Miracle-dz/UniFAR-FTUs huggingface dataset:
Reef fish and benthic community structures of the Santa Luzia Marine Reserve in the Cabo Verde islands, eastern central Atlantic Ocean

ABSTRACT Understanding ecological structures and the dynamics of reef fish assemblages is a fundamental step in current conservation biology. Patterns of abundance and biomass of reef fish communities of the tropical Cabo Verde Archipelago (eastern central Atlantic Ocean) have not been assessed previously. We studied general patterns of reef fish trophic groups and benthic cover at 11 sites around Santa Luzia Island, employing underwater visual census (UVC) and benthic photo-quadrats. Fish assemblage attributes were plotted against several descriptors, such as fishing intensity, water surge, and complexity and type of substrate, using multivariate analysis. The 15 most abundant species accounted for 94.12% of all fishes censused by UVC; nine of these were also among the 15 species with the highest biomass. The families Muraenidae, Pomacentridae and Labridae were the most speciose, while Chromis spp. (Pomacentridae) and Labridae were the dominant groups in terms of both density and biomass. In terms of trophic groups of fishes, planktivores dominated fish density (69%, with 4 species), followed by mobile invertebrate feeders (17.9%, with 13 species), with other groups such as carnivores (3.6%) and roving herbivores (2.7%) being less prevalent. The benthic community was partially dominated by crustose coralline algae and macroalgae (more than 25% of total coverage). The low densities of large piscivorous and carnivorous fishes in the reserve might be directly linked to overfishing. The highest fish and benthic biodiversity were detected in the northwestern Santa Luzia reef sites, indicating this area as a priority for establishment of a no-take zone in the future.
The global biogeography of lizard functional groups

Understanding the mechanisms determining species richness is a primary goal of biogeography. Richness patterns of sub‐groups within a taxon are usually assumed to be driven by similar processes. However, if richness of distinct ecological strategies respond differently to the same processes, inferences made for an entire taxon may be misleading. We deconstruct the global lizard assemblage into functional groups and examine the congruence among richness patterns between them. We further examine the species richness – functional richness relationship to elucidate the way functional diversity contributes to the overall species richness patterns.
Comprehensive analysis of the NAC gene family in Elaeis guineensis

The NAC gene family encode transcriptional regulator that contain a conserved NAM domain near the N-terminus and participate in the regulation of plant development and response to different abiotic stresses. In this study, 129 EgNAC genes were identified from the genome sequence of Elaeis guineensis and 97 EgNAC located on the chromsomes with an average of 4.56 EgNAC genes per chromosome. About 60% of EgNACs contained three exons and the gene sizes varied from 541 bp to 37,294 bp. Genomic duplication analysis showed that 10 EgNAC genes were involved in segmental duplication events and two genes were from tandem duplication. The gene expression profiles of EgNACs based on transcriptome database for different oil palm tissues showed that 30 EgNACs with low or no expression and 24 EgNACs were specifically expressed in one tissue. The trancriptome comparison between the control and cold stress samples demonstrated that thirty-seven EgNACs were down-regulated and 82 EgNACs were up-regulated under cold stress. Further RT-qPCR showed that the expression for 24 out of 32 validated EgNACs were induced under both cold, drought and salt stresses. Our comprehensive analysis of EgNAC genes has provided clues for candidate genes involved in abiotic stress tolerance.
Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning

Understanding plant growth processes is important for many aspects of biology and food security. Automating the observations of plant development—a process referred to as plant phenotyping—is increasingly important in the plant sciences, and is often a bottleneck. Automated tools are required to analyze the data in microscopy images depicting plant growth, either locating or counting regions of cellular features in images. In this paper, we present to the plant community an introduction to and exploration of two machine learning approaches to address the problem of marker localization in confocal microscopy. First, a comparative study is conducted on the classification accuracy of common conventional machine learning algorithms, as a means to highlight challenges with these methods. Second, a 3D (volumetric) deep learning approach is developed and presented, including consideration of appropriate loss functions and training data. A qualitative and quantitative analysis of all the results produced is performed. Evaluation of all approaches is performed on an unseen time-series sequence comprising several individual 3D volumes, capturing plant growth. The comparative analysis shows that the deep learning approach produces more accurate and robust results than traditional machine learning. To accompany the paper, we are releasing the 4D point annotation tool used to generate the annotations, in the form of a plugin for the popular ImageJ (FIJI) software. Network models and example datasets will also be available online.
A plan to diversify a transgenic blight‐tolerant American chestnut population using citizen science

 Breeding trees is potentially an efficient method to rescue the genetic diversity and adaptive of the American population large-scale  To develop a breeding plan to diversify a transgenic blight-tolerant population, we simulated pedigrees to estimate inbreeding coefficients and effective population 17 size in scenarios involving outcrossing 1 to 4 transgenic founders to a maximum 18 of 1500 wild-type trees over 1 to 5 generations. We also simulated marker-19 assisted introgression scenarios to minimize the extent of the transgenic founder 20 genome, especially on the transgene carrier chromosome. 21  Simulations suggest that the effective population size may be increased to > 500, and the average inbreeding coefficient reduced to < 0.01, by outcrossing a single transgenic founder over five generations to 2, 25, 50, 150, and 450 (677 total) wild-type parents. Three generations of marker-assisted introgression is predicted to decrease the length of the founder genome to between 7% to 13% of the transgene carrier chromosome length as compared to 42% with event selection only. Transgenic outcross selections may be intercrossed to select progeny homozygous for the transgene for planting in seed orchards.  A diversified population of transgenic blight-tolerant American chestnut is estimated to be available for use in large-scale forest restoration 20 to 35 years after federal approval to distribute the trees. In contrast, trees from earlier generations would be available almost immediately after federal approval for personal or horticultural plantings. Methods to accelerate pollen production outcrossing are discussed.
The Application of Molecular Methods in Diagnostics of Phytopathogenic Viruses, Fungi and Fungus−Like Organisms

The aim of this chapter is to describe some of the protocols which are used in the diagnostics of plant viruses, fungi and fungus-like organisms. Special adaptation of certain protocols is required for each of this group of pathogens and even more, for every type of virus, fungus or fungus-like organism, each type of raw material in terms of plant organs, plant host species, time of year and conditions in the laboratory. The protocols of molecular methods for detection, identification and characterization of phytopathogenic organisms cited here in include detailed instructions for its application. This chapter contains specific recommendations for selection of plant material, extraction of total RNAs or DNAs, detailed procedure for RT-PCR or PCR depending on phytopathogenic organisms and instruction for interpretation of obtained results. The chapter also focuses on application of DNA cloning in plant virology. The text on DNA cloning contains instruction for basic steps including amplification of DNA fragment that we want to clone, ligation of PCR product with vector DNA, insertation of recombinant DNA into bacteria cells, the reproduction How to cite this book chapter: Stanković, I. and Vučurović, A. 2019. The Application of Molecular Methods in Diagnostics of Phytopathogenic Viruses , Fungi and Fungus−Like Organisms. In: Vucelić Radović, B. , Lazić, D. and Nikšić, M. (eds.) Application of Molecular Methods and Raman Microscopy/ Spectroscopy in Agricultural Sciences and Food Technology, Pp. 59–82. London: Ubiquity Press. DOI: https://doi.org/10.5334/bbj.e.
Temporal preparation and short-term temporal memory in depression

