The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

Cotton is economically and evolutionarily important crop for its fiber. In order to improve fiber quality and yield, and to exploit the natural genetic potential inherent in genotypes, understanding genome structure and function of cultivated cotton is important. In order to achieve this, a functional understanding of bioinformatics resources such as databases, software solutions, and analysis tools is required. "ut currently, there are very few unified reports on bioinformatics tools and even fewer repositories to access cotton genomic information. "lso, resourceful developers and bioinformatics scientists actively addressing complex genomic challenges in cotton genomes are much in need. The primary goal of this chapter is to provide a review of such tools and resources for analyzing the structure and function of the cotton genome with preferential emphasis on this complex and economically important plant species. This discourse begins with a description of concurrent advances in high-throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources for analysis of genomes transcriptomes small RN"s and epigenomes. In each section, recent advances in cotton have been discussed. Cotton genome sequencing and annotation efforts are outlined within these sections. This review discusses the availability of genome information of both diploid and tetraploid species that have impelled cotton genome research into the post-genomics era, opening new avenues for exploring regulatory mechanisms associated with fine-tuning of gene expression of fiberrelated genes. Finally, the potential impacts of these rapid advances, especially the challenges in handling and analyzing the large datasets are discussed.

Preservation of milk is important as it relates to Capra aegagrus hircus (Alpine goat) milk DNA extraction. We examined the difference in concentration and quality of DNA resulting from the use of a preservation tablet (BronopolTM) versus a preservation solution by Norgen Biotek. When examining the concentration and quality of DNA in goat milk for studies using somatic cells from goat milk, it is ideal to use a substance that has a long-term preservation potential. The concentrations and quality of DNA obtained from goat milk was compared. Two separate trial samples of Alpine goat milk were obtained. The preservation tablet commonly known as B-14 or Bronopol™ was dissolved into one sample of milk. Another sample of goat milk without a tablet used a preservation solution from a Norgen Biotek. All DNA extraction methods followed the Norgen Biotek Corp. manufacturer's protocol. DNA quantity and quality was analyzed using a Thermo Scientific NanodropLite spectrophotometer. The study showed that the traditional Bronopol™ was a better method of preserving and maintaining the integrity of DNA in the somatic cells that are present in Alpine goat milk. This is based on the results obtained following determination of quantity and A260/A280 readings for quality assessment. Thus, the use of Bronopol™ is the preferred method of preserving goat milk for DNA extraction.

Abstract:The Giant River Prawn is an important commercial species from southeastern Asia and has a large global market. It has a complex life cycle in which it undergoes several molting sequences. Many arthropods require firm perches on which they can perform ecdysis. We investigated preference for substrate slope and its influence on ecdysis. We discovered that prawns occupy horizontal surfaces more frequently than others, but during pre-molt and molt stages, they shift their habitat use to non-horizontally sloped surfaces. Here, they will flex their shell and later molt. We recommend modification of cannibalism management in commercial facilities by providing sufficient vertical (strongly preferred) or high-sloped (greater than 30 degrees) surfaces to facilitate ecdysis, while providing much horizontal space for foraging and other activities. This should create habitat separation between foraging and highly susceptible freshly-molted prawns, thus leading to reduced cannibalism-related mortality.