Stacking disorder: the hexagonal polymorph of tris(bicyclo[2.1.1]hexeno)benzene and related examples

X-ray diffractograms of tris(bicyclo[2.1.1]hexeno)benzene, crystallized at the interface between a benzene solution and a layer of acetonitrile, show hexagonal symmetry and streaks of diffuse scattering along c*. The heavily faulted layer stacking is analyzed qualitatively and quantitatively in terms of a systematic protocol. This protocol requires partitioning the crystal structure into layers in such a way that pairs of adjacent layers may be stacked in different, but geometrically equivalent ways, which are dictated by the layer group symmetry. This approach is shown to provide a consistent alternative for analysis of a number of related cases provided the layers are defined on the basis of geometrical criteria rather than chemical intuitio

The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted

Synthesis and assembly of ribosomal components are fundamental cellular processes and generally well-conserved within the main groups of organisms. Yet, provocative variations to the general schemes exist. We have discovered an unusual processing pathway of pre-rRNA in extreme thermophilic archaea exemplified by Pyrococcus furiosus. The large subunit (LSU) rRNA is produced as a circularly permuted form through circularization followed by excision of Helix 98. As a consequence, the terminal domain VII that comprise the binding site for the signal recognition particle is appended to the 5´ end of the LSU rRNA that instead terminates in Domain VI carrying the Sarcin-Ricin Loop, the primary interaction site with the translational GTPases. To our knowledge, this is the first example of a true post-transcriptional circular permutation of a main functional molecule and the first example of rRNA fragmentation in archaea.publishedVersio

Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans

In all free-living organisms a late-stage checkpoint in the biogenesis of the small ribosomal subunit involves rRNA modification by an RsmA/Dim1 methyltransferase. The hyperthermophilic archaeon Nanoarchaeum equitans, whose existence is confined to the surface of a second archaeon, Ignic-occus hospitalis, lacks an RsmA/Dim1 homolog. We demonstrate here that the I. hospitalis host possesses the homolog Igni_1059, which dimethylates the N-6-positions of two invariant adenosines within helix 45 of 16S rRNA in a manner identical to other RsmA/Dim1 enzymes. However, Igni_1059 is not transferred from I. hospitalis to N. equitans across their fused cell membrane structures and the corresponding nucleotides in N. equitans 16S rRNA remain unmethylated. An alternative mechanism for ribosomal subunit maturation in N. equitans is suggested by sRNA interactions that span the redundant RsmA/Dim1 site to introduce 2'-O-ribose methylations within helices 44 and 45 of the rRNA

Last Planner Systems påvirkning på økonomisk- og miljømessig bærekraft i byggeprosjekter

Masteroppgaven vår er en kvalitativ flere-casestudie i tre entreprenørvirksomheter. Vår studie innebærer å se på bærekrafts muligheter og utfordringer ved anvendelse av Lean Construction verktøyet Last Planner System i byggeprosjekter. Formålet vårt er å finne hvilken effekt metodikken har på økonomiske- og miljømessige- bærekrafts aspekter som kostnadsbevissthet, tid, ressursforbruk, miljøvennlige materialer, redusering av utslipp og energiforbruk. Vi har fått fram nyanser, kompleksitet, motsetninger og likheter. For å svare på vår problemstilling, har vi intervjuet fem informanter med førstehåndserfaring på emnet. Vi har gjennom transkribering, analyse og diskusjon avdekket spennende funn om Last Planner System som har positive og negative innvirkninger på bærekraft. De positive effektene blir skapt ettersom de involverte i prosjektet føler eierskap, får bedre flyt i aktivitetene og samarbeider godt om målene. Derimot, blir de negative effektene skapt ved at er for ressurskrevende, krever høy grad av forankring, krever høy grad av trening og verktøyet kan ikke alltid brukes i helhet. Dette betyr at dersom ikke forutsetningene er på plass i organisasjonene, vil dette skape ineffektivitet som videre resulterer i økte kostnader for hver aktivitet i prosjektene. I tillegg, vil det resultere i økte utslipp ettersom man må bruke flere materialer og ressurser på byggeplassen. Vi har også fått fram hvordan det i mange bygge kontekster er naturlig å ta elementer fra Last Planner System og inkorporere dette i sin egen planleggingstilnærming. Her er de to viktigste delene - slank planlegging og involverende planlegging. Supplerende til disse to elementene, anvendes sterk milepælstyring og bakover planlegging. Last Planner System inngår også i et større rammeverk som heter VDC. Det har vært sentralt for oss å fremheve hvor elementært det er å se planleggingsmetodikken i et holistisk bilde. Vi har også utforsket forholdet mellom Last Planner System og miljøstandarden BREEAM. Her fant vi både signifikans og motsetninger.Our master ́s thesis is a qualitative multiple-case study in three construction companies. Our study involves looking at the opportunities and challenges of sustainability when using the Lean Construction tool Last Planner System in construction projects. Our reasoning for the thesis is to find the effect the method has on economic and environmental sustainability aspects. The aspects would revolve around cost awareness, time, resource consumption, environmentally friendly materials, reduction of emissions and energy consumption. We have brought nuances, complexity, contradictions, and similarities. To answer our problem, we have interviewed five informants with first-hand experience of the subject. Through transcriptions, analysis, and discussion, we have uncovered exiting findings about the Last Planner System that have positive and negative impacts on sustainability. The positive effects are created because the participants in the project get a higher level of ownership, better flow within the activities, and high collaboration towards common goals. However, negative effects are created because of the high demand for resources that keep the system going, high degree of anchoring, and tools cannot be used in their entirety. This means if the prerequisites are not in place in the organization, this will have potential to create inefficiency which further results in increased cost for each activity in the projects. In addition, it will result in increased emissions as more materials and resources must be used on the construction site. In addition, we have also shown in how many construction contexts it is natural to take elements from the Last Planner System and incorporate this into your own planning approach. This is the most important parts – Lean Planning and collaborative planning. Complementary to these elements, strong milestone management and backward planning are used. The Last Planner System also involves part of a larger framework called Virtual Design and Construction (VDC). It has been central for us to highlight how important it is to see planning methodology in a holistic view. We have also explored the relationship between The Last Planner System and the environmental standard BREEAM. Within this subject, both significance and contradictions were discovered

