Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security.

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

Short-term effects of thinning on the development and communities of understory vegetation of Chinese fir plantations in Southeastern China.

BACKGROUND: High-density conditions are global issues that threaten the sustainable management of plantations throughout the world. Monocultures and untimely management practices have identically resulted in the simplex of community structures, decreases in biodiversity, and long-term productivity losses in plantations China. The most popular measure which is commonly used to address these issues is thinning, which potentially results in increases in the development of understory plants in plantations. However, there is limited information currently available regarding the community composition of understory vegetation and the associated environmental factors, which has limited the sustainable management of China's fir plantation ecosystems. METHOD: In the present study, a thinning experiment was implemented which included a control check (CK: no thinning), as well as low intensity thinning (LIT: 20%), moderate intensity thinning (MIT: 33%), and high intensity thinning (HIT: 50%) in Chinese fir plantations located in the Southeastern China. During the investigation process, the understory vegetation examined three years after thinning measures were completed, in order to analyze the impacts of different thinning intensities on the growth and community composition of the understory plants. At the same time, the associated environmental factors in the fir plantations were also investigated. RESULTS: The species richness, total coverage, and biomass of the understory vegetation were observed to be apparently increased with increasing thinning intensity. In addition, it was found that the thinning measures had prominently influenced the soil nutrients. The community compositions of the understory vegetation were significantly different among the four thinning intensity levels, especially between the CK and the HIT. Furthermore, the development of the understory vegetation was found to be significantly correlated with the soil nutrient contents, and the community compositions of the understory vegetation were prominently driven by the tree densities, slope positions, and soil nutrient contents.

The relationships between water storage and biomass components in two conifer species.

BACKGROUND: Water storage is a significant physiological index of vegetation growth. However, information on water storage at the individual tree level and its relationship to climatic conditions and productivity is scarce. METHODS: We performed a comparative analysis of water storage using field measurements acquired three age classes of Chinese fir (Cunninghamia lanceolata) and Korean larch (Larix olgensis). The distributions of water storage, water content ratio and dry mass were presented, and regression analyses were used to confirm the relationships of water storage and water content ratio to dry mass components, respectively. RESULTS: Our results indicated that water was mostly concentrated in the stem xylem, which aligned well with the distribution of dry mass in both conifer species. However, the water storage of the stem xylem was always higher in Chinese fir than in Korean larch. The average water content ratio of both conifer species decreased with age, but that of Chinese fir was always higher than that of Korean larch. There was a significant difference in the water storage proportion in the components of Chinese fir (P < 0.001) and Korean larch (P < 0.001). The effects of age class on the water storage of Chinese fir (P = 0.72) and Korean larch (P = 0.077) were not significant. Interestingly, significant positive linear correlations were found between fine root water and leaf water and mass in Chinese fir (P < 0.001, R 2 ≥ 0.57) and Korean larch (P < 0.001, R 2 ≥ 0.74). The slopes showing that the linear relationship between tree size and water content ratio of stem xylem were always steeper than that of other components for the two conifers. CONCLUSION: Our study indicates the similar water related characteristics and their close relations to biomass accumulation and growth in both fast growing species at contrasting climates, illustrating the same coherent strategies of fast growing conifers in water utilization.

Image classification based on the linear unmixing and GEOBIA.

Geographic Object-Based Image Analysis and linear unmixing are common methods in image classification. The purpose of this study is to analyze the classification efficiency by integrating these two methods in the mountain area. This research selected Jiangle County, Fujian, as a study area. Two Landsat8 OLI images, which covered the county, were used. Linear spectral mixture model, multi-scale segmentation, and decision tree were applied in the classification. After image preprocessing, linear spectral mixture model was used to unmix the image into three fraction images-vegetation, shade, and soil. The principal component analysis and tasseled cap transformation were used to derived three principal components and the brightness, wetness, and greenness. Multi-scale segmentation is applied by eCognition. Under scale 40, the image was divided into vegetation and non-vegetation area, then under scale 20, the vegetation area was divided into different types by integrating the fraction with different methods. The accuracy assessment of the classification map was done using the forestry resource survey and the high-resolution image of Google Earth. This study indicated that the unmixed bands could improve the classification accuracy. The overall classification accuracy was 92.40% with a Kappa coefficient of 0.9032. Therefore, there is a conclusion that this approach is an efficient way to classify different plantation.

Status and Magnitude of Grey Wolf Conflict with Pastoral Communities in the Foothills of the Hindu Kush Region of Pakistan.

Pastoralist-wolf conflict over livestock depredation is the main factor affecting conservation of grey wolf worldwide. Very limited research has been carried out to evaluate the pattern and nature of livestock depredation by wolf. This study aims to determine the status and nature of human-wolf conflict across different villages in the Hind Kush region of Pakistan during the period January 2016-December 2016. For this purpose, a total of 110 local male respondents from all walks of life were interviewed using a semi-structured questionnaire. The grey wolf was declared as a common species in the area by 51.3% of the locals with an annual sighting rate of 0.46 each. During the year (2016), a total of 358 livestock were lost to grey wolf predation and disease. Of the total livestock loss, grey wolf was held responsible for a total 101 livestock losses. Goat and sheep were the most vulnerable prey species as they accounted for 80 (79.2%) of the total reported depredations. Out of the total economic loss (USD 46,736, USD 424.87/household), grey wolf was accountable for USD 11,910 (USD 108.27 per household), while disease contributed 34,826 (USD 316.6 per household). High depredation was observed during the summer season 58.42% (n = 59) followed by spring and autumn. Unattended livestock were more prone to grey wolf attack during free grazing in forests. Most of the respondents (75.45%) showed aggressive and negative attitudes towards grey wolf. The herders shared more negative attitude (z = -3.21, p = 0.001) than businessman towards the species. Herders having larger herd size displayed more deleterious behavior towards wolves than those having smaller herd size. Active herding techniques, vaccinating livestock, educating locals about wildlife importance, and initiating compensating schemes for affected families could be helpful to decrease negative perceptions.

Monitoring and predicting land use and land cover changes using remote sensing and GIS techniques-A case study of a hilly area, Jiangle, China.

Land use and land cover change research has been applied to landslides, erosion, land planning and global change. Based on the CA-Markov model, this study predicts the spatial patterns of land use in 2025 and 2036 based on the dynamic changes in land use patterns using remote sensing and geographic information system. CA-Markov integrates the advantages of cellular automata and Markov chain analysis to predict future land use trends based on studies of land use changes in the past. Based on Landsat 5 TM images from 1992 and 2003 and Landsat 8 OLI images from 2014, this study obtained a land use classification map for each year. Then, the genetic transition probability from 1992 to 2003 was obtained by IDRISI software. Based on the CA-Markov model, a predicted land use map for 2014 was obtained, and it was validated by the actual land use results of 2014 with a Kappa index of 0.8128. Finally, the land use patterns of 2025 and 2036 in Jiangle County were determined. This study can provide suggestions and a basis for urban development planning in Jiangle County.

Models for Predicting the Biomass of Cunninghamialanceolata Trees and Stands in Southeastern China.

Using existing equations to estimate the biomass of a single tree or a forest stand still involves large uncertainties. In this study, we developed individual-tree biomass models for Chinese Fir (Cunninghamia lanceolata.) stands in Fujian Province, southeast China, by using 74 previously established models that have been most commonly used to estimate tree biomass. We selected the best fit models and modified them. The results showed that the published model ln(B(Biomass)) = a + b * ln(D) + c * (ln(H))2 + d * (ln(H))3 + e * ln(WD) had the best fit for estimating the tree biomass of Chinese Fir stands. Furthermore, we observed that variables D(diameter at breast height), H (height), and WD(wood density)were significantly correlated with the total tree biomass estimation model. As a result, a natural logarithm structure gave the best estimates for the tree biomass structure. Finally, when a multi-step improvement on tree biomass model was performed, the tree biomass model with Tree volume(TV), WD and biomass wood density conversion factor (BECF),achieved the highest simulation accuracy, expressed as ln(TB) = -0.0703 + 0.9780 * ln(TV) + 0.0213 * ln(WD) + 1.0166 * ln(BECF). Therefore, when TV, WD and BECF were combined with tree biomass volume coefficient bi for Chinese Fir, the stand biomass (SB)model included both volume(SV) and coefficient bi variables of the stand as follows: bi = Exp(-0.0703+0.9780*ln(TV)+0.0213 * ln(WD)+1.0166*ln(BECF)). The stand biomass model is SB = SV/TV * bi.

Clinical and laboratory features of community-associated methicillin-resistant Staphylococcus aureus: is it really new?

OBJECTIVE: To review the epidemiologic and molecular characteristics of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in Detroit, Michigan, to assess the risk factors for infection and the response to therapy. DESIGN: Prospective clinical and laboratory study of 2003-2004 CA-MRSA isolates. Molecular features were compared with CA-MRSA isolates from 1980. SETTING: A 600-bed urban academic medical center. PATIENTS: Twenty-three patients with CA-MRSA infections from 2003-2004 were evaluated. In addition, laboratory analysis was performed on 13 CA-MRSA isolates from 1980. MAIN OUTCOME MEASURES: Laboratory analysis of isolates included antimicrobial susceptibility testing, pulsed-field genotyping, testing for Panton-Valentine leukocidin (PVL) genes, and staphylococcal cassette chromosome mec typing. RESULTS: Patients were predominantly young African American males and presented with skin and soft-tissue infections. All isolates were resistant to erythromycin and highly susceptible to other agents. Patients were generally treated successfully with combination incision and drainage and systemic antibiotics. Among the 23 isolates, 20 (87%) were the same strain. This strain carried the staphylococcal cassette chromosome mec type IV and PVL genes and is genetically identical to USA 300. Thirteen isolates of patients from our community who presented with CA-MRSA infections in 1980 represented a single clone that is unique compared with the 2003-2004 isolates. This strain carried staphylococcal cassette chromosome mec type IVA but did not carry the PVL genes. CONCLUSIONS: In our community, CA-MRSA is largely due to a single clone with a type IV mec gene and PVL gene. The type IV staphylococcal cassette chromosome mec type can be demonstrated in CA-MRSA isolates from a remote period, suggesting that earlier outbreaks were not related to healthcare exposure.

Persistence in Staphylococcus aureus bacteremia: incidence, characteristics of patients and outcome.

Staphylococcus aureus bacteremia often persists. The reasons for persistence and its outcome are poorly defined. We conducted a prospective-observational study among 245 consecutive S. aureus (MRSA: n=125; MSSA: n=120) bacteremias (>or=1 positive blood cultures (BC)) among 234 adults (18-103-y-old; median=59 y) hospitalized during 1 January 2002-31 December 2002 at a 600-bed teaching hospital. Measurements included bacteremia duration, complication-rate (metastatic infection, relapse or attributable mortality) and outcome. Bacteremia duration was measured based on follow-up BC among 193 patients and estimated based on symptoms resolution in the rest. Measured (1-59 d; median=2) and estimated (median=1 d) duration correlated (r=0.885) though positive follow-up BC was often detected without fever (57/105 patients, 54.3%). Persistence (defined as bacteremia for >or=3 d) was noted in 84 cases (38.4%). Complication-rate increased steadily with bacteremia duration (6.6%, 24.0% and 37.7% in bacteremia for 1-2, 3 and >or=4 d, respectively; p=0.05). Cox regression analysis revealed that bacteremia duration correlated positively with endovascular sources (p=0.006), vancomycin treatment (p=0.016), cardiovascular prosthesis (p=0.025), metastatic infections (p=0.025) and diabetes (p=0.038). It is concluded that persistent bacteremia is a feature of S. aureus infection, irrespective of oxacillin susceptibility, associated with worse outcome. Risk factors include endovascular sources, cardiovascular prosthesis, metastatic infections, vancomycin treatment and diabetes. Patients at risk may benefit from novel treatment strategies.

Time to positivity in Staphylococcus aureus bacteremia: possible correlation with the source and outcome of infection.

BACKGROUND: Staphylococcus aureus bacteremia often persists and causes metastatic infections. It is unknown whether the time between blood culture incubation and growth detection (i.e., the time to positivity) in a continuously monitored system--a probable surrogate marker of bacteremia severity--correlates with outcome. METHODS: We performed a prospective, observational study involving adult inpatients who had S. aureus bacteremia between 1 January 2002 and 30 June 2003 at a 600-bed teaching hospital. Measurements included time to positivity in initial blood culture series, duration of bacteremia, rate of metastatic infection, and outcome. RESULTS: A total of 376 S. aureus bacteremias (> or = 1 positive blood culture result) were reported for 357 patients aged 18-103 years (median age, 59 years); 64 bacteremias were excluded because blood was drawn after antibiotic therapy was started (n = 59) or through an intravascular catheter (n = 5). The source of infection was identified in 244 series (78.2%). Metastatic infection was detected in 25 bacteremias (8.0%). The mortality rate was 25.6%. The duration of bacteremia (determined in 251 series) was 1-59 days (median duration, 1 day; 70th percentile, 3 days). The time to positivity ranged from 4.2 to 98.2 h (median time to positivity, 15.5 h) and was significantly shorter for patients with an endovascular source of infection (14.9+/-5.4 vs. 19.5+/-10.6 h; P < .0005), extended duration (i.e., > or = 3 days) of bacteremia (14.1+/-4.2 vs. 18.6+/-9.2 h; P < .0005), and metastatic infection (12.9+/-5.9 vs 18.0+/-9.3 h; P = .007). Analysis of a range of cutoff values demonstrated that a time to positivity of < or = 14 h yielded the best sensitivity and specificity for predicting the source and outcome of infection. Logistic regression analyses revealed that a time to positivity of < or = 14 h was an independent predictor of an endovascular source of infection (P < .0005), extended bacteremia (P < .0005), metastatic infection (P < .0005), and attributable mortality (P = .017). CONCLUSIONS: Time to positivity in S. aureus bacteremia may provide useful diagnostic and prognostic information. Growth of S. aureus within 14 h after the initiation of incubation may identify patients with a high likelihood of endovascular infection sources, delayed clearance, and complications.