bluuebunny/crossref_metadata_2025 huggingface dataset:
Extension of shelf life of chilled hake (Merluccius capensis) by high pressure/Prolongación de la vida útil de merluza (Merluccius capensis) sometida a altas presiones conservada en refrigeración
Authors: Hurtado J.L. , Montero P. , Borderias A.J.
Published: January 2008

Vacuum packed hake muscle subjected to 400 MPa (three 5-min cycles) at 7 °C proved to be more stable at chilled temperatures (2-3 °C), and sensorially acceptable, until 43 days of storage in comparison with the nine days for the non-pressurized hake. The lot pressurized at 400 MPa had the appearance of cooked muscle. The microbial load was initially reduced by two log units by pressurization at 400 MPa. Trimethylamine nitrogen (TMA-N) values were also very low. Pressurization had no effect on dimethylamine nitrogen (DMA-N) production. The lot pressurized at 400 MPa showed slower increase in drip loss from day 15 of storage. In the lot subjected to 200 MPa (three 5-min cycles) at 7 °C, which retained the appearance of raw fish, microorganisms were one log unit lower than in the non-pressurized sample and TMA-N was lower. In conclusion, the chilled shelf life was prolonged by about one week in the lot pressurized at 200 MPa and about two weeks in the lot pressurized at 400 MPa.
Composición química y calidad nutritiva de garbanzo (Cicer arietinum L.) fresco y endurecido después de la fermentación en estado sólido (FES)/Chemical composition and nutritional quality of fresh and hardened chickpea (Cicer arietinum L) after the solid state fermentation (SSF)
Authors: Reyes-Moreno C. , Romero-Urias C.A. , Milan-Carrillo J. , Gomez-Garza R.M.
Published: January 2008

Solid state fermentation (SSF) represents a technological alternative for a great variety of legumes and cereals, or combinations of them, to improve their nutritional quality and to obtain edible products with palatable sensorial characteristics. Chickpeas (Cicer arietinum L.) are prone to develop the hardening phenomenon, also known as hard-to-cook (HTC) defect, when stored under adverse conditions of high temperature (≥ 25 °C) and high relative humidity (≥ 65%). This hard-to-cook phenomenon causes increases in cooking time, decreases in nutritional quality and deterioration of sensorial attributes of chickpea. The objective of this work was to study the effect of SSF on chemical composition and nutritional quality of fresh and hardened chickpeas. The hardening of chickpea ( Cicer arietinum L. Blanco Sinaloa 92 variety) for human consumption, was produced by accelerated storage (33-35 °C, RH = 75%, 180 days). A Rhizopus stolonifer spore suspension (1 x 106 spores/mL) was used as starter for the fermentation. The temperature and time of the SSF process were 35.8 °C and 42.7 h, respectively. The tempeh was obtained from fresh and hardened chickpea. The SSF process caused a significant increase ( p ≤ 0.05) in crude protein, true protein (19.6-19.9 to 23.2-23.4%), protein solubility, in vitro digestibility (68.6-73.1% to 79.9-80.5%), available lysine (2.19-3.04 to 3.19-4.07 g lysine/ 16 N), palmitic acid, and stearic acid, and a significant decrease ( p ≤ 0.05) in lipids, minerals, linoleic acid, phytic acid (8.82-10.73 to 2.11 g phytic acid/g dry matter), and tannins (16.1-22.4 to 3 mg catechin/g dry matter). The SSF process improved significantly the quality of fresh and hardened chickpea.
Student Evaluation in the Hospitality Curriculum
Authors: Hayes David K. , Tanke Mary L.
Published: January 2008

The authors outline a series of successful techniques they have employed for strengthening their testing and grading procedures. Items of particular note include the evaluation of test reliability, difficulty level, dispersion and the use of standard scores in determining course grades.

The intent is to provide information on how sound educational evaluation methods may be developed in a hospitality curriculum.

The system described is based on established norm referenced grading techniques, yet is applicable to criterion referenced grading in many respects.
Students as Consultants: a New Alternative in Experiential Learning
Authors: Haywood K. Michael
Published: January 2008

The student consulting project, as implemented in a marketing management course, is a demanding approach in experiential learning that can be successfully applied to senior-level courses in an undergraduate hospitality management program. It allows students to operate in the field and to overcome the limitations associated with textbook and in-class learning. It also provides valuable managerial insights and experiences in a specific functional area in the operational and competitive business environment in which small businesses exist. From a learning point of view, the consulting project places the student into a quasi-managerial role. In other words, the student learns about being a manager operating in a functional area and the vital role of personal values, perceptions, and behavior in directing a business toward its goals.
Students Study Energy Usage for . Heat Processing Pizzas
Authors: Unklesbay Nan , Heyne Linda , Ellersieck Mark
Published: January 2008

Undergraduate students in Food Service and Lodging Management participated in a foodservice energy research project during one semester. They determined the effect of oven paranteters upon energy consuniption during infrared and convective heating of siiyiulated pizzas. Three different oven temperatures and times were studied for infrared and convection ovens. Because of different process materials used, energy comparisons were made within each oven type, rather than between infrared and convective heating. This paper includes guidelines for the organization of suclr a project. The need for the recommended laboratory controls is illustrated by providing their research findings. To illustrate the practical application of the research findings, two scenarios are given, one for a pizza establishnrent, and one for a school foodservice operation.
A Survey of Attitudes Toward Tourism Growth in Rhode Island
Authors: Tyrrell Timothy J. , Spaulding lrving A.
Published: January 2008

A survey of Rhode Island households, businesses and town officials was conducted in 1982 in order to pravide background information for the first Governor's Conference on Tourism held in the state. The three objectives of the survey were to identify specific benefits and problems associated with tourism growth, to measure differences in attitudes held by the three groups sampled, and to identify regional differences in attitudes within the state. In order to accomplish the second and third objectives, a tourism attitude scale was developed.
From Practice-based Knowledge to the Practice of Research: Revisiting Constructivist Research Works on Knowledge
Authors: Charreire Petit Sandra , Huault Isabelle
Published: January 2008

Research studies within organizational knowledge are good examples for both analyzing and illustrating the debate regarding a paradigm shift in management. Most articles in the field focus on knowledge complexity and its socially constructed side. Researchers have noted a great deal of similarity between this socially constructed nature and the shaping elements of constructivism. They argue for a paradigm shift, rejecting positivism. To more fully understand this paradigm shift, and to address the number of methodological questions it raises, we carried out a content analysis on a sample of the main articles dealing with organizational knowledge. Our research points out that the principles of constructivism are difficult to adhere to within research design. It underlines the lack of specific methodological devices and lack of adaptation with the epistemological system of reference. This study highlights the methodological perspectives that underpin constructivist research in organizational knowledge.
Animal-Assisted Therapy with Children Suffering from Insecure Attachment Due to Abuse and Neglect: A Method to Lower the Risk of Intergenerational Transmission of Abuse?
Authors: Parish-Plass Nancy
Published: January 2008

Children suffering from insecure attachment due to severe abuse and/or neglect are often characterized by internal working models which, although perhaps adaptive within the original family situation, are inappropriate and maladaptive in other relationships and situations. Such children have a higher probability than the general population of becoming abusing or neglecting parents. Besides the usual goals of psychotherapy, an overall goal is to stop the cycle of abuse in which abused children may grow up to be abusing parents. Therapy with these children is complicated by their distrust in adults as well as difficulties in symbolization due to trauma during the preverbal stage. Animal-Assisted Therapy (AAT) provides avenues for circumventing these difficulties, as well as providing additional tools for reaching the inner world of the client. This article gives a brief background of the connection between insecure attachment and intergenerational transmission of abuse and neglect as well as a brief overview of the principles of AAT in a play therapy setting. A rationale for the use of AAT as a unique therapy technique for children having suffered from abuse and neglect is followed by a number of clinical examples illustrating AAT.
Use of the ADOS and ADI-R in Children with Psychosis: Importance of Clinical Judgment
Authors: Reaven Judith A. , Hepburn Susan L. , Ross Randal G.
Published: January 2008

The Autism Diagnostic Observation Schedule (ADOS) and the Autism Diagnostic Interview — Revised (ADI-R) are considered to be the `gold standard' in diagnostic evaluations for autism. Developed as research tools and now gaining wide clinical use, the ADOS/ADI-R assessment package has been demonstrated to differentiate children with autism from those with other developmental disabilities; however, little work concerning the reliability and validity of the tools in children with a known history of psychosis has been undertaken. We report on the administration of the ADOS, ADI-R and clinical judgment in three cases of Childhood-Onset Schizophrenia. All 3 children met both ADOS and ADI-R criteria for an autism spectrum diagnosis, even though none of them received a clinical diagnosis of autism from either a research child psychiatrist or an experienced clinically trained, research psychologist with expertise in autism. Issues concerning overlap of symptom presentation and implications for research and clinical use of these assessment tools are discussed.
Coping, Social Relations, and Communication: A Qualitative Exploratory Study of Children of Parents with Cancer
Authors: Thastum Mikael , Johansen Mikael Birkelund , Gubba Lotte , Olesen Louise Berg , Romer Georg
Published: January 2008