Organ and tissue level properties are more sensitive to age than osteocyte lacunar characteristics in rat cortical bone

Modeling and remodeling induce significant changes of bone structure and mechanical properties with age. Therefore, it is important to gain knowledge of the processes taking place in bone over time. The rat is a widely used animal model, where much data has been accumulated on age-related changes of bone on the organ and tissue level, whereas features on the nano- and micrometer scale are much less explored. We investigated the age-related development of organ and tissue level bone properties such as bone volume, bone mineral density, and load to fracture and correlated these with osteocyte lacunar properties in rat cortical bone. Femora of 14 to 42-week-old female Wistar rats were investigated using multiple complementary techniques including X-ray micro-computed tomography and biomechanical testing. The body weight, femoral length, aBMD, load to fracture, tissue volume, bone volume, and tissue density were found to increase rapidly with age at 14-30 weeks. At the age of 30-42 weeks, the growth rate appeared to decrease. However, no accompanying changes were found in osteocyte lacunar properties such as lacunar volume, ellipsoidal radii, lacunar stretch, lacunar oblateness, or lacunar orientation with animal age. Hence, the evolution of organ and tissue level properties with age in rat cortical bone is not accompanied by related changes in osteocyte lacunar properties. This suggests that bone microstructure and bone matrix material properties and not the geometric properties of the osteocyte lacunar network are main determinants of the properties of the bone on larger length scales

Quantitative proteogenomics of human pathogens using DIA-MS.

The increasing number of bacterial genomes in combination with reproducible quantitative proteome measurements provides new opportunities to explore how genetic differences modulate proteome composition and virulence. It is challenging to combine genome and proteome data as the underlying genome influences the proteome. We present a strategy to facilitate the integration of genome data from several genetically similar bacterial strains with data-independent analysis mass spectrometry (DIA-MS) for rapid interrogation of the combined data sets. The strategy relies on the construction of a composite genome combining all genetic data in a compact format, which can accommodate the fusion with quantitative peptide and protein information determined via DIA-MS. We demonstrate the method by combining data sets from whole genome sequencing, shotgun MS and DIA-MS from 34 clinical isolates of Streptococcus pyogenes. The data structure allows for fast exploration of the data showing that undetected proteins are on average more amenable to amino acid substitution than expressed proteins. We identified several significantly differentially expressed proteins between invasive and non-invasive strains. The work underlines how integration of whole genome sequencing with accurately quantified proteomes can further advance the interpretation of the relationship between genomes, proteomes and virulence

Mapping the 3D orientation of nanocrystals and nanostructures in human bone: Indications of novel structural features

Bone is built from collagen fibrils and biomineral nanoparticles. In humans, they are organized in lamellar twisting patterns on the microscale. It has been a central tenet that the biomineral nanoparticles are co-aligned with the bone nanostructure. Here, we reconstruct the three-dimensional orientation in human lamellar bone of both the nanoscale features and the biomineral crystal lattice from small-angle x-ray scattering and wide-angle x-ray scattering, respectively. While most of the investigated regions show well-aligned nanostructure and crystal structure, consistent with current bone models, we report a localized difference in orientation distribution between the nanostructure and the biomineral crystals in specific bands. Our results show a robust and systematic, but localized, variation in the alignment of the two signals, which can be interpreted as either an additional mineral fraction in bone, a preferentially aligned extrafibrillar fraction, or the result of transverse stacking of mineral particles over several fibrils

Polychromatic neutron phase contrast imaging of weakly absorbing samples enabled by phase retrieval

We demonstrate the use of a phase retrieval technique for propagation-based phase contrast neutron imaging with a polychromatic beam. This enables imaging samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time resolved measurements. A metal sample, designed to be close to a pure phase object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratio were significantly improved and in case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration-contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone