Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis

Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine–cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.

DNA BARCODING EDELWEISS (Anaphalis longifolia) ASAL SUMATERA UTARA MENGGUNAKAN SEKUEN GEN maturase K

Anaphalis longifolia merupakan anggota dari family Asteraceae yang tersebar di dataran tinggi Eropa, Amerika, hingga Asia. Penelitian tentang tanaman ini masih terbatas pada studi habitat, sedangkan penelitian terkait identifikasi molekuler masih belum dilakukan. Penelitian ini bertujuan untuk menganalisis DNA barcode dari A. longifolia menggunakan sekuen matK gene. Sampel yang diperoleh dari Sumatera Utara kemudian di Isolasi DNA, di amplifikasi menggunakan primer spesifik, lalu disequencing. Hasil sequencing dianalisis menggunakan program Molecular Evolution Genetics Analysis (MEGA) Version X. Hasil penelitian menunjukkan bahwa sekuen matK gen berhasil diamplifikasi pada panjang 800-850 kb. Hasil analisis pohon filogenetik menunjukkan bahwa sekuen matK gene dapat mengelompokkan A. longifolia. Pada sekuen matK gene A. longifolia, AT content lebih tinggi dibandingkan dengan GC conten. Jarak genetik yang diperoleh berkisar 0-0.0014. Hasil analisis alignment sekuen matK gene menunjukkan terdapat 1521 karakter yang dapat diamati, 1403 karakter conserved site, 118 karakter variable site, 9 karakter parsimony informative site, dan 7 karakter single nucleotide polymorphism (SNP) site. Sekuen matK gene dapat digunakan sebagai DNA barcoding untuk mengidentifikasi A. longifolia. Hasil penelitian ini diharapkan dapat memberikan informasi penting dalam konservasi A. longifolia.

Sequence analyses of insulin-like growth factor 1 gene in Nigerian indigenous and arbor acre chickens

Alpha % Indigenous chicken % Gene % Sequence KR nema The chicken Insulin-like growth factor 1 (IGF1) is a candidate gene for growth, body composition and metabolism, skeletal characteristics and growth of adipose tissue and fat deposition in chickens. It is mapped to 165.95 cM on chromosome 1 and composed of four exons and three introns, spanning more than 50 kb. Genomic DNA was extracted from blood samples collected from the experimental birds using Qiagen DNA extraction kits. Polymersae chain reaction (PCR) was carried out using established primers. The PCR amplicon involving 5?untranslated region were sequenced. The sequences were analysed to identify polymorphisms, their genetic diversities and evolutionary relationships among three strains of Nigerian indigenous chickens [Frizzle Feathered (7), Normal Feathered (19) and Naked Neck (19), and the Arbor Acre broiler chicken (17)]. Nucleotide sequences generated were edited and aligned using Codon Code Aligner. Diversity analysis was done using DnaSp while MEGA6 software was used to plot phylogenetic tree using maximum likelihood method. A total of nineteen single nucleotide polymorphisms (SNPs) were detected from 560 bp portions of the 5?UTR among the four chicken populations studied with none detected in the Frizzle feathered chicken. The Naked neck chicken had the highest number of SNP?s (13), haplotypes (6), haplotype diversity (0.778), nucleotide diversity (0.00487), average number of nucleotide differences (2.725), highest number of polymorphic (segregating) sites (13), parsimony informative site (5) and singleton variable site (8). The Naked neck chicken therefore had the highest rate of mutation and degree of allelic variation compared to other chicken strains used in this study. The phylogenetic tree showed that small genetic differentiation exists among the chicken populations studied. Some of the SNPs are newly discovered; hence, association between these alleles and productive traits in Nigerian native chickens is desirable in future studies.

Genetic Stability The Protein Encoding Envelope (E) Genes Dengue Virus Serotype-4 Passaged in Vero Cell As A Candidate Chimera Vaccine Material

This study aims to analyze genetic stability of the gene encoding the envelope protein (E) dengue virus serotype-4 passaged in vero cells, Denv-4 passaged in vero cells serially then continued with RNA extraction at passage 0, 10, 20, 30, 40 ,50 , and 60, and then continued with two step PCR and amplification, and sequencing then analyze the nucleotide stability with BLAST and MEGA 5 software. The result shows that there are many variable site in nucleotide and amino acid with high mutation rate 57.4% for nucleotide and 71.9% for amino acid ,while the similarity between passages are high ranging from 91% - 98%. The conclusion for this study is Denv-4 after analyzed shows that the gene encoding protein E has many variable site but high in similarity.

Lessons from a Small Local Earthquake (Mw 3.2) That Produced the Highest Acceleration Ever Recorded in Mexico City

A reliable estimation of seismic hazard-facing Mexico City from local earthquakes has suffered from poor seismic instrumentation, complex crustal structure, large and variable site amplification, and lack of knowledge of recurrence period of earthquakes on the mapped faults. Owing to recent improvement in local seismic networks, an earthquake swarm activity, which occurred in June–August 2019, was well recorded. The largest event of the sequence, an Mw 3.2 earthquake, caused panic in the city and produced peak ground acceleration (PGA) exceeding 0.3g at the closest station (MHVM) about 1 km away. An analysis of the event shows that it had normal-faulting focal mechanism, consistent with northeast–southwest-oriented mapped faults in the region. It was located at a depth of ∼1 km and had a low stress drop (∼0.1 MPa). We find that the high PGA for this low stress-drop event resulted from high-frequency amplification at MHVM (about factor of ∼6 around 13 Hz), likely due to topographic site effects, superimposed on a pervasive broadband amplification of seismic waves at hill-zone sites in the Valley of Mexico (up to ∼10 in the frequency band of 0.2–10 Hz). Simulation of ground motion for a scenario Mw 5.0 earthquake, using an empirical Green’s function technique, reveals that such an event may give rise to significant seismic intensities in the lake-bed zone of Mexico City. The results emphasize the need to re-evaluate the seismic hazard to Mexico City from local crustal earthquakes in the Valley of Mexico.

