Carrier-Envelope Phase-Dependent Strong-Field Excitation.

We present a joint experimental-theoretical study on the effect of the carrier-envelope phase (CEP) of a few-cycle pulse on the atomic excitation process. We focus on the excitation rates of argon at intensities in the transition between the multiphoton and tunneling regimes. Through numerical simulations, we show that the resulting bound-state population is highly sensitive to both the intensity and the CEP. The experimental data clearly agree with the theoretical prediction, and the results encourage the use of precisely tailored laser fields to coherently control the strong-field excitation process. We find a markedly different behavior for the CEP-dependent bound-state population at low and high intensities with a clear boundary, which we attribute to the transition from the multiphoton to the tunneling regime.

Genomics informed design of a suite of real-time PCR assays for the specific detection of each Xylella fastidiosa subspecies.

AIMS: Existing methods for the identification of the subspecies of Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and the associated plant health response to outbreaks and interceptions. METHODS AND RESULTS: Diagnostic markers were identified using a comparative genomics approach to allow fine differentiation of the very closely related subspecies. Five qPCR assays were designed to allow specific detection of X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, X. fastidiosa subsp. pauca, X. fastidiosa subsp. morus and X. fastidiosa subsp. sandyi. All assays were validated according to the European and Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2). CONCLUSIONS: All of the assays were shown to be specific to the target subspecies and all the assays could be used to detect femtogram quantities of X. fastidiosa DNA. SIGNIFICANCE AND IMPACT OF THE STUDY: At present, diagnosing the subspecies of X. fastidiosa requires multiple conventional PCR assays (although only available for three of the five subspecies) or multi-locus sequence typing which takes several days. By comparison, the new assays provide a substantial reduction in the turnaround time for direct identification to the subspecies level in as little as 75 min.

Relativistic Nondipole Effects in Strong-Field Atomic Ionization at Moderate Intensities.

We present a detailed experimental and theoretical study on the relativistic nondipole effects in strong-field atomic ionization by near-infrared linearly polarized few-cycle laser pulses in the intensity range of 10^{14}-10^{15} W/cm^{2}. We record high-resolution photoelectron momentum distributions of argon using a reaction microscope and compare our measurements with a truly ab initio fully relativistic 3D model based on the time-dependent Dirac equation. We observe counterintuitive peak shifts of the transverse electron momentum distribution in the direction opposite to that of laser propagation as a function of laser intensity and demonstrate an excellent agreement between the experimental results and theoretical predictions.

Laser-Based Metastable Krypton Generation.

We demonstrate the generation of metastable krypton in the long-lived 1s^{5} state using laser excitation. The atoms are excited through a two-photon absorption process into the 2p^{6} state using a pulsed optical parametric oscillator laser operating near 215 nm, after which the atoms decay quickly into the metastable state with a branching ratio of 75%. The interaction dynamics are modeled using density matrix formalism and, by combining this with experimental observations, we are able to calculate photoionization and two-photon absorption cross sections. When compared to traditional approaches to metastable production, this approach shows great potential for high-density metastable krypton production with minimal heating of the sample. Here, we show metastable production efficiencies of up to 2% per pulse. The new experimental results gained here, when combined with the density matrix model we have developed, suggest that fractional efficiencies up to 30% are possible under optimal conditions.

The complete genome sequence of Piper yellow mottle virus (PYMoV).

This study reports the first complete genome sequence of Piper yellow mottle virus (PYMoV, KC808712) identified in black pepper. The genome is 7,622 nucleotides long, possessing four open reading frames (ORFs). ORF1, ORF2 and ORF4 of PYMoV are reported as hypothetical proteins of unknown function with a predicted molecular mass of 15.7, 17.1 and 17.9 kDa, respectively. ORF3 of PYMoV encodes a polyprotein of 218.6 kDa and consists of a viral movement protein (MP), trimeric dUTPase, zinc finger, retropepsin, RT-LTR, and RNAse H. Detailed PYMoV genome analysis confirmed that it is a member of the family Caulimoviridae, genus Badnavirus. Fragments of two additional novel sequences resembling those found in members of the family Caulimoviridae were also identified in the black pepper sample, and the viruses from which they were derived were tentatively named Piper DNA virus 1 and 2.

