GATA-3 expression is crucial for T cell development and peaks during commitment to the T-cell lineage, midway through the CD4−CD8− (DN) 1-3 stages. We used RNA interference and conditional deletion to reduce GATA-3 protein acutely at specific points during T-cell differentiation in vitro. Even moderate GATA-3 reduction killed DN1 cells, delayed progression to DN2 stage, skewed DN2 gene regulation, and blocked appearance of DN3 phenotype. Although a Bcl-2 transgene rescued DN1 survival and improved DN2 cell generation, it did not restore DN3 differentiation. Gene expression analyses (qPCR, RNA-seq) showed that GATA-3-deficient DN2 cells quickly upregulated genes including Spi1 (PU.1) and Bcl11a and downregulated genes including Cpa3, Ets1, Zfpm1, Bcl11b, Il9r and Il17rb, with gene-specific kinetics and dose-dependencies. These targets could mediate two distinct roles played by GATA-3 in lineage commitment, as revealed by removing wildtype or GATA-3-deficient early T-lineage cells from environmental Notch signals. GATA-3 worked as a potent repressor of B-cell potential even at low expression levels, so that only full deletion of GATA-3 enabled pro-T cells to reveal B-cell potential. The ability of GATA-3 to block B-cell development did not require T-lineage commitment factor Bcl11b. In prethymic multipotent precursors, however, titration of GATA-3 activity using tamoxifen-inducible GATA-3 showed that GATA-3 inhibits B and myeloid developmental alternatives at different threshold doses. Furthermore, differential impacts of a GATA-3 obligate repressor construct imply that B and myeloid development are inhibited through distinct transcriptional mechanisms. Thus, the pattern of GATA-3 expression sequentially produces B-lineage exclusion, T-lineage progression, and myeloid-lineage exclusion for commitment.

Summary Mammalian T lymphocytes are a prototype for development from adult pluripotent stem cells. While T-cell specification is driven by Notch signaling, T-lineage commitment is only finalized after prolonged Notch activation. However, no T-lineage specific regulatory factor has been reported that mediates commitment. We used a gene-discovery approach to identify additional candidate T-lineage transcription factors and characterized expression of >100 regulatory genes in early T-cell precursors using realtime RT-PCR. These regulatory genes were also monitored in multilineage precursors as they entered T-cell or non-T-cell pathways in vitro; in non-T cells ex vivo; and in later T-cell developmental stages after lineage commitment. At least three major expression patterns were observed. Transcription factors in the largest group are expressed at relatively stable levels throughout T-lineage specification as a legacy from prethymic precursors, with some continuing while others are downregulated after commitment. Another group is highly expressed in the earliest stages only, and is downregulated before or during commitment. Genes in a third group undergo upregulation at one of three distinct transitions, suggesting a positive regulatory cascade. However, the transcription factors induced during commitment are not T-lineage specific. Different members of the same transcription factor family can follow opposite trajectories during specification and commitment, while factors co-expressed early can be expressed in divergent patterns in later T-cell development. Some factors reveal new regulatory distinctions between αβ and γδ T-lineage differentiation. These results show that T-cell identity has an essentially complex regulatory basis and provide a detailed framework for regulatory network modeling of T-cell specification.

The relationship of C1 -inhibitor (C1 -INH) concentration and apparent functional activity was investigated in 111 plasma samples from 21 patients with the common form of hereditary angioedema (HAE). Functional C1 -INH was analyzed by means of a modified version of immunodiffusion assay. Down to a C1-INH level of approximately 0.075 g/1 (38% of normal) apparent C1-INH functions were found within the normal range, while below this level functional adequacy of C1-INH could no longer be ascertained. When C4 concentrations, considered to reflect approximately functional C1-INH, were related to C1- INH antigen levels of individual samples, a relationship emerged which was identical to that between C1-INH concentration and apparent function. No attacks of edema could be associated with C1 -INH concentrations above 0.07 5 g/1, while it was possible to associate attacks with concentrations below this level. In experiments where patient plasma and normal plasma were mixed in various ratios or where HAE plasma was replaced by purified C1-INH, an increase in C1-INH antigen to concentrations of 0.06-0.08 g/1 was followed by a sharp rise in apparent functions to normal values. The rise of functional C1-INH became moderate when C1-INH antigen further increased. The results supported the idea of a functionally critical level of C1 -INH in the common form of HAE.

