141 research outputs found
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Scaling the nexus: towards integrated frameworks for analysing water, energy and food
The emergence of the water-energy-food (WEF) nexus concept following the 2011 Bonn Nexus Conference has resulted in a change to the way we perceive our natural resources. Global pressures such as climate change, and population growth have highlighted the fragility of our WEF systems, necessitating integrated solutions across multiple scales and levels. Whilst a number of frameworks and analytical tools have been developed since 2011, a comprehensive WEF nexus tool remains elusive, hindered in part by our limited data and understanding of the interdependencies and connections across the WEF systems. To achieve this, the community of academics, practitioners and policy-makers invested in WEF nexus research are addressing several critical areas that currently remain as barriers. Firstly, the plurality of scales (e.g., spatial, temporal, institutional, jurisdictional) necessitates a more comprehensive effort to assess interdependencies between water, energy and food, from household to institutional and national levels. Secondly, and closely related to scale, a lack of available data often hinders our ability to quantify physical stocks and flows of resources. In this paper, we elucidate many of the challenges that have arisen across nexus research, including the impact of multiple scales in operation across the nexus, and concomitantly, what impact these scales have on data accessibility. We review some of the critical frameworks and tools that are applied by nexus researchers and discuss some of the steps required to develop from nexus thinking to an operationalizable concept, with a consistent focus on scale and data availability
Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum
Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism
Scaling the nexus: Towards integrated frameworks for analyzing water, energy and food
The emergence of the water-energy-food (WEF) nexus has resulted in changes to the way we perceive our natural resources. Stressors such as climate change and population growth have highlighted the fragility of our WEF systems, necessitating integrated solutions across multiple scales. Whilst a number of frameworks and analytical tools have been developed since 2011, a comprehensive WEF nexus tool remains elusive, hindered in part by our limited data and understanding of the interdependencies and connections across the WEF systems. To achieve this, the community of academics, practitioners and policy-makers invested in WEF nexus research are addressing several critical areas that currently remain as barriers. Firstly, the plurality of scales (e.g., spatial, temporal, institutional, jurisdictional) necessitates a more comprehensive effort to assess interdependencies between water, energy and food, from household to institutional and national levels. Secondly, and closely related to scale, a lack of available data often hinders our ability to quantify physical stocks and flows of resources. Overcoming these barriers necessitates engaging multiple stakeholders, and using experiences and local insights to better understand nexus dynamics in particular locations or scenarios, and we exemplify this with the inclusion of a UK-based case-study on exploring the nexus in a particular geographical area. We elucidate many challenges that have arisen across nexus research, including the impact of multiple scales in operation, and concomitantly, what impact these scales have on data accessibility. We assess some of the critical frameworks and tools that are applied by nexus researchers and articulate some of the steps required to develop from nexus thinking to an operationalizable concept, with a consistent focus on scale and data availability
What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor?
Ubiquitin (Ub)-conjugating enzymes (E2) are key enzymes in ubiquitination or Ub-like modifications of proteins. We searched for all proteins belonging to the E2 enzyme super-family in seven species (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Arabidopsis thaliana) to identify families and to reconstruct each family’s phylogeny. Our phylogenetic analysis of 207 genes led us to define 17 E2 families, with 37 E2 genes, in the human genome. The subdivision of E2 into four classes did not correspond to the phylogenetic tree. The sequence signature HPN (histidine–proline–asparagine), followed by a tryptophan residue at 16 (up to 29) amino acids, was highly conserved. When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN. The secondary structures were characterized by a canonical alpha/beta fold. Only family 10 deviated from the common organization because the proteins were devoid of enzymatic activity. Family 7 had an insertion between beta strands 1 and 2; families 3, 5 and 14 had an insertion between the active cysteine and the conserved tryptophan. The three-dimensional data of these proteins highlight a strong structural conservation of the core domain. Our analysis shows that the primitive eukaryote ancestor possessed a diversified set of E2 enzymes, thus emphasizing the importance of the Ub pathway. This comprehensive overview of E2 enzymes emphasizes the diversity and evolution of this superfamily and helps clarify the nomenclature and true orthologies. A better understanding of the functions of these enzymes is necessary to decipher several human diseases
Gender-Associated Genes in Filarial Nematodes Are Important for Reproduction and Potential Intervention Targets
