Rapid, CRISPR-Based, Field-Deployable Detection Of White Spot Syndrome Virus In Shrimp

Rapid, sensitive, point-of-care diagnostics are critical for managing infectious diseases. Here we adapt the CRISPR-based SHERLOCK method to develop a rapid, accurate, single copy detection assay for White Spot Syndrome Virus, the most devastating virus impacting global shrimp aquaculture. Further, we combine paper matrix nucleic acid extraction and lateral flow colorimetric reporting to create a fully field-deployable, next-generation diagnostic with potential to transform veterinary pathology, disease ecology, and animal production.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Bose Hubbard Model in a Strong Effective Magnetic Field: Emergence of a Chiral Mott Insulator Ground State

Motivated by experiments on Josephson junction arrays, and cold atoms in an optical lattice in a synthetic magnetic field, we study the "fully frustrated" Bose-Hubbard (FFBH) model with half a magnetic flux quantum per plaquette. We obtain the phase diagram of this model on a two-leg ladder at integer filling via the density matrix renormalization group approach, complemented by Monte Carlo simulations on an effective classical XY model. The ground state at intermediate correlations is consistently shown to be a chiral Mott insulator (CMI) with a gap to all excitations and staggered loop currents which spontaneously break time reversal symmetry. We characterize the CMI state as a vortex supersolid or an indirect exciton condensate, and discuss various experimental implications.Comment: 4 pages, 4 figs, Significantly revised version, to appear in PRA-Rapi

Genetic Susceptibility of Cultured Shrimp (\u3ci\u3ePenaeus vannamei\u3c/i\u3e) to Infectious Hypodermal and Hematopoietic Necrosis Virus and \u3ci\u3eBaculovirus penaei\u3c/i\u3e: Possible Relationship with Growth Status and Metabolic Gene Expression

Offspring of four crosses (I, II, III, and IV) of Penaeus vannamei from known high- and low-growth families were challenged with infectious hypodermal and hematopoietic necrosis virus (IHHNV) and Baculovirus penaei (BP) to compare their susceptibility to these viral agents and examine the genetic component involved in disease resistance or susceptibility. Family crosses were made using broodstock from five families developed by the U.S. Marine Shrimp Farming Program. The prevalence of IHHNV infection was highest in cross I and lowest in cross III. Cross I was developed using male and female broodstock from the low-growth family 1.6, and cross III was developed using a female from the high-growth family 1.3 and a male from the low-growth family 1.6. The prevalence of BP infection at Day 4 was highest (100%) in cross IV, which was developed using a female from the low-growth family 1.4 and a male from the high-growth family 1.5. The reciprocal cross, cross III, had the lowest (68%) prevalence at Day 4 postexposure. Both crosses I and II had 88% prevalence of infection at Day 4. Despite 100% prevalence of BP infection in cross IV at 4 days, animals from this cross and cross II exhibited high survival by Day 18 (85 and 77%). On the other hand, crosses I and III (with 88 and 68% prevalence at Day 4, respectively) showed low survival at Day 18 (19 and 24%). On the basis of prevalence of infection and mortality rates, it was concluded that the susceptibility to BP in penaeid shrimp is governed by the genetic background of the parental crosses. The random amplified polymorphic DNA polymorphisms for crosses I, II, III, and IV, were 43, 45, 53, and 51%, respectively, showing no clear relationship between IHHNV and BP prevalence of infection and levels of nuclear genetic diversity. Though the mtDNA haplotypes in offspring from the different crosses were the same, major differences were observed in both steady-state levels and patterns of expression of the mitochondrial 12s rRNA in offspring obtained at various early developmental stages from each of the four crosses. The possible relationship among disease susceptibility, growth status, and expression of mitochondrial 12s rRNA is discussed in the context of a complex nuclear-cytoplasmic genetic system involved in the regulation of gene expression

Human heterochromatin protein 1 isoforms HP1(Hsα) and HP1(Hsβ) interfere with hTERT-telomere interactions and correlate with changes in cell growth and response to ionizing radiation

Telomeres are associated with the nuclear matrix and are thought to be heterochromatic. We show here that in human cells the overexpression of green fluorescent protein-tagged heterochromatin protein 1 (GFP-HP1) or nontagged HP1 isoforms HP1(Hsα) or HP1(Hsβ), but not HP1(Hsγ), results in decreased association of a catalytic unit of telomerase (hTERT) with telomeres. However, reduction of the G overhangs and overall telomere sizes was found in cells overexpressing any of these three proteins. Cells overexpressing HP1(Hsα) or HP1(Hsβ) also display a higher frequency of chromosome end-to-end associations and spontaneous chromosomal damage than the parental cells. None of these effects were observed in cells expressing mutants of GFP-ΔHP1(Hsα), GFP-ΔHP1(Hsβ), or GFP-ΔHP1(Hsγ) that had their chromodomains deleted. An increase in the cell population doubling time and higher sensitivity to cell killing by ionizing radiation (IR) treatment was also observed for cells overexpressing HP1(Hsα) or HP1(Hsβ). In contrast, cells expressing mutant GFP-ΔHP1(Hsα) or GFP-ΔHP1(Hsβ) showed a decrease in population doubling time and decreased sensitivity to IR compared to the parental cells. The effects on cell doubling times were paralleled by effects on tumorigenicity in mice: overexpression of HP1(Hsα) or HP1(Hsβ) suppressed tumorigenicity, whereas expression of mutant HP1(Hsα) or HP1(Hsβ) did not. Collectively, the results show that human cells are exquisitely sensitive to the amount of HP1(Hsα) or HP1(Hsβ) present, as their overexpression influences telomere stability, population doubling time, radioresistance, and tumorigenicity in a mouse xenograft model. In addition, the isoform-specific effects on telomeres reinforce the notion that telomeres are in a heterochromatinized state

System of crop intensification for more productive, resource-conserving, climate-resilient, and sustainable agriculture: experience with diverse crops in varying agroecologies

With continually increasing demand for food accompanied by the constraints of climate change and the availability and quality of soil and water, the world’s farmers are challenged to produce more food per hectare with less water, and with fewer agrochemical inputs if possible. The ideas and methods of the system of rice intensification which is improving irrigated rice production are now being extended/adapted to many other crops: wheat, maize, finger millet, sugarcane, tef, mustard, legumes, vegetables, and even spices. Promoting better root growth and enhancing the soil’s fertility with organic materials are being found effective means for raising the yields of many crop plants with less water, less fertilizer, reduced seeds, fewer agrochemicals, and greater climate resilience. In this article, we review what is becoming known about various farmer-centred innovations for agroecological crop management that can contribute to agricultural sustainability. These changes represent the emerging system of crop intensification, which is being increasingly applied in Asian, African, and Latin American countries. More research will be needed to verify the efficacy and impact of these innovations and to clarify their conditions and limits. But as no negative effects for human or environmental health have been identified, making these agronomic options more widely known should prompt more investigation and, to the extent justified by results, utilization of these methodologies

Genetic Signature of Rapid IHHNV (Infectious Hypodermal and Hematopoietic Necrosis Virus) Expansion in Wild Penaeus Shrimp Populations

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is a widely distributed single-stranded DNA parvovirus that has been responsible for major losses in wild and farmed penaeid shrimp populations on the northwestern Pacific coast of Mexico since the early 1990's. IHHNV has been considered a slow-evolving, stable virus because shrimp populations in this region have recovered to pre-epizootic levels, and limited nucleotide variation has been found in a small number of IHHNV isolates studied from this region. To gain insight into IHHNV evolutionary and population dynamics, we analyzed IHHNV capsid protein gene sequences from 89 Penaeus shrimp, along with 14 previously published sequences. Using Bayesian coalescent approaches, we calculated a mean rate of nucleotide substitution for IHHNV that was unexpectedly high (1.39×10−4 substitutions/site/year) and comparable to that reported for RNA viruses. We found more genetic diversity than previously reported for IHHNV isolates and highly significant subdivision among the viral populations in Mexican waters. Past changes in effective number of infections that we infer from Bayesian skyline plots closely correspond to IHHNV epizootiological historical records. Given the high evolutionary rate and the observed regional isolation of IHHNV in shrimp populations in the Gulf of California, we suggest regular monitoring of wild and farmed shrimp and restriction of shrimp movement as preventative measures for future viral outbreaks

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Complete Genome Sequence of a Novel Mutant Strain of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei)

The acute hepatopancreatic necrosis disease (AHPND) of Penaeus vannamei shrimp is caused by Vibrio parahaemolyticus carrying toxin genes, pirA and pirB We report the complete genome sequence of the novel V. parahaemolyticus strain R14, which did not display AHPND symptoms in P. vannamei despite containing the binary toxin genes.College of Agriculture & Life Sciences, University of Arizona, Tucson, AZOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei)

Vibrio parahaemolyticus carrying the toxin genes pirA and pirB causes acute hepatopancreatic necrosis disease in shrimp. A genome sequence of V. parahaemolyticus strain R13 was determined that showed deletions of the entire pirA gene and the 5' end of the pirB gene and does not cause the disease in experimental challenge.College of Agriculture & Life Sciences, The University of Arizona, Tucson, AZ; USDA National Institute of Food and Agriculture, Animal Health Project [1006512]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Acute hepatopancreatic necrosis disease (AHPND)) and hepatopancreatic microsporidiosis (HPM):): Two threats to sustainable shrimp aquaculture

Infectious diseases caused by viruses and bacteria are a major threat to sustainable shrimp farming globally. Since early 80’s viral diseases such as White Spot Disease, Taura Syndrome disease have caused enormous losses to shrimp aquaculture both in eastern and western hemisphere. As the shrimp industry tried to recover from the onslaught of these diseases, a bacterial, Acute Hepatopancreatic Necrosis Disease (AHPND), also known as Early Mortality Syndrome, and a fungal disease Hepatopancreatic Microsporidiosis (HPM) caused by Enterocytozoon hepatopenaei (EHP) are now posing new threat to shrimp aquaculture. Acute Hepatopancreatic Necrosis Disease is caused by Vibrio spp. expressing plasmidborne binary toxins, PirA and PirB that is similar to entomopathogenic bacterium, Photorhabdus encoded toxin. In 2009, AHPND emerged in China and since then spread to many countries in East Asia and in the Americas. Another disease that has caused alarm in recent year is Hepatopancreatic Microsporidiosis (HPM) caused by Enterocytozoon penaei (EHP), a microsporidium. While AHPND causes acute infection and large-scale mortalities, EHP causes chronic infection and results growth retardation and size variation in population reducing marketability of the infected shrimp. Both diseases affect hepatopancreas, an organ involved in metabolism and humoral immunity in shrimp. The binary toxin, PirA/ PirB are the primary virulence factor for AHPND, but specific virulence factor(s) for EHP is not known. It is, however, known that EHP does not have mitochondria and appears to transport ATP from the cytoplasm of infected cells as it contains ATP transporter genes in its genome. EHP has been shown to be a risk factor for AHPND. Due to lack of therapeutics, preventative measures remain as a corner stone for managing these diseases and efforts are underway to develop genetically improved lines of shrimp having resistance to AHPND and EHP