Although laccase has been recognized as a wonder molecule, and green enzyme, the use of low yielding fungal strains, poor production, purification, and low enzyme kinetics have hampered its larger-scale applications. Hence the present research was aimed to select high yielding fungal strains and to optimize the production, purification, and kinetics of laccase of Aspergillus sp. HB_RZ4. Aspergillus sp. HB_RZ4 produced a copious amount of laccase on under meso-acidophillic shaking conditions in a medium containing glucose and yeast extract. A 25 µM of CuSO4 enhanced the enzyme yield. The enzyme was best purified on Sephadex G-100 column. Purified enzyme resembled with the laccase of A. flavus. Kinetics of purified enzyme revealed the high substrate specificity and good velocity of reaction with ABTS as substrate. The enzyme was stable over a wide range of pH and temperature. The peptide structure of the purified enzyme resembled with the laccase of A. kawachii IFO 4308. The fungus decolorized various dyes independent of the requirement of a laccase mediator system (LMS). Aspergillus sp. HB_RZ4 came out as a potent natural producer of laccase, it decolorized the dyes even in absence of LMS and thus can be used for bioremediation.

Invasion ecology has a long tradition of searching for traits distinguishing alien invasive and non-invasive plants. Surprisingly, this approach has been so far poorly used to understand why some arable weeds are abundant and widespread while others are rare and narrowly distributed. In the present study, we focused on the characteristics of successful weeds occurring in maize fields, one of the most import crop worldwide. Two national weed surveys conducted in France were used to identify increasing and decreasing species based on 175 and 484 surveyed fields in the 1970s and the 2000s, respectively. Weed trait values related to regional frequency, local abundance and specialization to maize were identified with Phylogenetic Generalized Least-Squares (PGLS). We found a positive relationship between regional frequency and local abundance, i.e. the most widespread weeds were also locally more abundant. We highlighted that weeds with the C4 photosynthetic pathway and summer emergence were more abundant, more frequent and more specialized to maize crops. More generally, we highlighted two successful strategies: on the one hand, traits related to a general weediness syndrome with rapid resource acquisition (high SLA and Ellenberg-N) and high colonization capacity (seed longevity, fecundity and wind dispersal), on the other hand, traits related to specific adaptation to spring cultivation (thermophilous species with summer emergence, late flowering and C4 photosynthetic pathway). Deviations from the abundancy-frequency relationships also indicated that species of the Panicoideae sub-family, species with Triazine-resistant populations and neophyte species were more abundant than expected by their regional frequency. To some extent, it is therefore possible to predict which species can be troublesome in maize crops and use this information in weed risk assessment tools to prevent new introductions or favor early detection and eradication. This study showed how tools developed in functional and macro-ecology can be used to improve our understanding of weed ecology and to develop more preventive management strategies.

Three-dimensional structure of six closely related hydrogenases from purple bacteria has been modeled by combining template-based and ab initio modeling approach. The results lead to conclusion that there should be 4Fe3S-cluster in the structure of these enzymes. Thus, these hydrogenases could drive attention for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of 4Fe3S-cluster's microenvironment showed intragroup heterogeneity. Possible function of the C-terminal part of the small subunit in membrane binding has been discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) has been carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in number of hydrophobic interactions and number of ionic interactions. Molecular tunnels were mapped in the models and compared with structures from PDB. Protein-protein docking showed that these enzymes could exchange electrons in oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E.coli, H. marinus, R. eutropha, S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvx. gelatinosus.

Controlled atmosphere (CA) storage, under atmospheres with low O₂ and high CO₂ concentrations, is effective for extending the shelflife of horticultural products. We investigated the influence of CA storage (O₂/CO₂: 2.5%/6.0% or 2.5%/0.0%) at 1C for 21 d versus normoxia (normal air) on the physicochemical and biological properties of broccoli (Brassica oleracea var. italica, Plenck, 1794) via amounts and activities of terminal oxidases of electron transport chain. Mass loss, a sensitive index of freshness for broccoli heads under CA, was significantly lower under CA than under normoxia. The effect for depressing mass loss was observed 7 d earlier under CA including 6.0% CO₂ than under CA without CO₂. Environmental CO₂ was also effective for depressing loss of L-ascorbate. The alternative oxidase (AOX) level under CA was lower than under normoxia during storage, while the level of cytochrome c oxidase (COX), and the AOX/COX activity ratio (based on oxygen isotope discrimination), were stable during storage. Our results indicate that CA storage is effective for retaining freshness of broccoli heads during storage by depressing the induction of AOX. However, depression of AOX level was found to be independent of environmental CO₂.

In recent years, the biomimetic potential of lignified or partially lignified fruit pericarps has moved into focus. For the transfer of functional principles into biomimetic applications, a profound understanding of the structural composition of the role models is important. The aim of this study was to qualitatively analyse and visualize the functional morphology of the coconut endocarp on several hierarchical levels, and to use these findings for a more precise evaluation of the toughening mechanisms in the endocarp. Eight hierarchical levels of the ripe coconut fruit were identified using different imaging techniques, including light and scanning electron microscopy as well as micro-computer-tomography. These range from the organ level of the fruit (H0) to the molecular composition (H7) of the endocarp components. A special focus was laid on the hierarchical levels of the endocarp (H3-H6). This investigation confirmed that all hierarchical levels influence the crack development in different ways and thus contribute to the pronounced fracture toughness of the coconut endocarp. By providing relevant morphological parameters at each hierarchical level with the associated toughening mechanisms, this lays the basis for transferring those properties into biomimetic technical applications.

No single evolutionary event has been identified as the cause for the final emergence of our species. I propose that a mutation on CD155 receptor gene occurred to establish a symbiosis with poliovirus, which exerted its beneficial impact via RNA dependent non-genetic transgenerational inheritance, which caused a qualitative enhancement of cognitive functions. I posit that this mutation occurred in what we call, Anatomically Modern Humans, our immediate ancestor species and that the disruption of this symbiosis causes autism spectrum disorder. Positive selection of CD155 to the extent of becoming a species defining characteristic, the chronology of autism spectrum disorder prevalence increase and continued increase, the multigenerational nature of RNA inheritance, the universal infection of humans by poliovirus and a very low associated mortality rate, and several other factors support this hypothesis. Specific genetic, epidemiological and sperm miRNA content studies are suggested to test this hypothesis.

The genus Naegleria, of free-living amoeba (FLA) group, has been investigated mainly due to its human health impact resulting in deadly infections and their worldwide distribution on freshwater systems. Naegleria fowleri, colloquially known as the “brain-eating amoeba”, is the most studied Naegleria species because it causes Primary Amoebic Meningoencephalitis (PAM) of high lethality. The assessment of FLA biodiversity is fundamental to evaluate the presence of pathogenic species and the possibility of human contamination. However, the knowledge of FLA distribution in Brazil is unknown, and to rectify this situation we present a research on identifying Naegleria spp. in the Monjolinho River, as a model study. The river is a public Brazilian freshwater source that crosses the city of São Carlos. Five distinct sampling sites were examined through limnological features, trophozoites culturing and PCR against internal transcribed spacers (ITS) regions and 5.8S rRNA sequence. The results identified N. philippinensis, N. canariensisi, N. australiensis, N.gruberi, N. dobsoni sequences, as well as a Vahlkampfia sequence. The methodology delineated here represents the first Brazilian Naegleria spp. study on a freshwater system. Our result stresses the urgency of a large scale evaluation of the presence of free-living amoebas in Brazil.

Two cases of cutaneous nocardiosis in a cat and in a dog have been described. Diagnosis was made on basis of direct microscopy and cultural mycological analysis. Phenotypic characteristics of two indigenous Nocardia strains are presented. The strain isolated from cat was presumably identified as N. asteroids. There have been no reports of suchlike cases in pets in Russia so far.

Development and deployment of wheat varieties with high yields, wide adaptability, good quality, multiple-resistance to abiotic and biotic stresses, and efficient response to fertilizers have greatly contributed to global wheat sustainable production. The genomic composition of key commercial wheat variety can help understand the genetic basis underlying the development of new variety and permit increased breeding efficiency. In this study, we report the chromosomal and genomic compositions of BN207, presently the leading wheat variety in the southern region of Huang-Huai River Valley, the most important wheat producing area in China through an integrated analysis using fluorescent in situ hybridization (FISH) and wheat 15 K SNP array. Our results showed that BN207 inherited 55.3% and 40.7% of its genome from its male parent BN64 and female parent ZM16, respectively, and generating 64 novel or recombined loci. Besides, we detected nine chromosomal variations in Bn207 and its parents and ten sister lines, and physically mapped two variations, the pericentric inversion of chromosome 6B, and large tandem repeat sequence block at the long arm of 5A, both had positive effects on agronomic traits, by integration of FISH and SNP loci recombination analyses. These results will provide a reference for breeding of high yield wheat varieties as BN207, and the application of founder parents BN64 and ZM16, which are being utilized frequently in wheat breeding programs in Henan Province and surrounding areas.

Biological Hotspot research of fish larvae in estuarine waters of Timbulsoko Village, Demak was conducted in April-June 2019 in Timbulsoko Village. Timbulsloko has fertile waters because many fishermen make this location as a fishing ground area. Timbulsloko has the potential to become a nursery ground area and feeding ground for fish due to natural mangrove habitat but the abrasion disaster resulted in the degradation of the nursery ground habitat for early stage fish. The results showed that fish larvae caught in the waters of Timbulsloko Village consisted of 13 families. The composition of the types of fish larvae caught are Mugilidae, Siganidae, Gobiidae, Leiognathidae, Scatophagidae, Chanidae, Latidae, Engraulidae, Gerreidae, Carangidae, Bagridae, Sillaginidae, Ambassidae. The most common types of fish larvae are Ambassidae fish larvae, which are 46.98%, while the least caught are Carangidae fish larvae, Sillaginidae which is 1.01%. The largest abundance of fish larvae is 428,271 ind / m3 found at D2P2, while the abundance of fish larvae is at least at E1P1270 point with an abundance value of 51,498 ind / m3. The similarity of ecological habitat values at D2P2 and A2G1 points based on PCA analysis and the similarity of contours from spatial depth interpolation indicate the biological hotspot in the mangrove waters of Timbulsloko Village.

The Cape Restionaceae species, an endemic of the Fynbos Biome, is threatened by urbanization, alien plant invasion, agricultural expansion, and groundwater extraction. This is further worsened by the semi-arid conditions and hydrological variability factors, which influences species niche dynamics. Therefore, it is important to assess and monitor the Restionaceae species for preservation of their endemism and richness. This study models the hydrological niche and distribution changes of Restionaceae species at the New Years Peak (NYP) at microclimate level for biodiversity conservation. MaxEnt modelling and GIS analytical approaches were applied at various stages in niche modelling process as follows: (i) microclimatic input raster layers’ generation, (ii) ecological modelling and hydrological niche manipulation, and (iii) spatial distributional change mapping. The hydrological niches of the Restionaceae were effectively examined under the recent climate and compared with RCP2.6 and RCP8.5 future climate scenarios as the microscale environmental inputs. The results showed that most of the studied Restionaceae species positioned themselves along a hydrological gradient. Each species tolerated a range of hydrological conditions, which formed their hydrological niche. Changing climate would cause both positive and negative species range shifts. The study assists in plant species conservation and future climate change impact analysis on endangered plant species.

Plants are immobile, and, to overcome harsh environmental conditions, such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA-signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, the perception of the stress signal (abiotic and biotic) and the response network of ABA-signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA-signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.

Two cases of cutaneous nocardiosis in a cat and in a dog have been described. Diagnosis was made on basis of direct microscopy and cultural mycological analysis. Phenotypic characteristics of two indigenous Nocardia strains are presented. The strain isolated from cat was presumably identified as N. asteroids. There have been no reports of suchlike cases in pets in Russia so far.

It is well known that human activities and climate change have increased steppe habitat loss and fragmentation in Northwest China. Carabid beetles are often used as bioindicators of environmental change because they are extremely sensitive to disturbance. We chose 42 landscapes (18 fragmented and 24 continuous) in both desert and typical steppes of Northwest China to examine the influence of habitat loss and fragmentation on carabid beetle communities. The results showed the largest correlation coefficient between carabid communities and landscape compositions within a 7-km spatial scale in both desert and typical steppes. Further, the response of carabid communities to habitat fragmentation was species-specific in both desert and typical steppes. Habitat fragmentation in the desert steppe had positive effects on the richness and abundance of carabid communities, while in the typical steppe, the effects were negative. Additionally, habitat fragmentation significantly decreased the abundance of two common carabid species in the desert steppe. Therefore, the effects of habitat fragmentation on carabid biodiversity differ with species characteristics and habitat traits, where plant communities, soil structure, and microclimate vary in the different steppe types. The results of this study provide experimental evidence and technical support for biodiversity conservation management in the steppes of Northwest China.

Sixty years ago in the lab adjacent to Fred Sanger (1958 Nobel Prize for protein chemistry), I discovered the cell surface hydroxyproline-rich glycoproteins. Nature keeps some of her secrets longer than others. It has taken many years to dissect the molecular function and biological role of extensins and arabinogalactan proteins (AGPs). Extensins template the formation of new cell walls. AGPs remained baffling and enigmatic until a Eureka moment when computer prediction of AGP calcium binding depicted paired glucuronic acid residues and thus the likely role of a cell surface AGP-Ca²⁺capacitor: In conjunction with the auxin-activated proton pump that releases bound Ca²⁺ it led us to formulate the Hechtian Growth Oscillator as A Global Paradigm with a pivotal role in Ca²⁺ homeostasis. The ramifications are profound. They cannot be shrugged off with sceptical disdain but demand critical reappraisal of current dogma. Phyllotaxis is an ancient problem; it involves an essential role for auxin and the auxin efflux “PIN” proteins together with mechanotransduction of stress-strain as phyllotactic determinants. However, a general explanation remains elusive despite much effort, particularly by mathematicians. Here we propose a novel biochemical algorithm: Hechtian oscillator transduction of cell wall stress generates phyllotactic patterns quite independent of a mathematical approach. Plants simply use different rules and follow a different route.

In this review article, the occurrence of nor-lignans and their biological activities are explored and described. Nor-lignans have proven to be present in several different families also belonging to chemosystematically distant orders as well as to have many different beneficial pharmacological activities. This review article represents the first one on this argument and is thought to give a first overview on these compounds with the hope that their study may continue if not raise after this.

Background and Objective: Although whole body-electromyostimulation (WB-EMS) has been shown to favorably improve body composition in several research studies, it has not been confirmed how it affects adipose tissue-derived biomarkers and circumferences of the abdomen and thighs. Materials and Methods: Twenty participants of obese elderly women were randomly classified into an EMS group (EMSG; n = 10) or a non-EMS group (CON; n = 10). The WB-EMS suits used in this study enabled the simultaneous activation of 8 muscle groups with selectable intensities for each phase. Stimulation frequency was selected at 85 Hz, impulse-width at 350 μ seconds, and impulse-rise as a rectangular application. Impulse duration was 6 seconds with a 4-second break between impulses. The EMS sessions were combined with aerobic dancing 3 times a week for 12 weeks. Both groups received the same program; however, the CON did not receive electrical stimuli. Biomarkers and body composition including circumferences of the abdomen and thighs were measured on Week 0 and Week 12. Results: Compared with the CON, 1) a significant effect of the EMS-intervention concerning decreased body weight (p = 0.032) and increased basal metabolic rate (p = 0.029) were evident. The thigh subcutaneous fat and total fat of EMSG were not significantly changed, but those of CON were significantly increased after 12 weeks. 2) The biomarkers of CON either increased or showed no change, although the interleukin (IL)-6 was significantly (p = 0.028) decreased in EMSG. Specifically, C-reactive protein (CRP; p = 0.005) and alpha-fetoprotein (p = 0.050) of CON were significantly increased after 12 weeks. In addition, the IL-6 (p = 0.034), CRP (p = 0.001), carcinoembryonic antigen (p = 0.017), and low density lipoprotein (p = 0.005) of EMSG were lower than those of CON in the end of experiment. 3) Conclusions: The results indicate that EMS intervention improved body composition and reduced negative biomarkers, thus highlighting its effectiveness.

This study was undertaken to elucidate the role of trehalose (Tre) in mitigating oxidative stress under salinity and low P in maize. Eight-day-old maize seedlings of two maize varieties, BARI Hybrid Maize-7 and BARI Hybrid Maize-9 were subjected to salinity (150 mM NaCl), low P (5 µM KH2PO4) and their combined stress with or without 10 mM Tre for 15-d.Salinity and combined stress significantly inhibited the shoot length, root length, and root volume, whereas, low P increased the root length and volume in both genotypes. Exogenous Tre in the stress treatments increased all of the growth parameters as well as decreased the salinity, low P and combined stress-mediated Na+/K+, ROS, MDA, LOX activity and MG in both genotypes. Under salinity and low P stress, the SOD activity increased in both genotypes, but the activity decreased in combined stress. POD activity increased in all stress treatments. Interestingly, Tre application enhanced the SOD activity in all the stress treatments but inhibited the POD activity. Both CAT and GPX activity were increased by saline and low P stress while the activities inhibited in combined stress. Similar results were found for APX, GR, and DHAR activities in both genotypes. However, MDHAR activity was inhibited in all the stresses. Interestingly, Tre enhanced CAT APX, GPX, GR, MDHAR and DHAR activities suggesting the amelioration of ROS scavenging in maize under all the stresses. Increased GST activity in presence or absence of Tre might involve in detoxification of hydroperoxides as well as leaf senescence. On the other hand, increased glyoxalase activities in saline and low P stress in BHM-9 suggested better MG detoxification system because of down-regulation of Gly-I activity in BHM-7 in those stresses. Tre also increased the glyoxalase activities in both genotypes under all the stresses. Tre improved the growth in maize seedlings by decreasing Na+/K+, ROS, MDA, and MG through regulating antioxidant and glyoxalase systems.

To elucidate the chemical compositions of the sugar fall maple leaves, the methanol extracts were firstly fractionated by ethyl acetate and n-butanol respectively. The phenolic acids-rich fractions (ethyl acetate extracts) were further purified by various chromatographic columns including XAD macroporous resin, Sephadex LH-20, ODS and semi-preparative HPLC to yield the compounds. The isolated compounds were characterized by ¹H-Nuclear Magnetic Resonance (¹H-NMR), ¹³C-NMR, and high resolution electrospray ionisation mass spectral (HR-ESI-MS) spectroscopy. Twenty eight phenolics including fourteen flavonoids (1-14), five quinic acid derivatives (15-19), five galloyl tannins (20-24) and four other phenolic acids (25-28) were isolated and their structures were identified. The isolated compounds were evaluated for their antioxidant and α-glucosidase inhibitory activities. All of the phenolics constituents showed DPPH scavenging antioxidant activities. While, glycosides of quercetin and myricetin, galloyl tannins were showed promising α-glucosidase inhibitory activity. All of the compounds except 4, 11, 12 and 28 were isolated from sugar maple for the first time. Moreover, Compounds 9, 10, 14, 20, 21, 23, 25 and 26 were isolated from the Acer species for the first time.

Nervous systems and brains’ computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signaling originated in cells’ communication with the outside world and with each other, in order to cooperate toward adaptive construction and repair of multicellular bodies. Here we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering, cognitive science, and even machine learning and artificial intelligence. One of the predictions of this view is that regeneration and regulative development are able to restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states - in this case, pattern memories. Based on this idea, we propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution, and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology, and biomedicine of information processing in vivo.

Pathogen fitness landscapes change when transmission cycles establish in non-native environments or spill over into new vectors and hosts. The introduction of Leishmania infantum in the Americas into the Neotropics during European colonization represents a unique case study to investigate mechanisms of ecological adaptation of this important parasite. Defining the evolutionary trajectories that drive L. infantum fitness in this new environment are of great public health importance as they will allow unique insight into pathways of host/pathogen co-evolution and their consequences for region-specific changes in disease manifestation. This review summarizes current knowledge on L. infantum genetic and phenotypic diversity in the Americas and its possible role in the unique epidemiology of VL in the New World. We highlight the importance of appreciating adaptive molecular mechanisms in L. infantum to understand the parasites’ successful establishment on the continent.

Complex systems exhibit critical thresholds at which they transition among alternative phases. Complex systems theory has been applied to analyze disease progression, distinguishing three stages along progression: (i) a normal non-infected state, (ii) a pre-disease state in which the host is infected and responds; therapeutic interventions could still be effective, (iii) an irreversible state, where the system is seriously threatened. The Dynamical Network Biomarker (DNB) theory sought for early-warnings of the transition from health to disease. Such DNBs might range from individual genes to complex structures in transcriptional regulatory or protein-protein interaction networks. Here we revisit transcriptomic data obtained during infection of tobacco plants with tobacco etch potyvirus to identify DNBs signaling the transition from mild/reversible to severe/irreversible disease. We identified genes showing a sudden transition in expression along disease. Some of these genes cluster in modules that show the properties of DNBs. These modules contain both genes known to be involved in response to pathogens (e.g., ADH2, CYP19, ERF1, KAB1, LAP1, MBF1C, PR1, or TPS5) and other genes not previously related to biotic stress responses (e.g., ABCI6, BBX21, NAP1, OSM34, or ZPN1).

A recent report in PNAS that Candidatus Nanohaloarchaeum antarcticus requires haloarchaeon Halorubrum lacusprofundi for growth expands the list of known symbiotic or parasitic associations between the members of DPANN archaea, which are relatively small cells with reduced genomes and limited metabolic capacity, and free-living archaea. In line with previous studies addressing the enigmatic mechanism(s) for the transfer of metabolites from Ignicoccus hospitalis to Nanoarchaeum equitans, this new study presents additional evidence supporting a direct cytoplasmic connection facilitated by the fusion of parasite’s membrane with that of its host. Here I show that this novel mechanism for accessing the host resources by a membrane fusing mechanism, which eliminates the need for sophisticated multivalent transport systems, is fundamentally similar to that employed by several viral lineages. These new findings support an evolutionary model on the origin of incipient viral lineages from parasitic cellular lineages that started their parasitic life cycle by fusing with their host cells.

1) Background: One of the most common cancer that affects men worldwide and North American men is prostate cancer. Gleason score is a pathological grading system to examine the potential aggressiveness of the disease in the prostate tissue. The advancement in computing and next-generation sequencing technology now allow us to study the genomic profiles of patients in association with their different Gleason score more accurately and effectively. 2) Methods: In this study, we used a novel machine learning method to analyze gene expression of prostate tumors with different Gleason scores, and identify potential genetic biomarkers for each Gleason group. We obtained a publicly-available RNA-Seq dataset of a cohort of 104 prostate cancer patients from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) repository, and categorized patients based on their Gleason scores to create a hierarchy of disease progression. A hierarchical model with standard classifiers in different Gleason groups, also known as nodes, was developed to identify and predict nodes based on their mRNA or gene expression. In each node, patient samples were analyzed via class imbalance and hybrid feature selection techniques to build the prediction model. The outcome from analysis of each node is a set of genes that can differentiate each Gleason group from the remaining groups. To validate the proposed method, the set of identified genes are used to classify a second dataset of 499 prostate cancer patients collected from cBioportal [1]. 3) Results: The overall accuracy of applying this novel method to the first dataset was 93.3%, and further validated to 87% accuracy using the second dataset. This method also identified genes that were not previously reported as potential biomarkers for specific Gleason groups. In particular, PIAS3 was identified as a potential biomarker for Gleason score 4+3=7, and UBE2V2 for Gleason score 6. 4) Insight: Previous reports show that the genes predicted by this newly proposed method strongly correlate with prostate cancer development and progression. Furthermore, pathway analysis shows that both PIAS3 and UBE2V2 share similar protein interaction pathways, the JAK/STAT signaling process.

Biological control is widely successful for controlling pests, but effective biocontrol agents are now more difficult to obtain due to more restrictive international trade laws. Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, applying genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them, incorporating evolutionary and ecological principles. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined to better target their selection, followed by how to implement this information into a breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depends on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci (QTL) analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices include marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

1) Background: One of the deadliest cancers that affect men worldwide and North American men is prostate cancer. This disease motivates parts of the cells in the prostate to lose control of their growth and division. 2) Methods: We are proposing a machine learning method used to analyze gene expressions of prostate tumors with different Gleason scores, and to identify potential genetic biomarkers for each group. A publicly-available RNA-Seq dataset of a cohort of 104 prostate cancer patients have been retrieved from the National Center for Biotechnology Information's (NCBI) Gene Expression Omnibus (GEO) repository. We categorize patients by their Gleason scores into different groups to create a hierarchy of disease progression. A hierarchical model with standard classifiers in different Gleason groups (hereinafter called nodes) to identify and predict nodes based on their mRNA or gene expressions. At each node, patient samples are analyzed via class imbalance and hybrid feature selection techniques to build the prediction model. The outcome of each node is a set of genes that can separate the Gleason group from the remaining groups. To validate the proposed method, the set of identified genes are used to classify a second dataset of 499 prostate cancer patients that have been collected from cBioportal.. 3) Results: Two genes have been found to be potential biomarkers of specific Gleason groups; PIAS3 has been identifed for Gleason score 4+3=7, while UBE2 could be a poteintial biomarker for Gleason score 6. Other proposed genes that were not found in the literature might be potential biomarkers. 4) Conclusion: The latest literature supports that the genes predicted by the proposed method are strongly correlated with prostate cancer progression and tumour development processes. Furthermore, pathway analysis shows that both PIAS3 and UBE2 share the same protein interaction pathway, the JAK/STAT signaling process.

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arseniate up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a GC content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.

Pseudomonas aeruginosa (P. aeruginosa) produces a suite of virulence factors that are coordinated by Quorum Sensing (QS) contributing to its disease-causing ability in aquaculture. The present study is first of its kind to obtain information regarding the presence and distribution of five QS genes, three virulence genes viz: lasI, lasR, rhlI, rhlR, rhlAB, toxA, aprA and plcH and seven of the Extended-spectrum βlactamases (blaVEB, blaPER, blaTEM,, blaSHV, blaCTX-M1, blaCTX-M2 and blaCTX-M3) of Pseudomonas species isolated from fish meat by direct PCR. Bacterial identification was based mainly on conventional biochemical techniques using the Vitek 2, automated system. Phenotypic sensitivity of antibiotics was established by the agar disc diffusion technique through 16 various antimicrobial drugs. Quantification of their in vitro production of numerous virulence genes outside the cell that are QS dependent namely, pyocyanin, elastase, alkaline protease, biofilm and cytotoxicity of Vero cell was as well executed. Fifteen genes demonstrated an enormous variety in their association. The total number of Pseudomonas species isolates were 30/100 to be identified by the API 20NE system as P. aeruginosa 12/30 (40%), P. fluorescens 8/30 (27%), P. putida 6/30 (20%) and P. alkylphenolia 4/30 (13%). The outcomes of this study have great significance for the strategic designation of QS quenching.

The transition to reproduction is a crucial step in the life cycle of any organism. In Arabidopsis thaliana the establishment of reproductive growth can be divided into two phases: Firstly, cauline leaves with axillary meristems are formed and internode elongation begins. Secondly, lateral meristems develop into flowers with defined organs. Floral shoots are usually determinate and suppress the development of lateral shoots. Here, we describe a transposon insertion mutant in the Nossen accession with defects in floral development and growth. Most strikingly is the outgrowth of stems from the axillary bracts of the primary flower carrying secondary flowers. Therefore, we named this mutant flower-in-flower (fif). However, the transposon insertion in the annotated gene is not the cause for the fif phenotype. By means of classical and genome sequencing-based mapping, the mutation responsible for the fif phenotype was found to be in the LEAFY gene. The mutation, a G-to-A exchange in the second exon of LEAFY, creates a novel lfy allele and results in a cysteine-to-tyrosine exchange in the α1-helix of LEAFY´s DNA-binding domain. This exchange abolishes target DNA-binding, whereas subcellular localization and homomerization are not affected. To explain the strong fif phenotype against this molecular findings, several hypotheses are discussed.

Today massive amounts of sequenced metagenomic and -transcriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the various flavours of biological sequence data, and how this information can be interpreted to increase our scientific knowledge and understanding. We argue that a mechanistic understanding is required to consistently interpret experimental observations, and that this understanding is greatly facilitated by the generation and analysis of dynamic mathematical models. We conclude that, in order to construct mathematical models and to test mechanistic hypotheses, time-series data is of critical importance. We review diverse techniques to analyse time-series data and discuss various approaches by which time-series of biological sequence data was successfully used to derive and test mechanistic hypotheses. Analysing the bottlenecks of current strategies in the extraction of knowledge and understanding from data, we conclude that combined experimental and theoretical efforts should be implemented as early as possible during the planning phase of individual experiments and scientific research projects.

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy, and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3), and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.

Changes in land-use have been observed in banana-based systems in the African Great Lakes region affected by Xanthomonas wilt disease (XW) of banana. Through participatory focus group discussions (FGDs) and the 4-cell method, changes in land-use were retrospectively assessed in 13 XW-affected landscapes/villages along a 230 km transect from Masisi (XW arrived in 2001) to Bukavu (XW arrived around 2014) in eastern Democratic Republic of Congo during 2015. The four-cell chart ranked land-use by mapping the area under production and the number of households involved in production. Farmers’ perceptions on the sustainability of new land-uses were also documented. Soil nutrient content and erosion levels were measured for five major land-use options/ trajectories on 147 fields across 55 farms in three landscapes along the transect. From being ranked the most important crop (92% of landscapes i.e. produced on large areas of land and by many households) before XW outbreaks, its importance had declined with most households in 36% of the landscapes growing it on smaller farms while in 64% of cases by few households on smaller pots. Farmers uprooted entire banana mats or fields, expanding land under other crops, mainly beans, taro, sweet potato, cassava, maize, coffee and eucalyptus. Species richness did not change at landscape level, though 21 crops were introduced at farm level. Land-use for banana is however still perceived to be more sustainable due to its multi-functional roles. Soils under banana plots were found in general to be better in their chemical attributes while high erosion levels (Mg ha-1 year-1) were observed under cassava (1.7-148.9) compared with banana (0.3-10.7) and trees (0.3-5.9). The current shift away from banana could thus have profound effects on supply of key services and sustainability of the production systems. This study offers a good basis/entry point for interventions in the XW-affected landscapes.

Key features of glycogen metabolism in excitable tissues are not well-explained by current concepts. Glycogen stores in brain and skeletal muscle are generally considered to function as local glucose reserves, to be utilized during transient mismatches between glucose supply and demand; however, quantitative measures show that blood glucose supply is likely never rate-limiting for energy metabolism in either brain or muscle under physiological conditions. These tissues nevertheless do normally utilize glycogen during intervals of increased energy demand, despite the availability of free glucose, and despite the ATP cost of cycling glucose through glycogen polymer. This seemingly wasteful shunt can be explained by considering the effect of glycogenolysis on the amount of energy derived from ATP (ΔG’ATP). ΔG’ATP is diminished by elevations in Pi, such as occur at sites of rapid ATP hydrolysis and net phosphocreatine consumption. Glycogen utilization counters this effect by sequestering Pi in glycolytic metabolites (glycogen_n + Pi → glycogen_n-1 + glucose-1-phosphate → phosphorylated glycolytic intermediates), and thereby maintains the amount of energy obtained from ATP at sites of rapid ATP consumption. This thermodynamic effect may be particularly important in the narrow, spatially constricted astrocyte processes that ensheath neuronal synapses. This effect can also explain the co-localization of glycogen and cytosolic phosphocreatine in brain astrocytes, glycolytic super-compensation in brain when glycogen is not available, and aspects of exercise physiology in muscle glycogen phosphorylase deficiency (McArdle’s disease).

Edible coating gels developed from the Aloe vera plant have been used as a traditional medicine for about 3000 years. Aloe vera contains 110 potentially active constituents from six different classes: chromone and its glycoside derivatives; anthraquinone and its glycoside derivatives; flavonoids; phenylpropanoids and coumarins; phenylpyrone and phenol derivatives; and phytosterols and others. Apart from medicinal uses, Aloe gels have an important role in food preservation as edible coatings. They provide an edible barrier for atmospheric gases and moisture, and help to reduce the respiration and transpiration of fresh produce, which helps to preserve its postharvest quality. To date, numerous studies have been conducted on the postharvest use of Aloe vera gel. The present review article summarizes and discusses existing available information about the chemical constituents, antimicrobial activity, and food preservative characteristics of Aloe vera.

A previous study involving whole genome sequencing of the white shark suggested unique molecular evolution accounting for gigantism and the enhanced longevity of sharks including positive selection of dozens of protein-coding genes potentially involved in genome stability. We performed a reanalysis on some of the genes and identified serious flaws in their results. In this short article, we scrutinize one of the serious problems we identified, report other concerns, and point out a potential bias in analyzing iconic shark species in general.

Membrane-coupled RNA transport is an emerging theme in fungal biology. This review focuses on the RNA cargo and mechanistic details of transport via two inter-related sets of organelles: endosomes and extracellular vesicles for intra- and intercellular RNA transfer. Simultaneous transport and translation of messenger RNAs (mRNAs) on the surface of shuttling endosomes is a conserved process pertinent to highly polarised eukaryotic cells, such as hyphae or neurons. Here we detail the endosomal mRNA transport machinery components and mRNA targets of the core RNA-binding protein Rrm4. Extracellular vesicles (EVs) are newly garnering interest as mediators of intercellular communication, especially between pathogenic fungi and their hosts. Landmark studies in plant-fungus interactions indicate EVs as a means of delivering various cargos, most notably small RNAs (sRNAs), for cross-kingdom RNA interference. Recent advances and implications of the nascent field of fungal EVs are discussed and potential links between endosomal and EV-mediated RNA transport are proposed.

Chan and colleagues in their paper titled “Human origins in a southern African palaeo-wetland and first migrations” (https://www.nature.com/articles/s41586-019-1714-1) report 198 novel whole mitochondrial DNA (mtDNA) sequences and infer that ‘anatomically modern humans’ originated in the Makgadikgadi–Okavango palaeo-wetland of southern Africa around 200 thousand years ago. This claim relies on weakly informative data. In addition to flawed logic and questionable assumptions, the authors surprisingly disregard recent evidence and debate on human origins in Africa. As a result, the emphatic and high profile conclusions of the paper are unjustified.

RNA epigenetics is perhaps the most recent aspect of interest for translational epigeneticists. RNA modifications create such an extensive network of epigenetically driven combination whose role in physiology and pathophysiology is still far from being elucidated. Not surprisingly, some of the players determining changes into RNA structure are in common with those involved in DNA and chromatin structure regulation, while other molecules seem very specific to RNA. It is envisaged, then, that new small molecules, acting selectively on RNA epigenetic changes, will be reported soon, opening new therapeutic interventions based on the correction of the RNA epigenetic landscape. In this review, we shall summarize some aspects of RNA epigenetics limited to those in which the potential clinical translatability to cardiovascular disease is emerging.

The Populus L. genus unites tree species, which are botanically grouped into several sections. The species successfully hybridize both in the same section and between some sections. The poplar hybridization widely occurs in nature and in variety breeding. Therefore, the development of poplar species specific molecular markers is very actual. The effective markers for trees of the Aigeiros Daby section have been recently developed using the polymorphism of the 5S rDNA non-transcribed spacers (NTSs). In this article, the 5S rDNA NTS based markers were designed for several species of the Leuce Daby section. The alb9 marker amplifies one fragment with DNA matrix of P. alba and P. × canescens (natural hybrid P. alba × P. tremula). The alb2 marker works the same way except the case with P. bolleana. In this case, the amplification of three fragments was observed. The tremu1 marker amplification is detected with DNA matrix of P. tremula and P. × canescens. Thus, the developed markers may be applied as useful tool for the P. alba, P. tremula, P. × canescens and P. bolleana identification in such areas of plant science as botany, dendrology, genetics of populations, variety breeding etc.

Ecosystem surveillance monitoring is critical to managing natural resources and especially so under changing environments. Despite this importance, the design and implementation of monitoring programs across large temporal and spatial scales has been hampered by the lack of appropriately standardised methods and data streams. To address this gap, we outline a surveillance monitoring method based on permanent plots and voucher samples suited to rangeland environments around the world that is repeatable, cost-effective, appropriate for large-scale comparisons and adaptable to other global biomes. The method provides comprehensive data on vegetation composition and structure along with soil attributes relevant to plant growth, delivered as a combination of modules that can be targeted for different purposes or available resources. Plots are located in a stratified design across vegetation units, landforms and climates to enhance continental and global comparisons. Changes are investigated through revisits. Vegetation is measured to inform on composition, cover and structure. Samples of vegetation and soils are collected and tracked by barcode labels and stored long-term for subsequent analysis. Technology is used to enhance the accuracy of field methods, including differential GPS r plot locations, instrument based Leaf Area Index (LAI) measures, and three dimensional photo-panoramas for advanced analysis. A key feature of the method is the use of electronic field data collection to enhance data delivery into a publicly-accessible database.Our method is pragmatic, whilst still providing consistent data, information and samples on key vegetation and soil attributes. The method is operational and has been applied at more than 704 field locations across the Australian rangelands as part of the Ecosystem Surveillance program of the Terrestrial Ecosystem Research Network (TERN). The methodology enables continental analyses, and has been tested in communities broadly representative of rangelands globally, with components being applicable to other biomes. Here we also recommend the consultative process and guiding principles that drove the development of this method as an approach for development of the method into other biomes. The consistent, standardised and objective method enables continental, and potentially global analyses than were not previously possible with disparate programs and datasets.

The PI3K/AKT pathway is a key target in oncology where most efforts are focussed on phenotypes such as cell proliferation and survival. Comparatively little attention has been paid to PI3K in stemness regulation, despite the emerging link between acquisition of stem cell-like features and therapeutic failure in cancer. The aim of this review is to summarise current known and unknowns of PI3K-dependent stemness regulation, by integrating knowledge from the fields of developmental, signalling and cancer biology. Particular attention is given to the role of the PI3K pathway in pluripotent stem cells (PSCs) and the emerging parallels to dedifferentiated cancer cells with stem cell-like features. Compelling evidence suggests that PI3K/AKT signalling forms part of a ‘core molecular stemness programme’ in both mouse and human PSCs. In cancer, the oncogenic PIK3CA^H1047R variant causes constitutive activation of the PI3K pathway and has recently been linked to increased stemness in a dose-dependent manner, similar to observations in mouse PSCs with heterozygous versus homozygous Pten loss. There is also evidence that the stemness phenotype may become ‘locked’ and thus independent of the original PI3K activation, posing limitations for the success of PI3K monotherapy in cancer.Ongoing therapeutic developments for PI3K-associated cancers may therefore benefit from a better understanding of the pathway’s two-layered and highly context-dependent regulation of cell growth versus stemness.

Between 2011 and 2016 small-scale farm trials were run across three dairy regions of New Zealand (Waikato, Canterbury, Otago) to compare the performance of typical regional farm systems with farm systems implementing a combination of mitigation options most suitable to the region. The trials ran for at least three consecutive years with detailed recording of milk production and input costs. Nitrate leaching per hectare of the milking platform (where lactating cows are kept) was estimated using either measurements (suction cups), models, or soil mineral nitrogen measurements. Post-trial, detailed farm information was used in the New Zealand greenhouse gas inventory methodology to calculate the emissions from all sources; dairy platform, dairy support land used for wintering non-lactating cows (where applicable) and replacement stock, and imported supplements. Nitrate leaching was also estimated for the support land and growing of supplements imported from off-farm using the same methods as for the platform. Operating profit (NZ$/ha/year), nitrate leaching (kg N/ha/year), and greenhouse gas emissions (t CO₂-e/ha/year) were all expressed per hectare of milking platform to enable comparisons across regions. Nitrate leaching mitigations adopted in lower-input (less imported feed and N fertiliser) farm systems reduced leaching by 22 to 30 percent, and greenhouse gas emissions by between nine and 24 percent. The exception was the wintering barn system in Otago where nitrate leaching was reduced by 45 percent but greenhouse gas emissions were unchanged due to greater manure storage and handling. Important drivers of a lower environmental footprint are reducing nitrogen fertiliser and imported feed. Their effect is to reduce nitrogen surplus and feed flow through the herd and drive down both greenhouse gas emissions and nitrate leaching. Emission reductions in the lower-input systems of Waikato and Canterbury came at an average loss of profit of approximately NZ$100/t CO₂-e (three to five percent of industry average profit per hectare).

Red djulis (Chenopodium formosanum) is a native cereal plant in Taiwan; it contains abundant polyphenols, betalian and dietary fiber. The appearance of red djulis is bright red. Therefore, it is also called the “ruby of cereals”. The antioxidative activity of red djulis extract is well-understood. However, the antiaging function still remains unclear. This study examined the potential of red djulis extract for enhancing collagen secretion and preventing cutaneous aging using red djulis extracts. The red djulis extracts are comprised of an abundant active component that can effectively enhance the ability of collagen secretion of dermal fibroblasts, prevent the glycation of collagen and resist the damage of ultraviolet light exposure. After fibroblast treatment with red djulis extracts, TGM1, KRT1, KRT10 and SOD2 genes were up-regulated significantly by 2.3, 4.3, 4.4 and 27.3 times, respectively, compared to those of the control group. Additionally, it can increase COL1A2 gene expression by 43% and decrease MMP9 gene expression 33%. Therefore, it was demonstrated that red djulis extracts affect gene expressions related to the skin barrier, antioxidation and collagen. Moreover, we found positive effects on skin barrier integrity, endogenous antioxidant activity and skin collagen-preservation. The preparation of the red djulis extracts is environmental friendly and can promote the economic value of Chenopodium formosanum; thus, the proposed extract is suitable for applications in the development of food products, especially beverages, skin care and cosmetic products.

Marula seed cake (MSC) is a nutritionally-rich natural feed resource that can enhance the healthiness of animal-derived foods (ADFs) for human consumption. This study compared the health-related fatty acid (FA) profiles of MSC products from South Africa and Eswatini. Composite samples monthly collected from both countries were analysed for FAs. MSC products from both countries were found to be dominated by oleic acid (>70%), followed by palmitic, linoleic and stearic acids. Consequently, both products had their FA totals dominated by ƩMUFA followed by ƩSFA, ƩPUFA, Ʃn-6 PUFA and Ʃn-3 PUFA. Both oleic and stearic acids were higher (P < 0.01) whilst linoleic (P < 0.001), α-linolenic (P < 0.05), margaric (P < 0.05), palmitoleic (P < 0.05) and eicosatrienoic (P < 0.05) acids were lower in South African in comparison to Eswatini MSC. Consequently, South African MSC had higher ƩMUFA (P < 0.01) but lower ƩPUFA (P < 0.001), Ʃn-6 PUFA (P < 0.001) and Ʃn-3 PUFA (P < 0.05). Also, Eswatini MSC had higher n-6 : n-3 PUFA, PUFA : SFA (P = 0.001) and PUFA : MUFA (P < 0.05) ratios. Further, MSC products from both countries had similarly (P > 0.05) low atherogenicity and high desaturase indices. In conclusion, both country products are rich particularly in oleic acid and their incorporation into farm animal diets would increase content of the MUFA in ADFs and, consequently, improve health benefits to human consumers.

Porcine circovirus type 2 (PCV2) is a small non-enveloped DNA virus that causes swine immunosuppression by inducing apoptosis in lymphocytes. The ORF3 protein plays a major role in PCV2-induced apoptosis in porcine kidney cells, but there is little information regarding this protein in PCV2-infected lymphocytes. In this study, hybridoma screening and epitope mapping were determined by using an indirect ELISA. The mAb 7D3 against ORF3 peptide (residues 35–65) of PCV2 were generated in this study. In vivo situation, the mAb 7D3 recognized ORF3 protein existed in PCV2-infected apoptotic porcine PBMCs. It is noteworthy that thimerosal interfered with the binding of mAb 7D3 to epitope and it was diminished by adding cysteine. Additionally, thimerosal interacting with cysteine-containing peptide was demonstrated by the PTI assay. Furthermore, thimerosal specifically interacted with the antigen-binding sites of mAb 7D3. This study suggested that thimerosal blockade the occlusion of the antigen-binding sites of mAb 7D3 to bind ORF3 peptide (residues 35–65) via thimerosal interacting with cysteine residues which should be located within the antigen-binding sites of mAb 7D3. Overall, the mAb 7D3 has been characterized and it will be a valuables tool in future studies of ORF3 function and the wider mechanism of cell apoptosis caused by PCV2 infection. Similarly, these techniques will be useful for applications in detecting thimerosal too.

Bacterial Calcium-carbonate Precipitation (BCP) has been studied for multiple applications such as remediation, consolidation and cementation. Isolation and screening of strong calcifying bacteria is the main task of BCP-technique. In this paper we studied CaCO₃ precipitation by different bacteria isolated from a rhizospheric soil in both solid and liquid media. It has been found, through culture-depending studies, that bacteria belonging to Actinobacteria, Gammaproteobacteria and Alphaproteobacteria are the dominant bacteria involved in CaCO₃ precipitation in this environment. Pure and mixed cultures of selected strains were applied for sand biocementation experiments. Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS) analyses of the biotreated samples revealed the biological nature of the cementation and the effectiveness of the biodeposition treatment by mixed cultures. X-ray diffraction (XRD) analysis confirmed that all the calcifying strains selected for sand biocementation precipitated CaCO₃, mostly in the form of calcite. In this study Biolog® Eco-plate is evaluated as a useful method for a more targeted choice of the sampling site with the purpose of obtaining interesting candidates for BCP applications. Furthermore, ImageJ software was investigated, for the first time to our knowledge, as a potential method to screen high CaCO₃ producer strains.

The mechanical hill wet-seeded rice machine is benefits to establish uniform seedling, and ditches were established by using this machine. However, little knowledge is known on the effect of the establishment of ditches on growth, lodging and yield, and their relationship with root traits. In this study, two field experiments were conducted during 2012 and 2013 with using two super rice varieties (i.e. hybrid rice ‘Peizataifeng’ and inbred rice ‘Yuxiangyouzhan’) grown under three ditches establishment treatments (i.e. T1: both water ditches and seed ditches were established by the machine, T2: seed ditches were established by the machine, T3: neither water nor seed ditches were established by the machine). The lodging index and lodging resistance traits, the grain yield and above-ground dry weight and the root traits were measured. The results showed that the lodging index was significantly affected by the treatments with ditches. The strongest lodging resistance was detected in mechanical hill wet-seeded rice with ditches treatment in both 2012 and 2013. The lodging resistance was strongly related to the breaking resistance, the root volume and root superficial area at the heading stage and maturity stage and the total root length at the heading stage. No significant difference was investigated in grain yield or dry weight of mechanical hill wet-seeded rice. Yuxiangyouzhan showed higher grain yield, dry weight and better lodging resistance but unfavorable root growth attributes than Peizataifeng. Therefore, the mechanical hill wet-seeded rice with ditches treatment increased rice lodging resistance is related to root traits.

The present review provides an in-depth look into the complex topic of delimiting species in sea anemones. For most part of history this has been based on a small number of variable anatomic traits, many of which are used indistinctly across multiple taxonomic ranks. Early attempts to classify this group succeeded to comprise much of the diversity known to date, yet numerous taxa were mostly characterized by the lack of features rather than synapomorphies. Of the total number of species names within Actiniaria, about 77% are currently considered valid and more than half of them have several synonyms. Besides the nominal problem caused by large intraspecific variations and ambiguously described characters, genetic studies show that morphological convergences are also widespread among molecular phylogenies. On the contrary, spatial distribution has been emerging as a more reliable parameter to explain cryptic relationships among sea anemones. Integrative approaches and genome-wide data have been especially helpful to unveil the mechanisms behind the speciation process, which is typically marked by large genetic differences among populations, even from neighbouring localities. This paper further discusses current gaps in our knowledge and offers some future directions on how to address the issue of species delimitation in the extremely polymorphic group of sea anemones.

Desmoglein 3 (Dsg3) plays a crucial role in cell-cell adhesion and tissue integrity. Increasing evidence suggests that Dsg3 acts as a regulator of cellular mechanotransduction, but little is known about its direct role in mechanical force transmission. The present study investigated the impact of cyclic strain and substrate stiffness on Dsg3 expression and its role in mechanotransduction in keratinocytes. A direct comparison was made with E-cadherin, a well-characterized mechanosensor. Exposure of oral and skin keratinocytes to equiaxial cyclic strain promoted changes in expression and localization of junction assembly proteins. Knockdown of Dsg3 by siRNA blocked strain-induced junctional remodeling of E-cadherin and Myosin IIa. Importantly, the study demonstrated that Dsg3 regulates the expression and localization of YAP, a mechanosensor and an effector of the Hippo pathway. Furthermore, we showed that Dsg3 forms a complex with phospho-YAP and sequestered it to the plasma membrane, while Dsg3 depletion had an impact on both YAP and phospho-YAP in their response to mechanical forces, increasing the sensitivity of keratinocytes to strain- or substrate rigidity-induced nuclear relocation of YAP and phospho-YAP. PKP1 seemed to be crucial in recruiting the complex containing Dsg3/phospho-YAP to the cell surface since its silencing affected both Dsg3 junctional assembly with concomitant loss of phospho-YAP at cell periphery. Finally, we demonstrated that this Dsg3/YAP pathway has an influence on the expression of YAP1 target genes and cell proliferation. Together, these findings provide evidence of a novel role for Dsg3 in keratinocyte mechanotransduction.

Poor survival of human pluripotent stem cells (hPSCs) following freezing, thawing, or passaging hinders maintenance and differentiation in stem cell research. Rho-associated kinases (ROCKs) play a crucial role in hPSC survival. To date, a typical ROCK inhibitor, Y-27632, has been the primary agent used in hPSC research. Here, we report that another ROCK inhibitor, fasudil, can be used as an alternative. Fasudil increased hPSC growth due to survival rather than proliferation following thawing and passaging, similar to Y-27632. It did not affect pluripotency and genetic integrity including mitochondrial genome (mtDNA). Notably, the genes related to metabolism, mTORC1, and TP53 have mainly displayed a faster recovery pattern with ROCK inhibitors than control. Furthermore, fasudil was confirmed as useful for the single dissociation of hPSCs and for aggregation. It also increased retinal pigment epithelium (RPE) differentiation and the survival of neural crest cells during differentiation. These findings suggest that fasudil can replace Y-27632 for use in stem cell research.

Two desirable functions of healthy soil are nutrient cycling and pest suppression. We review recent literature on the contributions of soil microarthropods to soil health through their intersecting roles in decomposition and nutrient cycling and direct and indirect suppression of plant pests. Microarthropods can impact soil and plant health directly by feeding on pest organisms or serving as alternate prey for larger predatory arthropods, and indirectly, by mediating the ability of crop plants to resist or tolerate insect pests and diseases through interactions with the decomposition food web in support of plant nutrition. Soil fauna, including microarthropods, are key regulators of decomposition at local scales but their role at larger scales is unresolved. Future research priorities include the incorporation of multi-channel omnivory into food web modeling and understanding the vulnerability of our soil carbon to increased global temperatures.

The dorsal column nuclei (DCN) are organised by both somatotopy and modality, and have a diverse range of afferent inputs and projection targets. The functional organisation and connectivity of the DCN implicate them in a variety of sensorimotor functions, beyond their commonly accepted role in processing and transmitting somatosensory information to the thalamus, yet this is largely underappreciated in the literature. In this review, we examine the morphology, organisation, and connectivity of the DCN and their associated nuclei, to improve understanding of their sensorimotor functions. First, we briefly discuss the receptors, afferent fibres, and pathways involved in conveying tactile and proprioceptive information to the DCN. Next, we review the modality and somatotopic arrangements of the constituents of the dorsal column nuclei complex (DCN-complex), which includes the gracile, cuneate, external cuneate, X, and Z nuclei, and Bischoff’s nucleus. Finally, we examine and discuss the functional implications of the myriad of DCN-complex projection targets throughout the midbrain, and hindbrain, in addition to their modulatory inputs from the cortex. The organisation and connectivity of the DCN-complex suggest that these nuclei should be considered a complex integration and distribution hub for sensorimotor information.

The study of vegetation community and structural change has been central to ecology for over a century, yet how disturbances reshape the physical structure of forest canopies remains relatively unknown. Moderate severity disturbance including fire, ice storms, insect and pathogen outbreaks, affects different canopy strata and plant species, which may give rise to variable structural outcomes and ecological consequences. Terrestrial lidar (light detection and ranging) offers an unprecedented view of the interior arrangement and distribution of canopy elements, permitting the derivation of multidimensional measures of canopy structure that describe several canopy structural traits with known linkages to ecosystem functioning. We used lidar-derived canopy structural measured within a machine learning framework to detect and differentiate among various disturbance agents, including moderate severity fire, ice storm damage, age-related senescence, hemlock woolly adelgid, beech bark disease, and chronic acidification. We found that disturbance agents such as fire and ice storms primarily affected the amount and position of vegetation within canopies, while acidification, pathogen and insect infestation, and senescence altered canopy arrangement and complexity. Only two of the six disturbance agents significantly reduced leaf area, indicating that this commonly quantified canopy feature is insufficient to characterize many moderate severity disturbances. Rather, measures of canopy structure, including those that describe multidimensional change, are needed to characterize disturbance at moderate severities because structural changes from these events are spatially and quantitatively variable. Our findings suggest that standard disturbance detection methods, such as optical based remote sensing platforms, may currently be limited in their ability to detect, differentiate, and characterize disturbance. Further, we conclude that a more broadly inclusive definition of ecological disturbance that incorporates multiple aspects of canopy structure change will improve the modeling, detection, and prediction of functional implications of moderate severity disturbance.

Industrial pig farming is associated with negative technological pressure on the bodies of pigs. Leg weakness and lameness are the sources of significant economic loss in raising pigs. Therefore, it is important to identify predictors of limb condition. This work presents assessments of the state of limbs using indicators of growth and meat characteristics of pigs based on machine learning algorithms. We have evaluated and compared the accuracy of prediction for several ML classification algorithms (Random Forest, K-Nearest Neighbors, Artificial Neural Networks, C50Tree, Support Vector Machines, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) and have identified the Random Forest and K-Nearest Neighbors as the best performing algorithms for predicting pig leg weakness using a small set of simple measurements that can be taken at an early stage of animal development. Muscle Thickness, Back Fat amount, and Average Daily Gain serve as significant predictors of conformation of pig limbs. Our work demonstrates the utility and relative ease of using machine learning algorithms to assess the state of limbs in pigs based on growth rate and meat characteristics.

This paper presents a study of a field trial experiment at olive orchard irrigated by runoff harvesting system under a dry climate which was carried out on 5-year-old olive trees (Olea europaea. L, cv. Barnea) in the middle of Negev desert, starting right after the floods, onwards during the summer growing season. The beginning of the experiment occurred after 2 years with little rain and no run-off events. The olive trees were under severe drought stress when we first initiated controlled flooding in 2017. In the second research year (2018), a massive natural flood had occurred at the end of April. Results show that the water distribution within the soil was highly inhomogeneous even under flood conditions. Soil water loss rate, due to transpiration was mainly correlated with the total amount of soil water and not atmospheric conditions. The relative root water uptake from shallow soil layers (0.3-1.5m) gradually reduced along the season, while the relative water uptake from the deeper layers (1.5-4m) became more pronounced.

Increased connectivity between coastal lagoons and the sea is expected to entail a greater proportion of marine species in the former. Chetumal Bay, estuary of the Hondo river into the Caribbean, had a limited access to the sea until the opening of the Zaragoza Canal. We sought changes in the fish community from 1999-2001 (just after an expansion of the canal) to 2015-2018. The same fishing gear was used, in the same localities, during all seasons. Total fish abundance and mean local richness decreased, although total abundance increased in the polyhaline zone. Diversity was greater in the oligohaline zone in 1999-2001, but in the mesohaline zone in 2015-2018. Three guilds were absent in 2015-2018: medium-sized herbivores, large piscivores, and medium-sized planktivores. Abundance of small benthivores decreased by decade; medium-sized piscivores and small planktivores became more abundant in 2015-2018 in the polyhaline zone. These changes may be due to the opening of the channel, but illegal fishing outside the bay may explain the decrease in juveniles of large piscivores, and erosion in the innermost part may be destroying important habitats. Our findings can be a reference for similar situations, as coastal development and climate change interact and affect tropical estuaries.

As time progresses and technology improves, biological data sets are continuously increasing in size. New methods and new implementations of existing methods are needed to keep pace with this increase. In this paper, we present a high performance computing(HPC)-capable implementation of Iterative Random Forest (iRF). This new implementation enables the explainable-AI eQTL analysis of SNP sets with over a million SNPs. Using this implementation we also present a new method, iRF Leave One Out Prediction (iRF-LOOP), for the creation of Predictive Expression Networks on the order of 40,000 genes or more. We compare the new implementation of iRF with the previous R version and analyze its time to completion on two of the world's fastest supercomputers Summit and Titan. We also show iRF-LOOP's ability to capture biologically significant results when creating Predictive Expression Networks. This new implementation of iRF will enable the analysis of biological data sets at scales that were previously not possible.

Estrogen decline during menopause is associated with altered metabolism, weight gain and increased risk for cardiometabolic diseases. The gut microbiota also plays a role in the development of cardiometabolic dysfunction and is also subject to changes associated with age-related hormone changes. Phytoestrogens are plant-based estrogen mimics that have gained popularity as dietary supplements for treatment or prevention of menopause-related symptoms. These compounds have the potential to both modulate and to be metabolized by the gut microbiota. Hops (Humulus lupulus L.) contain potent phytoestrogen precursors, which rely on microbial biotransformation in the gut to estrogenic forms. We supplemented ovariectomized (OVX) or sham-operated (SHAM) C57BL/6 mice, with oral estradiol (E2), a flavonoid-rich extract from hops, or a placebo carrier oil to observe effects on adiposity, inflammation, and gut bacteria composition. Hops extract and E2 protected against increased visceral adiposity and liver triglyceride accumulation in OVX animals. Surprisingly, we found no evidence of OVX having a significant impact on the overall gut bacterial community structure. We did find differences in abundance of Akkermansia muciniphila, which was lower with HE treatment relative to the OVX E2 treatment and to placebo in the SHAM group.

A naked human eye can perceive objects down to a millimeter length. While lenses and microscopes have overcome this limit, the human mind still lacks perspective when navigating conventional scales (1), especially in the range that are less palpable to naked human eye (2,3). This problem is particularly acute in the context of science communication, where the conventional scale bar units facilitate little comprehension regarding the perception for factorial size differences (3). Here we aim to bridge the gap of scale factors and perspectives using a universal toolkit of objects, which can help comprehend the relative change in length dimensions up to 13 orders of magnitude difference. We further have demonstrated the use of such a universal object toolkit as a length perceptive scale by illustrating and narrating biological phenomena. The meter to picometer ‘length perceptive scale’ proposed here has the potential to cover majority of length scales present in the biological realm, and is analogous to the time compression methods widely used in explaining cosmos timeline (4). Our toolkit can also be calibrated according to the users need in their scientific communication and illustrations, which will aid the readers’ benefit in understanding the length scale perception of illustrated phenomenon.

Biological invasions have reached an unprecedented level and the number of introduced species is still increasing worldwide. Despite major advances in invasion science, the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions are still debated. Empirical studies show divergent impacts of non-native populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of non-native populations; this is hindering the emergence of a unified theory of biological invasions. We propose a synthesis that merges perspectives from population, community, and ecosystem levels. Along a timeline of ecosystem transformation driven by non-native species, from historical to human-modified ecosystems, we order invasion concepts and theories to clarify their chaining and relevance during each step of the invasion process. This temporal sorting of invasion concepts shows that each concept is relevant at a specific stage of the invasion. Concepts and empirical findings on non-native species may appear contradictory. However, we suggest that, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

Immobilization of enzymes is a good field of study to expand the life of enzyme in and lowering the cost of the chemical processes such as separation processes. Urease is an important enzyme with medical and industrial applications. The aim of the present study is to prepare an immobilized urease on a strong cation exchange resin (Amberlite IR120 -Na) and study of its activity and stability. We monitored the liberation of Na ions in the collected fractions and searching for protein in the fractions as an indicators of immobilization by ion exchange phenomenon. Sodium is measured using atomic absorption spectroscopy techniques, while protein tested by Bradford’s method. Immobilized urease activity was evaluated by salicylate-hypochlorite method. The results indicated a complete immobilization of urease enzyme on the resin surface with reserving 92% of the activity of free enzyme. The immobilized urease enzyme on resin showed good stability and it has a 62% of its activity after 154 days of storage at room temperature. It is concluded that a new immobilized urease enzyme system is prepared with good enzyme activity and stability.

Biological invasions have reached an unprecedented level and the number of introduced species is still increasing worldwide. Despite major advances in invasion science, the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions are still debated. Empirical studies show divergent impacts of non-native populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of non-native populations; this is hindering the emergence of a unified theory of biological invasions. We propose a synthesis that merges perspectives from population, community, and ecosystem levels. Along a timeline of ecosystem transformation driven by non-native species, from historical to human-modified ecosystems, we order invasion concepts and theories to clarify their chaining and relevance during each step of the invasion process. This temporal sorting of invasion concepts shows that each concept is relevant at a specific stage of the invasion. Concepts and empirical findings on non-native species may appear contradictory. However, we suggest that, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

Static standing postural stability has been measured by multiscale entropy (MSE), which is used to measure complexity. In this study, we used the average entropy (AE) to measure the static standing postural stability, as AE is a good measure of disorder. The center of pressure (COP) trajectories were collected from 11 subjects under four kinds of balance situation, from stable to unstable: bipedal with open eyes, bipedal with closed eyes, unipedal with open eyes, and unipedal with closed eyes. The AE, entropy of entropy (EoE), and MSE methods were used to analyze these COP data, and EoE was found to be a good measure of complexity. The AE of the 11 subjects sequentially increased by 100%as the balance situations progressed from stable to unstable, but the results of EoE and MSE did not follow this trend. Therefore, AE, rather than EoE or MSE, is a good measure of static standing postural stability. Furthermore, the comparison of EoE and AE plots exhibited an inverted U curve, which is another example of a complexity versus disorder inverted U curve.

Collagen type I production decreases with aging, leading to wrinkles and impaired skin function. Prostaglandin E2 (PGE2), a lipid-derived signaling molecule produced from arachidonic acid by cyclo-oxygenase, inhibits collagen production and induces matrix metallopeptidase 1 (MMP1) expression by fibroblasts in vitro. PGE2-induced collagen expression inhibition and MMP1 promotion are aging mechanisms. This study investigated the role of E-prostanoid 1 (EP1) in PGE2 signaling in normal human dermal fibroblasts (NHDFs). When EP1 expression was inhibited by EP1 small interfering RNA (siRNA), there were no significant changes in messenger RNA (mRNA) levels of collagen, type I, alpha 1 (COL1A1)/MMP1 between siRNA-transfected NHDFs and siRNA-transfected NHDFs with PGE2. This result showed that EP1 is a PGE2 receptor. Extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation after PGE2 treatment significantly increased by ~2.5 times. In addition, PGE2 treatment increased the intracellular Ca²⁺ concentration in NHDFs. These results indicated that PGE2 is directly associated with EP1 pathway–regulated ERK1/2 and inositol trisphosphate (IP₃) signaling in NHDFs.

Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. The most striking difference in phylogenetic signal reflected relative solvent accessibility; analyses of exposed sites (on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge-ctenophore clade. These differences in phylogenetic signal were not ameliorated when we repeated our analyses using the CAT model, a mixture model that is often used for analyses of protein datasets. In fact, the heterogeneous CAT model resulted in several rearrangements that are unlikely to represent evolutionary history. However, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acids both trees supported placement of ctenophores sister to all other animals. These results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.

High antioxidants level in food is gradually becoming popular because of the enhanced risk of oxidative stress in humans. Bread wheat is rich in vital antioxidants but its major bioactive compounds are not available for the human. This study was conducted with the aim to enhance the phytochemical constituents and antioxidative activity of wheat grains by fermenting it with the use of Bacillus subtilis KCTC 13241. The antioxidative potential was determined by DPPH (2,2-diphenyl-1-picryl- hydrazyl) and ABTS (3-ethyl-benzothiazo- line-6-sulfonic acid) radical scavenging assay as well by the concentration of amino acids, flavonoids, minerals, carbohydrates, and phenolic compounds. Different varieties showed different free radical scavenging potential on fermentation, which was significantly high with respect to their corresponding unfermented wheat varieties. The highest potential was found in a fermented wheat variety named Namhae and this combination can be used in the pharmaceutical and food industries.

EuAP2 genes are famous for their role in flower development. A legacy of the founding member of this subfamily of transcription factor, whose mutants lacked petals in Arabidopsis. However, studies of other euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.

Macro and micronutrients, essential for the maintenance of human metabolism, are daily assimilated through the diet. Wheat and other major cereals are a good source of nutrients, such as carbohydrates and proteins, but cannot supply enough amounts of essential micronutrients which includes provitamin A. As vitamin A deficiency (VAD) lead to several serious diseases spread worldwide, the biofortification of a major staple crop, such as wheat, represents an effective way to preserve human health in developing countries. In the present work, a key enzyme involved in the branch of carotenoids pathway producing β-carotene, lycopene epsilon cyclase, has been targeted by a TILLING approach in a “Block strategy” perspective. The null mutant genotype showed a strong reduction in the expression of lcyE gene and also interesting pleiotropic effects on an enzyme (β-ring hydroxylase) acting downstream in the pathway. Biochemical profiling of carotenoids in the wheat mutant lines showed an increase of roughly 75% in β-carotene in the grains of the complete mutant line vs. the control. In conclusions, here we describe the production and the characterization of a new wheat line biofortified in provitamin A obtained through a non-transgenic approach also shading new light on the molecular mechanism governing carotenoids biosynthesis in durum wheat.

Paenibacillus sp. tmac-D7 was isolated from coastline growing Trifolium macraei (double-head clover) root nodules from Bodega Bay, California. The draft genome is 5,567,337 bp with a G+C% of 52.4%, an N50 of 114,261 bp, and 5,282 predicted protein-coding genes. Paenibacillus, while found in many other environments, is frequently isolated from root nodules, with many acting as plant pathogen antagonists. Paenibacillus sp. tmac-D7 is the first genome of a non-rhizobial endophyte isolate from wild Trifolium macraei (double-head clover).

The maintenance of high quality standards for prolonging shelf life of fruit and maintaining sensory and nutritional quality is a priority the horticultural products. The aim of this work was to test the effectiveness of a single treatment of edible coating based on Aloe arborescens and a combined treatment of 1-Methylcycyclopropene and edible coating to prolong the shelf-life of "Settembrina" white flesh peach fruit. White flesh peach fruit were harvested at the commercial ripening stage and treated with edible coating (EC) or 1-MCP +EC and stored for 28 days at 1°C. After 7, 14, 21 and 28 days fruits were removed from cold storage, transferred at 20°C and then analyzed immediately (cold out) and after 6 days (shelf life) to evaluate the combined effect of cold storage and room temperature. Weight loss, physical, chemical and sensory parameters were measured. Fruit treated with EC and 1-MCP +EC kept their marketing values better than CTR after 14 days of storage and 6 days of simulated shelf life, in terms of flesh firmness, total soluble solids and titratable acidity as well as sensory parameters. After 21 days of storage, all treatments showed a deterioration of the quality parameters. The single and combined application of Aloe-based coating (with 1-MCP) slowed down the maturation processes of the fruit, limited the weight loss and preserved its organoleptic characteristics.

Here, we report the draft genome sequence of the type strain of Ideonella azotifigens DSMZ21438^T (formally 1a22^T = JCM15503^T). Ideonella azotifigens DSMZ21438T a novel betaproteobacterial non-symbiotic nitrogen-fixing grass rhizosphere dwelling microbe. The 891,561 paired-end shotgun reads were quality filtered and decontaminated with the ATLAS pipeline, then assembled with Unicycler. The genome size is 6,257,981 bp, an N50 size of 7,849 bp, with a G+C content of 66.71%, and with 5,882 predicted protein-coding genes. I. azotifigens DSMZ21438^T represents the first member of the genus isolated from rhizosphere soil, providing a framework for further study into non-alphaproteobacterial nitrogen fixation and synthetic biology applications.

Chronic myelogenous leukemia (CML) was the first malignancy for which clinical outcome was drastically improved by kinase inhibitor therapy. Kinase inhibitors targeting other well-known oncogenes have been introduced into clinical practice, but none have shown the same magnitude of clinical benefit as ABL1 inhibition in CML. We argue that early detection is an underappreciated, but critically important factor in success of ABL1 inhibitors in treatment of CML. We show that CML provides a window into how many types of cancer may look and behave at an early stage, prior to diagnosis and the development of additional genomic alterations. The remarkable clinical benefits of ABL1 inhibition is likely due to early detection of CML at a stage in which the tumor is driven by single oncogenic alteration which can be successfully controlled by the inhibitor. Thinking of CML as a prototype for effective systemic treatment based on early cancer detection may help to develop strategies for improving treatment for other types of cancer.

During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous insects represent model systems for the study of this evolutionary process. The host-plants on which these insects feed and often spend parts of their life cycle constitute ideal agents of divergent selection for these organisms. Adaptation to feeding on different host-plant species can potentially lead to ecological specialization of populations and subsequent speciation. This process is thought to have given birth to the astonishing diversity of phytophagous insects and is often put forward in macroevolutionary scenarios of insect diversification. Consequently, numerous phylogenetic studies on phytophagous insects have aimed at testing whether speciation driven by host-plant adaptation is the main pathway for the diversification of the groups under investigation. The increasing availability of comprehensive and well-resolved phylogenies and the recent developments in phylogenetic comparative methods are offering an unprecedented opportunity to test hypotheses on insect diversification at a macroevolutionary scale, in a robust phylogenetic framework. Our purpose here is to review the contribution of phylogenetic analyses to investigate the importance of plant-mediated speciation in the diversification of phytophagous insects and to present suggestions for future developments in this field.

Red djulis (Chenopodium formosanum) is a native cereal plant in Taiwan; it contains abundant polyphenols, betalian and dietary fiber. The appearance of red djulis is bright red. Therefore, it is also called the “ruby of cereals”. The antioxidative activity of red djulis extract is well-understood. However, the antiaging function still remains unclear. This study examined the potential of red djulis extract for enhancing collagen secretion and preventing cutaneous aging using red djulis extracts. The red djulis extracts are comprised of an abundant active component that can effectively enhance the ability of collagen secretion of dermal fibroblasts, prevent the glycation of collagen and resist the damage of ultraviolet light exposure. After fibroblast treatment with red djulis extracts, TGM1, KRT1, KRT10 and SOD2 genes were up-regulated significantly by 2.3, 4.3, 4.4 and 27.3 times, respectively, compared to those of the control group. Additionally, it can increase COL1A2 gene expression by 43% and decrease MMP9 gene expression 33%. Therefore, it was demonstrated that red djulis extracts affect gene expressions related to the skin barrier, antioxidation and collagen. Moreover, we found positive effects on skin barrier integrity, endogenous antioxidant activity and skin collagen-preservation. The preparation of the red djulis extracts is environmental friendly and can promote the economic value of Chenopodium formosanum; thus, the proposed extract is suitable for applications in the development of food products, especially beverages, skin care and cosmetic products.

Using the Yellow-River-Source National Park (YRSNP) as a study site, an unmanned aerial vehicle (UAV) remote sensing and line transect method was used to investigate the number of wild herbivorous animals and livestock, including the kiang (Equus kiang) and Tibetan gazelle (Procapra picticaudata). A downscaling algorithm was used to generate the forage yield data in YRSNP based on 30 m spatial resolution. On this basis, we estimated the forage–livestock balance, which included both wild animals and livestock, and analyzed the effects of functional zone planning in national parks on the forage–livestock balance in YRSNP. The results showed that the estimates of large herbivore population numbers in YRSNP based on population density in the aerial sample strips, which were compared and validated with statistical data and warm season survey results, indicated that the number of kiangs and Tibetan gazelles in the 2017 cold season was 12900 and 12100, respectively. The number of domestic yaks, Tibetan sheep, and horses was 53400, 76800, and 800, respectively, and the total number of sheep units was 353200. The ratio of the number of large wild herbivores and livestock sheep units was 1:5; Large wild herbivores have different preferences for functional zones, preferring ecological restoration areas consisting mainly of degraded grassland; The grazing pressure indices of the core reserve areas and ecological restoration areas were 0.168 and 0.276, respectively, indicating that these two regions still have high grazing potential. However, the grazing pressure index of the traditional utilization areas was 1.754, indicating that these grasslands are severely overloaded; After the planning and implementation of functional zones, the grazing pressure index of YRSNP was 1.967. Under this measure, the number of livestock was not reduced and the grazing pressure nearly doubled, indicating that forage–livestock conflict has become more severe.

Fire-tolerant eucalypt forests of south eastern Australia are assumed to fully recover from even the most intense fires but surprisingly very few studies have quantitatively assessed that recovery. Accurate assessment of horizontal and vertical attributes of tree crowns after fire is essential to understand the fire’s legacy effects on tree growth and on forest structure. In this study, we quantitatively assessed individual tree crowns 8.5 years after a 2009 wildfire that burnt extensive areas of eucalypt forest in temperate Australia. We used airborne lidar data validated with field measurements to estimate multiple metrics that quantified the cover, density, and vertical distribution of individual-tree crowns in 51 plots of 0.05 ha in fire-tolerant eucalypt forest across four wildfire severity types (unburnt, low, moderate, high). Significant differences in the field-assessed mean height of fire scarring as a proportion of tree height, and in the proportions of trees with epicormic (stem) resprouts were consistent with the gradation in fire severity. Linear mixed-effects models indicated persistent effects of both moderate- and high-severity wildfire on tree crown architecture. Trees at high-severity sites had significantly less crown projection area and live crown width as a proportion of total crown width than those at unburnt and low-severity sites. Significant differences in lidar-based metrics (crown cover, evenness, leaf area density profiles) indicated that tree crowns at moderate- and high-severity sites were comparatively narrow and more evenly distributed down the tree stem. These conical-shaped crowns contrasted sharply with the rounded crowns of trees at unburnt and low-severity sites, and likely influenced both tree productivity and the accuracy of biomass allometric equations for nearly a decade after the fire. Our data provide a clear example of the utility of airborne lidar data for quantifying the impacts of disturbances at the scale of individual trees. Quantified effects of contrasting fire severities on the structure of resprouter tree crowns provide a strong basis for interpreting post-fire patterns in forest canopies and vegetation profiles in lidar and other remotely-sensed data at larger scales.

