Third-color CD45 staining of paraformaldehyde-fixed peripheral blood lymphocytes

Third-color CD45 gating is a useful procedure in various clinical applications (Borowitz et al.: Am J Clin Pathol 100:534-540, 1993; Steltzer et al.: Ann NY Acad Sci 677:267-280, 1993) allowing for the selective immunophenotyping of abnormal cell populations. In laboratories where dual-color protocols are in place, the need for CD45 gating may not become evident until after cells have been exposed to fixatives. This brief study demonstrates that third-color CD45 staining and gating is possible with paraformaldehyde fixed lymphocytes, eliminating the need to restain fresh cells with the entire antibody panel, and with a significant saving of time and money. Gates must be modified from those obtained by fresh cell staining in order to include both bright and dim CD45 populations. In a standard protocol, third-color CD45 staining intensity was decreased 10-fold post-fixation with paraformaldehyde except, unexpectedly, for CD8+ cells. The latter phenomenon could be explained if the spatial arrangement of CD45 and CD8 is such that the CD45 epitope is protected from cross-linking by paraformaldehyde fixation in CD8+ cells, but not others.     

Freezing behavior of water in small pores and the possible role in the freezing of plant tissues

Two model systems were used to study the freezing of water in small diameter pores. Water in pores having a diameter of less than 100 nanometers froze at lower temperatures than bulk water. Data obtained with a range of pore sizes were consistent with predicted values based on equations developed by Mazur (1965 Ann NY Acad Sci 125: 658-676), and Homshaw (1980 J Soil Sci 31: 399-414). The addition of solutes lowered the freezing point of water in small pores. We propose that the freezing behavior of water in small pores may account for some of the freezing patterns observed in plant tissues. In tissues where cells are tightly packed, share common walls, and lack intercellular spaces, the presence of water in cell wall microcapillaries would alter the freezing temperature of tissue water, impede the spread of ice, and facilitate supercooling.     

Probable cloning artefacts previously interpreted as unusual leader sequences of rodent ornithine decarboxylase mRNAs--a cautionary tale

Messenger RNAs that have structurally unusual 5' leaders attract interest and provoke conjecture. Cloning and sequencing of two rodent ornithine decarboxylase (ODC) cDNAs, those for mouse [Kahana and Nathans, Proc. Natl. Acad. Sci. USA 82 (1985) 1673-1677] and, recently as published in this journal, for rat [Van Kranen et al., Gene 60 (1987) 145-155], have indicated the presence of such features. In both cases, the leader is unusually long and contains multiple AUG start codons preceding that which encodes the N terminus of the protein. In addition, the leader of the rat clone contains a 54-nt perfect inverted repeat. Because ODC expression appears to be regulated translationally, functional implications immediately suggest themselves. Certain unusual features of the mouse cDNA have proven artefactual [Brabant et al., Proc. Natl. Acad. Sci. USA 85 (1988) 2200-2204; Katz and Kahana, J. Biol. Chem. 263 (1988) 7604-7609]. It is likely that the putative leader sequence of rat ODC cDNA also resulted from a cloning artefact.     

A small plasmid for recombination-based screening.

We reported recently the construction of the 4.4-kb R6K-derived pMAD1 plasmid carrying supF [Stewart et al., Gene 106 (1991) 97-101] that does not share nt sequences with ColE1 and therefore permits recombination-based screening of lambda libraries that contain ColE1 sequences. Here we describe the construction of the 2.5-kb R6K-derived plasmid, pMAD3, that lacks the pi-encoding pir gene required for R6K replication. To supply pi [Inuzuka and Helinski, Proc. Natl. Acad. Sci. USA 75 (1978) 5381-5385] in trans, we employed pPR1 delta 22pir116, referred to henceforth as pPR1 [McEachern et al., Proc. Natl. Acad. Sci. USA 86 (1989) 7942-7946; Dellis and Filutowicz, J. Bacteriol. 173 (1991) 1279-1286]. Plasmid pMAD3 is small enough to be amplified readily by PCR [Saiki et al., Science 230 (1985) 1350-1354]. This permits the insertion of larger fragments and the retrieval of larger lambda inserts, as well as the use of a simplified PCR-based cloning protocol which utilizes annealing rather than ligation to create recombinants in pMAD3 [Nisson et al., PCR Methods and Applications 1 (1991) 120-123].     

