Final state effects on superfluid 4^{\bf 4}He in the deep inelastic regime

A study of Final State Effects (FSE) on the dynamic structure function of superfluid $^4$He in the Gersch--Rodriguez formalism is presented. The main ingredients needed in the calculation are the momentum distribution and the semidiagonal two--body density matrix. The influence of these ground state quantities on the FSE is analyzed. A variational form of $\rho_2$ is used, even though simpler forms turn out to give accurate results if properly chosen. Comparison to the experimental response at high momentum transfer is performed. The predicted response is quite sensitive to slight variations on the value of the condensate fraction, the best agreement with experiment being obtained with $n_0=0.082$. Sum rules of the FSE broadening function are also derived and commented. Finally, it is shown that Gersch--Rodriguez theory produces results as accurate as those coming from other more recent FSE theories.Comment: 20 pages, RevTex 3.0, 11 figures available upon request, to be appear in Phys. Rev.

Description of recent large-qq neutron inclusive scattering data from liquid 4^4He

We report dynamical calculations for large-$q$ structure functions of liquid $^4$He at $T$=1.6 and 2.3 K and compare those with recent MARI data. We extend those calculations far beyond the experimental range q\le 29\Ain in order to study the approach of the response to its asymptotic limit for a system with interactions having a strong short-range repulsion. We find only small deviations from theoretical $1/q$ behavior, valid for smooth $V$. We repeat an extraction by Glyde et al of cumulant coefficients from data. We argue that fits determine the single atom momentum distribution, but express doubt as to the extraction of meaningful Final State Interaction parameters.Comment: 37 pages, 13 postscript fig

Numerical study of the spherically-symmetric Gross-Pitaevskii equation in two space dimensions

We present a numerical study of the time-dependent and time-independent Gross-Pitaevskii (GP) equation in two space dimensions, which describes the Bose-Einstein condensate of trapped bosons at ultralow temperature with both attractive and repulsive interatomic interactions. Both time-dependent and time-independent GP equations are used to study the stationary problems. In addition the time-dependent approach is used to study some evolution problems of the condensate. Specifically, we study the evolution problem where the trap energy is suddenly changed in a stable preformed condensate. In this case the system oscillates with increasing amplitude and does not remain limited between two stable configurations. Good convergence is obtained in all cases studied.Comment: 9 latex pages, 7 postscript figures, To appear in Phys. Rev.

High-momentum dynamic structure function of liquid 3He-4He mixtures: a microscopic approach

The high-momentum dynamic structure function of liquid 3He-4He mixtures has been studied introducing final state effects. Corrections to the impulse approximation have been included using a generalized Gersch-Rodriguez theory that properly takes into account the Fermi statistics of 3He atoms. The microscopic inputs, as the momentum distributions and the two-body density matrices, correspond to a variational (fermi)-hypernetted chain calculation. The agreement with experimental data obtained at $q=23.1$ \AA$^{-1}$ is not completely satisfactory, the comparison being difficult due to inconsistencies present in the scattering measurements. The significant differences between the experimental determinations of the 4He condensate fraction and the 3He kinetic energy, and the theoretical results, still remain unsolved.Comment: 18 pages, 11 figures, to appear in Phys. Rev.

From a movement-deficient grapevine fanleaf virus to the identification of a new viral determinant of nematode transmission

Grapevine fanleaf virus (GFLV) and arabis mosaic virus (ArMV) are nepoviruses responsible for grapevine degeneration. They are specifically transmitted from grapevine to grapevine by two distinct ectoparasitic dagger nematodes of the genus Xiphinema. GFLV and ArMV move from cell to cell as virions through tubules formed into plasmodesmata by the self-assembly of the viral movement protein. Five surface-exposed regions in the coat protein called R1 to R5, which differ between the two viruses, were previously defined and exchanged to test their involvement in virus transmission, leading to the identification of region R2 as a transmission determinant. Region R4 (amino acids 258 to 264) could not be tested in transmission due to its requirement for plant systemic infection. Here, we present a fine-tuning mutagenesis of the GFLV coat protein in and around region R4 that restored the virus movement and allowed its evaluation in transmission. We show that residues T258, M260, D261, and R301 play a crucial role in virus transmission, thus representing a new viral determinant of nematode transmission

