Genomewide screen reveals a wide regulatory network for di/tripeptide utilization in Saccharomyces cerevisiae

Small peptides of two to six residues serve as important sources of amino acids and nitrogen required for growth by a variety of organisms. In the yeast Saccharomyces cerevisiae, the membrane transport protein Ptr2p, encoded by PTR2, mediates the uptake of di/tripeptides. To identify genes involved in regulation of dipeptide utilization, we performed a systematic, functional examination of this process in a haploid, nonessential, single-gene deletion mutant library. We have identified 103 candidate genes: 57 genes whose deletion decreased dipeptide utilization and 46 genes whose deletion enhanced dipeptide utilization. On the basis of Ptr2p-GFP expression studies, together with PTR2 expression analysis and dipeptide uptake assays, 42 genes were ascribed to the regulation of PTR2 expression, 37 genes were involved in Ptr2p localization, and 24 genes did not apparently affect Ptr2p-GFP expression or localization. The 103 genes regulating dipeptide utilization were distributed among most of the Gene Ontology functional categories, indicating a very wide regulatory network involved in transport and utilization of dipeptides in yeast. It is anticipated that further characterization of how these genes affect peptide utilization should add new insights into the global mechanisms of regulation of transport systems in general and peptide utilization in particular.     

Deciphering human prehistory through the geoarcheological study of cave sediments

Throughout human history, caves and rockshelters have been favored habitation places. These unique environments preserve sediments derived from an assortment of geological and human processes that are typically absent or masked at open‐air sites. Cave sediments are parts of larger stratigraphic frameworks that can reflect environmental changes, shifting microenvironments, and the nature of human activity within these confined and sheltered spaces. Stone tools and faunal material compose the artifact assemblages from caves that are typically studied. Cave sediments, on the other hand, which encase the archeological finds and which have both geological and human origins, have been understudied relative to traditional artifacts, in spite of their ubiquity and importance. Thus, anthropogenic sediments, the most striking of which are organic‐rich deposits, and combustion features merit the same attention as any other artifacts that result from human activities and behaviors. The purpose of this paper is to highlight some of the most salient aspects of prehistoric cave sediments and the processes revealed by recent studies of these accumulations. We review methods and techniques that are used to analyze cave sediments and illustrate how their careful study can be used to reconstruct local and regional cave environments, as well as the nature of the human activities that produced them. Finally, we show how such study can place important constraints on our archeological interpretations, ultimately having a profound effect on how we decipher human prehistory.     

Negatively charged self-assembling DNA/poloxamine nanospheres for in vivo gene transfer

Over the past decade, numerous nonviral cationic vectors have been synthesized. They share a high density of positive charges and efficiency for gene transfer in vitro. However, their positively charged surface causes instability in body fluids and cytotoxicity, thereby limiting their efficacy in vivo. Therefore, there is a need for developing alternative molecular structures. We have examined tetrabranched amphiphilic block copolymers consisting of four polyethyleneoxide/polypropyleneoxide blocks centered on an ethylenediamine moiety. Cryo-electron microscopy, ethidium bromide fluorescence and light and X-ray scattering experiments performed on vector–DNA complexes showed that the dense core of the nanosphere consisted of condensed DNA interacting with poloxamine molecules through electrostatic, hydrogen bonding and hydrophobic interactions, with DNA molecules also being exposed at the surface. The supramolecular organization of block copolymer/DNA nanospheres induced the formation of negatively charged particles. These particles were stable in a solution that had a physiological ionic composition and were resistant to decomplexation by heparin. The new nanostructured material, the structure of which clearly contrasted with that of lipoplexes and polyplexes, efficiently transferred reporter and therapeutic genes in skeletal and heart muscle in vivo. Negatively charged supramolecular assemblies hold promise as therapeutic gene carriers for skeletal and heart muscle-related diseases and expression of therapeutic proteins for local or systemic uses.     

Indirect approach to C-3 branched 1,2-cis-glycofuranosides: synthesis of aceric acid glycoside analogues

Aceric acid (3-C-carboxy-5-deoxy-alpha-l-xylofuranose) residues are present in pectic polysaccharide rhamnogalacturonan II (RG II) in the form of synthetically challenging 1,2-cis-glycofuranosides. To access synthetic fragments of RG II incorporating aceric acid, a four-step procedure based on C-2 epimerisation of initially prepared 1,2-trans-glycofuranoside was developed. Readily available derivatives of branched-chain l-lyxofuranose bearing a 3-C-vinyl group as a masked 3-C-carboxyl group were investigated as potential precursors of aceric acid units. In the first step of the procedure, installation of a participating group at C-2 of the furanose ring ensured stereocontrol of the O-glycosylation, which was carried out with the thioglycoside of 2-O-acetyl-3,5-di-O-benzyl-3-C-vinyl-L-lyxofuranose. After the glycosylation step, the 2-O-acetyl group was removed, the free 2-OH group was oxidised and the resulting ketone was finally reduced to form the C-3-vinyl-L-xylofuranoside. The use of L-Selectride in the key reduction reaction was essential to achieve the required stereoselectivity to generate 1,2-cis-furanoside.     

