From the Cover: Electronic resonance with anticorrelated pigment vibrations drives photosynthetic energy transfer outside the adiabatic framework

The delocalized, anticorrelated component of pigment vibrations can drive nonadiabatic electronic energy transfer in photosynthetic light-harvesting antennas. In femtosecond experiments, this energy transfer mechanism leads to excitation of delocalized, anticorrelated vibrational wavepackets on the ground electronic state that exhibit not only 2D spectroscopic signatures attributed to electronic coherence and oscillatory quantum energy transport but also a cross-peak asymmetry not previously explained by theory. A number of antennas have electronic energy gaps matching a pigment vibrational frequency with a small vibrational coordinate change on electronic excitation. Such photosynthetic energy transfer steps resemble molecular internal conversion through a nested intermolecular funnel.     

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device

We show how a bird’s-eye view of genomic structure can be obtained at ∼1-kb resolution from long (∼2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.Despite the sequencing of thousands of genomes (1), no human genome—reference or individual—has been described to completion (2): gaps remain in the genome reference sequence and there is a discontinuity between the resolution of next-generation sequencing and the resolution of cytogenetics. This gap leaves structure in the kilobase-to-megabase range partly unmapped. The nature and extent of highly repetitive regions—the centromeres, rDNA on the short arms of acrocentric chromosomes, the long arm of the Y chromosome—remain to be fully delineated, as do the sequences embedded in these regions. Sequencing of individual genomes (3) has also revealed that chromosome-scale amounts of sequence do not align to the human reference genome (4, 5), suggesting that substantial levels of sequence insertions are specific to individuals or subpopulations. Structural variation (SV) comprising rearrangement, loss, or gain of genomic regions is increasingly linked to phenotype and disease (6, 7). In cancer genomes, SV can be extreme (8) and difficult to deconvolve.All types and scales of SV pervade the human genome, but a single approach cannot capture them all (9). For example, though unbalanced SV can be readily ascertained by array technology, balanced SV cannot; a comprehensive analysis by paired-end sequencing is challenging and cost-prohibitive. Single-molecule optical mapping (10–13) facilitates assembly of genomes and detects SV, but haplotype phase is not preserved, because it requires construction of a consensus map from many molecules. These molecules cannot be recovered for further analysis, requiring larger amounts of sample for analysis, which may not be available, e.g., single-cell sequencing and clinical samples. An attempt to combine haplotyping and sequencing on Illumina flow cells was limited to sequencing only at the ends of short fragments (≤8 kb) (14).Microfluidic laboratory-on-a-chip devices have been used to separate individual chromosomes and extract genomic DNA (15, 16), enabling haplotype-phased genotype and sequence to be obtained. Meanwhile, laboratory-on-a-chip systems incorporating nanofluidics have been used to stretch and map DNA (17–19), but their application to detecting SV has remained theoretical due to technical limitations of the designs used. Existing platforms either do not stretch and hold DNA well enough to consistently produce accurate maps from a single molecule (20, 21), or they use inefficient labeling chemistry (22) and consequently cannot differentiate between poor matches and actual structural variation within a single molecule. These platforms also require purified input DNA, which is typically sheared during handling steps, cannot produce maps longer than a few hundred kilobases, and cannot readily recover the mapped DNA molecules to perform conventional genomic analysis. Finally, although confinement in nanochannels can provide high stretching under extreme buffer conditions (23), it is desirable to achieve full stretching independently of buffer composition.Here we describe a laboratory-on-a-chip design that overcomes these technical limitations and a procedure that offers an integrated view of human genome structure. By integrating a nanofluidic system with elongation flow into a laboratory-on-a-chip, (i) haplotype-phased chromosome substructures can be visualized on single megabase-scale molecules, (ii) structural variation ranging in size from a few kilobases to megabases can then be detected, (iii) our experimental maps can be compared with theoretical maps based on different genome assemblies, and variations can be detected, and (iv) interrogation of the same molecule can be zoomed out to the cytogenetic level and zoomed in to the sequence level.     

