Genomic organization and chromosomal location of the human gene encoding the B-lymphocyte activation antigen B7

The human B lymphocyte activation antigen B7 provides regulatory signals for T lymphocytes as a consequence of binding to its ligands CD28 and CTLA-4. The cDNA for B7 has previously been isolated and predicted to encode a type I membrane protein. The predicted polypeptide has a secretory signal peptide followed by two contiguous Ig-like domains, a hydrophobic transmembrane region and a short cytoplasmic tail. Here we report the exon-intron genomic organization of human B7 and the chromosomal location. The gene has six exons that span approximately 32 kilobases of DNA. Exon 1 is not translated and the second exon contains the initiation ATG codon and encodes a predicted signal peptide. This gene structure is characteristic for several eukaryotic genes with tissue-specific expression. The third and fourth exons correspond to two Ig-like domains whereas the fifth and sixth exons encode respectively the trans-membrane portion and the cytoplasmic tail. This close relationship between exons and functional domains is a characteristic feature of genes of the Ig superfamily. Cell surface expression of the B7 gene product has previously been mapped to human chromosome 12 by antibody reactivity with the B7-specific monoclonal antibody BB-1. We here demonstrate that theB7 gene is located to theq21-qter region of chromosome 3 by DNA blot analysis of human × rodent somatic cell hybrids.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M83071-M83075, M83077. Address correspondence and offprint requests to: B. Dupont, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue (Room S709), New York, NY 10021, USA.     

The JmjN Domain of Jhd2 Is Important for Its Protein Stability,and the Plant Homeodomain (PHD) Finger Mediates Its Chromatin Association Independent of H3K4 Methylation

Histone lysine methylation is a dynamic process that plays an important role in regulating chromatin structure and gene expression. Recent studies have identified Jhd2, a JmjC domain-containing protein, as an H3K4-specific demethylase in budding yeast. However, important questions regarding the regulation and functions of Jhd2 remain unanswered. In this study, we show that Jhd2 has intrinsic activity to remove all three states of H3K4 methylation in vivo and can dynamically associate with chromatin to modulate H3K4 methylation levels on both active and repressed genes and at the telomeric regions. We found that the plant homeodomain (PHD) finger of Jhd2 is important for its chromatin association in vivo. However, this association is not dependent on H3K4 methylation and the H3 N-terminal tail, suggesting the presence of an alternative mechanism by which Jhd2 binds nucleosomes. We also provide evidence that the JmjN domain and its interaction with the JmjC catalytic domain are important for Jhd2 function and that Not4 (an E3 ligase) monitors the structural integrity of this interdomain interaction to maintain the overall protein levels of Jhd2. We show that the S451R mutation in human SMCX (a homolog of Jhd2), which has been linked to mental retardation, and the homologous T359R mutation in Jhd2 affect the protein stability of both of these proteins. Therefore, our findings provide a mechanistic explanation for the observed defects in patients harboring this SMCX mutant and suggest the presence of a conserved pathway involving Not4 that modulates the protein stability of both yeast Jhd2 and human SMCX.     

Topological and phylogenetic analyses of bacterial holin families and superfamilies

Holins are small “hole-forming” transmembrane proteins that mediate bacterial cell lysis during programmed cell death or following phage infection. We have identified fifty two families of established or putative holins and have included representative members of these proteins in the Transporter Classification Database (TCDB; www.tcdb.org). We have identified the organismal sources of members of these families, calculated their average protein sizes, estimated their topologies and determined their relative family sizes. Topological analyses suggest that these proteins can have 1, 2, 3 or 4 transmembrane α-helical segments (TMSs), and members of a single family are frequently, but not always, of a single topology. In one case, proteins of a family proved to have either 2 or 4 TMSs, and the latter arose by intragenic duplication of a primordial 2 TMS protein-encoding gene resembling the former. Using established statistical approaches, some of these families have been shown to be related by common descent. Seven superfamilies, including 21 of the 52 recognized families were identified. Conserved motif and Pfam analyses confirmed most superfamily assignments. These results serve to expand upon the scope of channel-forming bacterial holins.     

Streptomyces sp. LK3 mediated synthesis of silver nanoparticles and its biomedical application

In the present study, the marine actinobacteria mediated biosynthesis of silver nanoparticles (AgNps) was achieved using Streptomyces sp LK3. The synthesized AgNps showed the characteristic absorption spectra in UV–vis at 420 nm, which confirmed the presence of nanoparticles. XRD analysis showed intense peaks at 2θ values of 27.51°, 31.87°, 45.57°, 56.56°, 66.26°, and 75.25° corresponding to (210), (113), (124), (240), (226), and (300) Bragg’s reflection based on the fcc structure of AgNps. The FTIR spectra exhibited prominent peaks at 3,417 cm^?1 (OH stretching due to alcoholic group) and 1,578 cm^?1 (C=C ring stretching). TEM micrograph showed that the synthesized AgNps were spherical in shape with an average size of 5 nm. Surface morphology and topographical structure of the synthesized AgNps were dignified by AFM. The synthesized AgNps showed significant acaricidal activity against Rhipicephalus microplus and Haemaphysalis bispinosa with LC₅₀ values of 16.10 and 16.45 mg/L, respectively. Our results clearly indicate that AgNps could provide a safer alternative to conventional acaricidal agents in the form of a topical antiparasitic formulation. The present study aimed to develop a novel, cost-effective, eco-friendly actinobacteria mediated synthesis of AgNps and its antiparasitic activity.     

Acute Neuronal Injury and Blood Genomic Profiles in a Nonhuman Primate Model for Ischemic Stroke

The goal of this study was to characterize acute neuronal injury in a novel nonhuman primate (NHP) ischemic stroke model by using multiple outcome measures. Silk sutures were inserted into the M1 segment of the middle cerebral artery of rhesus macaques to achieve permanent occlusion of the vessel. The sutures were introduced via the femoral artery by using endovascular microcatheterization techniques. Within hours after middle cerebral artery occlusion (MCAO), infarction was detectable by using diffusion-weighted MRI imaging. The infarcts expanded by 24 h after MCAO and then were detectable on T2-weighted images. The infarcts seen by MRI were consistent with neuronal injury demonstrated histologically. Neurobehavioral function after MCAO was determined by using 2 neurologic testing scales. Neurologic assessments indicated that impairment after ischemia was limited to motor function in the contralateral arm; other neurologic and behavioral parameters were largely unaffected. We also used microarrays to examine gene expression profiles in peripheral blood mononuclear cells after MCAO-induced ischemia. Several genes were altered in a time-dependent manner after MCAO, suggesting that this ischemia model may be suitable for identifying blood biomarkers associated with the presence and severity of ischemia. This NHP stroke model likely will facilitate the elucidation of mechanisms associated with acute neuronal injury after ischemia. In addition, the ability to identify candidate blood biomarkers in NHP after ischemia may prompt the development of new strategies for the diagnosis and treatment of ischemic stroke in humans.Abbreviations: MCAO, middle cerebral artery occlusion; NHP, nonhuman primate; PBMC, peripheral blood mononuclear cellsStroke is a debilitating neurologic condition, and little progress has been made in the development of neuroprotective treatments for acute stroke. The Stroke Therapy Academic Industry Roundtable (STAIR) report suggested that preclinical candidates for stroke therapy should be validated by testing in large animals with similarities to humans, such as nonhuman primates (NHP).²⁶ NHP stroke models have been developed in several species, including rhesus monkeys, marmosets, and baboons, by using a variety of techniques for middle cerebral artery occlusion (MCAO).^{4,10,12,13,14,25,32} The rhesus macaque is ideal for stroke studies because of its structural similarities to human brain. The rhesus brain is gyrencephalic, which makes it preferable to those of lissencephalic primates (for example, marmosets) and is functionally similar to human brain.⁶ In addition, the immunologic profile of rhesus macaques is similar to that of humans; therefore these animals are the preferred model for the study of immune responses to infectious diseases such as HIV/SIV, Dengue virus, and others.^17,23,30In addition to their use for neuroprotection assessment, NHP stroke models can facilitate efforts to develop diagnostic tools for identifying and treating stroke symptoms. The use of genomics in peripheral blood cells has been shown to be an excellent method to identify candidate biomarkers and cellular mechanisms associated with stroke.^28,29 Blood biomarkers can be used to rapidly determine the occurrence, timing, subtype, and severity of stroke.^11,15 One possible reason for the lack of viable stroke biomarkers may be the research models used to search for these markers. Although rodent stroke models have yielded a wealth of information on the mechanisms associated with brain ischemia, the findings have not translated well to human clinical trials.²⁶ Recent studies in human patients showed promising results when genomic tools have been used to screen for novel stroke biomarkers.^3,16,27 However, validation of human studies is limited by the need for large data sets in light of heterogeneity in stroke onset, subtype, comorbidities, and other factors. In addition, it is also impossible to know the exact time of stroke onset in most patients.Here we characterized acute neuronal injury in a novel, minimally invasive permanent ischemic stroke model involving rhesus macaques. Using endovascular catheterization techniques, we introduced silk sutures into the M1 segment of the middle cerebral artery and permanently occluded it. This procedure reliably produced infarcts that could be measured by MRI of the macaque brains during the acute phase period. The procedure resulted in discrete and limited neurobehavioral deficits, indicating the potential of this stroke model for chronic neuroprotection studies in the future. In addition, we used microarrays to identify blood genomic profiles that were altered in a time-dependent manner after ischemia. These studies characterize a preclinical model that is suitable for elucidating the mechanisms associated with cerebral ischemia and that may aid in identifying strategies for the diagnosis and treatment of stroke in humans.     

Aerobic biodegradation of Azo dye by Bacillus cohnii MTCC 3616; an obligately alkaliphilic bacterium and toxicity evaluation of metabolites by different bioassay systems

An obligate alkaliphilic bacterium Bacillus cohnii MTCC 3616 aerobically decolorized a textile azo dye Direct Red-22 (5,000 mg?l^?1) with 95 % efficiency at 37 °C and pH?9 in 4 h under static conditions. The decolorization of Direct Red-22 (DR-22) was possible through a broad pH (7–11), temperature (10–45 °C), salinity (1–7 %), and dye concentration (5–10 g?l^?1) range. Decolorization of dye was assessed by UV–vis spectrophotometer with reduction of peak intensity at 549 nm (λ _max). Biodegradation of dye was analyzed by Fourier transform infrared spectroscopy (FTIR) and high-performance liquid chromatography (HPLC). The FTIR spectrum revealed that B. cohnii specifically targeted azo bond (N=N) at 1,614.42 cm^?1 to break down Direct Red-22. Formation of metabolites with different retention times in HPLC analysis further confirmed the degradation of dye. The phytotoxicity test with 5,000 mg?l^?1 of untreated dye showed 80 % germination inhibition in Vigna mungo, 70 % in Sorghum bicolor and 80 % in Vigna radiata. No germination inhibition was noticed in all three plants by DR-22 metabolites at 5,000 mg?l^?1. Biotoxicity test with Artemia salina proved the lethality of the azo dye at LC₅₀ of 4 and 8 % for degraded metabolites by causing death of its nauplii compared to its less toxic-degraded metabolites. Bioaccumulation of dye was observed in the mid-gut of A. salina. The cytogenotoxicity assay on the meristematic root tip cells of Allium cepa further confirmed the cytotoxic nature of azo dye (DR-22) with decrease in mitotic index (0.5 % at 500 ppm) and increase in aberrant index (4.56 %) over 4-h exposure period. Genotoxic damages (lagging chromosome, metaphase cluster, chromosome bridges, and dye accumulation in cytoplasm) were noticed at different stages of cell cycle. The degraded metabolites had negligible cytotoxic and genotoxic effects.     

Effect of Experimental Temperature on the Permeation of Model Diffusants Across Porcine Buccal Mucosa

The influence of experimental temperature on the permeability of model diffusants across porcine buccal mucosa was investigated in vitro. The permeability increased significantly as the experimental temperature was increased in increments of approximately 7°C. It was observed that the apparent permeability and temperature were related by an exponential relationship that conformed to the Arrhenius equation. Diffusants with higher lipophilicities—buspirone and bupivacaine—had lower activation energies for diffusion when compared to hydrophilic diffusants—antipyrine and caffeine. The activation energy for diffusion of the model diffusants decreased linearly with increasing distribution coefficients across porcine buccal mucosa. The results suggested that the buccal mucosa acts as a stronger barrier to the diffusion of hydrophilic diffusants than the lipophilic ones. The log-linear relationship between permeability and temperature indicates that temperature should be carefully controlled in diffusion experiments. These results also point to the possibility of developing heat-generating buccal delivery devices, especially for hydrophobic diffusants.