Long non-coding RNAs (lncRNAs) represent a novel class of non-coding RNAs having a crucial role in many biological processes. The identification of long non-coding homologs among different species is ...essential to investigate such roles in model organisms as homologous genes tend to retain similar molecular and biological functions. Alignment-based metrics are able to effectively capture the conservation of transcribed coding sequences and then the homology of protein coding genes. However, unlike protein coding genes the poor sequence conservation of long non-coding genes makes the identification of their homologs a challenging task.
In this study we compare alignment-based and alignment-free string similarity metrics and look at promoter regions as a possible source of conserved information. We show that promoter regions encode relevant information for the conservation of long non-coding genes across species and that such information is better captured by alignment-free metrics. We perform a genome wide test of this hypothesis in human, mouse, and zebrafish.
The obtained results persuaded us to postulate the new hypothesis that, unlike protein coding genes, long non-coding genes tend to preserve their regulatory machinery rather than their transcribed sequence. All datasets, scripts, and the prediction tools adopted in this study are available at https://github.com/bioinformatics-sannio/lncrna-homologs .
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This paper provides an overview of the Curiosity rover's exploration at Vera Rubin ridge (VRR) and summarizes the science results. VRR is a distinct geomorphic feature on lower Aeolis Mons ...(informally known as Mount Sharp) that was identified in orbital data based on its distinct texture, topographic expression, and association with a hematite spectral signature. Curiosity conducted extensive remote sensing observations, acquired data on dozens of contact science targets, and drilled three outcrop samples from the ridge, as well as one outcrop sample immediately below the ridge. Our observations indicate that strata composing VRR were deposited in a predominantly lacustrine setting and are part of the Murray formation. The rocks within the ridge are chemically in family with underlying Murray formation strata. Red hematite is dispersed throughout much of the VRR bedrock, and this is the source of the orbital spectral detection. Gray hematite is also present in isolated, gray‐colored patches concentrated toward the upper elevations of VRR, and these gray patches also contain small, dark Fe‐rich nodules. We propose that VRR formed when diagenetic event(s) preferentially hardened rocks, which were subsequently eroded into a ridge by wind. Diagenesis also led to enhanced crystallization and/or cementation that deepened the ferric‐related spectral absorptions on the ridge, which helped make them readily distinguishable from orbit. Results add to existing evidence of protracted aqueous environments at Gale crater and give new insight into how diagenesis shaped Mars' rock record.
Plain Language Summary
Vera Rubin ridge is a feature at the base of Mount Sharp with a distinct texture and topography. Orbiter observations showed hematite, a mineral that sometimes forms by chemical reactions in water environments, was present atop the ridge. The presence of both water and chemical activity suggested the area preserved a past habitable environment. In this paper, we detail how the Curiosity science team tested this and other orbital‐based hypotheses. Curiosity data suggested that most ridge rocks were lain down in an ancient lake and had similar compositions to other Mount Sharp rocks. Curiosity confirmed that hematite was present in the ridge but no more abundantly than elsewhere. Larger grain size or higher crystallinity probably account for the ridge's hematite being more visible from orbit. We conclude Vera Rubin ridge formed because groundwater recrystallized and hardened the rocks that now make up the ridge. Wind subsequently sculpted and eroded Mount Sharp, leaving the harder ridge rocks standing because they resisted erosion compared with surrounding rocks. The implication of these results is that liquid water was present at Mount Sharp for a very long time, not only when the crater held a lake but also much later, likely as groundwater.
