Fgf-driven Tbx protein activities directly induce myf5 and myod to initiate zebrafish myogenesis.

Skeletal muscle derives from dorsal mesoderm formed during vertebrate gastrulation. Fibroblast growth factor (Fgf) signalling cooperates with Tbx transcription factors to promote dorsal mesoderm formation, but their role in myogenesis has been unclear. Using zebrafish, we show that dorsally derived Fgf signals act through Tbx16 and Tbxta to induce slow and fast trunk muscle precursors at distinct dorsoventral positions. Tbx16 binds to and directly activates the myf5 and myod genes, which are required for commitment to myogenesis. Tbx16 activity depends on Fgf signalling from the organiser. In contrast, Tbxta is not required for myf5 expression, but binds a specific site upstream of myod that is not bound by Tbx16 and drives (dependent on Fgf signals) myod expression in adaxial slow precursors, thereby initiating trunk myogenesis. After gastrulation, when similar muscle cell populations in the post-anal tail are generated from tailbud, declining Fgf signalling is less effective at initiating adaxial myogenesis, which is instead initiated by Hedgehog signalling from the notochord. Our findings suggest a hypothesis for ancestral vertebrate trunk myogenic patterning and how it was co-opted during tail evolution to generate similar muscle by new mechanisms.This article has an associated 'The people behind the papers' interview.

A lily membrane-associated NAC transcription factor LlNAC014 is involved in thermotolerance via activation of the DREB2-HSFA3 module.

The NTL (NAC with transmembrane motif 1-like) transcription factors with a conserved transmembrane motif are members of the NAC family and are important in plant development and in response to stress. However, knowledge of their regulatory pathways is scarce, especially under heat stress. Here, we cloned and identified a novel lily (Lilium longiflorum) NTL gene, LlNAC014, that increases thermotolerance. High temperature repressed LlNAC014 expression but activated its protein. LlNAC014 contained a typical transmembrane motif at its far C-terminus and was normally located on membranes, but under heat stress it entered the nucleus as a transcription factor. LlNAC014 also has a transactivation domain at its C-terminus, and its active form, LlNAC014ΔC, could function as a trans-activator in both yeast and plant cells. LlNAC014ΔC overexpression in lily and Arabidopsis increased thermotolerance, and also caused growth defects; silencing LlNAC014 in lily decreased thermotolerance. LlNAC014ΔC could constitutively activate the heat stress response by inducing the expression of heat-responsive genes, some of which were dependent on the HSF (heat stress transcription factor) pathway. Further analysis showed that LlNAC014 was a direct regulator of the DREB2-HSFA3 module, and bound to the CTT(N7)AAG element in the promoters of LlHSFA3A, LlHSFA3B, and LlDREB2B to activate their expression. Thus, LlNAC014 increased thermotolerance by sensing high temperature and translocating to the nucleus to activate the DREB2-HSFA3 module.

A tell tail sign: a conserved C-terminal tail-anchor domain targets a subset of pathogen effectors to the plant endoplasmic reticulum.

The endoplasmic reticulum (ER) is the entry point to the secretory pathway and, as such, is critical for adaptive responses to biotic stress, when the demand for de novo synthesis of immunity-related proteins and signalling components increases significantly. Successful phytopathogens have evolved an arsenal of small effector proteins which collectively reconfigure multiple host components and signalling pathways to promote virulence; a small, but important, subset of which are targeted to the endomembrane system including the ER. We identified and validated a conserved C-terminal tail-anchor motif in a set of pathogen effectors known to localize to the ER from the oomycetes Hyaloperonospora arabidopsidis and Plasmopara halstedii (downy mildew of Arabidopsis and sunflower, respectively) and used this protein topology to develop a bioinformatic pipeline to identify putative ER-localized effectors within the effectorome of the related oomycete, Phytophthora infestans, the causal agent of potato late blight. Many of the identified P. infestans tail-anchor effectors converged on ER-localized NAC transcription factors, indicating that this family is a critical host target for multiple pathogens.

CNN-Based Spectral Super-Resolution of Panchromatic Night-Time Light Imagery: City-Size-Associated Neighborhood Effects.

Data on artificial night-time light (NTL), emitted from the areas, and captured by satellites, are available at a global scale in panchromatic format. In the meantime, data on spectral properties of NTL give more information for further analysis. Such data, however, are available locally or on a commercial basis only. In our recent work, we examined several machine learning techniques, such as linear regression, kernel regression, random forest, and elastic map models, to convert the panchromatic NTL images into colored ones. We compared red, green, and blue light levels for eight geographical areas all over the world with panchromatic light intensities and characteristics of built-up extent from spatially corresponding pixels and their nearest neighbors. In the meantime, information from more distant neighboring pixels might improve the predictive power of models. In the present study, we explore this neighborhood effect using convolutional neural networks (CNN). The main outcome of our analysis is that the neighborhood effect goes in line with the geographical extent of metropolitan areas under analysis: For smaller areas, optimal input image size is smaller than for bigger ones. At that, for relatively large cities, the optimal input image size tends to differ for different colors, being on average higher for red and lower for blue lights. Compared to other machine learning techniques, CNN models emerged comparable in terms of Pearson's correlation but showed performed better in terms of WMSE, especially for testing datasets.

Street-Scale Analysis of Population Exposure to Light Pollution Based on Remote Sensing and Mobile Big Data-Shenzhen City as a Case.

Most studies on light pollution are based on light intensity retrieved from nighttime light (NTL) remote sensing with less consideration of the population factors. Furthermore, the coarse spatial resolution of traditional NTL remote sensing data limits the refined applications in current smart city studies. In order to analyze the influence of light pollution on populated areas, this study proposes an index named population exposure to light pollution (PELP) and conducts a street-scale analysis to illustrate spatial variation of PELP among residential areas in cites. By taking Shenzhen city as a case, multi-source data were combined including high resolution NTL remote sensing data from the Luojia 1-01 satellite sensor, high-precision mobile big data for visualizing human activities and population distribution as well as point of interest (POI) data. Results show that the main influenced areas of light pollution are concentrated in the downtown and core areas of newly expanded areas with obvious deviation corrected like traditional serious light polluted regions (e.g., ports). In comparison, commercial-residential mixed areas and village-in-city show a high level of PELP. The proposed method better presents the extent of population exposure to light pollution at a fine-grid scale and the regional difference between different types of residential areas in a city.

tbx6l and tbx16 are redundantly required for posterior paraxial mesoderm formation during zebrafish embryogenesis.

BACKGROUND: T-box genes encode a large transcription factor family implicated in many aspects of development. We are focusing on two related zebrafish T-box genes, tbx6l and tbx16, that are expressed in highly overlapping patterns in embryonic paraxial mesoderm. tbx16 mutants are deficient in trunk, but not tail, somites; we explored whether presence of tail somites in tbx16 mutants was due to compensatory function provided by the tbx6l gene. RESULTS: We generated two zebrafish tbx6l mutant alleles. Loss of tbx6l has no apparent effect on embryonic development, nor does tbx6l loss enhance the phenotype of two other T-box gene mutants, ta and tbx6, or of the mesp family gene mutant msgn1. In contrast, loss of tbx6l function dramatically enhances the paraxial mesoderm deficiency of tbx16 mutants. CONCLUSIONS: These data demonstrate that tbx6l and tbx16 genes function redundantly to direct tail somite development. tbx6l single mutants develop normally because tbx16 fully compensates for loss of tbx6l function. However, tbx6l only partially compensates for loss of tbx16 function. These results resolve the question of why loss of function of tbx16 gene, which is expressed throughout the ventral and paraxial mesoderm, profoundly affects somite development in the trunk but not the tail. Developmental Dynamics 246:759-769, 2017. © 2017 Wiley Periodicals, Inc.

Subcellular Distribution of NTL Transcription Factors in Arabidopsis thaliana.

NAC with a transmembrane (TM) motif1-like (NTL) transcription factors, containing three regions: the N-terminal NAC domain (ND), the middle regulation region (RR), and the C-terminal TM domain, belong to the tail-anchored proteins. Although these NTLs play numerous essential roles in plants, their subcellular distribution and the mechanism of translocation into the nucleus (NU) remain unclear. In this study, we found that most of the full-length NTLs were localized in the endoplasmic reticulum (ER), with the exception of NTL11 and NTL5, which were restricted to the NU. Furthermore, we found that NTL11 contains a TM domain, whereas NTL5 does not. The ND of all of the NTLs was responsible for nuclear localization in plants. After truncation of the TM domain, NTL8_NR, NTL10_NR and NTL13_NR localized in the cytoplasm (CT) and NU, and other NTL_NRs were only localized in the NU, suggesting that the RR of NTL8, NTL10 and NTL13 contains some inhibitory region to mask the nuclear localization signal sequence in the ND domain and permit their diffusion between CT and NU. Furthermore, the N-terminus of NTL11 was translocated to the NU, but the C-terminus was degraded in Arabidopsis mesophyll protoplasts. The chimeric construct of NTL11_ND with NTL10_RR and TM domain (11ND-10RT) was localized exclusively in the ER, and not in the NU. However, 10ND-11RT was found mainly in the NU. Our results indicated that the TM domain is essential for NTL targeting the ER and the N-terminal fragment, including ND and RR, is translocated into the NU after activation through proteolytic cleavage events upon stimulation by internal and external environmental signals.

Fast-folding proteins under stress.

Proteins are subject to a variety of stresses in biological organisms, including pressure and temperature, which are the easiest stresses to simulate by molecular dynamics. We discuss the effect of pressure and thermal stress on very-fast-folding model proteins, whose in vitro folding can be fully simulated on computers and compared with experiments. We then discuss experiments that can be used to subject proteins to low- and high-temperature unfolding, as well as low- and high-pressure unfolding. Pressure and temperature are prototypical perturbations that illustrate how close many proteins are to instability, a property that cells can exploit to control protein function. We conclude by reviewing some recent in-cell experiments, and progress being made in simulating and measuring protein stability and function inside live cells.

Natalisin, a tachykinin-like signaling system, regulates sexual activity and fecundity in insects.

An arthropod-specific peptidergic system, the neuropeptide designated here as natalisin and its receptor, was identified and investigated in three holometabolous insect species: Drosophila melanogaster, Tribolium castaneum, and Bombyx mori. In all three species, natalisin expression was observed in 3-4 pairs of the brain neurons: the anterior dorso-lateral interneurons, inferior contralateral interneurons, and small pars intercerebralis neurons. In B. mori, natalisin also was expressed in two additional pairs of contralateral interneurons in the subesophageal ganglion. Natalisin-RNAi and the activation or silencing of the neural activities in the natalisin-specific cells in D. melanogaster induced significant defects in the mating behaviors of both males and females. Knockdown of natalisin expression in T. castaneum resulted in significant reduction in the fecundity. The similarity of the natalisin C-terminal motifs to those of vertebrate tachykinins and of tachykinin-related peptides in arthropods led us to identify the natalisin receptor. A G protein-coupled receptor, previously known as tachykinin receptor 86C (also known as the neurokinin K receptor of D. melanogaster), now has been recognized as a bona fide natalisin receptor. Taken together, the taxonomic distribution pattern of the natalisin gene and the phylogeny of the receptor suggest that natalisin is an ancestral sibling of tachykinin that evolved only in the arthropod lineage.

Maternal Vsx1 plays an essential role in regulating prechordal mesendoderm and forebrain formation in zebrafish.

Prechordal mesendoderm (PME) is a derivative of gastrula organizer underlying the anterior neural plate of vertebrate embryos. It has been firmly established that PME is critical for head induction and anterior-posterior patterning. Therefore, the establishment of PME in a desired shape and size at a correct position during early embryogenesis is crucial for normal head patterning. However, it remains largely unclear how the desired form and size of PME is generated at a predestined position during early embryogenesis. Here we show that in zebrafish a maternal transcription repressor Vsx1 is essential for this early developmental regulation. Knocking down maternal vsx1 resulted in impaired PME formation and progression associated with a deficient and posteriorized forebrain. Loss- and gain-of-function experiments showed that maternal Vsx1 is essential for repressing ntl ectopic expression in more animal region at early gastrula stages. Chromatin immunoprecipitation assay in combination with core consensus sequence mutation analysis further revealed that maternal Vsx1 can directly repress ntl transcription by binding to the proximal promoter at a specific site. Simultaneous inhibition of ntl function could successfully suppress the defects of both PME and forebrain formation in maternal Vsx1 knockdown embryos. Our results reveal a pivotal role for maternal Vsx1 as a direct transcriptional repressor of ntl expression at the margin of the zebrafish gastrula to ensure directional cell polarization and migration of PME cells.

Urbanization and agricultural land loss in India: comparing satellite estimates with census data.

We examine the impacts of urbanization on agricultural land loss in India from 2001 to 2010. We combined a hierarchical classification approach with econometric time series analysis to reconstruct land-cover change histories using time series MODIS 250 m VI images composited at 16-day intervals and night time lights (NTL) data. We compared estimates of agricultural land loss using satellite data with agricultural census data. Our analysis highlights six key results. First, agricultural land loss is occurring around smaller cities more than around bigger cities. Second, from 2001 to 2010, each state lost less than 1% of its total geographical area due to agriculture to urban expansion. Third, the northeastern states experienced the least amount of agricultural land loss. Fourth, agricultural land loss is largely in states and districts which have a larger number of operational or approved SEZs. Fifth, urban conversion of agricultural land is concentrated in a few districts and states with high rates of economic growth. Sixth, agricultural land loss is predominantly in states with higher agricultural land suitability compared to other states. Although the total area of agricultural land lost to urban expansion has been relatively low, our results show that since 2006, the amount of agricultural land converted has been increasing steadily. Given that the preponderance of India's urban population growth has yet to occur, the results suggest an increase in the conversion of agricultural land going into the future.

Measurement of flood peak effects as a result of soil and land management, with focus on experimental issues and scale.

As a result of several serious flood events which have occurred since 2000, flooding across Europe is now receiving considerable public and media attention. The impact of land use on hydrology and flood response is significantly under-researched, and the links between land use change and flooding are still unclear. This study considers runoff data available from studies of arable in-field land use management options, applied with the aim of reducing diffuse pollution from arable land, in order to investigate whether these treatments also have potential to reduce downstream flooding. Intensive monitoring of 17 hillslope treatment areas produced a record of flood peak data covering different mitigation treatments for runoff which occurred in the winter of 2007-2008. We investigated event total runoff responses to rainfall, peak runoff, and timing of the runoff peaks from replicates of different treatments, in order to assess whether there is a significant difference in flood peak response between different mitigation options which could be used to mitigate downstream flood risk. A mixed-modelling approach was adopted in order to determine whether differences observed in runoff response were significant. The results of this study suggest that changes in land use management using arable in-field mitigation treatments can affect local-scale runoff generation, with differences observed in the size, duration and timing of flood peaks as a result of different management practices, but the study was unable to allow significant treatment effects to be determined. We suggest that further field studies of the effects of changes in land use and land use management need to upscale towards farm and catchment scale experiments which consider high quality before-and-after data over longer temporal timescales. This type of data collection is essential in order to allow appropriate land use management decisions to be made.

Recent advances in plant membrane-bound transcription factor research: emphasis on intracellular movement.

Transcription factors constitute numerous signal transduction networks and play a central role in gene expression regulation. Recent studies have shown that a limited portion of transcription factors are anchored in the cellular membrane, storing as dormant forms. Upon exposure to environmental and developmental cues, these transcription factors are released from the membrane and translocated to the nucleus, where they regulate associated target genes. As this process skips both transcriptional and translational regulations, it guarantees prompt response to external and internal signals. Membrane-bound transcription factors (MTFs) undergo several unique steps that are not involved in the action of canonical nuclear transcription factors: proteolytic processing and intracellular movement. Recently, alternative splicing has also emerged as a mechanism to liberate MTFs from the cellular membranes, establishing an additional activation scheme independent of proteolytic processing. Multiple layers of MTF regulation add complexity to transcriptional regulatory scheme and ensure elaborate action of MTFs. In this review, we provide an overview of recent findings on MTFs in plants and highlight the molecular mechanisms underlying MTF liberation from cellular membranes with an emphasis on intracellular movement.

Advances in membrane-tethered NAC transcription factors in plants.

Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.

TT3.1: a journey to protect chloroplasts upon heat stress.

Rice (Oryza sativa L.) is a staple crop that feeds over half the world's population. High temperature stress is a great threaten to sustainable agriculture and leads to yield loss and impaired grain quality in major crops. Rice is sensitive to heat stress at almost all the growth stages and the molecular mechanisms underlying responses to heat stress in rice is emerging. Through quantitative trait locus (QTL) mapping, a recent study conducted by Zhang et al. shows that one genetic locus Thermo-tolerance 3 (TT3) contains two genes that are required for thermotolerance in rice. The TT3.1-TT3.2 genetic module in rice links the plasma membrane to chloroplasts to protect chloroplasts from heat stress damage and increases grain yield under heat stress conditions. This breakthrough provides a promising strategy for future breeding of high temperature resilient crops.

Pescoids and Chimeras to Probe Early Evo-Devo in the Fish Astyanax mexicanus.

The fish species Astyanax mexicanus with its sighted and blind eco-morphotypes has become an original model to challenge vertebrate developmental evolution. Recently, we demonstrated that phenotypic evolution can be impacted by early developmental events starting from the production of oocytes in the fish ovaries. A. mexicanus offers an amenable model to test the influence of maternal determinants on cell fate decisions during early development, yet the mechanisms by which the information contained in the eggs is translated into specific developmental programs remain obscure due to the lack of specific tools in this emergent model. Here we describe methods for the generation of pescoids from yolkless-blastoderm explants to test the influence of embryonic and extraembryonic tissues on cell fate decisions, as well as the production of chimeric embryos obtained by intermorph cell transplantations to probe cell autonomous or non-autonomous processes. We show that Astyanax pescoids have the potential to recapitulate the main ontogenetic events observed in intact embryos, including the internalization of mesodermal progenitors and eye development, as followed with zic:GFP reporter lines. In addition, intermorph cell grafts resulted in proper integration of exogenous cells into the embryonic tissues, with lineages becoming more restricted from mid-blastula to gastrula. The implementation of these approaches in A. mexicanus will bring new light on the cascades of events, from the maternal pre-patterning of the early embryo to the evolution of brain regionalization.

Quantifying Spatiotemporal Changes in Human Activities Induced by COVID-19 Pandemic Using Daily Nighttime Light Data.

The COVID-19 pandemic caused drastic changes in human activities and nighttime light (NTL) at various scales, providing a unique opportunity for exploring the pattern of the extreme responses of human community. This study used daily NTL data to examine the spatial variations and temporal dynamics of human activities under the influence of COVID-19, taking Chinese mainland as the study area. The results suggest that the change in the intensity of NTL is not correlated to the number of confirmed cases, but reflects the changes in human activities and the intensity of epidemic prevention and control measures within a region. During the outbreak period, the major provincial capitals and urban agglomerations were affected by COVID-19 more than smaller cities. During the recovery, different regions showed different recovery processes. The cities in West and Northeast China recovered steadily while the recovery in coastal cities showed relatively greater fluctuations due to an increase in imported cases. Wuhan, the most seriously affected city in China, did not recover until the end of March. Nevertheless, as of 31 March, the overall NTL across China had recovered to an 89.5% level of the same period in the previous year. The high consistency between the big data of travel intensity and NTL further proved the validity of the results of this study. These findings imply that daily NTL data are effective for rapidly monitoring the dynamic changes in human activities, and can help evaluate the effects of control measures on human activities during major public health events.

An Impact Analysis of Artificial Light at Night (ALAN) on Bats. A Case Study of the Historic Monument and Natura 2000 Wisloujscie Fortress in Gdansk, Poland.

The artificial light at night (ALAN) present in many cities and towns has a negative impact on numerous organisms that live alongside humans, including bats. Therefore, we investigated if the artificial illumination of the historic Wisloujscie Fortress in Gdansk, Poland (part of the Natura 2000 network), during nighttime events, which included an outdoor electronic dance music (EDM) festival, might be responsible for increased light pollution and the decline in recent years of the pond bat (Myotis dasycneme). An assessment of light pollution levels was made using the methods of geographical information system (GIS) and free-of-charge satellite remote sensing (SRS) technology. Moreover, this paper reviewed the most important approaches for environmental protection of bats in the context of ecological light pollution, including International, European, and Polish regulatory frameworks. The analysis of this interdisciplinary study confirmed the complexity of the problem and highlighted, too, the need for better control of artificial illumination in such sensitive areas. It also revealed that SRS was not the best light pollution assessment method for this particular case study due to several reasons listed in this paper. As a result, the authors' proposal for improvements also involved practical recommendations for devising suitable strategies for lighting research and practice in the Natura 2000 Wisloujscie Fortress site located adjacent to urban areas to reduce the potential negative impact of ALAN on bats and their natural habitats.

Lamin-like Proteins Negatively Regulate Plant Immunity through NAC WITH TRANSMEMBRANE MOTIF1-LIKE9 and NONEXPRESSOR OF PR GENES1 in Arabidopsis thaliana.

Nuclear lamins are involved in multiple biological processes in metazoan cells. The proteins of the CROWDED NUCLEI (CRWN) family are considered lamin-like candidates in Arabidopsis, although the functions of these proteins are largely unknown. In this article we show that crwn1 crwn2 double mutant displays an enhanced resistance against virulent bacterial pathogens, and both virulent bacteria and salicylic acid (SA) induce transcription of CRWN1 gene as well as proteasome-mediated degradation of CRWN1 protein. We also show that CRWN1 interacts with NAC WITH TRANSMEMBRANE MOTIF1-LIKE9 (NTL9), a NAC transcription factor involved in plant immunity. The interaction between CRWN1 and NTL9 enhances the binding of NTL9 to the promoter of the PATHOGENESIS-RELATED1 (PR1) gene, and inhibits PR1 expression. Further genetic experiments indicated that the defense-related phenotypes of crwn1 crwn2 double mutant are dependent on NONEXPRESSOR OF PR GENES1 (NPR1), a transcriptional cofactor of PR1. These findings revealed a regulatory network composed of lamin-like protein CRWN1, NTL9, and NPR1 for the regulation of PR1 expression.

Gibberellic acid-mediated salt signaling in seed germination.

Seed germination initiates the postembryonic development of plants, which determines successful seedling establishment and plant propagation. It is therefore tightly regulated by diverse environmental conditions, including high salinity and drought, as well as by intrinsic developmental programs, among which gibberellic acid (GA) is best understood. Regulatory roles of GA in seed germination have been extensively studied. It is also known that high salinity inhibits germination by repressing genes encoding GA biosynthetic enzymes. However, it is still unclear how salt signals are coordinately incorporated into the GA signaling pathway at the molecular level. We recently demonstrated that a membrane-bound NAC transcription factor, NTL8, mediates salt signaling, primarily through a RGL2-independent GA pathway, in regulating seed germination. High salinity promotes NTL8 transcription and proteolytic activation of NTL8. Notably, the NTL8-mediated salt signaling is independent of abscisic acid (ABA). These observations indicate that membrane-mediated transcription control is an important component of salt signaling during seed germination.