The purpose of this qualitative study of families where a parent has cancer was to explore ways of informing the child of the parent's illness, how the child perceives the parent's emotional state, how the child copes with the parent's illness, and how this coping relates to the parent's coping and concerns for the child. Twenty-one children from 15 families and their parents were interviewed. In 13 families the mother was ill, in two the father. Children were aware of the facts of the illness, but there was limited emotional communication between the generations. The children were very observant of both the ill and the healthy parent's emotional condition. The children's observations and expressions led us to identify five coping strategies the younger generation used: Helping others, parentification, distraction, keeping it in the head, and wishful thinking. Both adaptive and destructive examples of parentification were found. Communication patterns and parental coping seemed to be highly related to the child's coping repertoire. Even though most children seemed to manage rather well, all children were strongly affected by the illness. The `healthiest' adaptation related to factors within the family system, which has implications for the provision of help.
Psychoanalytic Psychotherapy Assessment in a Child and Adolescent Mental Health Setting: An Exploratory Study
Authors: Petit Cécile , Midgley Nick
Published: January 2008

Undertaking assessment is a significant component of a Child Psychotherapist's work within Child and Adolescent Mental Health Services (CAMHS), yet as an activity it has been relatively neglected in the research literature. This study made use of a small-scale, qualitative design to explore the nature and function of psychoanalytic assessment work within a single CAMHS team. After an initial audit of child psychotherapy assessment work, indepth interviews with 5 Child and Adolescent Psychotherapists, exploring the nature of assessment work, were analysed using Interpretative Phenomenological Analysis (IPA). Results suggested that assessment is a major part of the Child Psychotherapist's work, although there are different types of assessment done in different contexts. Among the participants there was a certain shared understanding of the psychoanalytic approach to assessment, although with significant differences in regard to process, technique (e.g. use of interpretation, the role of countertransference) and the reporting of assessments. The analysis also suggested tensions between the role of the assessor as an `expert' and as a `therapist'.
Public opinion and tax aversion in Australia
Authors: Blount Simon
Published: January 2008

The passage of the GST legislation through the Senate brings to an end 25 years of debate over whether Australia should radically alter its tax system. This paper investigates the empirical problem of whether there were patterns of public opinion indicating that voters may have been averse to one particular aspect of taxation more than any other. The paper also addresses the methodological problems involved in investigating the suggestion that voters expressed intransitive preferences in regard to taxing and spending.
The bureaucratisation of Australian unions ? Evidence from a national survey
Authors: Hall Richard , Harley Bill , Tomkins Matthew
Published: January 2008

Using data drawn from the authors' own 1996 Australian National Trade Union Survey, this paper examines the size and implications of union bureaucracies in Australia. In particular, we critically evaluate the arguments of Bramble (1995b) that the growth of Australia's 'new generation' of union officials has had the effect of 'deterring democracy'. We find that while the evidence of increasing numbers of union officials is mixed, there are some trends that are contributing to higher union official density rates while other trends are lowering those rates. However, we find no support for Bramble's central claims that union bureaucratisation and managerial-service unionism have led to less democratic practices in Australian unions. Rather than being concerned with the number or class character of officials, we suggest that organisational features such as delegate structures are more relevant to the issue of union democracy.
Nowhere is as at home: adjustment strategies of recent immigrant women from the former Yugoslav Republics in southeast Queensland
Authors: Markovic Milica , Manderson Lenore
Published: January 2008

This paper analyses adjustment strategies of women from the former Yugoslav Republics who have settled in Australia since 1991. The majority of these recent immigrants have been humanitarian settlers and refugees, and this has had specific implications for their adjustment strategies. In-depth interviews were conducted during 1996-97 with 52 former Yugoslavian-born women who resided in southeast Queensland. The women's assessments of their decision to immigrate resulted in three adjustment strategies: (1) loss orientation, (2) ambivalence and (3) future orientation. Described separately, this typology delineates only ideal types, but is predictive of the kinds of settlement and coping issues that are faced by individual immigrants. The adjustment strategies are primarily affected by the women's status as independent immigrants or refugees and humanitarian settlers, social capital and social constraints in the host country.
A profile of New Agers: social and spiritual aspects
Authors: Possamai Adam
Published: January 2008

In the literature, New Agers are profiled as urban, educated, middle-class and middle-aged, the majority being women-a portrait mainly based on quantitative analyses. This article aims at providing a richer sociological description through a qualitative analysis of thirty-five interviews conducted in 1996-97 in Melbourne. This qualitative approach to New Agers will describe them as religious individualists, as technical mystics, and as people who locate authority in their inner self. However, even if they perceive themselves as unique in this spirituality, they also mix with other people in 'affinitive' networks. They tend to move in or toward New Age through crises and through a consumption of New Age symbols that predispose, provoke and reinforce alternation to New Age.
The Pattern of Antenatal Visits with Emphasis on Gestational Age at Booking in Riyadh Health Centres
Authors: Al-Shammari Sulaiman A , Khoja Towfik , Jarallah Jamal S
Published: January 2008

1344 expectant mothers were selected by random sampling from the catchment population of 15 health centres in Riyadh. The health centres were taken to represent all areas of urban Riyadh. These mothers were asked to complete apre-designed questionnaire in Arabic and undergo a structured interview by trained midwives to explore their knowledge, attitude and practice toward antenatal visits. It was found that the average gestational age at booking was 13 weeks. The number of antenatal visits achieved during the current pregnancy was 6. 97% of expectant mothers were aware of the importance of antenatal visits. Various demographic characteristics were studied in relation to the number of antenatal visits achieved and the gestational age at booking. It was found that the level of education of both husband and wife and poor obstetric history significantly affected gestational age at booking, (P-values were less than 0.03 and 0.002 respectively). However the family income and gestational age at booking affected the number of antenatal visits (P-values were less than 0.0003 and 0.0001 respectively). The respondents' most striking reason for non-compliance was related to accessibility to health centre. 23.3% thought that the health centres were far away from their residence and they needed to involve the husbands in driving them to health centres. Recommendations were given to improve aspects of accessibility and inviting more antenatal visits in addition to improving quality of such service.
Brute luck and responsibility
Authors: Vallentyne Peter
Published: January 2008

The concept of agent-responsibility for an outcome (that is, of the outcome reflecting the autonomous choice of the agent) is central to both ethics and political philosophy. The concept, however, remains radically under-explored. In particular, the issue of partial responsibility for an outcome needs further development. I propose an account of partial responsibility based on partial causal contribution. Agents who choose autonomously in full knowledge of the consequences are agent-responsible, I claim, for the shift in the objective probability of the outcome in question that her choice induces. Thus, agents will typically be only partially agent-responsible (that is, for a shift of less than 100 percent) for any given outcome. The model has an implication that is generally rejected: that agents who purchase lottery tickets and win are agent-responsible for only part of the winnings.
Contractualism and risk imposition
Authors: Lenman James
Published: January 2008

The article investigates the resources of contractualist moral theory to make sense of the ethics of risk imposition. In some ways, contractualism seems well placed to explain how it can be reasonable to accept exposure to risk of harms whose direct imposition would not be acceptable. However, there are difficulties getting clear about what directness comes to here, especially given the difficulty of adequately motivating traditional views that assign ethical significance to what the agent intends as opposed to merely foreseeing. The article considers two principles which might help the contractualist: the Redistribution Principle, which, while attractive, is perhaps somewhat too restrictive, and the Aim Consistency Principle , which grants ethical significance to the aims with which our actions are in principle consistent whatever our actual intentions may be. The article also considers the relative significance of ex ante and ex post perspectives from which to evaluate actions and principles.
Historical review: megakaryopoiesis and thrombopoiesis
Authors: Kaushansky Kenneth
Published: January 2008

The study of thrombopoiesis has evolved greatly since an era when platelets were termed “the dust of the blood,” only about 100 years ago. During this time megakaryocytes were identified as the origin of blood platelets; marrow-derived megakaryocytic progenitor cells were functionally defined and then purified; and the primary regulator of the process, thrombopoietin, was cloned and characterized and therapeutic thrombopoietic agents developed. During this journey we continue to learn that the physiologic mechanisms that drive proplatelet formation can be recapitulated in cell-free systems and their biochemistry evaluated; the molecular underpinnings of endomitosis are being increasingly understood; the intracellular signals sent by engagement of a large number of megakaryocyte surface receptors have been defined; and many of the transcription factors that drive megakaryocytic fate determination have been identified and experimentally manipulated. While some of these biologic processes mimic those seen in other cell types, megakaryocytes and platelets possess enough unique developmental features that we are virtually assured that continued study of thrombopoiesis will yield innumerable clinical and scientific insights for many decades to come.
Altered intracellular and extracellular signaling leads to impaired T-cell functions in ADA-SCID patients
Authors: Cassani Barbara , Mirolo Massimiliano , Cattaneo Federica , Benninghoff Ulrike , Hershfield Michael , Carlucci Filippo , Tabucchi Antonella , Bordignon Claudio , Roncarolo Maria Grazia , Aiuti Alessandro
Published: January 2008

Mutations in the adenosine deaminase (ADA) gene are responsible for a form of severe combined immunodeficiency (SCID) caused by the lymphotoxic accumulation of ADA substrates, adenosine and 2′-deoxy-adenosine. The molecular mechanisms underlying T-cell dysfunction in humans remain to be elucidated. Here, we show that CD4+ T cells from ADA-SCID patients have severely compromised TCR/CD28-driven proliferation and cytokine production, both at the transcriptional and protein levels. Such an impairment is associated with an intrinsically reduced ZAP-70 phosphorylation, Ca2+ flux, and ERK1/2 signaling and to defective transcriptional events linked to CREB and NF-κB. Moreover, exposure to 2′-deoxy-adenosine results in a stronger inhibition of T-cell activation, mediated by the aberrant A2A adenosine receptor signaling engagement and PKA hyperactivation, or in a direct apoptotic effect at higher doses. Conversely, in T cells isolated from patients after gene therapy with retrovirally transduced hematopoietic stem/progenitor cells, the biochemical events after TCR triggering occur properly, leading to restored effector functions and normal sensitivity to apoptosis. Overall, our findings provide a better understanding of the pathogenesis of the immune defects associated with an altered purine metabolism and confirm that ADA gene transfer is an efficacious treatment for ADA-SCID. The trials in this study are enrolled at www.ClinicalTrials.gov as #NCT00598481 and #NCT0059978.
Novel biphasic role for lymphocytes revealed during resolving inflammation
Authors: Rajakariar Ravindra , Lawrence Toby , Bystrom Jonas , Hilliard Mark , Colville-Nash Paul , Bellingan Geoff , Fitzgerald Desmond , Yaqoob Muhammad M. , Gilroy Derek W.
Published: January 2008

Acute inflammation is traditionally described as the influx of polymorphonuclear leukocytes (PMNs) followed by monocyte-derived macrophages, leading to resolution. This is a classic view, and despite subpopulations of lymphocytes possessing innate immune-regulatory properties, seldom is their role in acute inflammation and its resolution discussed. To redress this we show, using lymphocyte-deficient RAG1−/− mice, that peritoneal T/B lymphocytes control PMN trafficking by regulating cytokine synthesis. Once inflammation ensues in normal mice, lymphocytes disappear in response to DP1 receptor activation by prostaglandin D2. However, upon resolution, lymphocytes repopulate the cavity comprising B1, natural killer (NK), γ/δ T, CD4+/CD25+, and B2 cells. Repopulating lymphocytes are dispensable for resolution, as inflammation in RAG1−/− and wild-type mice resolve uniformly. However, repopulating lymphocytes are critical for modulating responses to superinfection. Thus, in chronic granulomatous disease using gp91phox−/− mice, not only is resolution delayed compared with wild-type, but there is a failure of lymphocyte re-appearance predisposing to exaggerated immune responses upon secondary challenge that is rescued by resolution-phase lymphocytes. In conclusion, as lymphocyte repopulation is also evident in human peritonitis, we hereby describe a transition in T/B cells from acute inflammation to resolution, with a central role in modulating the severity of early onset and orchestrating responses to secondary infection.
GSK3β is a negative regulator of platelet function and thrombosis
Authors: Li Dongjun , August Shelley , Woulfe Donna S.
Published: January 2008

Glycogen synthase kinase (GSK)3β is a ser-thr kinase that is phosphorylated by the kinase Akt. Although Akt has been shown to regulate platelet function and arterial thrombosis, its effectors in platelets remain unknown. We show here that agonist-dependent phosphorylation of GSK3β in platelets is Akt dependent. To determine whether GSK3β regulates platelet function, platelets from mice lacking a single allele of GSK3β were compared with those of wild-type (WT) controls. GSK3β+/− platelets demonstrated enhanced agonist-dependent aggregation, dense granule secretion, and fibrinogen binding, compared with WT platelets. Treatment of human platelets with GSK3 inhibitors renders them more sensitive to agonist-induced aggregation, suggesting that GSK3 suppresses platelet function in vitro. Finally, the effect of GSK3β on platelet function in vivo was evaluated using 2 thrombosis models in mice. In the first, 80% of GSK3β+/− mice (n = 10) formed stable occlusive thrombi after ferric chloride carotid artery injury, whereas the majority of wild-type mice (67%) formed no thrombi (n = 15). In a disseminated thrombosis model, deletion of a single allele of GSK3β in mice conferred enhanced sensitivity to thrombotic insult. Taken together, these results suggest that GSK3β acts as a negative regulator of platelet function in vitro and in vivo.
Novel markers of normal and neoplastic human plasmacytoid dendritic cells
Authors: Marafioti Teresa , Paterson Jennifer C. , Ballabio Erica , Reichard Kaaren K. , Tedoldi Sara , Hollowood Kevin , Dictor Michael , Hansmann Martin-Leo , Pileri Stefano A. , Dyer Martin J. , Sozzani Silvano , Dikic Ivan , Shaw Andrey S. , Petrella Tony , Stein Harald , Isaacson Peter G. , Facchetti Fabio , Mason David Y.
Published: January 2008