Key Points
We summarize Curiosity's campaign at Vera Rubin ridge (Sols 1726–2302) and the high‐level results from articles in this special issue
Vera Rubin ridge formed when diagenesis hardened rocks along the base of Aeolis Mons; wind subsequently etched the feature into a ridge
Results add evidence for protracted aqueous environments at Gale crater and give new insight into how diagenesis shaped Mars' rock record
IMPORTANCE: Antisocial behavior (ASB) places a large burden on perpetrators, survivors, and society. Twin studies indicate that half of the variation in this trait is genetic. Specific causal genetic ...variants have, however, not been identified. OBJECTIVES: To estimate the single-nucleotide polymorphism–based heritability of ASB; to identify novel genetic risk variants, genes, or biological pathways; to test for pleiotropic associations with other psychiatric traits; and to reevaluate the candidate gene era data through the Broad Antisocial Behavior Consortium. DESIGN, SETTING, AND PARTICIPANTS: Genome-wide association data from 5 large population-based cohorts and 3 target samples with genome-wide genotype and ASB data were used for meta-analysis from March 1, 2014, to May 1, 2016. All data sets used quantitative phenotypes, except for the Finnish Crime Study, which applied a case-control design (370 patients and 5850 control individuals). MAIN OUTCOME AND MEASURES: This study adopted relatively broad inclusion criteria to achieve a quantitative measure of ASB derived from multiple measures, maximizing the sample size over different age ranges. RESULTS: The discovery samples comprised 16 400 individuals, whereas the target samples consisted of 9381 individuals (all individuals were of European descent), including child and adult samples (mean age range, 6.7-56.1 years). Three promising loci with sex-discordant associations were found (8535 female individuals, chromosome 1: rs2764450, chromosome 11: rs11215217; 7772 male individuals, chromosome X, rs41456347). Polygenic risk score analyses showed prognostication of antisocial phenotypes in an independent Finnish Crime Study (2536 male individuals and 3684 female individuals) and shared genetic origin with conduct problems in a population-based sample (394 male individuals and 431 female individuals) but not with conduct disorder in a substance-dependent sample (950 male individuals and 1386 female individuals) (R2 = 0.0017 in the most optimal model, P = 0.03). Significant inverse genetic correlation of ASB with educational attainment (r = –0.52, P = .005) was detected. CONCLUSIONS AND RELEVANCE: The Broad Antisocial Behavior Consortium entails the largest collaboration to date on the genetic architecture of ASB, and the first results suggest that ASB may be highly polygenic and has potential heterogeneous genetic effects across sex.
Vera Rubin ridge (VRR) is an erosion-resistant feature on the northwestern slope of Mount Sharp in Gale crater, Mars, and orbital visible/short-wave infrared measurements indicate it contains ...red-colored hematite. The Mars Science Laboratory Curiosity rover performed an extensive campaign on VRR to study its mineralogy, geochemistry, and sedimentology to determine the depositional and diagenetic history of the ridge and constrain the processes by which the hematite could have formed. X-ray diffraction (XRD) data from the CheMin instrument of four samples drilled on and below VRR demonstrate differences in iron, phyllosilicate, and sulfate mineralogy and hematite grain size. Hematite is common across the ridge, and its detection in a gray-colored outcrop suggested localized regions with coarse-grained hematite, which commonly forms from warm fluids. Broad XRD peaks for hematite in one sample below VRR and the abundance of FeOT in the amorphous component suggest the presence of nano-crystalline hematite and amorphous Fe oxides/oxyhydroxides. Well-crystalline akaganeite and jarosite are present in two samples drilled from VRR, indicating at least limited alteration by acid-saline fluids. Collapsed nontronite is present below VRR, but samples from VRR contain phyllosilicate with d(001) = 9.6 Å, possibly from ferripyrophyllite or an acid-altered smectite. The most likely cementing agents creating the ridge are hematite and opaline silica. We hypothesize late diagenesis can explain much of the mineralogical variation on the ridge, where multiple fluid episodes with variable pH, salinity, and temperature altered the rocks, causing the precipitation and crystallization of phases that are not otherwise in equilibrium.
Visible/short‐wave infrared spectral data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) show absorptions attributed to hematite at Vera Rubin ridge (VRR), a topographic ...feature on northwest Mt. Sharp. The goals of this study are to determine why absorptions caused by ferric iron are strongly visible from orbit at VRR and to improve interpretation of CRISM data throughout lower Mt. Sharp. These goals are achieved by analyzing coordinated CRISM and in situ spectral data along the Curiosity Mars rover's traverse. VRR bedrock within areas that have the deepest ferric absorptions in CRISM data also has the deepest ferric absorptions measured in situ. This suggests strong ferric absorptions are visible from orbit at VRR because of the unique spectral properties of VRR bedrock. Dust and mixing with basaltic sand additionally inhibit the ability to measure ferric absorptions in bedrock stratigraphically below VRR from orbit. There are two implications of these findings: (1) Ferric absorptions in CRISM data initially dismissed as noise could be real, and ferric phases are more widespread in lower Mt. Sharp than previously reported. (2) Patches with the deepest ferric absorptions in CRISM data are, like VRR, reflective of deeper absorptions in the bedrock. One model to explain this spectral variability is late‐stage diagenetic fluids that changed the grain size of ferric phases, deepening absorptions. Curiosity's experience highlights the strengths of using CRISM data for spectral absorptions and associated mineral detections and the caveats in using these data for geologic interpretations and strategic path planning tools.
Plain Language Summary
Satellites orbiting Mars map the composition of the planet's surface, tell us about past environments, and guide rovers to interesting locations on the surface. The Curiosity rover investigated a ridge named Vera Rubin ridge where indications of the mineral hematite (Fe2O3) was suggested from orbital data. In this paper, we investigate why the hematite detection on the ridge was so clear from orbit and what the implications are for how the hematite formed. We found several factors influence the orbital data, but the biggest reason hematite at Vera Rubin ridge was so easily detected from orbit was because the bedrock there was unique. Water had interacted with rocks at the ridge sometime after they were deposited, and this interaction affected the properties of the hematite and made it more visible from orbit. Curiosity's data help us reinterpret the orbital data over Mt. Sharp and reveal hematite is probably present in most of the bedrock there. Furthermore, there are other areas with particularly clear hematite detections that likely formed in a similar manner as Vera Rubin ridge. We end this paper with a discussion of lessons learned from this experience for using orbital data to guide rovers in the future.
Key Points
Areas on Vera Rubin ridge with deep ferric absorptions from orbit also have deep ferric absorptions in Curiosity spectral data sets
Ferric phases are more widespread on Mt. Sharp than originally reported. Diagenesis deepened ferric absorptions in several locations
Combining orbital and in situ observations enhances planetary exploration
Mars early crust is more complex than homogenously basaltic with evolved magmatism evidenced by intermediate and felsic igneous rocks found in various locations in the southern hemisphere and martian ...meteorites. Geophysical constraints argue against a dense thick basaltic crust in the southern hemisphere, rather consistent with a buried light crust (<3,100 kg m−3), possibly evolved, underneath a basaltic surface. One of the oldest crustal components accessible at the surface of Mars, Terra Cimmeria/Sirenum (TSC), presents geochemical anomalies potentially suggesting an evolved crustal component at depth. Using visible/near infrared spectroscopy, we identify nine excavated feldspar‐rich locations in this region, and thermal infrared data suggest a silica concentration corresponding to intermediate compositions. The low density of such terrains compared to basalts supports that TSC crustal component is evolved. Early crusts of planetary bodies in the solar system were thus not restricted to basaltic compositions, and evolved crusts might have been widespread.
Plain Language Summary
Despite basaltic terrains widely observed at the surface of Mars, recent missions and a martian meteorite evidenced evolved magmatism (SiO2 > 53 wt.%), highlighting a heterogeneous crust on Mars. Geophysical and seismic constraints suggest the presence of buried evolved crustal components with low density compared to basalts, below subsequent basaltic lava flows. We investigate one of the most ancient region accessible at the surface of Mars using visible/near infrared and thermal infrared spectroscopy to verify that hypothesis. Nine feldspar‐rich terrains excavated by impact, fractures, and erosion are detected with evolved compositions. One of the oldest crustal component on Mars thus presents an evolved crust underneath the surface, in agreement with geophysical/seismic data. Hence, planetary bodies early crusts are not systematically basaltic as generally thought, but could be evolved too as inferred from several rare evolved meteorites (e.g., Erg Chech 002).
Key Points
Nine feldspar‐rich regions of intermediate silica compositions were identified in Terra Sirenum/Cimmeria (TSC)
The feldspar‐rich terrains are excavated crustal materials supporting a pre‐Noachian evolved crust at TSC
An early evolved crust on Mars suggests that early crusts in the solar system were not restricted to basaltic
Alteration of fresh rock surfaces proceeds very rapidly in most terrestrial environments so that initial stages of modification of newly exposed surfaces are quickly masked by subsequent aqueous ...weathering processes. The hyper-arid and hypo-thermal environment of Beacon Valley, Antarctica, is limited in terms of available liquid water and energy available for alteration, which severely slows weathering processes so that the initial stages of alteration can be studied in detail. We report on the nature of initial chemical alteration of the Ferrar Dolerite in Beacon Valley, Antarctica, using a multiplicity of approaches to characterize the process. We suggest that initial chemical alteration is primarily driven by cation migration in response to the oxidizing environment. Morphological studies of altered rock surfaces reveal evidence of small-scale leaching and dissolution patterns as well as physical erosion due to surface weakening. Within the alteration front, mineral structures are largely preserved and alteration is only indicated by discrete zones of discoloration. Mineralogical investigations expose the complexity of the alteration process; visible/near-infrared reflectance and mid-infrared emission spectroscopy reveal significant variations in mineralogical contributions that are consistent with the introduction of oxide and amorphous phases at the surfaces of the rocks, while X-ray diffraction analyses reveal no definitive changes in mineralogy or material properties. Chemical analyses reveal large-scale trends that are consistent with cation migration and leaching, while small-scale electron microprobe analyses indicate that chemical variations associated with magmatic processes are still largely preserved within the alteration rind. This work confirms the incomplete and immature chemical alteration processes at work in the McMurdo Dry Valleys. Liquid water is not a significant contributor to the alteration process at this early stage of rind development, but assists in the removal of alteration products and their local accumulation in the surrounding sediments. These results also suggest that the McMurdo Dry Valleys (and Beacon Valley, in particular) are relevant terrestrial analogs to hyper-arid and hypo-thermal alteration processes that may be dominant on the martian surface.
