Intact Site Research Articles

Victims of Heritage Crimes: Aspects of Legal and Socio-Economic Justice

Abstract The aim of this research is to show how different groups of stakeholders are suffering as a result of heritage crime. Research primarily addresses Latvian situation (with international comparisons) in relation to archaeological sites as the most vulnerable, however, the findings can be applicable to other heritage objects and broader territory as well. Most of these stakeholders are currently limited in, if not denied, access to justice and rights for an effective remedy within the traditional criminal law system. Insufficient level of social awareness of socio-economic benefits and rights stemming from integrity, development, and use of archaeological sites together with existing legal constraints results in poor self-recognition by individuals and groups as victims of heritage crime. While suffered parties abstain from protecting their rights, there is lack of information and proactive action from public authorities including law enforcement. Current research analyses the nature and scope of immediate harm resulted from the damage of archaeological sites and the extended consequences of the heritage crime for the different stakeholders’ groups. It points at the inefficiency of standard retributive approach and evaluates benefits of restorative justice elements in reaching justice for heritage crime victims. The results could be used for better recognition of benefits, and therefore rights, stemming from intact archaeological sites, amending legal regulation, providing access to justice for suffered individual and collective parties, allowing recognition of mass victimisation and facilitating prevention of heritage crime.

Active Zone Trafficking of CaV2/UNC-2 Channels Is Independent of β/CCB-1 and α2δ/UNC-36 Subunits.

The CaV2 voltage-gated calcium channel is the major conduit of calcium ions necessary for neurotransmitter release at presynaptic active zones (AZs). The CaV2 channel is a multimeric complex that consists of a pore-forming α1 subunit and two auxiliary β and α2δ subunits. Although auxiliary subunits are critical for channel function, whether they are required for α1 trafficking is unresolved. Using endogenously fluorescent protein-tagged CaV2 channel subunits in Caenorhabditis elegans, we show that UNC-2/α1 localizes to AZs even in the absence of CCB-1/β or UNC-36/α2δ, albeit at low levels. When UNC-2 is manipulated to be trapped in the endoplasmic reticulum (ER), CCB-1 and UNC-36 fail to colocalize with UNC-2 in the ER, indicating that they do not coassemble with UNC-2 in the ER. Moreover, blocking ER-associated degradation does not further increase presynaptic UNC-2 channels in ccb-1 or unc-36 mutants, indicating that UNC-2 levels are not regulated in the ER. An unc-2 mutant lacking C-terminal AZ protein interaction sites with intact auxiliary subunit binding sites displays persistent presynaptic UNC-2 localization and a prominent increase of UNC-2 channels in nonsynaptic axonal regions, underscoring a protective role of auxiliary subunits against UNC-2 degradation. In the absence of UNC-2, presynaptic CCB-1 and UNC-36 are profoundly diminished to barely detectable levels, indicating that UNC-2 is required for the presynaptic localization of CCB-1 and UNC-36. Together, our findings demonstrate that although the pore-forming subunit does not require auxiliary subunits for its trafficking and transport to AZs, it recruits auxiliary subunits to stabilize and expand calcium channel signalosomes.SIGNIFICANCE STATEMENT Synaptic transmission in the neuron hinges on the coupling of synaptic vesicle exocytosis with calcium influx. This calcium influx is mediated by CaV2 voltage-gated calcium channels. These channels consist of one pore-forming α1 subunit and two auxiliary β and α2δ subunits. The auxiliary subunits enhance channel function and regulate the overall level of channels at presynaptic terminals. However, it is not settled how these auxiliary subunits regulate the overall channel level. Our study in C. elegans finds that although the auxiliary subunits do not coassemble with α1 and aid trafficking, they are recruited to α1 and stabilize the channel complex at presynaptic terminals. Our study suggests that drugs that target the auxiliary subunits can directly destabilize and have an impact on CaV2 channels.

Interpreting and validating complexity and causality in lesion-symptom prognoses.

This paper considers the steps needed to generate pragmatic and interpretable lesion-symptom mappings that can be used for clinically reliable prognoses. The novel contributions are 3-fold. We first define and inter-relate five neurobiological and five methodological constraints that need to be accounted for when interpreting lesion-symptom associations and generating synthetic lesion data. The first implication is that, because of these constraints, lesion-symptom mapping needs to focus on probabilistic relationships between Lesion and Symptom, with Lesion as a multivariate spatial pattern, Symptom as a time-dependent behavioural profile and evidence that Lesion raises the probability of Symptom. The second implication is that in order to assess the strength of probabilistic causality, we need to distinguish between causal lesion sites, incidental lesion sites, spared but dysfunctional sites and intact sites, all of which might affect the accuracy of the predictions and prognoses generated. We then formulate lesion-symptom mappings in logical notations, including combinatorial rules, that are then used to evaluate and better understand complex brain-behaviour relationships. The logical and theoretical framework presented applies to any type of neurological disorder but is primarily discussed in relationship to stroke damage. Accommodating the identified constraints, we discuss how the 1965 Bradford Hill criteria for inferring probabilistic causality, post hoc, from observed correlations in epidemiology-can be applied to lesion-symptom mapping in stroke survivors. Finally, we propose that rather than rely on post hoc evaluation of how well the causality criteria have been met, the neurobiological and methodological constraints should be addressed, a priori, by changing the experimental design of lesion-symptom mappings and setting up an open platform to share and validate the discovery of reliable and accurate lesion rules that are clinically useful.

A large-scale field experiment across six rivers illustrates how the effects of resource enrichment are context dependent

Resource supplementation can increase species richness and change the faunal composition of communities, but experiments have produced variable outcomes. An often overlooked element is that species richness can only increase if new taxa can disperse to resource-rich locations and invade established, local communities. We experimentally increased a basal resource (detritus) in six rivers in south-eastern Australia by driving wooden stakes into the riverbed to increase retention of detritus. Control sites were left untreated. Sites were located in agricultural sections with mostly cleared vegetation, but with intact (uncleared) reference sites upstream to provide sources of prospective colonists. We measured channel retentiveness and sampled benthic detritus and invertebrates before and after manipulation. We tested whether: greater retentiveness increased detritus densities, species richness and abundances and altered faunal composition; manipulation sites reached bio-equivalence with reference sites; new species arose from upstream reference areas; and whether outcomes were consistent across rivers. Only three rivers gained increases in detritus densities. All had low pre-existing amounts of in-stream wood compared with rivers that did not respond to treatment. Two rivers (Hughes Creek, Seven Creeks) gained higher species richness and invertebrate densities within 12 months and reached bio-equivalence with reference sites. In contrast, Turtons Creek showed species turnover through replacement of individuals. Only in Hughes Creek was there evidence of successful dispersal from the upstream reference area. The outcomes show that the effects of resource supplementation vary between rivers and suggest that pre-existing conditions (e.g. channel retentiveness) may cause these differences, providing clear evidence of context dependence.

Structural insights into SARS-CoV-2 main protease conformational plasticity.

The spread of different severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin-like protease (3CL MPRO ), belonging to the class of cysteine hydrolases, plays an indispensable role in processing viral polyproteins that are involved in viral replication and transcription. Studies have successfully demonstrated the role of MPRO as an attractive drug target for designing antiviral treatments because of its importance in the viral life cycle. Herein, we report the structural dynamics of six experimentally solved structures of MPRO (i.e.,6LU7, 6M03, 6WQF, 6Y2E, 6Y84, and 7BUY including both ligand-free and ligand-bound states) at different resolutions. We have employed a structure-based balanced forcefield, CHARMM36m through state-of-the-art all-atoms molecular dynamics simulations at µ-seconds scale at room temperature(303K) and pH 7.0 to explore their structure-function relationship. The helical domain-III responsible for dimerization mostly contributes to the altered conformational states and destabilization of MPRO . A keen observation of the high degree of flexibility in the P5 binding pocket adjoining domain II-III highlights the reason for observation of conformational heterogeneity among the structural ensembles of MPRO . We also observe a differential dynamics of the catalytic pocket residues His41, Cys145, and Asp187, which may lead to catalytic impairment of the monomeric proteases. Among the highly populated conformational states of the six systems, 6LU7 and 7M03 forms the most stable and compact MPRO conformation with intact catalytic site and structural integrity. Altogether, our findings from this extensive study provides a benchmark to identify physiologically relevant structures of such promising drug targets for structure-based drug design and discovery of potent drug-like compounds having clinical potential.

