Introductory Analysis and Validation of CUT&RUN Sequencing Data.

The CUT&RUN technique facilitates detection of protein-DNA interactions across the genome. Typical applications of CUT&RUN include profiling changes in histone tail modifications or mapping transcription factor chromatin occupancy. Widespread adoption of CUT&RUN is driven, in part, by technical advantages over conventional ChIP-seq that include lower cell input requirements, lower sequencing depth requirements, and increased sensitivity with reduced background signal due to a lack of cross-linking agents that otherwise mask antibody epitopes.

Conformational switching of Arp5 subunit regulates INO80 chromatin remodeling.

The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80's ATPase activity to nucleosome movement. We find two distinct regions of Arp5 binding near the acidic pocket of nucleosomes.

Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling.

The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80's ATPase activity to nucleosome movement. Our investigation reveals that the grappler domain of Arp5 interacts with the acidic pocket of nucleosomes through two distinct mechanisms: an arginine anchor or a hydrophobic/acidic patch.

Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment.

RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators.

The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development.

ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins.

New insights into the mechanism and DNA-sequence specificity of INO80 chromatin remodeling.

The INO80 complex stood out in a large family of ATP-dependent chromatin remodelers because of its ATPase domain binding and translocating on DNA at the edge of nucleosomes, rather than at two helical turns from the center of DNA that is wrapped around nucleosomes. This unique property of INO80 was thought to account for its singular role in nucleosome placement at gene promoters in a DNA-sequence dependent manner that is crucial for transcription regulation. Now, we uncover INO80 functions differently than previously thought with its ATPase domain translocating on DNA close to the center of nucleosomes, like other remodelers.

The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming.

The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA.

Borylated 2,3,4,5-Tetrachlorophthalimide and Their 2,3,4,5-Tetrachlorobenzamide Analogues: Synthesis, Their Glycosidase Inhibition and Anticancer Properties in View to Boron Neutron Capture Therapy.

Tetrachlorinated phthalimide analogues bearing a boron-pinacolate ester group were synthesised via two synthetic routes and evaluated in their glycosidase modulating and anticancer properties, with a view to use them in boron neutron capture therapy (BNCT), a promising radiation type for cancer, as this therapy does little damage to biological tissue. An unexpected decarbonylation/decarboxylation to five 2,3,4,5-tetrachlorobenzamides was observed and confirmed by X-ray crystallography studies, thus, giving access to a family of borylated 2,3,4,5-tetrachlorobenzamides. Biological evaluation showed the benzamide drugs to possess good to weak potencies (74.

Synthesis of ()()-Tiruchanduramine.

The absolute stereochemistry of the marine alkaloid ()-()-tiruchanduramine was established via a convergent total synthesis in six steps and 15.5% overall yield from Fmoc-D-Dab(Boc)-OH.

B.M.Barthol. & K.Armstr., sp. nov. (Dipentodontaceae), a new species from northwestern Yunnan Province, China and northern Kachin State, Myanmar and a re-examination of the Asian and Australasian taxa of .

from the Dulong Jiang valley in northwestern Yunnan Province, China and the Babulongtan mountain range in northern Kachin State, Myanmar is here described as a new species of the Dipentodontaceae. It is the third species of the genus to be recognized for China and the first to be reported for Myanmar. It is similar to but differs by characters of its leaf margins, inflorescences, and fruit.

Video-assisted reflection: improving OSCE feedback.

Background: Objective Structured Clinical Examinations (OSCEs) are commonly used to provide feedback to students on their performance in formative examinations. However, students are often unable to act independently on the feedback they receive. This study explored how the use of video-assisted reflection in OSCEs can enhance students' ability to reflect and engage in sustainable feedback.

Grade of Membership models reveal geographical and environmental correlates of floristic structure in a temperate biodiversity hotspot.

Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south-central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors. With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai-Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns.

Temperate Zone Plant Natural Products-A Novel Resource for Activity against Tropical Parasitic Diseases.

The use of plant-derived natural products for the treatment of tropical parasitic diseases often has ethnopharmacological origins. As such, plants grown in temperate regions remain largely untested for novel anti-parasitic activities. We describe here a screen of the PhytoQuest Phytopure library, a novel source comprising over 600 purified compounds from temperate zone plants, against in vitro culture systems for , , and .

