Analysis of the tryptic search space in UniProt databases

In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding International Protein Index, reference sequence, Ensembl, and UniRef100 (where UniRef is UniProt reference clusters) organism‐specific data sets. All protein forms annotated in UniProtKB (both the canonical sequences and isoforms) were evaluated in this study. In addition, natural and disease‐associated amino acid variants annotated in UniProtKB were included in the evaluation. The peptide unicity was also evaluated for each data set. Furthermore, the peptide information in the UniProtKB data sets was also compared against the available peptide‐level identifications in the main MS‐based proteomics repositories. Identifying the peptides observed in these repositories is an important resource of information for protein databases as they provide supporting evidence for the existence of otherwise predicted proteins. Likewise, the repositories could use the information available in UniProtKB to direct reprocessing efforts on specific sets of peptides/proteins of interest. In summary, we provide comprehensive information about the different organism‐specific sequence data sets available from UniProt, together with the pros and cons for each, in terms of search space for MS‐based bottom‐up proteomics workflows. The aim of the analysis is to provide a clear view of the tryptic search space of UniProt and other protein databases to enable scientists to select those most appropriate for their purposes.     

The impact of Arabidopsis thaliana SNF1‐related‐kinase 1 (SnRK1)‐activating kinase 1 (SnAK1) and SnAK2 on SnRK1 phosphorylation status: characterization of a SnAK double mutant

Arabidopsis thaliana SNF1‐related‐kinase 1 (SnRK1)‐activating kinase 1 (AtSnAK1) and AtSnAK2 have been shown to phosphorylate in vitro and activate the energy signalling integrator, SnRK1. To clarify this signalling cascade in planta, a genetic‐ and molecular‐based approach was developed. Homozygous single AtSnAK1 and AtSnAK2 T‐DNA insertional mutants did not display an apparent phenotype. Crossing of the single mutants did not allow the isolation of double‐mutant plants, whereas self‐pollinating the S1?/? S2+/? sesquimutant specifically gave approximatively 22% individuals in their offspring that, when rescued on sugar‐supplemented media in vitro, were shown to be AtSnAK1 AtSnAK2 double mutants. Interestingly, this was not obtained in the case of the other sesquimutant, S1+/? S2?/?. Although reduced in size, the double mutant had the capacity to produce flowers, but not seeds. Immunological characterization established the T‐loop of the SnRK1 catalytic subunit to be non‐phosphorylated in the absence of both SnAKs. When the double mutant was complemented with a DNA construct containing an AtSnAK2 open reading frame driven by its own promoter, a normal phenotype was restored. Therefore, wild‐type plant growth and development is dependent on the presence of SnAK in vivo, and this is correlated with SnRK1 phosphorylation. These data show that both SnAKs are kinases phosphorylating SnRK1, and thereby they contribute to energy signalling in planta.     

RNAi-mediated Double Gene Knockdown and Gustatory Perception Measurement in Honey Bees (Apis mellifera)

This video demonstrates novel techniques of RNA interference (RNAi) which downregulate two genes simultaneously in honey bees using double-stranded RNA (dsRNA) injections. It also presents a protocol of proboscis extension response (PER) assay for measuring gustatory perception.RNAi-mediated gene knockdown is an effective technique downregulating target gene expression. This technique is usually used for single gene manipulation, but it has limitations to detect interactions and joint effects between genes. In the first part of this video, we present two strategies to simultaneously knock down two genes (called double gene knockdown). We show both strategies are able to effectively suppress two genes, vitellogenin (vg) and ultraspiracle (usp), which are in a regulatory feedback loop. This double gene knockdown approach can be used to dissect interrelationships between genes and can be readily applied in different insect species.The second part of this video is a demonstration of proboscis extension response (PER) assay in honey bees after the treatment of double gene knockdown. The PER assay is a standard test for measuring gustatory perception in honey bees, which is a key predictor for how fast a honey bee''s behavioral maturation is. Greater gustatory perception of nest bees indicates increased behavioral development which is often associated with an earlier age at onset of foraging and foraging specialization in pollen. In addition, PER assay can be applied to identify metabolic states of satiation or hunger in honey bees. Finally, PER assay combined with pairing different odor stimuli for conditioning the bees is also widely used for learning and memory studies in honey bees.     