Plasmacytoid dendritic cells (pDCs) are involved in innate immunity (eg, by secreting interferons) and also give rise to CD4+CD56+ hematodermic neoplasms. We report extensive characterization of human pDCs in routine tissue samples, documenting the expression of 19 immunohistologic markers, including signaling molecules (eg, BLNK), transcription factors (eg, ICSBP/IRF8 and PU.1), and Toll-like receptors (TLR7, TLR9). Many of these molecules are expressed in other cell types (principally B cells), but the adaptor protein CD2AP was essentially restricted to pDCs, and is therefore a novel immunohistologic marker for use in tissue biopsies. We found little evidence for activation-associated morphologic or phenotypic changes in conditions where pDCs are greatly increased (eg, Kikuchi disease). Most of the molecules were retained in the majority of pDC neoplasms, and 3 (BCL11A, CD2AP, and ICSBP/IRF8) were also commonly negative in leukemia cutis (acute myeloid leukemia in the skin), a tumor that may mimic pDC neoplasia. In summary, we have documented a range of molecules (notably those associated with B cells) expressed by pDCs in tissues and peripheral blood (where pDCs were detectable in cytospins at a frequency of < 1% of mononuclear cells) and also defined potential new markers (in particular CD2AP) for the diagnosis of pDC tumors.
The Average Mutual Information Profile as a Genomic Signature
Authors: Bauer Mark , Schuster Sheldon M , Sayood Khalid
Published: January 2008

Background

Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discriminating organisms using genomic data. Species specific genomic signatures are useful in a variety of contexts such as evolutionary analysis, assembly and classification of genomic sequences from large uncultivated microbial communities and a rapid identification system in health hazard situations.

Results

We have analyzed genomic sequences of eukaryotic and prokaryotic chromosomes as well as various subtypes of viruses using an information theoretic framework. We confirm the existence of a species specific average mutual information (AMI) profile. We use these profiles to define a very simple, computationally efficient, alignment free, distance measure that reflects the evolutionary relationships between genomic sequences. We use this distance measure to classify chromosomes according to species of origin, to separate and cluster subtypes of the HIV-1 virus, and classify DNA fragments to species of origin.

Conclusion

AMI profiles of DNA sequences prove to be species specific and easy to compute. The structure of AMI profiles are conserved, even in short subsequences of a species' genome, rendering a pervasive signature. This signature can be used to classify relatively short DNA fragments to species of origin.
Lactation failure in Src knockout mice is due to impaired secretory activation
Authors: Watkin Harriet , Richert Monica M , Lewis Andrew , Terrell Kristina , McManaman James P , Anderson Steven M
Published: January 2008

Background

Mammary gland development culminates in lactation and is orchestrated by numerous stimuli and signaling pathways. The Src family of nonreceptor tyrosine kinases plays a pivotal role in cell signaling. In order to determine if Src plays a role in mammary gland development we have examined mammary gland development and function during pregnancy and lactation in mice in which expression of Src has been eliminated.

Results

We have characterized a lactation defect in the Src-/- mice which results in the death of over 80% of the litters nursed by Src-/- dams. Mammary gland development during pregnancy appears normal in these mice; however secretory activation does not seem to occur. Serum prolactin levels are normal in Src-/- mice compared to wildtype controls. Expression of the prolactin receptor at both the RNA and protein level was decreased in Src-/- mice following the transition from pregnancy to lactation, as was phosphorylation of STAT5 and expression of milk protein genes. These results suggest that secretory activation, which occurs following parturition, does not occur completely in Src-/- mice. Failed secretory activation results in precocious involution in the mammary glands of Src-/- even when pups were suckling. Involution was accelerated following pup withdrawal perhaps as a result of incomplete secretory activation. In vitro differentiation of mammary epithelial cells from Src-/- mice resulted in diminished production of milk proteins compared to the amount of milk proteins produced by Src+/+ cells, indicating a direct role for Src in regulating the transcription/translation of milk protein genes in mammary epithelial cells.

Conclusion

Src is an essential signaling modulator in mammary gland development as Src-/- mice exhibit a block in secretory activation that results in lactation failure and precocious involution. Src appears to be required for increased expression of the prolactin receptor and successful downstream signaling, and alveolar cell organization.
The P450 oxidoreductase, RedA, controls development beyond the mound stage in Dictyostelium discoideum
Authors: Gonzalez-Kristeller Daniela C , Farage Layla , Fiorini Leonardo C , Loomis William F , da Silva Aline M
Published: January 2008

Background

NADPH-cytochrome-P450 oxidoreductase (CPR) is a ubiquitous enzyme that belongs to a family of diflavin oxidoreductases and is required for activity of the microsomal cytochrome-P450 monooxygenase system. CPR gene-disruption experiments have demonstrated that absence of this enzyme causes developmental defects both in mouse and insect.

Results

Annotation of the sequenced genome of D. discoideum revealed the presence of three genes (redA, redB and redC) that encode putative members of the diflavin oxidoreductase protein family. redA transcripts are present during growth and early development but then decline, reaching undetectable levels after the mound stage. redB transcripts are present in the same levels during growth and development while redC expression was detected only in vegetative growing cells. We isolated a mutant strain of Dictyostelium discoideum following restriction enzyme-mediated integration (REMI) mutagenesis in which redA was disrupted. This mutant develops only to the mound stage and accumulates a bright yellow pigment. The mound-arrest phenotype is cell-autonomous suggesting that the defect occurs within the cells rather than in intercellular signaling.

Conclusion

The developmental arrest due to disruption of redA implicates CPR in the metabolism of compounds that control cell differentiation.
Preimplantation expression of the somatic form of Dnmt1 suggests a role in the inheritance of genomic imprints
Authors: Cirio M Cecilia , Ratnam Sarayu , Ding Feng , Reinhart Bonnie , Navara Chris , Chaillet J Richard
Published: January 2008

Background

Identical DNA methylation differences between maternal and paternal alleles in gametes and adults suggest that the inheritance of genomic imprints is strictly due to the embryonic maintenance of DNA methylation. Such maintenance would occur in association with every cycle of DNA replication, including those of preimplantation embryos.

Results

The expression of the somatic form of the Dnmt1 cytosine methyltransferase (Dnmt1s) was examined in cleavage-stage preimplantation mouse embryos. Low concentrations of Dnmt1s are found in 1-, 2-, 4-, and 8-cell embryos, as well as in morulae and blastocysts. Dnmt1s is present in the cytoplasm at all stages, and in the nuclei of all stages except the 1-cell, pronuclear-stage embryo. The related oocyte-derived Dnmt1o protein is also present in nuclei of 8-cell embryos, along with embryo-synthesized Dnmt1s. Dnmt1s protein expressed in 1-cell and 2-cell embryos is derived from the oocyte, whereas the embryo synthesizes its own Dnmt1s from the 2-cell stage onward.

Conclusion

These observations suggest that Dnmt1s provides maintenance methyltransferase activity for the inheritance of methylation imprints in the early mouse embryo. Moreover, the ability of Dnmt1o and Dnmt1s proteins synthesized at the same time to substitute for one another's maintenance function, but the lack of functional interchange between oocyte- and embryo-synthesized Dnmt1 proteins, suggests that the developmental source is the critical determinant of Dnmt1 function during preimplantation development.
IS4 family goes genomic
Authors: De Palmenaer Daniel , Siguier Patricia , Mahillon Jacques
Published: January 2008

Background

Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family.

Results

A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus.

Conclusion

The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.
hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions
Authors: Brocchieri Luciano , Conway de Macario Everly , Macario Alberto JL
Published: January 2008

Background

Hsp70 chaperones are required for key cellular processes and response to environmental changes and survival but they have not been fully characterized yet. The human hsp70-gene family has an unknown number of members (eleven counted over ten years ago); some have been described but the information is incomplete and inconsistent. A coherent body of knowledge encompassing all family components that would facilitate their study individually and as a group is lacking. Nowadays, the study of chaperone genes benefits from the availability of genome sequences and a new protocol, chaperonomics, which we applied to elucidate the human hsp70 family.