Patient suffering of Major Depressive Disorder (MDD) often complain that subjective time seems to ‘drag’ with respect to physical time. This may point towards a generalized dysfunction of temporal processing in MDD. In the present study, we investigated temporal preparation in MDD. “Temporal preparation” refers to an increased readiness to act before an expected event; consequently, reaction time should be reduced. MDD patients and age-matched controls were required to make a saccadic eye movement between a central and an eccentric visual target after a variable duration preparatory period. We found that MDD patients produced a larger number of premature saccades, saccades initiated prior to the appearance of the expected stimulus. These saccades were not temporally controlled; instead, they seemed to reflect increased oculomotor impulsivity. In contrast, the latency of visually-guided saccades was strongly influenced by temporal preparation in controls; significantly less so, in MDD patients. This observed reduced temporal preparation in MDD was associated with a faster decay of short-term temporal memory. Moreover, in patients producing a lot of premature responses, temporal preparation to early imperative stimuli was increased. A reduction in premature saccades, however, was associated with reduced temporal preparation to late imperative stimuli. In conclusion, reduced temporal preparation and short-term temporal memory in the oculomotor domain supports the hypothesis that temporal processing was altered in MDD patients. These observed deficits could reflect other underlying aspects of abnormal time experience in MDD.
Habitat affinity and density-dependent movement as indicators of fish habitat restoration efficacy

In mark-recapture assays from four different study years, the affinity of young-of-the-year Chinook Salmon (Oncorhynchus tschawytscha) and steelhead (O. mykiss) for stream pools restored with or created by engineered log structures was greater than that for pools without restoration, though with high interannual variability. From corresponding distribution and abundance data, it was clear that behavioral data are not always concordant with single observations of abundance. The same was true of the correlation between either behavior or abundance and physical characteristics of pools, although depth and current velocity had some explanatory power for both responses in Chinook. Density-dependent immigration into pools by Chinook indicated that restored pools have greater capacity for this species than unrestored pools; however no such pattern emerged for steelhead. Variation among individuals in body condition has implications for population-wide fitness and low variation was correlated with stronger affinity for pools. This suggests that pools mediate habitat-related trade-offs and that restoring them might have positive effects on fitness. Thus, behavioral data appear to provide stronger indications of restoration effectiveness than observational data alone.
Pseudoleucochloridium ainohelicis nom. nov. (Trematoda: Panopistidae), a Replacement for Glaphyrostomum soricis Found from Long-Clawed Shrews in Hokkaido, Japan, with New Data on its Intermediate Hosts

Members of the genus Glaphyrostomum Braun, 1901 (Trematoda: Brachylaimidae) are parasites of birds. However, an exception occurs in Glaphyrostomum soricis Asakawa, Kamiya and Ohbayashi, 1988, which was described from the longclawed shrew, Sorex unguiculatus Dobson, 1890, in Hokkaido, Japan. A recent DNA barcode-based trematode survey of land snails clearly showed that Ainohelix editha (A. Adams, 1868), a bradybaenid snail indigenous to Hokkaido, serves as the first and second intermediate hosts for a species of the genus Pseudoleucochloridium Pojmańska, 1959 (Panopistidae). Its adult stage was furthermore confirmed from S. unguiculatus. A comparison of adult morphology between Pseudoleucochloridium sp. and G. soricis revealed that both should be considered the same species. However, Pseudoleucochloridium soricis comb. nov. cannot be applied because P. soricis (Sołtys, 1952) already exists as the type species of the genus. We, therefore, propose Pseudoleucochloridium ainohelicis nom. nov. as a replacement name for G. soricis.
NBR1-mediated p62-liquid droplets enhance the Keap1-Nrf2 system

p62/SQSTM1 is a multivalent protein that has an ability to cause a liquid-liquid phase separation and serves as a receptor protein that participates in cargo isolation during selective autophagy. This protein is also involved in the non-canonical activation of the Keap1-Nrf2 system, a major oxidative stress response pathway. Here we show a role of Neighbor of BRCA1 gene 1 (NBR1), an autophagy receptor structurally similar to p62/SQSTM1, in the p62-liquid droplet formation and the Keap1-Nrf2 pathway. The overexpression of NBR1 blocked selective degradation of p62/SQSTM1 through autophagy and promoted the accumulation and phosphorylation of p62/SQSTM1 in liquid-like bodies, which is required for the activation of Nrf2. NBR1 was induced in response to oxidative stress, and then the p62-mediated Nrf2 activation was up-regulated. Conversely, loss of Nbr1 suppresses not only the formation of p62/SQSTM1-liquid droplets but also p62-dependent Nrf2 activation during oxidative stress. Taken together, our results show that NBR1 mediates p62/SQSTM1-liquid droplet formation to activate the Keap1-Nrf2 pathway.
Assessment of genetic diversity and structure among populations of Epioblasma triquetra in the Laurentian Great Lakes drainage

The endangered freshwater mussel (Bivalvia:Unionidae) Epioblasma triquetra, or Snuffbox, has the largest distribution of any extant species in its highly threatened genus. The Laurentian Great Lakes populations of E. triquetra are among the most important remaining strongholds. Genetic data are needed to inform managers how best to conserve and, where necessary, restore populations in the region. We used genotypes from 8 polymorphic microsatellite loci to examine the genetic diversity and structure of the 12 locations (n = 277 individuals) where E. triquetra are known to persist in the Great Lakes region. Similar levels of heterozygosity and allelic richness were observed in these populations. Only 1 of the 12 sampling locations (Embarrass River, Wisconsin) showed any evidence of a recent bottleneck and none showed evidence of significant inbreeding. Genetic structure followed the geographic distribution of the sampling locations in the 3 major drainages sampled: the Green Bay drainage, Wisconsin; the Grand River drainage, Michigan; and the Huron–St Clair–Erie corridor. Epioblasma triquetra in rivers that drain into the Huron–St Clair–Erie corridor showed some substructure in the Clinton, Ausable, and Sydenham rivers. The genetic structure across the Great Lakes region is consistent with multiple post-glacial colonization events by E. triquetra into the Great Lakes after the retreat of the Wisconsin ice sheet. We found evidence that Lake Michigan acts as a physical barrier to gene flow based on Monmonier’s algorithm and comparisons of hierarchical AMOVAs using AICc tests. All analyses supported entry of E. triquetra into the Great Lakes region via multiple colonization routes as the best fitting hypothesis to the genetic data. The clear pattern of genetic structure and diversity observed for E. triquetra in the Great Lakes region suggests that conservation efforts and management decisions should take genetic profiles into context before allowing for admixture among genetic populations via translocations or hatchery propagation of juveniles.
Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. In addition, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium. We demonstrated growth on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium, but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to M. nodulans, and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.
Efficacy of Flecainide in Catecholaminergic Polymorphic Ventricular Tachycardia Is Mutation-Independent but Reduced by Calcium Overload

Background The dual Na+ and cardiac Ca2+-release channel inhibitor, Flecainide (FLEC) is effective in patients with catecholaminergic polymorphic ventricular tachycardia (CPVT), a disease caused by mutations in cardiac Ca2+-release channels (RyR2), calsequestrin (Casq2), or calmodulin. FLEC suppresses spontaneous Ca2+ waves in Casq2-knockout (Casq2−/−) cardiomyocytes, a CPVT model. However, a report failed to find FLEC efficacy against Ca2+ waves in another CPVT model, RyR2-R4496C heterozygous mice (RyR2R4496C+/−), raising the possibility that FLEC efficacy may be mutation dependent. Objective To address this controversy, we compared FLEC in Casq2−/− and RyR2R4496C+/− cardiomyocytes and mice under identical conditions. Methods After 30 min exposure to FLEC (6 μM) or vehicle (VEH), spontaneous Ca2+ waves were quantified during a 40 s pause after 1 Hz pacing train in the presence of isoproterenol (ISO, 1 μM). FLEC efficacy was also tested in vivo using a low dose (LOW: 3 mg/kg ISO + 60 mg/kg caffeine) or a high dose catecholamine challenge (HIGH: 3 mg/kg ISO + 120 mg/kg caffeine). Results In cardiomyocytes, FLEC efficacy was dependent on extracellular [Ca2+]. At 2 mM [Ca2+], only Casq2−/− myocytes exhibited Ca2+ waves, which were strongly suppressed by FLEC. At 3 mM [Ca2+] both groups exhibited Ca2+ waves that were suppressed by FLEC. At 4 mM [Ca2+], FLEC no longer suppressed Ca2+ waves in both groups. Analogous to the results in myocytes, RyR2R4496C+/− mice (n = 12) had significantly lower arrhythmia scores than Casq2−/− mice (n = 9), but the pattern of FLEC efficacy was similar in both groups (i.e., reduced FLEC efficacy after HIGH dose catecholamine challenge). Conclusion FLEC inhibits Ca2+ waves in RyR2R4496C+/− cardiomyocytes, indicating that RyR2 channel block by FLEC is not mutation-specific. However, FLEC efficacy is reduced by Ca2+ overload in vitro or by high dose catecholamine challenge in vivo, which could explain conflicting literature reports.
A report of four unrecorded Proteobacteria species isolated from soil in Korea

peat pH, relatively low plant In 2015 and 2017, the National Institute of Biological Resources has isolated four unrecorded prokaryotic species designated as R-1-5, R-2-13, R-2-1, and R-1-8 from the peatland soil of Yongneup. Phylogenetic analysis based on 16S rRNA gene sequence similarity determined the four strains (R-1-5, R-2-13, R-2-1, R-1-8) were most closely related to Curvibacter lanceolatus (99.93%), Massilia brevitalea (98.7%), Pseudomonas lini (99.54%), and Pseudomonas vancouverensis (99.93%), respectively. The four unrecorded strains belong to the phylum Proteobacteria , in which the genera Curvibacter and Massilia are assigned to the class Betaproteobacteria , and the genus Pseudomonas to the class Gammaproteobacteria . Since there are no publications or official reports on these four strains, these four species are new records to Korea. The strains were further characterized by Gram reaction, colony and cell morphology, basic biochemical properties, and phylogenetic position. Descriptive information of the four unrecorded species is provided.
Seasonal flooding affects habitat and landscape dynamics of a gravel-bed river floodplain

Floodplains are comprised of aquatic and terrestrial habitats that are reshaped frequently by hydrologic processes that operate at multiple spatial and temporal scales. It is well established that hydrologic and geomorphic dynamics are the primary drivers of habitat change in river floodplains over extended time periods. However, the effect of fluctuating discharge on floodplain habitat structure during seasonal flooding is less well understood. We collected ultra-high resolution digital multispectral imagery of a gravel-bed river floodplain in western Montana on 6 dates during a typical seasonal flood pulse and used it to quantify changes in habitat abundance and diversity associated with annual flooding. We observed significant changes in areal abundance of many habitat types, such as riffles, runs, shallow shorelines, and overbank flow. However, the relative abundance of some habitats, such as backwaters, springbrooks, pools, and ponds, changed very little. We also examined habitat transition patterns throughout the flood pulse. Few habitat transitions occurred in the main channel, which was dominated by riffle and run habitat. In contrast, in the near-channel, scoured habitats of the floodplain were dominated by cobble bars at low flows but transitioned to isolated flood channels at moderate discharge. The areal abundance of habitat types in near-channel floodplain areas varied as discharge fluctuated. These areas were most diverse and dissimilar in habitat composition at intermediate flows during both the rising and falling limbs of the hydrograph. The geomorphically stable areas of the floodplain were dominated by herbaceous habitat, and we observed fewer transitions from one habitat type to another during the seasonal flood pulse. However, the largest habitat diversity occurred during peak flow, which highlights the influence of flooding on the development and expansion of a broad array of aquatic habitats during the annual cycle of flooding. We conclude that the response of floodplain habitat abundance and diversity is strongly influenced by location on the riverscape.