Synchronous reluctance (Syn-Rel) machines with embedded permanent magnets (PMs) are research hotspots in variable speed motor drives due to their robust rotor structure and wide constant power speed ...range (CPSR). In this article, the potential of PM-assisted Syn-Rel machine to be next generation heavy duty traction motor solution has been investigated, with special attention put on one key geometric parameter, i.e., airgap length. Careful machine design and optimization has been conducted based on geometric parametrization including airgap length variation, for 15000 rpm peak speed and 350 kW peak power output. In low speed operations, the influence of airgap length on different torque components has been analyzed in detail based on the frozen permeability method. In field weakening region, the variation trend of several key parameters such as output power, torque ripple, and power losses have been investigated along with airgap length. It is found that with high electric and magnetic loading, reducing the electromagnetic airgap length is not always beneficial. There exists a suitable airgap length value to comprehensively balance torque/power density, cooling capability, efficiency and reliability. Numerical FEA and experimental tests of the prototype are combined to verify the conclusions.
There is a great need for antiviral drugs to treat enterovirus (EV) and rhinovirus (RV) infections, which can be severe and occasionally life-threatening. The conserved nonstructural protein 2C, ...which is an AAA+ ATPase, is a promising target for drug development. Here, we present a structure-activity relationship study of a previously identified compound that targets the 2C protein of EV-A71 and several EV-B species members, but not poliovirus (PV) (EV-C species). This compound is structurally related to the Food and Drug Administration (FDA)-approved drug fluoxetine-which also targets 2C-but has favorable chemical properties. We identified several compounds with increased antiviral potency and broadened activity. Four compounds showed broad-spectrum EV and RV activity and inhibited contemporary strains of emerging EVs of public health concern, including EV-A71, coxsackievirus (CV)-A24v, and EV-D68. Importantly, unlike (S)-fluoxetine, these compounds are no longer neuroactive. By raising resistant EV-A71, CV-B3, and EV-D68 variants against one of these inhibitors, we identified novel 2C resistance mutations. Reverse engineering of these mutations revealed a conserved mechanism of resistance development. Resistant viruses first acquired a mutation in, or adjacent to, the α2 helix of 2C. This mutation disrupted compound binding and provided drug resistance, but this was at the cost of viral fitness. Additional mutations at distantly localized 2C residues were then acquired to increase resistance and/or to compensate for the loss of fitness. Using computational methods to identify solvent accessible tunnels near the α2 helix in the EV-A71 and PV 2C crystal structures, a conserved binding pocket of the inhibitors is proposed.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long ...non-coding RNAs from transcripts assembled with high throughput RNA-seq data. Several classes of sequence-based features have been proposed to distinguish between coding and non-coding transcripts. Among them, open reading frame, conservation scores, nucleotide arrangements, and RNA secondary structure have been used with success in literature to recognize intergenic long non-coding RNAs, a particular subclass of non-coding RNAs.
In this paper we perform a systematic assessment of a wide collection of features extracted from sequence data. We use most of the features proposed in the literature, and we include, as a novel set of features, the occurrence of repeats contained in transposable elements. The aim is to detect signatures (groups of features) able to distinguish long non-coding transcripts from other classes, both protein-coding and non-coding. We evaluate different feature selection algorithms, test for signature stability, and evaluate the prediction ability of a signature with a machine learning algorithm. The study reveals different signatures in human, mouse, and zebrafish, highlighting that some features are shared among species, while others tend to be species-specific. Compared to coding potential tools and similar supervised approaches, including novel signatures, such as those identified here, in a machine learning algorithm improves the prediction performance, in terms of area under precision and recall curve, by 1 to 24%, depending on the species and on the signature.
Understanding which features are best suited for the prediction of long non-coding RNAs allows for the development of more effective automatic annotation pipelines especially relevant for poorly annotated genomes, such as zebrafish. We provide a web tool that recognizes novel long non-coding RNAs with the obtained signatures from fasta and gtf formats. The tool is available at the following url: http://www.bioinformatics-sannio.org/software/ .
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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