Goldilocks meets Polycomb.

The Polycomb system modulates chromatin structure to maintain gene repression during cell differentiation. Polycomb repression involves methylation of histone H3K27 (H3K27me3) by Polycomb repressive complex 2 (PRC2), monoubiquitylation of H2A (H2Aub1) by noncanonical PRC1 (ncPRC1), and chromatin compaction by canonical PRC1 (cPRC1), which is independent of its enzymatic activity. Puzzlingly, Polycomb repression also requires deubiquitylation of H2Aub1 by Polycomb repressive deubiquitinase (PR-DUB). In this issue of Genes & Development, Bonnet and colleagues (pp. 1046-1061) resolve this paradox by showing that high levels of H2Aub1 in Drosophila lacking PR-DUB activity promotes open chromatin and gene expression in spite of normal H3K27me3 levels and PRC binding. Pertinently, gene repression is restored by concomitant loss of PRC1 E3 ubiquitin ligase activity but depends on its chromatin compaction activity. These findings suggest that PR-DUB ensures just-right levels of H2Aub1 to allow chromatin compaction by cPRC1.

PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of chromatin compaction.

The Polycomb repressive complexes PRC1, PRC2, and PR-DUB repress target genes by modifying their chromatin. In Drosophila, PRC1 compacts chromatin and monoubiquitinates histone H2A at lysine 118 (H2Aub1), whereas PR-DUB is a major H2Aub1 deubiquitinase, but how H2Aub1 levels must be balanced for Polycomb repression remains unclear. We show that in early embryos, H2Aub1 is enriched at Polycomb target genes, where it facilitates H3K27me3 deposition by PRC2 to mark genes for repression. During subsequent stages of development, H2Aub1 becomes depleted from these genes and is no longer enriched when Polycomb maintains them repressed. Accordingly, Polycomb targets remain repressed in H2Aub1-deficient animals. In PR-DUB catalytic mutants, high levels of H2Aub1 accumulate at Polycomb target genes, and Polycomb repression breaks down. These high H2Aub1 levels do not diminish Polycomb protein complex binding or H3K27 trimethylation but increase DNA accessibility. We show that H2Aub1 interferes with nucleosome stacking and chromatin fiber folding in vitro. Consistent with this, Polycomb repression defects in PR-DUB mutants are exacerbated by reducing PRC1 chromatin compaction activity, but Polycomb repression is restored if PRC1 E3 ligase activity is removed. PR-DUB therefore acts as a rheostat that removes excessive H2Aub1 that, although deposited by PRC1, antagonizes PRC1-mediated chromatin compaction.

Computational Investigation of Conformational Properties of Short Azapeptides: Insights from DFT Study and NBO Analysis.

Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential application in the peptide drug design, remain largely unknown. In this work, we systematically investigated the conformational preferences of three azaamino acid residues in tripeptide models, Ac-azaXaa-Pro-NHMe [Xaa = Asn (4), Asp (5), Ala (6)], using the popular DFT functionals, B3LYP and B3LYP-D3. A solvation model density (SMD) was used to mimic the solvation effect on the conformational behaviors of azapeptides in water. During the calculation, we considered the impact of the amide bond in the azapeptide models on the conformational preferences of models 4-6. We analyzed the effect of the HB between the side-chain main chain and main-chain main-chain on the conformational behaviors of azapeptides 4-6. We found that the predicted lowest energy conformation for the three models differs depending on the calculation methods. In the gas phase, B3LYP functional indicates that the conformers tttANP-1 and tttADP-1 of azapeptides 4 and 5 correspond to the type I of ß-turn, the lowest energy conformation with all-trans amide bonds. Considering the dispersion correction, B3LYP-D3 functional predicts the conformers tctANP-2 and tctADP-3 of azapeptide 4 and 5, which contain the cis amide bond preceding the Pro residue, as the lowest energy conformation in the gas phase. The results imply that azaAsx and Pro residues may involve cis-trans isomerization in the gas phase. In water, the predicted lowest energy conformer of azapeptides 4 and 5 differs from the gas phase results and depends on the calculational method. For azapeptide 6, regardless of calculation methods and phases, tttAAP-1 (ß-I turn) is predicted as the lowest energy conformer. The results imply that the effect of the side chain that can form HBs on the conformational preferences of azapeptides 4 and 5 may not be negligible. We compared the theoretical results of azaXaa-Pro models with those of Pro-azaXaa models, showing that incorporating azaamino acid residue in peptides at different positions can significantly impact the folding patterns and stability of azapeptides.

Characterization of Asx Turn Types and Their Connate Relationship with ß-Turns.