In previous work from our laboratories a synthetic gene encoding a peptide (“Sulpeptide 1” or “S1”) with a high proportion of methionine and cysteine residues had been designed to act as a sulfur sink and was inserted into the dsz (desulfurization) operon of Rhodococcus erythropolis IGTS8. In the work described here this construct (dszAS1BC) and the intact dsz operon (dszABC) cloned into vector pRESX under control of the (Rhodococcus) kstD promoter were transformed into the desulfurization-negative strain CW25 of Rhodococcus qingshengii. The resulting strains (CW25[pRESX-dszABC] and CW25[pRESX-dszAS1BC]) were subjected to adaptive selection by repeated passages at log phase (up to 100 times) in minimal medium with dibenzothiophene (DBT) as sole sulfur source. For both strains DBT metabolism peaked early in the selection process and then decreased, eventually averaging four times that of the initial transformed cells; the maximum specific activity achieved by CW25[pRESX-dszAS1BC] exceeded that of CW25[pRESX-dszABC]. Growth rates increased by 7-fold (CW25[pRESX-dszABC]) and 13-fold (CW25[pRESX-dszAS1BC]) and these increases were stable. The adaptations of CW25[pRESX-dszAS1BC] were correlated with a 3-5X increase in plasmid copy numbers from those of the initial transformed cells; whole genome sequencing indicated that during its selection processes no mutations occurred to any of the dsz, S1, or other genes and promoters involved in sulfur metabolism, stress response, or DNA methylation, and that the effect of the sulfur sink produced by S1 is likely very small compared to the cells’ overall cysteine and methionine requirements. Nevertheless, a combination of genetic engineering using sulfur sinks and increasing Dsz capability with adaptive selection may be a viable strategy to increase biodesulfurization ability.

The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species.

Rhogocytes are morphologically distinct cells distributed throughout connective tissues of crustaceans and molluscs. Using light microscopy, rhogocytes of the vetigastropod Megathura crenulata were identified by their ovoid shape, and their cytoplasm filled with spherical inclusions which contained lysosomal enzymes, based on uptake of neutral red and staining with LysoTracker dye. Rhogocytes were most abundant in the digestive gland (2,824 rhogocytes/mm 2 ), followed by the connective tissue layer surrounding the middle and posterior esophagus and intestine (1,431 rhogocytes/mm 2 , 872 rhogocytes/mm 2 , and 1,190 rhogocytes/mm 2 , respectively), and were lowest in abundance in the foot (154 rhogocytes/ mm 2 ). At the transmission electron microscopy level, characteristic features of rhogocytes were inclusions showing a variety of electron densities, abundant vesicles, and rough endoplasmic reticulum in the cytoplasm, and regions of plasma membrane folded to produce slits connected by thin diaphragms. Although several functions have been proposed for gastropod rhogocytes, much attention has been focused on their possible role in the synthesis of the respiratory pigment hemocyanin. In M. crenulata, this molecule exists in several isoforms called keyhole limpet hemocyanin (KLH). One isoform, KLH1, is a large didecamer and has been used extensively in studies on vertebrate immunology and cancer therapy. We present four lines of evidence indicating rhogocytes in M. crenulata synthesize KLH1. First, at the transmission electron microscopy (TEM) level, dilated cisternae of RER containing material similar in size and shape to KLH were observed in rhogocytes examined throughout the year. Second, KLH1 mRNA was identified exclusively in tissue samples that contained rhogocytes; no mRNA for KLH1 was identified in samples containing only hemocytes. Third, immunoperoxidase staining with antibodies specific to KLH was localized only to rhogocytes. Fourth, in situ hybridization with a probe specific for M. crenulata KLH1 demonstrated KLH1-specific mRNA was present only in rhogocytes. Identification of the cells responsible for the synthesis of KLH is important because of the clinical significance of this molecule.Additional key words: hemocyanin, respiratory pigment, pore cell, gastropod Rhogocytes are large, ovoid to irregularly shaped cells surrounded by a basal lamina, and are distributed throughout the hemal spaces and connective tissue of gastropods. They are further characterized by a suite of morphological features (reviewed by Haszprunar 1996) including (1) the presence of dilated cisternae of rough endoplasmic reticulum (RER) containing material that resembles hemocyanin (HCN), (2) folded regions of the plasma membrane that create pores connected by thin diaphragms, and (3) large (1-5 lm diameter), spher-ical cytoplasmic inclusions, thought to be lysosomes, which vary in electron density. Haszprunar (1996) also summarizes the presence of cells with similar morphologies in a variety of invertebrates, and the multitude o...

The 32O-Y/32O-W culture may be a useful starting point for development of an improved thermophilic petroleum biodesulfurization process.

Clostridium sporogenes PA 3679 is a non-toxic endospore former that is widely used as a surrogate for Clostridium botulinum by the food processing industry to validate thermal processing strategies. PA 3679 produces spores of exceptionally high heat resistance without botulinum neurotoxins, permitting the use of PA 3679 in inoculated pack studies while ensuring the safety of food processing facilities. To identify genes associated with this heat resistance, the genomes of C. sporogenes PA 3679 isolates were compared to several other C. sporogenes strains. The most significant difference was the acquisition of a second spoVA operon, spoVA2, which is responsible for transport of dipicolinic acid into the spore core during sporulation. Interestingly, spoVA2 was also found in some C. botulinum species which phylogenetically cluster with PA 3679. Most other C. sporogenes strains examined both lack the spoVA2 locus and are phylogenetically distant within the group I Clostridium, adding to the understanding that C. sporogenes are dispersed C. botulinum strains which lack toxin genes. C. sporogenes strains are thus a very eclectic group, and few strains possess the characteristic heat resistance of PA 3679.