Detecting and characterizing gene conversions between multigene family members

We used a variety of methods to detect known gene conversions in the actin gene families of five angiosperm species, the beta-globin gene families of two primate species, and the Zfx/Zfy gene families of seven mammalian species. Our goal was to devise a working strategy which would allow the analysis of the members of a multigene family in order to determine whether there had been gene conversions between its members, identify the genes involved in the gene conversions, establish the lengths of the converted regions, and determine the polarities of the gene conversions. We show that three phylogenetic methods and the homoplasy test of Maynard Smith and Smith perform relatively poorly on our data sets because the sequences we analyzed had large levels of multiple substitutions. The method of Sawyer, the compatibility method of Jakobsen and Easteal, the partition matrix method of Jakobsen, Wilson, and Easteal, and the co-double method of Balding, Nichols, and Hunt can be used to identify the genes which have been involved in gene conversions. The co-double method is more powerful than other methods but requires orthologous sequences from related species. Compatibility, phylogenetic, and nucleotide substitution distribution statistics methods can be used to identify the location of the converted region(s). Site-by-site compatibility analyses can also be used to identify the direction of the conversion event(s). Combinations of these methods can therefore be used to establish the presence, locations, and polarities of gene conversions between multigene family members.     

Lizards cooperatively tunnel to construct a long-term home for family members

Constructing a home to protect offspring while they mature is common in many vertebrate groups, but has not previously been reported in lizards. Here we provide the first example of a lizard that constructs a long-term home for family members, and a rare case of lizards behaving cooperatively. The great desert skink, Liopholis kintorei from Central Australia, constructs an elaborate multi-tunnelled burrow that can be continuously occupied for up to 7 years. Multiple generations participate in construction and maintenance of burrows. Parental assignments based on DNA analysis show that immature individuals within the same burrow were mostly full siblings, even when several age cohorts were present. Parents were always captured at burrows containing their offspring, and females were only detected breeding with the same male both within- and across seasons. Consequently, the individual investments made to construct or maintain a burrow system benefit their own offspring, or siblings, over several breeding seasons.     

Complementary expression and heterophilic interactions between IgLON family members neurotrimin and LAMP

Neurotrimin (Ntm) and the limbic system-associated membrane protein (LAMP) are members of the IgLON (LAMP, OBCAM, Ntm) family of glycorylphosphatidylinositol anchored neural cell adhesion molecules. We previously reported that LAMP and Ntm promote adhesion and neurite outgrowth via a homophilic mechanism, suggesting that these proteins promote the formation of specific neuronal circuits by homophilic interactions. In this report, we have further characterized the expression and binding specificity of Ntm. Using a newly generated monoclonal antibody to Ntm, we demonstrated that this protein is largely expressed in a complementary pattern to that of LAMP in the nervous system, with co-expression at a few sites. Ntm is expressed at high levels in sensory-motor cortex and, of particular note, is transiently expressed in neurons of cortical barrel fields and corresponding thalamic "barreloids." Binding of a recombinant, soluble form of Ntm to CHO cells expressing either Ntm or LAMP demonstrates that Ntm and LAMP interact both homophilically and heterophilically. In contrast to conventional growth-promoting activity of Ig superfamily members, LAMP strongly inhibits the outgrowth of Ntm-expressing dorsal root ganglion (DRG) neurons in a heterophilic manner. These anatomical and functional data support the concept that homophilic and heterophilic interactions between IgLON family members are likely to play a role in the specification of neuronal projections via growth promoting and inhibiting effects, respectively.     

Health care professionals' perspectives on oral care for long-term care residents: nursing staff, speech-language pathologists and dental hygienists

doi: 10.1111/j.1741‐2358.2011.00513.x Health care professionals’ perspectives on oral care for long‐term care residents: Nursing staff, speech–language pathologists and dental hygienists Background: Oral health has been identified as a key factor in general health and systemic disease in long‐term care populations. To optimise oral health of this population, it is important to understand the oral care perspectives held by health care professionals involved in oral care provision. Objectives: To explore perspectives regarding oral care held by nursing staff, speech–language pathologists (SLPs) and dental hygienists (DHs) in long‐term care institutions and to understand how their perspectives impact activities and processes involved in the delivery of oral care. Methods: A focus group methodology was utilised. Separate focus groups for each targeted profession were held. Transcribed data were analysed using constant comparative analysis. Results: Daily oral health maintenance and monitoring was considered a role of nursing staff. SLPs and DHs have roles focusing on advocacy, education and supplemental care. Social factors motivate nursing staff to provide oral care, whereas factors related to the general health consequences of poor oral health underlined the motivations of SLPs and DHs. Conclusions: Education and training initiatives incorporating social aspects of oral health may be more effective for motivating nursing staff than approaches emphasising physical risk factors. Organisations can foster environments that support collaboration and communication amongst the members of multidisciplinary teams in order to promote oral health as a priority.     

miR-26家族与肿瘤关系的研究进展

miR-26家族是由miR-26a、miR-26b、miR-1297及miR-4465等序列相似、结构相仿、种子区序列相同(UCAAGUA)的微小RNA(microRNAs,miRNAs)组成。多种组织细胞分化过程中伴有mi R-26家族表达的增加,其异常表达与特发性肺纤维化、原发性胆汁性肝硬化、多发性硬化及阿尔茨海默病等有关。近年研究报道,多种肿瘤组织亦存在mi R-26基因表达紊乱,并与肿瘤的发生发展密切相关。就miR-26家族及其调控的靶基因与肿瘤关系的研究进展进行综述。     

Bcl-2 family members and disease

Apoptosis plays an important role during development and in the maintenance of multicellular organisms. Bcl-2 family members affect cell death in either a positive or negative fashion. Although some redundancy exists between family members, expression of certain family members is important during development in an organ-specific manner. The founding family member bcl-2 tends to be highly expressed in the embryo and declines postnatally following differentiation and maturation. Altered expression of bcl-2, as well as other family members, has been observed in disease states potentially affecting treatment modalities. Here we examine the distribution and role death repressors bcl-2, bcl-x(L) and bcl-w as well as death effectors bax and bak play regulating apoptosis in a tissue-specific manner. Understanding the normal role of these proteins during embryogenesis and in the mature organ will give us important insight into what goes awry in various disease states.     

Comparison of long-term care in an acute care institution and in a long-term care institution

BACKGROUND: Acute care hospitals in Quebec are required to reserve 10% of their beds for patients receiving long-term care while awaiting transfer to a long-term care facility. It is widely believed that this is inefficient because it is more costly to provide long-term care in an acute care hospital than in one dedicated to long-term care. The purpose of this study was to compare the quality and cost of long-term care in an acute care hospital and in a long-term care facility. METHODS: A concurrent cross-sectional study was conducted of 101 patients at the acute care hospital and 102 patients at the long-term care hospital. The 2 groups were closely matched in terms of age, sex, nursing care requirements and major diagnoses. Several indicators were used to assess the quality of care: the number of medical specialist consultations, drugs, biochemical tests and radiographic examinations; the number of adverse events (reportable incidents, nosocomial infections and pressure ulcers); and anthropometric and biochemical indicators of nutritional status. Costs were determined for nursing personnel, drugs and biochemical tests. A longitudinal study was conducted of 45 patients who had been receiving long-term care at the acute care hospital for at least 5 months and were then transferred to the long-term care facility where they remained for at least 6 months. For each patient, the number of adverse events, the number of medical specialist consultations and the changes in activities of daily living status were assessed at the 2 institutions. RESULTS: In the concurrent study, no differences in the number of adverse events were observed; however, patients at the acute care hospital received more drugs (5.9 v. 4.7 for each patient, p < 0.01) and underwent more tests (299 v. 79 laboratory units/year for each patient, p < 0.001) and radiographic examinations (64 v. 46 per 1000 patient-weeks, p < 0.05). At both institutions, 36% of the patients showed anthropometric and biochemical evidence of protein-calorie undernutrition; 28% at the acute care hospital and 27% at the long-term care hospital had low serum iron and low transferrin saturation, compatible with iron deficiency. The longitudinal study showed that there were more consultations (61 v. 37 per 1000 patient-weeks, p < 0.02) and fewer pressure ulcers (18 v. 34 per 1000 patient-weeks, p < 0.05) at the acute care hospital than at the long-term care facility; other measures did not differ. The cost per patient-year was $7580 higher at the acute care hospital, attributable to the higher cost of drugs ($42), the greater use of laboratory tests ($189) and, primarily, the higher cost of nursing ($7349). For patients requiring 3.00 nursing hours/day, the acute care hospital provided more hours than the long-term care facility (3.59 v. 3.03 hours), with a higher percentage of hours from professional nurses rather than auxiliary nurses or nursing aides (62% v. 28%). The nurse staffing pattern at the acute care hospital was characteristic of university-affiliated acute care hospitals. INTERPRETATION: The long-term care provided in the acute care hospital involved a more interventionist medical approach and greater use of professional nurses (at a significantly higher cost) but without any overall difference in the quality of care.     

