Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were size-selected to 500–600 bp, equipped with adapters, treated with bisulfite, PCR amplified, cloned and sequenced. We constructed RRBS libraries from murine ES cells and from ES cells lacking DNA methyltransferases Dnmt3a and 3b and with knocked-down (kd) levels of Dnmt1 (Dnmt[1(kd),3a(−/−),3b(−/−)]). Sequencing of 960 RRBS clones from Dnmt[1(kd),3a(−/−),3b(−/−)] cells generated 343 kb of non-redundant bisulfite sequence covering 66212 cytosines in the genome. All but 38 cytosines had been converted to uracil indicating a conversion rate of >99.9%. Of the remaining cytosines 35 were found in CpG and 3 in CpT dinucleotides. Non-CpG methylation was >250-fold reduced compared with wild-type ES cells, consistent with a role for Dnmt3a and/or Dnmt3b in CpA and CpT methylation. Closer inspection revealed neither a consensus sequence around the methylated sites nor evidence for clustering of residual methylation in the genome. Our findings indicate random loss rather than specific maintenance of methylation in Dnmt[1(kd),3a(−/−),3b(−/−)] cells. Near-complete bisulfite conversion and largely unbiased representation of RRBS libraries suggest that random shotgun bisulfite sequencing can be scaled to a genome-wide approach

A phoenix rising? The regeneration of the Ghana garment and textile industry

Some African countries’ premier industries, such as textiles, garments and agro-processing, which floundered in the face of market liberalization and stiff competition from cheap imports, are now going through regenerative changes, with some beginning to tell a cautionary tale of a leap upwards. Focusing on the Ghana garment and textile industry, we draw on a framework that integrates social practices and everyday general-purpose technologies to explore the rise, decline and regeneration of the industry. Explicating a fine analysis of how the performative reconfiguration of social practices and functional sources of innovation and technologies may combine to support innovation-driven growth, our study sheds light on how loosely connected actors within a hitherto floundering industry can learn to transform their situated practices to drive their ‘industrial regeneration’. Implications for the theory and practice of industrial regeneration are outlined

Application of International Standards to Evaluate the Potential of Sustainable Secondary Production of Tin and Tungsten in Portugal

The ambitious movement towards industry 5.0 technologies and the green transition drives the efforts towards securing critical metals’ supply chains globally. In Europe, highly economically important Tin and Tungsten are raising concerns regarding supply security due to geographical reserves’ uniformity and socio-political reluctance to mining. Nevertheless, mines that have seized operations in Portugal due to not being sustainable in the past are attracting renewed attention for further exploitation due to growing market demand and reclamation efforts for environmental concerns. Such abandoned resources need to be reassessed for their feasibility from economic, social, and environmental perspectives to ensure sustainable exploitation. Presenting the production criticality of Tin and Tungsten, this study implements the United Nations Framework Classification for Resources (UNFC) to assess the viability of abandoned mines and tailings dumps in Portugal, considering the indicators of Sustainable Development Goals (SDGs). The work indicates that Portugal’s abandoned Vale das Gatas Tin and Tungsten mine has good potential for further development. Furthermore, social perception towards new and abandoned mining is evaluated by collecting opinions from different parts of the country. It has been identified that sustainable technology and job opportunities are the driving parameters for the social acceptance of mining projects in Portugal

V3 Loop Truncations in HIV-1 Envelope Impart Resistance to Coreceptor Inhibitors and Enhanced Sensitivity to Neutralizing Antibodies

The V1/V2 region and the V3 loop of the human immunodeficiency virus type I (HIV-1) envelope (Env) protein are targets for neutralizing antibodies and also play an important functional role, with the V3 loop largely determining whether a virus uses CCR5 (R5), CXCR4 (X4), or either coreceptor (R5X4) to infect cells. While the sequence of V3 is variable, its length is highly conserved. Structural studies indicate that V3 length may be important for interactions with the extracellular loops of the coreceptor. Consistent with this view, genetic truncation of the V3 loop is typically associated with loss of Env function. We removed approximately one-half of the V3 loop from three different HIV-1 strains, and found that only the Env protein from the R5X4 strain R3A retained some fusion activity. Loss of V1/V2 (ΔV1/V2) was well tolerated by this virus. Passaging of virus with the truncated V3 loop resulted in the derivation of a virus strain that replicated with wild-type kinetics. This virus, termed TA1, retained the V3 loop truncation and acquired several adaptive changes in gp120 and gp41. TA1 could use CCR5 but not CXCR4 to infect cells, and was extremely sensitive to neutralization by HIV-1 positive human sera, and by antibodies to the CD4 binding site and to CD4-induced epitopes in the bridging sheet region of gp120. In addition, TA1 was completely resistant to CCR5 inhibitors, and was more dependent upon the N-terminal domain of CCR5, a region of the receptor that is thought to contact the bridging sheet of gp120 and the base of the V3 loop, and whose conformation may not be greatly affected by CCR5 inhibitors. These studies suggest that the V3 loop protects HIV from neutralization by antibodies prevalent in infected humans, that CCR5 inhibitors likely act by disrupting interactions between the V3 loop and the coreceptor, and that altered use of CCR5 by HIV-1 associated with increased sensitivity to changes in the N-terminal domain can be linked to high levels of resistance to these antiviral compounds