Cyclophosphamide potentiates the antitumor activity of v-p97NY

Previous work has demonstrated that a recombinant live vaccinia virus-based tumor vaccine, v-p97NY, induces an immune response in mice which can lead to the rejection of transfected lines of mouse melanoma cells expressing the human melanoma antigen p97 (S.-L. Hu et al., J. Virol. 62, 176, 1988; C. D. Estin et al., Proc. Natl. Acad. Sci. USA 85, 1052, 1988). We now show that the ability of v-p97NY to induce delayed-type hypersensitivity to p97 improved if the vaccinated mice were given cyclophosphamide (Cy) on the day of vaccination. Likewise, treatment of vaccinated mice with Cy increased the antitumor activity of vaccination so that tumor colony formation in the lungs was inhibited even when v-p9NY plus Cy was not given until 7 days after intravenous injection of tumor cells.     

Epstein-Barr virus DNA XII. A variable region of the Epstein-Barr virus genome is included in the P3HR-1 deletion.

The P3HR-1 subclone of Jijoye differs from Jijoye and from other Epstein-Barr virus (EBV)-infected cell lines in that the virus produced by P3HR-1 cultures lacks the ability to growth-transform normal B lymphocytes (Heston et al., Nature (London) 295:160-163, 1982; Miller et al., J. Virol. 18:1071-1080, 1976; Miller et al., Proc. Natl. Acad. Sci. U.S.A. 71:4006-4010, 1974; Ragona et al., Virology 101:553-557, 1980). The P3HR-1 virus was known to be deleted for a region which encodes RNA in latently infected, growth-transformed cells (Bornkamm et al., J. Virol. 35:603-618, 1980; Heller et al., J. Virol. 38:632-648, 1981; King et al., J. Virol. 36:506-518, 1980; Raab-Traub et al., J. Virol. 27:388-398, 1978; van Santen et al., Proc. Natl. Acad. Sci. U.S.A. 78:1930-1934, 1980). This deletion is now more precisely defined. The P3HR-1 genome contains less than 170 base pairs (and possibly none) of the 3,300-base pair U2 region of EBV DNA and is also lacking IR2 (a 123-base pair repeat which is the right boundary of U2). A surprising finding is that EBV isolates vary in part of the U2 region. Two transforming EB viruses, AG876 and Jijoye, are deleted for part of the U2 region including most or all of a fragment, HinfI-c, which encodes part of one of the three more abundant cytoplasmic polyadenylated RNAs of growth-transformed cells (King et al., J. Virol. 36:506-518, 1980; King et al., J. Virol. 38:649-660, 1981; van Santen et al., Proc. Natl. Acad. Sci. U.S.A. 78:1930-1934).     

Transient RNA interference in hematopoietic progenitors with functional consequences

Short interfering (si) RNAs have now been shown to inhibit gene expression in several species, including mammals (Elbashir et al.: Nature 411:494-498, 2001; Fire et al.: Nature 391:806-811, 1998). RNA inhibition in primary cells such as stem cells would facilitate rapid gene discovery in a postgenome era. While retroviruses can deliver siRNA expression cassettes for stable expression (Barton and Medzhitov: Proc Natl Acad Sci USA 99:14943-14945, 2002; Paddison et al.: Proc Natl Acad Sci USA 99:1443-1448, 2002; Rubinson et al.: Nat Genet 33:401-406, 2003), an efficient method for direct transfer of siRNA to stem cells is still lacking. Here, we established electroporation to deliver siRNA to hematopoietic progenitors. On average, at least 80% of cells take up the RNA, and these display nearly 100% knockout of marker gene expression at both the RNA and protein level. Moreover, knockdown of the hematopoietic regulator, CD45, results in 3-fold more hematopoietic colonies in a progenitor assay. These results demonstrate that transient transfection of siRNA to primary cells can have substantial functional consequences. This technology may be applicable to a variety of primary cell types.     

Recognition of centromeric histone variant CenH3s by their chaperones

Comment on: Zhou et al. Nature 2011; 47:234-237, Hu et al. Genes Dev 2011; 25:901-6 and Cho et al. Proc Natl Acad Sci USA 2011; 108:9367-71.     

Diffusion of molecules on biological membranes of nonplanar form. II. Diffusion anisotropy.

Molecules diffusing on nonplanar membranes, which have different amounts of corrugation in different directions, may experience dissimilar diffusion coefficients in each direction. Smith et al. (1979, Proc. Natl. Acad. Sci. USA, 76:5641-5644) measured diffusion anisotropy on fibroblast cell membranes in which the ratio of the diffusion coefficients, in different directions, was 0.27. In the present work we calculate the effect of anisotropic corrugation on the rate of diffusion of molecules on membranes. We find that part of the anisotropy reported by Smith et al. (1979, Proc. Natl. Acad. Sci. USA, 76:5641-5644) can be explained by the membrane nonplanarity, and we present the way of calculating this geometric factor.     

Signal sequence of alkaline phosphatase of Escherichia coli.

The amino acid sequence of the signal sequence of phoA was determined by DNA sequencing by using the dideoxy chain termination technique (Sanger et al., Proc. Natl. Acad. Sci. U.S.A. 74:5463-5467, 1977). The template used was single-stranded DNA obtained from M13 on f1 phage derivatives carrying phoA, constructed by in vitro recombination. The results confirm the sequence of the first five amino acids determined by Sarthy et al. (J. Bacteriol. 139:932-939, 1979) and extend the sequence in the same reading frame into the amino terminal region of the mature alkaline phosphatase (Bradshaw et al., Proc. Natl. Acad. Sci. U.S.A., 78:3473-3477, 1981). As was predicted (Inouye and Beckwith, Proc. Natl. Acad. Sci. U.S.A. 74:1440-1444, 1977), the signal sequence was highly hydrophobic. The alteration of DNA sequence was identified for a promoter mutation that results in the expression of phoA independent of the positive control gene phoB and in insensitivity to high phosphate.     

How do yeast cells sense glucose?

A glucose-sensing mechanism has been described in Saccharomyces cerevisiae that regulates expression of glucose transporter genes. The sensor proteins Snf3 and Rgt2 are homologous to the transporters they regulate. Snf3 and Rgt2 are integral plasma membrane proteins with unique carboxy-terminal domains that are predicted to be localized in the cytoplasm. In a recent paper Ozcan and colleagues [Ozcan S, et al. EMBO J 1998; 17:2556-2773 (Ref. 1)] present evidence that the cytoplasmic domains of Snf3 and Rgt2 are required to transmit a glucose signal. They provide additional evidence to support their earlier assertion [Ozcan S, et al. Proc Natl Acad Sci USA 1996;93:12428-12432 (Ref. 2)] that glucose transport via Snf3 and Rgt2 is not involved in glucose sensing but, rather, that these proteins behave like glucose receptors. Other examples of transporter homologs with regulatory functions have recently been described in fungi as well [Madi L, et al. Genetics 1997; 146:499-508 (Ref. 3). and Didion T, et al. Mol Microbiol 1998;27:643-650 (Ref. 4)]. The identification of this class of nutrient sensors is an important step in elucidating the complex of regulatory mechanisms that leads to adaptation of fungi to different environments.     

Horizontal gene transfer in microbial genome evolution

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).     

Biochemical detection of Abeta isoforms: implications for pathogenesis, diagnosis, and treatment of Alzheimer's disease