Taste Ratings of Healthier Main and Side Dishes among 4-to-8-Year-Old Children in a Quick-Service Restaurant Chain.

Restaurants are regular eating environments for many families. Children's consumption of restaurant foods has been linked with poorer diet quality, prompting emerging research examining strategies to encourage healthier eating among children in restaurants. Although taste is a primary determinant of restaurant meal choices, there is a lack of research considering children's perspectives on the taste of different healthier kids' meal options.

Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation.

Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA.

Iminosugar idoBR1 Isolated from Cucumber Reduces Inflammatory Activity.

Cucumbers have been anecdotally claimed to have anti-inflammatory activity for a long time, but the active principle was not identified. idoBR1, (2,3,4,5)-3,4,5-trihydroxypiperidine-2-carboxylic acid, is an iminosugar amino acid isolated from fruits of certain cucumbers, (Cucurbitaceae). It has no chromophore and analytically behaves like an amino acid making detection and identification difficult.

Simulated on-call: time well spent.

Background: Newly qualified doctors feel unprepared to take responsibility for patients and work independently, lacking confidence in skills essential during on-calls. We designed this study to assess the educational value of simulated on-calls and to explore the characteristics of this approach that contribute to improving students' preparedness.

Methods: A total of 38 final-year medical students attended two sessions, each including a simulated on-call followed by a one-to-one debriefing.

Author Correction: De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Once-daily tigecycline for outpatient parenteral antibiotic therapy: a single-centre observational study.

Background: Tigecycline has potential utility in the treatment of complex polymicrobial infections or those caused by MDR organisms in the ambulatory care setting owing to its breadth of antimicrobial coverage. Whilst licensed for twice-daily IV administration, its long half-life permits once-daily administration, which may facilitate successful outpatient parenteral antibiotic therapy (OPAT).

Methods: A retrospective case series of patients receiving once-daily tigecycline under OPAT was analysed at a single-centre NHS acute hospital (January 2016-June 2018).

De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens.

High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins.

Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling.

Nucleosomes are the fundamental building blocks of chromatin that regulate DNA access and are composed of histone octamers. ATP-dependent chromatin remodelers like ISW2 regulate chromatin access by translationally moving nucleosomes to different DNA regions. We find that histone octamers are more pliable than previously assumed and distorted by ISW2 early in remodeling before DNA enters nucleosomes and the ATPase motor moves processively on nucleosomal DNA.

Comparison of three different surgical techniques for designing pharyngeal flaps according to findings of videonasopharyngoscopy and multiplanar videofluoroscopy.

Background: Velopharyngeal insufficiency (VPI) occurs when the velopharyngeal sphincter (VPS) is unable to completely seal anatomical closure between the nasal and oral cavities during speech. Palatal repair can restore VPS function but the prevalence of VPI after repair has been reported ranging from 20% to 40%. The combination of flexible videonasopharyngoscopy (FVNP) and multiplanar videofluoroscopy (MPVF) has been reported as the best approach for assessing the VPS mechanism and planning effective surgical procedures aimed to correct VPI.

Regulation of ATP-dependent chromatin remodelers: accelerators/brakes, anchors and sensors.

All ATP-dependent chromatin remodelers have a DNA translocase domain that moves along double-stranded DNA when hydrolyzing ATP, which is the key action leading to DNA moving through nucleosomes. Recent structural and biochemical data from a variety of different chromatin remodelers have revealed that there are three basic ways in which these remodelers self-regulate their chromatin remodeling activity. In several instances, different domains within the catalytic subunit or accessory subunits through direct protein-protein interactions can modulate the ATPase and DNA translocation properties of the DNA translocase domain.

An Abies procera-derived tetracyclic triterpene containing a steroid-like nucleus core and a lactone side chain attenuates in vitro survival of both Fasciola hepatica and Schistosoma mansoni.

Two economically and biomedically important platyhelminth species, Fasciola hepatica (liver fluke) and Schistosoma mansoni (blood fluke), are responsible for the neglected tropical diseases (NTDs) fasciolosis and schistosomiasis. Due to the absence of prophylactic vaccines, these NTDs are principally managed by the single class chemotherapies triclabendazole (F. hepatica) and praziquantel (S.