Dissecting CTCF site function in a tense HoxD locus

In this issue of Genes & Development, Amândio and colleagues (pp. 1490–1509) dissect the function of a cluster of several CTCF binding sites in the HoxD cluster by iterative deletions in mice. They found additive functions for some, and intriguingly found that some sites function as insulators, while others function as anchors for enhancer–promoter interactions. These functions vary depending on developmental context. The work provides new insights into the roles played by CTCF in regulating developmental patterns and 3D chromatin organization.

Landscape design of “Tanjung Budaya Pemuteran” coast area based on landscape engineering

“Tanjung Budaya Pemuteran” is a place of coastal tourism and alternative tourism based on community culture in Pemuteran Village, Bali. The landscape characteristic and inherent local wisdom make this bay is a unique place. Gebug ende is the native rain harvesting ritual of Pemuteran society, which can be suggestive evidence. Currently, Tanjung Budaya Pemuteran landscapes not suitable to support the site function. This research aims to identify the existing landscape to make Tanjung Budaya Pemuteran use optimally without disregarding inherent local wisdom. Landscape analysis spatial with the quantitative and qualitative approach used to know the potential and constraint. The landscape engineering approach is used to measure the volume of rainwater to optimize the result of Gebug ende rain harvesting. The basic concept of this landscape design is named “Identities of Pemuteran”. Design concept generated through the transformation of Gebug ende. The block plan becomes a schematic design product that consists of a welcome area, a culture tourism area, a recreation area, and a service area. Each area is connected by primer and secondary circulation. Plants on-site are regulated based on vegetation groups of Barrington, Pes caprae, Mangroves, and existing. Visuals on the site are also arranged according to the design plan. The landscape engineering method produced the construction of a rainwater harvester with a volume of 10 m3. Site plan interpretations are explained in more detail through the site section, design details, and some illustrations.

VCS#9. Unapproved Materials From Approved Suppliers

This case study describes an abrupt and unexpected technical manufacturing problem caused by changes in the physical properties of a formulation ingredient. Manufacturing of a validated process could not be accomplished despite recently completed successful validation. Investigation determined a technical root cause, and also identified problems with practices in several site function areas. Practices in the site Materials Management function were significant in this event. Not all pharma personnel understand that materials from an approved supplier may not be universally acceptable in manufacturing – validation problems may have unlikely sources.

TRAIL - An Experimental Trace and Residue Reference Library for the functional analysis of stone tools in Liège

The document presents the experimental reference library for wear traces and residues on stone tools that has been created at TraceoLab, University of Liège, Belgium. This collection has been named TRAIL (“Traces In Liège”) and intends to provide a route (a trail) towards improved understanding of archaeological wear traces and residues. Through that means, it aims to contribute to an improved understanding of prehistoric stone tools, technologies, site function and past human behaviour. TRAIL has been gradually build up since the creation of TraceoLab in 2012. Since only part of the collection has been integrated in publications up to now, general details are included here on how the reference library is composed. This document serves as a basis to understand the composition of TRAIL and to gain insight in which publications of TraceoLab members contain what parts of the TRAIL reference library. This document will be gradually expanded upon as experiments proceed.

Towards an understanding of retouch flakes: A use-wear blind test on knapped stone microdebitage

The retouching and resharpening of lithic tools during their production and maintenance leads to the production of large numbers of small flakes and chips known as microdebitage. Standard analytical approaches to this material involves the mapping of microartefact densities to identify activity areas, and the creation of techno-typologies to characterise the form of retouch flakes from different types of tools. Whilst use-wear analysis is a common approach to the analysis of tools, it has been applied much less commonly to microdebitage. This paper contends that the use-wear analysis of microdebitage holds great potential for identifying activity areas on archaeological sites, representing a relatively unexplored analytical resource within microartefact assemblages. In order to test the range of factors that affect the identification of use-wear traces on small retouch flakes, a blind test consisting of 40 retouch flakes was conducted. The results show that wear traces can be identified with comparable levels of accuracy to those reported for historic blind tests of standard lithic tools suggesting that the use-wear analysis of retouch flakes can be a useful analytical tool in understanding site function, and in increasing sample sizes in cases where assemblages contain few tools.

Aboriginal plant use in the central Rocky Mountains: Macrobotanical records from three prehistoric sites in Birch Creek Valley, eastern Idaho

Recent excavations at three prehistoric sites in eastern Idaho recovered a moderate amount of culturally-introduced macrobotanical remains, including mountain ball and prickly pear cactus, goosefoot, sunflower, and tobacco, all of which came from contexts dating between 1500 B.C. and A.D. 1000. Within the greater region, cactus, goosefoot, and sunflower were first used by people between ca. 11,000 and 8500 B.C., whereas the archaeobotanical record for tobacco dates back to 10,300 B.C. The Birch Creek Valley data set allows us to explore aspects of local site function and settlement practices, as well as the temporal range and ubiquity of the above-listed taxa within the northern Intermountain West and adjacent portions of the central Rocky Mountains.