Growth and respiration in two mangrove species at a range of salinities

Growth and dark respiration rates were measured in leaves and roots of seedlings of Avicennia marina (Forsk.) Vierh, (grey mangrove), and Aegiceras corniculatum (L.) Blanco (river mangrove). Plants were grown in a soil mixture at ambient temperatures and watered with 0.25 and 100% sea-water. Oxygen uptake was measured in excised root and leaf samples. In both species growth was maximal in 25% sea-water, and root respiration was lowest in 100% sea-water. Differences were found between the two species in the responses of leaf respiration to salinity. In A. corniculatum leaf respiration was raised in both 25 and 100% sea-water, while in A. marina only leaves in 100% sea-water showed higher rates of respiration. These results are consistent with the view that A. marina is the more salt-tolerant of the two species. In A. corniculatum the respiration rates of the hypocotyl were also measured, and were much higher in 100% sea-water than in the other two treatments. The results suggest that at high salinities there is a high metabolic cost in the shoots of both species, and that at such salinities rates of root respiration may be limited by the supply of substrate from the shoots.     

Monoclonal Antibody RYSK173 Recognizes the Dinuclear Zn Center of Serum Carnosinase 1 (CN-1): Possible Consequences of Zn Binding for CN-1 Recognition by RYSK173

Background and Aims

The proportion of serum carnosinase (CN-1) recognized by RYSK173 monoclonal antibody negatively correlates with CN-1 activity. We thus hypothesized that the epitope recognized by RYSK173 is accessible only in a catalytically incompetent conformation of the zinc dependent enzyme and we mapped its position in the CN-1 structure. Since patients with kidney failure are often deficient in zinc and other trace elements we also assessed the RYSK173 CN-1 proportion in serum of these patients and studied the influence of hemodialysis hereon in relation to Zn²⁺ and Cu²⁺ concentration during hemodialysis.

Methods and Results

Epitope mapping using myc-tagged CN-1 fragments and overlapping peptides revealed that the RYSK173 epitope directly contributes to the formation of the dinuclear Zn center in the catalytic domain of homodimeric CN-1. Binding of RYSK173 to CN-1 was however not influenced by addition of Zn²⁺ or Cu²⁺ to serum. In serum of healthy controls the proportion of CN-1 recognized by RYSK173 was significantly lower compared to end-stage renal disease (ESRD) patients (1.12 ± 0.17 vs. 1.56 ± 0.40% of total CN-1; p<0.001). During hemodialysis the relative proportion of RYSK173 CN-1 decreased in parallel with increased serum Zn²⁺ and Cu²⁺ concentrations after dialysis.

Conclusions

Our study clearly indicates that RYSK173 recognizes a sequence within the transition metal binding site of CN-1, thus supporting our hypothesis that metal binding to CN-1 masks the epitope. The CN-1 RYSK173 proportion appears overall increased in ESRD patients, yet it decreases during hemodialysis possibly as a consequence of a relative increase in transition metal bound enzyme.     

