Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S

Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.

Ionophore-stimulation promotes re-organization of the invasion machinery of Toxoplasma gondii

Host cell invasion by intracellular, eukaryotic parasites, like the many important species within the phylum Apicomplexa, is a remarkable and active process involving the coordinated action of many apical organelles and other structures. To date, capturing how these various structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to generate images of the apical complex of Toxoplasma gondii tachyzoites under conditions that mimic resting parasites and those primed to invade through addition of a calcium ionophore. Using AI-based image-processing we were able to annotate 48 tomograms to identify and extract densities of the relevant subcellular organelles and accurately analyze features in 3D. We describe an interaction between an anteriorly located apical vesicle and a rhoptry tip that occurs only in the ionophore-stimulated parasites and that is associated with dramatic changes in the vesicle's shape in what appears to be a stalled fusion event. We also present information to support the presumption that this vesicle originates from the well-described vesicles that parallel the intraconoidal microtubules and that the latter two structures are linked by a novel tether. Lastly, we show that a previously described rosette is found associated with more than just the anterior-most apical vesicle, indicating that multiple such vesicles are primed to enable rhoptry secretion.

Highly Efficient Generation of Canker-Resistant Sweet Orange Enabled by an Improved CRISPR/Cas9 System

Sweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes, and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously [dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, citrus U6 (CsU6) to drive sgRNA expression], we further improved our CRISPR/Cas9 system by choosing superior promoters [Cestrum yellow leaf curling virus (CmYLCV) or Citrus sinensis ubiquitin (CsUbi) promoter] to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker-resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease-resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.

Prevalence of Microsporum canis from Pet Cats in Small Animal Hospitals, Chiang Mai, Thailand

Dermatophytosis is a disease caused by dermatophytes, a group of fungi that can cause disease both in humans and animals. The important genera that are pathogenic in animals include Trichophyton and Microsporum. Microsporum canis is an important species because it can cause zoonosis and is commonly found in domestic animals. Cats, which live very close to humans, may expose humans to this pathogen. This research focused on the epidemiology of M. canis found in cats. Hair samples were collected via the Mackenzie technique from cats with and without skin lesions, preliminarily examined with 10% KOH preparation, and cultured for fungal identification. Samples were confirmed with molecular techniques including polymerase chain reaction, gel electrophoresis, and sequencing. Samples were collected from 138 cats located in 93 households, 43 from cats with skin lesions (31.16%) and 95 from cats without skin lesions (68.84%). Eighteen cats with lesions (13.04%) and ten cats without lesions (7.2%) were found to carry M. canis. In eleven of the eighteen cats both with skin lesions and positive for M. canis (61.11%), the pathogen was found both at the site of the lesion and at other sites in the body. Because the pathogen can be found in the hair of cats with and without skin lesions, owners, keepers, veterinarians, and others who come into contact with these animals are at risk of infection if they are not aware or do not take precautions after contact with them.

Regeneration Status and Role of Traditional Ecological Knowledge for Cloud Forest Ecosystem Restoration in Ecuador

The importance of forests for biodiversity conservation has been well recognized by the global community; as a result, conservation efforts have increased over the past two decades. In Ecuador, the lack of integrated information for defining and assessing the status of local ecosystems is a major challenge for designing conservation and restoration plans. Thus, the objectives of this study were (1) to examine the regeneration status of cloud forest remnants, some of which had experienced past human disturbance events, (2) to explore a local rural community’s traditional ecological knowledge (TEK) relevant for restoration and (3) to investigate the integration between TEK and ecological science-based approaches. A survey of regeneration status was conducted in four remnants of cloud forests (n = 16) in Cosanga, Napo Province, in the Andes of northeastern Ecuador. The species of young trees (0.5–5 m height) were identified over 0.16 ha. In-depth interviews of individuals from local communities (n = 48) were conducted to identify socio-ecologically important native species. The results showed significant differences (p < 0.001) in species richness and the stem density of seedlings and saplings in gaps. The stem density of Chusquea sp., a bamboo species, explained 63% of the variation in species richness and 48% of the variation in the abundance of seedlings and saplings between plots. Informants cited 32 socio-ecologically important species, of which 26 species were cited as sources of food and habitats for wildlife. The ranking of species based on a relative importance index and a cultural value index—taking into account both the spread of knowledge among local informants and the multiplicity of uses—revealed that Hyeromina duquei, Citharexylum montanum, Eugenia crassimarginata and Sapium contortum were traditionally the most valuable species for both humans and wildlife. Informants also recommended 27 species for future planting, of which 19 species were amongst the rarest species in the regeneration survey. In conclusion, the results demonstrate a synergy between TEK and ecological science-based approaches (regeneration survey) to natural ecosystem research. Thus, traditional ecological knowledge can provide insights into ecosystem–plant–animal interaction, and to identify native species useful for both humans and wildlife for forest restoration projects to reconnect isolated cloud forest fragments.

Forensically Relevant Flesh Flies (Diptera, Sarcophagidae, Sarcophaginae) of Southern Brazil

Flesh flies comprise a large fly family distributed worldwide that has great importance for forensic entomology. A robust and updated checklist of Sarcophaginae flies recorded in Southern Brazil is presented, based on material collected in the Rio Grande do Sul state and on a literature review. The forensic importance (high, moderate, or none) of the recorded flesh flies for estimating the postmortem interval (PMI) or inferring cases of neglect was determined based on their ecological habits. A total of 2,831 specimens representing 38 taxa were collected from three studies. Oxysarcodexia was the most abundant and species-rich genus in all three studies. Dexosarcophaga carvalhoi (Lopes) was registered for the first time in Southern Brazil. The checklist for Southern Brazil comprises 91 species distributed in 19 genera, with Oxysarcodexia, Peckia, and Lepidodexia representing the richest genera. Considering the importance of species for PMI estimation, 10, 42, and 39 species were classified as having high, moderate, or no forensic relevance, respectively. Moreover, five myiasis-causing sarcophagine flies recorded in Southern Brazil were considered to have the potential to reveal cases of neglect or mistreatment. This study revealed that Microcerella halli (Engel) and Peckia (Euboettcheria) australis (Townsend) are the most important species for PMI estimation in Southern Brazil, as they are often found breeding in corpses in this region.

Effect of Industrial and Domestic Processing Techniques On the DNA Degradation of Anchovy

Food fraudulent activities have become a serious issue over the world recently. Seafood products have trading and profitable potential in Turkey owing to the abundance of fisheries and other species. While morphological features are commonly used for species identification in raw seafood products, this identification does not meet the correct classification in cryptic species and processed seafood products. Molecular techniques have been utilized for species authentication in processed seafood items successfully. In this study, the effect of different processing techniques on the DNA quality and DNA degradation isolated from raw and processed anchovy was investigated. Anchovy is one of the important species in both fisheries activities and processing and consumption in Turkey. For this aim, DNA was isolated from processed anchovy groups and un-processed anchovy groups as control by the same extraction methods and the quality of DNA was compared among the groups. The most common processing techniques, frying, baking, smoking, roasting, baking and grilling were applied to anchovy. The results revealed that not only different thermal processing but also treatment with acid and salt cause DNA degradation and quality loss of DNA parameters which are essential for authentication of species and traceability for public health.

BA and TDZ in the Morphogenesis in Vitro of Passiflora Setacea

Passiflora setacea DC (Passifloraceae) is considered an important species in the genetic breeding of passion fruit. However, its use is limited due to low seed germination. This paper aimed to study the effect of cytokinins 6-benzyladenine (BA) and thidiazuron (TDZ) on the in vitro morphogenesis of P. setacea using three explants: hypocotyl, nodal segment, and root segment. The explants were induced to morphogenesis in MS medium modified and with different concentrations of BA and TDZ. After 55 days, the percentage of calluses and shoots were evaluated, and anatomical characterization was performed. The three explants used in the in vitro morphogenesis of P. setacea showed callus and shoots formation, but in greater numbers in the nodal segments treated with BA. TDZ isolated affected equal to or less than BA on callus and shoots formation for the three explants. Direct and indirect organogenesis was observed in the three types of explants. From the results obtained for plant regeneration via in vitro morphogenesis of P. setacea, it is recommended to use a nodal segment in MSM medium and supplemented with 2.22 μmol L-1 of BA.

Temporal performance of the management effectiveness of a protected area in the Brazilian Atlantic Forest, São Paulo, Brazil

This work presents the monitoring of the effectiveness of the management of the Morro do Diabo State Park, Sao Paulo, Brazil, during fourteen years (2002-2016), divided into six-time cuts for which management effectiveness indices were obtained. This protected area (PA) of category II of the World Conservation Union is responsible for the conservation of important species of Brazilian biodiversity, especially the leonthopitecus chrysopygus, which until the 1980s was considered the most endangered primate of the planet and which this park has its largest free population in nature. The methodological procedure used was an adaptation of the one proposed by Cifuentes, Izurieta, and Faria (2000), commonly denominated EMAP, an acronym of the initials in Spanish. The results indicate that at the beginning of the analyzed period the AP had reasonable conditions for its management, although it presented difficulties related to planning and administration, problems solved from a joint organizational and local effort, prioritizing actions for results. The management quality standard gradually increased, with a greater perception of the scope of the area's management objectives, since in addition to the ecosystem services resulting from its existence, the PA started to offer real benefits to the community by improving and increasing public use and environmental education, for example. However, the effectiveness of management has decreased to previous levels, having as main factors endogenous aspects of the management system linked to indicators limited to management, with repercussions on other management components.

Design and Operation of “Siklob”, a Mechanised Falling Gear Operated in Northern Iloilo, Philippines

Fisheries in the Philippines is multispecies, and this is seen with the wide variety of fishing gears used in major and minor fishing grounds in the country. These gears constantly face modification and development to improve catch quality, quantity, and overall efficiency. This study investigated the features of “siklob”, a mechanised falling gear operated along the municipal waters of Northern Iloilo, Philippines. Some coastal residents claimed that fishers use fine mesh nets for this gear, and this was because of some incidences of the capture of very small fish. Results of this study, however, indicate that the mesh size of nettings used for “siklob” is 4.35 cm, which is above the minimum set by the national law (3 cm). The gear is operated offshore, in a fishing vessel, with lights and fish-finding devices. The catch included an array of pelagic to benthic species, with Sardinella gibbosa (Bleeker, 1849) as the top species. The catch per unit effort values for two fishing operations were 17.40 kg.cast-1 and 16.5 kg.cast-1, respectively. If a management plan for the gear is to be implemented in the area, it would be necessary first to study the spawning seasons of commercially important species and impose closed fishing seasons. Before any attempt to ban or control the use of the gear, it is necessary first to understand the gear design, performance, and selectivity.