Quantum multimode model of elastic scattering from Bose Einstein condensates

Mean field approximation treats only coherent aspects of the evolution of a Bose Einstein condensate. However, in many experiments some atoms scatter out of the condensate. We study an analytic model of two counter-propagating atomic Gaussian wavepackets incorporating dynamics of incoherent scattering processes. Within the model we can treat processes of elastic collision of atoms into the initially empty modes, and observe how, with growing occupation, the bosonic enhancement is slowly kicking in. A condition for bosonic enhancement effect is found in terms of relevant parameters. Scattered atoms form a squeezed state that can be viewed as a multi-component condensate. Not only are we able to calculate the dynamics of mode occupation, but also the full statistics of scattered atoms.Comment: 4 pages, 4 figure

On gene dosage balance in protein complexes: a comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression.

A comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol. 2008;2:

Proteolysis of microtubule associated protein 2 and sensitivity of pancreatic tumours to docetaxel

We have studied the state of microtubule associated protein 2 (MAP2) in the pancreatic ductal adenocarcinomas P03 and P02 (sensitive and refractory to docetaxel respectively) since they express the corresponding mRNA and MAP2-related peptides. Immunohistochemical localization showed that in tumour P03 the MAP2-related peptides are highly expressed and confined to the epithelial malignant cells while in P02 the intensity of the immunostaining is lower. However, anti α-tubulin staining followed a similar pattern suggesting that the net amount of macromolecular structures in the sensitive tumour is higher than in the refractory one. This may explain its higher sensitivity to docetaxel, because tubulin assembled into microtubules is the target of the drug. We found that protein extracts from both tumours differed in their proteolytic activity on rat brain MAP2. Since the proteolysis pattern obtained was similar to the one produced by Cathepsin D, we studied the effect of MAP2 proteolysed by this enzyme on microtubule formation in vitro. Proteolysis was found to increase the tendency of tubulin to assemble into macromolecular structures (microtubules and aggregates) in the presence of docetaxel. This suggests that in vivo proteolysis of MAP2 might increase microtubule alterations and potentiate the antitumour effect of docetaxel. © 2000 Cancer Research Campaig

Logic gates at the surface code threshold: Superconducting qubits poised for fault-tolerant quantum computing

A quantum computer can solve hard problems - such as prime factoring, database searching, and quantum simulation - at the cost of needing to protect fragile quantum states from error. Quantum error correction provides this protection, by distributing a logical state among many physical qubits via quantum entanglement. Superconductivity is an appealing platform, as it allows for constructing large quantum circuits, and is compatible with microfabrication. For superconducting qubits the surface code is a natural choice for error correction, as it uses only nearest-neighbour coupling and rapidly-cycled entangling gates. The gate fidelity requirements are modest: The per-step fidelity threshold is only about 99%. Here, we demonstrate a universal set of logic gates in a superconducting multi-qubit processor, achieving an average single-qubit gate fidelity of 99.92% and a two-qubit gate fidelity up to 99.4%. This places Josephson quantum computing at the fault-tolerant threshold for surface code error correction. Our quantum processor is a first step towards the surface code, using five qubits arranged in a linear array with nearest-neighbour coupling. As a further demonstration, we construct a five-qubit Greenberger-Horne-Zeilinger (GHZ) state using the complete circuit and full set of gates. The results demonstrate that Josephson quantum computing is a high-fidelity technology, with a clear path to scaling up to large-scale, fault-tolerant quantum circuits.Comment: 15 pages, 13 figures, including supplementary materia

Rolling quantum dice with a superconducting qubit

One of the key challenges in quantum information is coherently manipulating the quantum state. However, it is an outstanding question whether control can be realized with low error. Only gates from the Clifford group -- containing $\pi$, $\pi/2$, and Hadamard gates -- have been characterized with high accuracy. Here, we show how the Platonic solids enable implementing and characterizing larger gate sets. We find that all gates can be implemented with low error. The results fundamentally imply arbitrary manipulation of the quantum state can be realized with high precision, providing new practical possibilities for designing efficient quantum algorithms.Comment: 8 pages, 4 figures, including supplementary materia

Genomic Responses to Abnormal Gene Dosage: The X Chromosome Improved on a Common Strategy

This new primer, which discusses a study by Zhang et al., provides an overview of the process by which chromosomes achieve dose compensation and the mechanisms underlying this phenomenon in Drosophila S2 cells

