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Colorectal cancer (CRC), breast cancer, and chronic myeloid leukemia (CML) are life-threatening malignancies worldwide. Although potent therapeutic and screening strategies have been developed so far, these cancer types are still major public health problems. Therefore, the exploration of more potent and selective new agents is urgently required for the treatment of these cancers. Quinones represent one of the most important structures in anticancer drug discovery. We have previously identified a series of quinone-based compounds (ABQ-1-17) as anti-CML agents. In the current work, ABQ-3 was taken to the National Cancer Institute (NCI) for screening to determine its in vitro antiproliferative effects against a large panel of human tumor cell lines at five doses. ABQ-3 revealed significant growth inhibition against HCT-116 CRC and MCF-7 breast cancer cells with 2.00 mu M and 2.35 mu M GI(50) values, respectively. The MTT test also showed that ABQ-3 possessed anticancer effects towards HCT-116 and MCF-7 cells with IC50 values of 5.22 +/- 2.41 mu M and 7.46 +/- 2.76 mu M, respectively. Further experiments indicated that ABQ-3 induced apoptosis in both cell lines, and molecular docking studies explicitly suggested that ABQ-3 exhibited DNA binding in a similar fashion to previously reported compounds. Based on in silico pharmacokinetic prediction, ABQ-3 might display drug-like features enabling this compound to become a lead molecule for future studies., Scientific and Technological Research Council of Turkey (TÜBİTAK) European Commission (EC); European Union (EU); Horizon 2020; TÜBİTAK 2236; CoCirculation2; Scientific Research Projects Coordination Unit of Istanbul University

Faithful chromosome segregation in budding yeast requires correct positioning of the mitotic spindle along the mother to daughter cell polarity axis. When the anaphase spindle is not correctly positioned, a surveillance mechanism, named as the spindle position checkpoint (SPOC), prevents the progression out of mitosis until correct spindle positioning is achieved. How SPOC works on a molecular level is not well understood. Here we performed a genome-wide genetic screen to search for components required for SPOC. We identified the SWR1 chromatin-remodeling complex (SWR1-C) among several novel factors that are essential for SPOC integrity. Cells lacking SWR1-C were able to activate SPOC upon spindle misorientation but underwent mitotic slippage upon prolonged SPOC arrest. This mitotic slippage required the Cdc14-early anaphase release pathway and other factors including the SAGA (Spt-Ada-Gcn5 acetyltransferase) histone acetyltransferase complex, proteasome components and the mitotic cyclin-dependent kinase inhibitor Sic1. Together, our data establish a novel link between SWR1-C chromatin remodeling and robust checkpoint arrest in late anaphase., We thank Astrid Hofmann and Dorothee Albrecht for excellent technical assistance and Elmar Schiebel for strains and access to microscopes. This work was funded by the Deutsche Forschungsgemein-schaft (DFG) Collaborative Research Center SFB1036 (Project TP21 to G.P. and Project TP10 to M.K. and A.K.). A.K.C. was supported by the German Research Council (DFG, PE1883/1-2), MSCA Individual Fellowship (796599, COHEMEX), and EMBO-IG (3918). The work of G.P. is supported by the Heisenberg program (PE1883/3), SFB873/A14 and SFB1324/B09 of the DFG.

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); TÜBİTAK 2218 - National Postdoctoral Research Fellowship Program; TÜBİTAK 2232 International Outstanding Researchers Program; 2232 International Fellowship for Outstanding Researchers Program; European Union (EU); Horizon 2020; 2236 CoCirculation2 Program; TÜBİTAK 1001 Scientific and Technological Research Projects Funding Program

NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motif instances, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling was identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life., WD, MG-G were supported by the Narodowe Centrum Nauki (ncn.gov.pl) grant no. 2019/35/B/NZ2/03997. WD was also supported by the Wroclawskie Centrum Sieciowo-Komputerowe, Politechnika Wroclawska (wcss.pl), grant no.similar to 98. NS was supported by the Narodowe Centrum Badan i Rozwoju (ncbr.gov.pl) project no. POWR.03.02.00-00-I003/16. VC, SJS were supported by the Agence Nationale de la Recherche (anr.fr) grant no. SFAS R-17-CE11-0035. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

The circadian timing system controls absorption, distribution, metabolism, and elimination processes of drug pharmacokinetics over a 24-h period. Exposure of target tissues to the active form of the drug and cytotoxicity display variations depending on the chronopharmacokinetics. For anticancer drugs with narrow therapeutic ranges and dose-limiting side effects, it is particularly important to know the temporal changes in pharmacokinetics. A previous study indicated that pharmacokinetic profile of capecitabine was different depending on dosing time in rat. However, it is not known how such difference is attributed with respect to diurnal rhythm. Therefore, in this study, we evaluated capecitabine-metabolizing enzymes in a diurnal rhythm-dependent manner. To this end, C57BL/6J male mice were orally treated with 500 mg/kg capecitabine at ZT1, ZT7, ZT13, or ZT19. We then determined pharmacokinetics of capecitabine and its metabolites, 5?-deoxy-5-fluorocytidine (5?DFCR), 5?-deoxy-5-fluorouridine (5?DFUR), 5-fluorouracil (5-FU), in plasma and liver. Results revealed that plasma Cmax and AUC0-6h (area under the plasma concentration-time curve from 0 to 6 h) values of capecitabine, 5?DFUR, and 5-FU were higher during the rest phase (ZT1 and ZT7) than the activity phase (ZT13 and ZT19) (p < 0.05). Similarly, Cmax and AUC0-6h values of 5?DFUR and 5-FU in liver were higher during the rest phase than activity phase (p < 0.05), while there was no significant difference in liver concentrations of capecitabine and 5?DFCR. We determined the level of the enzymes responsible for the conversion of capecitabine and its metabolites at each ZT. Results indicated the levels of carboxylesterase 1 and 2, cytidine deaminase, uridine phosphorylase 2, and dihydropyrimidine dehydrogenase (p < 0.05) are being rhythmically regulated and, in turn, attributed different pharmacokinetics profiles of capecitabine and its metabolism. This study highlights the importance of capecitabine administration, The present work was supported by the Research Fund of Istanbul University. Project Number: TDK-2018-30939. The data used in this study were derived from PhD thesis of Yasemin Kubra Akyel. We would like to thank Dr. Ali Cihan Taskin for his valuable contribution to animal work.

