Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon in Mature Native Forests in Australia: The Role of Direct Weighing in the Derivation of Allometric Equations

Accurate estimates of forest biomass are essential to understand the contribution of forests to climate change mitigation efforts. In this manuscript, we report on biomass determinations for 586 directly weighed trees located in three important native forest areas in Australia. The sites were paired according to management strategy; i.e., managed for periodic cycles of harvest or conservation only. The key aim of the work was to test whether non-site specific available biomass relationships are reliable, especially in the estimation of the biomass of trees with a large diameter at breast height (DBH). The above-ground carbon (AGC) estimates for largely undisturbed forests ranged from approximately 200–400 t C ha−1. Existing allometric equations were generally poor at estimating biomass for mature trees, especially those of large DBH. Direct weighing of biomass ensured a degree of certainty in the results that cannot be associated with previous studies that relied on sub-sampling, or with studies that relied on existing allometric equations. Thus, caution should be exercised when interpreting the results of previous studies that did not rely on direct weighing of the biomass in the context of decisions around optimum forest management regimens, and the contribution of mature forest stands to the global carbon balance.
Kinetid structure of choanoflagellates and choanocytes of sponges does not support their close relationship

1 Department of Invertebrate Zoology, Biological Faculty, St. Petersburg State University, St. Petersburg, Russia 2 A.N. Severtzov Institute of Ecology and Evolution, Moscow, Russia 3 N.K. Koltzov Institute of Developmental Biology, Moscow, Russia 4 Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix Marseille University, CNRS, IRD, Avignon Université, Marseille France 5 Department of Embryology, Biological Faculty, St. Petersburg State University, St. Petersburg, Russia 6 Zoological Institute of Russian Academy of Science, St. Petersburg, Russia
CDK inhibitors as anticancer agents: Current status and future prospective

The cell-cycle is tremendously complex process and strictly controlled by cellular proteins called ‘Cyclin-dependent kinases’ (CDKs). Because of their critical contribution in cell division and their dysregulation in many cancers, CDKs have become an intense area of research for >20 years and several CDK-inhibitors (CDKIs) were developed. Initial results with broadly acting, first generation, pan-CDK inhibitors including flavopiridol, olomoucine, UCN-01 were almost disappointing due to limited efficacy and high toxicities observed in-vivo. To overcome these failures, Second-generation CDK inhibitors with high selectivity and specificity were enormously researched and developed. Based on impressive results in clinical investigations, FDA granted approval to three highly-specific CDK’4/6 inhibitors including; palbociclib (PD0332991), abemaciclib (LY2835219) and ribociclib (LEE011) for treatment of` patients with ‘HR-positive’, ‘HER2-negative’ advanced or metastatic` breast cancer. In this Review’, we’ll focus on CDKs, their contribution in cell-cycle and cancer, development and failure of pan-CDK inhibitors and currently approved CDK4/6 inhibitors with their preclinical’ and clinical study data that manifested their benefit in breast cancer’ treatment. In future, translational studies for coordinated assessment of the important biomarkers of clinical sensitivity and complete understanding of intersection of pharmacology’ and biology of CDKIs is required for more clinical success in the cancer treatment.
Id4 functional analysis during neurogenesis using zebrafish as a model organism

Id4 is a member of Id proteins which belong to a transcription factor family called “basic helix-loop-helix (bHLH)”proteins. bHLH family members contain a DNA binding domain and a helix-loop-helix domain that enables dimerisation between bHLH proteins. Id proteins are not capable of DNA binding due to absence of basic (DNA binding) domain. Therefore Id-bHLH heterodimerisation results in inhibition of bHLH activity which drives cellular differentiation. Id4 plays an important role in proliferating cells maintaining neural stem cell pool and controlling the timing of differentiation as well as apoptosis in the mouse. TALEN-mediated knockout of Id4 in zebrafish resulted in a reduction of Sox2 expression a marker for neural stem cells suggesting a reduction of the stem cell pool. In addition, premature GFAP expression a marker of astrocytes suggests that reduction of thestem cells pool is in part due to premature glial differentiation. HuC expression marking neurons was not changed however at 24 hpf. The observed phenotype was similar to that exhibited in mutants of the notch signalling pathwaysuggesting that Id4 could be a downstream target of notch. Indeed, Id4 expression was elevated in mind bomb mutants and embryos treated with DAPM an inhibitor of the notch signalling pathway suggesting that notch negatively regulates Id4 expression.
Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

We reviewed the availability of cytochrome c oxidase subunit I (COI) sequences for 2534 North American freshwater invertebrate genera in public databases (GenBank and Barcode of Life Data Systems) and assessed representation of genera commonly encountered in the Canadian Aquatic Biomonitoring Network (CABIN) database. COI sequence records were available for 61.2% of North American genera and 72.4% of Insecta genera in public databases. Mollusca (73.9%) and Nematoda (15.4%) were the best and worst represented groups, respectively. In CABIN, 85.4% of genera had COI sequence records, and 95.2% of genera occurring in >1% of samples were represented. Genera absent from CABIN tended to be uncommon or members of groups not routinely used for biomonitoring purposes. On average, 94.1% of genera in well-identified samples had associated sequence data. To leverage the full potential of genomics approaches, we must expand DNA-barcode reference libraries for poorly described components of freshwater food webs. Some genera appear to be well represented (e.g., Eukiefferiella), but deposited sequences represent few sampling localities or few species and lead to underestimation of sequence diversity at the genus level and reduced confidence in identifications. Public COI libraries are sufficiently populated to permit routine application of genomics tools in biomonitoring, and ongoing quality assurance/quality control should include re-evaluation as new COI reference sequences are added or taxonomic hierarchies change. Next, we must understand whether and how established biomonitoring approaches can capitalize on high-throughput sequencing tools. Biomonitoring approaches that use genomics data to facilitate structural and functional assessments are fertile ground for future investigation and will benefit from continued improvement of publicly available sequence libraries.
Efficacy of Dietary Antioxidants on Broiler Oxidative Stress, Performance and Meat Quality: Science and Market

Several production factors could exacerbate the biological formation of free radicals which, in turn, cause oxidative stress that impair the health, overall performance and meat quality of broiler chickens. Such factors could have a nutritional, pathological, physiological or environmental origin. The modern drive towards intensive commercial poultry production has elevated the exposure risk of broilers to these factors. In contrast, it has been demonstrated in many studies that dietary antioxidants could combat oxidative stress and improve broiler performance as well as meat quality. Interestingly, these efficacy claims have generated much attention from several feed additive companies which has spurred the development of certain commercial antioxidant products available in the global market. Information from recent studies suggests that both natural and synthetic antioxidants can be effective for augmenting broiler performance and meat quality particularly under conditions of oxidative stress. However, legislative restrictions may hinder the inclusion of high amounts of synthetic antioxidants required to achieve potency in oxidative-stressed broilers. The efficacy of dietary antioxidants depends on the age of the birds, dose and duration of supplementation. Moreover, supplementation of individual antioxidants on average seems to offer a better performance improvement than does a combination of antioxidants. Nonetheless, research efforts aimed at finding the right proportion of combining dietary antioxidants will offer tremendous economic benefits especially with the reduced use of costly synthetic vitamin E. This article gives further insights into research areas that could enhance the effective supplementation of antioxidants in broilers.
The role of hepatocyte nuclear factor 4α (HNF4α) in the metabolic regulation of its target genes

The nuclear receptor Hepatocyte Nuclear Factor 4a (HNF4a; NR2A1) regulates the transcription of many genes involved in glucose and lipid metabolism. Genetic linkage analyses have implicated HNF4a in the disease processes leading to Type 2 Diabetes Mellitus and dyslipidaemia. The aim of this study was to investigate the regulation of target genes in the metabolic pathways of glycolysis, lipogenesis and gluconeogenesis by HNF4a. Initally, the expression of HNF4a and its splice variants was investigated in three human hepatoma cell lines, HuH7, HepG2 and Hep3B, with the latter two cell lines shown to express the same range of HNF4a splice variants as human adult liver. The regulation of specific HNF4a target genes, L-PK, PEPCK and SREBP-1c, was subsequently investigated in HepG2 cells using a reporter gene approach. HNF4a was found to induce expression of reporter genes containing L-PK, PEPCK and SREBP-1c proximal promoter sequences. Insulin (1 ? M), but not high glucose (25 mM), was found to stimulate HNF4a-driven expression of the SREBP-1c reporter gene, while co-expression of HNF4a with the nuclear receptor coactivators, PGC-1a or p300, led to a reduction in SREBP-1c reporter gene expression. The changes in expression of various HNF4a target genes in response to physiological mediators of the fasting-fed cycle were characterised in HepG2 cells using a real-time quantitative PCR approach. The role of HNF4a, p300 and PGC-1a was further investigated by plasmid overexpression. HNF4a and PGC-1a were found to positively regulate PEPCK expression under cell culture conditions simulating fasting (cAMP), whilst overexpression of HNF4a, PGC1a and p300 reduced L-PK mRNA expression under fed conditions. In conclusion, the results indicate that HNF4a is a transcriptional activator of both glucagon- stimulated gluconeogenic gene expression and insulin-stimulated glycolytic and lipogenic gene expression. It is hypothesised HNF4a forms separate multi-protein complexes to differentially regulate metabolic pathways under different metabolic states.
Serial Dependence in Position Perception Occurs at the Time of Perception

Observers perceive objects in the world as stable over space and time, even though the visual experience of those objects is often discontinuous and distorted due to masking, occlusion, camouflage, noise, etc. How are we able to easily and quickly achieve stable perception in spite of this constantly changing visual input? It was previously shown that observers experience serial dependence in the perception of features and objects, an effect that extends up to 15 seconds back in time. Here, we asked whether the visual system utilizes an object’s prior physical location to inform future position assignments in order to maximize location stability of an object over time. To test this, we presented subjects with small targets at random angular locations relative to central fixation in the peripheral visual field. Subjects reported the perceived location of the target on each trial by adjusting a cursor’s position to match its location. Subjects made consistent errors when reporting the perceived position of the target on the current trial, mislocalizing it toward the position of the target in the preceding two trials (Experiment 1). This pull in position perception occurred even when a response was not required on the previous trial (Experiment 2). In addition, we show that serial dependence in perceived position occurs immediately after stimulus presentation, and is a fast stabilization mechanism that does not require a delay (Experiment 3). This indicates that serial dependence occurs for position representations and facilitates the stable perception of objects in space. Taken together with previous work, our results show that serial dependence occurs at many stages of visual processing, from initial position assignment to object categorization.
Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.
Conservation tillage and mulching effects on the adaptive capacity of direct-seeded upland rice (Oryza sativa L.) to alleviate weed and moisture stresses in the North Eastern Himalayan Region of India

ABSTRACT A field experiment was conducted to study the effects of tillage and mulch on weed growth, soil moisture storage, productivity and profitability of upland rice during 2012–2013 at Lembucherra, India. Tillage treatments included CT-RI: conventional tillage with 100% residue incorporation and NT-RR: no-till with 100% residue retention. Mulches included rice straw (SM), Gliricidia (GM), brown manuring (BM) and none (NM). CT-RI registered the highest total weed density (89–168 weeds m−2) and biomass (9.6–183 g dry weight m−2) than those for the NT-RR (75–161 weed m−2 and 8–155 g dry weight m−2). In addition, NT-RR stored (122–172 mm) more soil moisture (0–40 cm soil depth) in comparison with that for the CT-RI treatment (110–161 mm) during crop growing season. Tillage treatments did not have the significant effect on yields. NT-RR reduced the cost of cultivation by 31.5% compared with that for the CT-RI. Thus, the net returns under NT-RR were more than those for the CT-RI. The BM recorded the lowest weed biomass and density as compared to that under other mulches. Therefore, cultivation of upland rice using NT along with BM mulching enhanced productivity and profitability of rice cultivation in India.
Acute toxicity of nitrite in fat snook (Centropomus parallelus)

Abstract Oxidative stress and hypoxia responses in Centropomus parallelus exposed to three different concentrations of nitrite (0, 0.5, and 10 mg L−1) were evaluated. To determinate toxicity, we used enzymatic analyses and quantifications of oxygen consumption and opercular beats under conditions of normoxia and hypoxia. There was no significant difference in GST, CAT, or GPx enzymes in the liver or in GPx in the gills. Levels of GST were altered at a concentration of 10 mg L−1 in experiment I. Experiment II displayed alterations for GST and CAT in the liver at the same concentration, indicating that exposure to nitrite does not generate differentiated activation in the body’s defense system by the production of oxidative stress enzymes. When nitrite was associated with hypoxia, there was a significant increase in both enzymatic activity and opercular beating under hypoxia in the group exposed to 10 mg L−1 nitrite compared to the control.
Differences among Triticum dicoccum, T. monococcum and T. spelta in rate of nitrate uptake

Three groups of wheat cultivars Triticum dicoccum, T. monococcum and T. spelta were grown hydroponically under controlled conditions. At the age of 21 days, the plants were analysed to determine their rate of nitrate uptake, the net NO3 – uptake capacity and total nitrogen content. The rate of nitrate uptake varied from 2.7 (T. dicoccum) to 9.3 (T. monococcum) μmol NO3 –/g FW/h; in the economically important species T. spelta it ranged between 3.1–6.9 μmol NO3 –/g FW/h. In T. diccoccum and T. spelta these values represent about 80–90% estimated Vmax. Both groups were significantly different from T. monococcum. This collection was characterized by the highest Vmax but its nitrate uptake rate per g fresh weight reached only 45–67% Vmax. Within each group there were the intra-specific differences. Nitrate uptake capacity of the individual species or varieties was significantly affected by differences in development of root system. These results were compared with registered cultivar T. aestivum cv. Munk.
Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform

The recent call to reconstruct a detailed picture of the tree of life for all organisms has forever changed the field of molecular phylogenetics. Sequencing technology has improved to the point that scientists can now routinely sequence complete plastid/mitochondrial genomes and thus, vast amounts of data can be used to reconstruct phylogenies. These data are accumulating in DNA sequence repositories, such as GenBank, where everyone can benefit from the vast growth of information. The trend of generating genomic-region rich datasets has far outpaced the expasion of datasets by sampling a broader array of taxa. We show here that expanding a dataset both by increasing genomic regions and species sampled using GenBank data, despite the inherent missing DNA that comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We show that trnK intron is comparable to matK in terms of the proportion of variable sites, parsimony informative sites, the distribution of those sites among rate classes, and phylogenetic informativness across the history of the order. This is especailly useful since trnK intron is often sequenced concurrently with matK which saves on time and resources by increasing the phylogenetic utility of a single genomic region (rapidly evolving matK/trnK). Finally, we show that the inclusion of RNA edited sites in datasets for phylogeny reconstruction did not appear to impact resolution or support in the Gnetales indicating that edited sites in such low proportions do not need to be a consideration when building datasets. We also propose an alternate start codon for matK in Ephedra
Levantamento etnobotânico da família Cactaceae no estado de Sergipe

As Cactaceae ocorrem em uma ampla diversidade de clima, mas predominam em ambientes semiaridos e de solos rochoso-pedregosos. Familia monofiletica, distribuida em 127 generos e 1500 especies. No APG III, foi subdividida em quatro Subfamilias: Maihuenoideae, Pereskeoideae, Opuntioideae e Cactoideae e integra o segundo grupo botânico mais numeroso da regiao neotropical. No estado de Sergipe ocorrem 11 generos e 26 especies. O objetivo dessa pesquisa foi realizar um levantamento etnobotânico da familia Cactaceae no estado de Sergipe. As cactaceas apresentaram uma grande variedade de usos, a exemplo da ornamentacao, medicinal tradicional, alimenticia e manifestacoes culturais como inspiracao mistico-religioso, producao de poesias, cordeis e cancoes populares. Os resultados foram obtidos por meio de questionario semiestruturado, padronizado e aplicados a 36 individuos moradores de 11 localidades distribuidas nas regioes Leste, Agreste e Alto Sertao. Foi registrado no periodo de 2013 – 2015, 11 especies de cactos aplicadas em 55 usos pelas comunidades locais, as quais foram agrupadas em quatro categorias: medicinal; alimentacao humana e animal; construcao e producao de objetos; ornamental e mistico-cultural. Os cactos cabeca-de-frade, mandacaru, facheiro e palma forrageira tiveram a maior frequencia de citacoes de usos.
Metabolite profiling of core oil palm trunk (COPT) sap: The effects of different storage durations, conditions and temperatures

In Malaysia, core oil palm trunk (COPT) is one of the biomass that has been left underutilised due to its low properties. Nonetheless, metabolites contained in COPT sap may provide an alternative natural resources for bio-chemicals and pharmaceuticals. Metabolites such as sugars are easily affected by analytical factors during storage. In this study, the changes of metabolite contents in COPT sap stored at different storage durations, conditions and temperatures were observed by using gas chromatography-mass spectrometry (GC-MS) based metabolomics approach. The changes of metabolite contents, particularly sugars and organic acids were analysed using univariate and multivariate statistical analysis. The separation trends observed in the principal component analysis (PCA) score plot was greatly influenced by storage temperatures. However, two-way analysis of variance (ANOVA) revealed that the majority of significant metabolites (P<0.05) was strongly influenced by storage durations. The metabolite increased significantly when COPT was stored as raw rather than sap. The highest sugar concentrations in COPT were found at 10°C for one month (R-10-1M). Furthermore, the organic acids increased significantly when stored at 4°C for one month (R-4-1M). The results indicated different storage durations, conditions and temperatures led to variation in the COPT sap metabolite content.
The effect of adipokinetic hormones on the activity of digestive enzymes

The role of the adipokinetic hormone (AKH) in the control of protease, amylase and lipase activities is examined using the cockroach Periplaneta americana and the fruit fly Drosophila melanogaster as model species. The effects of Peram‐CAH‐I and ‐II on the activity of cockroach digestive enzymes in the gastric caeca and midgut are measured both in vivo and in vitro. The results show the activity of proteases, amylases and lipases in both parts of the gut: amylase activity is higher in the gastric caeca than in the midgut; lipase activity presents the opposite trend; and protease activity is similar in both organs. The applied hormones stimulate the activity of all digestive enzymes, although this stimulation is not uniform; AKHs affect enzymes selectively, and in some cases unequally, in the gastric caeca and midgut. No substantial differences between Peram‐CAH‐I and ‐II stimulation are recorded. The in vitro results demonstrate that AKH stimulates digestive enzyme activity directly. In agreement with the cockroach results, enzymatic activity in D. melanogaster larvae producing nonfunctional AKH is lower than that in the larvae with ectopically expressed Akh gene, where enzyme activity reaches or even exceeds that of the controls. Overall, the results demonstrate the active role of AKHs in the stimulation of digestive enzyme activity in insects.