1+1 = 3: A Fusion of 2 Enzymes in the Methionine Salvage Pathway of Tetrahymena thermophila Creates a Trifunctional Enzyme That Catalyzes 3 Steps in the Pathway

The methionine salvage pathway is responsible for regenerating methionine from its derivative, methylthioadenosine. The complete set of enzymes of the methionine pathway has been previously described in bacteria. Despite its importance, the pathway has only been fully described in one eukaryotic organism, yeast. Here we use a computational approach to identify the enzymes of the methionine salvage pathway in another eukaryote, Tetrahymena thermophila. In this organism, the pathway has two fused genes, MTNAK and MTNBD. Each of these fusions involves two different genes whose products catalyze two different single steps of the pathway in other organisms. One of the fusion proteins, mtnBD, is formed by enzymes that catalyze non-consecutive steps in the pathway, mtnB and mtnD. Interestingly the gene that codes for the intervening enzyme in the pathway, mtnC, is missing from the genome of Tetrahymena. We used complementation tests in yeast to show that the fusion of mtnB and mtnD from Tetrahymena is able to do in one step what yeast does in three, since it can rescue yeast knockouts of mtnB, mtnC, or mtnD. Fusion genes have proved to be very useful in aiding phylogenetic reconstructions and in the functional characterization of genes. Our results highlight another characteristic of fusion proteins, namely that these proteins can serve as biochemical shortcuts, allowing organisms to completely bypass steps in biochemical pathways

A truncating variant of RAD51B associated with primary ovarian insufficiency provides insights into its meiotic and somatic functions

Primary ovarian insufficiency (POI) causes female infertility by abolishing normal ovarian function. Although its genetic etiology has been extensively investigated, most POI cases remain unexplained. Using whole-exome sequencing, we identified a homozygous variant in RAD51B –(c.92delT) in two sisters with POI. In vitro studies revealed that this variant leads to translation reinitiation at methionine 64. Here, we show that this is a pathogenic hypomorphic variant in a mouse model. Rad51bc.92delT/c.92delT mice exhibited meiotic DNA repair defects due to RAD51 and HSF2BP/BMRE1 accumulation in the chromosome axes leading to a reduction in the number of crossovers. Interestingly, the interaction of RAD51B-c.92delT with RAD51C and with its newly identified interactors RAD51 and HELQ was abrogated or diminished. Repair of mitomycin-C-induced chromosomal aberrations was impaired in RAD51B/Rad51b-c.92delT human and mouse somatic cells in vitro and in explanted mouse bone marrow cells. Accordingly, Rad51b-c.92delT variant reduced replication fork progression of patient-derived lymphoblastoid cell lines and pluripotent reprogramming efficiency of primary mouse embryonic fibroblasts. Finally, Rad51bc.92delT/c.92delT mice displayed increased incidence of pituitary gland hyperplasia. These results provide new mechanistic insights into the role of RAD51B not only in meiosis but in the maintenance of somatic genome stability.This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Grant 2014/14231-0 (to MMF); FAPESP Grant 2013/02162-8, Nucleo de Estudos e Terapia Celular e Molecular (NETCEM), Conselho Nacional de Desenvolvimento Científico e Tecnológico Grant 303002/2016- 6 (to BBM); and FAPESP Grant 2014/50137-5 (to SELA). This work was supported by MINECO (PID2020-120326RB-I00) and by Junta de Castilla y León (CSI239P18 and CSI148P20). NFM, FSS, and MRMH are supported by European Social Fund/JCyLe grants (EDU/310/2015, EDU/556/2019 and EDU/1992/2020). YBC and RSU are funded by a grant from MINECO (BS-2015–073993 and BFU2017-89408-R). Experiments performed at CNIO were supported by grant PID2019-106707-RB to JM, co-sponsored by EU ERDF funds. SM was supported by an international postdoctoral contract “CNIO Friends”. The proteomic analysis was performed in the Proteomics Facility of Centro de Investigación del Cáncer, Salamanca, Grant PRB3(IPT17/0019 -ISCIII-SGEFI/ERDF). CIC-IBMCC is supported by the Programa de Apoyo a Planes Estratégicos de Investigación de Estructuras de Investigación de Excelencia cofunded by the Castilla–León autonomous government and the European Regional Development Fund (CLC–2017–01). Veitia’s Lab is supported by the University of Paris and the Centre National de la Recherche Scientifique