Physiology-phenology interactions in a productive semi-arid pine forest

This study explored possible advantages conferred by the phase shift between leaf phenology and photosynthesis seasonality in a semi-arid Pinus halepensis forest system, not seen in temperate sites. Leaf-scale measurements of gas exchange, nitrogen and phenology were used on daily, seasonal and annual time-scales. Peak photosynthesis was in late winter, when high soil moisture, mild temperatures and low leaf vapour pressure deficit (D(L)) allowed high rates associated with high water- and nitrogen-use efficiencies. Self-sustained new needle growth through the dry and hot summer maximized photosynthesis in the following wet season, without straining carbon storage. Low rates of water loss were associated with increasing sensitivity of stomatal conductance (g(s)) to soil moisture below a relative extractable water (REW) of 0.4, and decreased g(s )sensitivity to D(L) below REW of approx. 0.2. This response was captured by the modified Ball-Berry (Leuning) model. While most physiological parameters and responses measured were typical of temperate pines, the photosynthesis-phenological phasing contributed to high productivity under warm-dry conditions. This contrasts with reported effects of short-term periodical droughts and could lead to different predictions of the effect of warming and drying climate on pine forest productivity.     

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high‐quality 313.4‐Mb genome sequence of a bottle gourd inbred line, USVL1VR‐Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome‐level syntenic relationships between bottle gourd and other cucurbits, as well as lineage‐specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring‐spot virus (PRSV) resistance in bottle gourd, to a 317.8‐kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker‐assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high‐quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.     

Rate of homologous chromosome bivalents in spermatocytes may predict completion of spermatogenesis in azoospermic men

Abstract.The rate of bivalent formation during meiosis was correlated with the presence and amount of spermatozoa in the testes of azoospermic men. Four pairs of chromosomes, X-Y, 9, 15, and 18, were evaluated. In addition, left and right testes were compared. Three biopsies from each testis were undertaken to extract spermatozoa for intracytoplasmic sperm injection. In addition, one sample from each testis was used for histological definition, spermatozoa count and detection of chromosome bivalents in spermatocytes. A significantly higher rate of bivalents of all homologous chromosomes was found whenever spermatozoa were detected. The rate of bivalent X-Y was found to be the most sensitive predictor for detection of spermatozoa, with a cut-off value of 47%. The R(2) was 27% ( P=0.003) for the percent of spermatozoa in the minced sample as well as the number of mature spermatids per tubule in the histological section. All pairs of testes were in concord in regard to the likelihood of finding spermatozoa. In the testes where no spermatozoa were found on biopsy, the rate of X-Y bivalent indicated the presence of spermatozoa in the opposite side. Thus, it may be concluded that the rate of X-Y bivalent formation in spermatocytes may predict the presence and amount of spermatozoa in the testicular tissue of azoospermic men. It is suggested that when no spermatozoa are located by testicular fine-needle aspiration, X-Y bivalent evaluation may be conducted if spermatocytes are evinced. A high rate of X-Y bivalents may impel one to continue with testicular open biopsies.     

Phenols and phenol oxidases are involved in cadmium accumulation in the water plants Nymphoides peltata (Menyanthaceae) and Nymphaeae (Nymphaeaceae)

This comparative study investigates the mechanism of cadmium accumulation in the semiaquatic plant Nymphoides peltata (Menyanthaceae) and the aquatic plant Nymphaea (Nymphaeaceae). It was conducted as part of an ongoing study of the use of water plants for phytoremediation. Epidermal structures, known as hydropotes, are located on the abaxial epidermis of the leaf laminae of Nymphoides peltata and are shown to contain phenols, peroxidase and polyphenol oxidase activities. When plants are subjected to 50 mg/l of cadmium in the growth medium, these hydropotes accumulate cadmium. Cadmium-induced increases in phenols, peroxidase and polyphenol oxidase activities were determined in plant extracts. Cadmium binding by polymerized phenols was demonstrated in vivo. In comparison with Nymphaeae epidermal glands, N. peltata hydropotes are larger, open, and create bigger crystal, the latter principally composed of calcium and, proportionally, less cadmium. Although both plants showed similar levels of cadmium accumulation, N. peltata was sensitive while Nymphaeae was resistant to this cadmium level. It is suggested that in these water plants the main mechanism for cadmium accumulation is based on the trapping of cadmium crystals by polymerized phenols in specialized epidermal structures and this is due to peroxidase and polyphenol oxidase activities. Nymphaeae, with greater peroxidase activity and more polyphenols, is more resistant to this heavy metal than N. peltata.     

Damped oscillations in the adaptive response of the iron homeostasis network of E. coli

Living organisms often have to adapt to sudden environmental changes and reach homeostasis. To achieve adaptation, cells deploy motifs such as feedback in their genetic networks, endowing the cellular response with desirable properties. We studied the iron homeostasis network of E. coli, which employs feedback loops to regulate iron usage and uptake, while maintaining intracellular iron at non‐toxic levels. Using fluorescence reporters for iron‐dependent promoters in bulk and microfluidics‐based, single‐cell experiments, we show that E. coli cells exhibit damped oscillations in gene expression, following sudden reductions in external iron levels. The oscillations, lasting for several generations, are independent of position along the cell cycle. Experiments with mutants in network components demonstrate the involvement of iron uptake in the oscillations. Our findings suggest that the response is driven by intracellular iron oscillations large enough to induce nearly full network activation/deactivation. We propose a mathematical model based on a negative feedback loop closed by rapid iron uptake, and including iron usage and storage, which captures the main features of the observed behaviour. Taken together, our results shed light on the control of iron metabolism in bacteria and suggest that the oscillations represent a compromise between the requirements of stability and speed of response.     