Culture Shapes Efficiency of Facial Age Judgments

Background: Cultural differences in socialization can lead to characteristic differences in how we perceive the world. Consistent with this influence of differential experience, our perception of faces (e.g., preference, recognition ability) is shaped by our previous experience with different groups of individuals. Methodology/Principal Findings: Here, we examined whether cultural differences in social practices influence our perception of faces. Japanese, Chinese, and Asian-Canadian young adults made relative age judgments (i.e., which of these two faces is older?) for East Asian faces. Cross-cultural differences in the emphasis on respect for older individuals was reflected in participants ’ latency in facial age judgments for middle-age adult faces—with the Japanese young adults performing the fastest, followed by the Chinese, then the Asian-Canadians. In addition, consistent with the differential behavioural and linguistic markers used in the Japanese culture when interacting with individuals younger than oneself, only the Japanese young adults showed an advantage in judging the relative age of children’s faces. Conclusions/Significance: Our results show that different sociocultural practices shape our efficiency in processing facia

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development

While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators. Detailed analysis of the splicing dynamics and function of one such regulator, HMGA2, identified an alternative isoform that escapes miRNA-mediated targeting. We further identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development. Collectively, our study highlights molecular mechanisms by which alternative splicing and miRNA-mediated post-transcriptional regulation impact the molecular identity and stage-specific developmental features of human HSCs. Human hematopoietic stem cells (HSCs) display substantial transcriptional diversity during development. Here, we investigated the contribution of alternative splicing to such diversity by analyzing the dynamics of a key hematopoietic regulator, HMGA2. Next, we showed that CLK3, by regulating the splicing pattern of HMGA2, reinforces an HSC-specific program

Traditional circumcision during manhood initiation rituals in the Eastern Cape, South Africa: a pre-post intervention evaluation

<p>Abstract</p> <p>Background</p> <p>Circumcisions undertaken in non-clinical settings can have significant risks of serious adverse events, including death. The aim of this study was to test an intervention for safe traditional circumcision in the context of initiation into manhood among the Xhosa, Eastern Cape, South Africa.</p> <p>Methods</p> <p>Traditional surgeons and nurses registered with the health department were trained over five days on ten modules including safe circumcision, infection control, anatomy, post-operative care, detection and early management of complications and sexual health education. Initiates from initiation schools of the trained surgeons and nurses were examined and interviewed on 2^nd, 4^th, 7^thand 14^thday after circumcision.</p> <p>Results</p> <p>From 192 initiates physically examined at the 14th day after circumcision by a trained clinical nurse high rates of complications were found: 40 (20.8%) had mild delayed wound healing, 31 (16.2%) had a mild wound infection, 22 (10.5%) mild pain and 20 (10.4%) had insufficient skin removed. Most traditional surgeons and nurses wore gloves during operation and care but did not use the recommended circumcision instrument. Only 12% of the initiates were circumcised before their sexual debut and they reported a great deal of sexual risk behaviour.</p> <p>Conclusion</p> <p>Findings show weak support for scaling up traditional male circumcision.</p

Enhancing Horizon Scanning by utilizing pre-developed scenarios: analysis of current practice and specification of a process improvement to aid the identification of important 'weak signals'

This paper documents the Intuitive Logics scenario planning process and its relationship with horizon scanning activity in order to evaluate the separate and joint usefulness of these methods for anticipating the future. The specific objectives of this paper are to: (i) identify and differentiate scenario planning and horizon scanning methodologies (ii) discuss & evaluate their analytic underpinnings, and (iii) critically appraise their separate and combined value and effectiveness in relation to enhancing organizational preparedness for the future. Our analysis culminates with specifications to (iv) enhance the identification of ’weak signals’ in Horizon Scanning by utilizing a systematically broadened range of both negatively-valenced and positively-valenced scenario storylines

Neutrino Mass and μ→e+γ\mu \rightarrow e + \gamma from a Mini-Seesaw

The recently proposed "mini-seesaw mechanism" combines naturally suppressed Dirac and Majorana masses to achieve light Standard Model neutrinos via a low-scale seesaw. A key feature of this approach is the presence of multiple light (order GeV) sterile-neutrinos that mix with the Standard Model. In this work we study the bounds on these light sterile-neutrinos from processes like \mu ---> e + \gamma, invisible Z-decays, and neutrinoless double beta-decay. We show that viable parameter space exists and that, interestingly, key observables can lie just below current experimental sensitivities. In particular, a motivated region of parameter space predicts a value of BR(\mu ---> e + \gamma) within the range to be probed by MEG.Comment: 1+26 pages, 7 figures. v2 JHEP version (typo's fixed, minor change to presentation, results unchanged