Association between the PDGF receptor and members of the src family of tyrosine kinases.

We have examined the interaction between the platelet-derived growth factor (PDGF) receptor and three src family tyrosine kinases, pp60c-src, p59fyn, and pp62c-yes. The kinase activities of all three enzymes were elevated after PDGF stimulation of quiescent fibroblasts, coincident with association of the src family kinases with the PDGF receptor and other proteins. The presence of a protein of 81-85 kd in these complexes correlated with the detection of phosphatidylinositol (PI) kinase activity (previously described to associate with both the PDGF receptor and pp60c-src-middle T antigen). These results suggest that the physiological response to PDGF involves interaction of the receptor not only with serine/threonine and lipid kinases and a phospholipase, but also with other tyrosine kinases.     

Parameter dependence of correlation between the Shannon index and members of parametric diversity index family

We present detailed data on correlation of the Shannon diversity index with members of Hill's and Hurlbert's parametric index family. The correlation reaches its maximum in both cases at a definite parameter value. These specified data on correlation are exploitable when applying the above diversity indices. Namely, in case of their parallel use with the Shannon index a strong correlation between the indices should be avoided. The investigations were carried out on sets of moth and fly collections.Moreover, we hypothesized that a smaller distance between so-called sensitivity profiles of diversity indices predicts a larger correlation between the indices concerned. Based on investigations of the sensitivity profile distance between the Shannon index and members of parametric diversity index family as a function of index parameter, we point out that on the whole the above hypothesis is true. This makes possible to estimate the correlation of two diversity indices omitting troublesome index calculations on a large set of abundance lists.     

Homologies between members of the germin gene family in hexaploid wheat and similarities between these wheat germins and certain Physarum spherulins

By screening approximately 10(6) plaques in a wheat DNA library with a "full-length" germin cDNA probe, two genomic clones were detected. When digested with EcoRI, one clone yielded a 2.8-kilobase pair fragment (gf-2.8) and the other yielded a 3.8-kilobase pair fragment (gf-3.8). By nucleotide sequencing, each of gf-2.8 and gf-3.8 was found to encode a complete sequence for germin and germin mRNA, and to contain appreciable amounts of 5'- and 3'-flanking sequences. The "cap" site in gf-2.8 was determined by primer extension and the corresponding site in gf-3.8 was deduced by analogy. The mRNA coding sequences in gf-2.8 and gf-3.8 are intronless and 87% homologous with one another. The 5'-flanking regions in gf-2.8 and gf-3.8 contain recognizable sites of what are probably cis-acting elements but there is otherwise little if any significant similarity between them. In addition to putative TATA and CAAT boxes in the 5'-flanking regions of gf-2.8 and gf-3.8, there are AT-rich inverted-repeats, GC boxes, long purine-rich sequences, two 19-base pair direct-repeat sequences in gf-2.8, and a remarkably long (200-base pair) inverted-repeat sequence (approximately 90% homology) in gf-3.8. An 8% difference between the mature-protein coding regions in gf-2.8 and gf-3.8 is reflected by a corresponding 7% difference between the corresponding 201-residue proteins. Most significantly, the same 8% difference between the mature-protein coding regions in gf-2.8 and gf-3.8 is allied with no change whatever in a central part (61-151) of the encoded polypeptide sequences. It seems likely that this central, strongly conserved core in the germins is of first importance in the biochemical involvements of the proteins. When an equivalence is assumed between like amino acids, the gf-2.8 and gf-3.8 germins show significant (approximately 44%) similarity to spherulins 1a and 1b of Physarum polycephalum, a similarity that increases to approximately 50% in the conserved core of germin. Near the middle (87-96) of the conserved core in the germins is a rare PH(I/T)HPRATEI decapeptide sequence which is shared by spherulins (1a and 1b) and germins (gf-2.8 and gf-3.8). These similarities are discussed in the context of evidence which can be interpreted to suggest that the biochemistry of germins and spherulins is involved with cellular, perhaps cell-wall responses to desiccation, hydration, and osmotic stress.(ABSTRACT TRUNCATED AT 400 WORDS)     

Role of Bcl-2 family members in invertebrates

Proteins belonging to the Bcl-2 family function as regulators of 'life-or-death' decisions in response to various intrinsic and extrinsic stimuli. In mammals, cell death is controlled by pro- and anti-apoptotic members of the Bcl-2 family, which function upstream of the caspase cascade. Structural and functional homologues of the Bcl-2 family proteins also exist in lower eukaryotes, such as nematodes and flies. In nematodes, an anti-apoptotic Bcl-2 family protein, CED-9, functions as a potent cell death inhibitor, and a BH3-only protein, EGL-1, acts as an inhibitor of CED-9 to facilitate the spatio-temporal regulation of programmed cell death. On the other hand, the Drosophila genome encodes two Bcl-2 family proteins, Drob-1/Debcl/dBorg-1/dBok and Buffy/dBorg-2, both of which structurally belong to the pro-apoptotic group, despite abundant similarities in the cell death mechanisms between flies and vertebrates. Drob-1 acts as a pro-apoptotic factor in vitro and in vivo, and Buffy/dBorg-2 exhibits a weak anti-apoptotic function. The ancestral role of the Bcl-2 family protein may be pro-apoptotic, and the evolution of the functions of this family of proteins may be closely linked with the contribution of mitochondria to the cell death pathway.     

Novel PDGF family members: PDGF-C and PDGF-D

Platelet-derived growth factors (PDGFs) were discovered almost two decades ago. The classical PDGF polypeptide chains, PDGF-A and PDGF-B, are well studied and they regulate a number of physiological and pathophysiological processes in many types of mesenchymal cells via two receptor tyrosine kinases, PDGF receptors alpha and beta. Recently, two additional PDGF polypeptide chains were discovered, namely PDGF-C and PDGF-D. The discovery of two additional ligands for the two PDGF receptors suggests that PDGF-mediated signaling is more complex than previously anticipated.     

Transgenic analysis of the Smad family of TGF-beta signal transducers in Drosophila melanogaster suggests new roles and new interactions between family members

Smad signal transducers are required for transforming growth factor-beta-mediated developmental events in many organisms including humans. However, the roles of individual human Smad genes (hSmads) in development are largely unknown. Our hypothesis is that an hSmad performs developmental roles analogous to those of the most similar Drosophila Smad gene (dSmad). We expressed six hSmad and four dSmad transgenes in Drosophila melanogaster using the Gal4/UAS system and compared their phenotypes. Phylogenetically related human and Drosophila Smads induced similar phenotypes supporting the hypothesis. In contrast, two nearly identical hSmads generated distinct phenotypes. When expressed in wing imaginal disks, hSmad2 induced oversize wings while hSmad3 induced cell death. This observation suggests that a very small number of amino acid differences, between Smads in the same species, confer distinct developmental roles. Our observations also suggest new roles for the dSmads, Med and Dad, in dActivin signaling and potential interactions between these family members. Overall, the study demonstrates that transgenic methods in Drosophila can provide new information about non-Drosophila members of developmentally important multigene families.