Principles of Laser Spectroscopy and Quantum Optics is an essential textbook for graduate students studying the interaction of optical fields with atoms. It also serves as an ideal reference text for ...researchers working in the fields of laser spectroscopy and quantum optics.
The book provides a rigorous introduction to the prototypical problems of radiation fields interacting with two- and three-level atomic systems. It examines the interaction of radiation with both atomic vapors and condensed matter systems, the density matrix and the Bloch vector, and applications involving linear absorption and saturation spectroscopy. Other topics include hole burning, dark states, slow light, and coherent transient spectroscopy, as well as atom optics and atom interferometry. In the second half of the text, the authors consider applications in which the radiation field is quantized. Topics include spontaneous decay, optical pumping, sub-Doppler laser cooling, the Heisenberg equations of motion for atomic and field operators, and light scattering by atoms in both weak and strong external fields. The concluding chapter offers methods for creating entangled and spin-squeezed states of matter.
Instructors can create a one-semester course based on this book by combining the introductory chapters with a selection of the more advanced material. A solutions manual is available to teachers.
Rigorous introduction to the interaction of optical fields with atoms
Applications include linear and nonlinear spectroscopy, dark states, and slow light
Extensive chapter on atom optics and atom interferometry
Conclusion explores entangled and spin-squeezed states of matter
Solutions manual (available only to teachers)
The conversion of supplemental greenhouse light energy into biomass is not always optimal. Recent trends in global energy prices and discussions on climate change highlight the need to reduce our ...energy footprint associated with the use of supplemental light in greenhouse crop production. This can be achieved by implementing "smart" lighting regimens which in turn rely on a good understanding of how fluctuating light influences photosynthetic physiology. Here, a simple fit-for-purpose dynamic model is presented. It accurately predicts net leaf photosynthesis under natural fluctuating light. It comprises two ordinary differential equations predicting: 1) the total stomatal conductance to CO2 diffusion and 2) the CO2 concentration inside a leaf. It contains elements of the Farquhar-von Caemmerer-Berry model and the successful incorporation of this model suggests that for tomato (Solanum lycopersicum L.), it is sufficient to assume that Rubisco remains activated despite rapid fluctuations in irradiance. Furthermore, predictions of the net photosynthetic rate under both 400ppm and enriched 800ppm ambient CO2 concentrations indicate a strong correlation between the dynamic rate of photosynthesis and the rate of electron transport. Finally, we are able to indicate whether dynamic photosynthesis is Rubisco or electron transport rate limited.
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In
C. elegans, the transcription factor DAF-16 promotes longevity in response to reduced insulin/IGF-1 signaling or germline ablation. In this study, we have asked how different tissues interact to ...specify the lifespan of the animal. We find that several tissues act as signaling centers. In particular, DAF-16 activity in the intestine, which is also the animal's adipose tissue, completely restores the longevity of
daf-16(−) germline-deficient animals, and increases the lifespans of
daf-16(−) insulin/IGF-1-pathway mutants substantially. Our findings indicate that DAF-16 may control two types of downstream signals: DAF-16 activity in signaling cells upregulates DAF-16 in specific responding tissues, possibly via regulation of insulin-like peptides, and also evokes DAF-16-independent responses. We suggest that this network of tissue interactions and feedback regulation allows the tissues to equilibrate and fine-tune their expression of downstream genes, which, in turn, coordinates their rates of aging within the animal.
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In
C. elegans, removing the germ cells extends life span by triggering the nuclear localization and activation of the DAF-16/FOXO transcription factor in the intestine. In this study, we identify and ...analyze genes required for germline removal to extend life span. We find that the reproductive system communicates with the intestine through lipophilic-hormone signaling and that a gene called
kri-1 is likely to act in the intestine to promote DAF-16 nuclear localization in response to this signal. This lipophilic-signaling pathway and
kri-1 are not required for DAF-16's nuclear localization and life-span extension in animals with decreased insulin/IGF-1 signaling. Thus, this pathway specifically enables the integration of cues from the reproductive system with central DAF-16-activation pathways to influence the aging of the animal.
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Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining ...(NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR-based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator-like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology.
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The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. ...Currently, the most commonly used assay employs "mismatch nucleases" T7E1 or "Surveyor" that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR) can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an "all-in-one" CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation.
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Genetic diseases of blood cells are prime candidates for treatment through ex vivo gene editing of CD34
hematopoietic stem/progenitor cells (HSPCs), and a variety of technologies have been proposed ...to treat these disorders. Sickle cell disease (SCD) is a recessive genetic disorder caused by a single-nucleotide polymorphism in the β-globin gene (HBB). Sickle hemoglobin damages erythrocytes, causing vasoocclusion, severe pain, progressive organ damage, and premature death. We optimize design and delivery parameters of a ribonucleoprotein (RNP) complex comprising Cas9 protein and unmodified single guide RNA, together with a single-stranded DNA oligonucleotide donor (ssODN), to enable efficient replacement of the SCD mutation in human HSPCs. Corrected HSPCs from SCD patients produced less sickle hemoglobin RNA and protein and correspondingly increased wild-type hemoglobin when differentiated into erythroblasts. When engrafted into immunocompromised mice, ex vivo treated human HSPCs maintain SCD gene edits throughout 16 weeks at a level likely to have clinical benefit. These results demonstrate that an accessible approach combining Cas9 RNP with an ssODN can mediate efficient HSPC genome editing, enables investigator-led exploration of gene editing reagents in primary hematopoietic stem cells, and suggests a path toward the development of new gene editing treatments for SCD and other hematopoietic diseases.