Natural Progression of Canine Glycogen Storage Disease Type IIIa

Glycogen storage disease type IIIa (GSD IIIa) is caused by a deficiency of glycogen debranching enzyme activity. Hepatomegaly, muscle degeneration, and hypoglycemia occur in human patients at an early age. Long-term complications include liver cirrhosis, hepatic adenomas, and generalized myopathy. A naturally occurring canine model of GSD IIIa that mimics the human disease has been described, with progressive liver disease and skeletal muscle damage likely due to excess glycogen deposition. In the current study, long-term follow-up of previously described GSD IIIa dogs until 32 mo of age (n = 4) and of family-owned GSD IIIa dogs until 11 to 12 y of age (n = 2) revealed that elevated concentrations of liver and muscle enzyme (AST, ALT, ALP, and creatine phosphokinase) decreased over time, consistent with hepatic cirrhosis and muscle fibrosis. Glycogen deposition in many skeletal muscles; the tongue, diaphragm, and heart; and the phrenic and sciatic nerves occurred also. Furthermore, the urinary biomarker Glc₄, which has been described in many types of GSD, was first elevated and then decreased later in life. This urinary biomarker demonstrated a similar trend as AST and ALT in GSD IIIa dogs, indicating that Glc₄ might be a less invasive biomarker of hepatocellular disease. Finally, the current study further demonstrates that the canine GSD IIIa model adheres to the clinical course in human patients with this disorder and is an appropriate model for developing novel therapies.Abbreviations: CCR, curly-coated retriever; CPK, creatine phosphokinase; GSD IIIa, glycogen storage disease type IIIa; Glc₄, Glcα1-6Glcα1-4Glcα1-4GlcGlycogen storage disease type IIIa (GSD IIIa; OMIM, 232400) is an autosomal recessive disorder caused by mutations in the glycogen debranching enzyme gene (AGL), leading to various clinical signs. The tissues mainly affected are liver, heart, and skeletal muscle. Clinical manifestations include hypoglycemia, elevated serum concentrations of liver and muscle enzymes, hepatomegaly, growth retardation, muscle weakness, cardiac hypertrophy with arrhythmia risk, polycystic ovaries and neuropathy.^15,17,29 Current treatments are mainly symptomatic and are not curative. The most frequently used therapies are dietary, such as providing uncooked corn starch to prevent hypoglycemia at young ages and high-protein diets, which have been shown to reverse the extent of cardiomyopathy associated with GSD IIIa.^7,8,30,37 In addition, the use of medium-chain triglycerides has shown positive therapeutic effects in patients with GSD Ia and GSD IIIa.^11,22 However, dietary therapies do not prevent the long-term complications of GSD IIIa, including hepatic cirrhosis, hepatocellular adenoma, hepatocellular carcinoma, cardiomyopathy, neuropathy, and myopathy.³¹An appropriate animal model is necessary to test novel therapies and address the long-term effects of GSD IIIa. Recently a mouse model for GSD III has been described that may prove beneficial in testing new therapies.¹⁹ However, the limitations of mouse models include a short lifespan that curtails the study of the long-term effects of novel treatments. In addition, a large animal model often mimics human disease more closely than do mouse models, as occurs in GSD type Ia dog models, which exhibit lactic acidosis similar to human patients, a characteristic that mouse models of GSD Ia lack.¹⁶ Therefore a naturally occurring large animal model for GSD IIIa may be more effective in terms of the development of new treatments than are available mouse models.GSD IIIa (OMIA, 001577) has been reported to occur in curly-coated retriever dogs (CCR) and is caused by a naturally occurring homozygous frameshift mutation in exon 32 that leads to the deletion of 126 amino acids at the C-terminus of glycogen debranching enzyme.^12,40 The dogs in these previous studies proved to have abnormalities similar to those seen in humans affected with the disorder, namely progressive glycogen accumulation in muscle and liver, elevated liver and muscle enzymes (ALP, AST, creatine phosphokinase [CPK], and ALT), and eventual liver fibrosis. However, these animals were not followed beyond 16 mo of age in the earlier studies.^12,40 The goal of the current study is to provide biochemical follow-up on these animals and analyze more extensively other tissues and organs involved in GSD IIIa in the dog model. A brief analysis of the naturally high protein diets of GSD IIIa dogs, as well as the effects of an increased protein diet in 2 dogs for the last few months of life, is included.We also include the analysis of a urinary biomarker, Glcα1–6Glcα1– 4Glcα1–4Glc (Glc₄), which is a breakdown product of glycogen by α-amylase and neutral α-1,4-glucosidase.³² Elevated levels of Glc₄ have been found in urine from patients with GSD types II, III, IV, VI, and IX and may correlate with disease advancement.^1,18,24,32 To our knowledge, Glc₄ has not been evaluated previously in dogs; we therefore here evaluated the utility of Glc₄ as a biomarker of canine GSD IIIa. A correlation of Glc₄ levels with liver enzyme concentrations in blood might indicate a role of Glc₄ as a less-invasive biomarker for determining the advancement of liver disease in human and canine patients.     

Early induction of polyfunctional simian immunodeficiency virus (SIV)-specific T lymphocytes and rapid disappearance of SIV from lymph nodes of sooty mangabeys during primary infection

Although the cellular immune response is essential for controlling SIV replication in Asian macaques, its role in maintaining nonpathogenic SIV infection in natural hosts such as sooty mangabeys (SM) remains to be defined. We have previously shown that similar to rhesus macaques (RM), SM are able to mount a T lymphocyte response against SIV infection. To investigate early control of SIV replication in natural hosts, we performed a detailed characterization of SIV-specific cellular immunity and viral control in the first 6 mo following SIV infection in SM. Detection of the initial SIV-specific IFN-γ ELISPOT response in SIVsmE041-infected SM coincided temporally with a decline in peak plasma viremia and was similar in magnitude, specificity, and breadth to SIVsmE041-infected and SIVmac239-infected RM. Despite these similarities, SM showed a greater reduction in postpeak plasma viremia and a more rapid disappearance of productively SIV-infected cells from the lymph node compared with SIVmac239-infected RM. The early Gag-specific CD8(+) T lymphocyte response was significantly more polyfunctional in SM compared with RM, and granzyme B-positive CD8(+) T lymphocytes were present at significantly higher frequencies in SM even prior to SIV infection. These findings suggest that the early SIV-specific T cell response may be an important determinant of lymphoid tissue viral clearance and absence of lymph node immunopathology in natural hosts of SIV infection.