Deep Transfer Learning on Satellite Imagery Improves Air Quality Estimates in Developing Nations

Urban air pollution is a public health challenge in low- and middle-income countries (LMICs). However, LMICs lack adequate air quality (AQ) monitoring infrastructure. A persistent challenge has been our inability to estimate AQ accurately in LMIC cities, which hinders emergency preparedness and risk mitigation. Deep learning-based models that map satellite imagery to AQ can be built for high-income countries (HICs) with adequate ground data. Here we demonstrate that a scalable approach that adapts deep transfer learning on satellite imagery for AQ can extract meaningful estimates and insights in LMIC cities based on spatiotemporal patterns learned in HIC cities. The approach is demonstrated for Accra in Ghana, Africa, with AQ patterns learned from two US cities, specifically Los Angeles and New York

Characteristics of transposable element exonization within human and mouse

Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.Comment: 11 pages, 4 figure

RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

<p>Abstract</p> <p>Background</p> <p>Repetitive sequences are the major components of the eukaryotic genomes. Association of these repeats with transcribing sequences and their regulation in buffalo <it>Bubalus bubalis </it>has remained largely unresolved.</p> <p>Results</p> <p>We cloned and sequenced <it>RsaI </it>repeat fragments pDp1, pDp2, pDp3, pDp4 of 1331, 651, 603 and 339 base pairs, respectively from the buffalo, <it>Bubalus bubalis</it>. Upon characterization, these fragments were found to represent retrotransposons and part of some functional genes. The resultant clones showed cross hybridization only with buffalo, cattle, goat and sheep genomic DNA. Real Time PCR, detected ~2 × 10⁴copies of pDp1, ~ 3000 copies of pDp2 and pDp3 and ~ 1000 of pDp4 in buffalo, cattle, goat and sheep genomes, respectively. <it>RsaI </it>repeats are transcriptionally active in somatic tissues and spermatozoa. Accordingly, pDp1 showed maximum expression in lung, pDp2 and pDp3 both in Kidney, and pDp4 in ovary. Fluorescence <it>in situ </it>hybridization showed repeats to be distributed all across the chromosomes.</p> <p>Conclusions</p> <p>The data suggest that <it>RsaI </it>repeats have been incorporated into the exonic regions of various transcribing genes, possibly contributing towards the architecture and evolution of the buffalo and related genomes. Prospects of our present work in the context of comparative and functional genomics are highlighted.</p

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes. Prior analyses of expressed sequence tags show that almost all Alu-derived exons are alternatively spliced, and the vast majority of these exons have low transcript inclusion levels. In this work, we provide genomic and experimental evidence for diverse splicing patterns of exonized Alu elements in human tissues. Using Exon array data of 330 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific switch in their transcript inclusion levels. Most of such exons are derived from ancient Alu elements in the genome. In SEPN1, mutations of which are linked to a form of congenital muscular dystrophy, the muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity after the divergence of humans and chimpanzees. Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing

Aerosol chemistry, transport, and climatic implications during extreme biomass burning emissions over the Indo-Gangetic Plain

The large-scale emissions of airborne particulates from burning of agricultural residues particularly over the upper Indo-Gangetic Plain (IGP) have often been associated with frequent formation of haze, adverse health impacts, and modification in aerosol climatology and thereby aerosol impact on regional climate. In this study, short-term variations in aerosol climatology during extreme biomass burning emissions over the IGP were investigated. Size-segregated particulate concentration was initially measured and submicron particles (PM1.1) were found to dominate particulate mass within the fine mode (PM2.1). Particulate-bound water-soluble ions were mainly secondary in nature and primarily composed of sulfate and nitrate. There was evidence of gaseous NH3 dominating neutralization of acidic aerosol species (SO42−) in submicron particles, in contrast to crustal-dominating neutralization in coarser particulates. Diurnal variation in black carbon (BC) mass ratio was primarily influenced by regional meteorology, while gradual increase in BC concentration was consistent with the increase in Delta-C, referring to biomass burning emissions. The influence of biomass burning emissions was established using specific organic (levoglucosan), inorganic (K+ and NH4+), and satellite-based (UV aerosol index, UVAI) tracers. Levoglucosan was the most abundant species within submicron particles (649±177&thinsp;ng&thinsp;m−3), with a very high ratio (&gt;&thinsp;50) to other anhydrosugars, indicating exclusive emissions from burning of agriculture residues. Spatiotemporal distribution of aerosol and a few trace gases (CO and NO2) was evaluated using both spaceborne active and passive sensors. A significant increase in columnar aerosol loading (aerosol optical depth, AOD: 0.98) was evident, with the presence of absorbing aerosols (UVAI&thinsp;&gt;&thinsp;1.5) having low aerosol layer height ( ∼  1.5&thinsp;km). A strong intraseasonality in the aerosol cross-sectional altitudinal profile was even noted from CALIPSO, referring to the dominance of smoke and polluted continental aerosols across the IGP. A possible transport mechanism of biomass smoke was established using cluster analysis and concentration-weighted air mass back trajectories. Short-wave aerosol radiative forcing (ARF) was further simulated considering intraseasonality in aerosol properties, which resulted in a considerable increase in atmospheric ARF (135&thinsp;W&thinsp;m−2) and heating rate (4.3&thinsp;K&thinsp;day−1) during extreme biomass burning emissions compared to the non-dominating period (56&thinsp;W&thinsp;m−2, 1.8&thinsp;K&thinsp;day−1). Our analysis will be useful to improve understanding of short-term variation in aerosol chemistry over the IGP and to reduce uncertainties in regional aerosol–climate models.</p

Israel and a sports boycott: Antisemitic? Anti-Zionist?

The paper identifies and summarises the debates that surround the place of Israel in international sport and assesses how that place is increasingly being contested. The long-standing conflict between Israel and Palestine has begun to manifest in the world of sport with the paper sketching the debates of those calling for, and those opposed to, sport sanctions/boycott of Israel until the ‘Palestinian Question’ is resolved. Five related tasks are addressed: first, to summarise the call for sanctions/boycott emanating from the Boycott, Disinvestment and Sanctions movement. Second, to explore how this call is establishing itself in the world of sport. The responses of those opposed to any form of sanction/boycott are then considered. The confusion that surrounds the term antisemitism is addressed and the relationship between (anti-) Zionism and antisemitism unpacked. The discussion concludes with an assessment of the claim made by the Israeli state, and its supporters, that any action against the country’s participation in international sport would be an act of antisemitism. Offering a timely, integrated summary of the heated debates that surround the Israel/Palestine conflict, the paper contributes to a wider discussion on the relationship between sport and politics

Intronic Alus Influence Alternative Splicing

Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptom

Width of Gene Expression Profile Drives Alternative Splicing

Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection