3D genomics across the tree of life reveals condensin II as a determinant of architecture type

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional(3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedlyduring eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with theabsence of condensin II subunits. Moreover, condensin II depletion converts the architecture of thehuman genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state,centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physicalmodel in which lengthwise compaction of chromosomes by condensin II during mitosis determineschromosome-scale genome architecture, with effects that are retained during the subsequent interphase.This mechanism likely has been conserved since the last common ancestor of all eukaryotes.C.H. is supported by the Boehringer Ingelheim Fonds; C.H., Á.S.C., and B.D.R. are supported by an ERC CoG (772471, “CohesinLooping”); A.M.O.E. and B.D.R. are supported by the Dutch Research Council (NWO-Echo); and J.A.R. and R.H.M. are supported by the Dutch Cancer Society (KWF). T.v.S. and B.v.S. are supported by NIH Common Fund “4D Nucleome” Program grant U54DK107965. H.T. and E.d.W. are supported by an ERC StG (637597, “HAP-PHEN”). J.A.R., T.v.S., H.T., R.H.M., B.v.S., and E.d.W. are part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Work at the Center for Theoretical Biological Physics is sponsored by the NSF (grants PHY-2019745 and CHE-1614101) and by the Welch Foundation (grant C-1792). V.G.C. is funded by FAPESP (São Paulo State Research Foundation and Higher Education Personnel) grants 2016/13998-8 and 2017/09662-7. J.N.O. is a CPRIT Scholar in Cancer Research. E.L.A. was supported by an NSF Physics Frontiers Center Award (PHY-2019745), the Welch Foundation (Q-1866), a USDA Agriculture and Food Research Initiative grant (2017-05741), the Behavioral Plasticity Research Institute (NSF DBI-2021795), and an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375). Hi-C data for the 24 species were created by the DNA Zoo Consortium (www.dnazoo.org). DNA Zoo is supported by Illumina, Inc.; IBM; and the Pawsey Supercomputing Center. P.K. is supported by the University of Western Australia. L.L.M. was supported by NIH (1R01NS114491) and NSF awards (1557923, 1548121, and 1645219) and the Human Frontiers Science Program (RGP0060/2017). The draft A. californica project was supported by NHGRI. J.L.G.-S. received funding from the ERC (grant agreement no. 740041), the Spanish Ministerio de Economía y Competitividad (grant no. BFU2016-74961-P), and the institutional grant Unidad de Excelencia María de Maeztu (MDM-2016-0687). R.D.K. is supported by NIH grant RO1DK121366. V.H. is supported by NIH grant NIH1P41HD071837. K.M. is supported by a MEXT grant (20H05936). M.C.W. is supported by the NIH grants R01AG045183, R01AT009050, R01AG062257, and DP1DK113644 and by the Welch Foundation. E.F. was supported by NHGR

A qualitative study of the understanding among residents of vulnerable neighborhoods of those factors that attract migrant youth into illegal activities

The purpose of the study is to gain a deeper understanding of the perceptions, among the inhabitants of socially vulnerable areas, of the various factors that make immigrant youth participate in criminal activities. The essay is a qualitative case study with semi-structured interviews, each respondent hailing from a particular vulnerable area of Sweden. The data was processed in a thematic analysis which was then divided into different themes. The study begins with an introduction informing the reader of what to expect ahead as well as background information on vulnerable areas, criminal activity, and newcomers. The collected data has been analyzed theoretically with the help of Hirschi's social bond theory, Becker's labeling theory and Merton's strain theory. The results show that young immigrants choose to participate in illegal activities due to various factors. According to the respondents, the factors can be anything from housing situation, living conditions, financial resources and others that empower them to commit crimes. The norms and values that immigrant youth have are unlike established social norms and for this reason they are regarded as deviants and feel excluded from the majority society. Immigrant young people experience strain from an early age as they attempt to establish themselves and enjoy a similar level and standing as other Swedes

A qualitative study of the understanding among residents of vulnerable neighborhoods of those factors that attract migrant youth into illegal activities

The purpose of the study is to gain a deeper understanding of the perceptions, among the inhabitants of socially vulnerable areas, of the various factors that make immigrant youth participate in criminal activities. The essay is a qualitative case study with semi-structured interviews, each respondent hailing from a particular vulnerable area of Sweden. The data was processed in a thematic analysis which was then divided into different themes. The study begins with an introduction informing the reader of what to expect ahead as well as background information on vulnerable areas, criminal activity, and newcomers. The collected data has been analyzed theoretically with the help of Hirschi's social bond theory, Becker's labeling theory and Merton's strain theory. The results show that young immigrants choose to participate in illegal activities due to various factors. According to the respondents, the factors can be anything from housing situation, living conditions, financial resources and others that empower them to commit crimes. The norms and values that immigrant youth have are unlike established social norms and for this reason they are regarded as deviants and feel excluded from the majority society. Immigrant young people experience strain from an early age as they attempt to establish themselves and enjoy a similar level and standing as other Swedes

Evidence for and against a pathogenic role for reduced γ-secretase activity in familial Alzheimer’s disease

The majority of mutations causing familial Alzheimer’s disease (fAD) have been found in the gene PRESENILIN1 (PSEN1 ) with additional mutations in the related gene PRESENILIN2 (PSEN2 ). The best characterized function of PRESENILIN (PSEN) proteins is in γ-secretase enzyme activity. One substrate of γ-secretase is encoded by the gene AMYLOID BETA A4 PRECURSOR PROTEIN (A βPP/APP) that is a fAD mutation locus. AβPP is the source of the amyloid-β (Aβ) peptide enriched in the brains of people with fAD or the more common, late onset, sporadic form of AD, sAD. These observations have resulted in a focus on γ-secretase activity and Aβ as we attempt to understand the molecular basis of AD pathology. In this paper we briefly review some of the history of research on γ-secretase in AD. We then discuss the main ideas regarding the role of γ-secretase and the PSEN genes in this disease. We examine the significance of the “fAD mutation reading frame preservation rule” that applies to PSEN1 and PSEN2 (and A βPP ) and look at alternative roles for AβPP and Aβ in fAD. We present a case for an alternative interpretation of published data on the role of γ-secretase activity and fAD-associated mutations in AD pathology. Evidence supports a “PSEN holoprotein multimer hypothesis” where PSEN fAD mutations generate mutant PSEN holoproteins that multimerize with wild type holoprotein and dominantly interfere with an AD-critical function(s) such as autophagy or secretion of Aβ. Holoprotein multimerization may be required for the endoproteolysis that activates PSENs’ γ-secretase activity