Miracle-dz/UniFAR-FTUs huggingface dataset:
Fate of developmental mechanisms of myocardial plasticity in the postnatal heart

Whether the heart’s organ-founding, progenitor cell gene regulatory networks (CPC-GRNs) are sustained after birth and can be therapeutically evoked for regeneration in response to disease, remains elusive. Here, we report a spatiotemporally resolved analysis of CPC-GRN deployment dynamics, through the pan-CPC-GRN gene Isl1. We show that the Isl1-CPC-GRNs that are deployed during early cardiogenesis and generate the cardiomyocyte majority from mesoderm, undergo programmed silencing through proteasome- and PRC2-mediated Isl1 repression, selectively in the arterial pole. In contrast, we identify a neural crest (CNC)-specific Wnt/β-catenin/Isl1-CPC-GRN that is deployed through the venous pole during cardiac growth and partitioning, and contributes a minority of cardiomyocytes which, in turn, expand massively to build ~10% of the biventricular myocardium. These “dorsal CNCs” continue to sporadically generate cardiomyocytes throughout postnatal growth which, however, are non-proliferative, suggesting that partitioning-like, fetal proliferation signals could be therapeutically targeted to evoke clonal expansion capacity in postnatal CNC-cardiomyocytes for heart regeneration.
Assessment of Native Salmonids Above Hells Canyon Dam, Idaho

We investigated factors affecting the distribution and abundance of Yellowstone cutthroat trout (YCT), the abundance of all trout, and species richness in several drainages in the upper Snake River basin in Idaho. A total of 326 randomly selected sites were visited within the four study drainages, and of these, there was sufficient water to inventory fish and habitat in 56 of the sites in the Goose Creek drainage, 64 in the Raft River drainage, 54 in the Blackfoot River drainage, and 27 in the Willow Creek drainage. Fish were captured in 36, 55, 49, and 22 of the sites, respectively, and YCT were present at 17, 37, 32, and 13 of the sites, respectively. There was little consistency or strength in the models developed to predict YCT presence/absence and density, trout density, or species richness. Typically, the strongest models had the lowest sample sizes. In the Goose Creek drainage, sites with YCT were higher in elevation and lower in conductivity. In the Raft River drainage, trout cover was more abundant at sites with YCT than without YCT. In the Blackfoot River drainage, there was less fine substrate and more gravel substrate at sites with YCT than at sites without YCT. In the Willow Creek drainage, 70% of the sites located on public land contained YCT, but only 35% of private land contained YCT. The differences in variable importance between drainages suggests that factors that influence the distribution of YCT vary between drainages, and that for the most part the variables we measured had little influence on YCT distribution. In sites containing YCT, average cutthroat trout density was 0.11/m, 0.08/m, 0.10/m, and 0.08/m in the Goose Creek, Raft River, Blackfoot River, and Willow Creek drainages, respectively. In sites containing trout in general, average total trout density in these same drainages was 0.16/m, 0.15/m, 0.10/m, and 0.10/m. Models to predict YCT density, total trout density, and species richness were either weak (i.e., explained little variation) or contained small sample sizes. Based on our results, it appears that factors other than those we measured are affecting fish populations in these drainages.
Using MAP-Elites to Optimize Self-Assembling Behaviors in a Swarm of Bio-micro-robots

We are interested in programming a swarm of molecular robots that can perform self-assembly to form specific shapes at a specific location. Programming such robot swarms is challenging for two reasons. First, the goal is to optimize both the parameters and the structure of chemical reaction networks. Second, the search space is both high-dimensional and deceptive. In this paper, we show that MAP-Elites, an algorithm that searches for both high-performing and diverse solutions, outperforms previous state-of-the-art optimization methods.
Herb endozoochory by cockatoos: Is ‘foliage the fruit’?

Establishing whether herb seed endozoochory is accidental or has evolved independently or in combination with other dispersal mechanisms may be valuable in the study of plant – animal interactions, but it remains unexplored for birds. We tested whether an Australian cockatoo, the galah ( Eolophus roseicapilla ), swallows entire seeds when feeding on other tissues without subsequent seed digestion, thus enhancing seed dispersal (the ‘ foliage is the fruit ’ hypothesis). Our preliminary sampling provides strong evidence supporting that this seed predator also acts as a legitimate endozoochorous disperser. A large proportion of droppings contained numerous seeds of six herb species of three plant families, surviving gut passage to be dispersed as viable propagules. The wide range in the number of seeds found in combinations with up to ﬁ ve species in particular droppings suggests both simultaneous and sequential passive ingestion without seed digestion and/or focused seed predation and digestion. As expected for inadvertent ingestion and inef ﬁ cient digestion, our ﬁ ndings suggest that seed number and richness of dispersed plants are associated traits in this particular mutualistic interaction. This relationship can have important implications in community-wide processes, favouring herbs whose seeds are disseminated in a viable state over those predated or negatively affected by gut transit.
The complete mitogenome of the invasive Japanese mud snail Batillaria attramentaria (Gastropoda: Batillariidae) from Elkhorn Slough, California, USA

Abstract Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.
A Causal Role for Mouse Superior Colliculus in Visual Perceptual Decision-Making

The superior colliculus (SC) is arguably the most important visual structure in the mouse brain and is well known for its involvement in innate responses to visual threats and prey items. In other species, the SC plays a central role in voluntary as well as innate visual functions, including crucial contributions to selective attention and perceptual decision-making. In the mouse, the possible role of the SC in voluntary visual choice behaviors has not been established. Here, we demonstrate that the mouse SC of both sexes plays a causal role in visual perceptual decision-making by transiently inhibiting SC activity during an orientation change detection task. First, unilateral SC inhibition-induced spatially specific deficits in detection. Hit rates were reduced, and reaction times increased for orientation changes in the contralateral but not ipsilateral visual field. Second, the deficits caused by SC inhibition were specific to a temporal epoch coincident with early visual burst responses in the SC. Inhibiting SC during this 100-ms period caused a contralateral detection deficit, whereas inhibition immediately before or after did not. Third, SC inhibition reduced visual detection sensitivity. Psychometric analysis revealed that inhibiting SC visual activity significantly increased detection thresholds for contralateral orientation changes. In addition, effects on detection thresholds and lapse rates caused by SC inhibition were larger in the presence of a competing visual stimulus, indicating a role for the mouse SC in visual target selection. Together, our results demonstrate that the mouse SC is necessary for the normal performance of voluntary visual choice behaviors. SIGNIFICANCE STATEMENT The mouse superior colliculus (SC) has become a popular model for studying the circuit organization and development of the visual system. Although the SC is a fundamental component of the visual pathways in mice, its role in visual perceptual decision-making is not clear. By investigating how temporally precise SC inhibition influenced behavioral performance during a visually guided orientation change detection task, we identified a 100-ms temporal epoch of SC visual activity that is crucial for the ability of mice to detect behaviorally relevant visual changes. In addition, we found that SC inhibition also caused deficits in visual target selection. Thus, our findings highlight the importance of the SC for visual perceptual choice behavior in the mouse.
Does Drought Stress on Seedlings Have Longer Term Effects on Sapling Phenology, Reshooting, Growth and Plant Architecture in Quercus robur, Q. petraea and Their Morphological Intermediates?

Background and Objectives: Summer droughts are expected to increase in central and western Europe both in terms of frequency and intensity, justifying studies on longer term legacies of drought stress on tree species and their hybrids. Materials and Methods: We studied the longer-term after effects of water withholding and re-watering in the first growing season of potted seedlings from the sympatric species Quercus robur L. , Q. petraea (Matt.) Liebl. and their morphological intermediates. Phenology, growth, and plant architecture were examined after a cut-back of the stems at the end of the third growing season. Results: The legacy of the first-year water limitation is faded in the phenological response. Nonetheless, leaf senescence occurred later in offspring from Q. robur than in offspring from Q. petraea at the end of the fourth growing season and leafing out tended to be later in the subsequent growing season. Offspring from the intermediate forms displayed variable phenological responses. Height and radial growth were still affected by the drought stress in a taxon-dependent way, with the offspring from Q. petraea displaying growth reduction both in height and diameter, whereas offspring from Q. robur did not show any differences anymore between control and treated plants, demonstrating better post-stress recovery in Q. robur. Offspring from morphological intermediates responded again in a variable way. Although the number of reshoots after cutting back the stems was not affected anymore by the drought treatment in the first growing season, the number of side shoots on the reshoots was still reduced in the drought treated group of plants, independent of the taxon of the mother tree. Conclusions: Together, our results demonstrate the longer-lasting effects of drought stress on oak saplings with regard to growth and plant architecture, with the first being taxon dependent.
Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.
SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck

Background Technological advances in genomic sequencing are facilitating the reconstruction of transmission histories during outbreaks in the fight against infectious diseases. However, accurate disease transmission inference using this data is hindered by a number of challenges due to within-host pathogen diversity and weak transmission bottlenecks, where multiple genetically-distinct pathogenic strains co-transmit. Results We formulate a combinatorial optimization problem for transmission network inference under a weak bottleneck from a given timed phylogeny and establish hardness results. We present SharpTNI, a method to approximately count and almost uniformly sample from the solution space. Using simulated data, we show that SharpTNI accurately quantifies and uniformly samples from the solution space of parsimonious transmission networks, scaling to large datasets. We demonstrate that SharpTNI identifies co-transmissions during the 2014 Ebola outbreak that are corroborated by epidemiological information collected by previous studies. Conclusions Accounting for weak transmission bottlenecks is crucial for accurate inference of transmission histories during outbreaks. SharpTNI is a parsimony-based method to reconstruct transmission networks for diseases with long incubation times and large inocula given timed phylogenies. The model and theoretical work of this paper pave the way for novel maximum likelihood methods to co-estimate timed phylogenies and transmission networks under a weak bottleneck.
Turanose mediated WOX5 expression rescues symbiosis in cytokinin perception mutant cre1

Rhizobia-legume interaction recruits cytokinin for the induction of nodule primordia in the cortex. In Medicago truncatula, cytokinin signalling involves flavonoid mediated local alteration of polar auxin transport for triggering cortical cell division. Since sugar signalling is widely evidenced to trigger auxin responses, we explored whether sugar treatment could compensate for cytokinin signalling in M. truncatula cytokinin perception mutant cre1. Herein we demonstrate that turanose, a non-metabolizable sucrose analogue can trigger auxin response and show signs of recovery of symbiosis in cre1. Additionally, turanose upregulated the expression of WUSCHEL-related homeobox 5 (MtWOX5) which prompted us to check if overexpression of WOX5 could rescue cre1. Intriguingly, while overexpression of MtWOX5 failed, WOX5 from Arachis hypogaea (AhWOX5) completely restored functional symbiosis in cre1 with an efficiency resembling the wildtype. This indicate that indeterminate and determinate WOX5 responds to differential cues for nodule development and is consistent with their distinct clustering in distance trees. The mechanism of compensation of cytokinin signalling for recovery of symbiosis in cre1 was distinct for turanose treatment and AhWOX5 expression. Turanose increased MtHK2 level by ~5-fold and doubled the level of MtRR4 whereas AhWOX5 elevated the level of MtRR4 by ~12-fold without affecting the level of MtHK2/3. Thus, turanose compensated MtCRE1 at receptor level whereas WOX5 restored the signalling at the level of response regulators. We propose a working model to discuss how sugar mediated WOX5 signalling have compensated MtCRE1 to recover normal progress of symbiosis in cre1.
N,n-dibenzyl-3-nitrobenzenesulfenamide

In the title mol­ecule, C20H18N2O2S, all bond lengths and angles are within normal ranges. Weak inter­molecular C—H⋯O inter­actions link the mol­ecules into centrosymmetric dimers. The crystal packing is further stabilized by van der Waals forces.
Differential responses to low salinity on gene expression, physiological and biochemical indexes between the golden and brown noble scallopsChlamys nobilis

Low salinity is one of important environmental factors which often led to mass mortality of the noble scallop Chlamys nobilis cultivated in the South coast of China. It is well known that enzymic system and non‐enzymic system both play crucial roles in all living organisms against severe environments. To investigate how change about enzymic system and non‐enzymic system in the stenohaline marine bivalve under low salinity stress, an acute challenge lasting 48 hr was conducted using golden and brown noble scallops in the present study. The serine proteinase inhibitor from the noble scallop (CnSPI) was first cloned and expressed in different tissues. After low salinity stress, the gene expression levels were determined in haemocytes and compared between golden and brown scallops. Meanwhile, total carotenoids content (TCC) in adductor, superoxide dismutase (SOD) enzymatic activity and methylenedioxyamphetamine (MDA) content in gill and haemocytes were also determined and compared between the two colours scallops. Results showed that the CnSPI gene expression levels were significantly decreased after low salinity stress, and the golden scallops had higher gene expression levels than brown scallops (p < .05) at most times. Moreover, after low salinity stress, TCC, SOD enzymatic activity and MDA content also fluctuated, and the golden scallops contained higher TCC and SOD, but lower MDA than the brown ones. The present results indicated that enzymic system and non‐enzymic system were both changed under low salinity stress in the noble scallop and significantly different responses to the stress existed between golden and brown individuals. The SPI gene and carotenoids (CAR) both play a resistant role to low salinity stress in the noble scallop.
Divergence in hormone signalling links local adaptation and hybrid failure

Natural selection is a major driver for the origins of adaptations and new species1. Whether or not the processes driving adaptation and speciation share a molecular basis remains largely unknown2. Here, we show that divergence in hormone signalling contributed to the evolution of complex adaptations and intrinsic reproductive isolation in the Australian wildflower Senecio lautus. We provide evidence that differences in the auxin pathway, a hormone required for plant growth and development, has led to the repeated evolution of erect and prostrate forms along the Australian coast. Using multiple hybrid and natural populations, we show that adjacent erect and prostrate populations repeatedly diverged in auxin-related genes and auxin-dependent phenotypes, such as gravitropism. Analysis of a multi-year field selection experiment revealed that variation in fitness of an F10 hybrid population explained variation in gravitropism of their offspring. Genotyping of F11 hybrid individuals with extreme values of gravitropism revealed that variation in some of the most divergent genes explained both 65% of the variation in gravitropism and their probability of producing seed. Together, our results suggest that divergence in hormonal pathways can create a genetic link between rapid adaptation to new environments and the evolution of intrinsic reproductive isolation.
Functional organization of woody plant assemblages along precipitation and human disturbance gradients in a seasonally dry tropical forest

Chronic anthropogenic disturbances (CAD) and rainfall are important drivers of plant community assembly, but little is known about the role played by inter‐ and intraspecific trait variation as communities respond to these pervasive forces. Here, we examined the hypothesis that lower precipitation and higher CAD reduce both intra‐ and interspecific trait variation in Caatinga dry forests. We sampled woody plants across 15 plots along precipitation and CAD gradients and measured resource‐use traits. The effects of precipitation and CAD on RaoQ functional diversity were decomposed into species turnover and intraspecific variability. We used “T‐statistics” to assess the trait sorting from the regional pool to local communities (i.e., external filtering), and within‐community forces leading to low trait overlap (i.e., internal filtering) at individual and species levels. Intraspecific variability explained at least one‐third of the total trait variation and 46% of variation in multitrait diversity across communities. Increasing disturbance reduced multitrait diversity, while precipitation affected some particular traits, such as wood density. Overall, precipitation determined species sorting across communities, while disturbance relaxed internal filters, leading to higher trait overlap within communities due to higher intraspecific variability. Our results suggest that the woody Caatinga flora contains a substantial amount of both inter‐ and intraspecific trait variation. This variation is not randomly distributed within and across communities, but varies according to rainfall conditions and disturbance intensity. These findings reinforce the emerging idea that human disturbances can reorganize plant communities at multiple scales and highlight trait variability as a key biological asset for the resilience of dry forests.
A mitochondria-targeted antioxidant affects the carotenoid-based plumage of red crossbills

The mechanisms involved in the production of red carotenoid-based ornaments in vertebrates are still poorly understood. Those colours generated by red carotenoids often depend on the enzymatic production (ketolation) of these pigments from dietary yellow carotenoids. Recently, it has been proposed that this conversion takes place at the inner mitochondrial membrane (IMM). This implies that carotenoid ketolation and cell respiration could share the same biochemical pathways. Such a link would favour the evolution of red ketocarotenoid-based ornaments as reliable indices of individual quality under a sexual selection scenario. We exposed captive male red crossbills (Loxia curvirostra Linnaeus) to two different synthetic antioxidants designed to penetrate into the IMM: a synthetic ubiquinone (mitoQ) and a superoxide dismutase mimetic (mitoTEMPO). MitoQ decreased the blood levels of substrate yellow carotenoids and tocopherol. This could be attributed to the characteristics of the mitoQ molecule, which can distort the IMM structure, increasing free radical (superoxide) production and, potentially, antioxidant consumption. Contrarily, mitoTEMPO-treated birds increased the plasma levels of the second most abundant red ketocarotenoid of red crossbills (i.e. canthaxanthin). MitoTEMPO also increased plumage redness and total ketocarotenoid concentration in feathers among those birds exhibiting a redder plumage at the beginning of the study, rising the plasma values of the main red pigment (3-hydroxyechinenone) in paler birds. The results as a whole support the involvement of the mitochondrial antioxidant machinery in carotenoid biotransformation. The fact that the initial plumage redness determined the effect of mitoTEMPO suggests that the mitochondrial-based mechanism is intimately linked to individual quality. Summary statement Antioxidants designed to penetrate the mitochondrial membrane increased avian plumage redness but depending on pre-existing colouration. This supports mitochondrial involvement in the evolution of carotenoid-based ornaments as reliable quality signals.