Characteristics of dipeptide transport in normal and papain-treated brush border membrane vesicles from mouse intestine I. Uptake of glycyl-l-phenylalanine

Papain treatment of isolated brush border membrane vesicles was carried out to study peptide transport in the absence of hydrolytic events associated with the brush border membrane. Such a treatment allowed a 70% decrease in the activity of membrane-associated oligopeptidases and the study of peptide transport in the complete absence of free amino acids up to 1 min of incubation. A comparison between the time course curves of glycyl-l-phenylalanine uptake by normal and papain-treated vesicles showed that the overshoots seen in the presence of Na⁺ and K⁺ gradients (extravesicular intravesicular) when using normal vesicles were no longer evident after papain treatment. This result, together with the demonstration of uptake into an osmotically reactive intravesicular space and the analysis of uptake of free phenylalanine, allowed the coclusion that peptide transport was the result of two complementary mechanisms, uptake of free amino acids following hydrolysis by the membrane-bound oligopeptidases, and intact peptide transport down a concentration gradient by a non-Na⁺ (and non-K⁺)-dependent process. These results also showed the non-involvement of γ-glutamyltransferase and the γ-glutamyl cycle in peptide absorption. A linear relationship has been established between initial dipeptide uptake and glycyl-l-phenylalanine concentration for the intact peptide transport process. However, this process can be inhibited to various extents by other di- and tripeptides but the inhibition never exceeded 43%. These results are consistent with both passive and facilitated diffusion mechanisms of intact peptide transport, the latter occuring by either a low affinity-high capacity or a high affinity-low capacity system.     

Sensitivity of β-casein phosphopeptide-iron complex to digestive enzymes in ligated segment of rat duodenum

Binding iron to the phosphorylated β(1-25) peptide derived from β-casein improves iron bioavailability in the rat. The aim of the present work was to learn how injected β(1-25) and iron-β(1-25) complex behave in the duodenum of rats using the technique of intestinal ligation in situ and reversed-phase (RP)-high performance liquid chromatography-electrospray mass spectrometry analysis of the lumen contents. The results demonstrate that β(1-25) is sensitive to digestive enzymes including proteases/peptidases and phosphatases during duodenal transit. The lumen contents of rats perfused with iron free β(1-25) contained all peptidic sequences derived from β(1-25). In contrast, the phosphorylated part of β(1-25) [i.e., β(15-24)] was not detected in lumen of rats perfused with iron-β(1-25) complex.     

Contrasting breeding strategies of two sympatric orioles: first documentation of double brooding by Orchard Orioles

ABSTRACT.   Although many studies have revealed intraspecific variation in the number of broods raised per breeding season, less is known about the causes of variation between species. We monitored the breeding behavior of congeners traditionally thought to raise one brood per breeding season, Orchard Orioles ( Icterus spurius ) and Baltimore Orioles ( I. galbula ). Both species have similar habitat and nesting requirements. We captured and banded orioles at three study sites in Maryland in 2004 and 2005. No pairs of Baltimore Orioles ( N = 26) were double brooded, whereas 8 of 24 pairs (33%) of Orchard Orioles had a second brood and 7 of 16 pairs (44%) of Orchard Orioles that successfully raised a first brood also successfully raised a second brood during the same breeding season. Our findings provide the first documentation of double brooding by Orchard Orioles. The timing of molt and the amount of time and energy devoted to postfledgling parental care may contribute to this difference between species in terms of the number of broods per breeding season.     

Livestock Tick Predation by Chickens: The Rate of Digestion of Ticks in the Alimentary Tract of Chickens

Research on the predation of ticks by chickens is required to establish the potential rôle of chickens as biological control agents for ticks. In the present study, 26 local chickens were allowed to feed in groups of two or three for 1 hour on a meal containing adult unengorged Rhipicephalus appendiculatus and Amblyomma variegatum and slaughtered thereafter at different intervals ranging from 11 min to 24 h. The contents of the digestive tracts of the chickens were carefully examined under a dissecting microscope to determine the state of digestion of the ingested ticks.

All ticks found in the crop were not digested and a few A. variegatum were attached to the crop wall and were found dead. The gizzard contained partially and completely digested ticks while tick remnants were predominant in the small intestine. It was concluded that most of the digestion of tick proteins takes place in the small intestine. It was also concluded that, although the digestion rate of ticks varies in individual chickens, all ticks digested in a meal should have been completely digested and absorption of the tick nutrients should have started within 21–24 h although this could have been accomplished as early as 9 h by chickens with fast digestion rates.     

Potential of using lactic acid bacteria for therapy and immunomodulation in man

Abstract: There is in 1993 no proven medical indication of lactic acid bacteria (LAB) for therapy or immunomodulation in man. However, within the bulk of publications, rigorous trials have now opened rational fields of research on beneficial effects of LAB. These include lactose digestion, cholesterol metabolism, diarrheal disorders, prophylaxis of intestinal or urogenital infections, immunomodulation or even oral vaccination. We try here to analyse these studies, considering LAB as pharmacological agents, and conclude that pursuit of research could be promising for ecological therapy of mucosal diseases, and for development of original and flexible vectors for targeting in the gastrointestinal tract.     

A monomeric mutant of Clostridium symbiosum glutamate dehydrogenase: comparison with a structured monomeric intermediate obtained during refolding.

The refolding of Clostridium symbiosum glutamate dehydrogenase (GDH) involves the formation of an inactive structured monomeric intermediate prior to its concentration-dependent association. The structured monomer obtained after removal of guanidinium chloride was stable and competent for reconstitution into active hexamers. Site-directed mutagenesis of C. symbiosum gdh gene was performed to replace the residues Arg-61 and Phe-187 which are involved in subunit-subunit interactions, as determined by three-dimensional structure analysis. Heterologous over-expression in Escherichia coli of the double mutant (R61E/F187D) led to the production of a soluble protein with a molecular mass consistent with the monomeric form of clostridial GDH. This protein is catalytically inactive but cross-reacts with an anti-wild-type GDH antibody preparation. The double mutant R61E/F187D does not assemble into hexamers. The physical properties and the stability toward guanidinium chloride and urea of R61E/F187D were studied and compared to those of the structured monomeric intermediate.     

Chloroplast nucleoids in large number and large DNA amount with regard to maternal inheritance inChlamydomonas reinhardtii

Summary We studied the maternal chloroplast inheritance ofChlamydomonas reinhardtii by epifluorescence microscopy after staining with DNA specific fluorochrome DAPI and by genetic methods, using wild type cells and cells containing previously isolated mutation of cond-1 and cond-2. Wild type cells contained about 7 chloroplast (cp) nucleoids, while mutants, cond-1(+) and cond-2(+), contained about 14 and 23 cp nucleoids, respectively, after one week culture on agar plates. The total cpDNA contents were almost proportional to the numbers of cp nucleoids. When cells containing cond-1 or cond-2 mutation were used as a parental source to cross with wild type cells of the other parent, preferential digestion of cp nucleoids from male parent (mt^–) origin occurred in the zygotes, although the frequencies of the digestion were slightly lower than that in the zygotes from the cross between wild type cells. Western blot analysis of the protein ofzyslB gene, which has been found related to preferential digestion of mt^– origin cp-nucleoids DNA, showed that a high amount of this protein was detected with the initiation of preferential digestion of mt^– cp nucleoids and disappeared with the completion of the digestion. Cp genetic markers for antibiotic resistance were maternally inherited in all crosses. These results showed that although the preferential digestion of cp nucleoids consisting of large number and large cpDNA amount requires a slightly longer period to complete, this high ploidy of the cp nucleoids does not disturb maternal inheritance.