MmuPV1 E7's interaction with PTPN14 delays Epithelial differentiation and contributes to virus-induced skin disease.

Human papillomaviruses (HPVs) contribute to approximately 5% of all human cancers. Species-specific barriers limit the ability to study HPV pathogenesis in animal models. Murine papillomavirus (MmuPV1) provides a powerful tool to study the roles of papillomavirus genes in pathogenesis arising from a natural infection. We previously identified Protein Tyrosine Phosphatase Non-Receptor Type 14 (PTPN14), a tumor suppressor targeted by HPV E7 proteins, as a putative cellular target of MmuPV1 E7. Here, we confirmed the MmuPV1 E7-PTPN14 interaction. Based on the published structure of the HPV18 E7/PTPN14 complex, we generated a MmuPV1 E7 mutant, E7K81S, that was defective for binding PTPN14. Wild-type (WT) and E7K81S mutant viral genomes replicated as extrachromosomal circular DNAs to comparable levels in mouse keratinocytes. E7K81S mutant virus (E7K81S MmuPV1) was generated and used to infect FoxN/Nude mice. E7K81S MmuPV1 caused neoplastic lesions at a frequency similar to that of WT MmuPV1, but the lesions arose later and were smaller than WT-induced lesions. The E7K81S MmuPV1-induced lesions also had a trend towards a less severe grade of neoplastic disease. In the lesions, E7K81S MmuPV1 supported the late (productive) stage of the viral life cycle and promoted E2F activity and cellular DNA synthesis in suprabasal epithelial cells to similar degrees as WT MmuPV1. There was a similar frequency of lateral spread of infections among mice infected with E7K81S or WT MmuPV1. Compared to WT MmuPV1-induced lesions, E7K81S MmuPV1-induced lesions had a significant expansion of cells expressing differentiation markers, Keratin 10 and Involucrin. We conclude that an intact PTPN14 binding site is necessary for MmuPV1 E7's ability to contribute to papillomavirus-induced pathogenesis and this correlates with MmuPV1 E7 causing a delay in epithelial differentiation, which is a hallmark of papillomavirus-induced neoplasia.

Изменчивость биоразнообразия ассамблей жужелиц (Coleoptera, Carabidae) верхового болота при антропогенной трансформации их местообитаний