Optimizing the nitrogen (N) timings and rate can improve nutrient uptake, and nutrient-efficiencies, especially of N in wheat under the changing climate scenario. Climatic stress in the form of high temperature and drought resulted in the decreased crop physiology and, ultimately, grain yield. Taking the example of rainfed wheat, we quantified the impact of N application rates as full and split-dose at three variable sites of rainfed Pothwar, Pakistan by conducting field experiments for two years (2013-14 and 201-15). Treatments include, T1 = Control (No fertilizer applied), full dose of N applied at the time of crop sowing, i.e. T2 = 50 kg N ha^-1, T3 = 100 kg N ha^-1 and T4 = 150 kg N ha^-1 and split application of N at different timings during different stages of the crop called as split application of N, i.e. T5: Application of 50 kg N ha^-1 (15 kg N ha^-1 (Sowing) : 20 kg N ha^-1 (Tillering) :15 kg N ha^-1 (Anthesis), T6: Application of 100 kg N ha^-1 (30 kg N ha^-1 (Sowing): 40 kg N ha^-1 (Tillering) : 30 kg N ha^-1 (Anthesis) and T7: Application of 150 kg N ha^-1(45 kg N ha^-1 (Sowing) : 60 kg N ha^-1 (Tillering) : 45 kg N ha^-1 (Anthesis). Three study sites include viz. Islamabad (High rainfall with optimum temperature), University Research Farm (URF)-Koont (Medium rainfall with moderate temperature), and Talagang (low rainfall with high temperature). Results showed that the highest stomatal conductance (0.80 mole m^-2 sec^-1), net photosynthetic rate (20.07 μmole m^-2s^-1), transpiration rate (9.58 mmole m^-2s^-1), intercellular CO2 concentration (329.25 μmole CO₂ mol^-1 air), SPAD values (58.86 %) and proline contents (35.42 μg g^-1) were obtained for split application of N (T6 = Split N100) compared to control and full dose of N treatments. Among sites, these physiological traits remained highest at Islamabad and lowest at Talagang, while among years, maximum values of the measured parameters were obtained in 2013-14. A similar trend was observed for crop total N, N efficiencies, and agronomic traits of the crop. Our results suggest that optimum N application rate and its suitable timings can help to harvest real benefits of N as in our findings, split dose resulted in the maximum performance of the crop from physiological parameters to the agronomic traits of the rainfed wheat crop.

The pollen content of honey samples collected in the years 2017 and 2019 from experimental apiaries of Melipona seminigra pernigra Moure & Kerr 1950 installed in campo rupestre on canga (CRC) vegetation of the Serra dos Carajás, southeastern Amazonia, was analyzed to understand the local variability of floral resources occurring on natural and disturbed areas. Around one hundred pollen types were identified mainly belonging to Fabaceae, Myrtaceae and Euphorbiaceae (31, 6 and 5 types, respectively). The N5 mine presented the highest pollen richness with 95 pollen types identified, almost twice of those identified in the other areas, including the better preserved ones. Eighty percent of the pollen types are rare with concentrations ≤ 2,000 pollen grains/10 g; the remaining types are the most abundant and frequent, and are considered the primary bee sources (PBS). PBS correspond mostly to native plants such as Tapirira guianensis Aubl., Protium spp., Aparisthmium cordatum (A.Juss.) Baill., Mimosa acutistipula var. ferrea Barneby, Periandra mediterrânea (Vell.) Taub., Miconia spp., Pleroma carajasense K.Rocha, Myrcia splendens (Sw.) DC., Serjania spp. and Solanum crinitum Lam. All pollen types were identified during both seasons, but higher pollen concentration are related to the dry period (June-September). The statistical analysis indicated that there was no significant difference in honey pollen data between the natural and disturbed areas since the plant species considered as PBS in this work are intensively used in revegetation of degraded area (RDA) processes by mining activities.

1. Darwin’s naturalization hypothesis predicts that alien species closely related to native species are less likely to naturalize because of strong competition due to niche overlap. Closely related species are likely to attract similar herbivores and to release similar plant volatiles following herbivore attack, thus could attract the same predators. However, the importance of phylogenetic relatedness on the interaction between alien and native plants has never been tested in a multitrophic context. 2. In a mesocosm experiment we grew six alien target plant species alone and in competition with nine native plant species of varying phylogenetic relatedness. To test the effects of multitrophic interactions on the performance of alien target species, we used enclosure cages to expose plants to the presence and absence of herbivorous arthropods, predatory arthropods and nematodes. 3. Surprisingly, biomass and number of flowering structures increased with presence of competitors for some of the alien species, but overall there was no consistent competition effect. Similarly, we found that none of the multitrophic-interaction treatments affected survival, biomass or number of flowering structures of the alien species. 4. We conclude there was no significant relationship between performance measures of the alien species and their phylogenetic relatedness to the native competitors.

Blackberry is a fruit that has high nutritional value, a factor that has expanded its consumption worldwide. However, due to the fragility of the fruits and the high incidence of postharvest diseases, the fruits have a short shelf life. Thus, the objective of this study was to evaluate whether the application of coatings based on microfibrillated cellulose (NC) and lemongrass essential oil (EO) nanoparticles can prolong the shelf life of blackberry fruits after harvest. EO-coated blackberry fruits at nanocellulose concentrations were analyzed as follows: 0; 0.2; 0.4; 0.6 and 0.8%, in addition to the control treatment of which neither essential oil nor nanocellulose was used, for each treatment five repetitions were used. The fruits were analyzed soon after the application of the cover and at three and six days after storage. Fruit quality was assessed by soluble solids (SS), titratable acidity (TA), pH, fresh weight loss (FWL) and colorimetric parameters such as luminosity, hue angle and fruit peel chroma. Coating on EO (1000 ppm) blackberries combined with NC at concentrations of 0.2, 0.4 and 0.6% is promising in preserving blackberry fruits and reducing the process color reversal, up to six days of storage. The 0.4% NC + 1000 ppm EO conjugated coating showed no SS changes in blackberry fruits during the six days of storage.

This study was designed to investigate the effect of heat stress on body weight, physiological parameters, milk yield, and metabolome of milk and plasma in dairy cows by using Hydrogen-1Nuclear Magnetic Resonance Spectrometry (1HNMR)-based metabolomics approach. Ten Holstein cows in heat stress period (28 d) and another ten Holstein cows in thermo-neutral period (28 d) were maintained at the same feeding and management regime. Cows under both treatments were similar in parity, body weight, and days in milk at the beginning of each period. Bodyweight of each cow was recorded at the beginning and end of each period. Milk production, rectal temperature, and respiration rate were recorded weekly under each treatment while Blood samples and milk samples for 1HNMR analyses were collected at the end of each period. Cows in heat stress period had greater respiration rates (p<0.01), greater rectal temperatures (p< 0.01), lower milk yield (p< 0.01) and lower milk protein percentage (p=0.02) than cows in thermo-neutral period. Cows in heat stress period exhibited the greater milk concentrations of N-acetyl glycoprotein (NAG), choline, scylloinositol, pyridoxamine and lower milk concentrations of O-acetyl glycoprotein (OAG), citrate, glycerophosphocholine (GPC) and methyl phosphate than those in thermo-neutral period. Besides, cows in heat stress period showed greater plasma concentrations of alanine, glutamate, glucose, urea, histidine, 1-methylhistidine (1-MH) and formate. However, the plasma concentration of very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL), lipid, leucine, and 3-hydroxybutyrate (3-HB) were lower as compared to cows in the thermo-neutral period. In conclusion, heat stress affects the metabolites in milk and plasma in dairy cows. It is reflected by the alteration of 8 metabolites in milk and 12 metabolites in blood plasma. Which are mainly involved in gluconeogenesis, proteolysis, and milk fatty acid synthesis. Because of their capability to hit multiple targets, these metabolites could be selected as the potential biomarkers for dairy cows undergoing heat shock. The biological significances of the metabolite changes in the milk and plasma were also analyzed.

Optimizing the nitrogen (N) timings and rate can improve nutrient uptake, and nutrient-efficiencies, especially of N in wheat under the changing climate scenario. Climatic stress in the form of high temperature and drought resulted in the decreased crop physiology and, ultimately, grain yield. Taking the example of rainfed wheat, we quantified the impact of N application rates as full and split-dose at three variable sites of rainfed Pothwar, Pakistan by conducting field experiments for two years (2013-14 and 201-15). Treatments include, T₁ = Control (No fertilizer applied), full dose of N applied at the time of crop sowing, i.e. T₂ = 50 kg N ha^-1, T₃ = 100 kg N ha^-1 and T₄ = 150 kg N ha^-1 and split application of N at different timings during different stages of the crop called as split application of N, i.e. T₅: Application of 50 kg N ha^-1 (15 kg N ha^-1 (Sowing) : 20 kg N ha^-1 (Tillering) :15 kg N ha^-1 (Anthesis), T₆: Application of 100 kg N ha^-1 (30 kg N ha^-1 (Sowing): 40 kg N ha^-1 (Tillering) : 30 kg N ha^-1 (Anthesis) and T₇: Application of 150 kg N ha^-1(45 kg N ha^-1 (Sowing) : 60 kg N ha^-1 (Tillering) : 45 kg N ha^-1 (Anthesis). Three study sites include viz. Islamabad (High rainfall with optimum temperature), University Research Farm (URF)-Koont (Medium rainfall with moderate temperature), and Talagang (low rainfall with high temperature). Results showed that the highest stomatal conductance (0.80 mole m^-2 sec^-1), net photosynthetic rate (20.07 μmole m^-2s^-1), transpiration rate (9.58 mmole m^-2s^-1), intercellular CO₂ concentration (329.25 μmole CO₂ mol^-1 air), SPAD values (58.86 %) and proline contents (35.42 μg g^-1) were obtained for split application of N (T₆ = Split N₁₀₀) compared to control and full dose of N treatments. Among sites, these physiological traits remained highest at Islamabad and lowest at Talagang, while among years, maximum values of the measured parameters were obtained in 2013-14. A similar trend was observed for crop total N, N efficiencies, and agronomic traits of the crop. Our results suggest that optimum N application rate and its suitable timings can help to harvest real benefits of N as in our findings, split dose resulted in the maximum performance of the crop from physiological parameters to the agronomic traits of the rainfed wheat crop.

Microorganisms drive the biogeochemical cycles that link abiotic and biotic processes in the aqueous environment and are intricately associated with plastic debris. The detection of microplastics in water and sediment introduces new concerns as small particle size allows for yet unconsidered pathways for plastics in the food web and element cycles. In this review, we present current knowledge of microbe-plastic interactions and summarize the potential impact of biogeochemical processes on plastic distribution, cycling, transport, and sedimentation. We explore how microbe-plastic interactions influence the exposure of consumers to plastics and plastic degradation products. Key methods used to elucidate biofilm development, microbial biodegradation, and plastic detection in the aqueous environment are discussed. Finally, we comment on potential future questions and research directions needed to further define the role of microorganisms in the environmental fate of microplastics.

Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that would take into account the particular biological and biophysical properties of MSF complexes. Here we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes, and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.

Many studies were done in the development of drought stress-tolerant transgenic plants, including crop plants. Rice is considered to be a vital crop target for improving drought stress tolerance. Much transgenic rice showed improved drought stress tolerance was reported to date. They are genetically engineered plants that are developed by using genes that encode proteins involved in drought stress regulatory networks. These proteins include protein kinases, transcription factors, enzymes related to osmoprotectant or plant hormone synthesis, receptor-like kinase. Of the drought stress-tolerant transgenic rice plants described in this review, most of them display retarded plant growth. In crop crops, plant health is a fundamental agronomic trait that can directly affect yield. By understanding the regulatory mechanisms of retarded plant growth under drought stress, conditions are necessary precursors to developing genetically modified plants that result in high yields.

Growing acreage and changing consumer preferences cause increasing interest in the cereal products originating from organic farming. Lack of results of objective test, however, does not allow drawing conclusions about the effects of cultivation in the organic system and comparison to currently preferred conventional system. Field experiment was conducted in organic and conventional fields. Thirty modern cultivars of winter wheat were sown. They were characterized for disease infection including Fusarium head blight, seed sowing value, the amount of DNA of the six species of Fusarium fungi as well as concentration of ergosterol and trichothecenes in grain. The intensity Fusarium head blight was at a similar level in both systems. However, Fusarium colonization of kernels expressed as ergosterol level or DNA concentration was higher for the organic system. It did not reflect in an increased accumulation of trichothecenes in grain, which was similar in both systems, but sowing value of organically produced seeds was lower. Significant differences between analyzed cropping systems and experimental variants were found. The selection of the individual cultivars for organic growing in terms of resistance to diseases and contamination of grain with Fusarium toxins was possible. Effects of organic growing differ significantly from the conventional and grain obtained such way can be recommended to consumers. There are indications for use of particular cultivars bred for conventional agriculture in the case of organic farming, and the growing organic decreases plant stress resulting from intense fertilization and chemical plant protection.

Growing resistance is reported to carbamate insecticides in malaria vectors in Cameroon. However, the contribution of acetylcholinesterase (Ace-1) to this resistance remains uncharacterised. Here, we established that the G119S mutation is driving resistance to carbamates in Anopheles gambiae populations from Cameroon. Insecticide bioassay on field collected mosquitoes from Bankeng, a locality in southern Cameroon, showed high resistance to the carbamates bendiocarb (64.8 ± 3.5 % mortality) and propoxur (55.71 ± 2.9 %) but a full susceptibility to the organophosphate fenithrothion. The TaqMan genotyping of the G119S mutation in field-collected adults revealed the presence of this resistance allele (39%). A significant correlation was observed between the Ace-1^R and carbamate resistance at allelic [(bendiocarb; OR = 75.9; P<0.0001) and (propoxur; OR= 1514; P<0.0001)] and genotypic [RR vs SS (bendiocarb; OR = 120.8; P<0.0001) and (propoxur; OR= 3277; P<0.0001) levels. Furthermore, the presence of the mutation was confirmed by sequencing an Ace-1 portion flanking codon 119. The cloning of this fragment revealed a likely duplication of Ace-1 in Cameroon as mosquitoes exhibited at least three distinct haplotypes. Phylogenetic analyses showed that the predominant Ace-1^R allele is identical to that from West Africa suggesting a recent introduction of this allele in Central Africa from the West. The spread of this Ace-1^R represents a serious challenge to future implementation of IRS-based interventions using carbamates or organophosphates in Cameroon

Alpine forest gaps can distribute snowfall, solar radiation and rainfall, thus inducing a heterogeneous hydrothermal microenvironment between the inside and outside areas of forest gaps. Additionally, the characteristics of the heterogeneous microenvironment could vary greatly across the gap location properties during winter and the growing season. To determine the response of total phenol loss (TPL) from the litter to alpine forest gap disturbance during decomposition, we conducted a field litterbag experiment within a representative fir (Abies faxoniana Rehd.) forest based on the gap location properties. The TPL and abundances of fungi and bacteria from two typical shrub species (willow, Salix paraplesia Schneid., and bamboo, Fargesia nitida (Mitford) Keng f.) were measured during the following periods over two years: snow formation (SF), snow cover (SC) snow melting (ST), the early growing season (EG) and the later growing season (LG). At the end of the study, we found that the snow cover depth, frequencies of the freeze-thaw cycle and the fungal copy g-1 to bacterial copy g-1 ratio had significant effects on the litter TPL. The abundances of fungi and bacteria decreased from the gap center to the closed canopy during the two SF, SC, ST and LG periods and reversed during the two EG periods. The TPL closely followed the same trend as the microbial abundance during the first year of incubation. In addition, both species had larger TPLs in the gap center during the first winter, first year and entire two years. These findings suggest that alpine forest gap formation accelerates litter TPL and plays a dual role during specific critical periods by distributing abiotic and biotic factors directly and indirectly. In conclusion, reduced snow cover depth and duration during winter warming under current climate change scenarios or as gaps vanish may slow litter TPL in alpine biomes.

Phylogenies depict shared evolutionary patterns and structures on a tree topology, enabling the identification of hierarchical and historical relationships. Recent analyses indicate that phylogenetic signals extend beyond the primary structure of protein or DNA, and various aspects of codon usage biases are phylogenetically conserved. Several functional biases exist within genes, including the number of codons that are used, the position of the codons, and the overall nucleotide composition of the genome. Codon usage biases can significantly affect transcription and translational efficiencies, leading to differential gene expression. Although systematic codon usage biases originate from the overall GC content of a species, ramp sequences, codon aversion, codon pairing, and tRNA competition also significantly affect gene expression and are phylogenetically conserved. We review recent advances in analyzing codon usage biases and their implications in phylogenomics. We first outline common phylogenomic techniques. Next, we identify several codon usage biases and their effects on secondary structure, gene expression, and implications in phylogenetics. Finally, we suggest how codon usage biases can be included in phylogenomics. By incorporating various codon usage biases in common phylogenomic algorithms, we propose that we can significantly improve tree inference. Since codon usage biases have significant biological implications, they should be considered in conjunction with other phylogenetic algorithms.

Conventional fluorescent lamps used in tissue culture are costly light sources showing excessive wavelength emission-bandwidth that must be replaced by alternative, less costly and much lower power-consuming energy sources. The use of Light-Emitting Diodes (LEDs) is the best option due to their potential role as elicitors of secondary metabolite production in many plant models. Gynura procumbens(G. procumbens) is widely used for treating various diseases. Here, leaf explants were cultivated in MS medium supplemented with 0.5 mg/L of NAA and 2.0 mg/L of BAP for 30 days under white, blue, and red LEDs. Secondary metabolites were analyzed by HPLC and LC-MS. Blue LEDs elicited the highest antioxidant activity, total flavonoid, and phenolic content. Furthermore, the content of cyanidin-monoglucosides increased significantly increased under blue light.

Plants have evolved tightly regulated strategies to adapt and acclimate to a changing environment to ensure their survival. Various environmental factors affect plant distribution, growth and yield. Low temperature belongs to those abiotic factors which significantly constrain range boundaries of plant species. Exposing plants to low but non-freezing temperature induces a multigenic processes termed cold acclimation, which finally results in an increased freezing tolerance. Cold acclimation comprises reprogramming of the transcriptome, proteome and metabolome and affects communication and signaling between subcellular organelles. Reprogramming of the central carbohydrate metabolism plays a key role in cold acclimation. This review summarizes current knowledge about the role of carbohydrate metabolism in plant cold acclimation. A focus is laid on subcellular metabolic reprogramming, its thermodynamic constraints under low temperature and mathematical modelling of metabolism.

Lily–belong to the genus Lilium is one of the top cut flowers worldwide. Production and propagation of bulblets in vitro is an important approach for high-volume production, but not proved satisfactory. Hence, the aim of this study was to describe and compare the performances of morphological characteristics of the lily bulb in vivo produced by in vitro and conventional culture method and compare the production timelines in vitro vs conventional culture method. In results, it seems clear that in vitro re-culture of lily bulblet was able to be sustained and maintained its growth and so, ontogenic development after their performance in soil. Our results demonstrate that in the conventional pathway, the course of bulblet growth to bulb and ontogenic development took 3–4 growing seasons to reach the adult flowering phase. On the other hand, along with the re-culture in vitro, the course of bulb growth and ontogenic development took 1–2 growing seasons to reach the adult flowering phase because of the increasing initial bulb size and advancement of ontogenic development. Other than bulblet production through bulb scale explant, this study represents the first report on the method of in vitro bulb production of lily through re-culture by in vitro pathway with a comparison of the timelines and ontogenic development obtained from in vitro versus conventional pathway.

Proper bipolar spindle assembly underlies accurate chromosome segregation. A cohort of microtubule-associated proteins orchestrates spindle microtubule formation in a spatiotemporally coordinated manner. Among them, the conserved XMAP215/TOG family of microtubule polymerase plays a central role in spindle assembly. In fission yeast, two XMAP215/TOG members, Alp14 and Dis1, share essential roles in cell viability; however how these two proteins functionally collaborate remains undetermined. Here we show the functional interplay and specification of Alp14 and Dis1. Creation of new mutant alleles of alp14, which display temperature sensitivity in the absence of Dis1, enabled us to conduct detailed analyses of a double mutant. We have found that simultaneous inactivation of Alp14 and Dis1 results in early mitotic arrest with very short, fragile spindles. Intriguingly, these cells often undergo spindle collapse, leading to a lethal “cut” phenotype. By implementing an artificial targetting system, we have shown that Alp14 and Dis1 are not functionally exchangeable and as such are not merely redundant paralogues. Intriguingly, while Alp14 promotes microtubule nucleation, Dis1 does not. Our results uncover that the intrinsic specification, not the spatial regulation, between Alp14 and Dis1 underlies the collaborative actions of these two XMAP215/TOG members in mitotic progression, spindle integrity and genome stability.

Strigolactones (SLs) are a novel emerging plant hormones, which play important roles in regulating plant organ development and environmental stress tolerance. Even though the SL related genes have been identified and well characterized in some plants. The information of SL related genes in soybean is not fully established yet, especially in response to salt stress. In this study, we identified nine SL biosynthesis genes: two D27, two CCD7, two CCD8, and three MAX1, and seven SL signaling genes: two D14, two MAX2 and three D53 in soybean genome. We found that SL biosynthesis and signaling genes are conserved during evolution in different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as existence of ten pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthesis and signaling genes. By using quantitative real-time PCR (qRT-PCR), we confirmed that SL genes have different tissue expression in roots, stems and leaves. Further, we also explored the expression profiles of SL biosynthesis and signaling genes under salt stress. These results suggested that SL signaling genes may play important regulatory roles in response to salt stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthesis and signaling genes, and established a foundation for further functional analysis of soybean SL related genes in response to salt stress.

Transcriptome study of the desired crossbreed and comparing it with pure parental population is one of the methods for evaluating and selecting cross with appropriate productivity, and yet disease resistant, high tolerance to environmental stresses and adapted to the climate of the breeding tract. In this study, RNA-seq technology was employed to detect differential expression of genes in purebred Sistani and Sistani × Montbeliard crossbreed. Blood samples were collected from four cows (two pure and two its crossbreed). Total RNA was extracted in Media Teb Gene Laboratory of Iran. After the treatment of mRNA, cDNA was synthesized. Quality control was performed with FastQC. Following the assembling of the transcripts with bovine reference genome, Cuffdiff was used to detect differentially gene expression in purebred and its crossbred. In total, 45 significantly differentially expressed genes were detected (false discovery rate q < 0.05) between purebred Sistani and Sistani × Montbeliard crossbreed. Gene Ontology enrichment and pathway analysis revealed that these differentially expressed genes were highly enriched in Inflammation mediated by chemokine and cytokine signaling pathways. These genes are reported to have role in immune response, calving, fertility, resistance to mastitis and also may have a role in different levels of heat tolerance and disease resistance. Therefore, Sistani × Montbeliard crossbred could be suitable for the climatic conditions of the Sistan region in Iran.

Ixodes scapularis is the major vector of Lyme disease in the eastern United States. This species undergoes a life cycle consisting of eggs and three active stages: larva, nymph, and adult. Each active life stage takes a blood meal either for developing and molting to the next stage (larvae and nymphs) or for oviposition (adult females). This protein rich blood meal is the only food taken by Ixodes ticks. Most studies on blood digestion in ticks have shown that the initial stages of blood digestion are carried out by cathepsin proteases within endosomes of acidic digestive cells. However, in other hematophagous arthropods, the serine protease trypsin plays an important role in early protein degradation. In this study, we determined transcript expression of I. scapularis cathepsins and serine proteases, some with previously characterized roles in blood digestion. Gut pH was also determined and a trypsin-benzoyl-D, L-arginine 4-nitoanilide assay was used to measure active trypsin levels during blood digestion. Our data suggest that trypsin levels increase significantly after blood feeding and peaked in larvae, nymphs, and adults at 3, 1, and 1 days post host detachment, respectively. In addition, alkaline gut pH (8.0) conditions after I. scapularis blood feeding were similar to those required for trypsin activity in other arthropods suggesting these enzymes have an important and previously overlooked role in I. scapularis blood digestion.