Cytochrome b6f complex inhibition by antimycin-A requires Stt7 kinase activation but not PGR5

Ferredoxin-plastoquinone reductase (FQR) activity during cyclic electron flow (CEF) was first ascribed to the cytochrome b6f complex (b6f). However, this was later dismissed since b6f inhibition by antimycin-A (AA) could not be reproduced. AA presumably fails to ligate with haem bh, at variance with cytochrome bc1 complex, owing to a specific Qi-site occupation in b6f. Currently, PROTON GRADIENT REGULATION5 (PGR5) and the associated PGR5-Like1 are considered as FQR in the AA-sensitive CEF pathway. Here, we show that the b6f is conditionally inhibited by AA in a PGR5-independent manner when CEF is promoted. AA inhibition, demonstrated by single b6f turnover and electron transfer measurements, coincided with an altered Qi-site function which required Stt7 kinase activation by a strongly reduced plastoquinone pool. Thus, PGR5 and Stt7 were necessary for b6f activity and AA-sensitive electron transfer in CEF-favouring conditions. Extending previous findings, a new FQR activity model of the b6f is discussed.

Antibodies that conformationally activate ADAMTS13 allosterically enhance metalloprotease domain function

Plasma ADAMTS13 circulates in a folded conformation that is stabilized by an interaction between the central Spacer domain and the C-terminal CUB (complement components C1r and C1s, sea urchin protein Uegf, and bone morphogenetic protein-1) domains. Binding of ADAMTS13 to the VWF D4(-CK) domains or to certain activating murine monoclonal antibodies (mAbs) induces a structural change that extends ADAMTS13 into an open conformation that enhances its function. The objective was to characterize the mechanism by which conformational activation enhances ADAMTS13-mediated proteolysis of VWF. The activating effects of a novel anti-Spacer (3E4) and the anti-CUB1 (17G2) mAbs on the kinetics of proteolysis of VWF A2 domain fragments by ADAMTS13 were analyzed. mAb-induced conformational changes in ADAMTS13 were investigated by enzyme-linked immunosorbent assay. Both mAbs enhanced ADAMTS13 catalytic efficiency (kcat/Km) by ∼twofold (3E4: 2.0-fold; 17G2: 1.8-fold). Contrary to previous hypotheses, ADAMTS13 activation was not mediated through exposure of the Spacer or cysteine-rich domain exosites. Kinetic analyses revealed that mAb-induced conformational extension of ADAMTS13 enhances the proteolytic function of the metalloprotease domain (kcat), rather than augmenting substrate binding (Km). A conformational effect on the metalloprotease domain was further corroborated by the finding that incubation of ADAMTS13 with either mAb exposed a cryptic epitope in the metalloprotease domain that is normally concealed when ADAMTS13 is in a closed conformation. We show for the first time that the primary mechanism of mAb-induced conformational activation of ADAMTS13 is not a consequence of functional exosite exposure. Rather, our data are consistent with an allosteric activation mechanism on the metalloprotease domain that augments active site function.

Assessment of Functional Recovery and Subjective Donor-Site Morbidity Following Radial Forearm Flap Reconstruction in Small- to Moderate-Sized Palatal Defects

Context: Palatal defects are encountered following tumor extirpation, trauma, or congenitally. Among the known alternatives, radial artery free forearm flap (RAFF) is a versatile flap that confers good results in head and neck reconstruction, but donor-site morbidity has been an issue of discontent among the plastic surgeons. This limitation needs to be studied further and addressed considering the unmatched quality of this tissue. Aims: This study aims to weigh the impact of the functional edge of this flap against the unpopular donor-site morbidity on a group of patients. Settings and Design: This is a retrospective analysis of recuperation of palatal function and patient concerns with the donor-site function and cosmesis on 7 consecutive patients with small-to-moderate palatal defects reconstructed with RAFF. Methods and Materials: Postoperative recovery of speech, palatal movement, and restoration of oromaxillary interface was assessed using objective tests, such as speech intelligibility testing and articulation studies. Simultaneously, subjective donor-site function and cosmesis were assessed using Patient Scar Assessment Scale (PSAS), Upper Extremity Functional Index (UEFI), and donor limb sensory testing. Results and Conclusion: Mean PSAS score was 8.28/60, and UEFI score reported was 77/80, which reflect high patient satisfaction with the donor site. Nasoendoscopy shows remarkable restoration of palate anatomy. Intelligibility testing depicts near-normal speech understandability, whereas articulation studies revealed distortions post-palatal reconstruction with RAFF. Radial artery free forearm flap should be considered as the forerunner of reconstruction in palatal defects involving less than 50%.