The presented research demonstrated the features of the variability of the biodiversity of the carabid assemblages in the peat bog with the different degrees of transformation in the Belarusian Lake District. The material was collected using pitfall traps in a peat bog, part of which was drained by a network of reclamation canals. The studies were carried out on an intact site (control) with specialized peat bog vegetation and on three sites of different degrees of transformation: a site with a partially disturbed sphagnum cover, peat fields with a removed sphagnum cover (open peat), and drained sites with a removed sphagnum mat covered with trees and shrubs. Differentiation of a- and в-diversity in areas of different degrees of anthropogenic transformation was revealed. The average number of species (x2 = 10.72, p = 0.01) and individuals (F = 57.54, p = 0.001) in the samples differed significantly. If the sphagnum cover was disturbed or completely removed, the number of species decreases as compared to the control biotopes. Whereas during the formation of tree and bush cover, on the contrary, species richness increases. The average number of individuals decreases, except for sites with partially disturbed sphagnum cover. With an increase in anthropogenic transformation, species diversity and evenness was higher compared to the control (H’ = 1.54 ± 0.05, J’ = 0.42 ± 0.03) and reach a maximum in sites with woody vegetation (H’ = 2.48 ± 0.38, J’ = 0.97 ± 0.11). The values of the Shannon diversity index (x2 = 14.57, p = 0.002) and the Pielou evenness index (F = 18.44, p = 0.001) differed significantly in all studied habitats. The analysis of в-diversity demonstrated significant differences in the species composition of ground beetle assemblages in sites with different degrees of transformation (ANOSIM; R = 0.90, p = 0.0001). The species composition and dominance structure of ground beetle assemblages undergo the greatest changes when the sphagnum cover is completely removed. At the same time, the composition of the group of dominants is significantly expanding. Specialized raised bog species Agonum ericeti (Panzer, 1809), Pterostichus diligens (Sturm, 1824) and P. rhaeticus Heer, 1838 were replaced by open space dwellers and eurytopic species such as Cicindela sylvatica Linnaeus, 1758, Poecilus cupreus (Linnaeus, 1758), P. versicolor (Sturm, 1824), Agonum sexpunctatum (Linnaeus, 1758), Harpalus latus (Linnaeus, 1758).

Ecological River Water Quality Based on Macroinvertebrates Present in the Ecuadorian Amazon

The Yanaquincha River is one of the tributaries that crosses the canton of La Joya de los Sachas from north to south, where the increase in human activities is affecting the quality of water used for agricultural activities and in tourist resorts. The purpose of this research was to determine the biological quality of the water through the BMWP-Col index and physicochemical parameters. Five sampling sites were selected along the length of the river for this assessment. Relatively intact sites were classified as reference sites (BR and FR), moderately impacted sites (EPC and EFPC), and severely impacted sites (PC). Biological and physicochemical data were collected to examine the quality of the water. The Biological Monitoring Working Party Colombia (BMWP-Col) biotic index and Functional Feeding Group (FFG) grouping were used to evaluate river quality. The results showed that water temperature, depth, width, and turbidity are important parameters in the composition of families. In the sampling sites, the BMWP-Col index was a determinant for river water quality (moderate, poor, or bad). Good quality water was not found in any of the sampling sites. The composition of the macroinvertebrate community changes from the source of the river until it ends its journey in the city. In addition, the family abundance and the composition of the feeding group were observed in the sites that showed similar or the same quality of water. The diversity of families and FFGs was generally higher at sites of moderate water quality. Chironomidae and Annelida were the most abundant families while Leptoceridae was the least abundant. The diversity of families was higher in BR while it was lower in PC and EFPC, grouped in six and four (both PC and EFPC) FFGs, respectively. It is important to carry out this type of study in the Ecuadorian Amazon because there is a lack of knowledge about taxonomic and functional diversity and the physicochemical variables with water quality.

On the dependent recognition of some long zinc finger proteins.

The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many exhibiting short motifs. Here we use ZFY, CTCF, ZIM3, and ZNF343 as examples to address three closely related questions: What are the reasons that impede current motif discovery methods? What are the functions of those seemingly unused fingers and how can we improve the motif discovery algorithms based on long ZFPs' biophysical properties? Using ZFY, we employed a variety of methods and find evidence for 'dependent recognition' where downstream fingers can recognize some previously undiscovered motifs only in the presence of an intact core site. For CTCF, high-throughput measurements revealed its upstream specificity profile depends on the strength of its core. Moreover, the binding strength of the upstream site modulates CTCF's sensitivity to different epigenetic modifications within the core, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates the epigenetic control by CTCF. Our results establish that, because of irregular motif structures, variable spacing and dependent recognition between sub-motifs, the specificities of long ZFPs are significantly underestimated, so we developed an algorithm, ModeMap, to infer the motifs and recognition models of ZIM3 and ZNF343, which facilitates high-confidence identification of specific binding sites, including repeats-derived elements. With revised concept, technique, and algorithm, we can discover the overlooked specificities and functions of those 'extra' fingers, and therefore decipher their broader roles in human biology and diseases.

BZIP transcription factors repress the expression of wheat (Triticum aestivum L.) high molecular weight glutenin subunit genes in vegetative tissues

High molecular weight glutenin subunits (HMW GS) represent an important fraction of endosperm-specific seed-storage proteins that provide elasticity to bread dough. Previously, the second cis-regulatory module (CRM2) was found to be one of the most conserved part of HMW GS promoters, which indicated its pre-eminent role in their gene regulation. Here, we observed that deletion of CRM2 from the promoters of the Bx7 and By8 HMW GS genes increased the leakage of their transient expression in wheat leaf tissue. The effect of a VP1, an Myb and an antisense bZIP transcription factor (TF)-binding site, potentially involved in endosperm-specific regulation within CRM2, was then studied. The activity of a Bx7 gene promoter containing a mutant CRM2 with altered VP1 and Myb TF-binding sites, but an intact bZIP TF-binding site, was similarly low to that of the wild type in leaves. Transactivation analysis and EMSA indicated the binding of TFs TabZIP34 and TabZIP115 to the Skn-1 motif GTCAT in CRM2 and the repression of Bx7 and By8 HMW GS gene promoter activity in leaves. TabZIP34 and TabZIP115 may be involved in the downregulation of HMW GS gene expression in vegetative tissues and early-stage endosperm as well its modulation during seed maturation.

Spatial niche segregation between bird species in the Białowieża primeval forest (NE Poland)

Drivers of bird niche separation in temperate primeval forests have not yet been determined, due to the low number of intact forest sites. Here, we analyzed the general patterns of niche usage on trees by birds’ assemblages. We tested how tree species affect the sharing of space in an assemblage of birds and their level of specialization. We conducted our study in the Białowieża primeval forest (NE Poland). During two breeding seasons, we observed bird positions on trees, divided into three vertical and six horizontal zones in 768 observation points. Based on the interaction networks framework we calculated the Kullback-Leibler distance d′ as a metric of species specialization and the resource range RR index, which estimates the species’ specificity based on the fraction of space utilized with a non-zero performance. The d′ index was the highest in the lower understory for all parts of the tree on the basis of the position from the trunk. The RR index was the highest in the lower understory for all parts based on the position from the trunk. Regarding the tree species, the lowest d′ index was observed in all tree species together, and hornbeam, whereas the highest in oak. At the tree species level, the RR index was the lowest for hornbeam. We show tree species importance in forest space sharing in the case of bird assemblages. Hornbeam, alder, and spruce are universal species that were used by birds almost entirely. In contrast, oak, lime, and maple were only partially used. Tree species with less complex structures could shape bird assemblages, as they could offer birds much fewer niches to realize. Therefore, we showed that high specialization and niche separation are drivers of high bird diversity. Consequently maintaining a diverse stand structure is crucial for biodiversity conservation.

Post-operative ileo-ileal intussusception one week after hemicolectomy for ileo-colic intussusception

Intussusception is a common pediatric surgical emergency that results from the introversion of one loop of bowel into another. It is common in children between 3 months and 3 years. Recurrence of intussusception is said to be common in non-operative reduction and negligible after operative reduction. In this case report, we aim to discuss a case of post-operative ileo-ileal intussusception (POI) 7 days after a laparotomy and resection on account of gangrenous ileo-colic intussusception. A 13-month-old male patient presented with bloody stools associated with abdominal distention and fever. Clinical findings were suggestive of intussusception. Diagnosis was confirmed with an abdominopelvic ultrasound. A laparotomy revealed a gangrenous ascending colon extending to the terminal ileum so a right hemicolectomy was performed. The patient was well until post-operative day 7 when he developed abdominal distention associated with vomiting. An abdominal x-ray revealed multiple air fluid levels. A re-laparotomy was performed and a new intussusception was found proximal to an intact and patent anastomotic site. The involved bowel was reduced because it was viable. He was discharged on post-operative day 14. This was a rare case of recurrent intussusception with resection and anastomosis on account of intussusception in a 13-month-old boy.

