A high-density rice genetic linkage map with 2275 markers using a single F2 population

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.

microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer

The human genome is replete with long non-coding RNAs (lncRNA), many of which are transcribed and likely to have a functional role. Microarray analysis of >23,000 lncRNAs revealed downregulation of 712 (~3%) lncRNA in malignant hepatocytes, among which maternally expressed gene 3 (MEG3) was downregulated by 210-fold relative to expression in non-malignant hepatocytes. MEG3 expression was markedly reduced in four human hepatocellular cancer (HCC) cell lines compared with normal hepatocytes by real-time PCR. RNA in situ hybridization showed intense cytoplasmic expression of MEG3 in non-neoplastic liver with absent or very weak expression in HCC tissues. Enforced expression of MEG3 in HCC cells significantly decreased both anchorage-dependent and -independent cell growth, and induced apoptosis. MEG3 promoter hypermethylation was identified by methylation-specific PCR and MEG3 expression was increased with inhibition of methylation with either 5-Aza-2-Deoxycytidine, or siRNA to DNA Methyltransferase (DNMT) 1 and 3b in HCC cells. MiRNA-dependent regulation of MEG3 expression was studied by evaluating the involvement of miR-29, which can modulate DNMT 1 and 3. Overexpression of mir-29a increased expression of MEG3. GTL2, the murine homolog of MEG3, was reduced in liver tissues from hepatocyte-specific miR-29a/b1 knock-out mice compared with wild-type controls. These data show that methylation-dependent tissue-specific regulation of the lncRNA MEG3 by miR-29a may contribute to HCC growth and highlight the inter-relationship between two classes of non-coding RNA, miRNAs and lncRNAs, and epigenetic regulation of gene expression.

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

A new highly penetrant form of obesity due to deletions on chromosome 16p11.2

Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) >or= 40 kg m(-2) or BMI standard deviation score >or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

BACKGROUND

The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design.

RESULTS

This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific.

CONCLUSIONS

In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.

Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five inter-subspecific (indica/japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129-629 markers. Segregation distortion was determined based on chi-square analysis (P < 0.01) and was observed at 6.8-31.8%, of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated.

Two distinct nuclear receptor interaction domains in NSD1, a novel SET protein that exhibits characteristics of both corepressors and coactivators

NSD1, a novel 2588 amino acid mouse nuclear protein that interacts directly with the ligand-binding domain (LBD) of several nuclear receptors (NRs), has been identified and characterized. NSD1 contains a SET domain and multiple PHD fingers. In addition to these conserved domains found in both positive and negative Drosophila chromosomal regulators, NSD1 contains two distinct NR interaction domains, NID-L and NID+L, that exhibit binding properties of NIDs found in NR corepressors and coactivators, respectively. NID-L, but not NID+L, interacts with the unliganded LBDs of retinoic acid receptors (RAR) and thyroid hormone receptors (TR), and this interaction is severely impaired by mutations in the LBD alpha-helix 1 that prevent binding of corepressors and transcriptional silencing by apo-NRs. NID+L, but not NID-L, interacts with the liganded LBDs of RAR, TR, retinoid X receptor (RXR), and estrogen receptor (ER), and this interaction is abrogated by mutations in the LBD alpha-helix 12 that prevent binding of coactivators of the ligand-induced transcriptional activation function AF-2. A novel variant (FxxLL) of the NR box motif (LxxLL) is present in NID+L and is required for the binding of NSD1 to holo-LBDs. Interestingly, NSD1 contains separate repression and activation domains. Thus, NSD1 may define a novel class of bifunctional transcriptional intermediary factors playing distinct roles in both the presence and absence of ligand.

Reduced alpha-defensin expression is associated with inflammation and not NOD2 mutation status in ileal Crohn's disease

BACKGROUND AND AIMS

Reduced ileal Paneth cell alpha-defensin expression has been reported to be associated with Crohn's disease, especially in patients carrying NOD2 mutations. The aim of this study was to independently assess whether NOD2, alpha-defensins and Crohn's disease are linked.

METHODS

Using quantitative real-time polymerase chain reaction (RT-PCR), we measured the mRNA expression levels of key Paneth cell antimicrobial peptides (DEFA5, DEFA6, LYZ, PLA2G2A), inflammatory cytokines [interkelukin 6 (IL6) and IL8], and a marker of epithelial cell content, villin (VIL1) in 106 samples from both affected ileum (inflamed Crohn's disease cases, n = 44) and unaffected ileum (non-inflamed; Crohn's disease cases, n = 51 and controls, n = 11). Anti-human defensin 5 (HD-5) and haematoxylin/eosin immunohistochemical staining was performed on parallel sections from NOD2 wild-type and NOD2 mutant ileal Crohn's disease tissue.

RESULTS

In Crohn's disease patients, DEFA5 and DEFA6 mRNA expression levels were 1.9- and 2.2-fold lower, respectively, in histologically confirmed inflamed ileal mucosa after adjustment for confounders (DEFA5, p<0.001; DEFA6, p = 0.001). In contrast to previous studies, we found no significant association between alpha-defensin expression and NOD2 genotype. HD-5 protein data supports these RNA findings. The reduction in HD-5 protein expression appears due to surface epithelial cell loss and reduced Paneth cell numbers as a consequence of tissue damage.

CONCLUSIONS

Reduction in alpha-defensin expression is independent of NOD2 status and is due to loss of surface epithelium as a consequence of inflammatory changes rather than being the inciting event prior to inflammation in ileal Crohn's disease.

Hemocompatibility of titanium oxide films

Hemocompatibility is a key property of biomaterials that come in contact with blood. Surface modification has shown great potential for improving the hemocompatibility of biomedical materials and devices. In this paper, we describe our work of improving hemocompatibility with Ti-O thin films prepared by plasma immersion ion implantation and deposition and by sputtering. The structure and surface chemical and physical properties of the films were characterized by X-ray diffraction, Auger electron spectroscopy, atomic force microscopy (AFM), contact angle measurement, and Hall effect measurement. The behavior of fibrinogen adsorption was investigated by 125I radioactive isotope labeling and AFM. Systematic evaluation of hemocompatibility, including in vitro clotting time, thrombin time, prethrombin time, platelet adhesion, and in vivo implantation into dog's ventral aorta or right auricle from 17 to 90 days, proved that Ti-O films have excellent hemocompatibility. It is suggested that the significantly lower interface tension between Ti-O films and blood and plasma proteins and the semiconducting nature of Ti-O films give them their improved hemocompatibility.

Coibamide A, a potent antiproliferative cyclic depsipeptide from the Panamanian marine cyanobacterium Leptolyngbya sp

Coibamide A (1) is a new, potent antiproliferative depsipeptide which was isolated from a marine Leptolyngbya cyanobacterium collected from the Coiba National Park, Panama. The planar structure of 1 was elucidated by a combination of NMR spectroscopy and mass spectrometry. Exhaustive 1D and 2D NMR spectroscopy included natural abundance 15N and variable temperature experiments; mass spectrometry included TOF-ESI-MSn and FT-MSn experiments. Chemical degradation followed by chiral HPLC- and GC-MS analyses was used to assign the absolute configuration of 1. This highly methylated cyclized depsipeptide exhibited an unprecedented selectivity profile in the NCI 60 cancer cell line panel and appears to act via a novel mechanism.

PortLand

This paper considers the requirements for a scalable, easily manageable, fault-tolerant, and efficient data center network fabric. Trends in multi-core processors, end-host virtualization, and commodities of scale are pointing to future single-site data centers with millions of virtual end points. Existing layer 2 and layer 3 network protocols face some combination of limitations in such a setting: lack of scalability, difficult management, inflexible communication, or limited support for virtual machine migration. To some extent, these limitations may be inherent for Ethernet/IP style protocols when trying to support arbitrary topologies. We observe that data center networks are often managed as a single logical network fabric with a known baseline topology and growth model. We leverage this observation in the design and implementation of PortLand, a scalable, fault tolerant layer 2 routing and forwarding protocol for data center environments. Through our implementation and evaluation, we show that PortLand holds promise for supporting a ``plug-and-play" large-scale, data center network.

Antithrombogenic investigation of surface energy and optical bandgap and hemocompatibility mechanism of Ti(Ta(+5))O2 thin films

Recent improvements in the antithrombogenic properties of blood contacting biomaterials permit a hybrid design of layers for biomedical applications such as artificial heart valves and stents. Using magnetron sputtering and thermal oxidation, titanium oxide thin films containing tantalum. Ti(Ta(+5))O2, are fabricated to meet the challenge of enhanced hemocompatibility. The blood compatibility is evaluated in vitro by clotting time and platelet adhesion measurement, and in vivo experiments are also conducted. The Ti(Ta(+5))O2 films exhibit attractive blood compatibility exceeding that of low isotropic pyrolytic carbon. Physical properties such as surface energy and semiconductivity are found to play important roles. Our calculated results reveal that the smaller surface force gamma(s) of the film and the smaller blood film interfacial tension gamma(c,blood) are partially responsible for the enhancement of the blood compatibility. Based on the optical bandgap model, the film possesses better hemocompatibility because its optical bandgap of 3.2 eV is wider than that of fibrinogen having a bandgap of 1.8 eV. These factors result in thinner protein layers on the film surface, less protein denaturing, and overall excellent antithrombogenic properties.

Activation of platelets adhered on amorphous hydrogenated carbon (a-C:H) films synthesized by plasma immersion ion implantation-deposition (PIII-D)

Amorphous carbon films have attracted much attention recently due to their good biocompatibility. Diamond-like carbon (DLC), one form of amorphous carbon that is widely used in many kinds of industries, has been proposed for use in blood contacting medical devices. However, the blood coagulation mechanism on DLC in a biological environment is not well understood. Platelet adhesion and activation are crucial events in the interactions between blood and the materials as they influence the subsequent formation of thrombus. In this work, the behavior of platelets adhered onto hydrogenated amorphous carbon films (a-C:H) is investigated. Hydrogenated amorphous carbon films with different hydrogen contents, structures, and chemical bonds were fabricated at room temperature using plasma immersion ion implantation-deposition (PIII-D). The wettability of the films was investigated by contact angle measurements using several common liquids. Platelet adhesion experiments were conducted to examine the interaction of blood with the films in vitro and the activation of adherent platelets. The results show that the behavior of the platelets adhered on the a-C:H films is influenced by their structure and chemical bond, and it appears that protein interaction plays a key role in the activation of the adherent platelets.

Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping

By combining the amplified fragment length polymorphism (AFLP) technique with selective genotyping, we constructed a linkage map for rice and assigned each linkage group to a corresponding chromosome. The AFLP map, consisting of 202 AFLP markers, was generated from 74 recombinant inbred lines (RIL) which were selected from both extremes of the population (250 lines) with respect to the response to complete submergence. Map length was 1756 cM, with an average interval size of 8.5 cM. To assign linkage groups to chromosomes, we used 50 previously mapped AFLP markers as anchor markers distributed over the 12 chromosomes. Other AFLP markers were then assigned to specific chromosomes based on their linkage to anchor markers. This AFLP map is equivalent to the RFLP/AFLP map constructed previously as the anchors were in the same order in both maps. Furthermore, tests with two restriction fragment length polymorphism (RFLP) markers and two sequence-tagged site (STS) markers showed that they mapped in the expected positions. Using this AFLP map, a major gene for submergence tolerance was localized on chromosome 9. Quantitative trait loci (QTL) associated with submergence tolerance were detected on chromosomes 6, 7, 11, and 12. We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers.

Extracellular ATP is a mitogen for 3T3, 3T6, and A431 cells and acts synergistically with other growth factors

Extracellular ATP in concentrations of 5-50 microM displayed very little mitogenic activity by itself but it caused synergistic stimulation of [3H]thymidine incorporation in the presence of phorbol 12-tetradecanoate 13-acetate, epidermal growth factor, platelet-derived growth factor, insulin, adenosine, or 5'-(N-ethyl)carboxamidoadenosine. Cultures of Swiss 3T3, Swiss 3T6, A431, DDT1-MF2, and HFF cells were used. The percent of cell nuclei labeled with [3H]thymidine and cell number were also increased. ADP was equally mitogenic, while UTP and ITP were much less active. The effect of ATP was not due to hydrolysis by ectoenzymes to form adenosine, a known growth factor. Thus, the nonhydrolyzable analogue adenosine 5'-[beta, gamma-imido]triphosphate was mitogenic. In addition, it was found that ATP showed synergism in 3T6 and 3T3 cells when present for only the first hour of an incorporation assay, during which time no significant hydrolysis occurred. Furthermore, prolonged preincubation of cells with ATP reduced the mitogenic response to ATP but not to adenosine; preincubation with adenosine or N6-(R-phenylisopropyl)adenosine had the reverse effect. Finally, the effect of adenosine, but not of ATP, was inhibited by aminophylline. We conclude that extracellular ATP is a mitogen that interacts with P2 purinoceptors on the plasma membrane.

QTL x environment interactions in rice. I. heading date and plant height

One hundred twenty six doubled-haploid (DH) rice lines were evaluated in nine diverse Asian environments to reveal the genetic basis of genotype x environment interactions (GEI) for plant height (PH) and heading date (HD). A subset of lines was also evaluated in four water-limited environments, where the environmental basis of G x E could be more precisely defined. Responses to the environments were resolved into individual QTL x environment interactions using replicated phenotyping and the mixed linear-model approach. A total of 37 main-effect QTLs and 29 epistatic QTLs were identified. On average, these QTLs were detectable in 56% of the environments. When detected in multiple environments, the main effects of most QTLs were consistent in direction but varied considerably in magnitude across environments. Some QTLs had opposite effects in different environments, particularly in water-limited environments, indicating that they responded to the environments differently. Inconsistent QTL detection across environments was due primarily to non- or weak-expression of the QTL, and in part to significant QTL x environment interaction effects in the opposite direction to QTL main effects, and to pronounced epistasis. QTL x environment interactions were trait- and gene-specific. The greater GEI for HD than for PH in rice were reflected by more environment-specific QTLs, greater frequency and magnitude of QTL x environment interaction effects, and more pronounced epistasis for HD than for PH. Our results demonstrated that QTL x environment interaction is an important property of many QTLs, even for highly heritable traits such as height and maturity. Information about QTL x environment interaction is essential if marker-assisted selection is to be applied to the manipulation of quantitative traits.

Shear thickening of cornstarch suspensions as a reentrant jamming transition

We study the rheology of cornstarch suspensions, a non-Brownian particle system that exhibits shear thickening. From magnetic resonance imaging velocimetry and classical rheology it follows that as a function of the applied stress the suspension is first solid (yield stress), then liquid, and then solid again when it shear thickens. For the onset of thickening we find that the smaller the gap of the shear cell, the lower the shear rate at which thickening occurs. Shear thickening can then be interpreted as the consequence of dilatancy: the system under flow wants to dilate but instead undergoes a jamming transition because it is confined, as confirmed by measurement of the dilation of the suspension as a function of the shear rate.

In vitro investigation of blood compatibility of Ti with oxide layers of rutile structure

Structure characteristics of titanium oxide layer on titanium matrix were investigated by Rutherford Backscattering Spectroscopy (RBS), Auger Electron Spectroscopy (AES) and X-ray diffraction. It has been identified that the titanium oxide layers had rutile structure. The blood compatibility of the titanium oxide layers of different thickness was studied by blood clotting time measurement. It was shown that as the thickness of the titanium oxide layers increased, blood compatibility of these layers was obviously improved.

The effects of amorphous carbon films deposited on polyethylene terephthalate on bacterial adhesion

There is an increasing interest in developing new methods to reduce bacteria adhesion onto polymeric materials that are used in biomedical implants. The antibacterial behavior on polyethylene terephthalate (PET) treated by acetylene (C2H2) plasma immersion ion implantation-deposition (PIII-D) is investigated. The surface structure of the treated PET is determined by laser Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). The results show that a thin amorphous polymer-like carbon (PLC) layer is formed on the PET surface. Atomic force micrographs (AFM) show that C2H2 PIII-D significantly changes the surface morphology of PET. The capacities of Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE) to adhere onto PET are quantitatively determined by plate counting and Gamma-ray counting of 125I radio labeled bacteria in vitro. The results indicate that the adhesion of the two kinds of bacteria to PET is suppressed by PLC. The adhesion efficiency of SE on the coated surface is only about 14% of that of the untreated PET surface, and that of SA is about 35% of that of the virgin surface. The electrokinetic potentials of the bacterial cells and substrates are determined by zeta potential measurement. All the substrates as well as the bacterial strain have negative zeta potentials, and it means that bacterial adhesion is not mediated by electrostatic interactions. The surface energy components of the various substrates and bacteria are calculated based on measurements in water, formamide and diiodomethane. The surface free energies obtained are used to calculate the interfacial free energies of adhesion ( deltaFAdh ) of SA and SE onto various substrates, and it is found that bacterial adhesion is energetically unfavorable on the PLC deposited on PET by C2H2 PIII-D.

Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia

Rice double-haploid (DH) lines of an indica and japonica cross were grown at nine different locations across four countries in Asia. Genotype-by-environment (G x E) interaction analysis for 11 growth- and grain yield-related traits in nine locations was estimated by AMMI analysis. Maximum G x E interaction was exhibited for fertility percentage number of spikelets and grain yield. Plant height was least affected by environment, and the AMMI model explained a total of 76.2% of the interaction effect. Mean environment was computed by averaging the nine environments and subsequently analyzed with other environments to map quantitative trait loci (QTL). QTL controlling the 11 traits were detected by interval analysis using mapmaker/qtl. A threshold LOD of >/=3.20 was used to identify significant QTL. A total of 126 QTL were identified for the 11 traits across nine locations. Thirty-four QTL common in more than one environment were identified on ten chromosomes. A maximum of 44 QTL were detected for panicle length, and the maximum number of common QTL were detected for days to heading detected. A single locus for plant height (RZ730-RG810) had QTL common in all ten environments, confirming AMMI results that QTL for plant height were affected the least by environment, indicating the stability of the trait. Two QTL were detected for grain yield and 19 for thousand-grain weight in all DH lines. The number of QTL per trait per location ranged from zero to four. Clustering of the QTL for different traits at the same marker intervals was observed for plant height, panicle number, panicle length and spikelet number suggesting that pleiotropism and or tight linkage of different traits could be the possible reason for the congruence of several QTL. The many QTL detected by the same marker interval across environments indicate that QTL for most traits are stable and not essentially affected by environmental factors.

Microsatellite marker development, mapping and applications in rice genetics and breeding

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10,000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trail locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.

Gene therapy that inhibits nuclear translocation of nuclear factor kappaB results in tumor necrosis factor alpha-induced apoptosis of human synovial fibroblasts

OBJECTIVE

Tumor necrosis factor alpha (TNFalpha) increases the survival and proliferation of human rheumatoid arthritis (RA) cell lines. These experiments were designed to determine if inhibition of nuclear factor kappaB (NF-kappaB) nuclear translocation leads to increased apoptosis of TNFalpha-treated human RA cell lines.

METHODS

We constructed an inhibitor of nuclear factor kappaB(IkappaB) dominant-negative adenovirus (AdCMVIkappaB-DN) and an X-linked inhibitor of apoptosis (XIAP) antisense adenovirus (AdCMVXIAP-AS). Primary RA synovial fibroblast (RASF) cell lines were transfected in vitro, and SV40-transformed RA synovial cell lines in SCID mice were transfected in vivo. Cells were treated with TNFalpha and analyzed for apoptosis.

RESULTS

There was no apoptosis of primary RASF transfected in vitro with AdCMVIkappaB-DN alone. In contrast, there was apoptosis of >85% of cells treated with AdCMVIkappaB-DN plus TNFalpha. Primary RASF in SCID mice also exhibited high levels of apoptosis after in vivo transfection with AdCMVIkappaB-DN followed by treatment with TNFalpha. There was no apoptosis after treatment with AdCMVIkappaB-DN in the absence of TNFalpha. XIAP is an inhibitor of apoptosis which was up-regulated by TNFalpha, and this up-regulation was inhibited by AdCMVIkappaB-DN plus TNFalpha. Transfection of an AdCMVXIAP-AS gene therapy resulted in increased TNFa-induced apoptosis.

CONCLUSION

AdCMVIkappaB-DN gene therapy greatly enhances apoptosis due to inhibition of an NF-kappaB-mediated antiapoptosis signaling pathway, and XIAP is a TNFalpha-inducible specific inhibitor of apoptosis in RA synovial cell lines. This and other modulators of TNF receptor or the Fas apoptosis pathway may be therapeutically beneficial in facilitating apoptosis of synovial tissue in patients with RA.

Inhibition of IL-8 gene expression in Caco-2 cells by compounds which induce histone hyperacetylation

Ulcerative colitis, an idiopathic inflammatory disease of the colonic mucosa, can be effectively treated by enemas containing short chain fatty acids (SCFA) such as butyrate, propionate, and acetate. The molecular mechanisms that lead to this response have not been well characterized. It is well known that intestinal inflammation leads to an alteration in patterns of epithelial differentiation with an increase in epithelial proliferation and an expansion of cell populations in an undifferentiated state. SCFAs such as butyrate are capable of inhibiting cell proliferation and inducing a differentiated phenotype in vitro. The Caco-2 colon cancer cell line was used to study the effect of SCFAs and the process of cellular differentiation on the expression of the pro-inflammatory cytokine, interleukin 8 (IL-8). SCFAs and trichostatin A, structurally unrelated compounds which both induce histone hyperacetylation, both led to a dose-dependent inhibition of IL-8 gene expression. Furthermore, spontaneous differentiation of Caco-2 cells by growth to a post-confluent state also inhibited the expression of IL-8. A possible mechanism by which SCFAs may be effective in the treatment of ulcerative colitis may be through their ability to increase histone acetylation states and inhibit the production of pro-inflammatory substances by the intestinal epithelium.