DNA decay and limited Rad53 activation after liquid holding of UV-treated nucleotide excision repair deficient S. cerevisiae cells

The DNA damage checkpoint is a surveillance mechanism activated by DNA lesions and devoted to the maintenance of genome stability. It is considered as a signal transduction cascade, involving a sensing step, the activation of a set of protein kinases and the transmission and amplification of the damage signal through several phosphorylation events. In budding yeast many players of this pathway have been identified. Recent work showed that G1 and G2 checkpoint activation in response to UV irradiation requires prior recognition and processing of UV lesions by nucleotide excision repair (NER) factors that likely recruit checkpoint proteins near the damage. However, another report suggested that NER was not required for checkpoint function. Since the functional relationship between repair mechanisms and checkpoint activation is a very important issue in the field, we analyzed, under different experimental conditions, whether lesion processing by NER is required for checkpoint activation. We found that DNA damage checkpoint can be triggered in an NER-independent manner only if cells are subjected to liquid holding after UV treatment. This incubation causes a time-dependent breakage of DNA strands in NER-deficient cells and leads to partial activation of the checkpoint kinase. The analysis of the genetic requirements for this alternative activation pathway suggest that it requires Mec1 and the Rad17 complex and that the observed DNA breaks are likely to be due to spontaneous decay of damaged DNA.     

Abscisic Acid Sprays Significantly Increase Yield per Plant in Vineyard-Grown Wine Grape (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) cv. Cabernet Sauvignon Through Increased Berry Set with No Negative Effects on Anthocyanin Content and Total Polyphenol Index of Both Juice and Wine

In many cultivars of Vitis vinifera periods of mild water stress during ripening are thought to increase grape quality for winemaking, even though yields may be negatively affected. Because abscisic acid (ABA) is involved in the signaling of water stress in plants, we examine the effects of the ABA signal being given without the concomitant water stress. ABA at 250 mg l⁻¹ was sprayed weekly or biweekly from bud-burst until harvest onto the leaves of vineyard-grown plants of cv. Cabernet Sauvignon. For ABA-treated plants berry yield per bunch and per plant was significantly increased (1.5- to 2.0-fold) across three consecutive harvests (2005 through 2007). Number of berries per bunch and per plant was the primary basis for the significant crop increases, although bunches per plant also tended to increase (1.1- to 1.3-fold) across all three harvests. Other parameters assessed included number of internodes, shoot length, leaf area, leaf water potential at midday, photosynthesis, and stomatal conductance. These parameters showed no significant change with ABA treatment, although shoot length tended to be reduced, as was leaf area relative to control plants. The significantly increased fruit yields were thus accomplished without accompanying increases in leaf photosynthesis and leaf areas. Juice at harvest had equal levels of sugars (Brix) and somewhat higher levels of anthocyanins and total polyphenols relative to control values. The two latter trends continued for the resultant wine across two vintage years. In conclusion, three seasons of experimental trials have demonstrated that ABA application can significantly enhance yield per plant in the field-grown grape (cv. Cabernet Sauvignon) by favoring increased berry set without diminishing the quality of the fruit for winemaking use.     

Multiple mechanisms generate HLA class I altered phenotypes in laryngeal carcinomas: high frequency of HLA haplotype loss associated with loss of heterozygosity in chromosome region 6p21

Major histocompatibility complex (MHC) class I loss or downregulation in cancer cells is a major immune escape route used by a large variety of human tumors to evade anti-tumor immune responses mediated by cytotoxic T lymphocytes. Multiple mechanisms are responsible for such HLA class I alterations. However, the precise frequency of these molecular defects has not been clearly determined in tumors derived from specific tissues. To analyze such defects we aim to define the major HLA class I-altered phenotypes in different tumor types. In this paper we report on HLA class I expression in 70 laryngeal carcinomas. We used immunohistological techniques with a highly selective panel of anti-HLA monoclonal antibodies (mAb), and polymerase chain reaction (PCR) microsatellite amplification of previously selected microsatellite markers (STR) located in chromosome 6 and 15. DNA was obtained from microdissected tumor tissues and surrounding stroma to define the loss of heterozygosity (LOH) associated with chromosome 6p21. Our results showed that LOH in chromosome 6 produced HLA haplotype loss (phenotype II) in 36% of the tumors. In addition, HLA class I total loss (phenotype I) was found in 11%; HLA A or B locus downregulation (phenotype III) was detected in 20%; and HLA class I allelic loss (phenotype IV) in 10% of all cases. We sometimes observed two or more associated mechanisms in the same HLA-altered phenotype, such as LOH and HLA total loss in phenotype I. In only 23% of tumors it was not possible to identify any HLA class I alteration. We conclude that the combination of immunohistological techniques and molecular analysis of tumor DNA obtained from microdissected tumor tissues provides a means for the first time of determining the actual frequency of the major HLA class I-altered phenotypes in laryngeal carcinomas.     

Higher accumulation of F1-V fusion recombinant protein in plants after induction of protein body formation

Improving foreign protein accumulation is crucial for enhancing the commercial success of plant-based production systems since product yields have a major influence on process economics. Cereal grain evolved to store large amounts of proteins in tightly organized aggregates. In maize, γ-Zein is the major storage protein synthesized by the rough endoplasmic reticulum (ER) and stored in specialized organelles called protein bodies (PB). Zera^® (γ-Zein ER-accumulating domain) is the N-terminal proline-rich domain of γ-zein that is sufficient to induce the assembly of PB formation. Fusion of the Zera^® domain to proteins of interest results in assembly of dense PB-like, ER-derived organelles, containing high concentration of recombinant protein. Our main goal was to increase recombinant protein accumulation in plants in order to enhance the efficiency of orally-delivered plant-made vaccines. It is well known that oral vaccination requires substantially higher doses than parental formulations. As a part of a project to develop a plant-made plague vaccine, we expressed our model antigen, the Yersinia pestis F1-V antigen fusion protein, with and without a fused Zera^® domain. We demonstrated that Zera^®-F1-V protein accumulation was at least 3× higher than F1-V alone when expressed in three different host plant systems: Ncotiana benthamiana, Medicago sativa (alfalfa) and Nicotiana tabacum NT1 cells. We confirmed the feasibility of using Zera^® technology to induce protein body formation in non-seed tissues. Zera^® expression and accumulation did not affect plant development and growth. These results confirmed the potential exploitation of Zera^® technology to substantially increase the accumulation of value-added proteins in plants.     

Chain length-dependent association of distamycin-type oligopeptides with A·T and G·C pairs in polydeoxynucleotide duplexes

Different binding affinities of various distamycin analogs including the deformylated derivative with poly(dA-dC)·poly(dG-dT) were investigated using CD measurements. The inhibitory effect of distamycins on the DNAase I cleavage activity of DNA duplexes strongly supports the binding data. The base specificity of the ligand interaction with duplex DNA depends on the chain length of distamycin analogs. Netropsin, distamycin-2 and the deformylated distamycin-3 show no binding to dG·dC containing sequences at moderate ionic strength and are classified as highly dA·dT specific. In contrast distamycin having three, four or five methylpyrrolecarboxamide groups also forms more or less stable complexes with dG·dC-containing duplexes. These ligands possess a lower basepair specificity. The correlation between binding behavior and oligopeptide structure shows that presence of the number of hydrogen acceptor and donor sites determines the basepair and sequence specificity. The additional interaction with dG·dC pairs becomes essential when the number of hydrogen acceptor sites exceeds n = 3.     

Glutamate metabolism in cerebral mitochondria after ischemia and post‐ischemic recovery during aging: relationships with brain energy metabolism

Glutamate is involved in cerebral ischemic injury, but its role has not been completely clarified and studies are required to understand how to minimize its detrimental effects, contemporarily boosting the positive ones. In fact, glutamate is not only a neurotransmitter, but primarily a key metabolite for brain bioenergetics. Thus, we investigated the relationships between glutamate and brain energy metabolism in an in vivo model of complete cerebral ischemia of 15 min and during post‐ischemic recovery after 1, 24, 48, 72, and 96 h in 1‐year‐old adult and 2‐year‐old aged rats. The maximum rates (V _max) of glutamate dehydrogenase (GlDH ), glutamate‐oxaloacetate transaminase, and glutamate‐pyruvate transaminase were assayed in somatic mitochondria (FM ) and in intra‐synaptic ‘Light’ mitochondria and intra‐synaptic ‘Heavy’ mitochondria ones purified from cerebral cortex, distinguishing post‐ and pre‐synaptic compartments. During ischemia, none of the enzymes were modified in adult animals. In aged ones, glutamate‐oxaloacetate transaminase was increased in FM and GlDH in intra‐synaptic ‘Heavy’ mitochondria, stimulating glutamate catabolism. During post‐ischemic recovery, FM did not show modifications at both ages while, in intra‐synaptic mitochondria of adult animals, glutamate catabolism was increased after 1 h of recirculation and decreased after 48 and 72 h, whereas it remained decreased up to 96 h in aged rats. These results, with those previously published about Krebs’ cycle and Electron Transport Chain (Villa et al ., [2013] Neurochem. Int . 63, 765–781), demonstrate that: (i) V _max of energy‐linked enzymes are different in the various cerebral mitochondria, which (ii) respond differently to ischemia and post‐ischemic recovery, also (iii) with respect to aging.

     

High evolutionary rates and the origin of the Rosso Ammonitico Veronese Formation (Middle-Upper Jurassic of Italy) reptiles

The fossil record of metriorhynchids and plesiosaurians from the Rosso Ammonitico Veronese Formation (RAVFm, Middle–Upper Jurassic, Italy) is represented by elements collected between the eighteenth and twentieth centuries. All the metriorhynchid material is referred to the genus Neptunidraco. The first RAVFm plesiosaurian material was collected in the nineteenth century and referred to Plesiosaurus: elements are here described and interpreted as a chimerical association of crocodylomorph and plesiosaurian bones, providing the first co-occurrence of these clades in the RAVFm. The second plesiosaurian is the associated skeleton that we refer to Anguanax zignoi gen. et sp. nov. Bayesian phylogenetic analysis confirms the basal geosaurine affinities of Neptunidraco resulted by parsimony analysis. Using both methods, Anguanax was recovered as a basal pliosaurid, sister group of the clade including Marmornectes and Thalassophonea. Bayesian inference methods indicate that both Italian lineages diverged from other known lineages between 176 and 171 Mya, also showing divergence rates significantly higher than any other representative of their respective clades. We suggest a phase of rapid evolutionary adaptation to deeper marine environments in the ancestors of the Rosso Ammonitico Veronese reptiles as a response to the latest Liassic regressive regime in Northern Tethys.