The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses.

The complete nucleotide sequences of RNA 1 and RNA 2 of the nepovirus potato black ringspot virus (PBRSV) from two different isolates were determined, as well as partial sequences from two additional isolates. RNA1 is 7,579-7,598 nucleotides long and contains one single open reading frame (ORF), which is translated into a large polyprotein with 2,325 amino acids and a molecular weight of 257 kDa. The complete sequence of RNA2 ranges from 3857 to 3918 nt between the different isolates. It encodes a polyprotein of 1079-1082 amino acids with a molecular weight of 120 kDa. Sequence comparison using the Pro-Pol region and CP showed that all four isolates formed two distinct groups, corresponding to potato and arracacha, that were closely related to each other and also to tobacco ringspot virus (TRSV). Comparing our data to those obtained with other nepoviruses, our results confirm that PBRSV belongs to a distinct species and is a member of subgroup A in the genus Nepovirus based on its RNA2 size, genome organization, and nucleotide sequence.

Complete genome sequence of arracacha virus B: a novel cheravirus.

The complete genome sequences of RNA1 and RNA2 of the oca strain of the potato virus arracacha virus B were determined using next-generation sequencing. The RNA1 molecule is predicted to encode a 259-kDa polyprotein with homology to proteins of the cheraviruses apple latent spherical virus (ALSV) and cherry rasp leaf virus (CRLV). The RNA2 molecule is predicted to encode a 102-kDa polyprotein which also has homology to the corresponding protein of ALSV and, to a lesser degree, CRLV (30 % for RNA1, 24 % for RNA2). Detailed analysis of the genome sequence confirms that AVB is a distinct member of the genus Cheravirus.

Renal hypertension in rats immunized against angiotensin I and angiotensin II.

Rats, actively immunized against angiotensin I (AI) and angiotensin II (AII), were subjected to unilateral renal artery constriction to determine whether the resulting hypertension, which may still ensue in the animal immunized against AII, could be prevented by such combined immunity. Sustained immunity to both AI and AII neither changed preoperative blood pressures of the rats from those of control mock-immunized rats nor altered the incidence or severity of renal dip hypertension. Vascular hyperresponsiveness to small quantities of free angiotensin could not be invoked to explain the hypertension, for there was no significant difference between mock-immunized hypertensive animals, and those remaining normotensive, regarding pressor sensitivity to intravenous AI, AII, renin, and norepinephrine. (AI + AII)-immunized hypertensive rats required AI doses averaging 260 times greater than nonimmune hypertensives to elicit equipressor responses, and were refractory to renin, but not to norepinephrine. Thus, while previous studies have not excluded direct participation of endogenous AI in renal clip hypertension in rats, evidence from our experiments makes it extremely difficult to sustain any pressor function therein for circulating AI or AII. Our results also preclude involvement of AII produced from circulating AI by conversion within arteriolar walls, close to receptor sites, since AI immunity would block this mechanism of action.

Self-focusing in air with phase-stabilized few-cycle light pulses.

We investigate the nonlinear optical phenomenon of self-focusing in air with phase-stabilized few-cycle light pulses. This investigation looks at the role of the carrier-envelope phase by observing a filament in air, a nonlinear phenomenon that can be utilized for few-cycle pulse compression [Appl. Phys. B79, 673 (2004)]. We were able to measure the critical power for self-focusing in air to be 18+/-1 GW for a 6.3 fs pulse centered at 800 nm. Using this value and a basic first-order theory, we predicted that the self-focusing distance should deviate by 790 mum as the carrier-envelope phase is shifted from 0 to pi/2 rad. In contrast, the experimental results showed no deviation in the focus distance with a 3sigma upper limit of 180 mum. These counterintuitive results show the need for further study of self-focusing dynamics in the few-cycle regime.

The complete genome sequence of Canna yellow streak virus.

Canna yellow streak virus (Potyvirus, Potyviridae) was sequenced using the novel method of next-generation pyrosequencing. The complete genome was found to be 9,502 nucleotides excluding the poly-A tail with a predicted genome organisation typical for a member of the genus Potyvirus. As with other potyviruses that infect monocotyledons, some of the predicted cleavage sites of the polyprotein genome were unusual, such as a glutamic acid/threonine (E/T) between the CI and 6K2 proteins and a glutamic acid/aspartic acid (E/D) between the NIa and NIb proteins. Evidence of the presence of endogenous pararetroviruses in the canna genome was found from the large number of sequences obtained with this method.

The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence.

The complete genome sequence for an isolate of the Ugandan and Tanzanian strain types of Cassava brown streak virus have been determined using the novel approach of non-directed next generation sequencing. Comparison of the genome sequences revealed that CBSV is highly heterogeneous at the isolate level as well as the strain level. The isolate of the Ugandan strain was found to have a genome 9,070 nucleotides long coding for a polypeptide with 2,902 amino acid residues. The isolate of the Tanzanian strain was 9,008 nucleotides long and coded for a polypeptide with 2,916 amino acid residues. Nucleotide identity between the isolates across the genome was 76%, with protein encoding regions 57-77% and individual proteins had 65-91% amino acid similarity. In addition between the two strains four protein products (PIPO, CI, NIa-Vpg and coat protein) varied in size and an unusual HAM1-like protein, whilst of identical nucleotide length, was found to have the lowest homology. The implication of diversity of CBSV is discussed in the context of speciation, evolution, development of diagnostics, and breeding for resistance.

Early eutrophication in the lower great lakes:.

New Evidence from Biogenic Silica in Sediments New evidence from studies of biogenic silica and diatoms in sediment cores indicates that eutrophication in the lower Great Lakes resulted from nutrient enrichment associated with early settlement and forest clearance. Diatom production peaked from 1820 to 1850 in Lake Ontario, at about 1880 in Lake Erie, but not until 1970 in Lake Michigan. This is the first reported sediment record of the silica-depletion sequence for the Great Lakes.

Absolute metastable atom-atom collision cross section measurements using a magneto-optical trap.

We present a new technique to measure absolute total collision cross sections from metastable neon atoms. The technique is based on the observation of the decay rate of trapped atoms as they collide with room temperature atoms. We present the first measurement of this kind using trapped neon atoms in the (3)P(2) metastable state colliding with thermal ground state argon. The measured cross section has a value of 556+/-26 A(2).

Fas-mediated apoptosis in human prostatic carcinoma cell lines occurs via activation of caspase-8 and caspase-7.

We previously demonstrated that treatment with cycloheximide (CHX) converted the phenotype of Fas-resistant human prostatic carcinoma cell lines to Fas-sensitive and that resistance to Fas-mediated apoptosis was due to a dominant-negative protein(s). In this study, we investigated the sequential activation of caspase family members, to gain insight into the likely site of action of the suppressor protein(s). We did not find Tyr-Val-Ala-Aspase activity in any of the cell lines examined. Time-dependent Asp-Glu-Val-Aspase activity was detected during Fas-mediated apoptosis in Fas-sensitive cell lines PC3 and ALVA31. Asp-Glu-Val-Aspase activity in Fas-resistant cell lines DU145 and JCA1, was detected only under combined treatment with CHX and anti-Fas agonistic mAb. In experiments with caspase inhibitors we show that Fas-mediated apoptosis in PC3 is mainly executed by the caspase-3 subfamily, but another member(s) of the caspase family may be involved in Fas-mediated apoptosis in ALVA31, DU145, and JCA1. Western blot analysis revealed that Fas-ligation activated caspase-7, but not caspase-3. The activated form of caspase-8 was detected in DU145 only after 4 h of simultaneous treatment with CHX and anti-Fas mAb, whereas in PC3 caspase-8 was found to be activated after 1 h of Fas-ligation. We have also found that treatment with staurosporin did not activate caspase-8, whereas staurosporin induced apoptosis at the same levels in both Fas-resistant and Fas-sensitive cell lines. These results suggest that an inhibitory protein(s), which suppresses apoptosis in Fas-resistant cell lines, presumably acts at the apex of apoptotic cascade by preventing the activation of caspase-8.

