Detecting distant relatives of mammalian LPS-binding and lipid transport proteins.

In mammals, a family of four lipid binding proteins has been previously defined that includes two lipopolysaccharide binding proteins and two lipid transfer proteins. The first member of this family to have its three-dimensional structure determined is bactericidal/permeability-increasing protein (BPI). Using both the sequence and structure of BPI, along with recently developed sequence-sequence and sequence-structure similarity search methods, we have identified 13 distant members of the family in a diverse set of eukaryotes, including rat, chicken, Caenorhabditis elegans, and Biomphalaria galbrata. Although the sequence similarity between these 13 new members and any of the 4 original members of the BPI family is well below the "twilight zone," their high sequence-structure compatibility with BPI indicates they are likely to share its fold. These findings broaden the BPI family to include a member found in retina and brain, and suggest that a primitive member may have contained only one of the two similar domains of BPI.     

Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2^nd to 9^th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and ‘unrelated’ population samples. Using these bounds as a guide, we detected tens of thousands of 2^nd to 9^th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies.     

Cyanobacteria from Brazilian building walls are distant relatives of aquatic genera

The 16S-rDNA from 22 cyanobacteria isolated from biofilms on walls of modern and historic buildings in Brazil was partially sequenced (approximately 350 bp) using specific primers. The cyanobacteria with the closest matching sequences were found using the BLAST tool. The sequences were combined with 52 other cyanobacterial sequences already deposited in public data banks and a dendrogram constructed, after deletion from each sequence of one of the variable 16S rDNA regions (VI). The newly sequenced organisms fitted well within their respective families, but their similarities to other members of the groups were generally low, less than 96%. Close matches were found only with one other terrestrial (hot dry desert) cyanobacterium, Microcoleus sociatus, and with Anabaena variabilis. Phylogenetic analysis suggested that the deletion of the hypervariable regions in the RNA structure is essential for meaningful evolutionary studies. The results support the standard phylogenetic tree based on morphology, but suggest that these terrestrial cyanobacteria are distant relatives of their equivalent aquatic genera and are, indeed, a distinct population.     

Accessing and exploiting genes of breeding value of distant relatives of crop Brassicas

The Brassicas are an important group of crops in India yielding edible oils and many vegetables. For improving cultivated Brassicas, the wild relatives are of considerable value. The Brassica group of seed oil and vegetables comprises six cultivated species, out of which three are diploids and three are digenomic tetraploids. Brassica juncea is the major seed oil crop in India which can be improved for several traits by incorporating genes from its distant relatives. The early work in India relating to genome manipulation consisted of synthesis of B. juncea by crossing B. campestris with B. nigra, experimental resynthesis of Brassica species and non-homologous pairing and genetic exchange at the interspecific level. The alloploid species B. napus and B. carinata have not been successful in India due to agrometereological limitations. However, synthetic forms of B. napus have been produced which have a desirable maturity period with good yield potential. Also, through non-homologous pairing, pod shatter resistant B. napus has been obtained, B. napus ordinarily suffers from pod shattering. Similarly, synthetic forms of B. carinata have been derived from reciprocal crosses between morphotypes of B. oleracea and B. nigra and also through protoplast fusion of B. nigra with B. oleracea. Molecular analysis has revealed that one of the somatic hybrids had a novel cytoplasmic combination which carried B. nigra mitochondrial and B. oleracea chloroplast genomes. A range of wild and weedy species related to crop Brassicas possess extensive genetic variability. Work for utilizing this variability included hybridization between wild and crop species, analysis of chromosome pairing and induction of alloploidy. Among Brassicas of interest to India, protoplast culture and regeneration has been successful in the case of B. oleracea, B. juncea, B. nigra and B. carinata (cultivated species) and Eruca sativa and Diplotaxis muralis (related wild species). Polyethylene glycol mediated protoplast fusion has been the most commonly used method in India for producing somatic hybrids involving Brassicas. The eight somatic hybrids produced and studied showed that in the majority of cases the fusions led to symmetric hybrids combining the complete genomes of the donor species. For developing suitable male sterile lines, B. juncea, B. campestris and B. napus nuclei have been combined with the cytoplasm of six wild species and stable male steriles have been developed. Protoplast fusion methodology has been used extensively for improving these CMS by manipulating cytoplasmic organelles, including production of new combinations of cp and mt.     

Diacylglyceride kinases,sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases

Diacylglyceride kinases, sphingosine kinases, NAD kinases and 6-phosphofructokinases are thought to be related despite large evolution of their sequences. Discovery of a common signature has led to the suggestion that they possess a similar phosphate-donor-binding site and a similar phosphorylation mechanism. The substrate- and allosteric-binding sites are much more divergent and their delineation remains to be determined experimentally.     

Pannexins,distant relatives of the connexin family with specific cellular functions?

Intercellular communication (IC) is mediated by gap junctions (GJs) and hemichannels, which consist of proteins. This has been particularly well documented for the connexin (Cx) family. Initially, Cxs were thought to be the only proteins capable of GJ formation in vertebrates. About 10 years ago, however, a new GJ‐forming protein family related to invertebrate innexins (Inxs) was discovered in vertebrates, and named the pannexin (Panx) family. Panxs, which are structurally similar to Cxs, but evolutionarily distinct, have been shown to be co‐expressed with Cxs in vertebrates. Both protein families show distinct properties and have their own particular function. Identification of the mechanisms that control Panx channel gating is a major challenge for future work. In this review, we focus on the specific properties and role of Panxs in normal and pathological conditions.     

Interleukin-18 induces interferon-gamma production through NF-kappaB and NFAT activation in murine T helper type 1 cells.

Interleukin-18 (IL-18) combined with anti-CD3 monoclonal antibody (mAb) induced interferon-gamma (IFN-gamma) production by T helper type 1 (Th1) cells. Neither IL-18 nor anti-CD3 mAb alone induced production of IFN-gamma. Although treatment with IL-18 alone induced full activation of NF-kappaB in Th1 cells, it was not sufficient for the production of IFN-gamma. To examine the importance of NF-kappaB activation in IFN-gamma production, we established Th1 cells which expressed a transdominant IkappaBalpha mutant. In these cells, activation of NF-kappaB and production of IFN-gamma by IL-18 were suppressed. On the other hand, we examined the T cell receptor (TCR)/CD3-mediated signaling pathway. FK506, an inhibitor of NFAT activation, inhibited IFN-gamma production by IL-18 without any effect on the NF-kappaB activation. We conclude that dual signaling consisting of IL-18-induced NF-kappaB activation and TCR/CD3-mediated NFAT activation is crucial for IFN-gamma production by IL-18 in murine Th1 cells.     

Genome scanning for segments shared identical by descent among distant relatives in isolated populations.

In this paper, we address some of the statistical issues concerning false-positive rates that arise when the whole genome, or a portion thereof, is scanned in distantly related individuals, to search for a disease locus. We derive a method for correcting false-positive probabilities for the large number of comparisons that are performed when scanning a large portion of the genome. We consider both the idealized situation of a dense set of fully informative markers and the more realistic data-collection strategy of an initial scan at low resolution to identify promising areas, which then are typed with markers at high resolution. We also examine the accuracy of false-positive rates approximated using a conservative estimate of the separation distance between affected individuals in the current generation and the common ancestral couple. Calculation of false-positive rates when inbreeding is present in the pedigree also is considered.     

High-intensity-light-dependent and transient expression of new genes encoding distant relatives of light-harvesting chlorophyll-a/b proteins in Chlamydomonas reinhardtii

We identified four Lhc-like genes (Lhl) encoding proteins that are distant relatives of light-harvesting chlorophyll a/b-binding (LHC) proteins in the green alga Chlamydomonas reinhardtii. Their mRNA levels after transfer from low-intensity light to high-intensity light (HL) were examined and compared with those of Lhc genes encoding LHC proteins of PSII. The transfer caused a decrease in the mRNA level of Lhl3, a homolog of Arabidopsis thaliana Lil3, within 2 h, followed by gradual restoration depending on the intensity of HL. The response was similar to that of Lhc genes. In contrast, the mRNA levels of Lhl1, Lhl2 and Lhl4 significantly increased, reached a maximum within 1 h after the transfer and then rapidly returned to a low level. The intensity of HL little influenced the response of these genes. While the Lhl1 and Lhl2 proteins were homologs of early light-inducible protein (ELIP) and high-light-inducible protein (HLIP), respectively, Lhl4 encoded a novel protein. The HL-induced expression of Lhl4 was most prominent among the genes tested. Studies using various inhibitors indicate that the HL response is not mediated by the redox state of plastoquinone pool or reactive oxygen species, but required de novo protein synthesis in the cytosol.     

Calcineurin and NFAT4 induce chondrogenesis

Nuclear factor of activated T-cells (NFAT) and calcineurin are essential regulators of immune cell and mesenchymal cell differentiation. Here we show that elevated intracellular calcium induces chondrogenesis through a calcineurin/NFAT signaling axis that activates bone morphogenetic protein (BMP) expression. The calcium ionophore, ionomycin, induced chondrogenesis through activation of calcineurin. The calcineurin substrate, NFAT4, also induced chondrogenesis and chondrocyte gene expression. Significantly, the BMP antagonist, noggin, or dominant negative BMP receptors blocked the effects of elevated intracellular calcium on chondrogenesis. This suggested that calcineurin/NFAT4 activates BMP expression. Consistent with this, BMP2 gene expression was increased by ionomycin and suppressed by the calcineurin inhibitor, cyclosporine A. Furthermore, activated NFAT4 induced BMP2 gene expression. These results have important implications for the effects of NFATs during development and adaptive responses.     

Test of agronomic characteristics and amplified fragment length polymorphism analysis of new rice germplasm developed from transformation of genomic DNA of distant relatives

New rice lines, restorer line RB207 and maintainer line Yewei B, with better agronomic traits were separately developed from variant progeny of R207 (rice restorer line) and V20B (rice maintainer line) through transformation of genomic DNA ofEchinochloa crusgalli (C₄ plant) andOryza minuta, respectively. The phenotypes of the variant lines were apparently different from those of the receptors. Yewei B had stronger tolerance to high temperature than did V20B. The number of spikelets per panicle and the 1000-grain weight of RB207 increased by 40% over those of R207. The results of amplified fragment length polymorphism (AFLP) analysis indicated that the polymorphism rates were both 4.4% between genomes of the variant lines and their receptors. Results demonstrated that special DNA segments fromE. crusgalli andO. minuta might integrate into the genome of cultivated rice and could be stably passed on. The study further shows that transformation of genomic DNA of distant relatives is an effective approach for creating new rice germ plasm. These authors contributed equally to this work.