further increases, under high temperature and high space velocity, to reach a steady state reaction rate of 0.54 g(CH2) g(catalyst)(-1)h(-1), and a relatively high C5+ selectivity of about 90%. In addition, the catalyst also exhibits a relatively high stability as a function of time on stream. Co-59 zero field NMR analysis has indicates that the proportion of cobalt atoms engaged in the small hcp cobalt particles (

International audience; With the accumulation of knowledge for the intimate molecular mechanisms governing the processes inside the living cells in the later years, the ability to characterize the performance of elementary genetic circuits and parts at the single-cell level is becoming of crucial importance. Biological science is arriving to the point where it can develop hypothesis for the action of each molecule participating in the biochemical reactions and need proper techniques to test those hypothesis. Microfluidics is emerging as the technology that combined with high-magnification microscopy will allow for the long-term single-cell level observation of bacterial physiology. In this study we design, build and characterize the gene dynamics of genetic circuits as one of the basic parts governing programmed cell behavior. We use E. coli as model organism and grow it in microfluidics chips, which we observe with epifluorescence microscopy. One of the most invaluable segments of this technology is the consequent image processing, since it allows for the automated analysis of vast amount of single-cell observation and the fast and easy derivation of conclusions based on that data. Specifically, we are interested in promoter activity as function of time. We expect it to be oscillatory and for that we use GFP (green fluorescent protein) as a reporter in our genetic circuits. In this paper, an automated framework for single-cell tracking in phase-contrast microscopy is developed, combining 2D segmentation of cell time frames and graph-based reconstruction of their spatiotemporal evolution with fast tracking of the associated fluorescence signal. The results obtained on the investigated biological database are presented and discussed.

The growth rate of cultured mammalian cells can be influenced by chemical and physical methods such as electromagnetic fields (EMF), light, temperature and plasma. These physical methods have a number of well documented effects on mammalian cells including modification of gene expression, cell cycle, invasion, motility, cell viability, proliferation, apoptosis and mammosphere numbers. A study of the existing literature confirms that the impact of physical method on mammalian cells depends on the cell type, culture environment, exposure time, frequency, wave shape, and amount of dose. The modification of cell proliferation and apoptosis is necessary for cells products, tissue engineering, and therapy. In this article, we reviewed the impact of four physical methods on the growth rate and viability of cells. Plasma is the best method among fours because we can get desired result ranging from increasing cell proliferation to inducing apoptosis depending on the dose.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

WAP four disulfide core domain 2 (WFDC2) is a four disulfide core (4-DSC) protein secreted in the milk of the tammar wallaby. It is comprised of two 4-DSC domains assigned domain III at the NH2-terminal end and domain II at the COOH-terminal end. The WFDC2 gene was expressed only during pregnancy, early lactation, towards the end of lactation and involution. The WFDC2 protein showed antibacterial activity against Staphylococcus aureus, Salmonella enterica and Pseudomonas aeruginosa and this activity resided with domain II. There was no antibacterial activity detected against Enterococcus faecalis. The observed expression pattern of tammar WFDC2 and its antibacterial activity suggests a role to either reduce mastitis in the mammary gland caused by S. aureus or to protect the gut of the young at a time when it is not immune-competent. The latter effect could be achieved without disturbing the balance of commensal gut flora such as E. faecalis.

Cathelicidins secreted in milk may be central to autocrine feedback in the mammary gland for optimal development in addition to conferring innate immunity to both the mammary gland and the neonate. This study exploits the unique reproductive strategy of the tammar wallaby (Macropus eugenii) model to analyse differential splicing of cathelicidin genes and to evaluate the bactericidal activity and effect of the protein on mammary epithelial cell proliferation. Two linear peptides, Con73 and Con218, derived from the heterogeneous carboxyl end of cathelicidin transcripts, MaeuCath1 and MaeuCath7 respectively, were evaluated for antimicrobial activity. Both Con73 and Con218 significantly inhibited the growth of Staphylococcus aureus, Pseudomonas aureginosa, Enterococcus faecalis and Salmonella enterica. In addition both MaeuCath1 and MaeuCath7 stimulated proliferation of primary tammar wallaby mammary epithelial cells (WallMEC). Lactation-phase specific alternate spliced transcripts were determined for MaeuCath1 showing utilisation of both antimicrobial and proliferative functions are required by the mammary gland and the suckled young. The study has shown for the first time that temporal regulation of milk cathelicidins may be crucial in antimicrobial protection of the mammary gland and suckled young and mammary cell proliferation.

Substitution of Sc for Fe in CoFe2O4 spinel is investigated by powder XRD, magnetic measurements, and 57Fe Moessbauer spectroscopy.