Models of asparagine-containing dipeptides specifically designed to favor intrinsic folding into an Asx turn were characterized both theoretically, by using quantum chemistry, and experimentally, by using laser spectroscopy in the gas phase. Both approaches provided evidence for the spontaneous folding of both the Asn-Ala and Asn-Gly dipeptide models into the most stable Asx turn, a conformation stabilized by a C10 H-bond that was very similar to a type II' ß-turn. In parallel, analysis of Asx turns implicating asparagine in crystallized protein structures in the Protein Data Bank revealed a sequence-dependent behavior. In Asn-Ala sequences, the Asx turn was found in conjunction with a type I ß-turn for which the first of the four defining residues was Asn. The observation that the Asx turn in these structures is mostly of type II' (i. e., its most stable innate structure) suggests that this motif might foster the formation and/or enhance the stability of the backbone ß-turn. In contrast, the Asx turns observed in Asn-Gly sequences extensively adopted a type II Asx-turn structure, thus suggesting that their formation should be ascribed to other factors, such as hydration. The fact that the Asx turn in a Asn-Gly sequence is also often found in combination with a hydrated ß-bulge supports the premise that a Asn-Gly sequence might efficiently promote the formation of the ß-bulge secondary structure.

Role of astaxanthin in the modulation of brain-derived neurotrophic factor and spatial learning behavior in perinatally undernourished Wistar rats.

Objective: Maternal health and nutrition during the perinatal period is the predominant factor influencing the functional development of the brain. Maternal malnutrition during the perinatal period causes retardation of brain development. The current study investigates the role of Astaxanthin (AsX) in spatial learning and memory and BDNF in perinatally undernourished Wistar rats.Methods: The albino wistar rats were perinatally undernourished and administered with different dosages of AsX. The spatial learning and memory performance and BDNF level were assessed. Data were collected and analysed.Results: The % Correct choice during the acquisition phase, performance at the end of the acquisition phase and the mean BDNF level at the Hippocampus, Cerebellum, and Cerebral cortex showed significant decline (P<0.001) in the PUN group and significantly high (P<0.001) in the PUNA2 group compared to the control. However, the mean RME and mean WME during different days of the acquisition phase were significantly high (P<0.001) in the PUN group and insignificant (P>0.05) in PUNA2 compared to the control.Discussion: The results showed that AsX effectively modulated the cognitive deficit that occurred in perinatally undernourished rats. This can be attributed to BDNF upregulation as evidenced by the significant increase of the BDNF level.

Evaluation of hepatoprotective and antioxidant activity of astaxanthin and astaxanthin esters from microalga-Haematococcus pluvialis.

Effect of isolated astaxanthin (ASX) and astaxanthin esters (ASXEs) from green microalga-Haematococcus pluvialis on hepatotoxicity and antioxidant activity against carbon tetrachloride (CCl4) induced toxicity in rats was compared with synthetic astaxanthin (SASX). ASX, ASXEs, and SASX, all dissolved in olive oil, fed to rats with 100 and 250 µg/kg b.w for 14 days. They were evaluated for their hepatoprotective and antioxidant activity by measuring appropriate enzymes. Among the treated groups, the SGPT, SGOT and ALP levels were decreased by 2, 2.4, and 1.5 fold in ASXEs treated group at 250 µg/Kg b.w. when compared to toxin group. Further, antioxidant enzymes catalase, glutathione, superoxide dismutase and lipid peroxidase levels were estimated in treated groups, their levels were reduced by 30-50 % in the toxin group, however these levels restored by 136.95 and 238.48 % in ASXEs treated group at 250 µg/kg. The lipid peroxidation was restored by 5.2 and 2.8 fold in ASXEs and ASX treated groups at 250 µg/kg. The total protein, albumin and bilirubin contents were decreased in toxin group, whereas normalized in ASXEs treated group. These results indicates that ASX and ASXEs have better hepatoprotection and antioxidant activity, therefore can be used in pharmaceutical and nutraceutical applications and also extended to use as food colorant.

Additional sex combs-like family genes are required for normal cardiovascular development.

Congenital heart disease (CHD) is the most common birth defect. However, the majority of CHD cases have unknown etiology. Here we report the identification of ASXL2 and ASXL1, two homologous chromatin factors, as novel regulators of heart development. Asxl2(-/-) fetuses have reduced body weight and display congenital heart malformations including thickened compact myocardium in the left ventricle, membranous ventricular septal defect, and atrioventricular valval stenosis. Although most Asxl2(-/-) animals survive to term, the neonates have patent ductus arteriosus and consequent lung hemorrhage and die soon after birth. Asxl1(-/-) fetuses have reduced body weight and display cleft palate, anophthalmia as well as ventricular septal defects and a failure in lung maturation. From these results, we conclude that normal heart development requires both ASXL proteins. In particular, ASXL2 plays an important role in heart morphogenesis and the transition from fetal to postnatal circulation.

Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins.

The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1ß-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2ß-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond.

A quest for cytosolic sequons and their functions.

Evolution shapes protein sequences for their functions. Here, we studied the moonlighting functions of the N-linked sequon NXS/T, where X is not P, in human nucleocytosolic proteins. By comparing membrane and secreted proteins in which sequons are well known for N-glycosylation, we discovered that cyto-sequons can participate in nucleic acid binding, particularly in zinc finger proteins. Our global studies further discovered that sequon occurrence is largely proportional to protein length. The contribution of sequons to protein functions, including both N-glycosylation and nucleic acid binding, can be regulated through their density as well as the biased usage between NXS and NXT. In proteins where other PTMs or structural features are rich, such as phosphorylation, transmembrane ɑ-helices, and disulfide bridges, sequon occurrence is scarce. The information acquired here should help understand the relationship between protein sequence and function and assist future protein design and engineering.

Why Is the Australian Health Sector So Far behind in Practising Climate-Related Disclosures?

The health sector in Australia and the ASX100 is lagging far behind in the implementation of carbon management and climate risk analysis. This case study highlights the low quantity and quality of the sector compared to its market weight. The analysis of CDP disclosures for Australian healthcare companies shows this delay and a general lack of interest in the Task Force on Climate-Related Financial Disclosures' (TCFD) recommendations. Yet, the physical and transitory risks for these companies do exist. The reasons for this inaction represent a knowledge gap in the literature, but several hypotheses are formulated, such as the lack of pressure from public authorities. At the level of the ten largest healthcare companies in the world, this failure to act is not systemic, so the scope of analysis must be broadened to see a pattern emerging.

COVID-19 outbreak and sectoral performance of the Australian stock market: An event study analysis.

The outbreak of COVID-19 has weakened the economy of Australia and its capital market since early 2020. The overall stock market has declined. However, some sectors become highly vulnerable while others continue to perform well even in the crisis period. Given this new reality, we seek to investigate the initial volatility and the sectoral return. In this study, we analyse data for eight sectors such as, transportation, pharmaceuticals, healthcare, energy, food, real estate, telecommunications and technology of the Australian stock market. In doing so, we obtain data from Australian Securities Exchange (ASX) and analysed them based on 'Event Study' method. Here, we use the 10-days window for the event of official announcement of the COVID-19 outbreak in Australia on 27 February 2020. The findings of the study show that on the day of announcement, the indices for food, pharmaceuticals and healthcare exhibit impressive positive returns. Following the announcement, the telecommunications, pharmaceuticals and healthcare sectors exhibit good performance, while poor performance is demonstrated by the transportation industry. The findings are vital for investors, market participants, companies, private and public policymakers and governments to develop recovery action plans for vulnerable sectors and enable investors to regain their confidence to make better investment decisions.

Examination of information release on return volatility: A market and sectoral analysis.

This paper examines the role of information release in explaining the return volatility of the Australian equity market. The study applies proxies of greater accuracy to examine the effect of public and private information on return volatility. Analyst price targets (PTR) and Morningstar stock star ratings (MSR) were used as private information proxies while Australian Securities Exchange (ASX) announcements were used as the public information proxy. Daily data was collected for ASX 200 listed firms for the period 2013 to 2017. Analysis was conducted at both the aggregate market level and the sectoral level. Findings suggest that PTR have the largest effect on return volatility at both levels, with varied effects within each sector. This indicates that investors rely heavily on this information when undertaking investment decisions. In contrast, MSR had a negligible effect, likely due to the lower degree of informational content. Public information had a minor effect on return volatility at both the aggregate market and sectoral levels. These mixed results show that information flow varies depending on the information type (i.e. public or private) with each sector interpreting the same type of information differently. The research findings provide a valuable guide to investors regarding the appropriate information to generate excess returns as well as to hedge against future losses.

Structural Basis for the Activation of the Deubiquitinase Calypso by the Polycomb Protein ASX.

Ubiquitin C-terminal hydrolase deubiquitinase BAP1 is an essential tumor suppressor involved in cell growth control, DNA damage response, and transcriptional regulation. As part of the Polycomb repression machinery, BAP1 is activated by the deubiquitinase adaptor domain of ASXL1 mediating gene repression by cleaving ubiquitin (Ub) from histone H2A in nucleosomes. The molecular mechanism of BAP1 activation by ASXL1 remains elusive, as no structures are available for either BAP1 or ASXL1. Here, we present the crystal structure of the BAP1 ortholog from Drosophila melanogaster, named Calypso, bound to its activator, ASX, homolog of ASXL1. Based on comparative structural and functional analysis, we propose a model for Ub binding by Calypso/ASX, uncover decisive structural elements responsible for ASX-mediated Calypso activation, and characterize the interaction with ubiquitinated nucleosomes. Our results give molecular insight into Calypso function and its regulation by ASX and provide the opportunity for the rational design of mechanism-based therapeutics to treat human BAP1/ASXL1-related tumors.

