Some KpnI family members are associated with the Alu family in the human genome

The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI family sequence started several base-pairs downstream from the 3' end of the Alu family sequence. In both cases, the Alu family sequence was not flanked by the direct repeat sequence common to the Alu family. These two members showed no sequence homology in 3' terminal regions. Interestingly, the Alu family plus the KpnI family unit was found to be flanked by a direct repeat sequence of several base-pair length. Based on these findings, relationship between the Alu family and KpnI family is discussed.     

Male participation in family planning: results from a qualitative study in Mpigi District, Uganda

The aim of this study was to determine men's perceptions about family planning and how they participate or wish to participate in family planning activities in Mpigi District, central Uganda. Four focus group discussions were conducted with married men and with family planning providers from both the government and private sector. In addition, seven key informants were interviewed using a semi-structured interview guide. The results indicate that men have limited knowledge about family planning, that family planning services do not adequately meet the needs of men, and that spousal communication about family planning issues is generally poor. However, almost all men approved of modern family planning and expressed great interest in participating. The positive change of the beliefs and attitudes of men towards family planning in the past years has not been recognized by family planning programme managers, since available services are not in line with current public attitudes. A more couple-oriented approach to family planning is needed. Measures could include, for example, recruiting males as family planning providers, offering more family planning counselling for couples, and promoting female-oriented methods with men and vice versa.     

A novel polydnaviral gene family, BEN, and its immunosuppressive function in larvae of Plutella xylostella parasitized by Cotesia plutellae

A full genome sequence of the episomal form of Cotesia plutellae bracovirus (CpBV) suggests 11 BEN family genes. This study analyzed their expression and physiological function in the viral host, Plutella xylostella. All 11 BEN family genes were expressed during entire parasitization period of P. xylostella larvae. In addition, these BEN family genes were expressed in fat body, gut, epidermis, and hemocytes in final larval instar of parasitized P. xylostella. The 11 BEN family genes were transiently expressed in nonparasitized larvae by injection of each viral segment containing its corresponding BEN family gene. The transient expression of BEN family genes significantly suppressed hemocyte nodule formation in response to bacterial challenge. Subsequent injection of double-stranded RNA specific to each BEN family gene suppressed the expression of the BEN family gene and rescued the immunosuppression. These results indicate that 11 BEN family genes are expressed in larvae parasitized by C. plutellae and play crucial role in inducing immunosuppression. Homologous BEN family genes were found in other bracoviral genomes. We propose BEN domain-containing genes as a new functional gene family in polydnaviruses.     

TRP channels: an overview

The TRP ("transient receptor potential") family of ion channels now comprises more than 30 cation channels, most of which are permeable for Ca2+, and some also for Mg2+. On the basis of sequence homology, the TRP family can be divided in seven main subfamilies: the TRPC ('Canonical') family, the TRPV ('Vanilloid') family, the TRPM ('Melastatin') family, the TRPP ('Polycystin') family, the TRPML ('Mucolipin') family, the TRPA ('Ankyrin') family, and the TRPN ('NOMPC') family. The cloning and characterization of members of this cation channel family has exploded during recent years, leading to a plethora of data on the roles of TRPs in a variety of tissues and species, including mammals, insects, and yeast. The present review summarizes the most pertinent recent evidence regarding the structural and functional properties of TRP channels, focusing on the regulation and physiology of mammalian TRPs.     

Estimating heritability using family-pooled phenotypic and genotypic data: a simulation study applied to aquaculture

Estimating heritability based on individual phenotypic and genotypic measurements can be expensive and labour-intensive in commercial aquaculture breeding. Here, the feasibility of estimating heritability using within-family means of phenotypes and allelic frequencies was investigated. Different numbers of full-sib families and family sizes across ten generations with phenotypic and genotypic information on 10 K SNPs were analysed in ten replicates. Three scenarios, representing differing numbers of pools per family (one, two and five) were considered. The results showed that using one pool per family did not reliably estimate the heritability of family means. Using simulation parameters appropriate for aquaculture, at least 200 families of 60 progeny per family divided equally in two pools per family was required to estimate the heritability of family means effectively. Although application of five pools generated more within- and between- family relationships, it reduced the number of individuals per pool and increased within-family residual variation, hence, decreased the heritability of family means. Moreover, increasing the size of pools resulted in increasing the heritability of family means towards one. In addition, heritability of family mean estimates were higher than family heritabilities obtained from Falconer’s formula due to lower intraclass correlation estimate compared to the coefficient of relationship.Subject terms: Genome evolution     

Function and structure studies of GH family 31 and 97 α-glycosidases

A huge number of glycoside hydrolases are classified into the glycoside hydrolase family (GH family) based on their amino-acid sequence similarity. The glycoside hydrolases acting on α-glucosidic linkage are in GH family 4, 13, 15, 31, 63, 97, and 122. This review deals mainly with findings on GH family 31 and 97 enzymes. Research on two GH family 31 enzymes is described: clarification of the substrate recognition of Escherichia coli α-xylosidase, and glycosynthase derived from Schizosaccharomyces pombe α-glucosidase. GH family 97 is an aberrant GH family, containing inverting and retaining glycoside hydrolases. The inverting enzyme in GH family 97 displays significant similarity to retaining α-glycosidases, including GH family 97 retaining α-glycosidase, but the inverting enzyme has no catalytic nucleophile residue. It appears that a catalytic nucleophile has been eliminated during the molecular evolution in the same way as a man-made nucleophile mutant enzyme, which catalyzes the inverting reaction, as in glycosynthase and chemical rescue.     

水稻Trihelix转录因子家族全基因组分析及功能预测

Trihelix转录因子家族在植物生长发育以及响应逆境胁迫等方面发挥着重要作用,但目前基于水稻全基因组水平鉴定和分析该基因家族的研究尚未见相关报道。本文利用生物信息学方法在水稻基因组数据库中鉴定到Trihelix家族成员31个,序列聚类和功能结构域分析发现该家族均含有高度保守的、特征性的Trihelix结构域;根据亲缘关系远近和结构域特点,将其分为5个亚家族(Ⅰ~Ⅴ)。通过与拟南芥、二穗短炳草和高粱中Trihelix家族的聚类分析发现,这4个物种中Trihelix家族的分类相一致,但每个物种均含有不同亚家族的成员,表明该基因家族的分化早于物种的分化。基于MEME程序分析水稻Trihelix转录因子家族的保守基序与聚类分析结果具有较高的一致性。染色体区段复制分析表明,部分Trihelix家族成员在水稻以及水稻与其他物种之间存在种内和种间的染色体区段复制;生物芯片数据分析发现,Trihelix基因家族在水稻不同组织中、以及对6种不同植物激素的响应呈现多样化的表达谱。采用RiceFREND在线数据库分析发现,水稻Trihelix转录因子家族的20个成员与其他蛋白存在互作关系。本研究结果初步明确了水稻Trihelix转录因子家族的进化特点、染色体分布、染色体区段复制关系、组织表达、激素应答,以及该家族蛋白与其他蛋白质的互作情况,为进一步揭示Trihelix转录因子家族的分子进化规律和生物学功能奠定了基础。     

东方田鼠社群气味对家族群成员个体觅食行为的影响

东方田鼠家族群成员个体的觅食行为是否因食物斑块存有家族群自身及非亲缘家族群气味而发生变异,进而影响其摄入率。在新鲜马唐叶片构建的均质密集食物斑块上,分别配置家族群自身巢垫物及非亲缘家族群巢垫物作为社群气味,测定东方田鼠家族群在食物斑块觅食时,其成员个体觅食行为的序列过程及参数,检验家族群自身气味及非亲缘家族群气味对成员个体觅食行为的影响。结果表明,家族群自身气味能显著地缩短本群成员个体的觅食决定时间,通过减少成员个体的嗅闻及直立扫视动作时间比例、增大一般扫视、盯视及静听动作时间比例,降低觅食中断时间比例,提高其摄入率;而非亲缘家族群气味则能显著地延长家族群成员个体的觅食决定时间,通过增大家族群成员个体的嗅闻和一般扫视动作时间比例、减小直立扫视、盯视及静听动作时间比例,增大觅食中断时间比例,降低其摄入率。结果揭示,熟悉的社群气味会促使觅食活动中的家族群成员个体,在监测环境风险时,将精力更多地用于观察和监听群内其他成员个体的行为及其发出的警报信息,以便在有效规避环境风险的同时减缓个体间因干扰性竞争对觅食活动所造成的不利影响;而陌生的社群气味会迫使成员个体,将精力由依赖群内其他成员个体的行为转向凭借自身直接警觉周围环境。     

MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes

The miR-16 family, which targets genes important for the G1-S transition, is a known modulator of the cell cycle, and members of this family are often deleted or downregulated in many types of cancers. Here, we report the reciprocal relationship-that of the cell cycle controlling the miR-16 family. Levels of this family increase rapidly as cells are arrested in G0. Conversely, as cells are released from G0 arrest, levels of the miR-16 family rapidly decrease. Such rapid changes are made possible by the unusual instabilities of several family members. The repression mediated by the miR-16 family is sensitive to these cell-cycle changes, which suggests that the rapid upregulation of the miR-16 family reinforces cell-cycle arrest in G0. Upon cell-cycle re-entry, the rapid decay of several members allows levels of the family to decrease, alleviating repression of target genes and allowing proper resumption of the cell cycle.     

Explaining Mental Health Treatment Disparities: Ethnic and Cultural Differences in Family Involvement

In a large, representative sample of persons receiving public mental health treatment, we examined whether ethnic minority consumers were more likely than white consumers to live with their families and to receive family support. We then evaluated whether differences observed in family involvement explained treatment disparities observed in outpatient and inpatient mental health services. Results indicated that Asian American and Latino consumers, especially, were considerably more likely than white consumers to live with family members and to receive family support. Ethnocultural differences in living with family did explain treatment intensity disparities whether or not consumers described themselves as dependent on family support. The results support the hypothesis that cultural differences in family involvement and support play a role in explaining mental health treatment disparities.     

Function and Structure Studies of GH Family 31 and 97 α-Glycosidases

A huge number of glycoside hydrolases are classified into the glycoside hydrolase family (GH family) based on their amino-acid sequence similarity. The glycoside hydrolases acting on α-glucosidic linkage are in GH family 4, 13, 15, 31, 63, 97, and 122. This review deals mainly with findings on GH family 31 and 97 enzymes. Research on two GH family 31 enzymes is described: clarification of the substrate recognition of Escherichia coli α-xylosidase, and glycosynthase derived from Schizosaccharomyces pombe α-glucosidase. GH family 97 is an aberrant GH family, containing inverting and retaining glycoside hydrolases. The inverting enzyme in GH family 97 displays significant similarity to retaining α-glycosidases, including GH family 97 retaining α-glycosidase, but the inverting enzyme has no catalytic nucleophile residue. It appears that a catalytic nucleophile has been eliminated during the molecular evolution in the same way as a man-made nucleophile mutant enzyme, which catalyzes the inverting reaction, as in glycosynthase and chemical rescue.     

Evolutionary analysis of the mammalian M1 aminopeptidases reveals conserved exon structure and gene death

The members of the M1 aminopeptidase family share conserved domains, yet show functional divergence within the family as a whole. In order to better understand this family, this study analyzed the mammalian members in depth at exon, gene, and protein levels. The twelve human members, eleven rat members, and eleven mouse members were first analyzed in multiple alignments to visualize both reported and unreported conserved domains. Phylogenetic trees were then generated for humans, rats, mice, and all mammals to determine how closely related the homologs were and to gain insight to the divergence in the family members. This produced three groups with similarity within the family. Next, a synteny study was completed to determine the present locations of the genes and changes that had occurred. It became apparent that gene death likely resulted in the lack of one member in mouse and rat. Finally, an in-depth analysis of the exon structure revealed that nine members of the human family and eight in mouse, are highly conserved within the exon structure. Taken together, these results indicate that the M1 aminopeptidase family is a divergent family with three subgroups and that genetic evidence mirrors categorization of the family by enzymatic function.     