Lactation is a defining feature of mammals. The production of milk by the mammary gland during lactation is generally regarded as a mechanism required to supply nutrition to the neonates before they are able to digest other types of food. Increasing evidence suggests that components of milk have other functions in addition to nutrition. Monotremes, marsupials, and eutherians are all members of the class mammalia, but monotremes and marsupials have evolved a lactation pattern very different from that of eutherians. In eutherians, the gestation period is longer relative to the lactation period. However, in marsupials and monotremes the gestation period is relatively short. As a result, the newborn is relatively small and undeveloped, and most of the early development occurs postnatally. Eutherians produce milk of an approximately constant composition after the expression of the initial colostrum, whereas marsupials, such as the tammar wallaby (Macropus eugenii), have a short gestation, give birth to a highly immature young, and then commence a long lactation during which the milk production and composition change progressively to suit the needs of the developing young. The comparative study of monotreme, marsupial, and eutherian milk is of significant interest and may reveal the bioactives required for developmental processes. These factors may have been lost, downregulated, or altered/modified in eutherians, as most part of the development of the eutherian young occurs in utero with nutrition and developmental signaling provided by the amniotic fluid and supplemented from the mother via the placenta.

We consider the problem of comparing several nucleic acid sequences to identify words occurring imperfectly (patterns with no gap) with unusual frequency. Methods for computing, representing, and inspecting interactively the structure of such repeating motifs in nucleic acids and more generally any text are described. Multiple sequences are treated as one large concatenate. In a preprocessing step, a lexical index is created to provide rapid string matching for the enumeration of the words matching a pattern. For given word features (word length, minimal frequency), a sequence profile is displayed. The profile can be inspected interactively with on-line algorithms. Applications to the identification of regulatory elements in DNA regions involved in the control of gene expression are presented. Our program ('DNA-Lexemics') runs on the Macintosh.

The HfFe6Ge6-type ErMn6Ge6−xGax compounds (x=0.2, 0.4, 1.0) have been studied by powder neutron diffraction. The ErMn6Ge5.8Ga0.2 compound orders antiferromagnetically at 460 K in a collinear easy axis magnetic structure characterized by a doubling of the c-axis. Below Tt=270 K, a helimagnetic structure takes place and persists down to 50 K. Below this temperature, a ferrimagnetic structure with moments aligned along the c-axis is stable (μMn=2.21(5) μB and μEr=8.60(8) μB). The ErMn6Ge5.6Ga0.4 compound orders antiferromagnetically at 394 K. From 300 to 120 K, it is characterized by a helimagnetic arrangement. In both cases, the normal to the c-axis is perpendicular to the [001] direction. Below 110 K, a ferrimagnetic structure takes place and the direction of the ferromagnetic component is aligned along the c-axis. The Mn and Er moments refined at 2 K are μMn=2.21(6) μB and μEr=9.06(11) μB. The ErMn6Ge5Ga compound orders ferrimagnetically at 373 K and a moment reorientation takes place around 200 K. At high temperature the moments are close to the (001) plane whereas at low temperature they align along the c-axis. The Mn and Er moments refined at 2 K are μMn=2.23(6) μB and μEr=9.40(12) μB. Evolutions of the moment magnitudes, magnetocrystalline anisotropy and interlayer couplings, as a function of the Ga content and the nature of the rare earth element, are discussed.

Gene Expression Comparative Analysis allows bio-informatics researchers to discover the functional regulation of genes. This is achieved through comparisons between data-sets representing the quantities of substances in a biological system. Unnatural variations can be introduced during the data collection and digitization process so normalization algorithms must be applied to data before any accurate comparison can be made. There exist many different normalization methods each of which gives a different result. Comparing differently normalized datasets can allow for discovery of crucial regulated genes that may be otherwise hidden due to errors in a single normalization study. In this paper we introduce a web-based software package called EXP-PAC which makes use of a high performance computing platform of computer clusters to run multiple normalization methods in parallel. By generating multiple normalized datasets concurrently, we allow researchers the ability to improve the accuracy of their research with almost no extra time-cost.

The role of milk in providing nutrition for the young is well established. However, it is becoming apparent that milk has a more comprehensive role in programming and regulating growth and development of the suckled young, and an autocrine impact on the mammary gland so that it functions appropriately during the lactation cycle. This central role of milk is best studied in animal models, such as marsupials that have evolved a different lactation strategy to eutherians and allow researchers to more easily identify regulatory mechanisms that are not as readily apparent in eutherian species. For example, the tammar wallaby (Macropus eugenii) has evolved with a unique reproductive strategy of a short gestation, birth of an altricial young and a relatively long lactation during which the mother progressively changes the composition of the major, and many of the minor components of milk. Thus, in contrast to eutherians, there is a far greater investment in development of the young during lactation and it is likely that many of the signals that regulate development of eutherian embryos in utero are delivered by the milk. This requires the co-ordinated development and function of the mammary gland. Inappropriate timing of these signalling events in mammals may result in either limited or abnormal development of the young, and potentially a higher incidence of mature onset disease. The tammar is emerging as an attractive model to better understand the role of milk factors in these processes.

Lactation is an important characteristic of mammalian reproduction sometimes referred to as the quintessence of mammals. Comparative genomics and transcriptomics experiments are allowing a more in-depth molecular analysis of the evolution of lactation throughout the mammalian kingdom and these recent results are reviewed here. Milk cell and mammary gland gene expression analysis with sequencing methodology have started to reveal conserved or specific milk protein and components of the lactation system of monotreme, marsupial and eutherian lineages. These experiments have confirmed the ancient origin of the complex lactation system and provided useful insight into the function of specific milk proteins in the control of the lactation programme or the role of milk in the regulation of growth and development of the young beyond simple nutritive aspects.

Whey acidic protein (WAP) belongs to a family of four disulfide core (4-DSC) proteins rich in cysteine residues and is the principal whey protein found in milk of a number of mammalian species. Eutherian WAPs have two 4-DSC domains, whereas marsupial WAPs are characterized by the presence of an additional domain at the amino terminus. Structural and expression differences between marsupial and eutherian WAPs have presented challenges to identifying physiological functions of the WAP protein. We have characterized the genomic structure of tammar WAP (tWAP) gene, identified its chromosomal localization and investigated the potential function of tWAP. We have demonstrated that tWAP and domain III (DIII) of the protein alone stimulate proliferation of a mouse mammary epithelial cell line (HC11) and primary cultures of tammar mammary epithelial cells (Wall-MEC), whereas deletion of DIII from tWAP abolishes this proliferative effect. However, tWAP does not induce proliferation of human embryonic kidney (HEK293) cells. DNA synthesis and expression of cyclin D1 and cyclin-dependent kinase-4 genes were significantly up-regulated when Wall-MEC and HC11 cells were grown in the presence of either tWAP or DIII. These data suggest that DIII is the functional domain of the tWAP protein and that evolutionary pressure has led to the loss of this domain in eutherians, most likely as a consequence of adopting a reproductive strategy that relies on greater investment in development of the newborn during pregnancy.

This study has utilised comparative functional genomics to exploit animal models with extreme adaptation to lactation to identify candidate genes that specifically regulate protein synthesis in the cow mammary gland. Increasing milk protein production is valuable to the dairy industry. The lactation strategies of both the Cape fur seal (Artocephalus pusillus pusillus) and the tammar wallaby (Macropus eugenii) include periods of high rates of milk protein synthesis during an established lactation and therefore offer unique models to target genes that specifically regulate milk protein synthesis. Global changes in mammary gene expression in the Cape fur seal, tammar wallaby, and the cow (Bos taurus) were assessed using microarray analysis. The folate receptor alpha (FOLR1) showed the greatest change in gene expression in all three species [cow 12.7-fold (n = 3), fur seal 15.4-fold (n = 1), tammar 2.4-fold (n = 4)] at periods of increased milk protein production. This compliments previous reports that folate is important for milk protein synthesis and suggests FOLR1 may be a key regulatory point of folate metabolism for milk protein synthesis within mammary epithelial cells (lactocytes). These data may have important implications for the dairy industry to develop strategies to increase milk protein production in cows. This study illustrates the potential of comparative genomics to target genes of interest to the scientific community.

Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

Background The mammary gland undergoes a sophisticated programme of developmental changes during pregnancy/lactation. However, little is known about processes involving initiation of apoptosis at involution following weaning. We used fur seals as models to study the molecular process of involution as these animals display a unique mammary gland phenotype. Fur seals have long lactation periods whereby mothers cycle between secreting copious quantities of milk for 2 to 3 days suckling pups on land, with trips to sea alone to forage for up to 23 days during which time mammary glands remain active without initiating apoptosis/involution. Results We show the molecular basis by which alpha-lactalbumin (LALBA), a secreted milk protein, is absent in Cape fur seals and demonstrate an apoptotic function for LALBA when exposed to mammary cells. Conclusion We propose that apoptosis does not occur in fur seal mammary glands due to lack of LALBA in fur seal milk, allowing evasion of involution during a foraging trip. Our work identifies LALBA as a milk factor that feeds back on the mammary gland to regulate involution.

International audience; We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co- opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non- protein- coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

The mammalian totipotent and pluripotent lineage exhibits genome-wide dynamics with respect to DNA methylation content. The first phase of global DNA demethylation and de novo remethylation occurs during preimplantation development and gastrulation, respectively, while the second phase occurs in primordial germ cells and primary oocytes/prospermatogonia, respectively. These dynamics are indicative of a comprehensive epigenetic resetting or reprogramming of the genome in preparation for major differentiation events. To gain further insight into the mechanisms driving DNA methylation dynamics and other types of epigenetic modification, we performed an RNA expression microarray analysis of fetal prospermatogonia at the stage when they are undergoing rapid de novo DNA remethylation. We have identified a number of highly or specifically expressed genes that could be important for determining epigenetic change in prospermatogonia. These data provide a useful resource in the discovery of molecular pathways involved in epigenetic reprogramming in the mammalian germ line.

Publisher Summary This chapter presents a review of the current status of bovine milk genomics and functional genomics, and describes the roles, characteristics, and key bioactivities of the major bovine milk proteins and their encrypted peptides. As well as being the source of nutrition for the neonates of mammals, milk has long been considered to be a healthy source of dietary proteins and minerals for human consumption, and a global dairy industry has evolved to cater to that need. The next evolution of dairy products is to characterize, accentuate, and refine naturally occurring biological activities to develop dairy-based functional foods or “nutraceuticals.” Although a significant amount of information in relation to the biological activities present in the major bovine milk proteins is already available, the advances in genomic technologies and the utilization of comparative genomics approaches provide opportunities for further discovery and characterization of the bioactivities in bovine milk. The rapid advances in technology for both evaluating and understanding the structure of animal genomes and their functional significance have presented opportunities for scientists to more clearly understand the complexity of bovine milk proteins and the control of their expression. Used in conjunction with proteomic databases the knowledge of how milk proteins are processed into peptides, which represent much of the biological activity, can be increased. The application of analytical tools such as genomics and functional genomics to the full spectrum of lactation strategies adopted by eutherians, marsupials, and monotremes to improve understanding of the milk proteome is also discussed in the chapter.

This chapter describes two animals with extreme adaptation to lactation and explores approaches to exploit their unique reproductive strategies to identify new proteins in milk with bioactivity that have the potential to regulate mammary function and growth of the suckled young. The two animal models-the tammar wallaby (Macropus eugenii) and the Cape fur seal (. Arctocephalus pusillus pusillus)-are with very different lactation cycles. The tammar wallaby has adopted a reproductive strategy that includes a short gestation of 26.5 days, birth of an immature young, and a relatively long lactation period of 300 days. The composition of the milk changes progressively during the lactation cycle and this is controlled by the mother and not by the sucking pattern of the young. The tammar wallaby can practice concurrent asynchronous lactation demonstrating that the mammary gland is controlled locally. These changes in milk composition control the development of the young and therefore provide new opportunities to identify proteins regulating specific developmental processes in the pouch young. Cape fur seal has a lactation that is characterized by a repeated cycle of long at-sea foraging trips (up to 23 days) alternating with short suckling periods of 2-3 days on-shore. Lactation almost ceases while the seal is offshore but the mammary gland does not progress to apoptosis and involution. It is likely that specific milk proteins have a role both to reduce apoptosis in the mammary gland during foraging and to meet the challenges of growth and fasting physiology of the pup on-shore. Technology platforms using genomics, proteomics, and bioinformatics have been used to exploit these models to identify milk bioactive components. © 2008 Elsevier Inc. All rights reserved.

Antimicrobial peptides, such as cathelicidin, are an evolutionarily old defense system. However they have more complex actions than just simply their antimicrobial effects, including immunoregulation and interaction with the adaptive immune system. In this study we have characterized several novel cathelicidin-like peptides from the tammar wallaby (Macropus eugenii). The tammar cathelicidin-like (MaeuCath) mRNA were isolated based on the conservation of the cathelin-like amino terminus. Mature MaeuCath peptides were positively charged with hydrophobic carboxyl tails, features that are fundamental for antimicrobial function. MaeuCath1 was induced in tammar leukocytes in response to pathogen-associated molecular patterns from both gram positive and negative bacteria. In addition, we also examined the expression of MaeuCath1 in the primary and secondary lymphoid organs of the tammar neonate throughout early pouch life. The results from this study demonstrate the importance that MaeuCath1 may play in innate defense of the marsupial young, especially in the mucosal organs. Such expression of antimicrobial peptides may form part of the immune strategies of marsupials for neonatal survival during their post-partum development.

The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. In this study, we have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalization-specialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting protein-protein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. Our study had also demonstrated the flexibility of the two-layered generalization-specialization paradigm by using the same generalization layer for two specialized information extraction tasks.

Mammary gland involution requires co-ordination of milk production, immune responses, apoptosis and remodeling. Initiation and progression of each of these components involves integral control by the mammary gland. Although cell-based culture models and genetically manipulated animals have shed light on these processes, the factors controlling each step in the involution cascade are still poorly understood. The fur seal displays a unique lactation phenotype. During the lactation cycle the mammary gland downregulates milk production and initiates an immune response but fails to initiate the apoptotic phase of involution, allowing the female fur seal to undertake long foraging trips of up to 28 days between suckling bouts. Upon return to shore the female continues feeding her pup following resumption of lactation and milk production. Expression profiling of genes involved in this lactation cycle provides valuable tools for investigation of the factors responsible for the initiation of apoptosis at involution.

Marsupial young are born in an under-developed state without mature immune responses. Prior to the maturation of an immune system, marsupial young are heavily reliant upon immune factors secreted in the milk to defend them against potential microbial pathogens in the environment. In this study, we identified and characterized the immunoglobulin heavy chain constant regions, light chains, polymeric Ig receptor (pIgR), J chain, neonatal Fc receptor (alpha chain) (FcRn) and the chemokine CCL28 from the model marsupial species, the tammar wallaby (Macropus eugenii). Low levels of conservation were seen in motifs in C alpha and C gamma associated with receptor binding and or transcytosis, and this may have potential implications for functionality. We evaluated the expression of immunoglobulin genes in the tammar mammary gland throughout lactation and found that two periods of increased expression of immunoglobulin genes occur. These two periods coincide with the birth of the young, and with its first emergence from the pouch. This increased expression may represent a strategy for maternal immunological protection of the pouch young.

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

The fur seal (Arctocephalus spp. and Callorhinus spp., members of the pinniped family) is a mammal with the unusual capability to modulate its lactation cycle by turning milk production on and off without the typical mammalian regression and involution of the mammary gland. Lactation has evolved from constraints arising from the spatial and temporal separation of infant nursing and maternal foraging as the mother gives birth and feeds the pup on land while acquisition of nutrients for milk production occurs at sea. The lactation cycle begins with the female fur seal undergoing a perinatal fast of approximately 1 wk, after which time she departs the breeding colony to forage at sea. For the remainder of the long lactation period (116-540 days), the mother alternates between short periods ashore suckling the young with longer periods of up to 4 wk of foraging at sea. Milk production continues while foraging at sea, but at less than 20% the rate of production on land. Fur seals produce one of the richest milk reported, with a very high lipid content contributing up to 85% of total energy. This feature serves as an adaptation to the young's need to produce an insulating blubber layer against heat loss and to serve as an energy store when the mother is away foraging at sea. This atypical pattern of lactation means mothers have long periods with no suckling stimulus and can transfer high-energy milk rapidly while on land to minimize time away from foraging grounds. The absence of suckling stimulus and milk removal during foraging does not result in the onset of involution with associated apoptosis of mammary secretory cells and a subsequent progressive breakdown of the cellular structure of the mammary gland. The mechanisms controlling lactation in the fur seal mammary gland have been investigated using molecular and cellular techniques. These findings have shed light on the processes by which the unique features of lactation in the fur seal are regulated.

The fur seal ( Arctocephalus spp. and Callorhinus spp., members of the pinniped family) is a mammal with the unusual capability to modulate its lactation cycle by turning milk production on and off without the typical mammalian regression and involution of the mammary gland. Lactation has evolved from constraints arising from the spatial and temporal separation of infant nursing and maternal foraging as the mother gives birth and feeds the pup on land while acquisition of nutrients for milk production occurs at sea. The lactation cycle begins with the female fur seal undergoing a perinatal fast of approximately 1 wk, after which time she departs the breeding colony to forage at sea. For the remainder of the long lactation period (116–540 days), the mother alternates between short periods ashore suckling the young with longer periods of up to 4 wk of foraging at sea. Milk production continues while foraging at sea, but at less than 20% the rate of production on land. Fur seals produce one of the richest milk reported, with a very high lipid content contributing up to 85% of total energy. This feature serves as an adaptation to the young's need to produce an insulating blubber layer against heat loss and to serve as an energy store when the mother is away foraging at sea. This atypical pattern of lactation means mothers have long periods with no suckling stimulus and can transfer high-energy milk rapidly while on land to minimize time away from foraging grounds. The absence of suckling stimulus and milk removal during foraging does not result in the onset of involution with associated apoptosis of mammary secretory cells and a subsequent progressive breakdown of the cellular structure of the mammary gland. The mechanisms controlling lactation in the fur seal mammary gland have been investigated using molecular and cellular techniques. These findings have shed light on the processes by which the unique features of lactation in the fur seal are regulated.

We report a highly reproducible route to synthesize iron oxide nanoparticles (IONPs) with control over size and shape and with size dispersions around 10%. By tuning the relative ratio of squalane to dibenzyl ether, which were used as solvents in the synthesis, the size of the particles could be varied from 14 to around 100 nm, while their shape evolved from cubic (for size ranges up to 35 nm) to truncated octahedra and octahedra (for sizes from 40 nm up to 100 nm). Fine tuning of the size within each of these ranges could be achieved by varying the heating ramp and the iron precursor to decanoic acid ratio. We also demonstrate direct water transfer of the as-synthesized IONPs via in situ ligand exchange with gallol polyethylene glycol molecules, the latter simply added to the crude nanocrystal mixture at 70 degrees C. The specific absorption rate (SAR) values measured on the water transferred IONPs, at frequencies and applied magnetic fields that are considered safe for patients, confirmed their high heating performance. Finally, this method allows the transfer of 35 nm nanocubes as individually coated and stable particles to the water phase. For the first time, the heating performance of such large IONPs has been studied. This work uncovers the possibility of using large IONPs for magnetic hyperthermia in tumor therapy.

Oral squamous cell carcinoma (OSCC) is a disease with high incidence and mortality in India. There is no clinically proven biomarker for oral cancer and the 5-year survival rate has not improved for the past few years. Better understanding of deregulated process, pathways, and genes involved in the advanced stage tumor (stage III and IV) and further comparison with early stage tumor (Stage I and II) might lead to the discovery of biomarkers that can identify the tumor at an early onset. In this study we examined the gene expression profile of advanced OSCC tumors using an Affymetrix Human Gene 1.0ST array and compared the profile with control tissue surrounding normal margins. Microarray data analysis was performed using xRAY Biotique Systems to identify advanced OSCC gene profile that exhibited statistically significant differential expression of candidate marker genes. Intensive pathway analysis was performed using Ingenuity Systems to generate pathways deregulated in advanced OSCC. From the pathway analysis, it was found that hepatic stellate cell activation (myofibroblast activation), G2/M transition, interferon signaling, dendritic cell maturation, and oncostatin M signaling are the top significant pathways expressed in advanced tumor gene profile. These 5 pathways play pivotal role in promoting two important processes, fibrosis, and inflammation. Expression of significant targets identified from pathway analysis and current literature studies was validated by Quantitative-PCR and subsequently examined in early, advanced, and normal tissue samples. This comparison has led to identification of FN1 expression that can significantly distinguish early and advanced oral squamous cell carcinoma (OSCC) both at mRNA and protein level. Myofibroblast activation is essential for fibrosis condition and its presence was confirmed by the expression of alpha smooth muscle actin protein in early and advanced OSCC tissue samples. Furthermore, immunohistochemical analysis of inflammatory response mediators, SPP1 and ICAM1, showed significant higher expression in early and advanced OSCC tissues than in normal tissues. Meta-profiling analysis using present and external microarray data revealed that loss of KRT4 in pre-malignant stage might be an indicator for oral cancer progression. Down regulation of KRT4 gene in early and advanced OSCC was confirmed by Q-PCR. Early and advanced OSCC samples showed down regulation of anti-aging gene, Klotho, which acts as antagonist to proliferation promoting Wnt signaling pathway. Interestingly, it was observed that all 2-5A synthetase family genes, involved in immune response, were up regulated in early and advanced OSCC. A better understanding of molecular interactions in advanced OSCC samples has provided a clear insight of role of significant pathways and genes involved in the development of markers for early detection (FN1), prediction (loss of KRT4 in dysplasia condition) and therapeutic (targeting fibrosis and inflammation) purposes for improving the survival rate of patients. Through these findings, it can be incurred that fibrosis and inflammation are the key factors for oral cancer progression and using combination therapy of anti-fibrotic and anti-inflmmatory drugs might provide important insights into potential novel therapies for OSCC. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C37. Citation Format: Sivapriya Pavuluri, Christophe Lefevre, Julie Sharp, Sivalinga Prasad Vasireddi, Kevin R. Nicholas. Gene profiling predicts biomarkers in oral squamous cell carcinoma with diagnostic and therapeutic importance. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C37.

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human–CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1–15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single Eco RI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50–70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

We report on the multiferroic behavior of 2%-magnesium-doped Ga0.6Fe1.4O3 thin film at room temperature. The sample was grown by pulsed laser deposition on a Pt-coated Yttrium-Stabilized Zirconia substrate. Magnetic measurements indicate a net magnetization of 105 emu/cm(3) at 295 K, and the persistence of magnetic ordering above room temperature. Ferroelectric measurements show clear polarization switching with negligible contribution from leakage currents, with a polarization of 0.2 mu C/cm(-2) and a coercive field of 133 kV/cm. Scanning probe microscopy confirms the low leakage current and detects a stable piezoelectric signal. This could open original perspectives for the application of single-phased multiferroic systems. (C) 2013 AIP Publishing LLC.

