John Paul II's Pilgrimages to Poland - Native Context and Universal Message. Comments from a Participant and Researcher

The article concerns a relatively small but important fragment of John Paul II's pastoral activity, namely his pilgrimages to Poland: the nature of these pilgrimages, their historical background and teaching - especially to the extent that went beyond the immediate and Polish context. The text is the result not only of reading papal statements, but also of personal observation of the political and social atmosphere. The first two parts contain a concise description of the Pope's eight pilgrimages to Poland (before and after the political transformation). The third highlights out the main universal themes raised by the Pope: the dignity of the person, truth and freedom. During consecutive pilgrimages to Poland, he deepened and expanded the themes of his teaching. This collection of his sermons and speeches to Poles constitutes a comprehensive (devoid of redundant repetitions and omissions) treatment of important social, philosophical and theological issues. John Paul II, when speaking to Poles and about Poles, did not lose his universal perspective; he appealed both to Christians and to all people of good will. Papal pilgrimages to Poland are a significant part of modern Polish history, and their message is a valuable intellectual and spiritual gift.

Chemical reporters to study mammalian O-glycosylation

Glycans play essential roles in a range of cellular processes and have been shown to contribute to various pathologies. The diversity and dynamic nature of glycan structures and the complexities of glycan biosynthetic pathways make it challenging to study the roles of specific glycans in normal cellular function and disease. Chemical reporters have emerged as powerful tools to characterise glycan structures and monitor dynamic changes in glycan levels in a native context. A variety of tags can be introduced onto specific monosaccharides via the chemical modification of endogenous glycan structures or by metabolic or enzymatic incorporation of unnatural monosaccharides into cellular glycans. These chemical reporter strategies offer unique opportunities to study and manipulate glycan functions in living cells or whole organisms. In this review, we discuss recent advances in metabolic oligosaccharide engineering and chemoenzymatic glycan labelling, focusing on their application to the study of mammalian O-linked glycans. We describe current barriers to achieving glycan labelling specificity and highlight innovations that have started to pave the way to overcome these challenges.

A saturating mutagenesis CRISPR-Cas9–mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in murine ESCs

Regulatory elements (REs) consist of enhancers and promoters that occupy a significant portion of the noncoding genome and control gene expression programs either in cis or in trans. Putative REs have been identified largely based on their regulatory features (co-occupancy of ESC-specific transcription factors, enhancer histone marks, and DNase hypersensitivity) in mouse embryonic stem cells (mESCs). However, less has been established regarding their regulatory functions in their native context. We deployed cis- and trans-regulatory elements scanning through saturating mutagenesis and sequencing (ctSCAN-SMS) to target elements within the ∼12-kb cis-region (cis-REs; CREs) of the Oct4 gene locus, as well as genome-wide 2,613 high-confidence trans-REs (TREs), in mESCs. ctSCAN-SMS identified 10 CREs and 12 TREs as novel candidate REs of the Oct4 gene in mESCs. Furthermore, deletions of these candidate REs confirmed that the majority of the REs are functionally active, and CREs are more active than TREs in controlling Oct4 gene expression. A subset of active CREs and TREs physically interact with the Oct4 promoter to varying degrees; specifically, a greater number of active CREs, compared with active TREs, physically interact with the Oct4 promoter. Moreover, comparative genomics analysis reveals that a greater number of active CREs than active TREs are evolutionarily conserved between mice and primates, including humans. Taken together, our study demonstrates the reliability and robustness of ctSCAN-SMS screening to identify critical REs and investigate their roles in the regulation of transcriptional output of a target gene (in this case Oct4) in their native context.

The supramolecular landscape of growing human axons

During brain development, human axons must extend over great distances in a relatively short amount of time. How the subcellular architecture of the growing axon sustains the requirements for such rapid build-up of cellular constituents has remained elusive. Human axons have been particularly inaccessible to imaging at molecular resolution in a near-native context. Here we apply cryo-correlative light microscopy and electron tomography to growing axonal tracts from human cerebral organoids. Our data reveal a wealth of structural details on the arrangement of macromolecules, cytoskeletal components, and organelles in elongating axon shafts. In particular, the intricate shape of the endoplasmic reticulum is consistent with its role in fulfilling the high demand for lipid biosynthesis to support growth. Furthermore, the scarcity of ribosomes within the growing shaft suggests limited translational competence during expansion of this compartment. These data provide an unprecedented resource and reveal a molecular architecture that helps explain the unique biology of growing human axons.

At-home ethnography: a native researcher’s fieldwork reflections

PurposeIn last few decades, the native anthropology has been highlighted for its potential to immediately grasping cultural familiarity, contextual sensitivity, and rapport building. Nevertheless, detachment from the native context is also seen as a challenge for the native researcher. This paper aims to provide invaluable information about the fieldwork experience of the author as a native researcher in rural Punjab Pakistan. The author presents and reflects the fieldwork challenges faced and the strategies used to overcome the challenges. The primary objective of this paper is to discuss the methodological strategies to face the challenges of doing at-home ethnography.Design/methodology/approachThis paper is based on ethnographic fieldwork conducted in native context.FindingsDealing with contextual complexity and sensitivity with the author’s native learning, the author used native knowledge as a useful resource to investigate insider’s perspective on infant care belief practices. Furthermore, the author addressed the challenges related to building rapport, gaining friendly access to the families and children, and setting aside presumptions. The author discusses the strategies opted, such as selecting a research assistant, gaining access to the field, planning fieldwork and bracketing native presumptions.Practical implicationsThis paper provides important insight of at-home ethnography and technical understanding to conduct fieldwork in native contexts.Originality/valueBased on my ethnographic fieldwork, this article contributes in contemporary debates on the challenges in doing at-home ethnography.

Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo

T cells in vivo migrate primarily via undirected random walks, but it remains unresolved how these random walks generate an efficient search. Here, we use light sheet microscopy of T cells in the larval zebrafish as a model system to study motility across large populations of cells over hours in their native context. We show that cells do not perform Levy flight; rather, there is substantial cell-to-cell variability in speed, which persists over timespans of a few hours. This variability is amplified by a correlation between speed and directional persistence, generating a characteristic cell behavioral manifold that is preserved under a perturbation to cell speeds, and seen in Mouse T cells and Dictyostelium. Together, these effects generate a broad range of length scales over which cells explore in vivo.

Objects of Design

Design and social innovation is a developing field of study. The current lack of critical analysis of initiatives and the dominance of insights and methods from European cases in academic literature are not sufficient to construct an image that could be considered as comprehensive. This paper aims to address both issues by introducing Activity Theory as an analytical framework, as its ability to examine phenomena in their native context through multiple perspectives is considered to be well-suited to study design and social innovation initiatives. The analysis of data obtained during a field study investigating three social initiatives in Bangkok contributed to understanding how they work and why they exist, in addition to highlighting the influence of the Thai social and cultural context on the role of design in the social innovation process.

A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in murine ESCs

Regulatory elements (REs) consist of enhancers and promoters that occupy a significant portion of the non-coding genome and control gene expression programs either in –cis or in – trans. Putative REs have been identified largely based on their regulatory features (co-occupancy of ESC-specific transcription factors, enhancer histone marks and DNase hypersensitivity) in mouse embryonic stem cells (mESCs). However, less has been established regarding their regulatory functions in their native context. We deployed cis- and trans-regulatory elements scanning through saturating mutagenesis and sequencing (ctSCAN-SMS) to target elements within the ∼12kb cis-region (Cis-REs; CREs) of the Oct4 gene locus, as well as genome-wide 2,613 high-confidence trans-REs (TREs), in mESCs. ctSCAN-SMS identified 10 CREs and 12 TREs, as novel candidate REs of the Oct4 gene in mESCs. Furthermore, deletions of these candidate REs confirmed that the majority of the REs are functionally active, and CREs are more active than TREs in controlling Oct4 gene expression. A subset of active CREs and TREs physically interact with the Oct4 promoter to varying degrees; specifically, a greater number of active CREs compared to active TREs, physically interact with the Oct4 promoter. Moreover, comparative genomics analysis reveals that more number of active CREs than active TREs are evolutionary conserved between mouse and primates, including human. Taken together, our study demonstrates the reliability and robustness of ctSCAN-SMS screening to identify critical REs, and investigate their roles in the regulation of transcriptional output of a target gene (in this case Oct4) in their native context.

Control of clathrin-mediated endocytosis by NIMA family kinases

Endocytosis, the process by which cells internalize plasma membrane and associated cargo, is regulated extensively by posttranslational modifications. Previous studies suggested the potential involvement of scores of protein kinases in endocytic control, of which only a few have been validated within their native context. Here we show that the conserved NIMA-related kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (the NEKLs) control clathrin-mediated endocytosis in C. elegans. Loss of NEKLs leads to clathrin mislocalization and to a dramatic reduction in clathrin mobility at the apical membrane. Strikingly, reducing the levels of active AP2, the major clathrin adapter complex, rescues nekl mutant defects, whereas increased levels of active AP2 exacerbate nekl defects. Moreover, NEKL inhibition alleviates defects associated with reduced AP2 activity, attesting to the tight link between NEKL and AP2 functions. We also show that NEKLs are required for the clustering and internalization of membrane cargo and that human NEKs rescue defects in nekl mutant worms.