Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Y-Nauplii (Facetotecta) in Andaman Sea, India

The Facetotecta is among the lesser known groups in the world ocean. The present study recorded two types of Facetotecta in the Andaman Sea, off Andaman Islands. These two types of Facetotecta were observed during the period of August 2015, July 2016 and October 2017 and identified as Type I Hansenocaris corvinae and Type IX Hansenocaris leucadea. However, the cursory analysis suggested that the Type IX is a new type of Facetotecta and named it as Type XII Hansenocaris portblairenae sp. (nov). This finding suggests that this Facetotecta observation is the first report in the Andaman Sea, as well as in the Indian Ocean Region.
The toxicity of Cry1Ia5 transgenic soybean plants against Spodoptera littoralis

Three transgenic soybean lines expressing the Cry1Ia5 gene were developed using the Agrobacterium transformation system. The integration of the Cry1Ia5 gene in the genome of the transgenic plants was approved using specific primers for PCR and real time PCR analysis, respectively. The insecticidal activity of three transgenic lines (L1, L2 and L3) against 2nd larval instars Spodoptera littoralis was tested. The data indicate that L2 exhibited the highest mortality percentage 9 days post feeding (60%) followed by L3 (40%) then L1 (20%) while the control showed 0% mortality. The larvae fed transgenic material appeared smaller in size than compared to the control larvae. The reduction in insect size and weight was due to the accumulation of higher phenoloxidase activity in insect tissues. The higher mortality observed in L2 was due to a significant decrease in the acetylcholine esterase activity that leads to accumulation of acetylcholin at higher levels which causes paralysis and death. The developed transgenic line 2 could be used to construct an insect resistant soybean cultivar.
What’s ploidy got to do with it? Understanding the evolutionary ecology of macroalgal invasions necessitates incorporating life cycle complexity

Biological invasions represent grave threats to terrestrial, aquatic, and marine ecosystems, but our understanding of the role of evolution during invasions remains rudimentary. In marine environments, macroalgae account for a large percentage of invaders, but their complicated life cycles render it difficult to move methodologies and predictions wholesale from species with a single, free‐living ploidy stage, such as plants or animals. In haplodiplontic macroalgae, meiosis and fertilization are spatiotemporally separated by long‐lived, multicellular haploid and diploid stages, and gametes are produced by mitosis, not meiosis. As a consequence, there are unique eco‐evolutionary constraints that are not typically considered in invasions. First, selfing can occur in both monoicious (i.e., hermaphroditic) and dioicious (i.e., separate sexes) haplodiplontic macroalgae. In the former, fertilization between gametes produced by the same haploid thallus results in instantaneous, genome‐wide homozygosity. In the latter, cross‐fertilization between separate male and female haploids that share the same diploid parent is analogous to selfing in plants or animals. Separate sexes, therefore, cannot be used as a proxy for outcrossing. Second, selfing likely facilitates invasions (i.e., Baker's law) and the long‐lived haploid stage may enable purging of deleterious mutations, further contributing to invasion success. Third, asexual reproduction will result in the dominance of one ploidy and/or sex and the loss of the other(s). Whether or not sexual reproduction can be recovered depends on which stage is maintained. Finally, fourth, haplodiplontic life cycles are predicted to be maintained through niche differentiation in the haploid and diploid stages. Empirical tests are rare, but fundamental to our understanding of macroalgal invasion dynamics. By highlighting these four phenomena, we can build a framework with which to empirically and theoretically address important gaps in the literature on marine evolutionary ecology, of which biological invasions can serve as unnatural laboratories.
Which moths might be pollinators? Approaches in the search for the flower‐visiting needles in the Lepidopteran haystack

1. The natural history of pollination has been studied for centuries and is well documented for diurnal insect species, such as bees and butterflies, but less so for moths. There are notable cases of pollination systems among moths, but given their enormous diversity and primarily nocturnal habits, the role of moths as flower visitors is poorly understood. One potential issue with studying moth‐pollination systems is determining which approach to use in order to acquire data and reveal pollination patterns and dynamics. Based on reports from the literature and the authors' own research, this paper outlines eight approaches that can be employed to search for patterns of flower visitation by moths.
UJI POTENSI EKSTRAK DAUN TANAMAN KETEPENG (Cassia alata L) DALAM MENGHAMBAT PERTUMBUHAN BAKTERI Ralstonia solanacearum dan Streptococcus sobrinus

Ketepeng (Cassia alata L.) was a group of plants included in the Magnoliophyta division which can be found in tropical or subtropical areas. The purpose of this study was to determine the potential of Ketepeng leaves to inhibit the growth of R. solanacearum and S. sobrinus bacteria. The method used in this study is agar well diffusion with 3 replications. The sample used was Ketepeng leaf extract with several concentrations of 0.5%, 1%, 2%. Positive controls in this study were Chloramphenicol and negative control of 40% ethanol. The variables calculated are the calculation of water content, percentage of yield and percentage of area diameter barriers (DDH). In addition, the DDH results show the ethanol extract of Ketepeng leaves at concentrations of 0.5% and 1% not able to inhibit the growth of R. solanacearum, but at a concentration of 2% able to inhibit R.solanacearum with a diameter of 11,7 mm and the ethanol extract of Ketepeng leaves at concentrations was able to inhibit the growth of S. sobrinus bacteria with the highest diameter of 16 mm at a concentration of 2%.
Establishment and Utilization of Tools for Enhancing Foodfish Health

A good understanding of the normal immune responses in important aquaculture species is vital for evaluating the health status of the species of interest. However, basic information such as titers of immunoglobulin (Ig) is limited for fish, which could be attributed to the lack of available specific immunological probes to assess such immunity analytes. This study aimed to isolate, purify and characterize the IgM-like antibody from striped catfish (Pangasius hypophthalmus); and then to determine the reference intervals for this macromolecule of the immune system in the catfish species. An SDS-PAGE analysis of the purified striped catfish immunoglobulin revealed a heavy and a light chain with molecular weights of 70 and 25 kDa, respectively, and thus an estimated size of at least 760 kDa for the tetrameric form of this antibody isotype. A polyclonal rabbit anti-striped catfish antibody was produced with reactivity exhibited only against fish of the genus Pangasius, while also showing none against three nonPangasius species. The plasma levels of the IgM-like molecule in striped catfish were determined via a sandwich enzyme-linked immunosorbent assay (ELISA). The reference interval for this analyte had a range of 1.2 – 7.6 mg mL, and a median value of 3.3 mg mL. The findings of this study can help in monitoring changes in the health status of striped catfish * Manuscript to be submitted to Fish and Shellfish Immunology journal
Behavioural ontogeny of bearded seals Erignathus barbatus through the first year of life

Pinniped pups face special ontogenetic challenges as they are born and receive maternal care on solid substrates (land or ice) but must transition to feeding aquatically following weaning. In this study, satellite relay data loggers were used to study behavioural ontogeny of bearded seal Erignathus barbatus pups (n = 13) through their first year in Svalbard, Norway. Pups occupied shallow, coastal habitats and were found in areas with intermediate ice concentrations (in seasons with sea ice: late-autumn/winter). Most pups showed exploratory movement patterns that peaked in the weeks following weaning; maximum home range size occurred at 31 to 60 d of age. Thereafter, home range size decreased with pups settling into areas along the coast. Time spent diving, dive duration, dive depth and time at the bottom of dives increased during the first weeks of independence, stabilizing when pups were ~50 d old. Dive depth subsequently decreased to depths comparable to adult bearded seals (by the time pups were ~175 d old). Record maximum dive depth (368 m) and duration (16.5 min) were performed by pups that were 66 and 224 d old, respectively. Time spent hauled out decreased after weaning, with pups hauling out only sporadically after they were 75 d old. Bearded seal pups seem to be physiologically and behaviourally well developed by the time they are 2 mo old. Pups did not display the individually specialized diving behaviour seen in adults, which suggests that they continue to fine-tune their aquatic and other life-skills well past the end of the first year of life.
Morphology and metabarcoding: a test with stream diatoms from Mexico highlights the complementarity of identification methods

Diatoms are among the most commonly used bioindicators. Correct taxonomic identifications are critical to their use as bioindicators because closely related diatom species can respond differently to water physicochemical characteristics and pollutants. However, diatom identification based on morphology can be time consuming, and requires highly specialized taxonomic skills. To optimize diatom identification, DNA metabarcoding is increasingly used because it is generally less time consuming and may be more accurate than morphological identification. To date, however, neither DNA metabarcoding nor DNA barcoding diatom studies have been conducted in Mexico. Thus, we studied epilithic diatoms from streams in Central Mexico with a combination of morphological and metabarcoding techniques, and compared the diatoms identified and quantified by each method. We also assembled a barcode reference library based on clonal culturing. This library is composed of 190 strains that belong to 72 species in 24 genera. The morphological analysis of environmental samples resulted in the identification of 204 infrageneric taxa in 42 genera, but clonal culturing from the same samples retrieved 12 additional infrageneric taxa and 1 additional genus, thereby revealing concealed diversity. The metabarcoding approach resulted in the identification of 266 infrageneric taxa that belonged to 35 genera. Together, these methods detected 49 genera. Of these genera, 14 were identified only by morphology, 29 were identified by both methods, and 6 were only identified by metabarcoding. Of the 266 taxa we retrieved with metabarcoding, we confidently assigned 94 infrageneric taxa because a direct morphological or barcode sequence correlation was possible. Thirty-four of these 94 taxa were only detected with the metabarcoding method. One-fourth (23) of the assignments were only possible because of the barcode reference library we developed during this study, because there were no existing barcode sequences that matched these barcodes in the International Nucleotide Sequence Database Collaboration databases. Large disparities existed between relative abundances based on valve counts and sequence reads of the most abundant taxa, even after we corrected for cell biovolume. Overall, we conclude that the combination of morphological and molecular methods increases the detection and identification of diatoms.
A Kinetic Map of the Homomeric Voltage-Gated Potassium Channel (Kv) Family

The voltage-gated potassium (Kv) channels, encoded by 40 genes, repolarize all electrically excitable cells, including plant, cardiac, and neuronal cells. Although these genes were fully sequenced decades ago, a comprehensive kinetic characterization of all Kv channels is still missing, especially near physiological temperature. Here, we present a standardized kinetic map of the 40 homomeric Kv channels systematically characterized at 15, 25, and 35°C. Importantly, the Kv kinetics at 35°C differ significantly from commonly reported kinetics, usually performed at room temperature. We observed voltage-dependent Q10 for all active Kv channels and inherent heterogeneity in kinetics for some of them. Kinetic properties are consistent across different host cell lines and conserved across mouse, rat, and human. All electrophysiology data from all Kv channels are made available through a public website (Channelpedia). This dataset provides a solid foundation for exploring kinetics of heteromeric channels, roles of auxiliary subunits, kinetic modulation, and for building accurate Kv models.
A Computational Model of Normal and Impaired Lexical Decision: Graded Semantic Effects

Lexical decision is an important paradigm in studies of visual word recognition yet the underlying mechanisms supporting the activity are not well understood. While most models of visual word recognition focus on orthographic processing as the primary locus of the lexical decision, a number of behavioural studies have suggested a flexible role for semantic processing regulated by the similarity of the nonword foil to real words. Here we developed a computational model that interactively combines visual-orthographic, phonological and semantic processing to perform lexical decisions. Importantly, the model was able to differentiate words from nonwords by dynamically integrating measures of polarity across the key processing layers. The model was more reliant on semantic information when nonword foils were pseudowords as opposed to consonant strings. Moreover, the model was able to capture a range of standard reading effects in lexical decision. Damage to the model also resulted in reading patterns observed in patients with pure alexia, phonological dyslexia, and semantic dementia, demonstrating for the first time that both normal and neurologically-impaired lexical decision can be addressed in a connectionist computational model of reading.
The Mutational Features of Aristolochic Acid–Induced Mouse and Human Liver Cancers

Aristolochic acid (AA) exposure has been statistically associated with human liver cancers. However, direct evidence of AA exposure–induced liver cancer is absent. This study aims to establish a direct causal relationship between AA exposure and liver cancers based on a mouse model and then explores the AA‐mediated genomic alterations that could be implicated in human cancers with AA‐associated mutational signature.
Imaging the Dynamic Interaction Between Sprouting Microvessels and the Extracellular Matrix

Thorough understanding of growth and evolution of tissue vasculature is fundamental to many fields of medicine including cancer therapy, wound healing, and tissue engineering. Angiogenesis, the growth of new vessels from existing ones, is dynamically influenced by a variety of environmental factors, including mechanical and biophysical factors, chemotactic factors, proteolysis, and interaction with stromal cells. Yet, dynamic interactions between neovessels and their environment are difficult to study with traditional fixed time imaging techniques. Advancements in imaging technologies permit time-series and volumetric imaging, affording the ability to visualize microvessel growth over 3D space and time. Time-lapse imaging has led to more informative investigations of angiogenesis. The environmental factors implicated in angiogenesis span a wide range of signals. Neovessels advance through stromal matrices by forming attachments and pulling and pushing on their microenvironment, reorganizing matrix fibers, and inducing large deformations of the surrounding stroma. Concurrently, neovessels secrete proteolytic enzymes to degrade their basement membrane, create space for new vessels to grow, and release matrix-bound cytokines. Growing neovessels also respond to a host of soluble and matrix-bound growth factors, and display preferential growth along a cytokine gradient. Lastly, stromal cells such as macrophages and mesenchymal stem cells (MSCs) interact directly with neovessels and their surrounding matrix to facilitate sprouting, vessel fusion, and tissue remodeling. This review highlights how time-lapse imaging techniques advanced our understanding of the interaction of blood vessels with their environment during sprouting angiogenesis. The technology provides means to characterize the evolution of microvessel behavior, providing new insights and holding great promise for further research on the process of angiogenesis.
Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation

Changes in gene expression are required to orchestrate changes in cell state during development. Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and use changes in mRNA poly-A tail length to control protein production. Poly-A tail length is positively correlated with translation activation during early development. However, it is not clear how poly-A tail changes affect mRNA translation at a during vertebrate oocyte maturation. We used Tail-seq and polyribosome analysis to measure poly-A tail and translational changes during oocyte maturation in Xenopus laevis. We identified large-scale poly-A and translational changes during oocyte maturation and found that poly-A tail changes precede translation changes. Additionally, we identified a family of U-rich sequence elements that are enriched near the polyadenylation signal of polyadenylated and translationally activated mRNAs. A modest density of U-rich elements was correlated with polyadenylation while a high density of U-rich elements was required to activate translation, showing that polyadenylation and translation activation can be uncoupled. Collectively, our data show that changes in mRNA polyadenylation are a key mechanism regulating protein expression during vertebrate oocyte maturation and that these changes are controlled by a spatial code of cis-acting sequence elements. Our results provide insight into mechanisms of translational control in oocytes and identify novel proteins important for the completion of meiosis.
Cryptic species of a water hyacinth biological control agent revealed in South Africa: host specificity, impact, and thermal tolerance

The discovery that cryptic species are more abundant than previously thought has implications for weed biological control, as there is a risk that cryptic species may be inadvertently released with consequences for the safety of the practice. A cryptic species of a biological control agent released for the control of the invasive alien macrophyte, water hyacinth, Eichhornia crassipes (C. Mart.) Solms. (Pontederiaceae), was recently discovered in South Africa. The two species were considered a single species prior to genetic analysis and interbreeding experiments. The original biological control agent retains the name Eccritotarsus catarinensis (Carvalho) (Heteroptera: Miridae) whereas the new species has been described as Eccritotarsus eichhorniae Henry. In this study, we compared the host specificity, efficacy, and thermal physiologies of the two species. The host specificity of the two species within the Pontederiaceae was very similar and both are safe for release in South Africa. Comparison of the per capita impact of the two species indicated that E. eichhorniae was the more damaging species but this is likely to be influenced by temperature, with E. catarinensis being more effective under lower temperatures and E. eichhorniae being more effective under higher temperatures. Releasing the correct species for the thermal environment of each release site will improve the level of control of water hyacinth in South Africa. This example highlights the need to keep populations of biological control agents from different native range collection localities separate, and to screen for host specificity and efficacy.
Neuromagnetic activation dynamics of stimulus-locked processing during a naturalistic viewing

Naturalistic stimuli such as watching a movie while in the scanner provide an ecologically valid paradigm that has the potential of extracting valuable information on how the brain processes complex stimuli in a short period of time. Naturalistic viewing is also easier to conduct with challenging participant groups including patients and children. Given the high temporal resolution of MEG, in the present study, we demonstrate how a short movie clip can be used to map distinguishable activation dynamics underlying the processing of specific classes of visual stimuli such as face and hand manipulations, as well as auditory stimuli with words and non-words. MEG data were collected from 22 healthy volunteers (6 females, 3 left handed, mean age – 27.7 ± 5.28 years) during the presentation of naturalistic audiovisual stimuli. The MEG data were split into trials with the onset of the stimuli belonging to classes of interest (words, non-words, faces, hand manipulations). Based on the components of the averaged sensor ERFs time-locked to the visual and auditory stimulus onset, four and three time-windows, respectively, were defined to explore brain activation dynamics. Pseudo-Z, defined as the ratio of the source-projected time-locked power to the projected noise power for each vertex, was computed and used as a proxy of time-locked brain activation. Statistical testing using the mean-centered Partial Least Squares analysis indicated periods where a given visual or auditory stimuli had higher activation. Based on peak pseudo-Z differences between the visual conditions, time-frequency resolved analyses were carried to assess beta band desynchronization in motor-related areas, and inter-trial phase synchronization between face processing areas. Our results provide the first evidence that activation dynamics in canonical brain regions associated with the processing of particular classes of visual and auditory stimuli (words, faces, etc.) can be reliably mapped using MEG during presentation of naturalistic stimuli. Given the strength of MEG for brain mapping in temporal and frequency domains, the use of naturalistic stimuli may open new techniques in analyzing brain dynamics during ecologically valid sensation and perception. Highlights A time-locking analysis was employed in naturalistic stimuli paradigm. Specific visual and auditory stimuli from the movie were mapped in brain space. Motor β-suppression was evident in periods of watching hand manipulation. Increased synchronization between core face-processing areas was found around 200 and 300ms in the face condition. Naturalistic viewing paradigms provide a reliable approach for investigating brain dynamics.