Intact provirus and integration sites analysis in acute HIV-1 infection and changes after one year of early antiviral therapy

Background and objectivesHIV-1 provirus integration in host genomes provides a lifelong reservoir of virally infected cells. Although not able to generate viral progeny, the expression of defective proviruses has been associated with activation. Provirus integration may influence host gene transcription and shifts may occur during disease progression or antiretroviral therapy (ART). The study aimed to analyze intact/defective provirus and sites of provirus integration in acute infections: changes after 48 weeks of early therapy were also evaluated. MethodsDNA from peripheral blood lymphomonocytes of 8 acute HIV-1 infections at serodiagnosis (T0) and after 48 weeks of therapy (T1) was used to quantify intact and defective provirus by digital-droplet PCR and to analyze provirus integration sites, by next-generation sequencing of libraries derived from ligation-mediated PCR. ResultsA high variability in the amount of intact proviral DNA was observed at both T0 and T1, in the different subjects. Although the ratio of intact/total proviral HIV-1 DNA did not dramatically change between T0 (8.05%) and T1 (9.34%), after early therapy both intact and total HIV-1 DNA declined significantly, p = 0.047 and p = 0.008, respectively. The median number of different (IQR) integration sites in human chromosomes/subject was 5 (2.25-13.00) at T0 and 4 (3.00-6.75) at T1. Of all the integration sites observed at T1, 64% were already present at T0. Provirus integration was observed in introns of transcriptionally active genes. Some sites of integration, among which the most represented was in the neuregulin 2 gene, were shared by different patients, together with the orientation of the insertion. Provirus integration was also observed in intergenic regions, with median (IQR) % of 15.13 (6.81-21.40) at T0 and 18.46 (8.98-22.18) at T1 of all read matches. ConclusionsIn acute HIV-1 infection, the amount of intact proviral DNA in peripheral lymphomonocytes did not exceed 10% of total HIV-1 DNA, a percentage that was not substantially changed by early administrated ART. Provirus displayed a relatively small number of recurrent integration sites in introns of transcriptionally active genes, mainly related to cell-cycle control. Consideration should be given to therapeutic strategies able to target the cells harboring defective proviruses, that are not reached by conventional antiviral drugs, these potentially also impacting on replicative competent integrated provirus.

A Redox-Controlled Substrate Engineering Strategy for Site-Specific Enzymatic Fucosylation.

Fucosylation is one of the most common modifications of oligo-N-acetyllactosamine (oligo-LacNAc) glycans. However, none of known fucosyltransferases (FucTs) could install the α1,3-linked fucose to the oligo-LacNAc substrates in a site-specific manner. Here, we report a facile and general redox-controlled substrate engineering strategy for the site-specific α1,3-fucosylation of complex glycans containing multiple LacNAc units. This strategy takes advantage of an operationally simple oxidation enzyme module by using galactose oxidase (GOase) to convert the LacNAc unit into oxidized C6'-aldehyde LacNAc sequence, which is not a good substrate for recombinant α1,3-FucT from Helicobacter pylori strain 26695 (Hpα1,3FucT), enabling the site-specific α1,3-fucosylation at intact LacNAc sites. The general applicability and robustness of this strategy were demonstrated by the synthesis of a variety of structurally well-defined fucosides of linear and branched O- and N-linked glycans.

A Redox‐Controlled Substrate Engineering Strategy for Site‐Specific Enzymatic Fucosylation

AbstractFucosylation is one of the most common modifications of oligo‐N‐acetyllactosamine (oligo‐LacNAc) glycans. However, none of known fucosyltransferases (FucTs) could install the α1,3‐linked fucose to the oligo‐LacNAc substrates in a site‐specific manner. Here, we report a facile and general redox‐controlled substrate engineering strategy for the site‐specific α1,3‐fucosylation of complex glycans containing multiple LacNAc units. This strategy takes advantage of an operationally simple oxidation enzyme module by using galactose oxidase (GOase) to convert the LacNAc unit into oxidized C6′‐aldehyde LacNAc sequence, which is not a good substrate for recombinant α1,3‐FucT from Helicobacter pylori strain 26695 (Hpα1,3FucT), enabling the site‐specific α1,3‐fucosylation at intact LacNAc sites. The general applicability and robustness of this strategy were demonstrated by the synthesis of a variety of structurally well‐defined fucosides of linear and branched O‐ and N‐linked glycans.

Structure of the major oxidative damage 7,8-dihydro-8-oxoguanine presented into a catalytically competent DNA glycosylase.

If left unrepaired, the major oxidative DNA lesion 7,8-dihydro-8-oxoguanine (oxoG) promotes G-to-T transversions by favorably adopting a syn conformation and base pairing with dATP during replication. The human oxoG DNA glycosylase hOGG1 senses and removes oxoG amid millions-fold excess of guanine, thereby counteracting the genotoxic effects of the major oxidative damage. Crystal structures of hOGG1 in complex with oxoG-containing DNA have provided key insights into the lesion recognition and catalysis mechanisms of the enzyme. These lesion-recognition complex (LRC) structures typically involve a catalytically inactive hOGG1 mutant, where one of the catalytic-site amino acid residues is mutated to prevent the cleavage of oxoG. The use of a catalytically incompetent hOGG1 mutant has thus precluded understanding of unscathed interactions between oxoG and hOGG1 catalytic site as well as interactions among catalytic-site amino acid residues. As an orthogonal approach to visualize such interactions, we have co-crystallized a catalytically competent hOGG1 bound to 2'-fluoro-oxodG-containing DNA, a transition state destabilizing inhibitor that binds hOGG1 but is not processed by the enzyme. In this fluorinated lesion-recognition complex (FLRC), the 8-oxo moiety of oxoG is recognized by Gly42 and the Watson-Crick edge of oxoG is contacted by Gln315 and Pro266. The previously observed salt bridge between Lys249 and Cys253 is lacking in the FLRC, suggesting Lys249 is primed by Cys253 and poised for nucleophilic attack on C1' of oxodG. Overall, hOGG1 FLRC marks the first structure of oxoG presented into an intact catalytic site of hOGG1 and provides complementary insights into the glycosylase mechanisms of the enzyme.

Intramembranous bone regeneration in diversity outbred mice is heritable.

There are over one million cases of failed bone repair in the U.S. annually, resulting in substantial patient morbidity and societal costs. Multiple candidate genes affecting bone traits such as bone mineral density have been identified in human subjects and animal models using genome-wide association studies (GWAS). This approach for understanding the genetic factors affecting bone repair is impractical in human subjects but could be performed in a model organism if there is sufficient variability and heritability in the bone regeneration response. Diversity Outbred (DO) mice, which have significant genetic diversity and have been used to examine multiple intact bone traits, would be an excellent possibility. Thus, we sought to evaluate the phenotypic distribution of bone regeneration, sex effects and heritability of intramembranous bone regeneration on day 7 following femoral marrow ablation in 47 12-week old DO mice (23 males, 24 females). Compared to a previous study using 4 inbred mouse strains, we found similar levels of variability in the amount of regenerated bone (coefficient of variation of 86% v. 88%) with approximately the same degree of heritability (0.42 v. 0.49). There was a trend toward more bone regeneration in males than females. The amount of regenerated bone was either weakly or not correlated with bone mass at intact sites, suggesting that the genetic factors responsible for bone regeneration and intact bone phenotypes are at least partially independent. In conclusion, we demonstrate that DO mice exhibit variation and heritability of intramembranous bone regeneration that will be suitable for future GWAS.

Regional archaeological underwater survey method: Applications and implications

AbstractUnderwater cultural heritage (UCH) contributes to history, the arts, the economy and science. The number of intact and easily discoverable UCH sites is decreasing due to excavation in China. To conduct active surveys for mapping archaeological sites, rather than mapping based only on incidental reported finds from fishing operations, a regional archaeological underwater survey method is proposed according to independent geographical units and historical archives. This method is based on the approach used for systematic regional archaeological surveys on land and comprehensively examines similar survey examples. Old port districts, sea routes, fishing zones and naval battle areas are potential targets for this method. From 2012 to 2017, the survey method performed well when applied in the Haitan Strait, China, discovering intact sites, fragmented shipwrecks and numerous interfering objects. The method needs further refinement to eliminate interference and to obtain more detailed information about UCH. The main steps in this method include the selection of potential wreck site areas, the use of sequential equipment and survey line design. Cooperation between archaeologists and surveyors is essential.

Locking the Ultrasound-Induced Active Conformation of Metalloenzymes in Metal-Organic Frameworks.

Enhancing the enzymatic activity inside metal-organic frameworks (MOFs) is a critical challenge in chemical technology and bio-technology, which, if addressed, will broaden their scope in energy, food, environmental, and pharmaceutical industries. Here, we report a simple yet versatile and effective strategy to optimize biocatalytic activity by using MOFs to rapidly "lock" the ultrasound (US)-activated but more fragile conformation of metalloenzymes. The results demonstrate that up to 5.3-fold and 9.3-fold biocatalytic activity enhancement of the free and MOF-immobilized enzymes could be achieved compared to those without US pretreatment, respectively. Using horseradish peroxidase as a model, molecular dynamics simulation demonstrates that the improved activity of the enzyme is driven by an opened gate conformation of the heme active site, which allows more efficient substrate binding to the enzyme. The intact heme active site is confirmed by solid-state UV-vis and electron paramagnetic resonance, while the US-induced enzyme conformation change is confirmed by circular dichroism spectroscopy and Fourier-transform infrared spectroscopy. In addition, the improved activity of the biocomposites does not compromise their stability upon heating or exposure to organic solvent and a digestion cocktail. This rapid locking and immobilization strategy of the US-induced active enzyme conformation in MOFs gives rise to new possibilities for the exploitation of highly efficient biocatalysts for diverse applications.

Changes in Forest Conditions in a Siberian Larch Forest Induced by an Extreme Wet Event

The taiga forest, a semi-arid and nitrogen-limited ecosystem on permafrost, has changed under extreme wet events. This study aims to understand the changes that occurred in a larch forest in Eastern Siberia after the wet event of 2006–2007. In the summer of 2018, studies were conducted at the Spasskaya Pad Experimental Forest Station near Yakutsk, Russia, where a transect (60 m × 510 m) with 34 plots (30 m × 30 m) was set. It included intact sites and affected sites with different levels of forest damage, owing to the extreme wet event. We observed spatial variations in the normalized difference vegetation index (NDVI) calculated from Landsat satellite-observed data, and the foliar δ13C, δ15N, and C/N (carbon/nitrogen) ratio obtained from the needle samples of 105 mature larch trees. Our results reveal that the affected plots had a lower NDVI than the intact plots, resulting from a difference in tree stand density. In addition, the stand density is suggested to be a controlling factor in the spatial variations in the foliar C/N and δ13C values based on their significant relationships with the NDVI in June. We concluded that the larch trees from the regenerating forests in the affected areas have a higher nitrogen level and light availability (relatively low C/N and high δ13C) because of the slight competition for resources, owing to a low-stand density. This may lead to further succession of the larch forests after the extreme wet event.