Prior to the identification of the various abnormal proteins deposited as fibrillar aggregates in the Alzheimer's disease (AD) brain, there was tremendous controversy over the importance of the various lesions with respect to primacy in the pathology of AD. Nevertheless, based on analogy to systemic amyloidosis, many investigators believed that the amyloid deposits in AD played a causal role and that characterization of these deposits would hold the key to understanding this complex disease. Indeed, in retrospect, it was the initial biochemical purifications of the approximately 4 kDa amyloid beta-peptide (Abeta) from amyloid deposits in the mid 1980s that launched a new era of AD research (Glenner and Wong, Biochem. Biophys. Res. Commun. 122 (1984) 1121-1135; Wong et al., Proc. Natl. Acad Sci. USA 82 (1985) 8729 8732; and Masters et al., Proc. Natl. Acad Sci. USA 82 (1985) 4245-4249). Subsequent studies of the biology of Abeta together with genetic studies of AD have all supported the hypothesis that altered Abeta metabolism leading to aggregation plays a causal role in AD. Although there remains controversy as to whether Abeta deposited as classic amyloid or a smaller, aggregated, form causes AD, the relevance of studying the amyloid deposits has certainly been proven. Despite the significant advances in our understanding of the role of Abeta in AD pathogenesis, many important aspects of Abeta biology remain a mystery. This review will highlight those aspects of Abeta biology that have led to our increased understanding of the pathogenesis of AD as well as areas which warrant additional study.     

The human heat-shock genes HSPA6 and HSPA7 are both expressed and localize to chromosome 1.

HSPA6 is a member of the human heat-shock protein gene family, encoding a basic 70-kDa protein, with unique induction characteristics (Leung et al., 1990, Biochem. J. 267: 125-132). Hybridization analyses with a somatic cell hybrid DNA panel localized the gene to chromosome 1q. The highly related HSPA7 DNA sequence (Voellmy et al., 1985, Proc. Natl. Acad. Sci. USA 82: 4949-4953) colocalized. Both HSPA6 and HSPA7 represent functional genes, as determined by analyses of mRNA from heat-shocked human cells using specific oligonucleotides, although their pattern of expression differed. Neither mRNA was detected in the absence of heat stress. A BamHI polymorphism in the HSPA7 gene was present in a predominantly Asian population.     

Milk, revealed "silent" chemistry: new mode of cycloretinal synthesis

Bovine milk is by far the most commonly consumed milk in the western world. The protein composition in milk consists of casein and whey proteins, of which β-lactoglobulin (BLG) is the principal constituent of the latter. Here we provide biochemical evidence that this milk protein, in purified form and in pasteurized store-bought milk, promotes the formation of cycloretinal (all-trans retinal dimer), and a variety of other cycloterpenals of biological relevance [Fishkin et al., Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 7091-7096; Fishkin et al., Chirality, 2004, 16, 637-641; Kim et al., Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 19273-19278]. Cycloretinal is an eye metabolite and among several toxic byproducts of the visual cycle firmly established to cause age-related macular degeneration. Experiments in rabbits further demonstrate that BLG/milk can survive the digestive system and promote this reaction in vivo [Caillard et al., Am. J. Physiol., 1994, 266(6), G1053-G1059]. Proteomic studies on age-related macular degeneration patients have detected BLG in the eye of these patients further suggesting that this milk protein could contribute to disease progression [Crabb et al., Proc. Natl. Acad. Sci. U. S. A., 2002, 99(23), 14682-14687].     

Oversized flagellar membrane protein in paralyzed mutants of Chlamydomonas reinhardrii

A mutant strain of Chlamydomonas reinhardtii is shown to possess an oversized flagellar membrane protein. The mutant has paralyzed flagella, is temperature sensitive for flagellar assembly, and has an abnormal axonemal protein composition. All phenotypes appear to derive from a single Mendelian mutation, and genetic analysis suggests that the mutation, which call ts222, is in the gene pfl. Because pf1 mutants are known to have radial-spoke defects (Piperno et al., 1977, Proc. Natl. Acad. Sci. U. S. A. 74:1600-1604; and Witman et al., 1978, J. Cell Biol. 76:729-797), a relation as yet undefined appears to exist between radial-spoke and flagellar membrane biogenesis.     

How a mismatch repair enzyme balances the needs for efficient lesion processing and minimal action on undamaged DNA

Comment on: Maiti A, et al. Proc Natl Acad Sci USA 2012; 109:8091-6.     

A long way to stemness

Comment on: Tanaka Y, et al. Proc Natl Acad Sci USA 2012; 109:4515-20.     

A general requirement for FcγRIIB co-engagement of agonistic anti-TNFR antibodies

Comment on: Li F, et al. Proc Natl Acad Sci USA 2012; 109:10966-71.