Please cite this paper as: Klemens C, Berman D, Mozurkewich E. The effect of perinatal omega‐3 fatty acid supplementation on inflammatory markers and allergic diseases: a systematic review. BJOG ...2011;118:916–925.
Background Maternal supplementation with omega‐3 polyunsaturated fatty acids (n‐3 PUFA) may modulate immune responses and allergy in neonates and children.
Objective To determine if n‐3 PUFA supplementation during pregnancy and lactation reduces risk for childhood allergic disease.
Search strategy We searched Medline and all evidence‐based medicine reviews for randomised controlled trials comparing the effects of n‐3 PUFA and placebo supplementation during pregnancy and/or lactation on childhood allergic diseases and inflammatory cytokines.
Selection criteria We included studies reporting on food allergy, response to the egg skin prick test (SPT), atopy and asthma in infancy and childhood as well as production of interleukin‐13 and interferon‐gamma, two cytokines involved in the pathogenesis of asthma. For assessment of inclusion, two authors reviewed all s for suitability and independently extracted data.
Data collection and analysis Two‐by‐two tables were constructed and odds ratios (OR) were calculated for the outcomes: response to the SPT, food allergy, atopy and asthma in childhood. The assays differed so data on inflammatory markers were reported in narrative form.
Main results Five randomised controlled trials (n = 949) were included. n‐3 PUFA supplementation during pregnancy reduced 12‐month prevalence of positive egg SPT (two trials, 12/87 versus 32/100, OR 0.33, 95% CI 0.16, 0.70) and childhood asthma (two trials, 10/303 versus 17/179, OR 0.349, 95% CI 0.154, 0.788) and significantly reduced cord blood interleukin‐13 levels. Supplementation during lactation did not prevent asthma, food allergy or atopy.
Conclusion n‐3 PUFA supplementation during pregnancy decreases childhood asthma and response to SPT.
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NGLY1 deficiency, a rare disease with no effective treatment, is caused by autosomal recessive, loss-of-function mutations in the N-glycanase 1 (NGLY1) gene and is characterized by global ...developmental delay, hypotonia, alacrima, and seizures. We used a Drosophila model of NGLY1 deficiency to conduct an in vivo, unbiased, small molecule, repurposing screen of FDA-approved drugs to identify therapeutic compounds. Seventeen molecules partially rescued lethality in a patient-specific NGLY1 deficiency model, including multiple serotonin and dopamine modulators. Exclusive dNGLY1 expression in serotonin and dopamine neurons, in an otherwise dNGLY1 deficient fly, was sufficient to partially rescue lethality. Further, genetic modifier and transcriptomic data supports the importance of serotonin signaling in NGLY1 deficiency. Connectivity Map analysis identified glycogen synthase kinase 3 (GSK3) inhibition as a potential therapeutic mechanism for NGLY1 deficiency, which we experimentally validated with TWS119, lithium, and GSK3 knockdown. Strikingly, GSK3 inhibitors and a serotonin modulator rescued size defects in dNGLY1 deficient larvae upon proteasome inhibition, suggesting that these compounds act through NRF1, a transcription factor that is regulated by NGLY1 and regulates proteasome expression. This study reveals the importance of the serotonin pathway in NGLY1 deficiency, and serotonin modulators or GSK3 inhibitors may be effective therapeutics for this rare disease.
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Depositional ages and provenance of metasedimentary rocks provide constraints on the architecture of the interface between the Slave and Rae cratons and processes related to the Thelon Orogen. ...Clastic rocks analysed from the central Thelon tectonic zone are Paleoproterozoic in age and not remnants of the Archean Yellowknife Supergroup (Slave Province), as originally considered. Two assemblages are recognized. An older clastic assemblage deposited after 2.09 Ga contains detrital zircon age modes of 2.3 and 2.17 Ga, with subordinate Neoarchean and Paleoarchean detritus. Its deposition is interpreted to predate Thelon magmatic activity given that (1) it lacks ca. 2.01-1.97 Ga detritus of Thelon magmatic origin, and (2) correlative clastic rocks occur as inclusions in Thelon plutons and contain ca. 2.0 Ga metamorphic monazite. This assemblage is correlative with both the Mary Frances and Rutledge River groups, establishing a >800 km long basin at ca. 2.1 Ga that received detritus from the western Rae and (or) Buffalo Head terrane(s). Separation from the Slave Craton at this time is consistent with the absence of any Slave-affinity detritus. A younger assemblage deposited after 1.95 Ga and prior to 1.91 Ga contains mainly 2.02-1.95 Ga detrital zircon, age modes comparable with adjacent Thelon convergent-margin plutonic rocks. The younger assemblage records deposition of the uplifted and eroded Thelon magmatic arc in an intermontane or foreland basin setting during the later stages of post-collisional convergence. These U-Pb zircon data support a tectonic model for western Laurentia that reconciles differences between the Thelon and Taltson magmatic zones involving ca. 2.1 Ga rifting, ca. 2.01-1.97 Ga convergence, followed by <1.95 Ga thrust-driven exhumation.
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