The system biology approach has been applied to gene expression data to identify molecular mechanisms of isolated biological systems. Adapting this methodology to incorporate connections between different biological systems and extensive repositories of data can help find novel gene interactions. The devised distributed workflow uses normalized microarray gene expression data from which gene lists are extracted. Gene set enrichment is then applied to isolate data points which share genetic similarity. If an enriched gene set meets the enrichment score and p-value criteria, distributed correlation algorithms are applied to build network maps which are layered based on the time these two systems first interacted. Gene interactions are extracted using the network maps and given a score based on how often two or more genes show similar interactions. using this workflow, we have investigated the link between genes expressed during lactation and digestion of dairy products. Results found that genes expressed during the pregnancy period of the mouse (d3-d14) were also expressed after digestion of dairy products. Further investigation showed that while a majority of these genes had mitochondrial ribosomal protein related function, some anti-proliferative genes were present.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Room-temperature dielectric function e = e1 + ie2 spectra of magnetoelectric Ga2−xFexO3 (x = 0.9, 1.0, and 1.4) thin films are determined by spectroscopic ellipsometry (SE) as a function of Fe concentration x. The SE data are analysed by a multilayer model with a series of Tauc-Lorentz oscillators. While the threshold energies slightly decrease as x increases, the oscillator strength shows a strong composition-dependence for the major optical structure at ∼3.5 eV. The experimental data are compared to the e spectra obtained by density functional theory (DFT) calculations. Even though the overall shape of e spectra is consistent, the experimental data and calculated spectra show a clear discrepancy in the oscillator's strength ratio of the two optical structures at ∼3.5 and ∼6.0 eV. The DFT calculations suggest that a significant disordering in the cationic (Ga and Fe) sites in Ga2−xFexO3 is present in thin films, which influences their optical properties. This work demonstrates a successful application of optical characterization for determining the cationic sites occupation in thin films, which in turn improves our understanding of Physics and Chemistry in Ga2−xFexO3 thin films and paves a pathway to the development of new multifunctional devices.

The optical properties of polycrystalline Ga0.6Fe1.4O3 bulk are determined by spectroscopic ellipsometry from 0.73 to 6.45 eV. Complex dielectric function epsilon = epsilon(1) + i epsilon(2) spectra are obtained from the multilayer analysis. The ellipsometric data exhibit numerous optical structures, and the transition energies are accurately obtained by analyzing the second-energy derivatives of the data. The origins of the optical structures are explained in terms of Fe3+ ligand field transitions and ligand-to-metal charge transfer transitions. (C) 2012 American Vacuum Society. [http://dx.doi.org/10.1116/1.4721649]

Ga0.6Fe1.4O3 is predicted to be magnetoelectric with non zero magnetization at room temperature. However, in thin films, electric properties are overshadowed by strong leakage currents. In this Letter, we show that Mg doping in Ga0.6Fe1.4O3 thin films grown by pulsed laser deposition allows decreasing the leakage current density by four orders of magnitude and might simultaneously allow tuning the carriers' nature. These results suggest the possibility to develop a new class of material exhibiting room temperature magnetization, tunable transport properties, and magnetoelectric properties. (C) 2012 American Institute of Physics. This work was supported by the CNRS PICS program #5733 and the Leading Foreign Research Institute Recruitment Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (MEST) (2011-00267).

Background The marsupial early lactation protein (ELP) gene is expressed in the mammary gland and the protein is secreted into milk during early lactation (Phase 2A). Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine colostrum trypsin inhibitor (CTI) protein. Although ELP and CTI both have a single bovine pancreatic trypsin inhibitor (BPTI)-Kunitz domain and are secreted only during the early lactation phases, their evolutionary history is yet to be investigated. Results Tammar ELP was isolated from a genomic library and the fat-tailed dunnart and Southern koala ELP genes cloned from genomic DNA. The tammar ELP gene was expressed only in the mammary gland during late pregnancy (Phase 1) and early lactation (Phase 2A). The opossum and fat-tailed dunnart ELP and cow CTI transcripts were cloned from RNA isolated from the mammary gland and dog CTI from cells in colostrum. The putative mature ELP and CTI peptides shared 44.6%-62.2% similarity. In silico analyses identified the ELP and CTI genes in the other species examined and provided compelling evidence that they evolved from a common ancestral gene. In addition, whilst the eutherian CTI gene was conserved in the Laurasiatherian orders Carnivora and Cetartiodactyla, it had become a pseudogene in others. These data suggest that bovine CTI may be the ancestral gene of the Artiodactyla-specific, rapidly evolving chromosome 13 pancreatic trypsin inhibitor (PTI), spleen trypsin inhibitor (STI) and the five placenta-specific trophoblast Kunitz domain protein (TKDP1-5) genes. Conclusions Marsupial ELP and eutherian CTI evolved from an ancestral therian mammal gene before the divergence of marsupials and eutherians between 130 and 160 million years ago. The retention of the ELP gene in marsupials suggests that this early lactation-specific milk protein may have an important role in the immunologically naïve young of these species.

We consider the basic function which locates a specific string of symbols within a longer sequence. When one is expecting to do many substring searches it is worthwhile to build an auxiliary index to the sequence to aid in the search. We propose a method to generate a compact index that can be viewed as a small (partial) deterministic finite automaton recognizing the subword structure of a sequence. We present an algorithm for its construction on-line in linear time. Such a data structure permits the efficient localization of subwords in a sequence and can be used in the development of interactive sequence analysis software.

Nature 453, 175–183 (2008) In this Article, Mikhail Nefedov and Pieter J. de Jong were omitted from the author list.