Lymphatic filariasis is a neglected tropical disease that is caused by thread-like parasitic worms that live and reproduce in lymphatic vessels of the human host. There are no vaccines to prevent filariasis, and available drugs are not effective against all stages of the parasite. In addition, recent reports suggest that the filarial nematodes may be developing resistance to key medications. Therefore, there is an urgent need to identify new drug targets in filarial worms. The purpose of this study was to perform a genome-wide analysis of gender-associated gene transcription to improve understanding of key reproductive processes in filarial nematodes. Our results indicate that thousands of genes are differentially expressed in male and female adult worms. Many of those genes are involved in specific reproductive processes such as embryogenesis and spermatogenesis. In addition, expression of some of those genes is suppressed by tetracycline, a drug that leads to sterilization of adult female worms in many filarial species. Thus, gender-associated genes represent priority targets for design of vaccines and drugs that interfere with reproduction of filarial nematodes. Additional work with this type of integrated systems biology approach should lead to important new tools for controlling filarial diseases
Studies of and production in and Pb collisions
The production of and mesons is studied in proton-proton and
proton-lead collisions collected with the LHCb detector. Proton-proton
collisions are studied at center-of-mass energies of and ,
and proton-lead collisions are studied at a center-of-mass energy per nucleon
of . The studies are performed in center-of-mass rapidity
regions (forward rapidity) and
(backward rapidity) defined relative to the proton beam direction. The
and production cross sections are measured differentially as a function
of transverse momentum for and , respectively. The differential cross sections are used to
calculate nuclear modification factors. The nuclear modification factors for
and mesons agree at both forward and backward rapidity, showing
no significant evidence of mass dependence. The differential cross sections of
mesons are also used to calculate cross section ratios,
which show evidence of a deviation from the world average. These studies offer
new constraints on mass-dependent nuclear effects in heavy-ion collisions, as
well as and meson fragmentation.Comment: All figures and tables, along with machine-readable versions and any
supplementary material and additional information, are available at
https://lhcbproject.web.cern.ch/Publications/p/LHCb-PAPER-2023-030.html (LHCb
public pages
Fraction of decays in prompt production measured in pPb collisions at TeV
The fraction of and decays in the prompt
yield, , is measured by
the LHCb detector in pPb collisions at TeV. The study
covers the forward () and backward () rapidity
regions, where is the rapidity in the nucleon-nucleon
center-of-mass system. Forward and backward rapidity samples correspond to
integrated luminosities of 13.6 0.3 nb and 20.8 0.5
nb, respectively. The result is presented as a function of the
transverse momentum in the range 1 GeV/.
The fraction at forward rapidity is compatible with the LHCb
measurement performed in collisions at TeV, whereas the
result at backward rapidity is 2.4 larger than in the forward region
for GeV/. The increase of at low at backward rapidity is compatible with the suppression of the
(2S) contribution to the prompt yield. The lack of in-medium
dissociation of states observed in this study sets an upper limit of
180 MeV on the free energy available in these pPb collisions to dissociate or
inhibit charmonium state formation.Comment: All figures and tables, along with machine-readable versions and any
supplementary material and additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-028.html (LHCb
public pages
Observation of strangeness enhancement with charmed mesons in high-multiplicity collisions at TeV
The production of prompt and mesons is measured by the LHCb
experiment in proton-lead () collisions in both the forward
() and backward () rapidity regions at a
nucleon-nucleon center-of-mass energy of TeV.
The nuclear modification factors of both and mesons are
determined as a function of transverse momentum, , and
rapidity. In addition, the to cross-section ratio is measured
as a function of the charged particle multiplicity in the event. An enhanced
to production in high-multiplicity events is observed for the
whole measured range, in particular at low
and backward rapidity, where the significance exceeds six standard deviations.
This constitutes the first observation of strangeness enhancement in charm
quark hadronization in high-multiplicity collisions. The results
are also qualitatively consistent with the presence of quark coalescence as an
additional charm quark hadronization mechanism in high-multiplicity proton-lead
collisions.Comment: All figures and tables, along with machine-readable versions and any
supplementary material and additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-021.html (LHCb
public pages
Search for violation in the phase space of decays with the energy test
A search for violation in and decays is reported.
The search is performed using an unbinned model-independent method known as the
energy test that probes local violation in the phase space of the
decays. The data analysed correspond to an integrated luminosity of
fb collected in proton-proton collisions by the LHCb experiment at
a centre-of-mass energy of ~TeV, amounting to approximately 950000
and 620000 signal candidates for the and modes, respectively. The
method is validated using
and decays, where
-violating effects are expected to be negligible, and using
background-enhanced regions of the signal decays. The results are consistent
with symmetry in both the and the decays, with
-values for the hypothesis of no violation of 70% and 66%,
respectively.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-019.html (LHCb
public pages
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