Inclusive quasi-elastic electron-nucleus scattering

This article presents a review of the field of inclusive quasi-elastic electron-nucleus scattering. It discusses the approach used to measure the data and includes a compilation of data available in numerical form. The theoretical approaches used to interpret the data are presented. A number of results obtained from the comparison between experiment and calculation are then reviewed. The analogies and differences to other fields of physics exploiting quasi-elastic scattering from composite systems are pointed out.Comment: Accepted for publication in Reviews of Modern Physic

USP30 sets a trigger threshold for PINK1–PARKIN amplification of mitochondrial ubiquitylation

The mitochondrial deubiquitylase USP30 negatively regulates the selective autophagy of damaged mitochondria. We present the characterisation of an N-cyano pyrrolidine compound, FT3967385, with high selectivity for USP30. We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery, represents a robust biomarker for both USP30 loss and inhibition. A proteomics analysis, on a SHSY5Y neuroblastoma cell line model, directly compares the effects of genetic loss of USP30 with chemical inhibition. We have thereby identified a subset of ubiquitylation events consequent to mitochondrial depolarisation that are USP30 sensitive. Within responsive elements of the ubiquitylome, several components of the outer mitochondrial membrane transport (TOM) complex are prominent. Thus, our data support a model whereby USP30 can regulate the availability of ubiquitin at the specific site of mitochondrial PINK1 accumulation following membrane depolarisation. USP30 deubiquitylation of TOM complex components dampens the trigger for the Parkin-dependent amplification of mitochondrial ubiquitylation leading to mitophagy. Accordingly, PINK1 generation of phospho-Ser65 ubiquitin proceeds more rapidly in cells either lacking USP30 or subject to USP30 inhibition

Pharmacoinformatic investigation of medicinal plants from East Africa

Medicinal plants have widely been used in the traditional treatment of ailments and have been proven effective. Their contribution still holds an important place in modern drug discovery due to their chemical, and biological diversities. However, the poor documentation of traditional medicine, in developing African countries for instance, can lead to the loss of knowledge related to such practices. In this study, we present the Eastern Africa Natural Products Database (EANPDB) containing the structural and bioactivity information of 1870 unique molecules isolated from about 300 source species from the Eastern African region. This represents the largest collection of natural products (NPs) from this geographical region, covering literature data of the period from 1962 to 2019. The computed physicochemical properties and toxicity profiles of each compound have been included. A comparative analysis of some physico-chemical properties like molecular weight, H-bond donor/acceptor, logP(o/w), etc. as well scaffold diversity analysis has been carried out with other published NP databases. EANPDB was combined with the previously published Northern African Natural Products Database (NANPDB), to form a merger African Natural Products Database (ANPDB), containing similar to 6500 unique molecules isolated from about 1000 source species (freely available at http://african-compounds.org). As a case study, latrunculins A and B isolated from the spongeNegombata magnifica(Podospongiidae) with previously reported antitumour activities, were identified via substructure searching as molecules to be explored as putative binders of histone deacetylases (HDACs)

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne

The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types in polyubiquitin co-exist and are independently regulated in cells. This ‘ubiquitin code’ determines the fate of the modified protein1. Deubiquitinating enzymes of the Ovarian Tumour (OTU) family regulate cellular signalling by targeting distinct linkage types within polyubiquitin2, and understanding their mechanisms of linkage specificity gives fundamental insights into the ubiquitin system. We here reveal how the deubiquitinase Cezanne/OTUD7B specifically targets Lys11-linked polyubiquitin. Crystal structures of Cezanne alone and in complex with mono- and Lys11-linked diubiquitin, in combination with hydrogen-deuterium exchange mass spectrometry, enable reconstruction of the enzymatic cycle in exquisite detail. An intricate mechanism of ubiquitin-assisted conformational changes activate the enzyme, and while all chain types interact with the enzymatic S1 site, only Lys11-linked chains can bind productively across the active site and stimulate catalytic turnover. Our work highlights the fascinating plasticity of deubiquitinases, and indicates that new conformational states can occur when a true substrate, such as diubiquitin, is bound at the active site