Evaluation of astaxanthin incorporated collagen film developed from the outer skin waste of squid Doryteuthis singhalensis for wound healing and tissue regenerative applications.

The present investigation was aimed to evaluate in vivo wound healing activity of astaxanthin incorporated collagen hydrogel film biomaterials extracted from the outer skin waste of squid Doryteuthis singhalensis, to releases antibiotic, delivering potentialities of excisional and incisional wound model in Wistar rats. These results suggested that the astaxanthin incorporated collagen film (ACF) and gentamicin incorporated collagen film (GCF) exhibited excellent wound healing activity (71%) in both full thickness excision and linear incision in rats. The in-vitro antioxidant abilities of extracted astaxanthin exhibited strongly significant 1,1­diphenyl­2­picrylhydrazyl (DPPH) radical scavenging activity. In addition, tensile strength, epithelialization, hydroxyproline content and protein content in ACF and GCF treated groups were significantly increased. Histopathological assessment revealed an increase in collagen content, fibroblasts, granulation, thickness of scar formation, effective neovascularization and faster epithelialization within the short duration after the treatment of ACF and GCF compared to the control groups. The structure of prepared ACF and GCF biomaterials were characterized by SEM, EDS, and XRD. The in vivo biological study of the collagen-based film releases the antibiotic substance. The composite of collagen based biomaterials displays a promising biocompatibility through the dermal wound healing process as well as an evidence of biodegradability. Thus, the marine-derived biomaterials gave a substantial pledge for the development of biodegradable materials in drug delivery and soft tissue regeneration process.

Butelase 1-Mediated Ligation of Peptides and Proteins.

Structurally, butelase 1 is a cysteine protease of the asparaginyl endoprotease (AEP) family, but functionally, it displays intense Asn/Asp-specific (Asx) ligase activity and is virtually devoid of protease activity. Butelase 1 recognizes specifically a C-terminal Asx-containing tripeptide motif, Asx-His-Val, to form an Asx-Xaa peptide bond (Xaa = any amino acid), either intramolecularly or intermolecularly, resulting in cyclic peptides or site-specific modified peptides/proteins, respectively. Our work in the past 4 years has validated that butelase 1 is a potent and versatile tool for peptide and protein modification. Here we describe our protocols using butelase 1 for efficient and site-specific peptide and protein ligation, N-terminal labeling, preparation of thioesters, and bioconjugation of dendrimers. Additionally, we provide an example using butelase 1 for protein cyclization in combination with genetic code expansion in order to incorporate unnatural building blocks.

The major egg reserve protein from the invasive apple snail Pomacea maculata is a complex carotenoprotein related to those of Pomacea canaliculata and Pomacea scalaris.

Snails from the genus Pomacea lay conspicuous masses of brightly colored eggs above the water. Coloration is given by carotenoproteins that also which play important roles in protection against sun radiation, stabilizing and transporting antioxidant molecules and helping to protect embryos from desiccation and predators. They seem a key acquisition, but have been little studied. Here we report the characteristics of the major carotenoprotein from Pomacea maculata and the first comparison among these egg proteins. This particle, hereafter PmPV1, represents ~52% of perivitellin fluid protein. It is a glyco-lipo-carotenoprotein responsible for the bright reddish egg coloration. With VHDL characteristics, PmPV1 apparent molecular mass is 294kDa, composed of five non-covalently bound subunits of pI 4.7-9.8 and masses between 26 and 36kDa whose N-terminal sequences were obtained. It is a glyco-lipo-carotenoprotein scarcely lipidated (<1%) but highly glycosilated (13% by wt). Lipids include phospholipids, free fatty acids and carotenoids; mannose and galactose predominate over other monosaccharides. Main carotenoids are esterified and non-esterified astaxanthin (71 and 25%, respectively). Carotenoid removal does not seem to affect the structural characteristics of the oligomer, while deglycosilation reduces subunit number from five to a single one. The carotenoid-protein association protected the former against oxidation. PmPV1 cross reacts with polyclonal antibodies against the PcOvo, the major carotenoprotein from Pomacea canaliculata. The characterization of PmPV1 allows the first comparisons among snail carotenoproteins and further highlights the importance of these perivitellins in the reproductive strategy of Pomacea.