Clonality and inbreeding amplifies genetic isolation and mate limitation in a rare montane woody plant (Persoonia hindii; Proteaceae)

Small populations have genetic attributes that make them prone to extinction, including low effective population size (Ne), increased levels of inbreeding, and negative impacts from genetic drift. Some small populations are also clonal with low levels of genetic diversity, restricted seed dispersal, and high levels of genetic structure. Together, these attributes make species with small, isolated, clonal populations unlikely to persist under environmental change. We investigated an endangered woody plant species (Persoonia hindii) in eastern Australia to answer key questions about genetic differentiation, migration rates, population sizes, size of clones, mating system and Ne. We identified 587 single nucleotide polymorphisms. Of the 88 individual stems collected from 15 sites across the entire distribution of P. hindii, we identified 30 multi-locus genotypes (MLG). Additional fine-scale genotyping of two sites (49 and 47 stems) detected a dominant genet within each site occupying a minimum area of 20 m2. Global population differentiation was high (FST 0.22) with very low migration rates (0.048 - 0.064). We identified some population structure with variable site pairwise differentiation (0.015 - 0.32) with no detectable spatial autocorrelation. Species wide inbreeding coefficient was 0.42 (FIT), supporting the direct estimate of 82% selfing. Estimated Ne was extremely small (15), indicating that genetic drift may be reducing genetic diversity and increasing genetic load through fixation of deleterious alleles. Clonality and inbreeding combined with negligible gene flow suggests limited adaptive capacity to respond to climate challenges. Genetic rescue, through assisted gene migration and experimental translocations, would enhance the persistence of natural populations.

The Role of Woodlots in Forest Regeneration outside Protected Areas: Lessons from Tanzania

Promoting forest regeneration outside protected forests is an urgent challenge in densely settled, biodiverse areas like the East African Rift. Regenerating forests entails managing complex processes of ecological recovery as well as understanding the needs and motivations of local land users. Here, we evaluate pathways for attaining native tree regeneration across variable site conditions. We investigate two common strategies for attaining native tree regeneration—setting aside land for forest regeneration (‘Protect and Wait’) and native tree planting (‘Native Tree Planting’)—and a possible third, smallholder exotic tree-planting (‘Woodlots’). We measured native seedling regeneration patterns for each of the three strategies, all underway at a single site in Southern Tanzania. We also used historical aerial photograph analysis and interviews with smallholder farmers to understand past and present land use. Our results show that forest regeneration has been arrested for decades on land under ‘Protect and Wait’, and seedling survival appears to be limited under ‘Native Tree Planting’. In contrast, we found saplings of 28 native species growing spontaneously within pine, eucalyptus, and cypress woodlots planted <400 meters from native forest boundaries. Interviews showed that the citizens most likely to plant woodlots near the protected forest were those who owned additional land parcels elsewhere. Some saw woodlots as a means to avoid losing crops to wildlife at the forest edge. Our findings suggest: 1) Simply setting aside land for regeneration does not guarantee forest regrowth, even if it is adjacent to natural forest, 2) native seedlings will be more likely to survive if planted near shade trees, and 3) smallholders’ woodlots could hasten native tree regeneration at forest park edges if farmers have incentives to protect the native tree seedlings in their woodlots and they can find land elsewhere to plant food crops.

Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis

The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.

Effect of Predation, Competition, and Facilitation on Tree Survival and Growth in Abandoned Fields: Towards Precision Restoration

Tree seedlings planted in abandoned agricultural fields interact with herb communities through competition, tolerance, and facilitation. In addition, they are subject to herbivory by small mammals, deer or invertebrates. To increase the success of forest restoration in abandoned fields and reduce management costs, we should determine which species are tolerant to or facilitated by herbaceous vegetation and those which require protection from competition and predation. Eight native tree species were planted in plots covered by herbaceous vegetation, plots where herbaceous vegetation was removed, and plots where seedlings were surrounded by an organic mulch mat. Half of the seedlings were protected against small mammal damage. Results showed that two non-pioneer and moderately shade-tolerant species (yellow birch and red oak) were inhibited by herbaceous vegetation. Birch species were particularly affected by small mammal predation. No effects of predation or herbaceous competition were observed for conifer species. Rather, herbaceous vegetation had a positive effect on the survival and the height growth of tamarack (Larix laricina). None of the tested herb communities had a stronger competitive effect on tree growth than another. Restoration of abandoned fields using multi-tree species should be designed at the seedling scale rather than at the site scale to account for different tree responses to predation and competition as well as variable site conditions. An approach resembling precision agriculture is proposed to lower costs and any potential negative impact of more intensive vegetation management interventions.