Changes in the levels of major sulfur metabolites and free amino acids in pea cotyledons recovering from sulfur deficiency

Changes in levels of sulfur metabolites and free amino acids were followed in cotyledons of sulfur-deficient, developing pea seeds (Pisum sativum L.) for 24 hours after resupply of sulfate, during which time the legumin mRNA levels returned almost to normal. Two recovery situations were studied: cultured seeds, with sulfate added to the medium, and seeds attached to the intact plant, with sulfate added to the roots. In both situations the levels of cysteine, glutathione, and methionine rose rapidly, glutathione exhibiting an initial lag. In attached but not cultured seeds methionine markedly overshot the level normally found in sulfur-sufficient seeds. In the cultured seed S-adenosylmethionine (AdoMet), but not S-methylmethionine, showed a sustained rise; in the attached seed the changes were slight. The composition of the free amino acid pool did not change substantially in either recovery situation. In the cultured seed the large rise in AdoMet level occurred equally in nonrecovering seeds. It was accompanied by 6-fold and 10-fold increases in γ-aminobutyrate and alanine, respectively. These effects are attributed to wounding resulting from excision of the seed. ³⁵S-labeling experiments showed that there was no significant accumulation of label in unidentified sulfur-containing amino compounds in either recovery situation. It was concluded from these results and those of other workers that, at the present level of knowledge, the most probable candidate for a `signal' compound, eliciting recovery of legumin mRNA level in response to sulfur-feeding, is cysteine.     

Amino Acid Composition Along the Transport Pathway during Grain Filling in Wheat

The amino acid composition of endosperm cavity sap and of sieve tube saps from the flag leaf, peduncle, rachis, grain pedicel, and grain were determined for wheat plants just past the mid-half of grain filling. On a mole percent basis, glutamine accounted for almost half of the amino acids in sieve tube sap from the peduncle and ear. Other protein amino acids, plug γ-aminobutyrate, were present in varying, but mostly low (a few mole percent) proportions. The amino acid composition of phloem exudate resembled that of the mature wheat grain. The proportions of amino acids in the endosperm cavity were generally similar to those of the sieve tube sap supplying the grain. Cysteine, however, while virtually absent from sieve tube sap, comprised 1 to 2 mole percent of amino acids in the endosperm cavity, suggesting it is transported in a different form. Also, alanine and, to a lesser extent, glutamate were relatively more prominent in endosperm cavity sap than in the sieve tube sap. Thus, while most amino acids were more concentrated in the sieve tube sap than in the endosperm cavity sap, alanine and glutamate appeared to be moving from the sieve tube to the endosperm cavity in the absence of, or perhaps even against, their concentration gradients.     

Interleukin-23 is critical for full-blown expression of a non-autoimmune destructive arthritis and regulates interleukin-17A and RORγt in γδ T cells

Introduction

A protein analysis using a mass spectrometry indicated that there are serum proteins showing significant quantitative changes after the administration of infliximab. Among them, connective tissue growth factor (CTGF) seems to be related to the pathogenesis of rheumatoid arthritis (RA). Therefore, this study was conducted to investigate how CTGF is associated with the disease progression of RA.

Methods

Serum samples were collected from RA patients in active or inactive disease stages, and before or after treatments with infliximab. CTGF production was evaluated by ELISA, RT-PCR, indirect immunofluorescence microscopy, and immunoblotting. Osteoclastogenesis was evaluated using tartrate-resistant acid phosphatase (TRAP) staining, a bone resorption assay and osteoclasts specific catalytic enzymes productions.

Results

The serum concentrations of CTGF in RA were greater than in normal healthy controls and disease controls. Interestingly, those were significantly higher in active RA patients compared to inactive RA patients. Furthermore, the CTGF levels significantly were decreased by infliximab concomitant with the disease amelioration. In addition, tumour necrosis factor (TNF)α can induce the CTGF production from synovial fibroblasts even though TNFα can oppositely inhibit the production of CTGF from chondrocytes. CTGF promoted the induction of the quantitative and qualitative activities of osteoclasts in combination with M-CSF and receptor activator of NF-κB ligand (RANKL). In addition, we newly found integrin αVβ3 on the osteoclasts as a CTGF receptor.

Conclusions

These results indicate that aberrant CTGF production induced by TNFα plays a central role for the abnormal osteoclastic activation in RA patients. Restoration of aberrant CTGF production may contribute to the inhibition of articular destruction in infliximab treatment.     

The tangled core at the heart of the bryozoan suborder Phylloporinina

Abstract: The family Phylloporinidae was introduced in the late 19th century to accommodate a small number of Palaeozoic bryozoan genera characterized by irregularly fenestrated colonies generated by anastomosis of unilaminate branches. Among the first named of these genera were Chasmatopora Eichwald, 1855 and Phylloporina Ulrich in Foerste, 1887. The two names have been variously in fashion, and there has been confusion about whether they are subjective synonyms or are distinct genera. This taxonomic confusion has been due in large part to whether the single species (Retepora angulata Hall, 1847) assigned to Phylloporina in Foerste (1887) or the species that Ulrich intended (Retepora trentonensis Nicholson, 1875) is the type species and also because of lack of sufficient information about Foerste’s material to characterize it well. We here redescribe the pertinent species, erect the new species Chasmatopora foerstei for the species that Foerste incorrectly assigned to Phylloporina angulata (Hall), and suggest that Retepora trentonensis Nicholson be retained as type species of Phylloporina based on prevailing usage, until the issue is settled by the International Commission on Zoological Nomenclature.     

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

Background  

Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.     

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

Background

Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector.

Results

We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download.

Conclusion

Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms.