Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.

O presente estudo foi conduzido com o objetivo de avaliar as perdas fermentativas, a composição bromatológica e a estabilidade aeróbica de silagens provenientes de diferentes genótipos de milho produzidos com adubação orgânica. Os quatro tratamentos, avaliados em delineamento inteiramente casualizado, foram compostos pelos diferentes genótipos de milho: 1) híbrido simples (HS); e três variedades: 2) IPR114; 3) IPR164; e 4) ZMG01. Sessenta dias após a ensilagem foram quantificadas as perdas fermentativas, os silos foram abertos e amostrados para avaliações bromatológicas e de estabilidade aeróbica. As variedades apresentaram menor (p≤ 0,05) recuperação da matéria seca (MS) ensilada do que HS e a variedade ZMG01 apresentou o menor (p≤ 0,05) valor de pH dentre os genótipos. Os silos produzidos com HS e IPR114 apresentaram maiores teores de MS e menores (p≤ 0,05) concentrações de fibra em detergente neutro do que os silos de IPR164 e ZMG01. A variedade IPR114 reduziu o pH da silagem nas avaliações realizadas 48 e 72 horas, e a temperatura nas avaliações realizadas entre 40 e 64 horas após a exposição aeróbica, em relação aos demais genótipos avaliados. As variedades avaliadas no presente estudo apresentam maiores teores de fibra e menor recuperação da MS, em relação ao HS. Dentre as variedades avaliadas, IPR114 minimiza as perdas fermentativas e produz silagem com menor teor de fibra e maior estabilidade aeróbica, sendo, dentre as variedades estudadas, a variedade mais recomendada para sistemas orgânicos de produção.

AbstractMutations can occur throughout the virus genome and may be beneficial or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly that similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.

No abstract

Sugarcane silage (SS) is generally susceptible to yeast action, resulting in dry matter losses due to high soluble carbohydrate concentration. We evaluated the effects of adding corn grain and microbial inoculant at ensiling on fermentative profile, losses, chemical composition and degradation of silages. Forty experimental silos (PVC tubing) were assigned at random to a 5 × 2 factorial arrangement with: (1) 5 corn additions at ensiling: CONT -straight sugarcane silage; GC2 -sugarcane with ground corn (processed through a 2 mm sieve) added at ensiling; GC8 -sugarcane with ground corn (processed through an 8 mm sieve) added at ensiling; WC -sugarcane with whole corn grain added at ensiling; and RCS -rehydrated corn ensiled without sugarcane; and (2) 2 microbial inoculant additions at ensiling: 0 and 8 mg of commercial inoculant per kg of feed. Corn grain was added at the rate of 100 g per kg of fresh sugarcane. Adding corn grain to sugarcane at ensiling improved SS fermentation and silage chemical composition. There was no benefit from grinding the grain before adding it to sugarcane. Microbial inoculant had little effect on SS fermentation. Studies comparing corn grain with other energy sources, e.g. molasses or cassava, for addition at ensiling sugarcane seem warranted along with feeding studies with livestock to assess intake and subsequent performance. The overall benefits of adding the energy sources at ensiling versus feeding them directly to animals with untreated sugarcane silage should be determined. ResumenEl ensilaje de caña de azúcar es generalmente susceptible a la acción de levaduras resultando en pérdidas de materia seca (MS) debido a la alta concentración de carbohidratos solubles. En un estudio realizado en la Universidade Federal de São Carlos, Araras, Brazil, se evaluó el efecto de la adición, al momento de ensilar, de maíz en grano e inoculante microbiano en el perfil fermentativo, la pérdida de MS, la composición química y la degradación del ensilaje. Cuarenta silos experimentales (tubos de PVC) fueron distribuidos aleatoriamente en un diseño factorial 5 × 2. Se evaluaron: (1) cinco tratamientos de adición de maíz: CONT -ensilaje de caña de azúcar sin maíz; GC2 -ensilaje con maíz procesado por un tamiz de 2 mm; GC8 -ensilaje con maíz procesado por un tamiz de 8 mm; WC -ensilaje con granos enteros de Tropical Grasslands-Forrajes Tropicales (ISSN: 2346-3775) maíz; y RCS -ensilaje de maíz rehidratado sin caña de azúcar; y (2) dos tratamientos de adición de inoculante microbiano: 0 y 8 mg de inoculante comercial por kg de material a ensilar. Se utilizaron 100 g de maíz por kg de caña de azúcar fresca. Los resultados mostraron que la adición de maíz a la caña de azúcar al momento de ensilar mejoró la fermentación y composición química del ensilaje. La molienda del grano antes de adicionarlo a la caña de azúcar no mostró beneficios en la calidad del producto final. El inoculante microbiano tuvo poco efecto sobre la fermentación. Estudios para comparar el maíz en grano con otras fuentes de energía, p...