Results

We identified 47 hsp70 sequences, 17 genes and 30 pseudogenes. The genes distributed into seven evolutionarily distinct groups with distinguishable subgroups according to phylogenetic and other data, such as exon-intron and protein features. The N-terminal ATP-binding domain (ABD) was conserved at least partially in the majority of the proteins but the C-terminal substrate-binding domain (SBD) was not. Nine proteins were typical Hsp70s (65–80 kDa) with ABD and SBD, two were lighter lacking partly or totally the SBD, and six were heavier (>80 kDa) with divergent C-terminal domains. We also analyzed exon-intron features, transcriptional variants and protein structure and isoforms, and modality and patterns of expression in various tissues and developmental stages. Evolutionary analyses, including human hsp70 genes and pseudogenes, and other eukaryotic hsp70 genes, showed that six human genes encoding cytosolic Hsp70s and 27 pseudogenes originated from retro-transposition of HSPA8, a gene highly expressed in most tissues and developmental stages.

Conclusion

The human hsp70-gene family is characterized by a remarkable evolutionary diversity that mainly resulted from multiple duplications and retrotranspositions of a highly expressed gene, HSPA8. Human Hsp70 proteins are clustered into seven evolutionary Groups, with divergent C-terminal domains likely defining their distinctive functions. These functions may also be further defined by the observed differences in the N-terminal domain.
Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference
Authors: Kim Tae-Sung , Booth James G , Gauch Hugh G , Sun Qi , Park Jongsun , Lee Yong-Hwan , Lee Kwangwon
Published: January 2008

Background

Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs.

Results

We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST), which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC) and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations.

Conclusion

Taking our computational, statistical and experimental data together, we conclude that 1) the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2) the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3) there are different levels of evolutionary forces in variation of amino acid repeats, and 4) SSRs are stable molecular markers for genetic studies in N. crassa.
Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses
Authors: Gao Haichun , Wang Xiaohu , Yang Zamin K , Palzkill Timothy , Zhou Jizhong
Published: January 2008

Background

The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene.

Results

To understand the role of ArcA in S. oneidensis, an arcA deletion strain was constructed and subjected to both physiological characterization and microarray analysis. Compared to the wild-type MR-1, the mutant exhibited impaired aerobic growth and a defect in utilizing DMSO in the absence of O2. Microarray analyses on cells grown aerobically and anaerobically on fumarate revealed that expression of 1009 genes was significantly affected (p < 0.05) by the mutation. In contrast to E. coli ArcA, the protein appears to be dispensable in regulation of the TCA cycle in S. oneidensis. To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map. By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.

Conclusion

These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.
Discordant localization of WFA reactivity and brevican/ADAMTS-derived fragment in rodent brain
Authors: Ajmo Joanne M , Eakin Autumn K , Hamel Michelle G , Gottschall Paul E
Published: January 2008

Background

Proteoglycan (PG) in the extracellular matrix (ECM) of the central nervous system (CNS) may act as a barrier for neurite elongation in a growth tract, and regulate other characteristics collectively defined as structural neural plasticity. Proteolytic cleavage of PGs appears to alter the environment to one favoring plasticity and growth. Brevican belongs to the lectican family of aggregating, chondroitin sulfate (CS)-bearing PGs, and it modulates neurite outgrowth and synaptogenesis. Several ADAMTSs (a
disintegrin and metalloproteinase with thrombospondin motifs) are glutamyl-endopeptidases that proteolytically cleave brevican. The purpose of this study was to localize regions of adult CNS that contain a proteolytic-derived fragment of brevican which bears the ADAMTS-cleaved neoepitope sequence. These regions were compared to areas of Wisteria floribunda agglutin (WFA) reactivity, a common reagent used to detect "perineuronal nets" (PNNs) of intact matrix and a marker which is thought to label regions of relative neural stability.

Results

WFA reactivity was found primarily as PNNs, whereas brevican and the ADAMTS-cleaved fragment of brevican were more broadly distributed in neuropil, and in particular regions localized to PNNs. One example is hippocampus where the ADAMTS-cleaved brevican fragment is found surrounding pyramidal neurons, in neuropil of stratum oriens/radiatum and the lacunosum moleculare. The fragment was less abundant in the molecular layer of the dentate gyrus. Mostly PNNs of scattered interneurons along the pyramidal layer were identified by WFA. In lateral thalamus, the reticular thalamic nucleus stained abundantly with WFA whereas ventral posterior nuclei were markedly immunopositive for ADAMTS-cleaved brevican. Using Western blotting techniques, no common species were reactive for brevican and WFA.

Conclusion

In general, a marked discordance was observed in the regional localization between WFA and brevican or the ADAMTS-derived N-terminal fragment of brevican. Functionally, this difference may correspond to regions with varied prevalence for neural stability/plasticity.