A Newly Isolated Family of Short Interspersed Repetitive Elements (Sines) in Coregonid Fishes (Whitefish) with Sequences That Are Almost Identical to Those of the Smai Family of Repeats: Possible Evidence for the Horizontal Transfer of Sines

The SmaI family of repeats is present only in the chum salmon and the pink salmon, and it is not present in five other species in the same genus or in other species in closely related genera. In the present study, we showed that another short interspersed repetitive elements (SINEs) family, which is almost identical to the SmaI family, is present in all fishes in the subfamily Coregoninae, being regarded as the most primitive salmonids. This new family of SINEs was designated the SmaI-cor family (SmaI family of repeats in coregonids). The consensus sequence of the SmaI-cor family was found to be 98.6% homologous to that of the SmaI family. Accordingly, it is difficult to explain the high degree of homology between these two families of SINEs by any mechanism other than the horizontal transfer of SINEs. The estimates of the rate of neutral mutation of nuclear genes, comparing chum salmon and European whitefish, confirmed this possibility. Our results strongly suggest that a member(s) of the SmaI-cor family might have been transferred horizontally from one coregonid species to a common ancestor of chum and pink salmon or to these two species independently, to allow subsequent amplification of the SmaI family in their respective genomes.     

A study on family communication space (Part II)--A study on spatial utilization for, and familial consciousness of, family communication

Part II, based on the findings of Part I, tries to identify family Communication by delving into how it is actually practiced in view of spatial conditions within a house, and familial consciousness. Specific spatial conditions have been sampled of the housing of students at women's junior colleges, and how their family members mutually Communicate and evaluate it has been analyzed. Their views of "family" have also been examined. The findings are as follows: 1) The number of rooms, and the width of the room(s) used for family Communication are major determining factors in separating family Communication from other living activities. 2) The above separation is affected by whether family Communication is practiced in a Japanese-style room or a Western-style one. 3) The perceptual difference of the consent of "family" among a family members principally determines how they engage in family Communication and how they evaluate it. It has proved to be necessary to consider, for a spatial analysis, what kind of posture each member takes when mutually Communicating, seeking comfort and relaxation at home.     

Empowerment in family planning as viewed by Iranian women: a qualitative study

Women carry the primary responsibility for family planning in most parts of the world, and should be afforded the power of decision-making and control over their fertility. This study seeks to gain insight into Iranian women's perception of the meaning of empowerment in family planning. Using a qualitative study, seven focus group discussions and five individual interviews were conducted with 35 married Iranian women of reproductive age. The data were analysed using a conventional content analysis approach, in which themes and categories were explored to reveal women's experiences of empowerment in family planning. The results demonstrated four main categories: control over fertility plan, participative family planning, maintaining health and access to optimal family planning services. They viewed knowledge of family planning and autonomy of decision-making in fertility issues as essential elements for control of their fertility plan. Participants felt more empowered when joint family planning decisions were made with their partners in an atmosphere of agreement. Therefore, family planning policymakers should plan services with new approaches that focus on women's health and empowerment.     

PNMA family: Protein interaction network and cell signalling pathways implicated in cancer and apoptosis

Paraneoplastic Ma Family (PNMA) comprises a growing number of family members which share relatively conserved protein sequences encoded by the human genome and is localized to several human chromosomes, including the X-chromosome. Based on sequence analysis, PNMA family members share sequence homology to the Gag protein of LTR retrotransposon, and several family members with aberrant protein expressions have been reported to be closely associated with the human Paraneoplastic Disorder (PND). In addition, gene mutations of specific members of PNMA family are known to be associated with human mental retardation or 3-M syndrome consisting of restrictive post-natal growth or dwarfism, and development of skeletal abnormalities. Other than sequence homology, the physiological function of many members in this family remains unclear. However, several members of this family have been characterized, including cell signalling events mediated by these proteins that are associated with apoptosis, and cancer in different cell types. Furthermore, while certain PNMA family members show restricted gene expression in the human brain and testis, other PNMA family members exhibit broader gene expression or preferential and selective protein interaction profiles, suggesting functional divergence within the family. Functional analysis of some members of this family have identified protein domains that are required for subcellular localization, protein-protein interactions, and cell signalling events which are the focus of this review paper.     

CMTM家族成员在肿瘤细胞中的分子机制及潜在临床价值

恶性肿瘤已成为危害人类健康的重要杀手,针对肿瘤的研究也成为当今医学界的热点.含有MARVEL跨膜结构域的趋化素样因子基因家族(CKLF-like MARVEL transmembrane domain containing family of genes,CMTM family),原名人类趋化素样因子超家族(chemo...     

Isolation and characterization of two families of satellite DNA with repetitive units of 135 bp and 2.5 kb in the ant Monomorium subopacum (Hymenoptera, Formicidae)

Analyzing the satellite DNA in the ant species Monomorium subopacum we found two unrelated families of satellite DNA. Because these satellite DNA families were isolated using the two enzymes HaeIII and EcoRI we called the two families HaeIII and EcoRI family, respectively. The HaeIII family proved to be organized in a 135-bp basic unit repeat, the EcoRI family in a 2.5-kb basic unit repeat. The latter represents perhaps the longest satellite DNA isolated up to now in insects. The HaeIII family apparently comprises about 10% of the total genomic DNA whereas the EcoRI family represents only about 1-2%. A comparative analysis of the two satellite DNA sequences showed no homology between the two families although both sequences possessed long A and T stretches. Eight of the 34 chromosomes showed hybridization with the HaeIII family and hybridization signals are visible in six chromosomes with the EcoRI family. Analysis of the electrophoretic mobility of satellite DNA on non-denaturing polyacrylamide showed that the HaeIII family is only slightly curved. However, the unit of the EcoRI satellite DNA family has curvature, especially the first 1000 bp of the monomeric repeat, in which this DNA is AT rich and has numerous A and T stretches. There are also internal inverted subrepeats in each family. The sequences of satellite DNA families found in Monomorium subopacum are different from the sequences of other satellite DNAs cloned in insects, including other species of ants.     

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily.

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily (TC #2.A.66) consists of four previously recognized families: (a) the ubiquitous multi-drug and toxin extrusion (MATE) family; (b) the prokaryotic polysaccharide transporter (PST) family; (c) the eukaryotic oligosaccharidyl-lipid flippase (OLF) family and (d) the bacterial mouse virulence factor family (MVF). Of these four families, only members of the MATE family have been shown to function mechanistically as secondary carriers, and no member of the MVF family has been shown to function as a transporter. Establishment of a common origin for the MATE, PST, OLF and MVF families suggests a common mechanism of action as secondary carriers catalyzing substrate/cation antiport. Most protein members of these four families exhibit 12 putative transmembrane alpha-helical segments (TMSs), and several have been shown to have arisen by an internal gene duplication event; topological variation is observed for some members of the superfamily. The PST family is more closely related to the MATE, OLF and MVF families than any of these latter three families are related to each other. This fact leads to the suggestion that primordial proteins most closely related to the PST family were the evolutionary precursors of all members of the MOP superfamily. Here, phylogenetic trees and average hydropathy, similarity and amphipathicity plots for members of the four families are derived and provide detailed evolutionary and structural information about these proteins. We show that each family exhibits unique characteristics. For example, the MATE and PST families are characterized by numerous paralogues within a single organism (58 paralogues of the MATE family are present in Arabidopsis thaliana), while the OLF family consists exclusively of orthologues, and the MVF family consists primarily of orthologues. Only in the PST family has extensive lateral transfer of the encoding genes occurred, and in this family as well as the MVF family, topological variation is a characteristic feature. The results serve to define a large superfamily of transporters that we predict function to export substrates using a monovalent cation antiport mechanism.