Promotion of hematopoietic stem cell differentiation in vitro by a soluble mediator,allogeneic effect factor

This study was designed to investigate the effects of allogeneic effect factor (AEF), a soluble mediator derived from short-term mixed lymphocyte cultures (MLC) of in vitro alloantigen-primed T cells, on cultures of murine bone marrow cells. Cultures established under suboptimal conditions namely, in the absence of a pre-established adherent cell layer as required in conventional Dextertype cultures–declined and lost their stem cell activity rapidly. In contrast, supplementation of these cultures, at initiation and thereafter, with AEF, but not with T cell growth factor (TCGF), induced cell growth and proliferation for several weeks. Such AEF-supplemented cultures exhibited cellular heterogeneity and stem cell activity for significantly longer periods than the control cultures. Even in conventional Dexter cultures, established under optimal conditions, AEF had a beneficial effect on cellular growth and proliferation and myeloid progenitor cell (CFU-C) activity. Furthermore, cells capable of synergizing with suboptimal numbers of mature T cells in con A-induced mitogenic responses, shown by others to be pre-T cells, were detected in the AEF-supplemented cultures for several weeks.     

The implications of electronic health record for personalized medicine

The emerging concept of an electronic health record (EHR) targeted at a patient centric, cross-institutional and longitudinal information entity (possibly spanning the individuals lifetime) has great promise for personalized medicine. In fact, it is probably the only vehicle through which we may truly realize the personalization of medicine beyond population-based genetic profiles that are expected to become part of medication and treatment indications in the near future. The new EHR standards include mechanisms that integrate clinical data with genomic testing results obtained through applying research-type procedures, such as full DNA sequencing, to an individual patient. Although the most optimal process for the utilization of integrated clinical-genomic data in the EHR framework is still unclear, the new Health Level Seven (HL7) Clinical Genomics Draft Standard for Trial Use suggests using the 'encapsulate & bubble-up' approach, which includes two main phases: the encapsulation of raw genomic data and bubbling-up the most clinically significant portions of that data, while associating it with clinical phenotypes residing in the individual's EHR.     

Vibrationally enhanced hydrogen tunneling in the Escherichia coli thymidylate synthase catalyzed reaction

The enzyme thymidylate synthase (TS) catalyzes a complex reaction that involves forming and breaking at least six covalent bonds. The physical nature of the hydride transfer step in this complex reaction cascade has been studied by means of isotope effects and their temperature dependence. Competitive kinetic isotope effects (KIEs) on the second-order rate constant (V/K) were measured over a temperature range of 5-45 degrees C. The observed H/T ((T)V/K(H)) and D/T ((T)V/K(D)) KIEs were used to calculate the intrinsic KIEs throughout the temperature range. The Swain-Schaad relationships between the H/T and D/T V/K KIEs revealed that the hydride transfer step is the rate-determining step at the physiological temperature of Escherichia coli (20-30 degrees C) but is only partly rate-determining at elevated and reduced temperatures. H/D KIE on the first-order rate constant k(cat) ((D)k = 3.72) has been previously reported [Spencer et al. (1997) Biochemistry 36, 4212-4222]. Additionally, the Swain-Schaad relationships between that (D)k and the V/K KIEs reported here suggested that at 20 degrees C the hydride transfer step is the rate-determining step for both rate constants. Intrinsic KIEs were calculated here and were found to be virtually temperature independent (DeltaE(a) = 0 within experimental error). The isotope effects on the preexponential Arrhenius factors for the intrinsic KIEs were A(H)/A(T) = 6.8 +/- 2.8 and A(D)/A(T) = 1.9 +/- 0.25. Both effects are significantly above the semiclassical (no-tunneling) predicted values and indicate a contribution of quantum mechanical tunneling to this hydride transfer reaction. Tunneling correction to transition state theory would predict that these isotope effects on activation parameters result from no energy of activation for all isotopes. Yet, initial velocity measurements over the same temperature range indicate cofactor inhibition and result in significant activation energy on k(cat) (4.0 +/- 0.1 kcal/mol). Taken together, the temperature-independent KIEs, the large isotope effects on the preexponential Arrhenius factors, and a significant energy of activation all suggest vibrationally enhanced hydride tunneling in the TS-catalyzed reaction.     

SPAK kinase is a substrate and target of PKCtheta in T-cell receptor-induced AP-1 activation pathway

Protein kinase C-theta (PKCtheta) plays an important role in T-cell activation via stimulation of AP-1 and NF-kappaB. Here we report the isolation of SPAK, a Ste20-related upstream mitogen-activated protein kinase (MAPK), as a PKCtheta-interacting kinase. SPAK interacted with PKCtheta (but not with PKCalpha) via its 99 COOH-terminal residues. TCR/CD28 costimulation enhanced this association and stimulated the catalytic activity of SPAK. Recombinant SPAK was phosphorylated on Ser-311 in its kinase domain by PKCtheta, but not by PKCalpha. The magnitude and duration of TCR/CD28-induced endogenous SPAK activation were markedly impaired in PKCtheta-deficient T cells. Transfected SPAK synergized with constitutively active PKCtheta to activate AP-1, but not NF-kappaB. This synergistic activity, as well as the receptor-induced SPAK activation, required the PKCtheta-interacting region of SPAK, and Ser-311 mutation greatly reduced these activities of SPAK. Conversely, a SPAK-specific RNAi or a dominant-negative SPAK mutant inhibited PKCtheta- and TCR/CD28-induced AP-1, but not NF-kappaB, activation. These results define SPAK as a substrate and target of PKCtheta in a TCR/CD28-induced signaling pathway leading selectively to AP-1 (but not NF-kappaB) activation.