Dominant nature of the resistance to Fas- and tumor necrosis factor-alpha-mediated apoptosis in human prostatic carcinoma cell lines.

We have recently found (O. W. Rokhlin et al., Cancer Res., 57: 1758-1768, 1997) that, although Fas ligation induced apoptosis in two of six human prostatic carcinoma cell lines investigated, the apoptotic machinery involved in Fas-mediated killing is already in place in Fas-resistant cell lines. Here, we investigated Fas- and tumor necrosis factor-alpha (TNF-alpha)-mediated apoptosis in cell hybrids between resistant (DU145 and JCA1) and sensitive (ALVA31 and PC3) cell lines. All three types of hybrid cells investigated, F1(DU145 x PC3), F1(JCA1 x PC3), and F1(JCA1 x ALVA31), were found to be resistant to Fas- and TNF-alpha-mediated apoptosis at the same level as the corresponding parental resistant cell lines. These results indicate that resistance to Fas- and TNF-alpha-mediated apoptosis dominates over sensitivity in cell hybrids and suggest that resistance may be regulated by an apoptosis suppressor factor or factors acting in resistant but not in sensitive cells.

Fas-mediated apoptosis in human prostatic carcinoma cell lines.

Of six prostatic carcinoma cell lines examined (ALVA31, DU145, JCA1, LNCaP, ND1, and PC3) by flow cytometric analysis, all were found to be positive for Fas antigen. Furthermore, of the prostate tissue specimens studied (six cases), all revealed Fas expression in benign and malignant epithelial cells. The agonistic anti-Fas monoclonal antibody (IPO-4) induced apoptosis in only two of six cell lines investigated, PC3 and ALVA31. PCR analysis indicated that all cell lines expressed normal transmembrane and death domains of Fas antigen. Using Western blot analysis, we found abundant expression of p53 in the cytoplasm of two Fas-resistant cell lines, DU145 and ND1, and did not find p53 in two Fas-sensitive cell lines, PC3 and ALVA31. Western blot and PCR analysis did not show consistent differences between cell lines examined in the expression of Bcl-2, Bcl-X(L), Bcl-X(S), and Bak. In contrast, Bax protein was not detected in two Fas-resistant cell lines, DU145 and ND1. We also showed that three Fas-resistant cell lines, DU145, ND1, and JCA1, expressed CD40, whereas the two Fas-sensitive cell lines, PC3 and ALVA31, were CD40 negative. Fas-sensitive cell lines were transfected with the cDNA encoding CD40, and the CD40-positive transfectant became more resistant to growth inhibition mediated by treatment with TNF-alpha and anti-Fas monoclonal antibody. Treatment with cycloheximide converted the phenotype of resistant cell lines from Fas resistant to Fas sensitive. Moreover, anti-Fas treatment of both resistant and sensitive cell lines induced rapid tyrosine phosphorylation or dephosphorylation of multiple proteins. These results suggest that the apoptotic machinery involved in DNA fragmentation is already in place in Fas-resistant cell lines, and thus, Fas-mediated apoptosis could be a target for therapeutic intervention.

The interaction of excited atoms and few-cycle laser pulses.

This work describes the first observations of the ionisation of neon in a metastable atomic state utilising a strong-field, few-cycle light pulse. We compare the observations to theoretical predictions based on the Ammosov-Delone-Krainov (ADK) theory and a solution to the time-dependent Schrödinger equation (TDSE). The TDSE provides better agreement with the experimental data than the ADK theory. We optically pump the target atomic species and measure the ionisation rate as the a function of different steady-state populations in the fine structure of the target state which shows significant ionisation rate dependence on populations of spin-polarised states. The physical mechanism for this effect is unknown.

p53 is involved in tumor necrosis factor-alpha-induced apoptosis in the human prostatic carcinoma cell line LNCaP.

The human prostatic carcinoma cell line LNCaP is sensitive to TNF-alpha treatment and expresses wild-type p53. To analyse the possible role of p53 in TNF-alpha-mediated apoptosis, we generated a derivative of LNCaP, LN-56, expressing a dominant-negative element of p53, GSE56. P53 inactivation in LN-56 was associated with an increased resistance to apoptosis induced by TNF-alpha. Surface expression of TNF-alpha receptors was unchanged in LN-56 compared to LNCaP. TNF-alpha treatment resulted in accumulation of p53 in LNCaP and upregulation of p21/WAF1. Activation of caspase-7 and PARP proteolysis were delayed in LN-56 under TNF-alpha treatment. TNF-alpha-induced apoptosis in LNCaP cells was accompanied by caspase-dependent proteolysis of p21/WAF1 and Rb, which was significantly attenuated in LN-56. Cytochrome c release was induced by TNF-alpha treatment in both cell lines, but caspase-9 was not activated. LNCaP and LN-56 were injected s.c. in nude mice and tumors were identified in all LN-56, but not LNCaP, bearing mice indicating that p53 plays an important role in growth control of prostatic neoplasms. Interestingly, accumulation of p53 in TNF-alpha-treated LNCaP cells was decreased in the presence of the caspase inhibitor Z-VAD-FMK, suggesting a new role of activated caspases in acceleration of p53 response. In summary, these results indicate that p53 is involved in TNF-alpha-mediated apoptosis in LNCaP.

Lipopolysaccharide decreases oxygen consumption by Mono Mac 6 cells; an electron paramagnetic resonance oximetry study.

The rate of oxygen consumption in the human acute monocytic leukemia-derived cell line, Mono Mac 6, in response to lipopolysaccharide (LPS) in vitro was measured by electron paramagnetic resonance spectroscopy using an oxygen-sensitive spin-label, 4-oxo-2,2,6,6-tetramethylpiperidine-d16-1-oxyl (15N-PDT). Lipopolysaccharide impaired oxygen consumption in a dose-dependent manner which was shown to be mediated by mitochondrial dysfunction and could be augmented by pretreatment of the cells with interferon-gamma. Treatment of the cells with anti-CD14 monoclonal antibody failed to inhibit the LPS-induced effects on cellular respiration. These results suggest that LPS can directly reduce normal cellular oxygen consumption possibly via a CD14-independent pathway. This alteration of mitochondrial function by LPS may be responsible for the observed cell damage during sepsis.

A soluble neuronal factor alters contractile function of ventricular myocytes without effect on troponin T isoform expression.

OBJECTIVE: The purpose of this investigation was to establish a model system to facilitate identification of the sympathetic neuronal factor(s) that promotes improved contractility in neonatal cardiac myocytes. Conditioned medium from PC12 cells with sympathetic phenotype served as the source of the neuronal factor. METHODS: Contraction frequency, amplitude and velocity of cultured neonatal rat cardiac myocytes were measured by online video analysis. Interventions included in vitro sympathetic innervation, exposure to PC12 conditioned medium, neurotransmitters and antagonists. Metabolic activity was assayed by 2-deoxyglucose uptake. Troponin T isoform expression was analyzed by SDS-polyacrylamide gel electrophoresis. RESULTS: Medium conditioned by neuronal PC12 cells induced contractility changes similar to those induced by in vitro sympathetic innervation. These effects of PC12 conditioned medium and innervation were not suppressed by adrenergic or muscarinic antagonists nor reproduced by neuropeptide Y or somatostatin. Neuronal PC12 conditioned medium but not chromaffin PC12 conditioned medium, increased metabolic activity of the myocytes as detected by [3H]-2-deoxyglucose, indicating that the effect was specific to the neuronal PC12 cells. The in vitro switch of troponin T isoform expression was not altered by exposure to PC12 conditioned medium. CONCLUSIONS: Increased contractile function induced by sympathetic innervation is reproduced by PC12 conditioned medium, but neither is mediated by sympathetic or muscarinic neurotransmitters. Troponin T isoform expression is not related to the contractility changes. This model system will allow identification of the factor(s).