Comparison of ras activation during epidermal carcinogenesis in vitro and in vivo

Mouse epidermal cells have frequently been used to study the role of ras oncogenes in transformation in vivo and in vitro. After initiation with dimethylbenzanthracene (DMBA) in vivo, greater than 90% of the papillomas arising show the same A:T----T:A transversion at codon 61 of the H-ras gene, presumed to be the initiating event. On the other hand, initiation of epidermal cells in culture with carcinogens, followed by selection of initiated cells by resistance to calcium-induced differentiation, does not in general lead to the isolation of clones carrying mutant ras genes. Some other aspects of tumour progression in vivo can be reproduced using epidermal cells in culture: a rare DMBA transformant carrying the codon 61 mutation and expressing a 2:1 ratio of normal to mutant ras alleles gave rise upon transplantation to a more aggressive line in which the ratio of normal to mutant H-ras genes (and p21 products) was reversed. Similar alterations in ras gene dosage have been seen during progression of papillomas to carcinomas in vivo. We conclude that the mechanisms of initiation in vitro may differ substantially from in vivo, and depend on the particular culture conditions used. Moreover, the effects of mutant H-ras expression in mouse epidermal cells are variable depending on the genetic background of the cell.     

A controlled study of lifetime prevalence of affective and other psychiatric disorders in bulimic outpatients

The authors used structured diagnostic interviews to assess the lifetime prevalence of psychiatric disorders, by DSM-III criteria, among 70 women: 51 outpatients with active bulimia and 19 nonpatient subjects with remitted bulimia. Comparison groups consisted of 24 female outpatients with major depression and 28 nonpsychiatric control subjects. The active and remitted bulimic subjects closely resembled each other, with high lifetime rates of major affective disorder, anxiety disorders, and substance use disorders. Atypical depression was equally common among subjects with major affective disorder in all groups. These results are consistent with previous studies suggesting a phenomenologic relationship between bulimia and major affective disorder.     

Weather influences on intraocular pressure in patients with chronic glaucoma or ocular hypertension

From January 1979 to August 1984 intraocular pressure (IOP) was measured on the first Friday of each month under comparable conditions (same instruments, nearly always the same examiner) in a total of 109 patients in whom a primary chronic open-angle glaucoma or ocular hypertension had been diagnosed: The IOP was correlated to the local weather parameters (atmospheric pressure, cloud cover, relative air humidity, mean, maximum and minimum temperature, precipitation, duration of sunshine, mean and maximum wind velocity). In the large number of measurements a significant correlation was found only between IOP and atmospheric pressure: IOP was lower when air pressure was high. There was only a suggestion of a significant correlation between IOP and relative air humidity. However, further statistical analysis revealed that in fact both atmospheric pressure and relative air humidity account for only a negligible part of the variation in IOP values. From a practical point of view, therefore, the IOP of patients with primary chronic open-angle glaucoma or ocular hypertension is not influenced by weather conditions.     

Influence of early re-infusion of autologous shed mediastinal blood on clinical outcome after cardiac surgery.

Various strategies have been proposed to decrease allogeneic blood transfusion requirements after cardiac surgery. The aim of the study was to evaluate the efficacy of collected and re-infused autologous shed mediastinal blood on a patient's postoperative course. Ninety patients who underwent heart surgery with cardiopulmonary bypass (CPB) were studied. The patients were divided into two groups: Group 1 (n=41) received the centrifuged autologous shed mediastinal blood collected from the cardiotomy reservoir 4 hours after surgery; in Group 2 (n=49) all shed mediastinal blood was discarded (control group). Haemoglobin (Hb), haematocrit (Hct), C-reactive protein values, and leucocyte count were compared before surgery, at 4 h and 20 h after surgery, and on the fifth postoperative day. We have measured serum procalcitonin (PCT) concentration at 4 h and 20 h after CPB. We assessed drained blood loss within 20 postoperative hours. Leucocyte count, Hb, Hct values, C-reactive protein, and procalcitonin concentration did not differ between the groups before and at 4 h after surgery. Hb, Hct level, and leucocyte count were similar at 20 hours and on the fifth day after surgery. At 20 hours after surgery, an increase of serum PCT concentration (>0.5-2 ng/mL) was more frequent in Group 2 (58.3% vs. 33.3%; p = 0.03). On the fifth postoperative day, C-reactive protein concentration was lower in Group 1 (71.74 +/- 15.23; p <0.01) compared to Group 2 (93.53 +/- 20.3). Postoperative blood loss did not differ between the groups. Requirement for allogeneic blood transfusion was significantly lower in Group 1 (14.6% vs. 38.8%; p < 0.02). Patients in Group 1 developed less infective complications compared with Group 2 (2.4% and 16.3%, respectively; p < 0.05). The length of postoperative in-hospital stay was shorter in Group 1 compared with Group 2 (9.32 +/- 2.55 and 16.45 +/- 6.5, respectively; p < 0.05). We conclude that postoperative re-infusion of autologous red blood cells processed from shed mediastinal blood did not increase bleeding tendency and systemic inflammatory response and was effective in reducing the requirement for allogeneic transfusion, the rate of infective complications and the length of postoperative in-hospital stay.