1,319 research outputs found
Crustacean remains from the Yuka mammoth raise questions about non-analogue freshwater communities in the Beringian region during the Pleistocene
This work is licensed under a Creative Commons Attribution 4.0 International License.Frozen permafrost Pleistocene mammal carcasses with soft tissue remains are subject to intensive study and help elucidate the palaeoenvironment where these animals lived. Here we present an inventory of the freshwater fauna and flora found in a sediment sample from the mummified Woolly Mammoth carcass found in August 2010, from the Oyogos Yar coast near the Kondratievo River in the Laptev Sea region, Sakha (Yakutia) Republic, NE Russia. Our study demonstrates that the waterbody where the carcass was buried could be characterized as a shallow pond or lake inhabited mainly by taxa which are present in this area today, but additionally by some branchiopod crustacean taxa currently absent or unusual in the region although they exist in the arid zone of Eurasia (steppes and semi-deserts). These findings suggest that some “non-analogue” crustacean communities co-existed with the “Mammoth fauna”. Our findings raise questions about the nature of the waterbodies that existed in Beringia during the MIS3 climatic optimum when the mammoth was alive
Human Rhinovirus 16 Causes Golgi Apparatus Fragmentation without Blocking Protein Secretion
The replication of picornaviruses has been described to cause fragmentation of the Golgi apparatus that blocks the secretory pathway. The inhibition of major histocompatibility complex class I upregulation and cytokine, chemokine and interferon secretion may have important implications for host defense. Previous studies have shown that disruption of the secretory pathway can be replicated by expression of individual nonstructural proteins; however the situation with different serotypes of human rhinovirus (HRV) is unclear. The expression of 3A protein from HRV14 or HRV2 did not cause Golgi apparatus disruption or a block in secretion, whereas other studies showed that infection of cells with HRV1A did cause Golgi apparatus disruption which was replicated by the expression of 3A. HRV16 is the serotype most widely used in clinical HRV challenge studies; consequently, to address the issue of Golgi apparatus disruption for HRV16, we have systematically and quantitatively examined the effect of HRV16 on both Golgi apparatus fragmentation and protein secretion in HeLa cells. First, we expressed each individual nonstructural protein and examined their cellular localization and their disruption of endoplasmic reticulum and Golgi apparatus architecture. We quantified their effects on the secretory pathway by measuring secretion of the reporter protein Gaussia luciferase. Finally, we examined the same outcomes following infection of cells with live virus. We demonstrate that expression of HRV16 3A and 3AB and, to a lesser extent, 2B caused dispersal of the Golgi structure, and these three nonstructural proteins also inhibited protein secretion. The infection of cells with HRV16 also caused significant Golgi apparatus dispersal; however, this did not result in the inhibition of protein secretion. IMPORTANCE The ability of replicating picornaviruses to influence the function of the secretory pathway has important implications for host defense. However, there appear to be differences between different members of the family and inconsistent results when comparing infection with live virus to expression of individual nonstructural proteins. We demonstrate that individual nonstructural HRV16 proteins, when expressed in HeLa cells, can both fragment the Golgi apparatus and block secretion, whereas viral infection fragments the Golgi apparatus without blocking secretion. This has major implications for how we interpret mechanistic evidence derived from the expression of single viral proteins
Gauge links for transverse momentum dependent correlators at tree-level
In this paper we discuss the incorporation of gauge links in hadronic matrix
elements that describe the soft hadronic physics in high energy scattering
processes. In this description the matrix elements appear in soft correlators
and they contain non-local combinations of quark and gluon fields. In our
description we go beyond the collinear approach in which case also the
dependence on transverse momenta of partons is taken into consideration. The
non-locality in the transverse direction leads to a complex gauge link
structure for the full process, in which color is entangled, even at
tree-level. We show that at tree-level in a 1-parton unintegrated (1PU)
situation, in which only the transverse momentum of one of the initial state
hadrons is relevant, one can get a factorized expression involving transverse
momentum dependent (TMD) distribution functions. We point out problems at the
level of two initial state hadrons, even for relatively simple processes such
as Drell-Yan scattering.Comment: 25 pages, corrected typos and updated reference
Fully-Unintegrated Parton Distribution and Fragmentation Functions at Perturbative k_T
We define and study the properties of generalized beam functions (BFs) and
fragmenting jet functions (FJFs), which are fully-unintegrated parton
distribution functions (PDFs) and fragmentation functions (FFs) for
perturbative k_T. We calculate at one loop the coefficients for matching them
onto standard PDFs and FFs, correcting previous results for the BFs in the
literature. Technical subtleties when measuring transverse momentum in
dimensional regularization are clarified, and this enables us to renormalize in
momentum space. Generalized BFs describe the distribution in the full
four-momentum k_mu of a colliding parton taken out of an initial-state hadron,
and therefore characterize the collinear initial-state radiation. We illustrate
their importance through a factorization theorem for pp -> l^+ l^- + 0 jets,
where the transverse momentum of the lepton pair is measured. Generalized FJFs
are relevant for the analysis of semi-inclusive processes where the full
momentum of a hadron, fragmenting from a jet with constrained invariant mass,
is measured. Their significance is shown for the example of e^+ e^- -> dijet+h,
where the perpendicular momentum of the fragmenting hadron with respect to the
thrust axis is measured.Comment: Journal versio
Long term time variability of cosmic rays and possible relevance to the development of life on Earth
An analysis is made of the manner in which the cosmic ray intensity at Earth
has varied over its existence and its possible relevance to both the origin and
the evolution of life. Much of the analysis relates to the 'high energy' cosmic
rays () and their variability due to the changing
proximity of the solar system to supernova remnants which are generally
believed to be responsible for most cosmic rays up to PeV energies. It is
pointed out that, on a statistical basis, there will have been considerable
variations in the likely 100 My between the Earth's biosphere reaching
reasonable stability and the onset of very elementary life. Interestingly,
there is the increasingly strong possibility that PeV cosmic rays are
responsible for the initiation of terrestrial lightning strokes and the
possibility arises of considerable increases in the frequency of lightnings and
thereby the formation of some of the complex molecules which are the 'building
blocks of life'. Attention is also given to the well known generation of the
oxides of nitrogen by lightning strokes which are poisonous to animal life but
helpful to plant growth; here, too, the violent swings of cosmic ray
intensities may have had relevance to evolutionary changes. A particular
variant of the cosmic ray acceleration model, put forward by us, predicts an
increase in lightning rate in the past and this has been sought in Korean
historical records. Finally, the time dependence of the overall cosmic ray
intensity, which manifests itself mainly at sub-10 GeV energies, has been
examined. The relevance of cosmic rays to the 'global electrical circuit'
points to the importance of this concept.Comment: 18 pages, 5 figures, accepted by 'Surveys in Geophysics
Coupling models of cattle and farms with models of badgers for predicting the dynamics of bovine tuberculosis (TB)
Bovine TB is a major problem for the agricultural industry in several
countries. TB can be contracted and spread by species other than cattle and
this can cause a problem for disease control. In the UK and Ireland, badgers
are a recognised reservoir of infection and there has been substantial
discussion about potential control strategies. We present a coupling of
individual based models of bovine TB in badgers and cattle, which aims to
capture the key details of the natural history of the disease and of both
species at approximately county scale. The model is spatially explicit it
follows a very large number of cattle and badgers on a different grid size for
each species and includes also winter housing. We show that the model can
replicate the reported dynamics of both cattle and badger populations as well
as the increasing prevalence of the disease in cattle. Parameter space used as
input in simulations was swept out using Latin hypercube sampling and
sensitivity analysis to model outputs was conducted using mixed effect models.
By exploring a large and computationally intensive parameter space we show that
of the available control strategies it is the frequency of TB testing and
whether or not winter housing is practised that have the most significant
effects on the number of infected cattle, with the effect of winter housing
becoming stronger as farm size increases. Whether badgers were culled or not
explained about 5%, while the accuracy of the test employed to detect infected
cattle explained less than 3% of the variance in the number of infected cattle
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Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity
Background
Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps.
Results
We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes.
Conclusions
Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA
Chronic non-specific low back pain - sub-groups or a single mechanism?
Copyright 2008 Wand and O'Connell; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Low back pain is a substantial health problem and has subsequently attracted a
considerable amount of research. Clinical trials evaluating the efficacy of a variety of interventions
for chronic non-specific low back pain indicate limited effectiveness for most commonly applied
interventions and approaches.
Discussion: Many clinicians challenge the results of clinical trials as they feel that this lack of
effectiveness is at odds with their clinical experience of managing patients with back pain. A
common explanation for this discrepancy is the perceived heterogeneity of patients with chronic
non-specific low back pain. It is felt that the effects of treatment may be diluted by the application
of a single intervention to a complex, heterogeneous group with diverse treatment needs. This
argument presupposes that current treatment is effective when applied to the correct patient.
An alternative perspective is that the clinical trials are correct and current treatments have limited
efficacy. Preoccupation with sub-grouping may stifle engagement with this view and it is important
that the sub-grouping paradigm is closely examined. This paper argues that there are numerous
problems with the sub-grouping approach and that it may not be an important reason for the
disappointing results of clinical trials. We propose instead that current treatment may be ineffective
because it has been misdirected. Recent evidence that demonstrates changes within the brain in
chronic low back pain sufferers raises the possibility that persistent back pain may be a problem of
cortical reorganisation and degeneration. This perspective offers interesting insights into the
chronic low back pain experience and suggests alternative models of intervention.
Summary: The disappointing results of clinical research are commonly explained by the failure of
researchers to adequately attend to sub-grouping of the chronic non-specific low back pain
population. Alternatively, current approaches may be ineffective and clinicians and researchers may
need to radically rethink the nature of the problem and how it should best be managed
Determinants of Initiation Codon Selection during Translation in Mammalian Cells
Factors affecting translation of mRNA contribute to the complexity of eukaryotic proteomes. In some cases, translation of a particular mRNA can generate multiple proteins. However, the factors that determine whether ribosomes initiate translation from the first AUG codon in the transcript, from a downstream codon, or from multiple sites are not completely understood. Various mRNA properties, including AUG codon-accessibility and 5′ leader length have been proposed as potential determinants that affect where ribosomes initiate translation. To explore this issue, we performed studies using synthetic mRNAs with two in-frame AUG codons−both in excellent context. Open reading frames initiating at AUG1 and AUG2 encode large and small isoforms of a reporter protein, respectively. Translation of such an mRNA in COS-7 cells was shown to be 5′ cap-dependent and to occur efficiently from both AUG codons. AUG codon-accessibility was modified by using two different elements: an antisense locked nucleic acid oligonucleotide and an exon-junction complex. When either element was used to mask AUG1, the ratio of the proteins synthesized changed, favoring the smaller (AUG2-initiated) protein. In addition, we observed that increased leader length by itself changed the ratio of the proteins and favored initiation at AUG1. These observations demonstrate that initiation codon selection is affected by various factors, including AUG codon-accessibility and 5′ leader length, and is not necessarily determined by the order of AUG codons (5′→3′). The modulation of AUG codon accessibility may provide a powerful means of translation regulation in eukaryotic cells
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