One of the primary goals of conservation translocation programs should be the maintenance of both population demographic stability and genetic diversity. Here, we provide genetic management recommendations to inform a population reinforcement of the declining Egyptian Vulture population in the Balkans. Specifically, we examined whether the number of released individuals is sufficient to prevent genetic diversity loss due to random genetic drift and what the origin of the individuals should be that comprise the captive breeding pool. To this aim, we estimated and assessed genetic diversity levels and genetic structure of Egyptian Vulture populations across much of the species’ range using both neutral and non-neutral candidate loci involved in migration. We then evaluated the effects of the currently proposed population management scheme and candidate source populations on retaining allelic diversity. Our results show low differentiation values among populations and absence of genetic structure which point to past high gene flow. Furthermore, there was no predicted significant impact of different source populations on the genetic diversity of the recipient Balkan population. We also found that the declining Egyptian Vulture population in the Balkans still retains high levels of genetic diversity and therefore genetic diversity restoration is not currently needed. However, without any management, diversity is likely to decrease fast because of increased genetic drift as the population size continues to decline. Population reinforcement with nine birds per year for 20 years would provide sufficient demographic support for the population to retain > 85% of rare allelic diversity. Birds originating from the Balkans would ensure ecological and behavioral similarity and thus would be the best option for reinforcement. Nevertheless, our results demonstrate that to prevent further population contraction and loss of adaptive alleles, releasing individuals of different origin, European Union; HEAL-Link Greece; LIFE projects; “The Return of the Neophron” (LIFE programme); “Egyptian Vulture New LIFE” (LIFE programme, www.LifeNeophron.eu); Leventis Foundation and the MAVA Foundation; Israeli Academy of Science’s Adams Fellowship

Hematology is one of the best population health indicators, and the quickest way to gain insight into some hematological parameters is blood film evaluation. Sometimes, due to the inability to store blood, the unavailability of hematological instruments during field work, or the insufficient amount of blood for complete hematological analysis, blood film evaluation could be the only method for obtaining information about hematological changes. The population of brown bears (Ursus arctos) is often endangered, and is protected as an important integral species of terrestrial communities. Since any baseline hematological data of free-living endangered species are particularly important, the aim of this study was to test the possibility of using blood film evaluation, as the only source of hematological data, for assessment of an animal's hematological and, consequently, health status. Blood films of seventeen brown bears from eastern Turkey were evaluated to assess the morphology of erythrocytes and leukocytes, estimate the total leukocyte count, determine the differential leukocyte count, and look for the presence of cell inclusions or hemoparasites. Rouleaux formations were present in twelve animals, poikilocytosis in four, while parasitic nematodes, microfilariae, were found in nine out of seventeen bears. The results confirmed that blood film evaluation alone could be of use in assessing an animal's hematological status, but for more accurate assessment of health status, more blood parameters need to be analyzed. New findings in the study, such as the presence of rouleaux formations and microfilaria in brown bears from eastern Turkey, have opened the door for further investigation in this field., We are grateful to the Foundation Segré for providing most of the funding for this project. This research was also supported by other generous donors, including Arkadaşlar, Bilge Bahar, Faruk Eczacıbaşı, Seha İşmen, Ömer Külahçıoğlu, Burak Över, Batubay Özkan, Alan Peterson, Emin Özgür, Suna Reyent, Faruk Yalçın Zoo, National Geographic Society, Sigrid Rausing Trust, STGM, TANAP, Turkcell, the University of Utah, Iğdır University and the Whitley Fund. We thank the staff and volunteers of the KuzeyDoğa Society for their dedicated support.

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death throughout the world. Due to the shortcomings of traditional chemotherapy, targeted therapies have come into prominence for the management of NSCLC. In particular, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) therapy has emerged as a first-line therapy for NSCLC patients with EGFR-activating mutations. In this context, new indenopyrazoles, which were prepared by an efficient microwave-assisted method, were subjected to in silico and in vitro assays to evaluate their potency as EGFR TK-targeted anti-NSCLC agents. Compound 4 was the most promising antitumor agent towards A549 human lung adenocarcinoma cells, with an IC50 value of 6.13 µM compared to erlotinib (IC50 = 19.67 µM). Based on its low cytotoxicity to peripheral blood mononuclear cells (PBMCs), it can be concluded that compound 4 exerts selective antitumor action. This compound also inhibited EGFR TK with an IC50 value of 17.58 µM compared to erlotinib (IC50 = 0.04 µM) and induced apoptosis (56.30%). Taking into account in silico and in vitro data, compound 4 stands out as a potential EGFR TKI for the treatment of NSCLC., Anadolu University Scientific Research Projects Commission; Scientific and Technological Research Council of Turkey (TÜBİTAK)

Billions of birds annually migrate between breeding and nonbreeding grounds in North America. During fall 2020, there was a series of alarming mass-mortality events of migratory birds across the western United States, with estimates of 100,000 to 1 million birds having perished. One potential culprit behind these die-offs is wildfires, though there has been little research documenting the indirect effects of wildfires on actively migrating birds. We undertook a multi-year assessment of potential impacts that wildfires may have had on fall bird migration over the past decade, with a particular focus on fall 2020, using systematic bird banding data from southeastern Utah. We used a correlative approach to evaluate the relationship between estimates of acres burned by wildfires in western North America on several variables representing bird abundance and body condition. Notably, in our best fit models of birds banded at our research site during fall 2020, we found both a positive relationship for the number of bird captures and a negative relationship for body mass index with more daily burned acres. We provide an examination of incorporating lag effects of wildfires on different metrics of bird migration to account for potential impacts of fires on birds before migration and banding. Additionally, we assess the usefulness of different proxies of body condition in highly stressed land birds and introduce a scale for scoring emaciation of birds in the hand while banding. Our insights into avian migration ecology are one of the few studies that explore the role wildfires may have had in affecting migratory bird movements and health. / Des milliards d’oiseaux migrent chaque année entre les aires de nidification et celles en dehors de la saison de nidification en Amérique du Nord. Au cours de l’automne 2020, une série d’évènements alarmants de mortalité massive d’oiseaux migrateurs a eu lieu dans l’ouest des États-Unis, l’estimation d’oiseaux ayant péri oscillant entre 100, We are grateful for the generous support of the Hamit Batubay Ozkan Conservation Ecology Graduate Fellowship, Barbara J. Watkins Environmental Studies Graduate Fellowship, and the University of Utah Global Change and Sustainability Center, as well as Zach Lundeen for helping provide funds to support our bird banding operation.

Photorespiration, commonly viewed as a loss in photosynthetic productivity of C3 plants, is expected to decline with increasing atmospheric CO2, even though photorespiration plays an important role in the oxidative stress responses. This study aimed to quantify the role of photorespiration and alternative photoprotection mechanisms in Zostera marina L. (eelgrass), a carbon-limited marine C3 plant, in response to ocean acidification. Plants were grown in controlled outdoor aquaria at different [CO2]aq ranging from ~55 (ambient) to ~2121 ?M for 13 months and compared for differences in leaf photochemistry by simultaneous measurements of O2 flux and variable fluorescence. At ambient [CO2], photosynthesis was carbon limited and the excess photon absorption was diverted both to photorespiration and non-photochemical quenching (NPQ). The dynamic range of NPQ regulation in ambient grown plants, in response to instantaneous changes in [CO2]aq, suggested considerable tolerance for fluctuating environmental conditions. However, 60 to 80% of maximum photosynthetic capacity of ambient plants was diverted to photorespiration resulting in limited carbon fixation. The photosynthesis to respiration ratio (PE : RD) of ambient grown plants increased 6-fold when measured under high CO2 because photorespiration was virtually suppressed. Plants acclimated to high CO2 maintained 4-fold higher PE : RD than ambient grown plants as a result of a 60% reduction in photorespiration. The O2 production efficiency per unit chlorophyll was not affected by the CO2 environment in which the plants were grown. Yet, CO2 enrichment decreased the light level to initiate NPQ activity and downregulated the biomass specific pigment content by 50% and area specific pigment content by 30%. Thus, phenotypic acclimation to ocean carbonation in eelgrass, indicating the coupling between the regulation of photosynthetic structure and metabolic carbon demands, involved the downregulation of light harvesting by the, Financial support for this research was provided by the National Science Foundation (Award OCE-1061823 to RZ and VH), Virginia Sea Grant/NOAA (Award NA14OAR4170093 to RZ and BC-E) and the Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University (to BC-E). This research was performed in partial completion of the requirements for the Ph.D. degree (Oceanography) at Old Dominion University.

Epigenetic reprogramming to pluripotency requires extensive remodeling of chromatin landscapes to silence existing cell-type-specific genes and activate pluripotency genes. ATP-dependent chromatin remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of recently identified Bromodomain-containing protein 9 (BRD9) and the associated non-canonical BRG1-associated factors (ncBAF) complex in reprogramming remains unknown. Here, we show that genetic or chemical inhibition of BRD9, as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, increase human somatic cell reprogramming efficiency and can replace KLF4 and c-MYC. We find that BRD9 is dispensable for human induced pluripotent stem cells under primed but not under naive conditions. Mechanistically, BRD9 inhibition downregulates fibroblast-related genes and decreases chromatin accessibility at somatic enhancers. BRD9 maintains the expression of transcriptional regulators MN1 and ZBTB38, both of which impede reprogramming. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers chromatin-based barriers to reprogramming., Scientific and Technological Research Council of Turkey (TÜBİTAK); BİDEB Scholarship; Newton Advanced Fellowship; Arthritis Research UK; Cancer Research UK; LEAN project of the Leducq Foundation; European Union (EU); Seventh Frame-work Program; Marie Curie Actions

Colorectal cancer (CRC) and breast cancer are leading causes of death globally, due to significant challenges in detection and management. The late-stage diagnosis and treatment failures require the discovery of potential anticancer agents to achieve a satisfactory therapeutic effect. We have previously reported a series of plastoquinone analogues to understand their cytotoxic profile. Among these derivatives, three of them (AQ-11, AQ-12, and AQ-15) were selected by the National Cancer Institute (NCI) to evaluate their in vitro antiproliferative activity against a panel of 60 human tumor cell lines. AQ-12 exhibited significant antiproliferative activity against HCT-116 CRC and MCF-7 breast cancer cells at a single dose and further five doses. MTT assay was also performed for AQ-12 at different concentrations against these two cells, implying that AQ-12 exerted notable cytotoxicity toward HCT-116 (IC50 = 5.11 ± 2.14 ?M) and MCF-7 (IC50 = 6.06 ± 3.09 ?M) cells in comparison with cisplatin (IC50 = 23.68 ± 6.81 ?M and 19.67 ± 5.94 ?M, respectively). This compound also augmented apoptosis in HCT-116 (62.30%) and MCF-7 (64.60%) cells comparable to cisplatin (67.30% and 78.80%, respectively). Molecular docking studies showed that AQ-12 bound to DNA, forming hydrogen bonding through the quinone scaffold. In silico pharmacokinetic determinants indicated that AQ-12 demonstrated drug-likeness with a remarkable pharmacokinetic profile for future mechanistic anti-CRC and anti-breast cancer activity studies., Scientific Research Projects Coordination Unit of Istanbul University; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2236 CoCirculation2; European Union (EU); Horizon 2020

The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA predominantly interact with the acidic head of phosphatidyl-inositol-4,5-bisphosphate (PI(4,5)P2) inserted into the membrane. Our research group developed L-Heptanoylphosphatidyl Inositol Pentakisphosphate (L-HIPPO) and previously confirmed that this compound bound to the MA more strongly than PI(4,5)P2 and inositol hexakisphosphate (IP6) did. Therefore, herein we rationally designed eight new L-HIPPO derivatives based on the fact that the most changeable parts of L-HIPPO were two acyl chains. After that, we employed molecular docking for eight compounds via Maestro software using high-resolution crystal structures of MA in complex with IP6 (PDB IDs: 7E1I, 7E1J, and 7E1K), which were recently elucidated by our research group. The most promising docking scores were obtained with benzene-inserted compounds. Thus, we generated a library containing 213 new aromatic groupinserted L-HIPPO derivatives and performed the same molecular docking procedure. According to the results, we determined the nine new L-HIPPO derivatives most effectively binding to the MA with the most favorable scoring functions and pharmacokinetic properties for further exploration., Scientific and Technological Research Council of Turkey (TÜBİTAK); European Union (EU); Horizon 2020; Marie Sklodowska-Curie Actions Cofund program; European Commission; Co-Funded Brain Circulation2 Scheme; 2236 CoCirculation2 Program; European Research Council (ERC); Istanbul University

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these PLs, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an ?-helical and an ?/? domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc (6-4) PL. Further analysis of the Vc (6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478 to 484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc (6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Drosophila melanogaster (Dm, (6-4)) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; İstanbul Development Agency Grant; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program

Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers in both men and women and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we per-formed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9000 were singly quantified. Our in-depth analysis revealed 600 phosphopeptides to be significantly differentially regulated between tumor and normal tissues. Moreover, our data revealed that significantly up -regu-lated phosphoproteins are associated with protein syn-thesis and cytoskeletal re-organization which suggests proliferative and migratory behavior of renal tumors. This is supported by a mesenchymal profile of ccRCC phos-phorylation events. Our rigorous characterization of the renal phosphoproteome also suggests that both epidermal growth factor receptor and vascular endothelial growth factor receptor are important mediators of phos-pho signaling in RCC pathogenesis. Furthermore, we determined the kinases p21-activated kinase 2, cyclin-dependent kinase 1 and c-Jun N-terminal kinase 1 to be master kinases that are responsible for phosphorylation of many substrates associated with cell proliferation, inflammation and migration. Moreover, high expression of p21-activated kinase 2 is associated with worse survival outcome of ccRCC patients. These master kinases are targetable by inhibitory drugs such as fostamatinib, min-ocycline, tamoxifen and bosutinib which can serve as novel therapeutic agents for ccRCC treatment., NO acknowledges the Royal Society Newton Advanced Fellowship (NA170389) .

When combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based superresolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by*28 and*20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively., Scientific and Technological Research Council of Turkey (TÜBİTAK); Marmara University Scientific Research Projects Coordination Unit; Turkish Academy of Sciences (TÜBA)

English is widely recognized as the language of science, and English-language publications (ELPs) are rapidly increasing. It is often assumed that the number of non-ELPs is decreasing. This assumption contributes to the underuse of non-ELPs in conservation science, practice, and policy, especially at the international level. However, the number of conservation articles published in different languages is poorly documented. Using local and international search systems, we searched for scientific articles on biodiversity conservation published from 1980 to 2018 in English and 15 non-English languages. We compared the growth rate in publications across languages. In 12 of the 15 non-English languages, published conservation articles significantly increased every year over the past 39 years, at a rate similar to English-language articles. The other three languages showed contrasting results, depending on the search system. Since the 1990s, conservation science articles in most languages increased exponentially. The variation in the number of non-English-language articles identified among the search systems differed markedly (e.g., for simplified Chinese, 11,148 articles returned with local search system and 803 with Scopus). Google Scholar and local literature search systems returned the most articles for 11 and 4 non-English languages, respectively. However, the proportion of peer-reviewed conservation articles published in non-English languages was highest in Scopus, followed by Web of Science and local search systems, and lowest in Google Scholar. About 20% of the sampled non-English-language articles provided no title or abstract in English; thus, in theory, they were undiscoverable with English keywords. Possible reasons for this include language barriers and the need to disseminate research in countries where English is not widely spoken. Given the known biases in statistical methods and study characteristics between English- and non-English-language studies, non, Australian Government; University of Queensland; Centre for Biodiversity and Conservation Science; German Research Foundation (DFG); Germany’s Excellence Strategy; Universitat Hamburg Center for Earth System Research and Sustainability (CEN); Climate,Climatic Change, and Society (CLICCS); European Union (EU); Horizon 2020; Marie Sklodowska-Curie; Australian Research Council Future Fellowship

Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and dosed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; 1001 Scientific and Technological Research Projects Funding Program; U.S. Department of Energy; Office of Science; Office of Basic Energy Sciences; European Union (EU); Horizon 2020 ; European Research Council (ERC); SYBORG; U.S. Department of Energy Joint Genome Institute; DOE Office of Science User Facility; Max Planck Society; a Max-Planck-Partner Group; CONICYT; CONICYT Doctorado Nacional Grant; Fondo Nacional de Desarrollo Científico y Tecnológico (Fondecyt) Postdoctoral Fellowship; DOE Office of Science, Biological Environmental Research; National Institutes of Health; National Science Foundation Major Research Instrument Grant; NIGMS; Stanford PRECOURT Institute

Friedreich's ataxia (FRDA, OMIM#229300) is the most common hereditary ataxia, resulting from the reduction of frataxin protein levels due to the expansion of GAA repeats in the first intron of the FXN gene. Why the triplet repeat expansion causes a decrease in Frataxin protein levels is not entirely known. Generation of effective FRDA disease models is crucial for answering questions regarding the pathophysiology of this disease. There have been considerable efforts to generate in vitro and in vivo models of FRDA. In this perspective article, we highlight studies conducted using FRDA animal models, patient-derived materials, and particularly induced pluripotent stem cell (iPSC)-derived models. We discuss the current challenges in using FRDA animal models and patient-derived cells. Additionally, we provide a brief overview of how iPSC-based models of FRDA were used to investigate the main pathways involved in disease progression and to screen for potential therapeutic agents for FRDA. The specific focus of this perspective article is to discuss the outlook and the remaining challenges in the context of FRDA iPSC-based models., NA

Glioblastoma is the most malignant primary brain tumor, and a cornerstone in its treatment is radiotherapy. However, tumor cells surviving after irradiation indicates treatment failure; therefore, better understanding of the mechanisms regulating radiotherapy response is of utmost importance. In this study, we generated clinically relevant irradiation-exposed models by applying fractionated radiotherapy over a long time and selecting irradiation-survivor (IR-Surv) glioblastoma cells. We examined the transcriptomic alterations, cell cycle and growth rate changes and responses to secondary radiotherapy and DNA damage response (DDR) modulators. Accordingly, IR-Surv cells exhibited slower growth and partly retained their ability to resist secondary irradiation. Concomitantly, IR-Surv cells upregulated the expression of DDR-related genes, such as CHK1, ATM, ATR, and MGMT, and had better DNA repair capacity. IR-Surv cells displayed downregulation of hypoxic signature and lower induction of hypoxia target genes, compared to naive glioblastoma cells. Moreover, Chk1 inhibition alone or in combination with irradiation significantly reduced cell viability in both naive and IR-Surv cells. However, IR-Surv cells' response to Chk1 inhibition markedly decreased under hypoxic conditions. Taken together, we demonstrate the utility of combining DDR inhibitors and irradiation as a successful approach for both naive and IR-Surv glioblastoma cells as long as cells are refrained from hypoxic conditions., Scientific and Technological Research Council of Turkey (TÜBİTAK)

Cancer cachexia is a disorder of energy balance characterized by the wasting of adipose tissue and skeletal muscle resulting in severe weight loss with profound influence on morbidity and mortality. Treatment options for cancer cachexia are still limited. This multifactorial syndrome is associated with changes in several metabolic pathways in adipose tissue which is affected early in the course of cachexia. Adipose depots are involved in energy storage and consumption as well as endocrine functions. In this mini review, we discuss the metabolic reprogramming in all three types of adipose tissues - white, brown, and beige - under the influence of the tumor macro-environment. Alterations in adipose tissue lipolysis, lipogenesis, inflammation and adaptive thermogenesis of beige/brown adipocytes are highlighted. Energy-wasting circuits in adipose tissue impacts whole-body metabolism and particularly skeletal muscle. Targeting of key molecular players involved in the metabolic reprogramming may aid in the development of new treatment strategies for cancer cachexia., Scientific and Technological Research Council of Turkey (TÜBİTAK); TÜBİTAK-BİDEB

Wildlife are under continuous pressure to adapt to new environments as more land area is converted for human use and human populations continue to concentrate in suburban and exurban areas. This is especially the case for terrestrial mammals, which are forced to navigate these habitat matrices on foot. One way in which mammals may occupy urbanized landscapes is by altering their temporal activity behavior. Typically, studies have found that mammals increase their nocturnal activity within urbanized environments to avoid overlap with humans. However, to date, the majority of studies on this topic have focused on single species, and studying whether this trend holds across an entire community has important ecological implications. Specifically, understanding how differences in species temporal activity response alters predator-prey dynamics and sympatric interspecies competition can provide insight into urban wildlife community assembly and provide a mechanistic understanding of species co-occurrence within these systems. In this study, we used data from a community science camera trapping project in northern Utah to elucidate how human influence alters the temporal activity behavior of five medium- to largesized mammals and how differences in species response affect predator-prey, human, and sympatric competitor temporal niche overlap. We found community-wide changes in activity across study sites, with increases in late night and midday activity and decreases in crepuscular activity within the more-urbanized site. However, species-specific behavioral changes varied, and these changes resulted in reduced overlap, especially between coyotes (Canis latrans) and their potential prey species. These results provide information on how human influence may alter community assembly and species-species interactions within a wildland-urban interface., University of Utah of Graduate Research Fellowship

The Relict Dace is a small cyprinid and the only species in its genus, Relictus. It is naturally distributed in four drainage basins of central Nevada - Butte Valley, Ruby Valley, Steptoe Valley, and Goshute Valley. The species has experienced periods of isolation and connection within these four basins since the late Pliocene, with the last 100 years characterized by anthropogenic disturbance. To better inform conservation actions, we investigated range-wide and intra-basin genetic structure and diversity and conducted F-st outlier tests using RAD-sequencing. We found high levels of genetic structure and four main lineages on a broad scale corresponding primarily to geography, and on a very fine scale (<1 km) within drainage basins. Signatures of selection in the form of outlier loci were documented in multiple locations across the range. Our results provide baseline data for conservation efforts and highlight the degree of fine-scale genetic structuring that may be present in fishes of the Great Basin that are now restricted to small, isolated habitats-particularly wetland complexes. We caution against assuming that geographic distance is a proxy for genetic similarity in Great Basin fishes, encourage thorough genetic sampling, and note that broad-scale genetic surveys can overlook fine-scale genetic structure., U.S. Fish and Wildlife Service (USFWS) Cooperative Agreement Award

Amyotrophic lateral sclerosis (ALS) is a rapidly debilitating fatal neurodegenerative disorder, causing muscle atrophy and weakness, which leads to paralysis and eventual death. ALS has a multifaceted nature affected by many pathological mechanisms, including oxidative stress (also via protein aggregation), mitochondrial dysfunction, glutamate-induced excitotoxicity, apoptosis, neuroinflammation, axonal degeneration, skeletal muscle deterioration and viruses. This complexity is a major obstacle in defeating ALS. At present, riluzole and edaravone are the only drugs that have passed clinical trials for the treatment of ALS, notwithstanding that they showed modest benefits in a limited population of ALS. A dextromethorphan hydrobromide and quinidine sulfate combination was also approved to treat pseudobulbar affect (PBA) in the course of ALS. Globally, there is a struggle to prevent or alleviate the symptoms of this neurodegenerative disease, including implementation of antisense oligonucleotides (ASOs), induced pluripotent stem cells (iPSCs), CRISPR-9/Cas technique, non-invasive brain stimulation (NIBS) or ALS-on-a-chip technology. Additionally, researchers have synthesized and screened new compounds to be effective in ALS beyond the drug repurposing strategy. Despite all these efforts, ALS treatment is largely limited to palliative care, and there is a strong need for new therapeutics to be developed. This review focuses on and discusses which therapeutic strategies have been followed so far and what can be done in the future for the treatment of ALS., Scientific and Technological Research Council of Turkey (TÜBİTAK); European Union (EU); Horizon 2020 Marie Sklodowska-Curie Actions Cofund program; European Commission (EC); Co-Funded Brain Circulation2 Scheme; 2236 CoCirculation2 Program

Plants have paved the way for the attainment of molecules with a wide-range of biological activities. However, plant products occasionally show low biological activities and/or poor pharmacokinetic properties. In that case, development of their derivatives as drugs from the plant world has been actively performed. As plant products, plastoquinones (PQs) have been of high importance in anticancer drug design and discovery; we have previously evaluated and reported the potential cytotoxic effects of a series of PQ analogs. Among these analogs, PQ2, PQ3 and PQ10 were selected for National Cancer Institute (NCI) for in vitro screening of anticancer activity against a wide range of cancer cell lines. The apparent superior anticancer potency of PQ2 on the HCT-116 colorectal cancer cell line than that of PQ3 and PQ10 compared to other tested cell lines has encouraged us to perform further mechanistic studies to enlighten the mode of anti-colorectal cancer action of PQ2. For this purpose, its apoptotic effects on the HCT-116 cell line, DNA binding capacity and several crucial pharmacokinetic properties were investigated. Initially, MTT assay was conducted for PQ2 at different concentrations against HCT-116 cells. Results indicated that PQ2 exhibited significant cytotoxicity in HCT-116 cells with an IC50 value of 4.97 +/- 1.93 mu M compared to cisplatin (IC50 = 26.65 +/- 7.85 mu M). Moreover, apoptotic effects of PQ2 on HCT-116 cells were investigated by the annexin V/ethidium homodimer III staining method and PQ2 significantly induced apoptosis in HCT-116 cells compared to cisplatin. Based on the potent DNA cleavage capacity of PQ2, molecular docking studies were conducted in the minor groove of the double helix of DNA and PQ2 presented a key hydrogen bonding through its methoxy moiety. Overall, both in vitro and in silico studies indicated that effective, orally bioavailable drug-like PQ2 attracted attention for colorectal cancer treatment. The most important point to emer, Scientific Research Projects Coordination Unit of Istanbul University-Cerrahpasa; Scientific and Technological Research Council of Turkey (TÜBİTAK); European Union (EU); Horizon 2020 Marie Sklodowska-Curie Actions Cofund program; European Commission (EC); Co-Funded Brain Circulation2 Scheme; 2236 CoCirculation2 Program; European Research Council (ERC); European Union Seventh Framework Programme (FP7)

Pselesapseactoiontfeirmmpthoartaallclhoenatdroinlgolfevmeilcsaroreturbepurleesnenutceldecaotriorencatlny:d organization is critical for faithful segregation of cytoplasmic and genetic material during cell division and signaling via the primary cilium in quiescent cells. Microtubule-associated proteins (MAPs) govern assembly, maintenance, and remodeling of diverse microtubule arrays. While a set of conserved MAPs are only active during cell division, an emerging group of MAPs acts as dual regulators in dividing and nondividing cells. Here, we elucidated the nonciliary functions and molecular mechanism of action of the ciliopathy-linked protein CCDC66, which we previously characterized as a regulator of ciliogenesis in quiescent cells. We showed that CCDC66 dynamically localizes to the centrosomes, the bipolar spindle, the spindle midzone, the central spindle, and the midbody in dividing cells and interacts with the core machinery of centrosome maturation and MAPs involved in cell division. Loss-of-function experiments revealed its functions during mitotic progression and cytokinesis. Specifically, CCDC66 depletion resulted in defective spindle assembly and orientation, kinetochore fiber stability, chromosome alignment in metaphase as well as central spindle and midbody assembly and organization in anaphase and cytokinesis. Notably, CCDC66 regulates mitotic microtubule nucleation via noncentrosomal and centrosomal pathways via recruitment of gamma-tubulin to the centrosomes and the spindle. Additionally, CCDC66 bundles microtubules in vitro and in cells by its C-terminal microtubule-binding domain. Phenotypic rescue experiments showed that the microtubule and centrosome-associated pools of CCDC66 individually or cooperatively mediate its mitotic and cytokinetic functions. Collectively, our findings identify CCDC66 as a multifaceted regulator of the nucleation and organization of the diverse mitotic and cytokinetic microtubule arrays and provide new insight into noncil, European Union (EU); Horizon 2020; European Research Council (ERC); Starting Grant; European Molecular Biology Organization Installation Grant; European Molecular Biology Organization Young Investigator Award 2020; Scientific and Technological Research Council of Turkey (TÜBİTAK); BİDEB; Marie Sklodowska-Curie Fellowship

Human development and roads threaten wildlife through distinct mechanisms and understanding the influence of these elements can better inform mitigation and conservation strategies. We used camera traps to quantify the effects of major roads, environmental factors, and human development on the mammalian community composition between sites north and south of a major interstate highway in northern Utah, USA. We found no significant differences in species richness nor community similarity across the north-south divide of the highway. Through Bayesian hierarchical modeling, we compared the effects of the distance to the highway, housing and human population density, normalized difference vegetation index (NDVI), and the human footprint index to changes in mammalian community composition and species-specific habitat usage. Community occupancy response, similarity, and species richness were negatively affected by increased housing and human population densities and positively affected by increased NDVI and decreased human footprint, whereas their response to the highway was more inconclusive. We conclude that mammalian community composition in our study area is influenced by both environmental conditions and human development while the effect of the highway was more nuanced, possibly due to the presence of a newly constructed wildlife overpass. Taken together, the lack of differences in species richness or community composition across the highway suggests that it may not currently exacerbate the effects of other anthropogenic sources of habitat fragmentation and highlights the need for additional research into human-wildlife conflict mitigation strategies., NA

Human clock-gene variations contribute to the phenotypic differences observed in various behavioral and physiological processes, such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. However, little is known about the possible effects of identified variations at the molecular level. In this study, we performed a functional characterization at the cellular level of rare cryptochrome 2 (CRY2) missense variations that were identified from the Ensembl database. Our structural studies revealed that three variations (p.Pro123Leu, p.Asp406His, and p.Ser410Ile) are located at the rim of the secondary pocket of CRY2. We show that these variants were unable to repress CLOCK (circadian locomotor output cycles kaput)/BMAL1 (brain and muscle ARNT-like-1)-driven transcription in a cell-based reporter assay and had reduced affinity to CLOCK-BMAL1. Furthermore, our biochemical studies indicated that the variants were less stable than the WT CRY2, which could be rescued in the presence of period 2 (PER2), another core clock protein. Finally, we found that these variants were unable to properly localize to the nucleus and thereby were unable to rescue the circadian rhythm in a Cry1(-/-)Cry2(-/-) double KO mouse embryonic fibroblast cell line. Collectively, our data suggest that the rim of the secondary pocket of CRY2 plays a significant role in its nuclear localization independently of PER2 and in the intact circadian rhythm at the cellular level., Scientific and Technological Research Council of Turkey (TÜBİTAK); KBAG

Stroke is the second highest reason of death in the world and the leading cause of disability. The ischemic stroke makes up the majority of stroke cases that occur due to the blockage of blood vessels. Therapeutic applications for ischemic stroke include thrombolytic treatments that are in limited usage and only applicable to less than 10% of the total stroke patients, but there are promising new approaches. The main cause of ischemic neuronal death is glutamate excitotoxicity. There have been multiple studies focusing on neuroprotection via reduction of glutamate both in ischemic stroke and other neurodegenerative diseases that ultimately failed due to the obstacles in delivery. At that point, systemic glutamate grabbing, or scavenging is an ingenious way of decreasing glutamate levels upon ischemic stroke. The main advantage of this new therapeutic method is the scavengers working in the circulating blood so that there is no interference with the natural brain neurophysiology. In this review, we explain the molecular mechanisms of ischemic stroke, provide brief information about existing drugs and approaches, and present novel systemic glutamate scavenging methods. This review hopefully will elucidate the potential usage of the introduced therapeutic approaches in stroke patients., Scientific and Technological Research Council of Turkey (TÜBİTAK); Natural Science Engineering Council of Canada (NSERC); Instituto de Salud Carlos III; Research Council of Norway (RCN); EuroNanoMed III; GOTTARG project

The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography., National Science Foundation (NSF) Science and Technology Centers; BioXFEL; National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program of TÜBİTAK; 2244 Industrial PhD Program of TÜBİTAK; 1001 TÜBİTAK Supporting Scientific and Technological Research Projects Program; Linac Coherent Light Source (LCLS); Stanford Synchrotron Light Source (SSRL); SLAC National Accelerator Laboratory; U.S. Department of Energy, Office of Science, Basic Energy Sciences

Background: lung cancer is the primary cause of cancer deaths worldwide. Activation of epidermal growth factor receptor (EGFR) leads to lung cancer progression and poor prognosis while involuntary weight loss remains a major problem. Tumour-derived parathyroid hormone-related protein (PTHrP) emerged as a potential mediator of cachexia. Here, we investigated the modulatory role of EGFR signalling in PTHrP (encoded by Pthlh) gene expression and the impact of this relationship on cancer cachexia. Methods: global gene expression profiles of Lewis lung carcinoma (LLC) cells were analysed. Pthlh mRNA levels were measured by qRT-PCR in LLC cells treated with EGFR ligands and tyrosine kinase inhibitors (TKIs). LLC tumour-bearing mice received EGFR TKI erlotinib for 7 days via intraperitoneal injection or oral gavage. Tumour Pthlh mRNA, weight of fat/muscle tissue, and grip strength were assessed. RNA-seq data from The Cancer Genome Atlas and gene expression analysis tools were used to characterize expression profiles of PTHLH and EGFR along with correlation analysis of PTHLH with EGFR and transforming growth factor alpha (TGFA) in human lung cancer and head and neck squamous carcinoma (HNSC). Survival of lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) patients with EGFR gene alterations was analysed in regard to PTHLH expression. Results: expression of EGFR ligands, EGFR itself, and PTHrP co-clusters in LLC cells. Activation of EGFR signalling with its ligands significantly increases (3.8-fold, P < 0.0005) while EGFR TKIs significantly decrease (90%, P < 0.0005) Pthlh mRNA levels in LLC cells. Pthlh mRNA drops 65-75% (P < 0.0005) in tumours upon treatment of LLC tumour-bearing mice with erlotinib while their muscle mass and grip strength increase (9.2% P < 0.05, 23% P < 0.005, respectively) compared with tumour-bearing control mice. PTHLH is overexpressed in tumours of LUSC (45.8-fold, P < 0.05) and HNSC (17.5-fold, P < 0.05) compared with normal tissue., Scientific and Technological Research Council of Turkey (TÜBİTAK); European Molecular Biology Organization (EMBO)

Ayan et al. report two structures of the protein streptavidin - one at ambient temperature determined using serial femtosecond crystallography and a second one determined at cryogenic temperature. These results provide insights into the structural dynamics of apo streptavidin and reveal a cooperative allostery between monomers for binding to biotin, and the findings are supported by GNM analysis. Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 angstrom resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 angstrom resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature., National Science Foundation (NSF) Science and Technology Centers; 2232 International Fellowship for Outstanding Researchers Program; 1001 Scientific and Technological Research Projects Funding Program; Scientific and Technological Research Council of Turkey (TÜBİTAK); U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (OBES); National Institutes of Health, National Institute of General Medical Sciences (NIGMS)

Glioblastoma is the most common and malignant primary brain tumor, defined by its highly aggressive nature. Despite the advances in diagnostic and surgical techniques, and the development of novel therapies in the last decade, the prognosis for glioblastoma is still extremely poor. One major factor for the failure of existing therapeutic approaches is the highly invasive nature of glioblastomas. The extreme infiltrating capacity of tumor cells into the brain parenchyma makes complete surgical removal difficult; glioblastomas almost inevitably recur in a more therapy-resistant state, sometimes at distant sites in the brain. Therefore, there are major efforts to understand the molecular mechanisms underpinning glioblastoma invasion; however, there is no approved therapy directed against the invasive phenotype as of now. Here, we review the major molecular mechanisms of glioblastoma cell invasion, including the routes followed by glioblastoma cells, the interaction of tumor cells within the brain environment and the extracellular matrix components, and the roles of tumor cell adhesion and extracellular matrix remodeling. We also include a perspective of high-throughput approaches utilized to discover novel players for invasion and clinical targeting of invasive glioblastoma cells., Scientific and Technological Research Council of Turkey (TÜBİTAK)

Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their dysfunction causes cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of stable microtubules that maintain their length at a steady-state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified the Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that regulates microtubule organization and stability. Consistently, we observed an increase in tubulin polymerization and microtubule stability, as well as disrupted microtubule organization in ENKD1 overexpression. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results advance our understanding of the functional and regulatory relationship between MAPs and the primary cilium., European Molecular Biology Organization (EMBO) Installation Grant; EMBO Young Investigator Award; Scientific and Technical Research Council of Turkey (TÜBİTAK); European Union (EU); Horizon 2020; Research and Innovation Programme; Marie Sklodowska-Curie Grant

Ras GTPase interacts with its regulators and downstream effectors for its critical function in cellular signaling. Targeting the disrupted mechanisms in Ras-related human cancers requires understanding the distinct dynamics of these protein-protein interactions. We performed normal mode analysis (NMA) of KRas4B in wild-type or mutant monomeric and neurofibromin-1 (NF1), Son of Sevenless 1 (SOS1) or Raf-1 bound dimeric conformational states to reveal partner-specific dynamics of the protein. Gaussian network model (GNM) analysis showed that the known KRas4B lobes further partition into subdomains upon binding to its partners. Furthermore, KRas4B interactions with different partners suppress the flexibility in not only their binding sites but also distant residues in the allosteric lobe in a partner-specific way. The conformational changes can be driven by intrinsic residue fluctuations of the open state KRas4B-GDP, as we illustrated with anisotropic network model (ANM) analysis. The allosteric paths connecting the nucleotide binding residues to the allosteric site at alpha 3-L7 portray differences in the inactive and active states. These findings help in understanding the partner-specific KRas4B dynamics, which could be utilized for therapeutic targeting.

Objective: to compare the effectiveness of different mask types in limiting the dispersal of coughed air. Method: the Schlieren method with a single curved mirror was used in this study. Coughed air has a slightly higher temperature than ambient air, which generates a refractive index gradient. A curved mirror with a radius of curvature of 10 m and a diameter of 60 cm was used. The spread of the cough wavefront was investigated among five subjects wearing: (1) no mask; (2) a single surgical mask; (3) a double surgical mask; (4) a cloth mask; (5) a valveless N95 mask; and (6) a valved N95 mask. Results: all mask types reduced the size of the contaminated region significantly. The percentage reduction in the cross-sectional area of the contaminated region for the same mask types on different subjects revealed by normalized data suggests that the fit of a mask plays an important role. Conclusions: no significant difference in the spread of coughed air was found between the use of a single surgical mask or a double surgical mask. Cloth masks may be effective, depending on the quality of the cloth. Valved N95 masks exclusively protect the user. The fit of a mask is an important factor to minimize the contaminated region.

Globally, birds have been shown to respond to climate change by shifting their elevational distributions. This phenomenon is especially prevalent in the tropics, where elevational gradients are often hotspots of diversity and endemism. Empirical evidence has suggested that elevational range shifts are far from uniform across species, varying greatly in the direction (upslope vs. downslope) and rate of change (speed of elevational shift). However, little is known about the drivers of these variable responses to climate change, limiting our ability to accurately project changes in the future. Here, we compile empirical estimates of elevational shift rates (m/yr) for 421 bird species from eight study sites across the tropics. On average, species shifted their mean elevations upslope by 1.63 +/- 0.30 m/yr, their upper limits by 1.62 m +/- 0.38 m/yr, and their lower limits by 2.81 +/- 0.42 m/yr. Upslope shift rates increased in smaller-bodied, less territorial species, whereas larger species were more likely to shift downslope. When considering absolute shift rates, rates were fastest for species with high dispersal ability, low foraging strata, and wide elevational ranges. Our results indicate that elevational shift rates are associated with species' traits, particularly body size, dispersal ability, and territoriality. However, these effects vary substantially across sites, suggesting that responses of tropical montane bird communities to climate change are complex and best predicted within the local or regional context.

An estimated 17% of migratory bird species are threatened or near threatened with extinction. This represents an enormous potential loss of biodiversity and cost to human societies due to the economic benefits that birds provide through ecosystem services and ecotourism. Conservation of migratory bird species presents many unique challenges, as these birds rely on multiple geographically distinct habitats, including breeding grounds, non-breeding grounds, and stopover sites during migration. In particular, stopover habitats are seldom studied relative to breeding and non-breeding habitats, despite their importance as refueling stations for migratory birds. In this study, we summarize the current research on the use of temporary primary crops by birds during migration and we assess the species characteristics and agricultural practices most often associated with the use of cropland as stopover habitat. First, we conducted a systematic review of the literature to document the effects various farming practices and crop types have on the abundance and diversity of migratory birds using agricultural areas for stopovers. Second, we analyzed the ecological correlates of bird species in the Northern Hemisphere that predict which species may use these areas while migrating. We ran a GLMM to test whether primary diet, diet breadth, primary habitat, habitat breadth, or realm predicted stopover use of agricultural areas. Our review suggests that particular crop types (principally rice, corn, and sunflower), as well as farming practices that result in higher non-cultivated plant diversity, encourage the use of agricultural areas by migrating birds. We found that cropland is used as stopover habitat by bird species that can utilize a large breadth of habitats, as well as species with preferences for habitat similar in structure to agricultural areas.

Aurora kinase A (AURKA) is a conserved kinase that plays crucial roles in numerous cellular processes. Although AURKA overexpression is frequent in human cancers, its pleiotropic functions and multifaceted regulation present challenges in its therapeutic targeting. Key to overcoming these challenges is to identify and characterize the full range of AURKA interactors, which are often weak and transient. Previous proteomic studies were limited in monitoring dynamic and non-mitotic AURKA interactions. Here, we generate the proximity interactome of AURKA in asynchronous cells, which consists of 440 proteins involving multiple biological processes and cellular compartments. Importantly, AURKA has extensive proximate and physical interactions to centriolar satellites, key regulators of the primary cilium. Loss-of-function experiments identify satellites as negative regulators of AURKA activity, abundance, and localization in quiescent cells. Notably, loss of satellites activates AURKA at the basal body, decreases centrosomal IFT88 levels, and causes ciliogenesis defects. Collectively, our results provide a resource for dissecting spatiotemporal regulation of AURKA and uncover its proteostatic regulation by satellites as a new mechanism for its ciliary functions.

Background: androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10-100x more binding sites than differentially expressed genes. It is unclear how or if these excess binding sites impact gene transcription. Results: to characterize the regulatory logic of AR-mediated transcription, we generated a locus-specific map of enhancer activity by functionally testing all common clinical AR binding sites with Self-Transcribing Active Regulatory Regions sequencing (STARRseq). Only 7% of AR binding sites displayed androgen-dependent enhancer activity. Instead, the vast majority of AR binding sites were either inactive or constitutively active enhancers. These annotations strongly correlated with enhancer-associated features of both in vitro cell lines and clinical prostate cancer samples. Evaluating the effect of each enhancer class on transcription, we found that AR-regulated enhancers frequently interact with promoters and form central chromosomal loops that are required for transcription. Somatic mutations of these critical AR-regulated enhancers often impact enhancer activity. Conclusions: using a functional map of AR enhancer activity, we demonstrated that AR-regulated enhancers act as a regulatory hub that increases interactions with other AR binding sites and gene promoters.

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

The majority of the world's biodiversity occurs in the tropics, but human actions in these regions have precipitated an extinction crisis due to habitat degradation, overexploitation, and climate change. Understanding which ecological, biogeographical, and life-history traits predict extinction risk is critical for conserving species. The Philippines is a hotspot of biodiversity and endemism, but it is a region that also suffers from an extremely high level of deforestation, habitat degradation, and wildlife exploitation. We investigated the biological correlates of extinction risk based on the IUCN Red List threat status among resident Philippine birds using a broad range of ecological, biogeographical, and life history traits previously identified as correlates of extinction risk in birds. We found strong support across competing models for endemism, narrower elevational ranges, high forest dependency, and larger body size as correlates significantly associated with extinction risk. Additionally, we compared observed threat status with threat status fitted by our model, finding fourteen species that are not currently recognized by the IUCN Red List as threatened that may be more threatened than currently believed and therefore warrant heightened conservation focus, and predicted threat statuses for the four Philippine Data Deficient bird species. We also assessed species described in recent taxonomic splits that are recognized by BirdLife International, finding 12 species that have a fitted threat status more severe than their IUCN-designated ones. Our findings provide a framework for avian conservation efforts to identify birds with specific biological correlates that increase a species' vulnerability to extinction both in the Philippine Archipelago and elsewhere on other tropical islands.

Background: the histone H3 lysine 79 (H3K79) methyltransferase DOT1L is a key chromatin-based barrier to somatic cell reprogramming. However, the mechanisms by which DOT1L safeguards cell identity and somatic-specific transcriptional programs remain unknown. Results: we employed a proteomic approach using proximity-based labeling to identify DOT1L-interacting proteins and investigated their effects on reprogramming. Among DOT1L interactors, suppression of AF10 (MLLT10) via RNA interference or CRISPR/Cas9, significantly increases reprogramming efficiency. In somatic cells and induced pluripotent stem cells (iPSCs) higher order H3K79 methylation is dependent on AF10 expression. In AF10 knock-out cells, re-expression wild-type AF10, but not a DOT1L binding-impaired mutant, rescues overall H3K79 methylation and reduces reprogramming efficiency. Transcriptomic analyses during reprogramming show that AF10 suppression results in downregulation of fibroblast-specific genes and accelerates the activation of pluripotency-associated genes. Conclusions: our findings establish AF10 as a novel barrier to reprogramming by regulating H3K79 methylation and thereby sheds light on the mechanism by which cell identity is maintained in somatic cells.

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine beta-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic Cbs(Zn/Zn) mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1(-/-) mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, Cbs(Zn/Zn), Cry1(-/-), and Cry2(-/-) samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.

Oligomerization of Pr55(Gag) is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55(Gag). However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55(Gag) to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18-33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles' membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain's 2D layers during assembly and budding.

The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations., The authors thank Colin Grant (US Fish and Wildlife Service), who made many of the initial inquiries soliciting longfin smelt samples, and Josh Israel (US Bureau of Reclamation), who performed initial genetic analyses. The authors also thank the following individuals and agencies for help collecting samples: Hobbslab and staff -UC Davis; Matt Dekar and staff -US Fish and Wildlife Service; Kathy Hieb, Jennifer Giannetta, Jeremiah Bautista, Aaron Ng, Rebecca Garwood, James Ray, Justin Garwood, and Mike Wallace -California Department of Fish and Wildlife; Laurie Lloyd, Olaf Langness -Washington Department of Fish and Wildlife, Thomas Quinn, University of Washington; Eric Taylor -The University of British Columbia, John Kelson -Fish BiologistConsultant, Smithers, British Columbia; Mayumi Arimitsu -US Geological Survey, Alaska Science Center. Finally, the authors also thank a number of internal reviewers, Genomic Variation Lab Personnel, and other agency biologists who helped this project, including Matthew Campbell, Daphne Gille, Levi Lewis, Andrea Schreier, Josh Israel, and Alisha Goodbla. Funding for this project was generously provided by the California Department of Water Resources, Agreement Number 4600011196.

Predator-prey interactions and human presence are among the key factors shaping large mammal activity patterns. In human-dominated landscapes, large carnivores must balance their activity rhythms between optimizing feeding opportunities and avoiding encounters with humans. In northeastern Turkey, the Caucasian lynx (Lynx lynx dinniki), a threatened subspecies of the Eurasian lynx (Lynx lynx), occupies habitats that are heavily fragmented and dominated by human presence in the warm part of the year. Using camera traps and GPS-collar activity sensors, we investigated lynx circadian activity patterns across lunar phases and seasons. We compared the activity pattern of the lynx to the activity pattern of its primary prey, the European hare (Lepus europaeus), and humans. We found that during the warm season (May-October), lynx displayed a bimodal crepuscular activity pattern typical for this species and consistent with hare activity. During the cold season (November-April), both lynx and hares shifted to predominantly diurnal activity. During the full moon, hares reduced their activity due to the anti-predator behaviour, followed by a corresponding adjustment in lynx activity patterns. We conclude that lynx activity in our study area is an outcome of weather conditions, human presence and foraging behaviour. Our results also corroborate the suitability of camera trapping data in documenting multiple species' temporal activity patterns., National Geographic Society; Sigrid Rausing Trust; Europian Union (EU); Civil Society Development Center (STGM); The Trans-Anatolian Natural Gas Pipeline (TANAP); Whitley Fund; Foundation Segré; Bilge Bahar; Faruk Eczacıbaşı; Seha İşmen; Ömer Külahçıoğlu; Burak Över; Batubay Özkan; Alan Peterson; Emin Özgür; Suna Reyent; Faruk Yalçın Zoo

Protected areas are highly heterogeneous in their effectiveness at buffering human pressure, which may hamper their ability to conserve species highly sensitive to human activities. Here, we use 60 million bird observations from eBird to estimate the sensitivity to human pressure of each bird species breeding in the Americas. Concerningly, we find that ecoregions hosting large proportions of high-sensitivity species, concentrated in tropical biomes, do not have more intact protected habitat. Moreover, 266 high-sensitivity species have little or no intact protected habitat within their distributions. Finally, we show that protected area intactness is decreasing faster where high-sensitivity species concentrate. Our results highlight a major mismatch between species conservation needs and the coverage of intact protected habitats, which likely hampers the long-term effectiveness of protected areas at retaining species. We highlight ecoregions where protection and management of intact habitats, complemented by restoration, is urgently needed., NA

The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway., National Science Foundation (NSF) Science and Technology Centers; Science and Technology Centers; Scientifc and Technological Research Council of Turkey (TÜBİTAK); US Department of Energy Joint Genome Institute

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine beta-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic Cbs(Zn/Zn) mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1(-/-) mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, Cbs(Zn/Zn), Cry1(-/-), and Cry2(-/-) samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control., İstanbul Development Agency; Defense Advanced Research Projects Agency; National Institute of Neurological Disorders and Stroke; Scientific and Technological Research Council of Turkey (TÜBİTAK) BIDEB 2214-A Scholarship