Background A wide variety of animal models have been used to study human breast cancer. Murine, feline and canine mammary tumor cell lines have been studied for several decades and have been shown to have numerous aspects in common with human breast cancer. It is clear that new comparative approaches to study cancer etiology are likely to be productive. Results A continuous line of breast carcinoma cells (WalBC) was established from a primary breast cancer that spontaneously arose in a female tammar wallaby (Macropus eugenii). The primary tumor was 1.5 cm3 and although large, did not appear to invade the stroma and lacked vimentin expression. The WalBC cell line was cultured from the primary tumor and passaged for 22 months. WalBC cells displayed an epithelial morphology when grown on plastic, were not EGF responsive, stained strongly for cyto-keratin and negatively for vimentin. WalBC cells were shown to be non-invasive within a Matrigel invasion assay and failed to produce tumors following transplantation into nude mice. Gene expression profiling of WalBC cells was performed using a cDNA microarray of nearly 10,000 mammary gland cDNA clones and compared to normal primary mammary cells and profiles of human breast cancer. Seventy-six genes were down-regulated and sixty-six genes were up-regulated in WalBC cells when compared to primary mammary cells. WalBC cells exhibited expression of known markers of basal invasive human breast cancers as well as increased KRT17, KRT 14 and KRT 19, DSP, s100A4, NDRG-1, ANXA1, TK1 and AQP3 gene expression and decreased gene expression of TIMP3, VIM and TAGLN. New targets for breast cancer treatment were identified such as ZONAB, PACSIN3, MRP8 and SUMO1 which have human homologues. Conclusion This study demonstrates how novel models of breast cancer can provide new fundamental clues regarding cancer etiology which may lead to new human treatments and therapies.

The mammary explant culture model has been frequently used to mimic lactation and to examine the endocrine control of milk protein gene expression. Studies in the mouse show the expression of the milk protein genes in explants requires insulin in the presence of prolactin and cortisol. The role of insulin in milk protein synthesis in the dairy cow is not as clear. The bovine mammary explant culture model has been utilised to show that insulin is essential for alpha-s1-casein gene expression and the synthesis of the casein proteins. In addition, mouse culture experiments were undertaken to provide an insight into the underlying molecular mechanisms of insulin action in hte mammary gland. A global analysis of the genes induced in the cultured explants was done using Affymetrix microarray and showed 132 genes, including the major milk protein genes, required the complement of insulin, cortisol and prolactin for maximal expression. Twenty-seven genes showed a 3-fold change in gene expression in response to insulin. The function of these genes can be largely categorised into maintenance of cell integrity, signal transduction, transport mechanisms, cellular metabolism and a direct effect on gene transcription in the nucleus. The requirement for insulin in milk protein synthesis is highlighted by its role in inducing the STAT5 gene, known to be a key transcription factor for the milk protein genes. Interestingly, dairy cows of high genetic merit have unusually low serum concentrations of insulin. This has occured in association with a high selection pressure for milk volume that has altered the regulation of blood glucose homeostasis. Our study indicates that this intensity of selection for high milk volume could be compromising the dairy cow’s potential for milk protein production: Has selecting for milk volume in many populations of dairy cows been achieved by lowering circulating insulin levels with consequent effects on the efficiency for milk protein yield as well as compromised reproductive performance.

Representation of sequence similarity by dot matrix plots is a method widely used for comparing biological sequences. The user is presented with an overall view of similarity between two sequences. Computation of this plot has been reconsidered here. An improvement is proposed through the preprocessing of the data into an automation recognizing the word structure of a sequence. The main advantage of this approach is to systematically eliminate the repetitions during word comparison. Simple heuristics are also considered to greatly speed up pattern matching. As a result, large sequences are handled very efficiently. This is illustrated by a comparison of large genomic DNA. The algorithm has been implemented in an interactive application on a microcomputer.

The molecular basis for the pituitary-specific expression of the human growth hormone (hGH) gene was investigated, by gene transfer and protein footprinting experiments. Plasmid constructs in which CAT or Neo transcription units are fused to a 0.5 kb fragment of the hGH 5' sequences were efficiently expressed in GC and GH3 cells, derived from a pituitary tumor, but not in cell lines of other origins, indicating the presence of a tissue-specific promoter. DNaseI footprinting experiments have identified at least three factors that specifically bind to the hGH 5' region. While two of these factors were also detected in extracts of non-expressing cells, the third factor, GHF-1, was detected only in extracts of GH expressing pituitary tumor cells. Mutagenesis experiments suggest that binding of GHF-1 and some of the other more ubiquitous factors is required for optimal hGH promoter activity in vivo. Tissue specificity of the hGH promoter therefore seems to be determined by the binding of at least one tissue-specific trans-acting factor, acting in concert with several other more ubiquitous, yet specific, DNA binding proteins.